Kurts Notes

KURT'S NOTES
By Dr. Kurt Schaberg

KURT'S NOTES
By Dr. Kurt Schaberg
Diagnostic Guides
Gastrointestinal Tract: Inflammatory
Inflammatory Patterns of the GI tract

Inflammatory Bowel Disease
Medication injury in the GI tract
GI infections
Hirschsprung Disease
Gastrointestinal Tract: Tumors

Esophagus Tumors
Stomach Tumors
Colon Polyps
Colon Cancer
Appendix Tumors
Anal Tumors
Lower Anogenital Squamous Tract
Mesenchymal Tumors of the GI Tract
GI Tumor Syndromes
GI Neuroendocrine Tumors
Liver, Bile Ducts, Gallbladder, and Pancreas
Medical Liver
Liver Tumors
Pancreas Tumors
Bile Duct and Gallbladder Tumors
Cytology
Cytology Basics
Cervical Cytology
Effusion Cytology
Urine Cytology
Thyroid Cytology
Thorax
Lung Tumors
Lung Cancer Diagnoses on Small Biopsies (condensed)
Pleural & Peritoneal Tumors
Mediastinum Tumors
Head and Neck

Salivary Gland Tumors
Squamous Mucosa of the Upper Aeordigestive Tract
Sinonasal Tumors
Thyroid & Parathyroid tumors
Soft Tissue and Bone
Soft Tissue Tumors
Bone tumors
Breast
In Situ Lesions (Non-invasive)
Invasive Breast Carcinoma
Papillary Lesions
Fibroepithelial and Spindle Cell Lesions of the Breast
Non-neoplastic: reactive and non-proliferative
Diseases of the Nipple
Gynecologic
Vulva (Tumors and Inflammatory)
Cervical Tumors
Ovarian Tumors
Endometrial tumors
Mesenchymal Tumors of the Uterus
Tony’s Guide to Endometrium Frozen Sections
Tony’s Guide to Ovary Frozen Section
Skin
Epithelial Tumors
Dermal Tumors
Inflammatory Dermatopathology (Rashes)
Pediatrics
Small round blue cell tumors in kids
Genitourinary
Kidney Tumors
Bladder Tumors
Prostate Tumors
Prostate Cancer Grading (condensed)
Testicular Tumors
Adrenal and Paraganglia Tumors
Immunohistochemistry
Dr. Rouse’s Handout
NOTE: There is also now a convenient shorter

URL: kurtsnotes.net
Below are my quick diagnostic reference guides for a range of
conditions commonly encountered by anatomic pathologists. I
developed these as teaching aides for my resident didactic sessions
and for reference while signing out cases.
My suggestions on wording for streamlined, user-friendly

diagnostic report write ups can be found here.
CHAPTER 1
Gastrointestinal Tract:
Tumors
Adapted/inspired by: Atlas of Gastrointestinal Pathology. Arnold et al. 2015 Prepared by Kurt Schaberg
Last updated: 4/2/2020
Patterns of GI Tract Injury

Esophagus Non-keratinizing stratified Normal Esophagus
squamous mucosa
Benign Incidental Findings:
Gastric “Inlet Patch”- Heterotopic Muscularis mucosae
gastric mucosa in esophagus
Esophageal duct
Pancreatic Heterotopia/Metaplasia
Glycogenic Acanthosis – Epithelial Submucosal glands
hyperplasia with abundant, enlarged
superficial glycogenated cells;
clinically appears white (Muscularis propria: distal = smooth muscle; proximal = skeletal muscle)
Acute Esophagitis Intraepithelial Neutrophils with Erosion/Ulceration

GERD Often scattered Eos (usu. < 15/HPF),
Intercellular edema, Basal cell hyperplasia, Elongation
of vascular papilla. Worse distally (near GEJ). Ulcer!
Infections
Candida - Look for fungal hyphae, Get PAS-D/GMS
HSV - Look for Molding, Multinucleation,
Margination in epithelial cells.
CMV – Look for inclusions in mesenchymal cells.
Medications (“Pill esophagitis”) Look for crystals,
resins, and pill fragments; Polarize to help looking for
foreign material.
Eosinophilic Esophagitis Increased intraepithelial Eosinophils (report per HPF)

GERD
Eos typically < 15/HPF, Intraepithelial T lymphocytes
(“squiggle cells”), Intercellular edema, Basal cell hyperplasia,
Elongation of vascular papilla. Worse distally (near GEJ).
Eosinophilic Esophagitis
Typically >20 Eos/HPF. Often eosinophilic microabscesses
with degranulation. Often diffuse or worse proximally.
Associated with “Atopic Triad” (Allergies, Asthma, Eczema).
Presents with dysphagia, chest pain, food impaction, which
may cause a food aversion. Endoscopically can appear as
rings or furrows (“Trachealization/felinization”) Note: As EoE and GERD can appear
identical on a single bx, close clinical
Allergies/Systemic autoimmune disorders and endoscopic correlation is often
Medication Reaction necessary to distinguish between
the them!
Parakeratosis Pattern Superficial squamous cells with retained nuclei
GERD
Eos typically < 15/HPF, Intraepithelial T lymphocytes
(“squiggle cells”), Intercellular edema, Basal cell hyperplasia,
Elongation of vascular papilla. Worse distally (near GEJ).
Candida Esophagitis
Look for fungal hyphae at surface and get PAS-D or GMS,
particularly in immunosuppressed individuals. Budding yeast
are NOT good enough!
Esophagitis Dissecans Superficialis (“Sloughing
Esophagitis”) Superficial “mummified” layer (with ghost
nuclei) with variable necrosis and minimal inflammation.
Clinically can be quite dramatic with extensive peeling and
fissuring. Has been associated with thermal injury,
medications, and some autoimmune conditions.
Esophageal Leukoplakia
Lymphocytic Pattern Intraepithelial Lymphocytes
GERD
Lichen Planus
Band-like (“lichenoid”) infiltrate at junction between
epithelium and submucosa. Dyskeratotic keratinocytes
(“Civatte bodies”) are common. Associated with cutaneous
LP, certain medications, and viral infections. Often older
women. Risk of dysplasia → SCC
Graft Versus Host Disease
Donor T lymphocytes attack host tissue. Typically present
with Rash, Diarrhea, elevated LFT’s.
Intraepithelial lymphocytes with dyskeratotic keratinocytes
and scattered apoptotic bodies. Make sure CMV IHC is
neg.
Crohn’s Disease
Look in lamina propria for granulomas
“Contact Mucositis”
May be a generalized response to mucosal injury, for
example to an allergy to a medication or food.
Other
CVID, Celiac disease, Dysmotility, Etc…
Stomach
Oxyntic Mucosa (90% of stomach)
Present in body/fundus
Pink parietal cells make acid and intrinsic factor (B12 uptake)
Purple chief cells make pepsinogen
Antral Mucosa
Present in distal antrum and cardia
Gastrin-secreting G cells are found ONLY in antrum
Usu. extremely few inflammatory cells, except at the gastric Oxyntic Antral
cardia, which commonly has some chronic inflammation.
Reactive (Chemical) Gastritis/Gastropathy
Foveolar hyperplasia (“corkscrew glands”),
Mucin depletion, Edema, Minimal inflammation,
Extension of smooth muscle bands between glands
Often caused by chemical irritation by bile reflux,
Medications (particularly NSAIDs), or alcohol.
Portal Hypertensive Gastropathy
Above findings, plus dilated vessels in lamina propria. Seen in
patients with portal hypertension.
Endoscopically like “snake skin”
Gastric Antral Vascular Ectasia (“GAVE”)
Endoscopically looks like a watermelon. Fibrin thrombi
present in lamina propria capillaries.
Acute Gastritis Intraepithelial Neutrophils often with Erosion/Ulceration

Helicobacter pylori
Acute gastritis with characteristic superficial lymphoplasmacytic
inflammation and prominent lymphoid aggregates. Most common in
Antrum. Look hard in pits and consider getting Helicobacter IHC.
Risk of MALT and dysplasia/carcinoma.
Helicobacter heilmanni
Less acute inflammation. More common in kids. Organisms are
longer, more tightly spiraled, and less numerous
Medications
Esp. NSAIDs. Often associated ischemic or reactive changes.
“Focally Enhanced Gastritis”
Focally injured glands surrounded by inflammation. Associated in kids with IBD, particularly Crohn’s
disease.
CMV
Chronic Gastritis Chronic inflammation in the mucosa
Helicobacter pylori
Acute gastritis with characteristic superficial lymphoplasmacytic
inflammation and prominent lymphoid aggregates. Most common in
Antrum.
Autoimmune Metaplastic Atrophic Gastritis (AMAG)
Also known as autoimmune gastritis. Autoantibodies destroy parietal
cells/oxyntic mucosa → No intrinsic factor → B12 deficiency →
Pernicious anemia.
Body-predominant injury with loss of oxyntic mucosa and Deep
chronic inflammation → Intestinal and pyloric metaplasia & ECL cell
hyperplasia → Can make neuroendocrine tumors (type I)
Gastrin stain can help confirm sample came from body (negative) and
not antrum (positive).
Medications
Esp. NSAIDs. Often associated ischemic or reactive changes.
Other
CVID, Celiac disease
Lymphocytic Gastritis Intraepithelial Lymphocytes

Helicobacter pylori
Celiac Disease
Medications (E.g., Ticlopidine, Olmesartan)
HIV
Other Immune-mediated Disorders
CVID, Crohn’s Disease, Lymphocytic colitis, etc…
Lymphoma
Collagenous Gastritis Increased subepithelial collagen band with Intraepithelial

Lymphocytes (can highlight with trichrome stain)
Collagenous colitis/enteritis
Celiac Disease
Medications (E.g., Olmesartan)
Helicobacter
Other Immune-mediated Disorders
Eosinophilic Gastritis Increased Eosinophils
Although there is no strict cut-off, >30/HPF is likely too many and

any in the epithelium, submucosa, or muscle is abnormal
Eosinophilic Gastritis/Gastroenteritis
Diagnosis of exclusion. Can be associated with Eosinophil-rich
inflammation in other organs (e.g., esophagus and/or small
bowel). Layer of bowel involved determines symptoms.
Helicobacter
Parasites
Connective tissue diseases/Vasculitis
Food Allergies
Medications
Inflammatory bowel disease (particularly Crohn’s)
Oxyntic Gland Hyperplasia Dilated oxyntic glands with hypertrophic parietal cells
with “snouts”
Single/Sporadic Polyp → Fundic Gland Polyp
Associated with Proton Pump Inhibitor use (increases gastrin levels
through feedback, causing parietal cell hypertrophy).
Extremely low risk of dysplasia/progression
Innumerable or Dysplastic? Consider a Syndrome:

Familial Adenomatous Polyposis Can become dysplastic, but
still low rate of progression to carcinoma
MutYH-Associated Polyposis
Zollinger-Ellison Syndrome
Gastrinoma (usu. in small bowel) causes increased acid secretion
and ulcers. Associated with MEN1.
Foveolar Hyperplasia “Corkscrew glands”, Mucin depletion, Edema

Single/Sporadic Polyp → Hyperplastic Polyp
Associated with background inflammatory injury. extremely low risk
of dysplasia/progression
Innumerable or Dysplastic? Consider a Syndrome:

Ménétrier's Disease Whole stomach, protein-losing enteropathy
PTEN Syndromes (Cowden’s, etc…)
Cronkhite-Candada Syndrome
Juvenile Polyposis
Peutz-Jeghers Syndrome
Small Intestine Quick Checklist:
- Villi? Long and skinny? Go away or blunt with Celiac Disease
- Goblet Cells? Go away with autoimmune enteropathy
- Intraepithelial lymphocytes? Increased in Celiac (and others)
- Plasma cells? Go away with CVID
- Critters? Look between villi and on surface for Giardia, etc..
- Vessels ok? Look for amyloid and vasculitis
- Endocrine cells? Go away with endocrine dysgenesis
Acute Duodenitis Neutrophils in duodenal epithelium

Peptic Duodenitis
Additionally see Gastric foveolar metaplasia and chronic
inflammation. Associated with excess gastric acid and/or
Helicobacter
Infection Most commonly Helicobacter (can lead to ulcers →
Peptic Ulcer Disease). Sometimes Adenovirus, CMV, or other
viruses.
Medications Most commonly NSAIDs
Acute Ileitis Neutrophils in Ileal epithelium

Medications Most commonly NSAIDs
Infection Including common stool pathogens (bacterial and viral)
Inflammatory bowel disease Crohn’s disease is more likely to impact TI (so look for granulomas,
and signs of chronicity, including pyloric gland metaplasia). In UC, there is typically inflammation in
the nearby cecum (that is thought to “backwash”)
Eosinophilic Gastroenteritis Increased Eosinophils

any in the epithelium, submucosa, or muscle is abnormal Eosinophilic
Gastroenteritis Symptoms
Eosinophilic Gastroenteritis
Diagnosis of exclusion. Can be associated with Eosinophil-rich Layer Symptoms
inflammation in other organs (e.g., stomach or colon).
Layer of bowel involved determines symptoms. Mucosa Diarrhea,
malabsorption
Parasites
Connective tissue diseases/Vasculitis Muscle Ileus
Food Allergies
Serosa Ileus and ascites
Medications
Chronic Injury Architectural distortion: crypt branching, dropout, and pyloric gland
metaplasia often with villous blunting and a basal lymphoplasmacytosis
Often starts to look like colon with IBD!
Chronic ACTIVE inflammation, with cryptitis and crypt abscesses.
Particularly Crohn’s in the TI (and small bowel in general).
Look for granulomas and transmural inflammation in resections.
“Diaphragm Disease” Due to NSAIDS
Mild → erosions with associated acute inflammation
Severe → multiple episodes can cause scarring → stenosis
Usu. Less chronic inflammation than Crohn’s
Medications
Mycophenolate – Immunosuppressant (often given after
transplantation) that can cause epithelial/crypt damage with
increased apoptosis→ causes diarrhea
Crypt Distortion
Ischemia Severe pain. Coagulative necrosis. Crypt withering.

Lamina propria hyalinization and hemorrhage. Reperfusion brings
acute inflammation.
Radiation Most sensitive to damage. Endothelial injury → edema,

fibrin, and ischemic changes with enlarged/bizarre nuclei.
Graft vs. Host Disease (GVHD) Donor T-lymphocytes attack Pyloric Gland
host bowel. First see apoptotic bodies in crypts. Metaplasia
Severe damage shows crypt abscess, crypt distortion, and epithelial
destruction. Lerner System for Grading GVHD
Graft Rejection Host T-lymphocytes attack donor bowel. Grade Findings

Similar to GVHD: Inflammation (mostly lymphs) with crypt 1 Isolated apoptotic bodies
destruction and apoptosis.
2 Loss or damage of isolated crypts, w/
or w/o crypt abscesses
“IPAA” findings (given to patients with UC or FAP) 3 Loss of 2 or more contiguous crypts
Usu. NOT given to Crohn’s patients as high risk of
4 Extensive crypt loss with epithelial
complications destruction
Pouchitis Acute and chronic inflammation of ileal
reservoir. Unclear etiology, but often treated with
antibiotics/probiotics.
If refractory, consider Crohn’s.
vs
Cuffitis Chronic active inflammation of rectal cuff,
attributed often to residual/recurrent UC.
Malabsorption Villous atrophy with increased intraepithelial lymphocytes (IEL)
Causes Diarrhea clinically often with weight loss.
Gluten Sensitive Enteropathy (Celiac Disease)

Gluten exposure triggers inflammation, primarily in
duodenum. Positive serology for: Antigliaden, Tissue
transglutaminase (TTG), and antiendomysial (EMA) (if not
IgA deficient!). Associated with haplotypes HLA-DQ2 or
DQ8 (absence both of these essentially excludes
diagnosis). Number of IEL typically >20/100 enterocytes.
“Crescendo” at tip of villi.
Other Protein Sensitives (e.g., cow milk, soy, eggs)
Often increased Eosinophils in mucosa
Peptic duodenitis
Medications (e.g., Olmesartan and NSAIDs)
Small Bowel Bacterial Overgrowth excess anaerobic bacteria (often caused by decreased acid and
dysmotility) digest bile and carbohydrates→ variable local damage and bloating
CVID Immunodeficiency with impaired B-cell differentiation. Usually plasma cells ABSENT→ low serum
Ig’s → recurrent infections.
Tropical Sprue Unknown etiology, but likely infectious. After travel to Africa, Asia, or South America.
Must exclude other infections.
Autoimmune Enteropathy Gut autoantibodies → often absent goblet or Paneth cells. Most common
in infants.
Foamy Macrophages “Foamy” macrophages in mucosa
Mycobacterium avium intracellulare (MAI) Get a FITE stain!
Immunocompromised/AIDS-defining opportunistic infection.
Whipple Disease Get a PAS/D stain! Tropheryma whipplei causes
an infection often afflicting adult white men→ arthralgias, weight
loss, diarrhea. Treat with antibiotics.
Nonspecific Macrophages
Dilated Lacteal Engorged/dilated lymphatics
Primary Lymphangiectasia Poorly understood. Dilated
lymphatics→ lymph/albumin leakage into gut → diarrhea and
protein-losing enteropathy.
Secondary Lymphangiectasia Similar manifestations as primary,
but secondary to obstruction, tumor, adhesions, stricture, prior
surgery, etc….
Colon
Crypts should be oriented parallel to one another,
perpendicular to the surface (like test tubes),
resting on the muscularis mucosae
Regional Variation
Right Colon Left Colon
More lymphocytes Less lymphocytes
Paneth cells normal Paneth Cells abnormal
Fewer goblet cells More goblet cells
Some architectural distortion and muciphages in the rectum is considered normal.
Focal Active Colitis Rare collections of neutrophils in crypt epithelium

(Otherwise normal)
Medications (esp. NSAIDs)
Acute Self-limited Colitis Resolves in <4
weeks. Usually infectious (e.g., Campylobacter,
Salmonella, Shigella, or Yersinia) with abrupt
onset and coinciding fever.
Bowel preparation artifact
Ischemic Colitis
IBD Usu. More insidious onset.
Acute Colitis Extensive cryptitis and crypt abscesses, WITHOUT features of Chronicity
Infection Usu. acute bacterial or viral infections

(e.g. CMV, Salmonella, Shigella, Campylobacter,
etc…), so make sure this has been evaluated
clinically. Often food contamination (fecal-oral).
May see Pseudomembranes.
Medications Esp. NSAIDs. Also Resins

(Kayexalate and Sevelamer) and Ipilimumab.
IBD Usually has features of chronicity, so would
have to be emerging (very recent onset) or
partially treated.
Chronic Active Colitis Active colitis with features of Chronicity
Features of Chronicity include: Architectural distortion (crypt
branching, loss, and shortening), basal lymphoplasmacytosis, and
Paneth cell or pyloric metaplasia
Inflammatory Bowel Disease (IBD)
Chronic systemic autoimmune inflammatory disease.
On a mucosal colonic biopsy, can be impossible to
distinguish Crohn’s from UC and must rely on Think of those test
clinical/endoscopic impression. tubes being melted!
Look for Granulomas and Dysplasia.
(See IBD handout for Crohn’s vs UC)
Infection Always rule out CMV in refractory IBD (along
with other causes clinically)
Diverticular Disease Most common in older patients
in sigmoid colon. Can mimic IBD with Diverticulitis and
Segmental Colitis Associated with Diverticulosis (SCAD).
Diversion-Associated Colitis In bowel diverted from
fecal stream (causes short chain fatty acid deficiency).
Usu. see florid lymphoid hyperplasia with prominent
germinal centers.
STD Proctocolitis Sexually Transmitted Diseases: Esp. Syphilis and lymphogranuloma venereum
(Chlamydia). Often tons of plasma cells.
Cord Colitis Syndrome After Umbilical cord transplantation. Often see granulomas.
Medications NSAIDs, Ipilimumab, and resins
Ischemic Colitis Superficial epithelial damage, Crypt withering, Lamina propria

hyalinization and hemorrhage.
Occasional pseudomembranes and acute inflammation
(with reperfusion)
Ischemia Due to poor perfusion. Most common in “watershed”
areas (splenic flexure, rectosigmoid, and ileocecal regions) in older
patients with vascular occlusion or low-flow states.
Infection
E.coli 0157:H7 (EHEC)—Endothelial damage from toxin→ Fibrin
thrombi often seen. Associated with Hemolytic Uremic Syndrome
(Anemia, low platelets, renal failure)
C. Difficile—Pseudomembranes, less hyalinization and crypt
withering
Medications Esp. NSAIDs. Also Resins (Kayexalate and Sevelamer)
and Ipilimumab.
Eosinophilic Colitis Increased Eosinophils

any in the epithelium, submucosa, or muscle is abnormal
Eosinophilic Colitis/Gastroenteritis
Diagnosis of exclusion. Can be associated with Eosinophil-rich
inflammation in other organs (e.g., esophagus and/or small
bowel). Layer of bowel involved determines symptoms.
Parasites
Connective tissue diseases/Vasculitis
Food Allergies
Medications
Systemic mastocytosis
Lymphocytic Colitis Increased intraepithelial lymphocytes
Lymphocytic Colitis Watery diarrhea with normal endoscopic

findings. Increased intraepithelial lymphocytes (>20 lymphs/100
epithelial cells). Classically older women.
Collagenous Colitis Watery diarrhea with normal endoscopic
findings. Increased intraepithelial lymphocytes with Increased
subepithelial collagen layer (irregularly thickened, trapping
inflammatory cells, vessels, and fibroblasts). Highlight with
trichrome stain.
Medications (e.g., NSAIDs, Olmesartan, SSRIs, etc…)
Viral Infections
Granulomatous Colitis Granulomas! Rule out infection with FITE and GMS/PAS-D
Crohn’s Disease Loose, non-necrotizing. Seen in less than ½ of

cases. Note: In UC can see granulomatous reaction to crypt rupture!
Infections Esp. if Necrotizing! Rule out fungi and mycobacteria.
Look around for parasites (e.g., Schistosomiasis)
Nonspecific mucosal injury
Medications
Sarcoidosis
Cord Colitis Syndrome
Diverticular disease
CVID and Chronic Granulomatous Disease
Pigments and Inorganic Material
Iron Appears brown and granular on H&E; Blue on Iron Stain
Deposition Patterns:
A: Deposition in lamina propria/macrophages → prior mucosal
microhemorrhages
B: Coarse, crystals at surface → Iron pill
C: Subtle, uniform deposition in deep glands → Iron overload
Resins
Kayexalate: Used to treat hyperkalemia in renal failure →
causes ischemic and ulcerative changes. Linked to fatalities, so
urgent dx.
Purple on H&E with narrow fish-scale pattern.
Sevelamer: Used to treat hyperphosphatemia in renal failure

→ Associated with mucosal injury.
Bright pink to rusty yellow on H&E with irregular fish-scale
pattern.
Bile Acid Sequestrants: (e.g., cholestyramine) Binds bile acids

(lowers cholesterol). NOT associated with injury
Bright pink/orange on H&E with smooth, glassy texture.
Calcium Appears dark purple and often cracked on

H&E; Black on von Kossa
Can be: Metastatic (in normal tissue due to high serum calcium
levels), dystrophic (in damaged tissue due to injury), or idiopathic
90 Yttrium-labeled Microspheres
Appear as uniform dark/opaque perfect circles.
Given by interventional radiology as internal radiation therapy
for hepatic malignancies. Often also see radiation injury.
Melanosis
Coarse, brownish black pigment in
cytoplasm of macrophages.
Consists of deposited Lipofuscin.
Although classically associated with
laxative use, can be seen in any
disorder with increased epithelial cell
turnover, including constipation.
Tattoo Very black, coarse granules in

macrophages, often with a foreign body
giant cell reaction.
Used to mark lesions endoscopically
for later identification.
Muciphages
Mucin-containing macrophages in lamina propria
Presumably cleaning up after epithelial injury and

turnover. Very common, especially in rectum.
Air “Pseudolipomatosis” Pneumatosis Cystoides Intestinalis

Empty spaces, without a foreign body Empty spaces, WITH a foreign body reaction.
reaction. (which means it happened in vivo!!)
Attributed to insufflation artifact. Often iatrogenic or infectious cause.
No associated nuclei (not fat).
Prepared by Kurt Schaberg

Normal Colon
Crypts should be oriented parallel to one another,
perpendicular to the surface (like test tubes), resting
on the muscularis mucosae.
Regional Variation
Right Colon Left Colon
More lymphocytes Less lymphocytes
Paneth cells normal Paneth Cells abnormal
Fewer goblet cells More goblet cells
Some architectural distortion and muciphages in the rectum is considered normal.

Intraepithelial lymphocytes (and even rare neutrophils) over lymphoid follicles is also normal.
Patterns of Damage in IBD

The inflammation in IBD is characterized by the presence/absence of “Activity,” defined as neutrophilic
inflammation of the epithelium with epithelial damage, and “Chronicity,” including architectural
distortion, a basal lymphoplasmacytosis, and Paneth cell metaplasia.
These words are combined such that you can have an “Active colitis,” a “Chronic active colitis,” or a
“Chronic inactive colitis,” which is also sometimes called “Quiescent colitis.”
Crypt architectural distortion
Activity = PMNs Chronicity Crypt shortening
Crypt branching
Cryptitis Crypt Crypt dropout
Loss of crypt parallelism
Abscesses Villiform surface
Basal lymphoplasmacytosis
Paneth cell metaplasia and
hyperplasia
Pyloric gland metaplasia
Lamina propria and submucosal
fibrosis
Typical appearance IBD in recent

New onset, ~ 1 month
of active disease Treatment remission
untreated IBD untreated
Chronic Active Chronic inactive
Active Colitis (Quiescent) Colitis
Colitis
IBD is subclassified as either Ulcerative colitis (UC) or Crohn’s disease (CD):
Ulcerative Colitis
Chronic active inflammation in the rectum
proceeding proximally in continuous,
diffuse pattern
Typical findings:
Chronic Active Colitis limited to mucosa
and superficial submucosa with ulceration
Can see deeper inflammation with severe

“fulminant” colitis
Can have increased inflammation in cecum

near appendiceal orifice (“cecal patch”)
Can have inflammation in terminal ileum

(“backwash ileitis”)
Crohn’s Disease Patchy Transmural chronic active

inflammation in any part of the GI tract
Typical findings:
Transmural inflammation
Skip areas and patchy inflammation
Granulomas
Ulcers: superficial apthous to fissuring
Muscle and nerve hypertrophy
Pyloric gland metaplasia (esp. in TI)
Fibrosis and strictures
Fistulas
Indeterminate Colitis aka: IBD, type unclassified

Approximately 10% of patients unclassifiable, often due to the extensive pathologic and clinical
overlap between UC and CD. Placeholder term--this is NOT a specific entity. Often due to
insufficient data or fulminant colitis.
Differential Diagnosis:
Active Colitis Neutrophilic Cryptitis
But, Chronicity ABSENT
(aka Acute Self-limited Colitis)
Neutrophils in superficial lamina propria
Causes: E. Coli, Salmonella, Shigella, Crypt abscesses
Campylobacter, Viruses Hemorrhage, edema
E. coli O157:H7→ ischemic changes Possible erosions
Looks similar: Some medications (e.g., NSAIDS, Checkpoint inhibitors), New onset IBD
Focal Active Colitis FOCAL Neutrophilic Cryptitis

Chronicity ABSENT
Causes:
NSAIDS → + Increased apoptoses, ischemic-like changes
Bowel preparation artifact → + Increased apoptoses, edema, mucin depletion
Early infection → Days 0-4 after onset
Ischemic changes → often with lamina propria hyalinization, crypt withering
Microscopic Colitis Increased Intraepithelial Lymphocytes (IELs)

Neutrophils rare to absent
Lymphocytic Colitis Collagenous Colitis
IEL ≥20/100 surface epithelial cells IEL >10-20/100 surface epithelial cells
Normal architecture Increased Subepithelial Collagen
Chronic inflammation in lamina propria Entraps capillaries and lymphocytes
(usu. superficial) Highlighted by Trichrome stain
Additional DDX:
Ischemic colitis → Hyalinized lamina propria, withered crypts, minimal inflammation
Radiation colitis → Ischemic changes, Atypical stromal cells, Telangiectatic blood vessels
Diverticular disease–associated colitis → In colonic segment with diverticulosis
Diversion colitis → Colon isolated from fecal stream, Follicular lymphoid hyperplasia
Prolapse → Fibromuscular hyperplasia, Angulated diamond-shaped crypts
Vasculitis → Inflammatory destruction of vessels, Fibrinoid necrosis
Eosinophilic/Allergic Colitis → >60 Eos/10 HPF, Few PMNs, Absent chronicity
STD Proctitis → Often chlamydia or syphilis due to anal receptive intercourse. Lots of ulceration, plasma
cells, and histiocytes. Confined to rectum.
Medical Management
Usually 2 phases: 1) Induction (to induce remission) and 2) Maintenance (to maintain remission)
These may use same or different medications/dosages.
Typical management previously involved “Step-up therapy,” where you start with a mild drug (e.g.,
mesalamine) and only move up to a more powerful drug if they “fail” that drug. However, recent
clinical trails have shown better complication-free survival with a “Top down” model where you start
with a more powerful medication (e.g., monoclonal antibody).
Mesalamine (5-ASA) – mechanisms of action unknown. Low activity. Usually used orally or rectally for
mild UC.
Sulfasalazine – like 5-ASA (mechanism of action unknown). Usually used for mild ileocolic CD.
Budesonide – steroid taken orally with little system effect (mainly works on GI tract).
Prednisone – oral steroid often used to induce remission in active IBD. Long-term use limited due to
side effects. Use in both CD and UC.
Azathioprine/6-Mercaptopurine – Thiopurines, inhibit DNA synthesis, thereby reducing WBC
production and inflammation. Risk of lymphoma. Used in both CD and UC.
Tofacitinib (Xeljanz) – janus kinase (JAK) inhibitor. Currently only used in UC. Oral pill. Powerful.
Monoclonal antibodies:
Adalimumab (Humira) – recognizes TNFα. Used in both CD and UC.
Infliximab (Remicade) – recognizes TNFα. Used in both CD and UC.
Vedolizumab (Entyvio) – recognizes α4β7 (gut-specific) integrin, inhibiting diapedesis. Used in both CD
and UC, but likely better for UC. Very few side-effects as gut-specific.
Ustekinumab (Stelara) – recognizes interleukin (IL) 12 and 23. Used in CD.
Cancer Risk and Screening Cancer Risk:

Ulcerative colitis = ~2.4 fold risk
Crohn’s Disease = ~1.9 fold risk
(~ 2x risk)
Inflammation → DNA oxidation/damage → Cancer
Risk proportional to severity/duration of inflammation.
Screening recommendations:
First 8-10 yrs after diagnosis→ No increased screening (not enough time for carcinogenesis)
Years 10-20 → Every 1-3 yrs (shorter interval with worse, esp. if PSC)
Years 20 onward → 1-2 yrs
Treatment of Dysplasia
With modern techniques, including high-definition and chromoendoscopy, most dysplasia is visible. As
such, it can be completely resected endoscopically.
Once a dysplastic lesion has been resected, in the absence of surrounding dysplasia, ongoing meticulous
colonoscopic surveillance is appropriate.
Proctocolectomy is only recommended for dysplasia if endoscopic resection is not possible, or if
nonvisible high-grade dysplasia or adenocarcinoma is found.
From: Laine L. SCENIC international consensus statement on surveillance and management of dysplasia in inflammatory bowel disease.
Gastroenterology. 2015 Mar;148(3):639-651.
Pre-malignant and Malignant lesions in IBD:
Generally, follows stepwise progression of: Non-neoplastic → Low-grade dysplasia → High-grade
dysplasia → Adenocarcinoma. However, there are cases where it appears to go from low-grade (or even
normal appearing) to adenocarcinoma very quickly or directly.
Conventional Dysplasia (look like usual adenomas):
Indefinite for Dysplasia
Unable to classify as definitely reactive or dysplastic.
Often atypia in setting of severe inflammation or ulceration.
Sometimes surface not present for evaluation.
Management: Treat active disease and repeat biopsy in 3-12
months.
Low-Grade Dysplasia
Looks like a sporadic Adenoma.
Enlarged, hyperchromatic, smooth, “pencillate” nuclei.
Pseudostratified nuclei with maintained basal orientation.
Higher N:C ratios; Little to no surface maturation.
Often abrupt transition (corresponding with clone)
Prominent apoptoses.
Molecular: IBD-associated dysplasia show more copy number
aberrations and aneuploidy than sporadic adenomas. TP53
mutations are very frequently present early. Possibly reflecting a
faster progression toward cancer.
Management: Complete endoscopic resection if visible.

Otherwise proctocolectomy ± IPAA to exclude cancer. Hint: Try using a lymphocyte as what is
“normochromatic”
High-Grade Dysplasia
Enlarged, hyperchromatic, pleomorphic nuclei.
Often plumper than LGD.
Irregular nuclear contours. Prominent nucleoli.
Loss of nuclear polarity.
Complex architecture: Cribriforming, crypt
branching/budding.
P53 staining often highlights both grades:

Dysplasia→ Strong P53 staining (or null-type) at the
surface in atypical areas.
Negative/Indefinite→ weak staining at bottom of crypts (proliferative compartment), without strong
staining at the surface.
H&E is still the gold standard though, so only do it on cases that are equivocal!
Nonconventional lesions:
Serrated Epithelial Change
Serrations at top and bottom of crypts.
Distorted crypt architecture where some crypts do
not reach the muscularis mucosae. (unlike SSL)
Normal nuclei. Goblet cell-rich epithelium.
Controversial risk of CRC. Many studies show
increased risk of dysplasia/carcinoma. Note: The colon in IBD patients can frequently show
Emerging genetics, likely TP53 mutations. surface serrations/hyperplasia, particularly in the
distal colon, so strict criteria are necessary.
Non-Conventional Dysplasia May be present with conventional dysplasia in ~50%

of cases. More common on left side as polypoid mass.
Hypermucinous—Villous architecture with prominent

cytoplasmic mucin.
Traditional Serrated Adenoma (TSA)-like
Sessile serrated lesion (SSl)-like
Paneth cell differentiation
Goblet cell deficient—absence of goblet cells
“Terminal epithelial differentiation,” TED, or “Crypt
cell dysplasia,” CCD –flat lesions, round to oval
hyperchromatic nuclei. Can be just in crypts.
Adenocarcinoma
Invasive through basement membrane:
- Infiltrating glands/cells
- Broad, expansive confluent growth of glands
Compared to Sporadic, IBD-associated CRC is:

- More often multifocal (field defect)
- More often higher grade
- More often advances stage
- More often signet-ring or mucinous
Unique variant:
Low-grade tubuloglandular adenocarcinoma—very bland small to medium-sized round glands
that invade with little desmosplastic stroma. Often CK7 (+). Frequent IDH1 mutations.
Last Updated: 4/2/2020 Prepared by Kurt Schaberg
Medication Injury in the GI tract

Non-specific Injury
Pill Esophagitis Pill retained in esophagus (not enough water or laying supine) →
Caustic/osmotic injury
Often elderly women → odynophagia and retrosternal pain →

strictures and perforation
Often at site of aortic arch (mid-esophagus)
Common offenders: Antibiotics, NSAIDs, Iron, bisphosphonates
Findings: Ulceration, acute inflammation, granulation tissue

Helpful finding: polarizable crystalline material (pill fragments)
Reactive (Chemical) Gastropathy

Common offenders: EtOH and NSAIDs
Finding: foveolar hyperplasia with corkscrewing glands,
mucin depletion, edema, and few inflammatory cells
Colitis Can cause most patterns of colitis (see separate “Inflammatory Patterns of the GI tract” guide)
Pattern of Colitis Associated Drug
Eosinophilic colitis NSAIDs, gold, carbamazepine, antiplatelet agents, estrogens
Lymphocytic or NSAIDs, lansoprazole, ticlopidine, ranitidine, simvastatin, flutamide, carbamazepine,
collagenous colitis sertraline, penicillin, checkpoint inhibitors, Idelalisib
Focal active colitis NSAIDs, Bowel preparation (esp. oral sodium phosphate), checkpoint inhibitors,
Idelalisib
Ischemic colitis NSAIDs, antibiotics, amphetamines, digitalis, diuretics, chemotherapy, nasal

decongestants, constipation-inducing medications, laxatives, vasopressor agents,
cocaine, ergotamine, serotonin agonists/antagonists including sumatriptan, estrogen,
progesterone, glutaraldehyde, and immunomodulators such as interleukin
Apoptotic colitis Bowel preparation (esp. oral sodium phosphate), mycophenolate mofetil, laxatives,
chemotherapeutic agents (esp. 5-fluorouracil), NSAIDs, cyclosporine, checkpoint
inhibitors, Idelalisib
Pseudomembranous NSAIDs, antibiotic-associated Clostridium difficile colitis
colitis
Neutropenic colitis Chemotherapy
Modified from: Odze and Goldblum’s Surgical Pathology of the GI tract, Liver, Biliary tract, and Pancreas. 3 rd Edition. 2014.
More Specific Drug Patterns
NSAIDs
Non-Steroidal Anti-Inflammatory Drugs
Inhibit cyclooxygenase→ decrease prostaglandins →
decreased mucous, acid neutralizing bicarbonate, and
mucosal blood flow → mucosal injury; Also deplete
ATP
Inflammation and ulceration in any part of GI tract
Can cause strictures and “Diaphragm disease”
(concentric, thin mucosal webs)
Can cause erosion/ulceration in any part of GI tract
Esophagus→ acute esophagitis, ulceration, stricture
Stomach→ reactive gastropathy, ulceration
Intestines → Mostly active inflammation, with some
mild chronic architectural changes, ulceration;
lymphocytic/collagenous colitis,
PPI
Proton Pump Inhibitor
Used to treat esophagitis and peptic ulcer disease
Inhibit parietal cell acid secretion → less stomach acid →
gastrin secretion increases (trying to tell to make more
acid) → Parietal cell hypertrophy and neuroendocrine cell
hyperplasia
→ Increased fundic gland polyps
Colchicine
Used to treat gout.
Inhibits microtuble polymerization → interferes
with mitosis, chemotaxis, and PMN degranulation
Most characteristic finding: multiple “arrested”
metaphase mitoses, particularly in “rings.” Also
often apoptotic bodies and lots of reactive changes.
Cytotoxic Chemotherapy
Epithelial atypia, sometimes mimicking dysplasia
Taxol→ ring mitoses like colchicine
Severe neutropenia can cause “Neutropenic Colitis” where after
mucosal damage opportunistic bacteria invade causing necrosis
and pneumatosis → often septic shock
Antacids and Sucralfate

Gastric “Metastatic” calcifications (due to
Calcium/phosphate imbalances)→ small calcifications
under mucosal surface
Iron Iron appears brown and granular on H&E; Blue on Iron Stain
Usually associated with erosion/ulceration. Sometimes reactive chemical

gastropathy or chronic gastritis.
Iron Deposition Patterns:
A: Deposition in lamina propria/macrophages → prior mucosal
microhemorrhages
B: Coarse, crystals at surface → Iron pill
C: Subtle, uniform deposition in deep glands → Iron overload
Resins
Kayexalate: Used to treat hyperkalemia in renal failure → causes

ischemic and ulcerative changes. Linked to fatalities and perforation, so
urgent dx.
Purple on H&E with narrow fish-scale pattern.
Sevelamer: Used to treat hyperphosphatemia in renal failure →

Associated with mucosal injury also.
Bright pink to rusty yellow on H&E with irregular fish-scale pattern.
Bile Acid Sequestrants: (e.g., cholestyramine) Binds bile acids (lowers

cholesterol). NOT associated with injury
Bright pink/orange on H&E with smooth, glassy texture.
Doxycycline
Superficial mucosal necrosis/erosion
Capillary damage with microthrombi and

hyaline necrosis
Background reactive chemical gastritis and

chronic gastritis
Angiotensin II Receptor Blockers

The “-artan” drugs: Olmesartan and Losartan
Used to treat hypertension
Induces severe diarrhea
Duodenal changes often indistinguishable from

Celiac disease:
- Villous blunting
- Increased intraepithelial lymphocytes
Often more acute and chronic inflammation in

lamina propria
Sometimes see subepithelial collagen deposition
Mycophenolate Mofetil
Immunosuppressive drug usually used after solid
organ transplantation
GI toxic→ often limiting use
Resembles GVHD or Crohn’s disease:

• Increased crypt apoptoses
• Patchy neutrophilic inflammation
• Degenerating damaged crypts
• Architectural damage
• Granulomas
More Eos favors drug effect, more apoptoses

favors GVHD
Bowel Prep and Laxatives
Many act through increasing osmolarity of stool → traps water in
lumen → loose stool
Mucin depletion
Focal active colitis/cryptitis
Increased apoptotic bodies
Erosions
Melanosis Coli
Classically associated with irritant laxatives, but actually indicator of
increased epithelial cell turnover
Apoptosis → debris phagocytosed by macrophages → lipofuscin
accumulates → looks yellow or brown
Can see with many drugs including NSAIDs, etc..
Checkpoint Inhibitors
Anti-PD1, Anti-PDL1, and anti-CTLA therapy
Activate immune tumor destruction, but can also
cause autoimmune “immune related adverse events”
Respond to steroids
Colon, most patterns including:

• Lymphocytic colitis
• Collagenous colitis
• Acute self-limited colitis
• Apoptotic colitis
Stomach:
• Perigland inflammation/focal enhancing gastritis-
pattern
• NOT diffuse
Duodenum:
• Villous blunting
• Increased intraepithelial lymphocytes
• Apoptoses
• Brunner’s gland inflammation
Idelalisib
Specific small molecule drug used to treat
CLL/SLL and follicular lymphoma
Causes severe diarrhea
Changes seen in colon and small bowel:

• Increased apoptoses
• Lymphocytic colitis
• Focal active colitis/cryptitis
90 Yttrium-labeled Microspheres
Appear as uniform dark/opaque perfect circles.
Given by interventional radiology as internal radiation therapy for
hepatic malignancies. Often also see radiation injury.
Most common to see in upper GI due to shared circulation with
liver
Additional
Diuretics
Decrease circulatory volume→ bowel ischemia at usual watershed areas
See classic ischemic findings: crypt withering, lamina propria hyalinization.
Ergotamine
Given for migraines, induces vasospasm→ causes localized ischemia in GI tract
Small, localized ischemic ulcers. Not in watershed zones.
Gluteraldehyde
Used to disinfect colonoscopes. Used less now. Contact irritant in rectum and colon.
Hormone therapy/Oral contraceptives

Estrogen produces a hypercoagulable state → mesenteric venous thrombosis → ischemic colitis
From: Marginean EC. The Ever-Changing Landscape of Drug-Induced Injury of the Lower Gastrointestinal Tract. Archives of
Pathology & Laboratory Medicine 2016 140:8, 748-758
Last updated: 5/31/2020 Prepared by Kurt Schaberg
GI Infections
Bacteria
Helicobacter
H. pylori→ slender curved rods
Very common: Infects ½ the world population (esp. underdeveloped
countries, through person-to-person contact)
Acute infection→ Chronic active gastritis with superficial
lymphoplasmacytic infiltrate
More prevalent in antrum
Often erosions and germinal center formation→ can cause MALT
lymphoma
H. heilmannii→ milder inflammation, corkscrew appearance
May be acquired from domestic animals. Esp. prevalent in children.
Less likely to cause lymphoma.
Both stain with Giemsa, Silver, and same immunohistochemical stain
Treat with triple therapy (2 antibiotics + PPI)
Intestinal Spirochetosis Fuzzy, fringed layer of organisms at surface (Non-invasive)

Variable species, but most are Brachyspira
Usually no associated inflammatory infiltrate
Stain with silver stains: Warthin-Starry, Steiner
Clinical significance is somewhat unclear:
Diarrhea most common symptom, but unclear if actually
causative or coincidental
Classical association with men who have HIV is also being
questioned
Mycobacterium M. avium-intracellulare complex (MAI or MAC)

Abundant foamy macrophages in lamina propria often distending villi. Can
have poorly formed granulomas.
Usually immunocompromised (classically AIDS)
Present with Diarrhea, malabsorption, and weight loss
Organisms stain with AFB, FITE, PAS, and GMS
M. Tuberculosis
Classically necrotizing (caseating) granulomas,
Coalescence of large granulomas, often with associated cuff of
lymphocytes.
Organisms stain with AFB & FITE, but culture and/or PCR may be required.
Most common in ileocecum with sharply-defined ulcers and strictures
(mimicking Crohn’s disease), causing weight loss, fever, abdominal pain,
and diarrhea.
GI symptoms may precede pulmonary symptoms.
Whipple disease
Infection by Tropheryma whipplei
Present with weight loss, diarrhea, arthritis,
lymphadenopathy, endocarditis, and neuropsychiatric issues.
Most common in middle-aged white males with HLA-B27.
Most often infects small bowel, but can see changes
throughout GI tract and also brain, heart, and lymph nodes.
Massive infiltration of lamina propria by foamy macrophages
Variable acute inflammation.
Organisms stain with PAS. Can also identify with PCR.
(Negative for FITE and AFB, helping differentiate from MAI)
Yersinia
Gram-negative coccobacciform enteric bacteria
Infection caused by food contamination
Most commonly infects ilium, right colon, and appendix.
Can cause ulcers and edema.
Abundant epithelioid granulomas with lymphoid cuffs
Transmural lymphoid aggregates and giant cells common
Usually not necrotizing
→ Closely mimics Crohn’s disease
Stains not helpful→ consider culture, serologies, or PCR
Common cause of granulomatous appendicitis
Acute infectious colitis “Acute Self-limited Colitis”

Most commonly associated with bacterial enterocolitis
Usually acute onset of diarrhea and abdominal pain.
Often self-limited and resolves within several weeks.
Often discriminated from one another by microbiology testing
(classically culture, but now PCR NAATs)
Classically, Active colitis (cryptitis, crypt abscess formation,

epithelial damage), without features of chronicity (preserved
architecture, no metaplasia or basal lymphoplasmacytosis).
Nevertheless, can mimic IBD, particularly in the resolving phase
Most common bacteria include (Often food-borne illness):
Campylobacter—most common stool isolate in US.
Salmonella—can cause typhoid fever with hyperplastic Peyer’s patches, ulcers, and necrosis. Less PMNs.
Enterohemorrhagic E. coli (O157:H7)—Shiga-like toxins cause epithelial and endothelial injury→ see
fibrin thrombi and ischemic changes→ can cause hemolytic uremic syndrome (HUS) due to endothelial
injury and platelet activation causing 1) Thrombocytopenia, 2) Hemolytic anemia, and 3) Kidney injury
Clostridioides difficile—usually after recent antibiotic use. Watery diarrhea with pseudomembranes
Shigella, Yersinia
Also caused by some viruses (e.g., norovirus) and parasites
Sarcina
Spherical cells 2-3 μm in diameter
Occur in tetrads or packets of 8 or more
Most commonly found in the stomach
Unclear if pathogenic. Likely incidental finding.
Often seen in cases of delayed gastric emptying and gastric

outlet obstruction
→ Their presence can prompt further investigation as to
cause of dysfunction, such as occult malignancy
Actinomyces
Long, filamentous bacteria that stain purple
Look like “dust bunnies”
Frequently seen as incidental bacteria on

biopsies or part of mixed flora colonizing
lesions, especially in oral cavity.
Associated with poor hygiene.
Uncommon cause of appendicitis.
Positive on Gram stain and GMS.

Negative on AFB.
Normal Flora Most “normal” bacteria in the oral cavity and intestines are
gram-negative anaerobes
On GI biopsies, often see in esophagus and intestines
Bacteroides species are the most common, other common
ones include Prevotella and Veillonella.
Other organisms include gram-positive organisms like
Streptococcus.
Usually, these are commensal and do not cause disease.
Can cause periodontal disease
Elsewhere, most disease is due to spread to other regions (e.g.,
endocarditis, abscesses, septic arthritis, pneumonia, etc…)
Often polymicrobial clusters/infections
Highlighted by gram and silver stains
Histologic findings are nonspecific and further microbiology
gests (e.g., culture, MALDI-TOF, or NAAT) are necessary for
identification.
Viruses
Cytomegalovirus (CMV) Most common in immunocompromised hosts, esp. AIDS
Often causes ulcerations. Symptoms vary by site:
Esophagus→ dysphagia, odynophagia
Stomach/intestines→ Diarrhea, bloody or watery, pain
Ulceration, mixed inflammatory infiltrate with neutrophils
if severely immunocompromised, less inflammation
Viral inclusions, preferentially in mesenchymal cells:

Most commonly endothelium or other stromal cells
Nuclear→ “Owl’s eye” (Cowdry A), pink, nucleolus-like
Cytoplasmic→ granular and pink to purple, hof-like
Be sure to evaluate for in refractory IBD and GVHD cases
Can also look for with PCR
Herpes Simplex Virus (HSV)

Most commonly causes ulceration with variable inflammation,
predominantly acute. Can get vesicles in anorectum.
Viral inclusions at edges of ulcers in epithelial cells

3M’s→ Moulding, (chromatin) Margination, Multinucleation
#2 most common cause of infectious esophagitis→ dysphagia

Self-limited in healthy patients; may cause esophageal
perforation or disseminate in immunocompromised patients
Findings the same in HSV1&2
Adenovirus
Normal hosts: Common cause of childhood diarrhea.
Can cause intussusception due to lymphoid hyperplasia
Immunocompromised hosts: Diarrhea, potentially leading to
disseminated disease (including hepatitis and pneumonitis)
and death. Harder to control.
Characteristic smudgy inclusions that are basophilic to
eosinophilic
Tubular GI tract: Inclusions in surface epithelium, often in
goblet cells→ can be round or crescent shaped. Most often
in colon with increased apoptosis and epithelial sloughing.
Liver: Inclusions in hepatocytes, often at edges of
coagulative necrosis
Fungus
Candida Most common infection of the esophagus
More common in immunocompromised
Presents with dysphagia/odynophagia
Endoscopy: white plaques with underlying ulceration
Neutrophilic inflammation with ulceration, but less if
immunocompromised
Parakeratosis common
→ highlighted by PAS-D and GMS stains
→See mix of budding yeast and pseudohyphae
Histoplasmosis
Endemic to Ohio, Missouri, Mississippi river valleys.
Can cause localized or disseminated disease (more common
in immunocompromised). Lung most common site, but GI
common too.
Most common GI site of involvement is ileum. May cause
ulcers or mass.
Often lymphohistiocytic infiltrates without well-formed
granulomas
Intracellular 2-5 μm fungi
Positive with GMS and PAS
Cryptococcus Ubiquitous. Often from avian droppings (think “Pigeons”)

Usually immunocompromised (e.g., AIDS, organ transplant, etc…)
Can be localized or disseminated disease.
Other common sites are lung and meninges
Variable inflammatory response (depending on immune state). Can have
granulomas or suppurative necrosis.
4-7μm, very “pleomorphic” (lots of different sizes), round to oval,
Narrow-based buds. Unstained, refringent capsules give “halo” or “soap
bubble” appearance. Stain with GMS. Capsule stains with mucicarmine
Coccidioides
“Valley Fever.” Found in soil in southwestern United States and South and
Central America. Higher risk if immunocompromised. Can have localized or
disseminated disease.
In host, spores develop into large, thick-walled endospore-containing

spherules, which enlarge and rupture. There is often associated
granulomatous and chronic inflammation
Parasites
Strongyloides Nematode with worldwide distribution. Very common in Tropics and
southeastern US. Often get through skin when barefoot on contaminated
soil. Skin→ Lung→ GI tract → Feces → next host (or autoinfect)
Worse in immunocompromised patients
Can be asymptomatic and harbor for >30 yrs
When symptomatic, diarrhea, pain, bleeding
Inflammation with neutrophils and eosinophils often, may resemble IBD
Adult worms, larvae, and eggs all found IN crypts
Enterobius vermicularis “Pinworm”

Spread by fecal-oral route. Humans are the only host.
Most common in children.
Often asymptomatic, but can cause anal pruritis
Most commonly seen in appendix, often incidentally
Thick cuticle on adult worm
characteristic lateral spikes (ala)
Easily visible internal organs
Even invasive worms cause minimal inflammation
Schistosomiasis
Parasitic trematode (fluke)
Any species of “schisto” can be found in the gut
Endemic to Africa, Asia and parts of the Americas.
Highest prevalence in Sub-Saharan Africa and Middle East
Infected by contaminated water through the skin

→ snails are intermediate host
Most patients are asymptomatic, but can present with GI
bleeding (or hematuria or portal hypertension)
Ova: Found in the wall of the GI or GU tract. Often calcify

with time. Variable acute, chronic, or granulomatous
inflammation. Often prominent eosinophils.
Worms: often have no reaction to them, found in veins (of

bowel or bladder) or in liver → lay eggs into urine/stool
Three main species in humans:

Schistosoma mansoni-Usually GI tract. Lateral spine
Schistosoma japonicum-Usually GI tract. Later knob
Schistosoma haematobium-Usually GU tract. Terminal
spine
Liver flukes
Helminths occlude bile duct→ dilated ducts with wall
thickening→ Signs of biliary obstruction (jaundice, fever, RUQ
pain) → can cause cholangiocarcinoma long-term due to
chronic inflammation
Clonorchis sinensis, Opisthorchis species, and Fasciola species
Endemic primarily to Asia and acquired by eating raw or
undercooked fish or crawfish
Worms visible to naked eye
Echinococcus
Cestode (tapeworm) with wide geographic distribution
Definitive host = Dogs (or other carnivore)—humans infected
through exposure to feces→ Eggs hatch → larvae travel to liver
and form cysts→ cysts grow very slowly
Often asymptomatic, but can get symptoms from mass-effect
Treated with surgical resection; Ruptured cysts are very
antigenic→ can cause anaphylaxis
Inner most layer contains protoscolices (developing heads of
adult tapeworms), which contain 2 circles of hooklets and
sucker
This is surrounded by a layer of hyalinized, white laminated,
acellular material
Protozoans
Entamoeba Histolytica
Protozoan most common in subtropical and tropical regions
In US, most common in immigrants and travelers
Infected through fecal-oral route/contaminated food/water
Can be asymptomatic, or cause variably severe diarrhea

Can cause amoebic liver abscesses
Cause deep “flask-shaped” ulcers, extending into

submucosa, undermining nearby mucosa.
Architectural distortion may mimic IBD
Often abundant amorphous eosinophilic debris
Entamoeba: Round, red, eccentric nucleus

Distinct cell membranes with foamy cytoplasm
Ingested RBCs.
Giardia duodenalis Most common protozoa infection in US
Usually acquired from contaminated water. Can be STD.
More common in kids, with travel, and immunocompromised
Causes diarrhea (unclear pathogenesis), often watery and foul-smelling.
Can be chronic, esp. if immunocompromised
Usually see trophozoites with no associated inflammation

(sometimes mild villous blunting and chronic inflammation)
Trophozoites are pair-shaped with 2 oval nuclei

Look like “falling leaves” in bowel lumen
Cryptosporidia
Obligate intracellular world-wide parasite.
Can be from contaminated water or person-to-person
Diarrhea→ self-limited in normal hosts, but often chronic/relapsing
with weight loss and cramping in immunocompromised. No good
therapy.
Parasites appear as 2-5μm basophilic “blue beads” on lumina apical

surface.
Can see villous blunting and variable inflammatory infiltrate
Enveloped by microvilli→ less microvilli for absorption→ diarrhea
Cystoisospora Formerly just “isospora”

Obligate intracellular world-wide parasite.
Infected by contaminated food/water
Causes diarrhea, often chronic. Debilitating if immunocompromised
Villous blunting with mixed inflammation and prominent Eosinophils
Variable forms, all intraepithelial:
Some crescent/banana shaped
Others are round with prominent nucleoli
Cyclospora
Protozoan with world-wide distribution that causes diarrhea.
Infection often occurs through contaminated food/water
Variable villous blunting and inflammation
Round (2-3 µm) forms and crescentic merozoites (5-6 µm) in
parasitophorous vacuoles
Microsporidia
Fungus that causes intestinal infection, particularly in AIDS patients→
Diarrhea
Small spores (2-3 μm) and larger plasmodia
Located within supranuclear cytoplasm of epithelial cells
Prepared by Dr. Kurt Schaberg
Hirschsprung Disease
• Congenital absence of ganglion cells in both nerve plexuses (Submucosal and Myenteric)
→ leads to poor peristalsis and obstruction → Proximal dilation with narrowed, spastic distal aganglionic segment
→ Failure to pass meconium, abdominal distention, constipation → can get enterocolitis
• Always impacts distal-most part of GI tract (farther for neural crest cells to travel to make ganglion cells)
Physiologic Hirschsprung Transition

Anus Normal
Hypoganglionated Segment Zone Bowel
Segment
~2 cm
(shorter in newborns)
Mucosa
Submucosa
Inner Muscle
Outer Muscle
Ganglion Cells Absent to Few Absent Present, but fewer Present
Neural Absent, but nerves may be Present Present Absent

hypertrophy more prominent
Nerve Twigs Present Absent Present Present
Mucosa Squamous Colorectal Colorectal Colorectal Colorectal
Inadequate to confirm absence of ganglion

cells as physiologically hypoganglionated
Suction Biopsy Protocol:
• Preoperative rectal suction biopsies are done to establish a diagnosis.
• Biopsies should be >3mm in diameter and at least 1/3 of the thickness
should be submucosa.
• Should be >2 cm above dentate line to avoid physiologic area of fewer
ganglion cells.
• Multiple serial sections are examined initially
→ If no ganglion cells, order additional sections (75 levels) and
Calretinin IHC
Definition of Neural Hypertrophy:

Ancillary studies:
Submucosal nerves >40µm
Calretinin:
Shows granular staining of small, intrinsic nerve twigs in mucosa
and muscularis mucosae normally, which are absent in
Hirschsprung. Also highlights ganglion cells and nerve bundles.
Ganglion Cells
Hirschsprung Normal
(No Staining) (Excludes Hirschsprung
Segment in that area—could Mature/Adult Immature/Infant
still be transition zone) Often have less Nissl
Neuronal markers: substance and higher
(e.g., NSE, NeuN, and MAP-2) can be helpful in confirming the N/C ratios
presence of ganglion cells
CHAPTER 2
Gastrointestinal Tract:
Inflammatory
Last Updated: June 1, 2020 Prepared by Kurt Schaberg
Esophagus Tumors
Normal Non-keratinizing stratified
squamous mucosa
Benign Incidental Findings:
Pancreatic Heterotopia/Metaplasia Muscularis mucosae
“Multilayered Epithelium”– Epithelium Esophageal duct
at transition between squamous and
glandular mucosa with some features
Submucosal glands
of BOTH. Looks like squamous
metaplasia of the cervix.
Inlet Patch—Stomach epithelium in upper esophagus
(Muscularis propria: distal = smooth muscle; proximal = skeletal muscle)
Glandular Lesions “Barrett’s Esophagus”:

British (and Japanese) Columnar epithelium
Complete Intestinal Metaplasia Exact duplicate of (regardless of goblet cells!) extending ≥1 cm
intestinal mucosa with absorptive cells between above the gastric folds
goblet cells. Usually seen in stomach.
AGA 2011 Columnar epithelium with goblet cells
Incomplete Intestinal Metaplasia Goblet cells with in the esophagus (No length requirement)
intervening foveolar cells. More common at GEJ.
ACG 2016 Columnar epithelium with goblet cells
Higher risk for dysplasia
extending ≥1 cm above the gastric folds
Complete IM
Incomplete IM
Risk factors: GERD, Obesity, Male gender, Smoking, H. pylori
Pathogenesis: Acid/Bile reflux→ Intestinal metaplasia → Mutations → Low-grade dysplasia → TP53
mutation → High-grade Dysplasia → DNA/Chromosomal instability → Cancer
Negative for Dysplasia Should be most common Dx by far!

Surface maturation 1
“The Four Lines” (shows preserved cell polarity) 2

1- Apical mucin cap
3
2- Base of mucin cap
3- Cytoplasm (between mucin and nucleus) 4
4- Row of nuclei (maintained nuclear polarity)
“Wild-type” p53 staining
Management: Follow-up in 3-5 yrs
Indefinite for Dysplasia Used in cases where it is unclear if there is true dysplasia
Often obscuring inflammation or partial maturation. Could consider getting p53 IHC.
Management: Treat for reflux (hoping things calm down) and repeat biopsy in 3-6 months
Low-Grade Dysplasia
Adenoma-like (Truly dysplastic appearing)
(in typical “intestinal type”)
Penicillate, hyperchromatic nuclei
Extends to surface epithelium
Often abrupt transition from reactive to neoplastic
Loss of “the 4 lines,” but retained basal nuclei
Hyperchromatic nuclei
Management: Mucosal ablation
Nuclear Hyperchromasia and pleomorphism
Loss of cell and nuclear polarity
No surface maturation
Rounded, irregular nuclei
Complex architecture
Management: Mucosal ablation if flat

EMR if mucosal irregularity (to rule out carcinoma)
P53 IHC:
Considered indicative of dysplasia/neoplasia if:
1) Overexpressed (every nucleus, strong) or
2) “Null” phenotype (tumor cells all negative)
Other types of Glandular Dysplasia (other than “Intestinal”)

Foveolar Type
Few, if any, goblet cells (may arise independently)
Prominent cytoplasmic mucin
Hyperchromatic, slightly enlarged nuclei
Possible pseudo-stratification
Basal Crypt Dysplasia

Dysplasia at the base of the crypt that matures at
the surface
Small Cell Pattern
Proliferation of numerous tiny, monotonous
glands with loss of polarity and nuclear
hyperchromasia
Adenocarcinoma Invasion across the basement membrane
→ Lamina propria overrun by glands
→ May see single infiltrating cells, or expansively growing glands
Nearly all occur near
without intervening lamina propria
GE junction due to
Barrett’s esophagus. Features associated with EARLY invasion: Luminal necrosis, Prominent
nucleoli, glands growing parallel to the surface.
Often present with
dysphagia Features associated with DEEP invasion: Angulated glands, Prominent
desmoplasia (at least into submucosa likely), Pagetoid spread of
malignant cells in squamous epithelium.
Classification: Shows a mixed gastric/intestinal lineage.

Patterns of growth: Tubular (most common, see above), papillary,
mucinous, and signet-ring cell patterns (worse prognosis, see
figure to the left ). Often a mixture of patterns is seen.
Staging Challenges: Often in Barrett’s esophagus the muscularis

mucosae can be duplicated and/or distorted, which can make
determining the depth of invasion challenging, particularly on
EMR.
HER2: If amplified → approved for treatment with Trastuzumab
First, start with IHC, if equivocal (2+), then do FISH
(See next page for full grading and algorithm)
Management: If seems low stage clinically (i.e., just intramucosal)
→ EMR & Ablation
If advanced stage (Into the submucosa, or more) → Esophagectomy
(if not too advanced), possibly after chemo and radiation.
May be hard to distinguish Adenocarcinoma from SCC, requiring

stains. Undifferentiated carcinoma should be considered if the IHC
Her2: 3+ by IHC pattern is equivocal or if there are no definite morphologic features
Adenocarcinoma Squamous cell carcinoma
CK7+ CK7- (usually)
p63, p40, CK5/6 - p63, p40, CK5/6 +
PAS/mucin stain + PAS/mucin stain -
From: Bartley et al. HER2 Testing and Clinical Decision Making in Gastroesophageal Adenocarcinoma.
Arch Pathol Lab Med—Vol 140, December 2016
Squamous Lesions
Squamous Papilloma
Papillary proliferation of squamous epithelium with fibrovascular
core of lamina propria. Benign.
May contain koilocytes, but more dysplasia is rare.
Usually exophytic, but can be flat or endophytic.
Result from mucosal irritation stimulating a hyperregenerative
response. Common irritations include: HPV, GERD, trauma, etc..
Squamous Dysplasia
Cytologic atypia: Nuclear enlargement, pleomorphism,
hyperchromasia, loss of polarity, and nuclear overlap.
Architectural Atypia: Abnormal maturation
Low-grade dysplasia: Involvement of the lower ½ of the

epithelium only, with mild atypia
High-grade dysplasia: Involvement of more than ½ of the
epithelium OR severe cytologic atypia
Squamous Cell Carcinoma

Malignant epithelial neoplasm showing squamous differentiation
With keratinocyte-type cells with intercellular bridges and/or
keratinization
Risk factors: Tobacco, Alcohol, very hot beverages, achalasia,

caustic ingestion, etc.. Most prevalent in Asia
HPV is thought to NOT contribute significantly. Although it is

present in many cases, it not integrated or transcriptionally active.
Often presents with dysphagia.
Genetics: Complex cytogenetics, frequent TP53 mutations
Subtypes: Verrucous—often in setting of chronic irritation,

exceedingly well-differentiated with minimal atypia, papillary
surface, broad pushing invasion with associated inflammation
Spindle cell—polypoid growth with high-grade spindle cell
component.
Basaloid—Solid or nested growth of basaloid cells. No HPV
association (unlike basaloid SCC in oropharynx)
Stomach Tumors
Benign Tumors
Fundic Gland Polyps
Benign. Most common stomach polyp.
Hyperplastic expansion of deep oxyntic mucosa with
cystically dilated oxyntic glands and foveolar hypoplasia.
Parietal cell hyperplasia
Usually asymptomatic and incidental.
Associated with PPI use
Can have CTNNB1 (β-catenin) mutations
If numerous (esp. >20) in a young patient, consider a
polyposis syndrome, such as FAP.
Hyperplastic Polyps
Benign. Second most common gastric polyp
Elongated, tortuous, hyperplastic foveolar epithelium
Cystically dilated glands
Inflammatory changes and edema
Often eroded at surface.
Small, haphazardly distributed smooth muscle
Hyperproliferative response to tissue injury.
Usually arise in setting of long-standing gastritis
Precursor lesion = polypoid foveolar hyperplasia
May be hard to differentiate from hamartomatous

polyps (e.g., Cronkhite-Canada syndrome)
Pyloric Gland adenoma

Polypoid proliferation of pyloric-type gastric glands
(cuboidal to columnar cells with foamy, ground-
glass cytoplasm) and no well-formed apical mucin
cap. Often dilated glands. Basal round nuclei.
Usually older individuals with atrophic/metaplastic
autoimmune gastritis and/or H. pylori
Sometimes syndromic (e.g., FAP, GAPPs, etc…)
Activating GNAS and/or KRAS mutations and
inactivating APC mutations.
Can develop high-grade dysplasia → carcinoma
Stain with MUC6

Dysplasia Low-grade foveolar-type dysplasia
Neoplastic change of gastric epithelium without stromal invasion.
Can be gastric/foveolar or intestinal-type (or mixed):

Intestinal-type dysplasia: looks like a colonic adenoma with tall
columnar cells with hyperchromatic nuclei
Gastric/Foveolar-type dysplasia has tubulovillous or serrated fronds

lined by cuboidal to columnar cells resembling gastric foveolar cells.
Nuclei are round to oval. There is apical neutral mucin.
Regardless of type, graded as high vs low:

Low-grade dysplasia: preserved polarization (basal nuclei), relatively
preserved architecture
Intestinal: nuclei hyperchromatic, elongate (“cigar-shaped”)
Foveolar: nuclei round to oval
High-grade dysplasia: Prominent cytologic atypia with enlarged nuclei,

high N:C ratios, sometimes prominent nucleoli. Loss of polarity.
Complex architecture.
Indefinite for dysplasia: Not a biologic entity. Used when there are
questions as to if a lesion is neoplastic or reactive. Often very inflamed.
Intramucosal carcinoma
→ Invasion into lamina propria
Characterized by gland crowding, excessive branching, and budding.
Can see: Single cell infiltration, trabecular growth, intraglandular
necrotic debris, and irregular gland fusion.
High-grade intestinal-type dysplasia
Intestinal-type Adenoma
Localized, polypoid lesion (whereas dysplasia can be flat and
multifocal/non-localized) with dysplastic intestinalized epithelium.
Third-most common type of gastric polyp.
Any cause of gastric intestinalization is a risk factor (e.g., H. pylori,
autoimmune gastritis, etc…)
Look similar to colorectal adenomas and have similar genetics.
Rarer Polyps
Foveolar-type adenoma: Similar to foveolar dysplasia (discussed above), but localized, polypoid lesion.
Usually syndrome-associated (FAP or GAPPs), with no background of inflammation (unlike intestinal-type
adenomas)
Oxyntic gland adenoma: Neoplasm composed of columnar cells with chief cell differentiation (pale
basophilic cytoplasm) with mild nuclear atypia, mimicking oxyntic glands. High rate of progression to
invasive adenocarcinoma.
Malignant Tumors
Adenocarcinoma
Malignant epithelial neoplasm with invasion of lamina propria (or beyond) by neoplastic glandular cells.
Risk factors:
H. pylori—very strong risk factor. Chronic infection→ chronic inflammation → intestinal metaplasia →
dysplasia → carcinoma.
Also—smoking, EBV-infection, and dietary factors
Morphological subtypes:
Tubular—most common subtype. Branching tubules of variable
diameter. Solid growth with barely recognized tubules is included in
this group.
Poorly cohesive (including signet ring)—Second most common.

Neoplastic cells are isolated or arranged in small aggregates without
well-formed glands.
Signet-ring cell type is composed predominantly or exclusively of
signet ring cells, which are characterized by a central, optically clear,
globoid droplet of cytoplasmic mucin with an eccentric nucleus.
Mucinous—malignant epithelium in extracellular mucin pools. Must

be >50% of tumor. Tumor cells may be in glands or single cells.
Papillary—Relatively rare. Exophytic growth with elongated finger-

like processes lined by cuboidal to columnar cells supported by
fibrovascular cores. Well-differentiated with pushing invasion, but
nevertheless has a worse prognosis.
Gastric (adeno)carcinoma with lymphoid stroma—(aka

“lymphoepithelial-like carcinoma” or “medullary carcinoma”)
Syncytial growth of irregular sheets and tubules of polygonal tumor
cells with rich lymphocytic infiltrate. Often EBV-associated. A
separate subset are MMR-deficient (so get EBV and MMR IHC on any
case you are considering for this).
Hepatoid carcinoma—resemble liver (large polygonal eosinophilic

cells). May stain with Hepar-1 and/or AFP. Usually Arginase-1
negative.
Micropapillary adenocarcinoma—small clusters of tumor cells

without fibrovascular cores protruding into clear spaces. Worse
prognosis (like micropapillary carcinomas in other organs).
Fundic-gland type—develop from oxyntic gland adenomas. Very rare!
Mixed—contain two or more subtypes. Often worse prognosis.

Molecular subtypes:
Chromosomally unstable: Predominantly intestinal type morphology with extensive DNA copy
number variations. Frequent TP53 mutations. Most common subtype.
Genomically stable: Predominantly diffuse (signet-ring) morphology. Fewer genetic alterations.

Frequent CDH1 and RHOA alterations/mutations.
Microsatellite instability (MSI): mutations or promoter methylation of mismatch repair enzymes

(often MLH1). Better prognosis.
EBV-positive: usually histologically gastric carcinoma with lymphoid stroma. PIK3CA and ARID1A
mutations. Often PD-L1 amplified. Better prognosis.
Staging:
Tumors with an epicenter within 2 cm of the GE junction should be staged as esophageal cancers.
All tumors in the stomach that do not cross the GE junction (or have an epicenter in the stomach >2
cm from the GE junction) should be staged as gastric.
Stage Finding
Tis Carcinoma in situ = High-grade dysplasia
T1a Tumor invades lamina propria or muscularis mucosae
T1b Tumor invades submucosae
T2 Tumor invades muscularis propria
T3 Tumor invades subserosa
T4a Tumor perforates serosa
T4b Tumor invades adjacent structures
Predictive biomarkers:
Anti-HER2 (ERBB2) therapy is used in patients with unresectable or metastatic tumors. (see
esophageal guide for grading scheme)
EBV and MSI: tumors that are EBV-positive or MSI-high are better prognosis.
Well-Differentiated Neuroendocrine Tumors “NET”
Proliferation of cells with round nuclei, “salt and pepper” (speckled) chromatin and abundant
eosinophilic cytoplasm, arranged in nests, acini, trabeculae, and ribbons.
Express neuroendocrine (NE) markers: Synaptophysin, Chromogranin, INSM1
3 main clinical settings/types (see chart below):

Type 1: Associated with autoimmune gastritis→ destruction of parietal cells→ decreased stomach acid
→ compensatory hyperplasia of antral G-cells (to try to signal to make more acid)→ secrete gastrin →
ECL cell hyperplasia and NET formation
Type 2: Zollinger-Ellison syndrome with a duodenal or pancreatic gastrin-secreting NET, which stimulates
ECL cell hyperplasia and stomach NET formation
Type 3: Sporadic, often higher stage and more aggressive.
Size Requirements: (this can vary a little by source, but generally…)

NE cell hyperplasia: collections of >5 NE cells. Can be linear (chain) or micronodular (clusters), <0.15mm
NE cell dysplasia: nodules > 0.15 mm, fused nodules, or infiltrative nodules (pTis)
Micro-NET: cellular proliferation filling lamina propria. Nodule >0.15mm, but < 0.5mm (pTis)
NET: >0.5mm or invasion into submucosa
Grading: Ki67 Proliferation index based on evaluation of ≥ 500 cells in a “hot spot.” Mitotic count based
on evaluating 50 Hpfs, but reported per 10 Hpfs.
Grade Ki67 Proliferation Mitotic index

Index
Grade 1 <3% <2
Grade 2 3-20% 2-20
Grade 3 >20% >20
Type 1 Type 2 Type 3

Cause Autoimmune gastritis Zollinger-Ellison syndrome, Sporadic
often MEN1
Focality Multifocal Multifocal Unifocal
Cell of origin ECL (body/fundus) ECL (body/fundus) D,G, ECL, and EC-cells
% of Gastric NET’s ~85% ~5% ~10%
Hypergastrinemia Yes (secondary) Yes (primary) No
ECL-cell proliferation Yes Yes No
Acid secretion Low High Normal
Background mucosa Atrophic gastritis Parietal cell hyperplasia Normal
Stage at Dx: Low (Tx = EMR) Low (usually) Often advanced
5-year survival ~100% ~75% <50%
Neuroendocrine Carcinoma
Often arise from non-neuroendocrine tumors (and subsequently develop neuroendocrine differentiation.
Sheet-like growth
Not Graded. Ki67/Mitotic index >20% (often much higher).
Malignant! Very metabolically active/rapidly growing
→ see on normal FDG-PET scan
Molecular: p53, RB1 (and other carcinoma-associated mutations)
Treatment: Platinum-containing chemotherapy
Small Cell Neuroendocrine Carcinoma

Morphology: Fusiform nuclei, finely granular chromatin, scant
cytoplasm, and nuclear molding. Extensive necrosis.
Tons of mitoses. Ki67 almost 100%.
Large Cell Neuroendocrine Carcinoma

Morphology: Large, round nuclei, with prominent nucleoli, and
moderate amounts of cytoplasm. Sheet-like to nested growth.
Ki67 often in 60-80% range.
Other Malignancies
Lymphoma
The GI tract is the most common site of extranodal lymphomas and the stomach is the most commonly
involved site. The two most common are DLBCL and extranodal marginal zone lymphoma.
Diffuse Large B-Cell Lymphoma (DLBCL)—Diffuse infiltrate of atypical large lymphoid cells that show
immunoreactivity to B cell markers (CD20, PAX5, CD19, CD79a) and are negative for EBV. Most cells
resemble centroblasts. Tend to localize to one anatomical site and are less aggressive than their nodal
counterpart. However, like nodal disease, must still do full work-up to classify as Germinal center (GCB)
or Activated B Cell (ABC) subtypes and look for MYC and BCL2 alterations.
Extranodal Marginal Zone Lymphoma of Mucosa-associated Lymphoid Tissue (“MALT lymphoma”)—
Often associated with H. pylori infection. Diffuse to perifollicular infiltrate of small centrocyte-like to
monocytoid lymphocytes. Positive for B-cell markers (CD20, PAX5). CD43 and MNDA1±. Negative for
mantle cell markers (CD5, SOX11, and CyclinD1), CLL/SLL markers (CD5, CD23, LEF1), and Follicular
Lymphoma markers (CD10, BCL6). Indolent course. Often cured by eradication H. pylori.
Squamous cell carcinoma—carcinoma with exclusively squamous differentiation, with keratinocyte-cells

with intercellular bridges and/or keratinization. Very rare.
Adenosquamous carcinoma—carcinoma with both glandular and squamous differentiation (with each at
least 25%).
Undifferentiated carcinoma—carcinoma composed of anaplastic cells without histologic or
immunophenotypic evidence of differentiation. Diffuse malignant cells. Often patchy keratin. Dx of
exclusion—must rule out lymphoma, melanoma, EBV-associated gastric carcinoma, etc…
Gastroblastoma—Often young men. Biphasic tumor of gastric muscularis propria with spindled cells and
nests of epithelial cells. MALAT1-GLI1 gene fusion
Colon Polyps
Adenoma “Picket fence” nuclei: Elongated, Pencillate, pseudostratified, hyperchromatic
Nuclei retain basal orientation (bottom 1/2 of cell)
Low grade dysplastic changes should involve at least the upper half of the
crypts and the luminal surface Tubular Tubulovillous Villous
Tubules >75% 25-75% <25%
High-grade dysplasia (“carcinoma in situ”) Villi <25% 25-75% >75%
Significant cytologic pleomorphism
Rounded, heaped-up cells, ↑ nuclear:cytoplasmic ratio
Nuclei: “Open” chromatin, prominent nucleoli
Lose basal orientation, extend to luminal half of cell
Architectural complexity
Cribriforming, solid nests, intraluminal necrosis
Absence of definite breach of basement membrane
Intramucosal Carcinoma
Neoplastic cells through basement membrane
Into lamina propria but not through muscularis mucosae
Single cell infiltration, small and irregular/angulated tubules
Marked expansion of back-to-back cribriform glands
No metastatic risk (paucity of lymphatics in colonic mucosa)
Invasion into submucosa → implied by Desmoplastic response

Chromosomal Instability Pathway (most common): APC → KRAS→ p53 (also often β-Catenin and SMAD4)
Lynch Microsatellite Instability Pathway: Germline MMR mutation → Loss of heterozygosity
→ Microsatellite instability
Serrated Polyps
Hyperplastic polyp (HP): Superficial mucosal outgrowth characterized by elongated crypts lined by
nondysplastic epithelium with surface papillary infoldings → serrated luminal contour (like a knife)
Sessile serrated lesion (SSL):
(formerly sessile serrated polyp/adenoma (SSP/A)
Usually large (≥1 cm) sessile, right-sided lesions
Architectural disturbances at the bases of crypts is required
Serrations extending to bases, asymmetrical growth
→ Boot-shaped, “Duck” foot
Only ≥1 unequivocal distorted crypt is required
Size of polyp Left Colon Right Colon
1-5 mm Vast majority HP Mix of SSA and HP
6-9 mm Mix of SSA and HP Vast majority SSA
10+ mm Vast majority SSA Essentially all SSA
Sporadic Microsatellite Instability Pathway: Normal colon → BRAF V600E→ HP→ DNA methylation → SSL
→ MLH1 promoter methylation/deficiency → Microsatellite instability → Dysplasia → Carcinoma
Traditional Serrated Adenoma aka TSA
Serrated Adenomatous Polyps. Uncommon.
Prominent frilly serrations of glands
Columnar cells with mucin-depleted, eosinophilic cytoplasm
Cytologic low grade dysplasia throughout
Complex architecture with ectopic crypt formation
Often pedunculated, villous, and left sided
Can contain either KRAS mutations (derived from goblet-cell rich HPs)
or BRAF mutations (derived from microvesicular HPs/SSL)
Peutz-Jeghers Polyp Hamartomas (non-neoplastic)

Germline mutation in the STK11/LKB1 gene.
Most frequent in small intestine
Multilobated, may have papillary or frond-like surface
Arborizing smooth muscle
Generally cytologically bland epithelium
Mucocutaneous melanotic macules (lips and oral mucosa)
Increased risk of many cancers
(e.g., Stomach, Colon, Pancreas, Breast, etc…)
Juvenile Polyp Common in children, but may occur at any age

Usually smoothly spherical pedunculated polyp
Prominent cystically dilated glands
Abundant inflamed stroma
Surface may be eroded
Dysplasia and carcinoma are very rare in sporadic polyps
≥5 polyps or extra-colorectal location may indicate Juvenile
Polyposis syndrome
Prolapse Polyp Changes may be seen secondary to rectal mucosal prolapse

Often anterior rectal wall within 12 cm of anal verge
Superficial ulceration or erosion of mucosa
Thickened, disorganized muscularis mucosae with extension into lamina
propria→ Smooth muscle surrounds individual crypts
Regenerating mucosal epithelium (may appear adenomatous)
Distorted crypts, sometimes diamond-shaped
Clinical Follow-up Guidelines From: Gupta et al. Gastroenterology 2020 Mar;91(3):463-485
Starting at age 50.
Next follow-up in:

No polyps/Normal → 10 yrs
Adenomas: Serrated Polyps:
1-2 TAs (<1cm) → 7-10 yrs ≤ 20 HPs (<1cm) → 10 yrs
3-4 TAs (<1cm) → 3-5 yrs 1-2 SSP, < 1 cm → 5-10 yrs
5-10 TAs (<1cm) → 3 yrs 3-4 SSP, < 1 cm → 3-5 yrs
>10 TAs → 1 yr 5-10 SSP, < 1 cm → 3 yrs
≥1 TA >1 cm → 3 yrs SSP, > 1cm → 3 yrs
≥1 Villous Adenoma/TVA → 3 yrs SSP with dysplasia → 3 yrs
Adenoma with High-grade dysplasia → 3 yrs HP ≥ 1cm → 3-5 yrs
Piecemeal resection of adenoma ≥ 2 cm → 6 mo TSA → 3 yrs
Piecemeal resection of SSP ≥2 cm → 6 mo
Colorectal Cancer
Adenocarcinoma, NOS Characteristic morphology:
Architectural complexity (“cribriform growth”)
Abundant “dirty” necrosis
Most arise through Adenoma → Carcinoma sequence

3rd most common cancer in U.S.
Associated with processed food, obesity, red meat, low-
fiber diet, and alcohol
Subtypes Although most colon cancers are “NOS” (Not Otherwise Specified), some subtypes exist, many
of which have distinct morphology, clinical implications, and molecular alterations
Mucinous adenocarcinoma
>50% of tumor composed of pools of extracellular mucin (most common
subtype). No prognosis implications. Enriched for MSI-high tumors.
If <50%→ “Mucinous features” or “mucinous component”
Signet-ring cell carcinoma

>50% of tumor cells have prominent intracytoplasmic mucin displacing the
nucleus. Worse outcome. Associated with Lynch syndrome and MSI-high.
Medullary carcinoma Mucinous

Sheets of malignant cells with vesicular nuclei, prominent nucleoli,
abundant eosinophilic cytoplasm, and a prominent inflammatory infiltrate.
BRAF mutations→ MSI-high. Better prognosis.
Serrated adenocarcinoma
Morphologically similar to serrated polyps Signet-ring
Micropapillary adenocarcinoma
Small clusters of tumor cells with stromal retraction.
Worse outcome (like in all organs) with early metastasis to LN.
Adenoma-like adenocarcinoma
Pushing invasion with minimal desmoplasia. Hard to Dx on Bx. Good
prognosis.
Medullary
Adenosquamous carcinoma
Grading For “NOS” cancers Grade Differentiation Gland formation
Based on gland formation in the least Low-grade Well-differentiated >95%
differentiated component. Don’t include areas of
tumor budding or poorly differentiated clusters Moderately-differentiated 50-95%
(these are counted elsewhere). High-grade Poorly-differentiated <50%
Special Data to Report
Large Venous Invasion Tumor involving endothelium-lined spaces with an identifiable smooth
muscle layer or elastic lamina
Extramural venous invasion

(outside muscularis propria) is
a risk factor for liver metastasis
Tumor filling large vein

(destroying lumen)
“orphan” artery IEL
(without its paired vein)
Sometimes you might just see the

orphan artery and/or a large, rounded
“Tongue” of tumor next to it
EVG
H&E
The EVG stain can highlight the internal elastic lamina of both the artery and vein. If you don’t see large venous
invasion, consider getting an EVG to look for it .
Tumor Budding Poorly differentiated clusters

Single cells or small clusters of Clusters of ≥5 cells without gland
<5 cells at the advancing front formation
of the tumor
Associated with worse outcome
High tumor budding is a
significant risk factor for nodal
involvement/poor outcome.
Represents “epithelial-
mesenchymal transition”
Lymph Node Metastases Tumor Deposits

Must have residual lymphoid tissue A tumor focus in the fat, but without identifiable lymph node
Usually rounded contour tissue, nerve, or vascular structure → Staged as pN1c
Often irregular contours.
Unpaired artery or elastic lamina? → Large venous invasion!
Stage
Stage Criteria
pT0 No evidence of primary tumor
pTis Carcinoma in situ (High-grade dysplasia), intramucosal carcinoma (involvement of lamina

propria with no extension through muscularis mucosae) → Few lymphatics→ low risk of mets
pT1 Tumor invades the submucosa (through the muscularis mucosa but not into the muscularis
propria) → Usually elicits a desmoplastic response
pT2 Tumor invades the muscularis propria
pT3 Tumor invades through the muscularis propria into pericolorectal tissues
pT4a Tumor invades through the visceral peritoneum (including gross perforation of the bowel
through tumor and continuous invasion of tumor through areas of inflammation to the surface
of the visceral peritoneum)
pT4b Tumor directly invades or adheres to adjacent organs or structures
Colon
In this example, even though
Cancer
the tumor isn’t “at the surface,”
because it is continuous with
the surface through
inflammation, it is pT4a
Inflammation Mesothelial surface
“Pseudo-Invasion” (True) Invasion

Usually NO/little cytologic or architectural atypia Usually cytologic or architectural atypia
Inflamed/fibrotic stroma Desmoplastic stroma
Hemosiderin-laden macrophages Infiltrative/irregular growth
Glands accompanied by lamina propria NOT accompanied by lamina propria
Rounded/well-circumscribed Anywhere in colon
Mostly left colon
Some Molecular
Chromosomal Instability Pathway (Non-hypermutated Pathway): ~85% CRC.
Adenoma→ Carcinoma sequence. Large chromosome arm gains/losses.
Common mutations: APC (early, starts adenoma→ activates WNT pathway), KRAS, and P53.
RAS mutations (~50% of tumors)→ Resistant to anti-EGFR therapy (used to treat metastatic CRC)
Microsatellite Instability (MSI) Pathway (Hypermutated Pathway): ~15% of CRC.

Sporadic: BRAF mutation→ MLH1 promoter hypermethylation → Inactivation of mismatch repair
(MMR) enzymes → Serrated polyp → Carcinoma
Lynch-associated: Germline mutations in MMR proteins→ loss of heterozygosity→ Adenoma →

Carcinoma
→ Lots of mutations → more immunogenic → more inflammatory response to tumor → better

outcome. Also, response to check point inhibitors (e.g., anti-PD-L1 drugs)
Ultramutated Pathway: ~3% of CRC.

POLE (DNA replication enzyme) mutation → lots of mistakes with DNA replication → Ultramutated
tumor
Rectal Cancers Stuff

For RECTAL cancers: The quality of the surgical technique is a key determinant of local recurrence and
long-term survival. Grossly, asses the completeness of the non-peritonealized mesorectal excision.
Score according to worst area.
Complete:
Intact, bulky mesorectum with a smooth surface.
No visible muscle, only very minor irregularities (<5mm)
No “Coning” (where the specimen tapers dramatically distally)
Nearly Complete:
Moderately bulky mesorectum
Minor irregularities (>5mm), but no visible muscle
Incomplete:
Little bulk to mesorectum
Muscularis propria visible
“Coning”
And visible muscle
Circumferential Resection Margin: Considered positive if tumor is microscopically <1mm from inked
circumferential margin (non-peritonealized)
Appendix Lesions
Fibrous Obliteration
Non-neoplastic, benign process. Often incidental.
Replacement of lumen by fibrous tissue with varying
neural proliferation and adipocytes (so may stain with
S100).
Serrated Lesions and Polyps

Identical to those in the colon. May be incidental or cause acute
appendicitis. Associated with KRAS mutations.
Hyperplastic polyp: Polyp with serrations of superficial crypts only

More common
Sessile Serrated Lesion (formerly Sessile serrated adenoma/polyp):

Serrated polyp with distortion extending to crypt bases,
often circumferential.
→ Can develop (adenoma-like) dysplasia (high-grade or low-grade)
→ villous growth → eventual possible adenocarcinoma
Adenocarcinoma
Looks just like adenocarcinoma of the colon.
Can be NOS, mucinous, signet-ring, etc…
Frequent KRAS and GNAS mutations.
Staging very similar to colonic adenocarcinoma.
Irregular malignant glands infiltrating the stroma (often with a

desmoplastic response)
Neuroendocrine tumors Most common appendiceal tumor by far.

Incidence of ~1% of all appendectomies.
Majority in appendiceal tip (so be sure to sample this!)
Occur at younger age than NETs elsewhere in GI tract.
May present incidentally or with acute appendicitis.
Good prognosis (>95% survival) if confined to appendix.
Looks and is graded like other GI NETs (see separate guide for details)
Nests and cords of cells with monotonous nuclei with “salt and
pepper” chromatin
Unique Appendiceal Lesions
Appendiceal Mucinous Neoplasms
Low-grade Appendiceal Mucinous Neoplasm (LAMN):
Villous mucinous epithelium with tall cytoplasmic mucin
vacuoles
Low-grade cytology (nuclei compressed to pseudostratified)
Broad, pushing border with compression of lamina propria
and fibrosis
Mucin may dissect through wall (with or without epithelium)
Prognosis is very stage-dependent (earlier is much better)
High-grade Appendiceal Mucinous Neoplasm (HAMN):

Similar to LAMN, with additional complex architecture
(micropapillary or cribriform) and/or cytologic atypia
Infiltrative growth?! → Adenocarcinoma!
Both have frequent KRAS mutations.

Both are considered in situ [“pTis(LAMN)”], if confined by the muscularis
propria. If through muscle into subserosa → pT3.
If serosa involved → pT4a
Acellular peritoneal deposits→ pM1a
Cellular peritoneal deposits → pM1b (higher risk for spread/recurrence → pseudomyxoma peritonei)
Goblet Cell Adenocarcinoma Previously known as “Goblet cell carcinoid” or

“Adenocarcinoma ex Goblet cell carcinoid”
Amphicrine (having both endocrine and
exocrine features) tumor with goblet-like
mucinous cells, endocrine cells, and Paneth- Low-Grade
like cells. Pattern
Must have at least some low-grade pattern
for Dx.
Usually located at appendiceal tip.
Stage as an Adenocarcinoma.
Low-grade pattern: Tubules and clusters of High-grade
goblet-like mucinous cells; endocrine and Pattern
Paneth-like cells with granular eosinophilic
cytoplasm, mild nuclear atypia, and no Grade Tubular/Clustered Loss of tubular/clustered
stromal reaction. (Low-grade Pattern) growth (High-grade pattern)
High-grade pattern: Tumor cells 1 >75% <25%
infiltrating as single cells, complex
anastomosing tubules, cribriform 2 50-75% 25-50%
masses, or sheets. Signet-ring cells.
High-grade cytologic features. 3 <50% >50%
Desmoplastic response.
Tumors of the Anus

Benign Tumors
Inflammatory Cloacogenic Polyp
Non-neoplastic polyp arising at the anal transition zone
May involve lower rectum, often anterior.
Thought to be due to prolapse (on a spectrum with solitary
rectal ulcer syndrome and rectal prolapse)
Surface may include squamous, glandular, or transitional

epithelium, which is often hyperplastic, without dysplasia
Stromal inflammation, surface ulceration, and granulation
tissue are often present
Classic feature: Fibromuscular proliferation around glands
Squamous Intraepithelial Lesions (SIL)

Non-invasive cytologic and architectural abnormalities of
squamous epithelium, associated with HPV infection
See separate “Lower Anogenital Squamous Tract” (LAST)
guide for additional information
Low-grade Squamous Intraepithelial Lesion (LSIL)

(AIN1, Condyloma)
Cytologic atypia and mitotic figures in the lower 1/3 of
epithelium with associated superficial Koilocytic atypia.
“Atypia”= hyperchromatic nuclei with irregular nuclear
contours.
Koilocytes = large superficial cells with large, hyperchromatic,
“rasinoid” nuclei and perinuclear halos. Sometimes
multinucleated
If papillomatous exophytic growth→ Condyloma, often has
marked epithelial thickening, parakeratosis, broad rete pegs,
and koilocytic atypia.
High-grade Squamous Intraepithelial Lesion (HSIL)

Marked cytologic atypia and superficial mitotic figures
involving full thickness (for CIS/AIN3) or up to 2/3 (for AIN2).
Nuclei are hyperchromatic with irregular nuclear contours.
Loss of architectural polarity (Top looks like bottom)
Diffuse “Block positive” P16 staining
Can screen for Anal SIL in high risk populations (e.g., HIV+)
with anal Pap smears.
Fibroepithelial Polyp
Aka “Hypertrophic anal papillae” or “Skin tag”
Non-neoplastic, benign polypoid projections of anal
squamous epithelium with underlying subepithelial
connective tissue.
Very common! May resemble hemorrhoids clinically.
Surface: Squamous epithelium usually.

Core: Loose fibrovascular connective tissue.
May have multinucleated giant cells or fibroblasts

with bizarre nuclei (large, smudged, hyperchromatic),
which are thought to be degenerative (like “ancient
change” in a schwannoma), often CD34+.
If contain large dilated vascular spaces consider: a

Hemorrhoid.
Paget’s Disease
Pagetoid spread of malignant glandular cells within
the squamous epithelium (an in situ lesion)
Large pleomorphic cells with abundant pale
cytoplasm. May infiltrate singly or form glandular
structures in squamous epithelium.
Clinically, skin is erythematous and itchy.
May be Primary or Secondary:
Primary→ Likely derived from adnexal structures,
has an apocrine phenotype (IHC: CK7+, CK20/CDX2-,
GCDFP-15/GATA-3 +), Not associated with an
underlying neoplasm
Secondary→ Derived from an underlying rectal or
anal neoplasm (often rectal adenocarcinoma).
Phenotype depends on underlying malignancy (often
CK20 & CDX2 +)
Management: Must clinically (and with IHC) evaluate if this is primary or secondary and exclude rectal
origin. If primary, has a strong tendency to recur, and can become invasive.
DDX: Melanoma (S100, HMB45, SOX10, Melan-A +) and SCCIS (CK5/6+, often block positive P16)
Other Benign Tumors
Developmental and Acquired cysts:
Duplication cyst—Lined by columnar, organized GI epithelium with a well-formed, double muscle layer
and nerve plexus
Tailgut Cyst—(Retrorectal cystic hamartoma) Cystic mass near sacrum lined by any type of GI tract
epithelium, including squamous, with disorganized smooth muscle bundles
Also: Epidermoid cyst, Anal duct cyst, Median raphe cyst, Mature cystic teratomas, etc…
Ectopic breast tissue—the “milk line” extends to the perianal area, so you can have ectopic breast
tissue and even breast tumors (e.g., phyllodes tumors)
Hidradenoma Papilliferum–well-circumscribed nodule with papillary architecture of ducts lined by a
double layer of epithelial cells with decapitation secretion (essentially the cutaneous counterpart of a
breast intraductal papilloma). Almost exclusively in middle-aged women.
Malignant Tumors
General Considerations
If a lesion can be completely visualized with gentle traction of the buttocks, it is considered a Perianal
lesion (not anal), which is similar to skin lesions on other parts of the body.
Carcinomas above the dentate line → metastasize to perirectal and internal iliac nodes
Carcinomas below the dentate line → metastasize to inguinal and femoral lymph nodes

Malignant epithelial tumor derived from the anal squamous
mucosa with keratin production, intercellular bridges, and
frequent HPV infection.
Infiltrating squamous cell clusters and strands with malignant
nuclei and eosinophilic cytoplasm.
Most common in older patients and women.
HPV infection in ~90% of cases (most commonly type 16).
Risk factors: Immunodeficiency (particularly HIV), anal receptive

intercourse, and smoking
Histologically heterogeneous
Basaloid pattern—marked hyperchromasia, scant cytoplasm, and peripheral palisading (reminiscent of
BCC), formerly called cloacogenic carcinoma
Admixed mucin-containing cells (try to avoid using term mucoepidermoid carcinoma to avoid confusion)
Verrucous carcinoma—Bland, well-differentiated thickened epithelium with bulbous exophytic fronds

and endophytic “pushing” invasion. Lacks HPV cytopathic effect or significant atypia. Cannot Dx on
biopsy. Often associated inflammatory infiltrate. Locally destructive but does not metastasize.
Anal Adenocarcinoma
Adenocarcinoma that arises in the anal canal.
Can be extra or intramucosal:
Intramucosal→ Arises from luminal mucosa and is intestinal-type
Extramucosal→ Does NOT arise from lumina (no in situ
component) may be associated with an anal glands, fistula, or
other structures
Anal gland adenocarcinomas arise from the anal gland/duct.
They form infiltrative masses in the wall of the anus. IHC: CK7+,
CK20/CDX2-. Be sure to exclude a metastasis (e.g., GYN)
Most fistula-associated adenocarcinomas most often arise in the
setting of Crohn’s disease and are mucinous.
All types can show Pagetoid spread→ Secondary Paget's disease!
Histologic Mucin Classic IHC

Type Production
Intestinal +/- CK7+/-,

Mucosal origin CK20+,
CDX2+
Anal Gland - CK7+,
Primary CK20 -,
CDX2 -,
Fistula- + Variable, Dx
Extramucosal associated depends of
Adenocarcinoma origin h/o fistula!
involving the anal Non-anal Variable
canal +/-
gland, Non-
fistula
Intestinal +/- CK7 +/-,
CRC
CK20 +,
metastases
CDX2 +,
Secondary
Apocrine- - CK7+,
True Paget like GCDFB-15 +,
disease CK20 -,
CDX2 -,
Skin adnexa Skin CK7+,
(non-Paget -
Adnexal CK20 -,
type) CDX2 -,
Non-CRC Variable +/- Variable

metastases
Modified from: WHO Classificaiton of Tumours: Digestive System Tumours. 5th Ed.
Neuroendocrine Neoplasms
Neuroendocrine Carcinomas are much more common than well-differentiated neuroendocrine tumors.
Neuroendocrine Carcinomas:
Sheet-like growth
Not Graded. Ki67/Mitotic index >20% (often much higher).


Ki67 often in 60-80% range.
Melanoma
Malignant transformation of melanocytes present in the anal
mucosa/transition zone.
Very rare.
Typically old/elderly patients. More common in women.
Typically polypoid masses near dentate line.
Typically epithelial morphology. Large, malignant cells with

frequent Macronucleoli.
Dusky greyish cytoplasm with frequent pigmentation.
IHC: Typical melanocyte markers (S100, SOX10, HMB45, Melan-A)
Molecular/Therapeutics:
BRAF mutations→ BRAF inhibitors (e.g., vemurafenib)
CKIT mutations→ tyrosine kinase inhibitors (e.g., imatinib)
Poor prognosis.
Lower Anogenital Squamous Tract

Similar terminology is used for all HPV-associated squamous lesions of the lower anogenital tract (See LAST project)
HPV-infection: Type 1 → Infects epithelium to support virion production → LSIL/Condyloma (often transient, self-limited)
Type 2 → Viral oncogene overexpression drives a clonal production of undifferentiated cells → HSIL (precancerous)
Low-Grade Squamous High-Grade Squamous

Intraepithelial Lesion Intraepithelial Lesion
(LSIL) (HSIL)
Normal -IN 1 -IN 2 -IN 3 (SCCIS)
Koilocytosis None Present Maybe Maybe

Dysplastic Absent, but nerves may Limited to lowest 1/3 Extend to 2/3 Full-Thickness
basal cells be more prominent
Mitoses Basal layer only Limited to lowest 1/3 Extend to 2/3 Full-Thickness
P16 IHC Negative Negative Block Positive Block Positive
LAST Project: Darragh TM, et al. The Lower Anogenital Squamous Terminology Standardization Project for HPV-Associated Lesions. Arch Pathol Lab Med. 2012 Oct;136(10):1266-97.
Different abbreviations for different sites: When to use P16 Immunohistochemistry
Site abbreviation + IN Used as surrogate marker of High-risk HPV infection
AIN: Anal Intraepithelial Neoplasia • When the morphologic DDX is between HSIL (P16 +) and a mimic, such
PaIN: Perianal Intraepithelial Neoplasia as squamous metaplasia (P16 -)
PeIN: Penile Intraepithelial Neoplasia • When you are considering a Dx of -IN2, which should be P16+ (vs. LSIL,
CIN: Cervical Intraepithelial Neoplasia which should be P16 -)
VaIN: Vaginal Intraepithelial Neoplasia • When there is disagreement between pathologists
VIN: Vulvar Intraepithelial Neoplasia • When there is a high-risk for missed HSIL disease (e.g., HPV +)
LSIL Cytologic changes
Mature Keratinocytes (with lots of cytoplasm) with:
• Enlarged nuclei (>3x normal intermediate cells)
• Nuclear membrane irregularities
• Hyperchromasia (“Rasinoid”)
• Perinuclear halos
• Multinucleation
P16 Positive P16 Negative

Strong, diffuse, nuclear and cytoplasmic, Weak/Patchy
block staining along the basal layer going i.e., Anything but “Block” positive
at least 1/3 of the way up
When P16 Immunohistochemistry will NOT help

HSIL Cytologic changes
• When the biopsy is unequivocally LSIL, HSIL, or Negative morphologically
Immature keratinocytes (minimal cytoplasm, High N/C ratios)
• When the DDX is between LSIL and Negative, as both processes are P16
with:
negative.
• Irregular nuclear contours (Hint: think in 3-dimensions)
• Increased nuclear size
• Increased mitoses Human Papilloma Virus (HPV)
Sexually Transmitted Disease
Serotypes: 16 &18 → Most associated with HSIL/SCC
6 &11 → Most associated with LSIL/Condylomas
HPV-associated oncoprotein E6 inactivates p53, E7 inactivates Rb
Usually infects transition zone between squamous and glandular
mucosa.
Mesenchymal Tumors of the Gastrointestinal Tract

Gastrointestinal Stromal Tumors (GISTs)
Derived from interstitial cells of Cajal
Stains: (+) CD117 (cKit), DOG1, CD34
Most common in Stomach (60%) followed by Small Bowel (30%)
Most often spindled, but can be epithelioid or pleomorphic
Mutually exclusive cKIT (80%) or PDGFRA (10%) receptor tyrosine kinase mutations→ often shrink pre-
operatively with receptor tyrosine kinase inhibitors (e.g., imatinib)
Increased in NF1 patients
Can estimate risk of progressive disease (see table at end of guide)
SDH-mutated type (without a cKit mutation)→ pediatric/familial

Carney-Stathakis syndrome→ paraganglioma and GIST with germline SDH mutation
Carney’s Triad→ GIST, pulmonary chondroma, paraganglioma, somatic SDH mutation
Epithelioid, multinodular, metastasize to lymph nodes, don’t respond to RTK inhibitor therapy
(no Ckit mutations!), but overall more indolent; Characterized by loss of SDHB staining
Neural Origin (arise from myenteric plexus or other nerves)

Schwannoma
Benign nerve sheath tumor with Schwannian differentiation
Most common in stomach in muscularis propria. Well-circumscribed. Unencapsulated.
Spindle cell proliferation with varying cellularity. Often have a lymphoid cuff, but Verocay bodies and
hyalinized vessels often absent (unlike elsewhere)
Stains: (+) S100 (strong, diffuse)
Mucosal Schwann cell hamartoma

Small, sporadic, benign, presenting as a colon polyp
Uniform bland spindled cells expanding lamina propria between crypts.
Stains: (+) S100
Granular cell tumor

Benign neoplasm with neuroectodermal differentiation.
Often esophagus, submucosal→ look out for pseudoepitheliomatous hyperplasia (SCC mimic)
Epithelioid to spindled cells with abundant eosinophilic granular cytoplasm highlighted by PASd
Full of lysosomes due to inactivating mutations in ATP6AP1 or 2 (makes it so can’t break down
lysosomes)→ granular appearance
Stains: (+) S100, CD68, Inhibin, Calretinin
Perineurioma
Benign peripheral nerve sheath tumor composed of cells with perineurial differentiation
Typically, colonic, small, and solitary. Can be associated with a serrated polyps.
Bland spindled cells expanding lamina propria and distorting glands.
Stains: (+) EMA (weak), GLUT1, clauidin-1
Ganglioneuroma
Benign neoplasm composed of mature ganglion cells and nerves (unmyelinated axons with Schwann
cells). Usually in the colorectum.
When multiple/diffuse and/or syndrome-related (MEN 2b, Cowden, and NF1)→ Ganglioneuromatosis
Usually sporadic, small mucosal polyps detected incidentally.
Diffuse mural involvement strongly associated with MEN2B (RET mutation)
Stains: Schwann cells (+) S100, Ganglion cells (+) Synaptophysin, neurofilament
Gangliocytic paraganglioma
Most common in second part of the duodenum, mostly benign
3 characteristic elements: 1) Epithelioid neuroendocrine cells (think paraganglioma),
2) Ganglion cells,
3) Spindled Schwann cells
Stains: (+) S100 in Schwann cells, (+) Synaptophysin in neuroendocrine cells
Muscle Origin
Stains: (+) Desmin, Caldesmon, Actin; (-) Neural markers and GIST markers
Leiomyoma
Benign smooth muscle tumors, Most common in colorectum (< 1 cm, polypoid arising from muscularis
mucosae, pedunculated, asymptomatic) and esophagus (Larger, arising from muscularis propria,
symptomatic)
Bland, spindled cells, fascicular architecture
Minimal mitotic activity (<1 per 50 HPF) and no tumor-type necrosis
Leiomyosarcoma
Malignant smooth muscle tumors, aggressive. Spindle cell neoplasms with atypia, mitoses, and/or
necrosis.
If multiple smooth muscle tumors in an immunosuppressed patient→ consider an EBV-associated

smooth muscle tumor
Rhabdomyosarcoma
Malignant tumors with skeletal muscle differentiation.
Stains: (+) Myogenin, MyoD1
Multiple subtypes (see small round blue cell tumor guide)
Fibroblastic Origin
Fibromatosis (“Desmoid fibromatosis” or “Mesenteric fibromatosis”)
Most common in small bowel mesentery; usually large
Bland, spindled cells in long, sweeping fascicles. Infiltrative growth.
Locally aggressive, non-metastasizing.
Stains: + nuclear β-catenin (80%), may stain with smooth muscle actin
WNT/ β-catenin signaling dysregulation due to somatic CTNNB1 or germline APC mutations (so see with
Familial Adenomatous Polyposis)
Inflammatory fibroid polyp

Benign. Most common in stomach, proximal duodenum, or ileum→ can cause intussusception
Centered in submucosa but extend to mucosa
Spindled to plump cytologically bland spindled cells and associated eosinophils and lymphocytes; often
myxoid background. Cells proliferate/circle around vessels→”onion-skinning”
Stains: (+) CD34
Molecular: PDGFRA mutations
Inflammatory myofibroblastic tumor (“IMT”)
Usually in children and young adults
Bland, spindled to stellate cells in myxoid to collagenous stroma with associated lymphoplasmacytic
inflammation.
Stains: ~50% stain with ALK (also detect with FISH), variable staining with myoid markers
Molecular: ~60% have ALK rearrangements; ~5% show ROS1 fusions
Low risk for recurrence; very rare metastases
Solitary Fibrous Tumor (“SFT”)

Adults with slow-growing mass in any anatomic site
Bland ovoid to spindled cells with “patternless pattern” (haphazard), “Stag-horn vessels,” variable
cellularity and collagen.
Stains: (+) STAT6, CD34
Molecular: NAB2-STAT6 rearrangement→ best seen with STAT6 IHC
Vascular Origin
Glomus Tumor
Derived from modified smooth muscle cells of the perivascular glomus body.
Most common in stomach, usually benign.
Round, uniform nuclei with pale eosinophilic polygonal cytoplasm arranged in sheets and nests
Richly vascular, hyalinized stroma. Can be mistaken for NET morphologically.
Stains: (+) Smooth muscle actin
Lymphangioma
Benign, lymphatic tumor.
Most common in small intestine. Often congenital, presenting in childhood.
Thin-walled, dilated spaces with a single layer of endothelial-lined lymphatic spaces containing chylous
or serous material.
Lymphangiomatosis—multicentric or extensively infiltrating lymphangioma.
Stains: (+) CD31, D2-40
Hemangioma
Can be in any organ. Benign, but can bleed. Varying morphologies with different caliber vessels (e.g.,
Cavernous)
Should NOT see: Papillary growth, multilayering, cellular atypia, mitoses, and necrosis
Stains: (+) ERG, CD31, CD34
Kaposi Sarcoma
HHV8-associated vascular neoplasm often occurring in immunocompromised patients (classically AIDS)
Infiltrating small, irregular vascular channels and fascicles of non-pleomorphic spindled epithelioid cells.
Erythrocyte containing clefts. Hyaline globules. Associated inflammation.
Stains: (+) CD31, CD34, ERG, HHV8 (LANA-1)
Often asymptomatic, can bleed
Angiosarcoma
Malignant vascular tumor with endothelial differentiation. Aggressive.
Often high-grade malignant tumors with nuclear atypia, mitoses, and necrosis. Can be epithelioid.
Variably vasoformative, with anastomosing vessels to solid sheet-like growth
Stains: (+) ERG, CD31, CD34; Epithelioid angiosarcomas can stain with CK
Adipocytic differentiation
Lipoma
Benign tumor composed of mature adipocytes.
Can occur anywhere. Most common in colon in submucosa. If mucosal→ possible Cowden’s syndrome
Well-differentiated liposarcoma/Atypical lipomatous tumor

Malignant adipocytic tumor.
Often lipoblasts or atypical cells with smudged nuclei in fibrous septae
MDM2 amplifications by FISH
Rare
Plexiform Fibromyxoma
Benign tumors that arise in the stomach antrum/pylorus
Multinodular, centered in muscularis propria composed of bland spindled cells in myxoid stroma
Synovial Sarcoma
Malignant spindle cell (“monophasic”), possibly with epithelioid to glandular component (“biphasic”)
Uniform spindle cells with almost no matrix and somewhat vesicular nuclei
Characteristic SS18 gene rearrangements
Patchy keratin and EMA
Gastrointestinal Clear Cell Sarcoma-like tumor (GNET)

Malignant sarcoma with neuroectodermal differentiation (also called GNET)
Alveolar/nested architecture; epithelioid to spindled cells with eosinophilic to clear cytoplasm, vesicular
chromatin, and prominent nucleoli; scattered multinucleated giant cells.
Stains: (+) S100, HMB-45, MelanA, and MiTF FISH: EWSR1 translocation
Perivascular epithelioid cell tumor (“PEComa”)

Mostly epithelioid cells with some spindled component. Cytoplasm granular, eosinophilic to clear.
Admixture of adipocytes, epithelioid cells, and intimately associated thick-walled blood vessels.
Variable expression of smooth muscle and melanocytic markers
Stains: HMB-45, also often Melan-A, MITF (and smooth muscle markers)
Marked nuclear atypia and mitoses→ risk of metastatic behavior
Basic Mesenchymal GI tumor Immunohistochemistry Panel
First Round:
CD117 (ckit) →GIST
DOG1
Desmin → Smooth Muscle tumors
S100 → Neural Tumors (and other, rarer, neural crest tumors)
Second Round (less common tumors):

EMA→ Perineurioma
Nuclear β–Catenin→ Fibromatosis
ALK→ Inflammatory myofibroblastic tumor
Melan-A→ GNET, PEComa
Calretinin, CD68→ Granular cell tumor
SMA→ Myofibroblastic or muscle differentiation (or Glomus)
CD31 or ERG → Vascular tumors
CD34→ Vascular tumors, GIST, Inflammatory fibroid polyp, some NF cells
Gastrointestinal stromal tumor prognosis
Miettinen and Lasota, Arch Pathol Lab Med—Vol 130, October 2006
GI Tumor Syndromes
Lynch Syndrome aka Hereditary Nonpolyposis Colorectal Cancer (HNPCC)
Germline mutations with mismatch repair (MMR) enzymes. Autosomal Dominant
→ defective DNA repair → tons of mutations (“hypermutated”) → microsatellite unstable
Most common form of heritable CRC (colorectal cancer)
CRC usually develops before age 50, often with multiple primaries (~80% lifetime risk)
Also at risk for: Endometrial cancer, Upper urinary tract and other GI cancers, and Sebaceous skin tumors
Universal screening of all new CRC. Do IHC first (algorithm below), can also do MSI testing by PCR.
Looking for LOSS of staining. Normal is intact staining of all 4 MMR enzymes.
Lynch-related CRC is more often right-sided and arises from adenomas
(vs. sporadic MMR-deficient tumors, that come from SSP/A’s, and are associated with BRAF V600E
mutations and then MLH-1 promoter hypermethylation and MLH1 loss of expression)
Universal Testing in ALL newly diagnosed CRC: MMR IHC
MMR Intact MSH2, MSH6, or PMS2 MLH1 Deficient

Note: DNA polymerase (POL) Deficient
(with PMS2)
ε and δ mutations can result
with a similar clinical Probably Probably
BRAF
phenotype NOT lynch Lynch
(sporadic) Testing
Germline
Testing BRAF
No BRAF
Mutation
MMR-deficient CRC: Sporadic

MLH1 Methylation
testing
Associated with high-grade, mucinous differentiation, and
lymphocytic infiltrates (hypermutated state is immunogenic). No
Methylation
Methylation
Better survival compared to MMR-intact CRC (probably due to
host response). Automatically approved for anti-PDL1 therapy. Probably
Sporadic
Lynch
Peutz-Jeghers Mutation in the STK11/LKB1 gene on chromosome 19

Can be sporadic or inherited
Classic polyps are Hamartomas (non-neoplastic)
Most frequent in small intestine, can remove with polypectomy
Multilobated, may have papillary or frond-like surface
Arborizing smooth muscle
Generally cytologically bland epithelium
Often pedunculated → cause intussusception
Also see: Mucocutaneous melanotic macules (lips and oral mucosa)

Increased risk of many cancers
(e.g., Stomach, Colon, Pancreas, Breast, etc…)
Ovarian SCTAT’s, Sertoli cell tumors, Cervical adenoma malignum
Familial Adenomatous Polyposis aka FAP
Germline mutation in APC gene. Autosomal Dominant
Tumor suppressor → Loss leads to lots of tumors
Hundreds of colorectal adenomas carpeting colon, more on left side
Almost complete penetrance
Mean age of CRC diagnosis: 40 yrs (so often prophylactic colectomy in 20’s)
Also at risk for duodenal and gastric adenomas (less cancer risk though)
Need to undergo regular surveillance upper endoscopies also
First morphologic finding: Single dysplastic crypts (“unicryptal adenoma”)
Variants:
Attenuated FAP – Less than 100 adenomas, right-sided, older age of
presentation and CRC. Mutation in different part of APC gene.
Gardner’s – FAP with prominent extraintestinal manifestations (including:
Desmoid tumors, Osteomas, Epidermoid cysts, Papillary thyroid carcinoma
(classically the cribriform-morular variant variant), and nasopharyngeal
angiofibromas)
Turncot’s – “Glioma polyposis syndrome.” FAP with brain tumor (usu.
Medulloblastoma)
MYH-Associated polyposis
Autosomal recessive (need biallelic germline mutations for phenotype)
MYH gene involved in base excision repair → defects result in APC and RAS mutations
Multiple adenomas (usu. < 100), may have extraintestinal manifestations of FAP
Increased risk of CRC, usu. Right side, even in absence of polyps
Hereditary Diffuse Gastric Cancer

Most common mutation: CDH1 (E-cadherin). Autosomal Dominant
E-cadherin is important for cell adhesion and tumor suppression
→ Mutation causes uncontrolled growth of poorly-cohesive cells
Many families have other mutations, so use clinical criteria often
>70% risk of gastric cancer by 80 yrs

Endoscopic surveillance is likely inadequate as invisible in situ
Many get prophylactic gastrectomies
Women at increased risk for lobular breast cancer
Classic finding: Signet ring carcinoma in situ

Signet ring cells above basement membrane
Pagetoid spread
Can then progress to invasive, diffuse gastric cancer
Often Multifocal Q: What other tumor has loss of E-cadherin?
A: Lobular breast cancer! Makes sense, right?
Juvenile Polyposis JP’s can be sporadic (much more common, esp. if few) or Hereditary
Defined as ≥5 Juvenile polyps, or any number if positive family history

Germline mutations in SMAD4 or BMPR1A
Present with bleeding → anemia
Usu. 50 – 200 polyps
Can develop dysplasia and CRC. Age or CRC ~35 yrs
Need increased surveillance
Polyps are pedunculated with cystically dilated cysts
Loose, edematous with inflamed stroma and ulceration
Cronkhite-Canada Uncertain etiology (NOT clearly genetic), Non-familial

Often older male (~50 yo)
Hamartomatous polyps and protein-losing enteropathy
Diffusely nodular mucosa throughout GI tract
Broad, sessile polyps with edema and cystic dilations
In stomach, look like HP. In colon, look like JP
“Ectodermal” manifestations: onychodystrophy, alopecia,
cataracts, glossitis, vitiligo
Increased risk of colon cancer, but PLE is often more

dangerous!
COWden Syndrome Think of this cow

Uterine Cancer
(because of the bow… get it?
PTEN mutation. Autosomal dominant
Tumor suppressor → lots of different tumors
Other PTEN syndromes include: Bannayan-Riley
Ruvalcaba syndrome and Lhermitte-Duclos disease
Get:
Multiple hamartomas (mouth, GI tract)
Thyroid carcinoma (usually Follicular)
Breast Cancer (high risk) Thyroid Cancer
Endometrial Cancer
TrichileMMOOOOmas
Breast CA
Lipomas
Esophagus: Glycogen acanthosis
Stomach: Polyps that often resemble HP’s
Colon: Stroma-rich polyps with cystically dilated glands
Can mimic JP’s.
Can contain Adipocytes in lamina propria (relatively unique)
Can get ganlgioneuromatous polyps
Is it a Hamartoma?
Polyp with:
Epithelial hyperplasia,
Dilated & distorted glands,
Lamina propria edema,
Chronic inflammation
Does it have a prominent smooth muscle component?
Yes No
Does it have: Are there other cell types?

Arborizing smooth muscle, Adipocytes
Smooth Muscle wisps in the lamina propria, Nerves
Lobular configuration of glands?
Yes No
Yes No
Hamartomatous polyp
Consider Does thee background
Peutz-Jeghers Are there other cell
Polyp Cowden Syndrome mucosa show gastritis or
types present? (and other PTEN Intestinal metaplasia?
Adipocytes syndromes)
Nerves
Yes
Yes Most likely Hyperplastic polyp or

Inflammatory polyp
Nonspecific:
No Hamartoma vs Hyperplasia
DDX: Hyperplastic/inflammatory polyps,
Prolapse polyp, Juvenile polyp, Peutz-
Jegher’s polyp, etc… No Most likely Juvenile Polyp or
Inflammatory polyp
Consider Cronkhite-Canada
Background not sampled Syndrome
Background identical to polyps

Ganglion cells & Nerves Adipocytes
See either of these?

Think Cowden syndrome
Can confirm there are adipocytes
(and not air) with S100 IHC
Modified from: A Pattern-Based Approach to Neoplastic Biopsies: Atlas of Gastrointestinal Pathology. Lam-Himlin et al. 2019
GI Neuroendocrine Tumors
Neuroendocrine tumors “Neuro”→ contain secretory granules (like synaptic vesicles)
“Endocrine”→ secrete peptides and amines locally
Tumors can arise anywhere in the GI tract. They have characteristic morphology and protein expression.
Immunohistochemical markers: (Note, these may also recognize neurons and neuroblastic cells)
Synaptophysin and Chromogranin→ recognize the dense core granules
CD56 and Neural-Specific Enolase (NSE) → Less specific
Often “dot-like” perinuclear staining with cytokeratin; INSM1→ New NE transcription factor (nuclear stain)
Well-Differentiated Neuroendocrine Tumors

Morphology: Uniform, round nuclei
aka “carcinoid”
“Salt and Pepper” fine, speckled chromatin
Granular cytoplasm
Organoid architecture (i.e., nested, cords, glands-like rosettes, or ribbons)
No necrosis. Variable stroma. Can see amyloid deposition.
Molecular: MEN1, DAXX, ATRX mutations common

(particularly in the pancreas)
Malignant, but slow-growing, indolent progression.

Early NETs have a low risk of metastasis
Somatostatin receptors→ can detect with “DOTA” PET radiographically
Graded 1-3 based on Ki67/Mitoses (see next page)
Poorly-Differentiated Neuroendocrine Carcinomas

Sheet-like growth
Not Graded


Ki67 often in 60-80% range
Mixed Neuroendocrine-Non-neuroendocrine Neoplasms (MiNEN)
Adenocarcinoma A neuroendocrine tumor or carcinoma with a non-
neuroendocrine component (both >30% of tumor)
Can be adenocarcinoma, squamous cell carcinoma,

etc..
Presumed to be clonally related

(A non-neuroendocrine carcinoma
Small Cell NEC
dedifferentiates/transdifferentiates to a NEC)
Common sites
Most Neuroendocrine Tumors are well-differentiated. NETs are overall relatively rare.
In GI tract, they are often polypoid and centered in the submucosa or muscle with intact overlying
mucosa.
Small intestine—most common site, often in ileum. Tend to present later, with advanced disease (either
liver metastases, or large lymph node metastases at root of mesentery).
Appendix—often small and incidental.
Rectum
Stomach—three distinct setting/types (see separate stomach tumor guide)
Pancreas—arise in the pancreatic parenchyma (from islets) and grow into the peripancreatic fat, or, less
commonly, into the pancreatic duct.
Site of Origin NET metastasis with unknown primary? We can do a panel of stains to try to
locate the primary. Also, the clinician can do a DOTA-PET
CDX2→ Small intestine TTF1→ Lung IL1→ Pancreas/Rectum SATB2→ Rectum
Grading
Classification/Grade Ki67 Proliferation Index Mitotic index
Well-differentiated
Grade 1 <3% <2
Grade 2 3-20% 2-20
Grade 3 >20% >20
Poorly-differentiated
Small cell type >20% >20
Large Cell type
Ki67 Proliferation index based on evaluation of ≥ 500 cells in a “hot spot.”

Mitotic count based on evaluating 50 Hpfs, but reported per 10 Hpfs.
Noteworthy Variants
Cystic: although most NET’s are solid, some, particularly in the
pancreas, can undergo central cystic degeneration
Pleomorphic nuclei: “endocrine atypia” seen in endocrine organs can
be seen in WD-NET. These changes appear to be degenerative, are not
associated with a higher Ki67, and have no prognostic importance.
Oncocytic: abundant granular oncocytic cytoplasm with eccentric
nuclei, appearing rhabdoid. Can have pleomorphic nuclei to.
Somatostatinoma: often ampullary with a glandular appearance and
psammomatous calcifications. Can be mistaken for an adenocarcinoma.
Clear cytoplasm: associated with Von Hippel Lindau
Lipid-rich: lots of small lipid vacuoles
“Adenoma-Carcinoid:” Rarely, small neuroendocrine clusters are found
incidentally next to an adenoma in a polypectomy. The NE proliferation
is typically small, and is possibly reactive to the “tumor milieu.”
Tumor Syndromes “Functioning”→ hormone secreting → characteristic syndrome

Functioning tumors are often pancreatic and discovered sooner due to symptoms.
Non-functioning tumors are often discovered later (with metastases) or incidentally.
Insulinoma→ Usu. Small, present early with hypoglycemia
Gastrinoma→ Zollinger-Ellison Syndrome → acid hypersecretion → extensive peptic ulcers
Associated with MEN1, most commonly tumor in proximal duodenum
VIPoma→ Watery diarrhea with hypokalemia and achlorhydria
Glucagonoma→ Necrolytic migratory erythema, diabetes, stomatitis
Somatostatin → diabetes, cholelithiasis, diarrhea → can have glandular growth and psammoma bodies
“Carcinoid syndrome”→ Serotonin and Kallikrein secretion → Flushing, diarrhea, bronchoconstriction.
Usu. Only if liver metastases. Elevated serum 5-HT and/or urine 5-HIAA
Family Syndromes
MEN 1: Majority develop NETs (Pancreas > stomach/duodenal). Often multifocal proliferation of islets,
with microadenomas (<0.5 cm, non-functional) and WD-NET’s (>0.5 cm or functional). Also, Pituitary
adenoma, parathyroid hyperplasia, bronchial and thymic NETs.
Neurofibromatosis 1: Increased risk of WD-NET (in addition to lots of tumors, like neurofibromas,
MPNST’s, GISTs, etc…), particularly ampullary somatostatinomas.
Von Hippel Lindau: Can have WD-NET’s with clear cells. Also, hemangioblastomas, clear cell renal cell
carcinomas, and adrenal tumors.
Tuberous Sclerosis: Pancreatic insulin and somatostatin-producing NET. Also, angiomyolipomas and
other hamartomas
CHAPTER 3
Liver, Bile Ducts,

Gallbladder, and
Pancreas
Updated: 4/1/2020 Prepared by Kurt Schaberg
Medical Liver
Steatosis/Steatohepatitis Steatosis = Abnormal accumulation of fat within
hepatocytes
Steatohepatitis = Fat + inflammation, acidophil
bodies, and/or ballooning (active lobular injury)
These are part of the same disease process, and
both lead to fibrosis, but steatohepatitis leads to
fibrosis faster (essentially a difference in grading
activity).
Portal infiltrates may be present, but are usually
mild. If they are severe, consider additional Dx’s.
Ballooned hepatocytes: Enlarged (such that they

“stand out”) with no fat and thin, wispy
Macrovesicular cytoplasm. Most often Zone 3.
Represents a change in lipid metabolism
Predominant pattern = Nucleus pushed to the side by usually a single medium to large sized droplet
Ok to have smaller droplets mixed in also
Microvesicular
Usually represents mitochondrial injury
Nucleus remains central with innumerable, fine fat droplets
Only use this term if it is a diffuse change (not focal, or in a mostly macrovesicular case)
Quantifying Fat Amount of Fat Grade
Estimate the % of cells with macrovesicular steatosis <5% Normal

Average over the entire specimen 5-33% Mild
Report rounded to the nearest 10%
34-66% Moderate
Often found in zone 3 first. >67% Severe
Fibrosis
Fatty liver disease causes pericellular, pericentral
fibrosis first (where the most fat is)
→ Progresses to portal and pericentral fibrosis
→ Bridging fibrosis
→ Cirrhosis
Once cirrhotic, there may be relatively little fat!

Pericellular fibrosis
Alcoholic Hepatitis
Hepatocyte injury and inflammation resulting from
chronic alcohol consumption
AST/ALT ratio typically >2

Micro: Steatosis, Findings that Favor EtOH: More
hepatocyte ballooning, more neutrophilic lobular
inflammation (black arrow), More Mallory-Denk bodies
(red arrow), lobular cholestasis, and more, diffuse
pericellular fibrosis
Mallory-Denk Bodies = pink, ropey cytoplasmic

inclusions = ubiquitinated cytokeratins. Cells also loose
expression of CK8/18.
But Histology can be identical to NASH!
Non-Alcoholic Steatohepattis (NASH)

Associated with metabolic syndrome, including
obesity, type 2 diabetes, dyslipidemia, hypertension
Micro: Steatosis, Ballooning, Lobular lymphs and

Neuts (exception in pediatric patients, where
inflammation is more portal), acidophil bodies,
and Pericellular fibrosis.
Sometimes adults have mild portal inflammation,
mostly lymphs.
Grade/Stage using NASH-CRN system:
Fibrosis
0 None
1a Mild zone 3 sinusoidal fibrosis
1b Moderate zone 3 sinusoidal fibrosis
1c Portal fibrosis only
2 Zone 3 sinusoidal fibrosis and portal fibrosis
3 Bridging fibrosis
4 Cirrhosis
Steatosis Lobular Inflammation Hepatocellular Ballooning

0: <5% 0: None 0: None
1: 5-33% 1: <2 foci/20x field 1: Mild, few
2: 34-66% 2: 2-4 foci/20x field 2: Moderate-marked, many
3: >66% 3: >4 foci/20x field
Sum the individual components for a total grade (maximum of 8)

Wilson’s Disease Mutations of copper transport protein (ATP7B gene)
results in inability to excrete copper in bile → accumulate
copper in liver and other tissues
Variable presentation: Acute or chronic liver disease,
neurologic/psychiatric findings, hemolytic anemia, ±
Kayser-Fleischer rings
Labs: Low ceruloplasmin, Increased urine copper, AST/ALT
ratio >2.2, Alk phos/T. Bili <4
Micro: Variable! Steatohepatitis, possible Malory-Denk
bodies and glycogenated nuclei; Later chronic hepatitis
When considering diagnosis→ send block for copper

quantification
Total Parental Nutrition Variable steatohepatitis or cholestasis depending

on age
Infant Kids Adult
Steatosis/Steatohepatitis
Cholestasis
Other causes of Macrovesicular steatosis

Drugs including: Amiodarone, Glucocorticoids, methotrexate, tamoxifen, and certain chemotherapeutic
agents
Other conditions, including: Malnutrition (marasmus or kwashiorkor), hormone alterations (e.g.,

hypothyroidism, elevated cortisol, growth hormone deficiency), cystic fibrosis, and lipodystrophies.
Microvesicular steatosis
Finely divided fat cells accumulate in cytoplasm
as a result of Mitochondrial damage, which is
often serious
DDX: Reye’s syndrome, inborn errors of

metabolism, Drugs, Toxins, Acute fatty liver of
pregnancy
Portal Tract Chronic Inflammation Basic DDX: viral, autoimmune, drug
Chronic Hepatitis C ~90% Develop chronic infection; Bloodborne

Antibodies (anti-HCV) indicate exposure
Detection of HCV RNA indicates virus persistence
Newer Meds: Ledipasvir/sofosbuvir (Harvoni) → highly effective
Slow, silent, progressive disease (over decades)
→cirrhosis (risk of HCC)
Micro: Variably dense portal lymphocytic infiltrates
Periportal interface activity
Scattered lobular collections of inflammatory cells ±
acidophil bodies
Portal lymphoid aggregates
Rare plasma cells allowed.
Viral Hepatitis: Distinguishing Acute vs Chronic:
Often use clinical definition = elevated liver enzymes for ≥6 months.
Fibrosis also indicates chronic damage. Diffuse moderate lobulitis means acute or acute-on-chronic.
Stage viral hepatitis using Batts-Ludwig, Ishak, Sheuer, or METAVR systems (fairly similar)
Chronic Hepatitis B ~10% Develop chronic disease; Bloodborne

Micro: Portal chronic inflammatory infiltrates
Interface activity, Lobular hepatitis
Ground glass inclusions
Sanded nuclei
IHC: HBsAg = infected, HBcAg = actively replicating
Fibrosing Cholestatic Hep B: Variant with more

progressive/worse disease. Usu. Immunosuppressed state (e.g.,
post-transplant). Extensive cholestasis, bile ductular reaction,
hepatocyte swelling, and fibrosis
Hepatitis D: Requires Hep B → acute-on-chronic hepatitis
Autoimmune Hepatitis Strong Female Predominance

Elevated AST/ALT (often marked)
Serology: + anti-Smooth Muscle Antibody, ANA, LKM-1,
Elevated IgG
Micro: Dense portal infiltrates with marked interface
activity → Lymphs & Plasma Cells
Lobular injury
Regenerative rosette formation
Can have “Overlap” with PBC
See Scoring Rubric on next page.
Criteria for Autoimmune Hepatitis:
Finding Cutoff Points
Autoantibodies (maximum 2 points!)
ANA or SMA ≥ 1:40 1
ANA or SMA ≥ 1:80 2
LKM ≥ 1:40 2
SLA Positive 2
Serum IgG
> Upper limit of normal 1
> 1.10 times the upper 2
limit of normal
Histology
No evidence of hepatitis Disqualifying
(Not AIH!)
Atypical for AIH 0
Compatible with AIH 1
Typical of AIH 2
Absence of viral hepatitis
Viral serology all negative 2
Scoring:
≥6: Probable AIH
≥7: Definite AIH
Histology:
Typical: 1) Lymphoplasmacytic interface hepatitis extending into
the lobule, 2) Regenerative rosette formation, 3) Emperipolesis
Compatible: Chronic hepatitis with lymphocytic infiltration

without all the features considered typical
Atypical: Signs of another diagnosis, such as steatohepatitis
Modified from: Hennes EM et al. Simplified criteria for the diagnosis of autoimmune hepatitis. Hepatology. 2008 Jul;48(1):169-76.
Graft-vs-host Disease (GVHD)
Usually post-stem cell transplant (transplanted immunocompetent
T-cells attack new host)
Involves skin, liver, GI tract → rash, ↑LFTs, diarrhea, and vomiting
Micro: Bile duct epithelial injury (lymphocytic inflammation,
withering, drop out)
Mild portal inflammation; Possible endothelitis
Rejection Immune-mediated inflammation/damage in transplanted liver.
T cell-mediated rejection
Formerly: Acute Cellular Rejection
Micro: 1) Mixed portal tract inflammation (lymphs,
including activated lymphs, Eos, etc..), 2) Bile duct
damage/inflammation, 3) Endothelitis
Plasma cell-rich rejection

Formerly: de novo autoimmune hepatitis
Micro: Portal and/or central plasma cell-rich (>30%) infiltrates and lymphocytic cholangitis
Note: Original disease MUST not be autoimmune hepatitis (otherwise, classify as recurrent autoimmune
hepatitis likely)
Chronic rejection
Micro: Bile duct injury→ eventual loss/paucity; Also often lose hepatic arterioles.
Chronic vascular damage with foam cell arteriopathy and luminal narrowing
Antibody-mediated rejection
Micro: Portal vascular dilation, endothelial
hypertrophy, and arteritis, Often edematous portal
tract and cholestasis.
C4d IHC showing >50% staining of vein and capillaries;
Positive Serum Donor-specific Antibody (DSA)
C4d
Lobular Injury Indicates an acute process (too injurious to be chronic!)
Often very high transaminases.
Lobular disarray (normal plate structure disrupted)
Lobulitis (lymphs attacking hepatocytes in lobule)
Acidophil bodies (apoptotic hepatocytes)
Acute Viral Hepatitis

Usu. due to Hep. A or B
(Hep A and E are spread by fecal-oral; “the
vowels hit the bowels”)
Diagnosis confirmed with serology or serum PCR.
Micro: Lobular damage and disarray

Diffuse lobular inflammation
Hepatocyte ballooning/swelling
Hepatocyte necrosis and regeneration
May see mild portal and periportal inflammation
NO fibrosis
Drug reaction
2 chief mechanisms: Intrinsic (predictable, dose-dependent, less inflammation, more necrosis) vs.
Idiosyncratic (majority of cases, not dose-dependent, more inflammation)
Herbal and botanical drugs are important but often overlooked cause of hepatotoxicity
Very Diverse findings. Can mimic many other disorders (e.g., Autoimmune hepatitis)
https://livertox.nih.gov/
Idiopathic Neonatal Hepatitis

aka Neonatal giant cell hepatitis
Neonatal jaundice with hepatomegaly, elevated T. Bili and Conj.
Bili, variable AST/ALT
Diagnosis of exclusion (must exclude biliary atresia)
Loose association with hypopituitarism
Micro: Lobular disarray with prominent giant cell transformation

Absent to mild lobular inflammation (despite name)
Canalicular and hepatocellular cholestasis
Minimal portal tract changes and preserved bile ducts
Cholestasis/Biliary Labs: Elevated Alkaline phosphatase, GGT, and serum bilirubin.
Can highlight bile ducts with CK7 and CK19. Often see increased
copper deposition in periportal hepatocytes with cholestasis.
Large Duct Obstruction Mechanical blockage of bile ducts (by gallstones, stricture,
or tumor)→ usually diagnosed clinically
Micro: Portal tract edema, mixed inflammation with

prominent neutrophils, and bile ductular reaction
Canalicular and/or ductular cholestasis
Additional considerations:
Lots PMNs in duct epithelium or lumen→ consider
ascending cholangitis
Can see prominent bile ductular reaction with extensive
necrosis/hepatitis as part of liver regeneration (so look
for lobular injury!)
Primary Biliary Cholangitis aka Primary Biliary Cirrhosis
Autoimmune disease with destruction of intrahepatic bile

ducts
Usu. Older women with +AMA serology (M2 subtype)
Micro: Moderate portal chronic inflammation.
“Florid duct lesion”→ lymphocytic cholangitis with bile
duct injury, +/- Granulomas
Often causes bile ductular reaction and bile duct paucity
Primary Sclerosing Cholangitis

Progressive fibrosis and stricturing of bile ducts—predominantly seen
extrahepatic, but also intrahepatic
Often diagnosed by cholangiography (multiple strictures)
→ Increased risk of cholangiocarcinoma
Frequently young to middle-age men; Strong association with UC

Micro: Classically, Concentric fibrosis of ducts—“Onion Skin”
(but not often seen on bx)
Biliary obstruction pattern (edema, pmns, ductular reaction)
Eventual bile duct obliteration by fibrosis with ductopenia
Biliary Atresia
Idiopathic prenatal destruction/fibrosis of extrahepatic bile ducts—Most common cause of pathologic
infant jaundice. Usually present in first few weeks of life with jaundice and failure to thrive.
Hepatobiliary (HIDA) scan demonstrates failure of excretion of radiotracer into duodenum.
Surgical intervention with Kasai procedure and/or liver transplantation required.
Micro: Large bile duct obstruction findings—(non-specific, requires clinical/radiographic correlation)
Also consider in pediatric cholestatic liver disease: Bile salt deficiency diseases (formerly, Progressive Familial
Intrahepatic Cholestasis, or, PFIC), and inherited defects in bilirubin metabolism (mostly tested for with send-
out testing).
Neonatal Paucity of Intrahepatic Bile Ducts

Can by Non-syndromic or Syndromic (Alagille
syndrome—JAG1 mutations; associated with other
abnormalities such as cardiac and skeletal)
Micro: Interlobular bile ducts absent in > 50% of portal

tracts. Can highlight with CK7.
Ductular reaction may be present
Sepsis
Patients systemically ill, often with sepsis and/or bacteremia
Often jaundiced
Micro: Classically, Ductular cholestasis (“cholangitis lenta”)
However, this is challenged by some as this seems to be
common in any condition with cholestasis (including during
the hepatic dysfunction seen with sepsis)
Ductular reaction with inspissated bile and flattened, atrophic
epithelium.
Drug Reaction
Most common histologic pattern of drug-induced liver injury is cholestasis
Can have several patterns:
Bland/Pure cholestasis: Cholestasis with minimal inflammation (also see with systemic illness and
pregnancy)
Cholestatic hepatitis: Cholestasis with inflammation and hepatocellular damage
Prolonged cholestasis/ductopenia: > 3 months,
Sclerosing duct injury: Fibrosis affecting large bile ducts (similar to PSC)
https://livertox.nih.gov/
Neonatal Cholestasis Diagnostic Algorithm Disorder
Histologic
Pattern
Idiopathic
Serum GGT
Hypopituitarism
Neonatal
hepatitis
BASD
Low or Normal
PFIC 2
Bland
PFIC 1
cholestasis
Paucity of intrahepatic bile ducts

Biliary atresia
Neonatal
cholestasis
Choledochal
cyst
PFIC 3
Biliary
obstruction
High PNALD
Neonatal
hepatitis
Alagille
syndrome
A1AT deficiency
Most common causes of Neonatal Cholestasis:

1) Biliary atresia (BA)
2) Idiopathic Neonatal Hepatitis (INH)
Modified from a presentation from Grace Kim MD at USCAP March 2020

Clinical Neonatal Cholestasis Algorithm
Jaundice after 2
weeks of age
Laboratory studies
(Bili, AST, ALT, ALK,
GGT, INR, CBC)
Conjugated/direct
Liver Ultrasound
hyperbilirubinemia
Choledochal cyst Possible Biliary

Clinical “red flags” Normal
(or other mass) Atresia
Additional
Targeted, disease-
Surgery Liver biopsy laboratory work-up
specific evaluation
(A1AT typing, etc…)
Paucity of Possible
Biliary Obstructive Neonatal hepatitis
intrahepatic bile Next Gen
Pattern Pattern
ducts sequencing
Intraop
Cholangiogram +/-
HIDA scan
Biliary Atresia
Kasai Procedure
Modified from a presentation from Grace Kim MD at USCAP March 2020

Altered Blood Flow
“Shock Liver”
Liver hypoperfusion of any cause
Massive elevation in AST & ALT (thousands)
Micro: Central coagulative necrosis (zone 3)
Collapse of reticulin plates. No inflammation.
Other causes of bland Central Necrosis:
Acetaminophen toxicity (indistinguishable histologically)
Congestive Hepatopathy
Caused by hepatic venous outflow obstruction
Can be due to RHF, Budd-Chiari, etc…
Grossly: Nutmeg liver
Micro: Central zone sinusoidal dilatation,
congestion, hepatic plate atrophy, and necrosis
Chronic cases can lead to central vein and
sinusoidal fibrosis → Cirrhosis
Sinusoidal Obstruction Syndrome aka Veno-Occlusive Disease

Sinusoidal endothelial injury; Often due to chemotherapy or Stem Cell
Transplantation
Micro: Central vein obliteration (best seen on trichrome) →

Sinusoidal dilation/congestion; Sinusoidal endothelial edema
Cirrhosis
Common End-Stage for many liver disorders
Regenerative nodules surrounded by fibrosis

(want to see both for Dx)
Special type: “Biliary Cirrhosis” seen with long-standing cholestasis

Cholate stasis (ballooning, feathery degeneration at edges of nodules), “jigsaw” pattern of cirrhosis (instead
of round nodules, biliary cirrhosis is classically irregular), copper deposition in zone 1, ductopenia, periductal
fibrosis, bile infarcts.
Miscelaneous
Iron Overload aka Hemosiderosis
With excessive transfusions or iron supplementation
Iron accumulates in Kupffer cells (sinusoidal macrophages)
first. When those are saturated, then it is deposited in
hepatocytes
Iron Stains
Hereditary Hemochromatosis
Inherited disorder of iron metabolism
HFE gene mutations cause increased iron absorption & storage
Iron accumulates first in periportal hepatocytes
→progressively involves all zones & bile duct epithelium
Less Kupffer cell involvement (relatively)
Glycogenic Hepatopathy
Poorly-controlled diabetes→ abundant glycogen
stores → Hepatomegaly and elevated LFTs
A component of Mauriac Syndrome (with delayed

puberty and Cushingoid features)
Micro: Diffuse glycogenation of hepatocytes
Demonstrated by PAS stain (Diastase sensitive)
Absence of inflammation
α1-Antitrypsin Deficiency
Genetic disorder characterized by abnormal α-1-antitrypsin
protein synthesis
PiZZ phenotype accounts for most cases
→ Chronic liver disease and emphysema
Micro: Eosinophilic, PAS-D (+) globules within periportal

hepatocytes are characteristic
Neonatal hepatitis features cholestasis and hepatocyte injury
(too early for globule formation)
“Resolving Hepatitis”
Can look “almost normal”
Minimal/no lobulitis or portal inflammation
Mild lobular disarray (somewhat disorganized plates)

Kupfer cell hypertrophy (cleaning up debris)
Highlighted with a PASd stain
Most common causes: acute self-limited viral infection or
idiosyncratic drug reaction
Adenovirus/Herpes Hepatitis
Massive, bland azonal necrosis with characteristic
inclusions at edge of necrosis.
Usu. Immunocompromised. Poor prognosis.
CMV Hepatitis
Almost exclusively in immunocompromised individuals.
Inclusions can be subtle (so use stain liberally).
Classically: Neutrophilic microabscesses.
EBV Hepatitis
Often looks like a nondescript hepatitis with mild to
moderate portal and lobular inflammation (so often keep in
DDX, esp. if young or immunocompromised!)
Classically: Lots of activated lymphocytes in sinuses
Amyloid
Part of system illness, often plasma cell dyscrasias.
Required: Apple-green birefringence on Congo Red stain

Nodular Regenerative Hyperplasia
Think: “Cirrhosis-like nodules, but without the fibrosis”
Multiple hyperplastic parenchymal nodules (with normal to
enlarged hepatocytes) with intervening compressed/atrophied
parenchyma
No significant fibrosis
Best seen on reticulin stain
Results from changes in hepatic

blood flow from obliteration of
small portal veins → leads to
localized atrophy → other areas
grow to compensate.
Can cause portal hypertension.
Congenital Hepatic Fibrosis

Embryologic ductal plate malformation that leads to
bridging fibrosis (cirrhosis) with prominent malformed
ducts.
Ducts ectatic, anastomosing, and irregularly shaped.

No significant inflammation.
Few/abnormal portal veins → Leads to portal

hypertension.
Cystic Fibrosis
CFTR (Chloride ion channel) mutations result in
exocrine gland malfunction.
Autosomal recessive. Usually presents with
respiratory problems, meconium ileus, or pancreatic
insufficiency.
In liver, thick abnormal secretions are present in bile
ducts (similar to in lungs and pancreas) → biliary
obstruction → epithelial atrophy, bile ductular
proliferation, inflammation → fibrosis → biliary
cirrhosis.
Secretions stain with PAS-D

Laboratory Correlation
Acute Hepatitis Chronic Hepatitis
Marked Transaminitis (AST & ALT >5x normal) Mild Transaminitis (AST & ALT <5x normal)
Non-Hepatotropic Virus (CMV, EBV, Adeno) HBV: 5% develop chronic hepatitis
HAV & HEV: Fecal oral transmission; only acute AIH: + ANA, ASMA, Elevated IgG; Interface
necroinflammatory lymphoplasmacytic infiltrate
HBV: Ground Glass inclusions
HCV: 80% develop chronic hepatitis; nodular aggregates
AIH: Plasma cells of lymphocytes
Adverse drug reaction Hereditary Hemochromatosis: + HFE genetic mutation

Elevated Transferrin saturation and serum ferritin
Massive altered hepatic blood flow (e.g., Shock)
Wilson’s: Increased liver copper quantification; +
ATP7B gene; AST/ALT ratio >2.2, Alk. Phos./T. Bili <4
A1AT Deficiency: PiZZ phenotype, Hyaline globules in

hepatocytes stain with PAS with diastase stain
Cholestatic Hepatitis
Elevated Alk Phos. & GGT; +/- Bili Alcoholic: Clinical history of alcohol, AST:ALT > 2, more
Jaundice likely to show neutrophils and Mallory’s hyaline
NASH: Diabetes or metabolic syndrome, Obesity

Large duct obstruction
Drug reaction
PBC: Female, + AMA, IgM, lymphocytic cholangitis
and florid duct lesion
PSC: Male, IBD, diagnosed with cholangiography,

concentric fibrosis around bile ducts, risk of
cholangiocarcinoma
Drug reaction
Cirrhosis/Liver Failure
Synthetic Dysfunction (Elevated INR, Low Albumin, Low platelets)
Based on a presentation from Max Smith M.D., Mayo Clinic

(more) Differential Diagnoses
Acute Liver Failure
Histologically, typically lobulitis or necrosis patterns (as they are too injurious to be chronic)
• Acetaminophen toxicity (40 – 50%)
• Drug reaction (10 – 20%)
• Acute viral hepatitis (10 – 20%)
• Idiopathic (20 – 30%)
• Rare causes: Wilson’s disease, Autoimmune hepatitis, Budd-Chiari syndrome, Non-hepatotropic
viruses
Almost Normal Liver With Portal hypertension and/or ascites

With Elevated LFTs
• Hepatoportal sclerosis
• Systemic autoimmune conditions
• Portal venopathy
• Vascular outflow obstruction
• Peritoneal serositis (no liver disease)
• Intermittent ischemia
• Metabolic syndrome (even if fat-free)
• Medication
Fatty Liver • Drug effect

• Wilson’s disease (and other genetic disorders)
• Metabolic syndrome (NASH)
• Cystic fibrosis
• Alcohol use
• Elevated cortisol
Bland Lobular Necrosis

Necrosis with NO (or little) associated inflammation
Due to direct injury/toxicity (not secondary immune damage)
Zone 1 Zone 2 Zone 3 Azonal
Iron Toxicity Poisons Acetaminophen Herpes

Phosphorous Toxicity Beryllium Ischemia Adenovirus
Hepatitis A Yellow fever Some toxins Varicella
Some industrial chemicals
Based on: Atlas of Liver Pathology: A Pattern-based Approach, by Dr. Michael Torbenson
Granulomas
• Primary biliary cholangitis
• Sarcoidosis
• Drug effect
• Infection
• CVID and other systemic granulomatous diseases
• Paraneoplastic
Bland Lobular Cholestasis

• Drug effect
• Severe systemic illness/sepsis
• Paraneoplastic syndrome
Ductopenia (adult) • GVHD

• Drug effect
• Chronic obstruction
• Idiopathic
• Primary biliary cholangitis
• Chronic rejection
Chronic Hepatitis Pattern

• Viral Hepatitis
• Autoimmune hepatitis
• Drug effect
Microvesicular Steatosis • Alcohol foamy degeneration

• Genetic diseases (e.g., Alper’s syndrome)
• Medication (e.g., Reye’s syndrome)
• Infection (e.g., HDV + HBV)
• Toxin (e.g., arsenic)
• Acute fatty liver of pregnancy
Pediatric Cholestatic Disease • Sepsis

• TPN
• Biliary atresia (extrahepatic)
• Bile salt deficiency (PFIC’s)
• Paucity of intrahepatic bile ducts
• Genetic diseases (e.g., alpha-1 antitrypsin,
• Non-syndromic vs Syndromic
Niemann-Pick, etc…)
• Neonatal giant cell hepatitis
Cystic Biliary Malformations • Autosomal recessive polycystic kidney disease

• Autosomal dominant polycystic kidney
• Congenital hepatic fibrosis
disease
• Caroli syndrome/disease
Portal Hypertension • Sarcoidosis
• Nodular regenerative hyperplasia
Pre-hepatic
• Hepatoportal sclerosis
• Portal vein thrombosis
• Peliosis hepatitis
• Portal vein stricture
• Veno-occlusive disease
Hepatic
Post-Hepatic
• Cirrhosis
• Portal vein thrombosis
• Schistosomiasis
Veno-Occlusive Disease • Radiation therapy

• Herbal teas/remedies
• Bone marrow transplantation
• Chemotherapy medications
Congestive Hepatopathy • Veno-occlusive disease

• Sickle cell anemia
• Budd-Chiari syndrome
• Hemophagocytosis syndrome
• Right-sided heart failure
• Autoimmune diseases
• Compression of hepatic veins or IVC
• Paraneoplastic syndromes
• Medications (e.g., estrogen)
Things that are easy to overlook • Hepatoportal sclerosis

• Glycogenopathy • Early bile duct loss
• Alpha-1-antitrypsin deficiency • Amyloid
• Nodular regenerative hyperplasia • Stellate cell hyperplasia
Hepatocellular Lesions
Note: All of these lesions stain with Hepatocellular stains (Hepar-1 and Arginase)!
Also, canalicular staining with CD10 and pCEA. Cytoplasmic TTF-1. Negative MOC-31.
Macroregenerative Nodule An unusually large regenerative nodule (often >1 cm) that
develops in the setting of cirrhosis.
Hyperplastic liver parenchyma. Plates may be slightly thickened (usu. 1-2 cells thick, maybe focally 3).
Have normal constituents (bile ducts, arteries, veins, etc…). No atypia (Unless dysplastic).
Focal Nodular Hyperplasia (FNH) Not a true neoplasm; “Focal Cirrhosis”

Regenerative hyperplastic response of hepatocytes
secondary to vascular abnormalities
Very common
Well-circumscribed with central stellate scar with
fibrous septae with entrapped vessels, bile ducts,
and inflammatory cells
Normal plate thickness. No true portal tracts.
“Map-like” staining with glutamine-synthetase
Glutamine Synthetase IHC:

Strong “Map-like” staining
Normal, pericentral staining
Note: In cirrhosis it shows
weak, patchy periseptal
staining.
Hepatocellular Adenoma Benign liver neoplasm.

Assoc. with oral contraceptives/steroids.
Subtypes:
Risk of transformation to HCC and/or bleeding/rupture
Inflammatory/Telangiectatic (~45%) →
Stain with serum amyloid A and CRP; Benign-appearing hepatocytes, No significant atypia.
associated inflammatory infiltrate, peliosis, Normal plate thickness (1-2 cells thick)
and bile ductular reaction in fibrous septae. Unpaired arteries, absent bile ducts
Transformation to HCC occurs. No mitoses
Β-catenin activated (~15%) → Nuclear Β-

catenin (focal), Diffuse, strong glutamine
synthetase. Highest risk of malignant
transformation
Normal Liver
HNF1α-inactivated (~30%) → Loss of LFABP

staining. Associated with adenomatosis (>10
adenomas). Very low risk of transformation. Unpaired arteries
Unclassified (~10%) → None of the above

(~10%)
Hepatocellular Lesions
Hepatocellular Carcinoma Malignant tumor with hepatocellular differentiation
Often occurs in setting of cirrhosis (associated with chronic
liver damage such as viral hepatitis, EtOH, and NASH)
Dx often made clinically (Radiology + ↑ AFP = HCC)
Treat often with embolization, resection, or transplant
Widening of hepatic plates (>2 cells thick)
Absent portal tracts, often unpaired arteries.
Architecture and cytologic atypia varies and includes
pseudoacini/pseudogland formation and wide trabeculae.
Often bile production by tumor cells.
Staining:
Reticulin→ Widening of hepatic plates
CD34→ Diffuse sinusoidal (“capillarization”)
Glypican-3→ +/- (but negative in benign liver,
Positive staining supports malignancy)
Retic. CD34
Variants:
Fibrolamellar HCC → Often young, non-cirrhotic patients. Normal
AFP. Often large, solitary. Large oncocytic tumor cells with bands of
lamellar fibrosis. Cytoplasmic pale bodies. Recurrent DNAJB1-
PRKACA translocation. Stain with CD68 and CK7.
Classically thought to be better prognosis, but this is likely mostly
due to demographics (younger, non-cirrhotic patients)
Steatohepatitic HCC → Assoc with Hep C with NASH.

Macrovesicular steatosis, ballooning degeneration, M-D bodies.
Can be hard to recognize on biopsy (esp. if background NASH)!
Macrotrabecular-Massive HCC → Thick trabeculae coated by

endothelial cells and surrounded by vascular space. Aggressive
subtype with high AFP and TP53 mutations or FGF19 amplification.
Hepatoblastoma Embryonal
Most common liver tumor in Children. Pattern
Malignant. Assoc. w/ Beckwith-Wiedmann
Shows a variety of epithelial (e.g., fetal and
embryonal) and mesenchymal cell types
(“teratoid”) recapitulating hepatic ontogenesis.
Fetal
Frequent ẞ-Catenin mutations Pattern
Nuclear localization by IHC→ worse prognosis
Biliary Lesions
Note: The epithelium in all of these lesions stain with CK7, CK19, and MOC31 (among other stains).
These lesions are negative for hepatocellular stains (Hepar-1, Arginase, and Glypican-3).
Bile Duct Adenoma

Benign bile duct proliferation
Usu. <1 cm, subcapsular, and well-circumscribed.
Small, uniform, small ducts with cuboidal cells and regular nuclei.
Biliary adenofibroma→ more complex epithelial growth with
abundant fibroblastic stromal components
Clinically, may mistake intraoperatively for a metastasis
Bile Duct Hamartoma

Benign, may be multiple. aka Von Meyenburg Complex
Usu. small (several mm)
Irregular to round bile dilated bile ducts
Associated with fibrous/hyalinized stroma
Lumens contain bile and proteinaceous material
Adenocarcinoma arising from Cholangiocarcinoma

intrahepatic bile ducts
Inflammatory disorders can predispose (e.g., PSC or liver fluke
infection). Must clinically distinguish from metastasis as overlap.
Usu. tubular pattern. Sometimes large ducts. Often sclerotic center.
Non-specific IHC profile, but (+) Albumin ISH supports intrahepatic
Combined Hepatocellular - Cholangiocarcinoma

A single tumor with morphologically distinct areas of HCC
(Arginase and Hepar +) and Cholangiocarcinoma (CK7+).
Treated and prognosis similar to cholangiocarcinoma
(Worse than HCC, No transplantation).
Additional DX:
Intraductal Papillary Neoplasms → Similar to

IPMNs in the Pancreatic duct. Can progress to
cholangiocarcinoma.
Mucinous Cystic Neoplasms→ Just like in the

pancreas! Ovarian-type stroma surrounding
mucinous epithelium.
Vascular Lesions
Note: All of these lesions stain with endothelial markers, including CD31, ERG, and FLI-1.
Cavernous Hemangioma
Most common benign tumor of the liver.

Thought to be malformations and non-neoplastic.
Often asymptomatic and diagnosed radiographically.
More common in females
Fibrous septae lined by single layer for flat endothelial cells.
Can thrombose and calcify.
Epithelioid Hemangioendothelioma
Endothelial tumor of low-grade malignancy.
Eosinophilic, slightly epithelioid cells with signet ring-like
features representing intracytoplasmic lumina (often
contain RBCs). Associated dense fibrous stroma.
Often have intravascular papillary growth and infiltrate
sinusoidal spaces at edge of lesion
Translocation: WWTR1-CAMTA1 fusion
Sometimes focally positive for cytokeratins by IHC
Angiosarcoma
Malignant endothelial tumor. Most common liver sarcoma.
Spindled to epithelioid cells. Variably atypical endothelial
cells with multilayering and mitoses. Anastomosing spaces.
Like to grow along pre-existing vascular spaces.
Usually large and/or multifocal.
Assoc. with exposure to Vinyl Chloride or Thorothrast.
Poor prognosis.
Other Tumors:
PEComa/Angiomyolipoma→ Benign tumors, just like in the kidney! Think of this if you see fat.
Variable admixture of fat, smooth muscle, and thick-walled blood vessels. Associated with tuberous
sclerosus. Usu. Asymptomatic. Stain with HMB45. MelanA+/-
Embryonal Sarcoma→ Malignant tumor composed of undifferentiated mesenchymal cells. Usu. older
children. Loose myxoid tissue with immature and giant cells. Characteristic eosinophilic intracellular
hyaline globules. Can rupture. Previously bad prognosis, but improving.
Figure adapted from WHO
Diagnostic Algorithm for Pancreatic Tumors
Gross/Radiographic Appearance?
Solid Cystic
Epithelium/Stroma? Degenerative?
(No epithelium
Individual glands Solid, cellular epithelium lining cysts)
Desmoplastic stroma Minimal or hyalinized
Mucin production stroma
Be sure to
Ductal Predominant cellular consider a Epithelium
Adenocarcinoma differentiation? pseudocyst! Lined Cysts
Acinar Neuroendocrine Unknown Serous Mucinous

Stains: (+) Stains: (+) Stains: (+) β-catenin Cuboidal, clear Columnar, often
chymotrypsin, synaptophysin, (nuclear), CD10, cells, glycogen-rich mucin-filled
trypsin chromogranin CD56, E-Cadherin (PAS +; PASd -)
shows lost Stains: (+) Inhibin
membranous
Squamoid Ovarian-type
staining
nests? stroma, separate
from ducts
Yes No Yes No
Pancreatoblastoma Acinar Cell Pancreatic Solid- Serous Mucinous Cystic Intraductal Papillary
Carcinoma Neuroendocrine Pseudopapillary Cystadenoma Neoplasm (MCN) Mucinous Neoplasm
Most common in Tumor Neoplasm (SPPN) (IPMN)
Children Prominent nucleoli, Usu. Body or Tail,
Characteristic
granular cytoplasm, Usu. young woman, Almost exclusively in Papillary architecture,
radiology,
Lipase secretion Low malignant women Grossly visible (>0.5 cm),
Benign,
→Subcutaneous fat potential If tubular→ consider ITPN
Usu. Cystic, but
necrosis
can be solid
Pancreatic Ductal Adenocarcinoma
Invasive carcinoma with glandular/ductal differentiation
85% of Pancreatic tumors, PNI
Most common in head of pancreas→ resect with Pancreaticoduodenectomy (Whipple procedure)
Often unresectable at time of diagnosis, Poor Prognosis (often < 1 year)
Precursor lesions: IPMN, MCN, PanIN
Most are well to moderately-differentiated and show duct-like glandular structures that haphazardly
infiltrate and elicit a desmoplastic response (disrupting normal lobular architecture)
Genetics:
>90% show KRAS activation point mutations (also in PanIN)
Also often present are inactivating mutations in the tumor suppressors: TP53, P16, and/or SMAD4
Loss of SMAD4 (DPC4) is relatively specific to pancreatic adenocarcinomas and can be evaluated by IHC
Subtypes:
If squamous differentiation→ adenosquamous carcinoma (poorer prognosis)
If >80% of tumor has abundant extracellular mucin (often large and arise in an intestinal-type IPMN)→
Colloid Carcinoma (better prognosis)
If pleomorphic, no gland formation, +/- osteoclast-like giant cells→ Undifferentiated (anaplastic) carcinoma
(with osteoclast-like giant cells)
Other Rare subtypes: Hepatoid carcinoma, Medullary carcinoma, Invasive micropapillary carcinoma, Signet-
ring (poorly cohesive cell) carcinoma, Sarcomatoid carcinoma
Cytology requirements:
(best seen on Pap-stained slides)
1) Nuclear pleomorphism (>4:1)
2) Architectural disarray (“drunken honey comb”)
3) Irregular nuclear contours
4) Single malignant cells
Ancillary testing on cytology specimens:

1) Next-gen sequencing→ looking for KRAS mutations, etc..
2) FISH (e.g., Urovysion) looking for aneuploidy Normal “honeycomb”
pancreatic ductal
epithelium
Non-Invasive Glandular Lesions
Intraductal Papillary Mucinous Neoplasm (IPMN)
Grossly visible (often >5mm) proliferation of mucinous cells within the
main pancreatic duct (main-duct IPMN) or its branches (branch-duct
IPMN).
Grade based on worst area.
3 Subtypes: Gastric (most common, least aggressive, resembles foveolar
cells), Intestinal (tall, cuboidal cells), and pancreatobiliary (resembles
biliary epithelium, low cuboidal with amphophilic cytoplasm and
complex papillae)
Most often in head.
Molecular: KRAS mutations the most common (and seen in many GI

cancers). GNAS mutations are also common and seem to be relatively
unique to IPMNs
Gastric-type IPMN
If pre-invasive→ Benign, but have to submit entire capsule/lesion to
prove no invasion.
Decision to resect depends on size, location, symptoms, age, etc…
A solid nodule radiographically is suspicious for invasion.
Intraductal Oncocytic
Mucinous Neoplasms
Papillary Neoplasm
Cytology findings:
Essentially, an IPMN, but with
abundant eosinophilic granular Often a background of abundant, thick, neoplastic mucin.
cytoplasm, often forming cribriform Abundant cohesive groups of mucinous columnar cells
lumens. (must exclude GI luminal sampling!)
Almost all high-grade.
High-grade dysplasia (CIS) within a mucinous cyst looks
Stain with Hepar-1. identical on smears to invasive adenocarcinoma
Genetically distinct with Recurrent Cyst fluid CEA elevated (greater than 200 ng/mL is highly
Rearrangements in PRKACA and PRKACB suggestive of a mucinous cyst)
(includes same fusion as fibrolamellar HCC)
Non-Invasive Glandular Lesions
Intraductal Tubulopapillary Neoplasm
Intraductal epithelial neoplasm that forms predominantly back-to-back tubules.
Often have high-grade dysplasia, ductal differentiation, and no overt mucin production.
Can have focal papillary growth.
Often fill and distort glands making hard to evaluate for invasion.
Genetically distinct (No KRAS mutations).
Rare. Benign if non-invasive.
Mucinous Cystic Neoplasm

Cyst-forming, mucin-producing neoplasm with a wall of distinct ovarian-type subepithelial
stroma.
Epithelium is predominantly columnar, mucinous epithelium.
Does not connect to the ductal system (unlike IPMNs)
Ovarian stroma: densely packed spindled cells and stains with ER, inhibin, and calretinin.
Almost exclusively in women. Almost always in Body or tail.
Must be thoroughly sampled to exclude invasive component.
Simple Mucinous Cyst (Not in WHO)

Cysts >1 cm lined by nonpapillary mucinous epithelium without ovarian-type stroma
Usually gastric-type lining; Frequent KRAS mutations; Essentially a flat IPMN or dilated
PanIN for lesions that don’t fit into IPMN or MCN well
Pancreatic Intraepithelial Neoplasia (PanIN):

Non-invasive, non-mass forming neoplasia confined to the pancreatic ducts (In situ).
Main precursor to ductal adenocarcinoma. Harbors same genetic mutations (e.g., KRAS), with
increasing frequency with higher grades.
Low-grade PanIN: Basally located or pseudostratified with mild to moderate cytologic atypia.
Flat or papillary. Common. Low risk, so no need to report at margins.
High-grade PanIN (Carcinoma in situ/CIS): Severe cytologic atypia with loss of polarity and
often abnormal architecture (papillary, micropapillary, or cribriform). Higher risk, so report at
margins.
Pancreatic Neuroendocrine Tumors Can get anywhere in the pancreas.
Associated with MEN and VHL.
Well-differentiated Neuroendocrine tumors
Cytology: Discohesive, often
Morphology: Uniform, round nuclei with “Salt and
plasmacytoid cells with monomorphic
Pepper” fine, speckled chromatin
round nuclei and stippled chromatin
Organoid architecture (i.e., nested, cords, glands-like
rosettes, or ribbons)
Molecular: MEN1, DAXX, ATRX mutations common
IHC: express Synaptophysin, Chromogranin, INSM1
Malignant, but slow-growing, indolent progression.
Early NETs have a low risk of metastasis
Poorly-differentiated Neuroendocrine Carcinomas
If <0.5 cm & non-functional with no mitoses→ Often arise from non-neuroendocrine tumors (and subsequently develop neuroendocrine
“microadenoma” (benign and often incidental) differentiation.
Classification/ Ki67 Proliferation Mitotic Sheet-like growth
Grade Index index Malignant! Very metabolically active/rapidly growing
Well-differentiated PanNET
Grade 1 <3% <2 Treatment: Platinum-containing chemotherapy
Grade 2 3-20% 2-20
Grade 3 >20% >20
Morphology: Fusiform nuclei, finely granular chromatin, scant cytoplasm, and nuclear
Poorly-differentiated PanNET molding. Extensive necrosis.
Small cell type Tons of mitoses. Ki67 almost 100%.
>20% >20 Large Cell Neuroendocrine Carcinoma
Large Cell type
Morphology: Large, round nuclei, with prominent nucleoli,
Ki67 Proliferation index based on evaluation of ≥ 500 cells in a “hot spot.” and moderate amounts of cytoplasm. Sheet-like to nested growth.
Mitotic count based on evaluating 50 Hpfs, but reported per 10 Hpfs. Ki67 often 60-80% range
Pancreatoblastoma Carcinoma showing Acinar cell differentiation with squamoid nests

Most common in children (but can see in adults)
Associated with Beckwith-Wiedemann syndrome and FAP.
Much of the tumor looks like Acinar Cell Carcinoma, BUT defining findings is Squamoid nests.
IHC: Acinar component stains with Trypsin/Chymostrypsin. Squamoid nests stain with EMA,
Synaptophysin may show positivity. Often nuclear ẞ-catenin.
Often indolent, curable tumors.
Acinar Cell Carcinoma
Carcinoma showing Acinar cell differentiation
Most commonly older men
Lobular to trabecular pattern of growth, very cellular
Cells have moderate amounts of granular cytoplasm (full of zymogen
granules) with uniform nuclei and a single prominent nucleolus
Can be mixed with neuroendocrine or ductal carcinomas
Immunohistochemical evidence of acinar differentiation: trypsin,
chymotrypsin, lipase, or amylase; BCL10 is also good. No genetic hallmark
Can cause subcutaneous fat necrosis due to lipase hypersecretion
Poor prognosis (better than PDAC, but less than PNET; Median 19 months)
Solid Pseudopapillary Neoplasm

Most common in adolescent girls and young women
Solid and pseudopapillary/cystic growth

Solid tumor resembles neuroendocrine tumor (monomorphic round cells)
Pseudopapillae are formed when cells detach from fibrovascular cores
Commonly see hyaline globules and cholesterol clusters/foamy histiocytes.
IHC: Nuclear ẞ-catenin. Loss of E-cadherin. Positive for Cyclin D1, CD56, CD10, PR.
Sometimes express CK or CD117. Negative for Neuroendocrine and Acinar markers.
Low-grade malignant, with often good prognoses and surgical cure.
Serous Cystadenoma Benign. Often identified incidentally. Often older women in the body.
Composed of bland, uniform, cuboidal cells with clear, glycogen-rich cytoplasm.
Cysts lined by a single layer of cells, with well-defined cell borders.
Small, round nuclei.
Glycogen→ stains with PAS (and digested by diastase)
IHC: Stains with inhibin
Characteristic multilocular, sponge-like appearance with a central scar
(think of a cut orange!)
Associated with von Hippel-Lindau syndrome (VHL) (can get multiple).
Very Rare: If metastasizes→ Serous cystadenocarcinoma
Non-neoplastic Processes Ductal Adenocarcinoma Chronic Pancreatitis
Chronic Pancreatitis Haphazard, irregular Lobular, organized

Inflammation/destruction of gland with scarring and dysfunction architecture architecture
Often associated abdominal pain, elevated serum lipase and amylase Incomplete luminal spaces with Complete luminal spaces
Causes: EtOH (most common by far), obstruction, genetic gland rupture
Exocrine insufficiency → fat malabsorption → steatorrhea
Endocrine insufficiency (comes late) → diabetes mellitus Cellular pleomorphism (4:1 Less pleomorphic
variation in size)
Can resemble invasive ductal adenocarcinoma (see table→)
Microscopically: Fibrosis and glandular atrophy with retained lobular architecture. Perineural invasion Absent
Islets of Langerhans preserved until late→ may show “pseudo-hyperplasia.”
Vascular/perivascular invasion Absent
Pseudocyst Extrapancreatic invasion Absent
Pancreatic or peripancreatic collection of enzyme-rich fluid without an epithelial
lining (wall composed of fibrosis and granulation tissue) Mitoses and prominent Often absent
Often secondary to pancreatitis, and spontaneously resolves nucleoli often prominent
FNA fluid analysis: High amylase (>250 IU/mL) and low CEA (<100 ng/mL)
Fluid often contains amorphous debris and bile. Can extend outside of the Confined to pancreas
pancreas into fat, etc…
Autoimmune pancreatitis Note: Both can show edematous stroma
Type 1: IgG4-related lobular inflammation/destruction
Key features: 1)Dense lymphoplasmacytic infiltrate, 2)Storiform fibrosis,
3)Obliterative phlebitis; Increased IgG4+ plasma cells (>50/HPF on excision or
>10/HPF on biopsy). Clinically can mimic carcinoma. Often elevated serum IgG4.
Type 2: Duct-centric granulocytic destruction with epithelial damage
Acinar Cystic Transformation of the Pancreas

Multilocular cystic change of acini throughout the pancreas. Lined by cells with pale
or granular apical cytoplasm and acinar or ductal differentiation (not mucinous!).
Lymphoepithelial Cyst
Cystic lesion lined by squamous mucosa with surrounding lymphoid tissue.
Tumors of the Gallbladder and Bile Ducts

Benign Tumors
Biliary Intraepithelial Neoplasia (BilIN) Low-grade BilIN
Non-invasive (in situ) dysplastic epithelial lesion

within the biliary tree or gall bladder.
Can be low-grade or high-grade.
Chronic inflammation (e.g., with stones, PSC, or
parasite) can induce mutations→ dysplasia→ cancer
Molecular: KRAS mutations seen in ~40% cases, TP53
mutations are a late event in high-grade BilIN
Two-tiered grading system (see table below), grade the
area of worst cytoarchitectural atypia
Architecture can be flat or micropapillary. High-grade BilIN
Can colonize peribiliary glands and Rokitansky-Aschoff
sinuses→ don’t confuse for invasion!!
Factors favoring reactive atypia:
- Cellular atypia is worse deeper in the epithelium
and “matures” as you approach the surface
- Nuclei have fine chromatin
- Gradual transition from normal to atypical
(neoplastic processes often have an abrupt transition)
Feature Low-grade BilIN High-grade BilIN Note: On cytology

specimens (e.g., bile
(BilIN 1/2) (BilIN 3)
duct brushing), the
Microscopic Flat or micropapillary Flat or micropapillary distinction between
findings Hyperchromatic nuclei Hyperchromatic and irregular nuclei invasive and non-
Increased N:C ratio Pleomorphic cells with bizarre nuclei invasive disease cannot
Nuclear stratification Increased N:C ratio
be distinguished, so
Preserved nuclear polarity Complex nuclear stratification
Loss of nuclear polarity BilIN3 appear identical
to invasive carcinoma.
Biliary mucosa Relatively focal Relatively extensive
involvement
Outcomes: If confined
Involvement of Uncommon Common
to gallbladder, cured by
peribiliary glands
surgical excision.
Ki67 Low to intermediate Frequently high However, this can be a
“field defect” with
S100 Mild to moderate Diffuse and strong multifocal disease
IHC
p53 Wild-type Abnormal (Diffuse strong or null) throughout the biliary
tree with regional
p16 Preserved Decreased recurrences.
Modified from: WHO Classificaiton of Tumours: Digestive System Tumours. 5th Ed.
Intracholecystic Papillary Neoplasm (Essentially an IPMN, but in the gallbladder!)
A mass-forming (grossly visible), non-invasive neoplasm arising in
the gallbladder mucosa. (vs BilIN, which is microscopic)
Intraluminal growth of back-to-back epithelium with primarily
papillary architecture (sometimes tubulopapillary)
Grade dysplasia using same criteria as BilIN
Often adjacent BilIN; Frequent KRAS mutations.
Four morphological patterns, often intermixed, with no current
clinical significance:
Biliary→ Most common, cuboidal cells with clear to pink
cytoplasm, enlarge nuclei, and frequent nucleoli
Gastric→ Resemble foveolar cells (tall with abundant apical mucin)
Intestinal→ Resemble colonic adenomas
Oncocytic→ Least common, abundant eosinophilic granular
cytoplasm
An invasive carcinoma is identified in ~1/2 of cases (especially
biliary type with high-grade BilIN), so sample completely!
Intraductal Papillary Neoplasm of the Bile Ducts (Biliary IPMN)

Grossly visible papillary lesion predominantly growing in the bile duct
lumen (vs BilIN, which is microscopic—not grossly visible)
→ Can cause biliary obstruction→ Duct dilation
→ Can secrete abundant mucus
Papillary fronds with fine fibrovascular cores covered by cuboidal or
columnar neoplastic epithelium with variable cytologic atypia
Grade based on area of worst atypia
Risk factors: PSC, Liver flukes
Molecular: KRAS mutation→ Low-grade dysplasia→ P16 loss, TP53
mutation→ High-grade dysplasia→ Invasive carcinoma
Can subgroup same as above (ICPN), but often mixed
Outcome: ~50% have an associated invasive component, so sample well.
Still, better prognosis than conventional cholangiocarcinoma
Pyloric gland adenoma of the Gallbladder

Non-invasive, benign glandular neoplasm of the
gallbladder composed of mucinous glands with
pyloric to Brunner’s gland features
- small, tightly packed bland-looking glands with
abundant pale apical mucinous cytoplasm,
peripheral nuclei, and minimal intervening stroma.
- Some glands may be cystically dilated.
Can be pedunculated or sessile
Rarely, can have superimposed high-grade
dysplasia or carcinoma.
Malignant Tumors
Carcinoma of the Gallbladder
Malignant epithelial neoplasm in the gallbladder arising from the biliary epithelium
Most common biliary tract malignancy, most frequent in old women (long-standing gallstones)
Tumors are most often located in the fundus and flat.
Signs and symptoms overlap with cholelithiasis, often diagnosed incidentally.
Risk factors: Gallstones (most common), PSC, certain regional SNPs
Inflammation (chronic cholecystitis→ calcifications→ “Porcelain gallbladder”)→ BilIN→ Carcinoma
Most cases are associated with surrounding dysplasia, so if you find dysplasia, sample the
gallbladder well to see if there is an occult carcinoma!
Molecular: Frequent CTNNB1 (β-catenin) mutations, sometimes HER2 amplified or MMR-deficient
Subtypes:
Biliary-type Adenocarcinoma: Most common subtype. Similar in morphology and behavior to
pancreatic ductal adenocarcinoma. Infiltrating tubules lined but cuboidal cells in desmoplastic stroma.
Intestinal-type Adenocarcinoma: Resemble colonic adenocarcinomas. Tubular configuration with
columnar cells with elongated, pseudostratified cells. Rare→ must rule out a metastasis
Mucinous Adenocarcinoma: >50% of the tumor contains abundant extracellular mucin.
Poorly-cohesive carcinoma: Individual cells infiltrating diffusely through wall. Includes Signet-ring cells.
Other subtypes: Clear cell carcinoma, Squamous cell carcinoma, Adenosquamous carcinoma,
It can be hard to tell dysplasia involving a Rokitansky-Aschoff sinus from invasive tumor. Invasive tumor
glands are often smaller glands with irregular contours and increased cytologic atypia. In contrast, RA
sinuses are often larger, dilated, and have round contours.
Prognosis depends largely on stage:
If “Early” (not yet muscle invasive, so pTis/T1a/T1b)→ Good prognosis
If “Advanced” (Into or beyond muscle, ≥pT2)→ Aggressive
Note: pT2 is subdivided by if the tumor is on the hepatic or peritoneal side of the gallbladder:
pT2a→ Peritoneal side → Relatively better prognosis
pT2b→ Hepatic side → Relatively worse prognosis
Carcinoma of the Extrahepatic Bile Ducts
Malignant epithelial neoplasms arising in the extrahepatic bile ducts.
Most frequently Adenocarcinoma = Cholangiocarcinoma
Klatskin tumor: Perihilar tumor occurring at the confluence of right and left
hepatic ducts
Often older patients presenting with obstructive jaundice

Risk factors: PSC, Liver flukes, Choledochal cysts, and Gallstones
Two precursor lesions: BilIN and Intraductal papillary neoplasms
Molecular: Early KRAS mutations. Frequent late TP53 mutations.
Most carcinomas are pancreatobiliary-type: resemble pancreatic ductal
adenocarcinoma. Widely-spaced, irregular glands and small tumor clusters
infiltrating through desmoplastic stroma. Frequent perineural and
lymphovascular invasion.
Overall, very aggressive tumors with poor prognosis
Cytologic Diagnosis of Adenocarcinoma:

Since it so closely resembles pancreatic ductal
adenocarcinoma, we use the same cytologic criteria
(best seen on Pap-stained slides):
1) Nuclear pleomorphism (>4:1)
2) Architectural disarray (“drunken honeycomb”)
3) Irregular nuclear contours
4) Single malignant cells
Helpful additional clue: A clearly neoplastic

population and a separate distinct clearly benign
population.
If the person has PSC or a Stent, they may have Some advanced endoscopists can get tissue
considerable reactive atypia, so, in these cases, it is biopsies from common bile duct lesions via
often prudent to be more conservative and consider cholangioscopy (e.g., with “Spyglass”), often
downgrading your diagnoses accordingly. yielding small biopsies.
Ancillary testing on cytology specimens:

1) Next-gen sequencing→ looking for KRAS or TP53
mutations, etc..
2) FISH (e.g., Urovysion) looking for aneuploidy
NOTE: The distinction between high-grade BilIN (non-

invasive) and invasive carcinoma cannot be made by
brush cytology.
CHAPTER 4
Cytology
Cytology Basics
Benign Malignant
Round nuclei
“Smooth” evenly distributed chromatin
Think: Like a robin’s egg Irregular nuclear contours
Clumped, uneven, vesicular or
hyperchromatic chromatin
Think: Like a boulder or raisin
One approach: Mentally divide a nucleus

into quarters and compare the chromatin
and nuclear contours of each quarter.
Benign = Mostly the same
Malignant = Lots of variability
Cells/nuclei look similar to neighbors
Lots of variation in size/shape of

neighboring cells (Pleomorphism)
Benign Malignant
Organized cell clusters Irregular “Drunken” architecture
Polarized cells (that know which way is up) Tightly packed together
“Honeycomb” or “Picket-fence” glandular
architecture
Large, prominent nucleoli (sometimes)

Small, usually inconspicuous nucleoli
Frequent mitoses, especially atypical
Rare mitoses
Benign No nuclear molding
Nuclear molding Malignant
“Cannibalism”
(tumor cells eating other tumor cells)
The main phagocytosis of cells in benign

processes is by macrophages
Often High N:C ratios

Often Low N:C Ratios (There are plenty of exceptions to this, for
(However, there are obvious exceptions example mucinous carcinomas)
to this, like benign lymphocytes or
reserve cells having scant cytoplasm)
Basic Lines of Differentiation Always think broadly and first try to put things into a
“bucket,” then you can get more specific after.
Obviously, this is a gross oversimplification,

but you have to start somewhere! Basic Broad
Classification
Epithelial/ Lymphoid/ Mesenchymal/

Melanoma
Carcinoma Lymphoma Sarcoma
Squamous cell Neuroendocrine

Adenocarcinoma
carcinoma tumor/carcinoma
Epithelial cells/Carcinoma
Epithelial cells form structures, so even when
smeared, they remain in cohesive clusters
Compared to blood cells, they are also

relatively large in size
They often have moderate to abundant

cytoplasm (obviously not true of all
carcinomas though… I’m looking at you small
cell carcinoma!) and therefore appear
“epithelioid.”
Glandular Cells/ Adenocarcinoma
May form glands or papillae
Characteristically produce mucin, which may be visible in
cytoplasm.
Cytoplasm often appears “delicate” (fluffy to granular) with
less distinct cell borders. Blueish cytoplasm on Pap usually.
Often columnar with nucleus polarized at one end.
Can see Signet ring cells.
Intracytoplasmic lumina
Squamous cell cells/carcinoma

Produce keratin→ Bright orangish on Pap stains. Can see keratin pearls
Cytoplasm appears “dense” with distinct cell borders
Neuroendocrine Cells/ Tumors

Nuclear chromatin appears stippled
like “Salt and Pepper”
Cells are often discohesive
May have granular cytoplasm with
secretory granules.
Lymphocytes/Lymphoma
Discohesive small cells (remember, they must
circulate through vessels, so they have to be
small and loose)
Scant cytoplasm
Lymphoglandular bodies (pieces of
lymphocyte cytoplasm that peel off during
smearing →)
Consider sending for flow cytometry at time
of adequacy to evaluate for lymphoma
Melanocytes/Melanoma
Large, discohesive cells. Often very cellular aspirates.
Frequently prominent nucleoli

Double mirror image nuclei (DMIN)
(“bug-eyed demons”)
Cytoplasmic melanin pigment (→)
Intranuclear pseudoinclusions (→)
Mesenchymal/Sarcoma
Spindled cells = long, narrow cells with relatively scant
cytoplasm and cigar-like nuclei.
Frequent extracellular matrix
Neural tumors often have “buckled” or “fishhook” nuclei.
Very variable pleomorphism
Often paucicellular aspirates due to dense extracellular
fibrous stroma
Common Non-Neoplastic Findings
Abscess
Abundant Neutrophils (some of which may
be degenerating)
Necrosis and fibrin
Macrophages, bacteria, foreign material
At time of adequacy assessment one will see

frank pus. If this happens, remember to
culture it!
Clinically: Warm, Red, Tender
Granulomas
Nodular collections of epithelioid histiocytes
Often in loose syncytial aggregates
Can resemble a swirling school of fish
Histiocytes may be spindled or epithelioid with

elongated nuclei resembling bananas or
boomerangs
Can see Multinucleated Giant Cells
DDX: Infection (esp. TB & Fungi), Sarcoidosis,

foreign material→ so try to do cultures or at least
bug stains!
Necrosis
Lots of “grungy” particle fragments and fibrin
without any nucleated cells.
Can be seen in non-neoplastic processes and

neoplastic processes (so look around for viable
cells to suggest what might have caused it).
May see macrophages trying to clean up.

Reactive Lymphoid Hyperplasia
Often very cellular aspirate.
Mixture of small and large lymphocytes (range of
maturation) with a predominance of small
lymphocytes.
Frequently plasma cells and tingible macrophages (↓)
May see mitoses
Consider sending for flow cytometry at time of
adequacy to evaluate for lymphoma
Cyst Fluid
Paucicellular with scattered macrophages, which may
contain hemosiderin pigment
May see scattered debris.
These elements are often non-specific and don’t

indicate the composition of the cyst lining/wall, so
may be “unsatisfactory” for diagnosis.
If possible, drain the cyst and then reaspirate the area

in attempt to sample the cyst wall.
Ultrasound Gel
Coarsely granular metachromatic
material on Romanowsky stains.
Can obscure diagnostic material.

(some) Differential Diagnoses
Intranuclear Pseudoinclusions
Develop when the cytoplasm pushes into the nucleus (think: a balloon within a balloon)
• Papillary thyroid carcinoma
• Medullary thyroid carcinoma
• Melanoma
• Liver (benign and malignant hepatocytes)
• Meningioma
• Lung adenocarcinoma
Very Granular Cytoplasm

• Granular cell tumor (lysosomes)
• Acinar cell carcinoma (zymogens)
• Oncocytic/Hürthle cell neoplasms (mitochondria)
• Neuroendocrine tumors (neurosecretory granules)
• Hepatocytes/tumors
• Melanoma (melanosomes)
• Adrenal cortical/tumors
• Leydig cells/tumors
Tigroid Background
Seen with glycogen-rich lesions
• Seminoma/Dysgerminoma (most classic!)
• Clear cell renal cell carcinoma
• Ewing sarcoma/PNET
• Other glycogen-rich tumors
Psammoma Bodies
Frequently seen in papillary tumors
• Papillary thyroid carcinoma
• Serous ovarian tumors
• Mesothelioma
• Papillary renal cell carcinoma
• Meningioma
• Somatostatinoma (duodenum)
• Prolactinoma (pituitary)
• Lung micropapillary adenocarcinoma
Based on: The Book of Cells: A Breviary of Cytopathology, by Dr. Richard Mac DeMay
Cervical Cytology
Cell types Superficial Cells:
Small, pyknotic nucleus
Abundant cytoplasm (Often pink, can be blue)
Polygonal shape
Indicate abundant Estrogen
Intermediate Cells:
Abundant blue cytoplasm, polygonal shape
Larger, round to oval nuclei
Finer, normochromatic nuclei
→ Nuclei are important reference size
Basal/Parabasal Cell:
Minimal cytoplasm
Round to oval nuclei
Fine, but slightly dark chromatin
Usually few in number, unless atrophic
Endocervical Cells:
Uniform, Columnar cells
Polar, with round nucleus at one end
Majority of cytoplasm occupied by mucin
Arranged in flat sheets→ think “Honeycomb
Arranged in linear strips→ “Palisaded”
Endometrial Cells:
Small, High N:C ratio cells (almost all nucleus!)
Nucleus about the same size as an intermediate cell nucleus
Round nuclei with smooth chromatin, possible micronucleoli
Can be in large groups with outside epithelium and in inside stroma
Normal finding in first half of menstrual cycle if premenopausal
(Report if >50 yrs old)
Pap Smear Adequacy Criteria

(In practice, the number of cells is
Minimum number of well-visualized squamous cells for adequacy estimated based on sample photos,
Liquid-based preparation: 5,000 cells (ThinPrep and SurePath) and the cells aren’t counted).
Conventional Preparation: 8,000 to 12,000 cells
If obscuring elements cover >75% of epithelial cells → Unsatisfactory
Quality indicator: Presence of ≥10 endocervical cells or squamous metaplastic cells (reported, but not
required to be satisfactory for evaluation)
Any specimen with abnormal cells is considered adequate and should be reported!
Low-Grade Squamous Intraepithelial Lesion (LSIL)
Mature Keratinocytes (with lots of cytoplasm) AND:
• Enlarged nuclei (>3x normal intermediate cells)
• Nuclear membrane irregularities
• Hyperchromasia (“Rasinoid”)
• NO nucleoli
Optional:
• Perinuclear Halos = Koilocytes
• Large, irregular clearing
• Thick borders, like it was drawn with a
calligraphy pen
• Multinucleation
Caused by High and Low-risk HPV

May regress spontaneously!
Some findings, but “not enough”?

Consider “Atypical Squamous Cells of Undetermined
Significance” (ASCUS)
Can be either Quantitative (i.e., only rare atypical cells)
or Qualitative (e.g., only 2x nuclear enlargement)
High-Grade Squamous Intraepithelial Lesion (HSIL)

Immature keratinocytes (minimal cytoplasm, High N/C ratios) with:
• Markedly irregular nuclear contours
• (Hint: think in 3-dimensions)
• Look like boulders with all the irregularities
• Irregular chromatin and/or Hyperchromasia

Consider “Atypical Squamous Cells—Cannot exclude HSIL” (ASC-H)
Can be either Quantitative (i.e., only rare atypical cells) or
Qualitative (e.g., only moderate atypia)
Non-keratinizing SCC may look like HSIL (similar findings)
Clues to invasion: “Tumor diathesis” (Necrotic debris)

Prominent nucleoli
Keratinizing SCC: Pleomorphic cells with hyperchromatic, irregular nuclei,

prominent orangeophilic (keratinizing) cytoplasm, and bizarre shapes (like
“Tadpoles” or snakes)
Tadpole Cell
Glandular Abnormalities
Reactive Endocervical Cells

Nuclear enlargement (4-5x),
Hyperchromasia, BUT round nuclei with smooth contours and
N:C ratios maintained. Prominent nucleoli.
Not too crowded. Mitoses, but no apoptosis.
Can see tubal metaplasia→ look for cilia!
For AIS, think “Feathery,”
like a bird’s wing.
Endocervical Adenocarcinoma In Situ (AIS):
Nuclei enlargement and crowding (cigar-like, think GI adenoma)
High N:C ratios with coarse, dark chromatin.
Cellular crowding with rosettes and “feathery edges”
Mitoses and apoptosis. No nucleoli.
Most strongly associated with HPV18 subtype
Adenocarcinoma
Variable, depending on site of origin/type.
Generally, more pleomorphic/irregular.
Endometrial cell nuclei larger than intermediate cell.
Features suggesting invasion: 1)Macronucleoli, 2)Tumor

diathesis, 3)increased single cells, and 4)irregular chromatin
Factors favoring endometrial adenocarcinoma (vs endocervix):

Neutrophils, less cytoplasm, smaller nuclei
Practically speaking, often diagnose as simply: “Atypical

Glandular Cells” using Bethesda System unless very
pleomorphic
Squamous metaplasia
Thick, “Dense” cytoplasm (consistent, dark teal)
Sharply defined cell borders.
Round, usually central nuclei
Normal nuclear size
Count as sampling of transition zone
Reparative/Inflammatory Changes
Classic “Repair”
Enlarged nuclei with Prominent Nucleoli.
Round nuclear contours with fine, pale chromatin.
Normal N:C ratios, but variably sized
Cohesive flat sheets of cells with “streaming” like pulled taffy
Background inflammation
General inflammatory change

Mild nuclear enlargement (<2x size)
Fine, pale chromatin
Often nucleoli
Can see small perinuclear clearing, but smaller, and more
even than koilocytic halos
Atrophy
Seen in LOW estrogen states:
Postmenopausal
Postpartum
Premenarche
Turner syndrome
Predominance of basal and parabasal cells (High N:C ratios)

Prone to injury→ often inflammation
Immature cells that can mimic HSIL, BUT:

Finely granular chromatin
Smooth nuclear contours
Can see “Blue blobs” (see →) and granular debris (mimicking

tumor diathesis, but no karyorrhectic nuclear debris)
Radiation Changes
Cytomegaly: Big cells with Big
nuclei (proportion N:C
maintained)
Large, bizarre cells
Cytoplasmic vacuolation and

polychromasia
Multinucleation
Follicular Cervicitis
Abundant lymphocytes (small rim of cytoplasm
around round nucleus, unlike HSIL, which is irregular)
Numerous tingible body macrophages
Variably sized lymphocytes with plasma cells.
IUD-Effect
Two characteristic findings:
1) Cells with abundant vacuolated cytoplasm
(mimicking Adenocarcinoma)
2) Cells with small, dark nuclei and scant

cytoplasm (mimicking HSIL)
Always know history! 1 2
Herpes
3 M’s
Molding of nuclei
Multinucleation
Margination of chromatin
“Ground glass” chromatin with eosinophilic nuclear inclusions
Can treat with acyclovir

“Shift” in flora
“Clue Cells” = squamous cells covered with shaggy bacilli and mixed
bacteria rather than the normal lactobacilli
Thick, milky vaginal discharge with a foul “fishy” odor

(positive “whiff” test after adding KOH)
Most commonly attributed to Gardenerella vaginalis.
Treat if symptomatic.
Trichomonas Vaginalis
Pear-shaped protozoan STD
Pale, eccentric elongate nucleus
Red cytoplasmic granules
Often associated with Leptothrix (non-pathogenic

filamentous bacterium).
Often acute inflammation and inflammatory halos

Treat with antibiotics
Candida
Fungal species that can cause infectious
throughout the GYN tract (and other areas).
Thick, “cottage cheese” discharge
Eosinophilic yeast forms and pseudohyphae and
hyphae (“Spaghetti and meatballs”)
Often tangled or skewering squamous cells
Can have variable associated inflammation or
inflammatory halos
Usually only treat if symptomatic
Actinomyces
Gram-positive anaerobic bacteria
Commonly associated with IUD (or other foreign body)
Long, filamentous organisms

Tangled clumps of bacteria that look like “cotton balls”
or “dust bunnies”
No need to remove IUD or treat if asymptomatic

General Management
This is a very generalized and abbreviated (but hopefully still helpful) summarization!
For a full review of current management guidelines, please refer to the ASCCP website:
http://www.asccp.org/guidelines
Pap result → Next step

Unsatisfactory → Repeat Pap in 2-4 months
NILM, but HPV positive (> 30 yrs) → Repeat co-testing at 1 yr, OR, HPV subtyping, if high-risk→ colpo
ASCUS → HPV testing (“if you Ask Us, you should get an HPV test”), if positive → colpo; Neg→ routine
LSIL → Colposcopy, unless HPV negative, then can do repeat co-testing at 1 yr
21-24 yo with ASCUS or LSIL → follow-up in 12 months (likely to clear spontaneously)
ASC-H → Colposcopy
HSIL→ Colposcopy or LEEP
Atypical glandular cells → Colposcopy with endocervical sampling and endometrial sampling
Screening Recommendations (according to the USPSTF):

Women 21-65 Cytology alone every 3 years
OR Women 30-65 Co-testing (cytology + HPV testing) every 5 yrs
(Don’t do HPV testing if less than 30 as high rate of positivity, but also clearance)
(Don’t do any testing before age 21, after 65 if they have had good prior screening, or after a
hysterectomy for benign reasons)
Human Papilloma Virus (HPV)

Sexually Transmitted Disease.
Circular double stranded DNA virus
Infects transformation zone→ establishes itself and replicates in basal cells
Detected in the vast majority of cervical cancers.
Viral genes responsible for transforming host cells by integrating into the host DNA and disrupting tumor
suppressor genes.
E6→ inactivates p53 (blocks apoptosis)
E7→ inactivates Rb (gets rid of cell cycle arrest→ uncontrolled growth)
However, many infections are naturally cleared, so only a minority persist and lead to cancer.
HPV subtypes
High-risk (associated with cervical cancer and HSIL, but can also cause LSIL)
16, 18, 31, 33
Type 16 is most commonly detected in cervical cancers
Type 18 is associated with Endocervical Adenocarcinoma
Low-risk (Not associated with HSIL. Instead associated with LSIL/condylomas)

6, 11, 42, 43
Effusion Cytology
Normal Components Fluid sources: Peritoneum, Pleura, and Pericardium
(Mesothelium-lined cavities)
Mesothelial Cells “Mesos”
Diff Quick Round, central nucleus with coarse chromatin.
Abundant dense cytoplasm.
“Lacy skirt” (where the cytoplasm is denser closer

to the nucleus) due to surface microvilli (visible on
EM) → causes characteristic “windows” between
Window mesothelial
Pap
Can be multinucleated.
Variably prominent nucleoli.
In effusions:
Cells often present as dispersed single cells.
Mesos often adhere to each other in pairs
Cell block: H&E
In washes:
(take during surgery→ larger tissue fragments)
Mesos often present in large monolayer sheets
Well-organized, honey-comb appearance
Little nuclear overlap
Mesothelial cells can take on phagocytic roles and

essentially exist on a morphologic spectrum with
histiocytes, making them sometimes impossible to
tell apart morphologically.
In response to inflammation/trauma, mesothelial

cells can become “Activated” and look very scary!
Activated findings include:

Prominent nucleoli
Larger cell size and Multinucleation
Denser, two-toned cytoplasm
Mitotic figures
Vacuolization (mimicking signet ring cells)
Cytoplasmic blebs
Pericardial mesos are famous for being Hugging (engulfing/canibalization) other mesos
SUPER “activated” (think of all the trauma of BUT, they should still have smooth nuclear
continuous beating!). Be very cautious contours
diagnosing metastatic carcinoma there and
Positive stains: Calretinin, D2-40, CK AE1/AE3,
do stains!
CK7, CK5/6, WT-1, Mesothelin,
Histiocytes
Peripherally located grooved/folded/indented/curved nuclei
(smaller than mesothelial cell nucleus)
Abundant foamy cytoplasm, often containing debris

(more cytoplasm than lymphocyte)
Sometimes can also see monocytes

(which become macrophages after
activation), derived from marrow.
Smaller, rounder cells with oval,
indented nuclei.
“Raked” chromatin
Positive stains: CD68, CD163
Lymphocytes
Small cells with a single round nucleus.
Thin rim of cytoplasm.
A few is normal, especially in chronic effusions, but if

there are A LOT of lymphs think about:
- Lymphoma (Consider flow, or stain a cell block)
- Tuberculous effusion
- Chylous effusion
- Metastases
Collagen Balls
Sphere of collagen surrounded by a single layer of mesothelial cells.
See in pelvic washes, likely from ovary.
Benign, incidental finding.
Malignant Effusions
Metastatic Adenocarcinoma
Second population of “Foreign” epithelioid cells
(in addition to mesos)
Cytologic atypia (although sometimes bland)
Mucin production/intracytoplasmic lumina
Often larger than Medium-sized mesos
Well-defined cell borders (no lacy skirts)
Delicate cytoplasm (with mucin vacuoles)
Large cell groups (Often balls, papillae, or caterpillars)

“Cannon balls” → specifically suggests breast origin
Classically with “smooth community borders”
(Knobby borders favor mesos)
On cell block, often a “halo” around tumor cluster
(other cell/material retracted away)
Beware, some adenocarcinomas (notably lobular
breast and gastric signet-ring carcinoma) shed as
single-cells, making them hard to spot on H&E
Often best to have a low threshold for IHC.

IHC Panel to differentiate from mesos (Generally):
Metastatic Adenocarcinoma Mesothelial cells
BerEP4 Calretinin
MOC31 D2-40
B72.3 WT-1
Claudin-4 CK5/6
Adeno stains that can also get mesos: PAX8, CK7, AE1/AE3
Meso stains that can also get carcinomas: WT-1, CK5/6
Look at how BIG these cells are (note RBC for comparison)!
Intracytoplasmic
Lumen in lobular
breast cancer
Lymphoma
Often occur late (with an established Dx)
Cause chylous effusions often (milky white)
Dominated by lymphocytes
Single disclosive cells (of varying size depending on type)
If high-grade: Lots of big cells, mits, and karyorrhexis
Consider sending flow or staining cell block.
Primary Effusion Lymphoma:
Occurs in immunocompromised patients (often AIDs). Aggressive. Involves pleura, peritoneal fluid, or
pericardium without solid component. Big, ugly cells (high-grade). Positive: HHV8, EBV, CD30. MYC
overexpressed.
Interestingly, there is a form of this lymphoma that occurs in the setting of breast implants. However, this
seems to be rare and indolent in comparison.
Malignant Mesothelioma
Most commonly older men in pleural cavity due to asbestos exposure.
Poor prognosis. Classically forms rind-like encasement of lung.
Histologically, can be epithelioid, sarcomatoid, or both (biphasic)
First specimen often pleural fluid, but classically very hard to dx.
All mesothelial cells (no “foreign” second population)
Often maintain similar cytologic features (lacy skirts, etc…)
Can be cytologically malignant or relatively bland
“More and bigger cells, in more and bigger clusters.”
Large clusters with knobby, flower-like contours
The diagnosis of mesothelioma has medical and legal

implications, so the diagnosis often requires special studies or a
tissue biopsy for definitive diagnosis. Otherwise, often signed
out as “Atypical mesothelial proliferation.”
Special Studies that support the diagnosis of

mesothelioma with good specificity (not
fantastic sensitivity though):
IHC: BAP1 or MTAP loss Mesothelioma on Tissue biopsy:
• Stromal invasion usually apparent
FISH: CDKN2A (p16) deletion
• Dense cellularity
Multigene expression profiling panels • Complex papillae, tubules, and cellular
stratification
• Cells surrounded by stroma
Useful Article: Husain AN et al. Guidelines for Pathologic • Expansile nodules with disorganized growth
Diagnosis of Malignant Mesothelioma 2017 Update of the
Consensus Statement From the International Mesothelioma
• Minimal inflammation
Interest Group. Arch Pathol Lab Med. 2018 Jan;142(1):89-108.
Benign Effusions
Rheumatoid Effusion
Seen with Rheumatoid Arthritis.
Classically see, essentially, fragmented components of a
rheumatoid nodule (granuloma with central necrosis):
1. Granulomas, multinucleated giant cells, and
epithelioid histiocytes
2. Necrotic debris
Often very Bizarre, but benign, cells—so be careful!
Eosinophilic Effusion
Abundant eosinophils.
Rarely malignant.
Often idiopathic, but also associated with:

• Pneumothorax,
• Prior procedure,
• hypersensitivity reaction,
• infection,
Lupus Effusion
Seen in systemic lupus erythematosus (LE) due to pleuritis.
Classically see “LE” cells, which are neutrophils with a
phagocytosed nucleus.
Auto-antibodies (e.g., Anti-DNA) attack a cell → the cell dies

and the nucleus is shed creating a LE body → this is
phagocytosed by a neutrophil.
This finding is not too sensitive or specific, but it is classic and

can prompt further testing.
“Tart cells” (phagocytosed nucleus in a macrophage) are more

common and even less specific.
Chylous Effusion
Caused by leakage of thoracic duct→ leaks fatty lymphatic fluid.
Often caused by lymphoma.
Rich in triglycerides→ milky white.
Mostly lymphocytes with some lipophages and mesos.
Tuberculous effusion
Abundant lymphocytes (T-cells) with sparse mesos.
Histiocytes are present, but giant cells are rare.
Endosalpingiosis
Fallopian tube-type epithelium present elsewhere.

Columnar to cuboidal cells with bland nuclear features
Cilia are unique finding that can be very helpful.
Can have psammoma bodies
PAX8 positive (like many GYN tumors), so be careful!
Endometriosis
Can be hard to diagnose without history, but always something
to keep in the back of your mind.
Triad:
1. Hemosiderin-laden macrophages
2. Endometrial glands (small columnar cells, similar to mesos)
3. Endometrial stroma (like histiocytes or lymphs)
Cell block can be very helpful!

The Paris System for Urine Cytology

Figures from:
Additional Studies
UroVysion FISH
4 Markers:
1-3) Chromosome enumeration probes targeting pericentromeric region on chromosomes 3, 7,
and 17 (looking for aneuploidy)
4) Specific probe targeting 9p21 loci (p16 gene, looking for loss)
Analysis:
- Positive if ≥4 of 25 analyzed cells show two or more of chromosome 3, 7 or 17 (i.e.,
chromosome gain)
OR
- Positive if ≥12 of 25 analyzed cells show have total loss of 9p21
If not positive after 25 cells → keep counting until all cells are analyzed.
Note: Some reactive cells (e.g., Umbrella cells) can be tetraploid!

Thyroid Cytology
Adequacy Criteria Must see at least 6 groups of well-visualized follicular
epithelial cells, each consisting of at least 10 cells.
Exceptions:
1) Abundant colloid with radiographic findings compatible
with a colloid nodule
2) Abundant inflammation with a solid nodule
(lymphocytes, granulomas, or neutrophils)
3) Atypia
Ideally, follicular epithelium should be in nice big, flat (“monolayered”) sheets, with evenly
spaced (“Honeycomb-like”) dark, round nuclei with uniformly granular chromatin.
Benign Follicular Nodule Watery Colloid

Histologically represent nodular goiter, adenomatoid
nodules, and colloid nodules.
Variable amounts of: colloid, bland follicular cells,
Hürthle cells, and macrophages.
Should be sparse to moderately cellular with a good
amount of colloid (easiest to see on diff-quick)
Watery colloid – thin, watery, like cellophane
Dense Colloid – thick, hyaline
Cystic degeneration: macrophages, “reparative” stretched cells Dense Colloid
Lymphocytic Thyroiditis
Hypercellular smear with abundant, polymorphic lymphocytes.
Hürthle cell metaplasia common (Large cells with abundant
granular cytoplasm and prominent nucleoli).
Advanced cases may be hypocellular (due to fibrosis).
Often middle-aged women with associated circulating
autoantibodies.
Granulomatous Thyroiditis Aka subacute or de Quervain’s

Self-limited inflammatory condition, usually diagnosed clinically
Clusters of epithelioid histiocytes (i.e., granulomas) and
multinucleated giant cells, often ingesting colloid
Early can have neutrophils and eosinophils. Later have lymphocytes.
Papillary Carcinoma
Most common malignant thyroid neoplasm
Relatively good prognosis. Spreads via
lymphatics.
Classic findings:
-Intranuclear pseudoinclusions
-Powdery, pale chromatin with marginal
micronucleoli
-Enlarged, irregular nuclei
-Longitudinal nuclear grooves
-Dense, squamoid cytoplasm
-Multinucleated giant cells
-Dense, “Bubble gum” colloid
-Septate cytoplasmic vacuoles
-Papillary structures w/ and w/o fibrovascular
cores

Consider Atypia of Undetermined Significance
(AUS) or Suspicious for Malignancy.
Follicular Neoplasm/Suspicious for Follicular Neoplasm

Cannot differentiate between Follicular Adenoma
and Carcinoma on cytology specimens (need to
see capsular or vascular invasion on resection
specimen!)
Moderately or Markedly cellular
Significant alteration in follicular architecture
→ Repetitive microfollicular pattern or cell
crowding/overlapping in trabeculae
→ Minimal colloid
Minimal cytologic atypia. Microfollicle: less than 15 cells
arranged in a circle that is at
Hürthle Cell Lesions: least 2/3 complete
Look for: 1) nonmacrofollicular
architecture, 2) absence of colloid, 3) Some findings, but “not enough”?
absence of inflammation, and 4) presence Consider Follicular Lesion of Undetermined
of “Transgressing blood vessels” Significance (FLUS)
Medullary Carcinoma
Can be sporadic or inherited (part of MEN 2A&B)
Derived from Parafollicular C cells→ stain with Calcitonin!
Moderate to Marked Cellularity. Often discohesive.
Plasmacytoid, polygonal, to spindled cells.
Mild to moderate pleomorphism.
“Salt and Pepper” chromatin.
Granular cytoplasm with small granules.
Occasional intranuclear pseudoinclusions or amyloid fragments
Undifferentiated (Anaplastic) Carcinoma
Extremely aggressive. Poor prognosis.
Classically older women with rapidly growing, hard
neck mass → trouble breathing
Variable cellularity. Often discohesive.
Epithelioid to Spindled cells.
Enlarged, pleomorphic nuclei.
Often associated necrosis and inflammation.
Can see osteoclast-like giant cells
The Bethesda System and Genetics
With rare exception, FNAs should be classified into one of the Bethesda Categories.
If you have an equivocal AUS/FLUS case, consider sending for molecular testing.
Papillary Thyroid Carcinoma:
MAPK Pathway Diagnostic Category Risk of Management
BRAF (most classic PTC’s) Malignancy
V600E (most common)
I Unsatisfactory Repeat US-guided FNA
RAS (associated with
follicular variant & NIFTP)
II Benign 0-3% Clinical follow-up
Medullary Carcinoma:
RET (think MEN2A&B) III AUS/FLUS ~5-15% Repeat FNA and/or
Molecular testing
Follicular Neoplasms:
RAS most common IV Follicular 15-30% Lobectomy
PAX8/PPARG Neoplasm
PTEN
V Suspicious for 60-75% Near total or total
Poorly Differentiated and Malignancy thyroidectomy
Anaplastic
TP53 VI Malignant 97-99% Thyroidectomy
CTNNB1
(and others mentioned above)
CHAPTER 5
Thorax
Lung Tumors
Adenocarcinoma
Malignant epithelial tumor with glandular differentiation, mucin production, or pneumocyte marker
expression.
Lung Cancer (including other carcinoma types) is the most common cause of cancer death world-wide.
Strong association with tobacco smoking. Other risk factors: Radon, air pollution, occupational exposure
Symptoms vary depending on sites of involvement, and include chest pain and hemoptysis.
However, most patients present late with advanced or metastatic disease that is inoperable.
On CT, they are often peripheral with solid (invasive) areas and “ground-glass” (lepidic) areas.
Histologic Patterns:
Use for non-mucinous adenocarcinomas. If an
adenocarcinoma subtype/architectural pattern is identified
on biopsy, it should be reported. Report in 5% increments
and classify based on predominant pattern.
Lepidic
Subtype Characteristics
Lepidic Growing along the surface of alveolar
walls (like AIS), non-invasive
Acinar Round to oval glands with a central
lumen space surrounded by tumor cells
Papillary Glands growing along central Acinar
fibrovascular cores
Micropapillary Cells growing in papillary tufts forming
florets that lack fibrovascular cores
(poorer prognosis)
Solid Polygonal tumor cells growing in sheets
(poorer prognosis)
Papillary
If exclusively lepidic on biopsy, report as “Adenocarcinoma,

lepidic pattern” (or something similar). On resection, this could
represent Adenocarcinoma in situ (AIS), Minimally invasive
adenocarcinoma (MIA), or simply a lepidic component of an
invasive adenocarcinoma. Radiographic correlation is required
pre-operatively. Micropapillary
Criteria for invasion:
1) Histologic subtype other than lepidic (e.g., acinar),
2) Desmoplastic stroma associated with tumor,
3) Vascular or pleural invasion,
4) Spread through air spaces (STAS)
IHC: (+) TTF-1, Napsin-A, CK7
Solid
Variants of Adenocarcinoma:
Invasive Mucinous Carcinoma
An adenocarcinoma with goblet or columnar cells with
abundant intracytoplasmic mucin.
Any growth pattern may be seen. Even though often lepidic-
predominant, usually areas of invasion.
Frequently KRAS mutated. Often peripheral.
Usually CK7+, TTF-1 negative with frequent CK20 expression.
Need to clinically exclude mucinous metastasis (e.g.,
pancreas)
Colloid Adenocarcinoma
Adenocarcinoma where pools of abundant mucin replace
air spaces.
Mucin distends alveolar spaces and destroy walls, with
overtly invasive growth. Tumor cells often do not entirely
line alveoli and may be relatively bland.
IHC: Often express intestinal markers CDX2, CK20
(+/-) TTF-1, CK7, and Napsin-A
Enteric Adenocarcinoma
Adenocarcinoma resembling colorectal-type
adenocarcinoma.
Requires careful clinical evaluation (e.g., colonoscopy and
imaging) to exclude a metastasis from an occult primary.
Morphology and IHC identical to colon cancer:
Eosinophilic, tall columnar cells with pseudostratified
nuclei and abundant “dirty” necrosis.
Fetal Adenocarcinoma
Adenocarcinoma resembling fetal lung.
Complex glandular structures composed of
glycogen-rich, non-ciliated cells (resembling the
developing epithelium of the lung).
Frequent morule formation. Variable atypia.
Can be pure or combined with other types.
IHC: TTF-1(+). Frequent nuclear β-catenin,
neuroendocrine marker, and germ cell marker
expression
Precursor/Early/Lepidic Lesions:
Atypical Adenomatous Hyperplasia
A small (usually ≤ 0.5 cm) localized proliferation of
mildly to moderately atypical type II pneumocytes
and/or Clara cells lining alveolar walls (lepidic
growth).
Often peripheral.
Benign—cured if resected.
(Glandular counterpart of squamous dysplasia)
Adenocarcinoma in situ Formerly, “Brochoalveolar Adenocarcinoma” (BAC)
A small (≤ 3 cm), solitary, localized adenocarcinoma

with pure lepidic growth (no other patterns allowed).
NO stromal, vascular, or pleural invasion. No STAS.
Mostly non-mucinous.
Septal widening with sclerosis/elastosis is common.
Minimal to moderate nuclear atypia.
IHC: Express CK7, TTF-1, and Napsin-A.
Essentially Benign—100% survival if resected entirely.
Minimally Invasive Adenocarcinoma

Must fulfill all of the following criteria:
1) Small tumor ≤3 cm
2) Solitary adenocarcinoma
3) Predominantly lepidic growth
4) Invasive component ≤ 0.5 cm in greatest dimension
• Includes any subtype other than lepidic and
desmoplastic stroma
5) Does not contain:
• Lymphovascular invasion
• Pleural invasion
• Spread through air spaces (STAS)
• Tumor necrosis
Usually non-mucinous.
Essentially benign→ 100% disease-free survival if resected
Pneumonic-type Adenocarcinoma
Tumors should be considered pneumonic-type adenocarcinoma if there is diffuse distribution of
adenocarcinoma throughout a region(s) of the lung as opposed to a well-defined lesion(s)
- These are typically mucinous, but can be non-mucinous
- Often Lepidic-predominant, but can see any pattern
Squamous Lesions
Squamous Papilloma
Papillary proliferation covered by squamous epithelium.
HPV is involved in <½ of solitary lesions, but is involved in
essentially all cases of laryngotracheal papillomatosis.
Often present with obstruction or hemoptysis.
Malignant transformation is rare.
Squamous Cell Carcinoma in situ

Squamous dysplasia precursor lesion arising in squamous metaplasia
of the bronchial tree. Can be single or multifocal.
Part of a continuum with sequential molecular abnormalities and
can morphologically graded from mild dysplasia to SCCIS using
similar criteria to upper aerodigestive tract.
Respiratory epithelium→ irritant/carcinogen (e.g, smoking)→ hyperplasia→ squamous metaplasia →
squamous dysplasia → squamous cell carcinoma in situ → invasive squamous cell carcinoma

Malignant epithelial tumor that shows either
keratinization, intercellular bridges, or expresses
immunohistochemical markers of squamous
differentiation.
Strongly associated with smoking. Often central.

May be keratinizing or non-keratinizing
IHC: (+) p40, p63, CK5/6; (-) TTF-1, Napsin-A
Basaloid Squamous Cell Carcinoma

Proliferation of small with high N:C ratios, distinct
borders cells with lobular architecture and
peripheral palisading. No nuclear molding. Lack
overt squamous morphology, but express
squamous IHC markers. Lots of mitoses. Often
hyaline or mucoid stroma.
Most compose >50% of tumor.
IHC: Stain with same squamous markers. Ki67
often 50-80%. Only focal NE marker staining.
Worse prognosis than SCC otherwise
Neuroendocrine Tumors IHC Markers of Neuroendocrine Differentiation:
Synaptophysin, Chromogranin, INSM1. Less so CD56, NSE.
Cytokeratins often show perinuclear “dot-like” staining.
Note: Lung neuroendocrine neoplasms are graded based on mitoses and necrosis (counted in a hotspot).
Ki67 may be helpful to confirm your morphologic impression, but is not currently used for grading.
Typical Atypical Large cell Small cell carcinoma

carcinoid carcinoid neuroendocrine
carcinoma
Smoking association No Maybe Yes Yes
Mitoses/2mm2 0-1 2-10 >10 (median 70!) >10 (median 80!)

Necrosis No Focal, if any Yes Yes, extensive
Neuroendocrine Yes Yes Yes Yes

morphology
Ki-67 Proliferation Up to 5% Up to 20% 40-80% Almost 100%
index
TTF1 expression Usually not Usually not ~50% Usually, Yes (85%)
Combined with non- No No Sometimes Sometimes
small cell component
(e.g., squam)
Adapted from: WHO Classification of tumors of the lung, pleura, thymus, and heart. 2015.
Typical Carcinoid
Low-grade malignancy.
Often arise near central airway. Can grow in airway.
Occasionally peripheral (often spindled morphology).
Tumor syndromes are rare.
“Carcinoid morphology:” organoid or trabecular
growth, uniform polygonal cells, finely granular “salt
and pepper” chromatin, inconspicuous nucleoli, and
abundant eosinophilic cytoplasm)
<2 mitoses per 2 mm2, lacking necrosis, and >0.5cm

(if less than 0.5 cm, it is designated as a “tumorlet”).
On cytology, discohesive cells with stippled

chromatin.
Atypical Carcinoid
Intermediate-grade malignancy
A tumor with “carcinoid morphology” and 2-10
mitoses per 2 mm2 and/or necrosis (often
punctate).
Worse prognosis than typical carcinoid.
Diffuse Idiopathic Pulmonary Neuroendocrine Cell Hyperplasia
aka “DIPNECH”
Generalized proliferation of pulmonary neuroendocrine cells along airways.
May invade locally and eventually grow to tumorlets or even carcinoid tumors. Often older patients.
Tumor cells have neuroendocrine morphology (round to oval nuclei with salt and pepper chromatin)
and start in respiratory mucosa.
Patients often present with cough and wheezing misdiagnosed as asthma (or asymptomatic).
Chronic, slowly progressive disease
Small Cell Carcinoma

Often centrally located in major airways/hilar.
Often present with rapid growth, metastases (including bulky
mediastinal lymphadenopathy), and paraneoplastic
syndromes (e.g., hyponatremia, Cushing's, etc.)
Strongest association with heavy smoking of all lung cancers.
Small cell size (usually smaller than 3 resting lymphocytes)
Scant cytoplasm. Unclear borders. Frequent nuclear molding.
Densely cellular sheet-like growth. Cells fusiform to round.
Finely granular chromatin (no nucleoli)
High mitotic rate: >10 mitoses per 2 mm2 (median 80)
Frequent necrosis (often large zones) and apoptoses.
Ki67 often essentially 100%
Can be “combined” with other tumors, such as SCC.
Very poor prognosis

Smoking-related. Often peripheral.
“Neuroendocrine morphology” (architecture: organoid nesting,
palisading, rosettes, trabeculae)
Cytological features of non-small cell carcinoma: large cell size,
vesicular, coarse, or fine chromatin, frequent prominent nucleoli,
and abundant cytoplasm (low N:C ratio)
High mitotic rate: >10 mitoses per 2 mm2 (median 70)
Necrosis (often large zones)
Can be combined with other types of lung carcinoma (e.g., SCC)
Aggressive.
Other Carcinomas
Adenosquamous Carcinoma
Carcinoma with both a 1) squamous cell carcinoma 2
and 2) an adenocarcinoma component.
Each must constitute at least 10%.

Can only be diagnosed on resection specimen (can
suggest though on Bx) 1
Large Cell Carcinoma

Undifferentiated non-small cell carcinoma that lacks cytologic, architectural,
and IHC features of small cell carcinoma, adenocarcinoma, and SCC
DX of exclusion! (Therefore cannot be made on a Bx)
Prevalence is decreasing with increased IHC use.
Sheets or nests of large polygonal cells with vesicular nuclei and prominent
nucleoli. IHC: CK(+), TTF1 (-), p40(- or focal), neuroendocrine marker (-)
Sarcomatoid Carcinomas Diagnosis can only be definitively made on resection specimens.
Spindle Cell Carcinoma: a carcinoma consisting of almost

entirely pure spindle cells
Giant Cell Carcinoma: a carcinoma consisting of almost entirely
giant cells
Pleomorphic Carcinoma: contains at least 10% giant or spindle
cell carcinoma. This includes both of the above categories and is
essentially the current term for sarcomatoid carcinoma in the
lung.
IHC: Variable IHC
Carcinosarcoma: Mixture of NSCLC and a sarcoma containing
heterologous elements such as rhabdomyosarcoma,
chondrosarcoma, or osteosarcoma. Poor prognosis.
Lymphoepithelioma-like Carcinoma
Carcinoma with marked lymphoid infiltrate
EBV infection of neoplastic cells (EBER ish +)
Large cells with syncytial growth, large vesicular
nuclei and prominent nucleoli.
IHC: (+) CK AE1/AE3, CK5/6, p40, p63.
Improved survival.
Classification of Lung Carcinomas
with Limited Tissue
Diagnostic Algorithm Try to be as specific as you can be, while also sparing as much tissue as
you can for molecular testing (critical for lung cancer!)
Morphologically Carcinoma
Histology: Lepidic, papillary, micropapillary, or Keratinization, pearls, or

acinar growth. Cytology: Delicate foamy intercellular bridges
cytoplasm, fine chromatin, prominent nucleoli
Squamous cell
Adenocarcinoma carcinoma
Nested or trabecular growth, rosettes,

Note: You may still want to do a lung moderate amounts of cytoplasm,
adenocarcinoma marker to confirm lung origin vesicular nuclei with prominent
nucleoli
Speckled chromatin, scant

cytoplasm, lots of mitoses Synaptophysin,
chromogranin, or
CD56 +
Synaptophysin or
CD56+; CK+ Large cell
neuroendocrine
carcinoma
Small cell No clear line of

carcinoma differentiation?
Choose one squamous
Do Stains marker and one
adenocarcinoma marker
(to start with). More
p40 and TTF-1, +/- options on next page.
Mucin marker
P40 +; TTF1 and Both markers Both markers

TTF1 and/or
mucin marker negative positive, in
mucin +; p40 -
negative different cells
Non-small cell Cytokeratin(s) to

Non-small cell confirm epithelial Non-small cell
carcinoma, favor carcinoma,
carcinoma, favor
squamous cell possible
adenocarcinoma
carcinoma Adenosquamous
Non-small cell carcinoma
May want to do other stains or clinical carcinoma (NOS)
evaluation to exclude a metastasis
Classification Guidelines
Some carcinomas can only be diagnosed on resection (not on Bx): Adenocarcinoma in situ, Minimally
invasive carcinoma, Adenosquamous carcinoma, Large cell carcinoma, Sarcomatoid carcinoma
If you can make the diagnosis morphologically → can call Adenocarcinoma or Squamous cell carcinoma
If can’t tell morphologically, then do stains:

A simple panel of 2 stains (1 squamous and 1 adenocarcinoma) is usually adequate (e.g., p40 and TTF1)
A positive mucin stain (e.g., PAS-D, or mucicarmine) can also identify some adenocarcinomas.
Report as “Non-small cell carcinoma, favor….” (either adenocarcinoma or squamous cell carcinoma)
Do not do neuroendocrine stains unless there are morphologic findings to suggest neuroendocrine
differentiation (neuroendocrine differentiation in an SCC or Adeno doesn’t impact treatment/prognosis).
Immunohistochemical Staining Note: Some primary lung

Adenocarcinoma Squamous cell carcinoma adenocarcinomas, including Mucinous
adenocarcinoma, Colloid carcinoma,
TTF1 p40 (most specific) and Enteric adenocarcinoma, can be
Napsin A CK5/6 TTF-1 negative. They can even stain
with CK20 and CDX2. These cases
CK7 (less specific) p63 (less specific) require careful clinical correlation to
exclude a metastasis from the GI tract.
IHC typing of a Cytokeratin-positive, morphologically undifferentiated non-small cell lung carcinoma

(NSCLC). Mucin-negative. Sarcomatoid carcinoma and neuroendocrine tumors should also be considered.
TTF1 p63 p40 CK5/6 Resection Dx Biopsy Dx

Napsin-A
Adenocarcinoma NSCLC favor
+ - - - Adenocarcinoma
+ + - - Adenocarcinoma
+ + + (focal) - Adenocarcinoma
+ - - + (focal) Adenocarcinoma
Any one of the above diffusely Squamous cell NSCLC favor SCC
- positive carcinoma
Any one of the above focally positive Large cell NSCLC, NOS
- carcinoma
Large cell NSCLC, NOS
- - - - carcinoma
Multiple Tumors When more than 1 tumor nodule is identified in resection specimens, it is
important to attempt distinction of synchronous primary tumors from a
tumor with intrapulmonary metastasis.
Consider it a second primary if (and stage each separately):
- Tumors have different histologic types (e.g., 1 squamous and 1 adenocarcinoma)
- They are dramatically different morphologically after comprehensive review
- They are two squamous carcinomas with each having an in situ component
Consider it an intrapulmonary metastasis if:
- Identical genetic abnormalities are detected.
Relative arguments that favor a second primary:
- Different biomarker pattern
- Absence of nodal or systemic metastases
Relative arguments that favor an intrapulmonary metastasis:
- Matching appearance after comprehensive review
- The same biomarker pattern
- Significant nodal or systemic metastases
Pleural Invasion If tumor is approaching the visceral pleural surface, get an Elastin stain
(e.g., EVG) to see if it crosses the elastic layer for staging purposes.
Visceral Pleura Surface
Stage Depth of Invasion
PL0 Tumor does NOT completely
traverse elastic layer
PL1 Tumor extends through elastic layer,
but not to visceral pleural surface
PL2 Tumor extends to the visceral
pleural surface
PL3 Tumor invades parietal pleura
In this example, the tumor crosses the
elastic layer, but doesn’t go to the
visceral pleural surface, so it is PL1.
Lung
Spread Through Air Spaces (“STAS”)

Defined as micropapillary clusters, solid nests or single cells of tumor extending beyond the edge of
the tumor into the air spaces of the surrounding lung parenchyma.
- No strict distance cut-off.
- If present, cannot be considered AIS or minimally invasive adenocarcinoma.
- Associated with an increased incidence of recurrence in tumors that have
undergone limited resection (e.g., wedge resection).
- Should not be incorporated into the measurement of tumor size.
Major Genetic Changes ~70% of lung cancers are inoperable
→ Dx and all testing done on core Bx or FNA
Must test Adenocarcinoma for: EGFR, ALK, ROS1 in all cases (molecular/FISH/IHC); PD-L1 (IHC)
Consider testing for: BRAF, KRAS, HER2, RET,
(Can consider some of these tests in non-adenocarcinomas if mixed histology or small biopsy)
Alteration Small cell carcinoma Adenocarcinoma Squamous cell

(%) (%) carcinoma (%)
Mutation
EGFR Caucasian <1 10-20 <1
EGFR Asian <5 35-45 <5
KRAS Caucasian <1 15-35 <5
KRAS Asian <1 5-10 <5
BRAF 0 <5 0
PIK3CA <5 <5 5-15
RB >90 5-15 5-15
P53 >90 30-40 50-80
Amplification
EGFR <1 5-10 10
FGFR1 <1 <5 15-25
MYC 20-30 5-10 5-10
Gene Rearrangement
ALK 0 5 <1
ROS1 0 1-2 0
NTRK1 0 <1 0
Driver mutations are essential for tumor survival (“oncogene addiction”), so targeting them results
in cancer cell death.
EGFR mutations→ can treat with receptor tyrosine kinase inhibitors: Erlotinib, gefitinib, afatinib, etc.
→ Eventually develop acquired resistance (usu. < 1 yr); Most commonly T790M mutation
KRAS mutations→ resistant to EGFR-targeted therapy (and no current specific treatments)
ALK and ROS1 rearrangement→ respond to crizotinib
Adenocarcinomas: Associations
EGFR and ALK→ usually never smokers, Asian, non-mucinous, peripheral location
KRAS→ usually smokers, mucinous, non-Asians, perihilar location (like small cell and SCC)
ALK rearrangements→ usu. Young, never smokers, associated with cribriform morphology
Salivary Gland Tumors Arise from salivary-like glands in bronchi.
Often endobronchial in central airway→ present with wheezing, cough, obstruction
Mucoepidermoid Carcinoma: 3 cell-type present: 1)Mucin-secreting cells, 2)Squamous cells, and
3)Intermediate cells. MAML2 rearrangements detectable by FISH. Low-grade has good prognosis
Adenoid Cystic Carcinoma: Basaloid carcinoma with epithelial and myoepithelial cells arranged in
variable configurations including tubular, cribriform, and solid. Often myxoid or hyalinized material within
tubules. Frequent MYB rearrangements.
Epithelial-Myoepithelial Carcinoma: Low-grade malignancy with biphasic morphology consisting of ducts
made up of epithelial cells with surrounding myoepithelial cells, often with clear to spindled morphology.
Pleomorphic Adenoma: Benign tumor with epithelial cells and myoepithelial cells intermingled with
myxoid to chondroid stroma. PLAG1 rearrangements.
Adenomas
Sclerosing Pneumocytoma Old name: “Sclerosing hemangioma” (didn’t know origin!)
Pneumocytic origin with dual cell populations:
1) Surface cuboidal cells resembling type II pneumocytes
-Stain with Cytokeratins, TTF-1, Napsin-A 1
2) Round stromal cells
- Stain with TTF-1; CK-negative
Four growth patterns: 1)Solid, 2)Papillary, 3)Sclerotic,
4)Hemorrhagic. 2
Benign. Often asymptomatic. More commonly women.
Alveolar Adenoma
Solitary, well-circumscribed, peripheral tumor.
Network of cystic spaces line by a simple layer of
type II pneumocytes (resembling alveoli) overlying a
spindle cell-rich stroma, sometimes with myxoid
matrix
Benign. Very Rare. Often asymptomatic/incidental.
Other Adenomas
Glandular Papilloma: Benign papillary glandular tumor lined by ciliated or non-ciliated columnar cells
with varying numbers of cuboidal and goblet cells.
Papillary Adenoma: Benign circumscribed papillary neoplasm that consists of cytologically bland,
cuboidal to columnar cells covering fibrovascular cores.
Mucinous Gland Adenoma: Exophytic, well-circumscribed tumor of the tracheobronchial
seromucinous glands and ducts. Microacini, glands, and tubules of bland cells. Benign.
Mesenchymal Lesions
Pulmonary Hamartoma
Asymptomatic, solitary, well-circumscribed lesion.
Usually peripheral with “popcorn” calcifications on CT
Varying amounts of at least 2 mesenchymal elements
(e.g., cartilage, fat, smooth muscle, or fibrous tissue)
combined with entrapped epithelium.
Benign. Neoplasms, with frequent HMGA2 fusions.
Relatively common.
Cartilage only benign neoplasm?→ Chondroma→
associated with Carney Triad
Lymphangioleiomyomatosis aka “LAM”

Perivascular Epithelioid Cell tumor (PEComa)
Diffuse, bilateral multicystic proliferation
Low-grade destructive, metastasizing.
Almost exclusively young women.
Associated with Tuberous sclerosis.
Slowly take over lungs→ SOB, Dyspnea
Thin-walled cysts with plump spindled cells with
pale eosinophilic to clear cytoplasm (glycogen)
IHC: (+) HMB45, SMA, MelanA, CathepsinK, MiTF
Molecular: TSC mutations→ mTOR pathway
Clear Cell “Sugar” Tumor

Benign, localized PEComa. Very rare.
Not associated with tuberous sclerosis.
Solitary, well-circumscribed peripheral lesions.
Round to oval cells with abundant clear or
eosinophilic cytoplasm.
IHC: (+) HMB45, MelanA, CathepsinK, MiTF,
Solitary Fibrous Tumor

Usually benign.
“Patternless pattern” of varying cellularity of bland spindled
cells with varying amounts of collagenized stroma.
Prominent “Staghorn vessels” (dilated, thin-walled,
branching vessels).
Can be hyalinized or myxoid.
IHC: STAT6 (+). Also, CD34, CD99 (+, but variable).
Molecular: NAB2/STAT6 gene fusion
Intimal Sarcoma
Malignant.
Arises in large blood vessels of systemic and pulmonary
circulation. Characteristic predominantly intraluminal growth
with obstruction of blood flow and seeding tumor emboli.
Mild to severely pleomorphic spindled cells with necrosis,
nuclear pleomorphism, and mitoses. Can have myxoid or
fascicular areas.
IHC: MDM2 (+)
Molecular: Amplification of MDM2/CDK4 (like in ALT/WDL)
Inflammatory myofibroblastic Tumor

Relatively indolent (tend to recur, rarely metastasize).
Any age. Usually solitary. Frequently asymptomatic.
Bland spindled to stellate cells in myxoid to hyalinize stroma. Can
have loose, fascicular, or storiform growth.
Prominent lymphoplasmacytic infiltrate.
Most cells bland, but sometimes large cells with prominent nucleoli.
IHC: Variable staining with actin/desmin. ALK (+) in ~50%
Molecular: ~50% have ALK gene rearrangements.
Meningothelial-Like Nodule
Old name: “chemodectoma”
Benign. Common, incidental, often multiple.
Small (1-4mm)
Monotonous, bland, ovoid to spindle cells within septae
Indistinct cell borders. Oval nuclei with occasional intranuclear
pseudoinclusions. Prominent whorled architecture.
IHC: (+) SSTR2A, PR, EMA, CD56; (-)CK, S100, TTF1
Pulmonary blastoma Vs. Pleuropulmonary blastoma

Pulmonary Blastoma: Biphasic tumor that consists of low-grade
fetal adenocarcinoma and primitive mesenchymal stroma (may
or may not show specific line of differentiation like muscle or
bone). Uncommon carcinoma of adulthood. Poor prognosis.
Pleuropulmonary Blastoma: Sarcoma of the lung in infancy/

childhood. May be solid or cystic. Small round primitive cells
with variable sarcomatous differentiation (e.g.,
rhabdomyosarcoma). DICER1 mutations. Can be seen in with
germline DICER1 mutations, increasing risk of other
malignancies too.
SMARCA4-deficient Thoracic Sarcomas
Malignant. Centered in thorax. Very aggressive.
Diffuse sheets of mildly discohesive, relatively
monotonous, and undifferentiated epithelioid cells
with prominent nucleoli.
IHC: (+) CD34, SALL4, (+/-)CK
Molecular: SMARCA4 mutations (part of SWI/SNF
chromatin remodeling complex, like INI-1)
Pulmonary Myxoid Sarcoma with EWSR1-CREB1 translocation

Malignant. Usually arises in airways.
Lobules of delicate, lace-like strands and cords
of round to spindled cells within myxoid
stroma.
IHC: Pretty much all negative except vimentin
EWSR1 rearrangements with FISH.
Synovial Sarcoma
Malignant spindle cell neoplasm with characteristic
SS18 translocation. Poor prognosis.
Like in soft tissue, monophasic or biphasic
proliferation of spindled cells with stubby nuclei
and frequent Stag-horn vessels
Other Mesenchymal tumors

Epithelioid hemangioendothelioma Myoepithelial tumors
Congenital peribronchial myofibroblastic tumor Granular cell tumor
Diffuse pulmonary lymphangiomatosis
Other Lesions
Metastases!!! Always consider in the lung, especially if multiple/bilateral!
MALT Lymphoma—thought to arise secondary to inflammatory/autoimmune processes.
Lymphomatoid Granulomatosis—Pulmonary nodules composed of angiocentric/angiodestructive
polymorphous lymphoid infiltrate containing EBV-positive B cells with reactive T cells.
Pulmonary Langerhans Cell Histiocytosis—Strongly associated with smoking and in the lung is classified
as an interstitial lung disease in most cases (not a neoplasm)
Germ Cell Tumors—Mature teratomas most common
Intrapulmonary thymoma
Melanoma
Classification of Lung Carcinomas
with Limited Tissue Prepared by Kurt Schaberg
Diagnostic Algorithm Try to be as specific as you can be, while also sparing as much tissue as
you can for molecular testing (critical for lung cancer!)
Morphologically Carcinoma
Histology: Lepidic, papillary, micropapillary, or Keratinization, pearls, or

acinar growth. Cytology: Delicate foamy intercellular bridges
cytoplasm, fine chromatin, prominent nucleoli
Squamous cell
Adenocarcinoma carcinoma
Nested or trabecular growth, rosettes,

Note: You may still want to do a lung moderate amounts of cytoplasm,
adenocarcinoma marker to confirm lung origin vesicular nuclei with prominent
nucleoli
Speckled chromatin, scant

cytoplasm, lots of mitoses Synaptophysin,
chromogranin, or
CD56 +
Synaptophysin or
CD56+; CK+ Large cell
neuroendocrine
carcinoma
Small cell No clear line of

carcinoma differentiation?
Choose one squamous
Do Stains marker and one
adenocarcinoma marker
(to start with). More
p40 and TTF-1, +/- options on next page.
Mucin marker
P40 +; TTF1 and Both markers Both markers

TTF1 and/or
mucin marker negative positive, in
mucin +; p40 -
negative different cells
Non-small cell Cytokeratin(s) to

Non-small cell confirm epithelial Non-small cell
carcinoma, favor carcinoma,
carcinoma, favor
squamous cell possible
adenocarcinoma
carcinoma Adenosquamous
Non-small cell carcinoma
May want to do other stains or clinical carcinoma (NOS)
evaluation to exclude a metastasis
Classification Guidelines
Some carcinomas can only be diagnosed on resection (not on Bx): Adenocarcinoma in situ, Minimally
invasive carcinoma, Adenosquamous carcinoma, Large cell carcinoma, Sarcomatous carcinoma
If you can make the diagnosis morphologically → can call Adenocarcinoma or Squamous cell carcinoma
If can’t tell morphologically, then do stains:

A simple panel of 2 stains (1 squamous and 1 adenocarcinoma) is usually adequate (e.g., p40 and TTF1)
A positive mucin stain (e.g., PAS-D, or mucicarmine) can also identify some adenocarcinomas.
Report as “Non-small cell carcinoma, favor….” (either adenocarcinoma or squamous cell carcinoma)
Do not do neuroendocrine stains unless there are morphologic findings to suggest neuroendocrine
differentiation (neuroendocrine differentiation in an SCC or adeno doesn’t impact treatment/prognosis).
Immunohistochemical Staining Note: Some primary lung

Adenocarcinoma Squamous cell carcinoma adenocarcinomas, including Mucinous
adenocarcinoma, Colloid carcinoma,
TTF1 p40 (most specific) and Enteric adenocarcinoma, can be
TTF-1 negative. They can even stain
Napsin A CK5/6
with CK20 and CDX2. These cases
CK7 (less specific) p63 (less specific) require careful clinical correlation to
exclude a metastasis from the GI tract.
Adenocarcinoma Subtypes/Patterns
Use for non-mucinous adenocarcinomas. If an adenocarcinoma subtype/architectural pattern is identified
on biopsy, it should be reported. Report in 5% increments and classify based on predominant pattern.
Subtype Characteristics
Lepidic Growing along the surface of alveolar walls (like AIS), non-invasive
Acinar Round to oval glands with a central lumen space surrounded by
tumor cells
Papillary Glands growing along central fibrovascular cores
Micropapillary Cells growing in papillary tufts forming florets that lack
fibrovascular cores (poorer prognosis)
Solid Polygonal tumor cells growing in sheets (poorer prognosis)
If exclusively lepidic on biopsy report as “Adenocarcinoma, lepidic pattern” (or something

similar). On resection, this could represent Adenocarcinoma in situ (AIS), Minimally invasive
adenocarcinoma, or simply a lepidic component of an invasive adenocarcinoma. Radiographic
correlation is required pre-operatively.
Criteria for invasion: 1)histologic subtype other than lepidic (e.g., acinar), 2)desmoplastic stroma
associate with tumor, 3)vascular or pleural invasion, or 4)Spread through air spaces (STAS)
Lung Neuroendocrine Tumors
Note: Lung neuroendocrine neoplasms are graded based on mitoses and necrosis. Ki67 may be helpful to
confirm your morphologic impression, but is not currently used for grading (unlike in the GI tract).

carcinoma
Smoking association No Maybe Yes Yes
Neuroendocrine Yes Yes Yes Yes

morphology
Ki-67 Proliferation Up to 5% Up to 20% 40-80% Almost 100%
index
TTF1 expression Usually not Usually not ~50% Usually, Yes (85%)
Combined with non- No No Sometimes Sometimes

small cell component
(e.g., squam)
Criteria for Diagnosis:

Typical Carcinoid: A tumor with “carcinoid morphology” (organoid or trabecular growth, uniform
polygonal cells, finely granular “salt and pepper” chromatin, inconspicuous nucleoli, abundant
eosinophilic cytoplasm) and <2 mitoses per 2 mm2, lacking necrosis, and >0.5cm (if less than 0.5 cm, it is
designated as a “tumorlet”).
Atypical Carcinoid: A tumor with “carcinoid morphology” and 2-10 mitoses per 2 mm2 and/or necrosis
(often punctate).
Large Cell Neuroendocrine Carcinoma: A tumor with:

1) “Neuroendocrine morphology” (organoid nesting, palisading, rosettes, trabeculae)
2) High mitotic rate: >10 mitoses per 2 mm2 (median 70)
3) Necrosis (often large zones)
4) Cytological features of non-small cell carcinoma: large cell size, vesicular, coarse, or fine chromatin,
frequent nucleoli, and abundant cytoplasm (low N:C ratio)
Small Cell Carcinoma: A tumor with:
1) Small cell size (usually smaller than 3 resting lymphocytes)
2) Scant cytoplasm
3) Finely granular chromatin (no nucleoli)
4) High mitotic rate: >10 mitoses per 2 mm2 (median 80)
5) Frequent necrosis (often large zones)
Lung Cancer Molecular (basic)
Major Genetic Changes ~70% of lung cancers are inoperable
→ Dx and all testing done on core Bx or FNA
Must test Adenocarcinoma for: EGFR, ALK, ROS1 in all cases (molecular/FISH/IHC); PD-L1 (IHC)
Consider testing for: BRAF, KRAS, HER2, RET,
(Can consider some of these tests in non-adenocarcinomas if mixed histology or small biopsy)
Alteration Small cell carcinoma Adenocarcinoma Squamous cell
(%) (%) carcinoma (%)
Mutation
EGFR Caucasian <1 10-20 <1
EGFR Asian <5 35-45 <5
KRAS Caucasian <1 15-35 <5
KRAS Asian <1 5-10 <5
BRAF 0 <5 0
PIK3CA <5 <5 5-15
RB >90 5-15 5-15
P53 >90 30-40 50-80
Amplification
EGFR <1 5-10 10
FGFR1 <1 <5 15-25
MYC 20-30 5-10 5-10
Gene Rearrangement
ALK 0 5 <1
ROS1 0 1-2 0
NTRK1 0 <1 0
Driver mutations are essential for tumor survival (“oncogene addiction”), so targeting them results
in cancer cell death.
EGFR mutations→ can treat with receptor tyrosine kinase inhibitors: Erlotinib, gefitinib, afatinib, etc.
→ Eventually develop acquired resistance (usu. < 1 yr); Most commonly T790M mutation
KRAS mutations→ resistant to EGFR-targeted therapy (and no current specific treatments)
ALK and ROS1 rearrangement→ respond to crizotinib
Adenocarcinomas: Associations
EGFR and ALK→ usually never smokers, Asian, non-mucinous, peripheral location
KRAS→ usually smokers, mucinous, non-Asians, perihilar location (like small cell and SCC)
ALK rearrangements→ usu. Young, never smokers, associated with cribriform morphology
Mediastinum Tumors
General Region located between the lungs, sternum, spine, thoracic inlet, and diaphragm.
About half of tumors are asymptomatic→ identified on imaging.
Symptoms often result from compression/invasion of structures→ cough, pain, dyspnea.
May block superior vena cava→ “SVC syndrome”→ face swelling, distended neck veins, distended
collaterals→ often malignant→ Adults: think lung cancer or lymphoma; Kids: Leukemia/lymphoma.
Differential Diagnosis by Location:
Anterior Superior Middle Posterior The Classic 5 “T’s” of
Thymic tumors Thymic tumors Pericardial cyst Neurogenic tumors Anterior Mediastinal
Germ cell tumors Thyroid tumors Bronchial cyst Schwannoma Masses
Thyroid tumors Lymphoma Lymphoma Neurofibroma
Parathyroid Parathyroid Ganglioneuroma Thymus
tumors tumors MPNST Thyroid
Lymphoma Paraganglioma Teratoma
Paraganglioma Neuroblastoma Terrible lymphoma
Hemangioma Gastrointestinal cyst Thoracic Aorta
Lipoma Bronchogenic cyst
Developmental Cysts Congenital anomalies that develop during embryogenesis.
Bronchogenic Cyst 1
Abnormal tracheobronchial tree branching.
Often well-formed structures resembling bronchus.
Contain a combination of: Ciliated epithelium (1),
cartilage (2), submucosal glands (3), smooth muscle,
and/or degenerative changes. Unilocular.
Cured by excision. Can get infected.
Can be hard to distinguish from esophageal
3
duplication cysts if ciliated and no cartilage,
can say simply “Foregut cyst” 2
Gastrointestinal Duplication Cysts

Attached to the GI tract (but lumens not contiguous, unlike a
diverticulum), with epithelium that resembles some part of
the GI tract, and a well-developed double layer of smooth
muscle (resembling normal bowel layers). NO Cartilage.
Esophageal Duplication Cyst: Columnar (ciliated or non-
ciliated), squamous, or mixed epithelium. Can contain
heterotopic lung or thyroid.
Enteric Duplication Cyst: Variable epithelium, usually gastric

or duodenal.
Thymic Tumors
Thymoma Thymic epithelial neoplasms with a variety of histologic patterns.
Overall rare, but most common mediastinal tumor in adults.
Multiple subclassifications (see below), but stage is much more important prognostically!
(All subtypes can behave aggressively or indolently, mostly important to aid in recognition and DDX)
Frequent association with paraneoplastic syndromes:
Most common = Myasthenia gravis (autoantibodies block acetylcholine receptors between muscle &
nerves → weakness)
Other syndromes: Collagen and autoimmune disorders (e.g., lupus), immunodeficiencies, endocrine
disorders, dermatologic disorders, enterocolitis, etc..
Type Composition Proportion Proportion Prognosis
Epithelium Lymphocytes
Type A Bland spindled to ovoid cells, few Predominant, Few/none Excellent
or no admixed lymphocytes spindled/oval
Type AB Both lymphocyte poor (type A) and Significant Significant Very good
lymphocyte-rich (type B)
components, with a significant
proportion of immature T cells
Type B1 Predominantly lymphocytes with Low, no Predominant Very good

dispersed epithelial cells (that do clusters,
not form clusters) polygonal
Type B2 Predominantly lymphocytes, with Low, small Significant Fair

small clusters of epithelial cells clusters
Type B3 Predominantly atypical polygonal Predominant, Few Fair, often

epithelial cells in sheets. epithelioid high stage
Micronodular Multiple small tumors with bland Significant, Significant. B & Excellent
with lymphoid spindled cells surrounded by spindled T cells, without
stroma lymphoid stroma epithelial cells
Metaplastic Biphasic tumor consists of solid Predominant, Few/none Very good

polygonal epithelial cells in a epithelioid and
background of bland spindled cells spindled
Subtyping:
Some thymomas are heterogeneous and show multiple patterns of growth. In these cases, list the
different patterns quantified by %. Also, be careful definitely subtyping a thymoma on a limited
sampling (likely best to just Dx as “Thymoma” and give the pattern(s) present in the biopsy).
Note: Type AB thymomas are inherently heterogeneous.
Immunohistochemistry:
Most do not require IHC for subtyping. Often used to differentiate from Non-thymomas.
Thymic epithelial cells → AE1/AE3, p63, PAX8.
T-Cells in thymus → CD5, CD3, TdT (immature thymic T-cells)
Thymoma (continued) Thymic Tumor
Lymphoid Component
Yes Absent/sparse
Epithelial Cell Type Epithelial Cell Type

Epithelioid
Spindled Spindled Epithelioid
Epithelium Type AB Thymoma Type A Thymoma Type B3 Thymoma

Lymphocytes
Thymic Carcinoma
Type B1 Thymoma Adapted from: Twitter @lauraebrown, Laura Brown, MD, UCSF Hematopathology, 2019.
.
Type B2 Thymoma
Type B2 Thymoma
Type A Thymoma
Spindled/oval cells with few or no admixed
immature lymphocytes. Bland nuclei with
powdery chromatin. Can have a microcystic
appearance.
Usually low stage. Often lobulated and
circumscribed/encapsulated.
Excellent prognosis.
Type AB Thymoma
2 components: A) lymphocyte-poor
A B
spindle cell component and B)
lymphocyte-rich component
Varying proportions, but > 10% of tumor
with moderate infiltrate of immature TdT+
T-cells.
Usually low stage, lobulated, and very
good prognosis.
Type B1 Thymoma
Closely resembles normal thymus: Dispersed epithelial
cells that do not form clusters and are set in a dense
background of immature T cells mimicking thymic
cortex. Also has areas of medullary differentiation
(nodular pale areas ± Hassall's corpuscles; mostly TdT-
T cells with a substantial B-cell population).
Usually nodular with a very good prognosis.

Type B2 Thymoma
Polygonal neoplastic epithelial cells set in a
background of numerous immature T cells.
Epithelial cells denser than in B1 and are usually
clustered with round vesicular nuclei.
Often encapsulated with a fair to good prognosis.
Type B3 Thymoma
Mild or moderately atypical polygonal pink
epithelial cells with lobules of sheet-like or solid
growth with fibrous septae. Often few
intermingled immature T-cells.
Usually poorly circumscribed→ extensions into
mediastinal fat/organs→ most patients have local
symptoms (e.g., chest pain or SVC syndrome)→ fair
prognosis overall, frequent recurrences.
Micronodular Thymoma with

Lymphoid Stroma
Multiple epithelial nodules surrounded by prominent
lymphoid stroma containing mature B and T cells and
devoid of epithelial cells.
May contain germinal centers and/or plasma cells.
Excellent prognosis
Metaplastic Thymoma
Biphasic: Composed of alternating areas of solid
epithelial cells and bland slender spindle cells.
Absent to few lymphocytes.
Very rare. No paraneoplastic syndrome.
YAP1-MAML2 gene fusions
Microscopic Thymoma: Multifocal thymic epithelial proliferations, < 1mm, composed of bland spindled
to polygonal cells in well-circumscribed nodules embedded in the medulla or cortex. Very rare.
Sclerosing Thymoma: Abundant collagen-rich stroma in an otherwise conventional thymoma. Very rare.
Lipofibroadenoma: Benign thymic tumor that resembles a fibroadenoma of the breast. Very rare.
Thymic Carcinomas
Thymic epithelial tumor with malignant cytologic
features that lacks thymic organization.
Resembles conventional carcinomas in other organs.
Often unequivocal cytologic atypia.
Often unencapsulated and no fibrous septae.
Variable T cell infiltrate
IHC: (+) CK AE1/AE3, p63, PAX8, CD5, CD117, GLUT1,
MUC1. Focal Synaptophysin often.
Types of Thymic Carcinoma
Squamous Cell Carcinoma: Most common type of thymic carcinoma. Resembles SCC elsewhere. Lacks
normal thymic architecture (e.g., lobulation, lymphocytes, etc…). Frankly invasive into nearby structures
and often present with symptoms. Often eosinophilic cytoplasm and abundant stroma.
Basaloid Carcinoma: High N:C basaloid appearance with cystic and papillary architecture and peripheral
palisading. Lots of mitoses and necrosis. Very aggressive.
Mucoepidermoid Carcinoma: Like in other organs (Squamoid cells, mucus-producing cells, and
intermediate cells). MAML2 translocations.
Lymphoepithelioma-like Carcinoma: poorly-differentiated squamous cell carcinoma with an associated
rich lymphoplasmacytic infiltrate (resembles nasopharyngeal carcinoma). Often EBV-positive.
Clear Cell Carcinoma: Composed predominantly of cells with vacuolated clear cytoplasm.
Sarcomatoid Carcinoma: consists completely or partly of spindled cells.
If heterologous elements→ Carcinosarcoma.
NUT Carcinoma: Like elsewhere, NUT gene rearrangement. Monomorphic round cells with characteristic
abrupt keratinization. Often stain with squamous markers. NUT IHC +. Extremely aggressive.
Adenocarcinomas: Heterogeneous group showing glandular and/or mucin production.
Undifferentiated Carcinoma
Thymic Neuroendocrine Tumors IHC Markers of Neuroendocrine Differentiation:

Synaptophysin, Chromogranin, INSM1. Less so CD56.
Rare. Classified using same criteria as in lung.
Cytokeratins often show perinuclear “dot-like” staining.
No smoking association. Can see with MEN1.
(See Lung Tumor Notes for more info)
carcinoma
Morphology Organoid or trabecular growth, Large cell size, vesicular to Small fusiform to round
uniform polygonal cells, finely coarse chromatin, frequent cells, scant cytoplasm,
granular “salt and pepper” chromatin prominent nucleoli, and finely granular chromatin,
abundant cytoplasm Lots of mitoses
Ki-67 Up to 5% Up to 20% 40-80% Almost 100%
Combined with No No Sometimes Sometimes
non-small cell
component
Germ Cell Tumors Note: For more info, refer to the Testicle and Ovary guides
Morphologically identical to gonadal counterparts! Seminoma
Associated with Klinefelter syndrome (XXY)
Prepubertal→ Mostly teratomas or Yolk Sac
Women→ Mostly teratomas
Men→ Teratomas, Seminoma, YST, and mixed
Seminoma
Large polygonal cells with clear to eosinophilic cytoplasm,
distinct cell membranes, vesicular chromatin, and prominent
nucleoli. Fibrous septae and nested architecture
Yolk Sac Tumor
Lymphocytic infiltrate; Sometimes granulomas
Yolk Sac Tumor
Many patterns/architecture. Often hypocellular myxoid areas
Most common = reticular/microcystic
Can also be solid, papillary, etc…
Classic: Schiller-Duval Bodies
Hyaline globules. Elevated Serum AFP
Embryonal Carcinoma Embryonal Carcinoma
Large “Primitive” cells
Vesicular nuclei with prominent nucleoli
Coarse, basophilic chromatin. Amphophilic cytoplasm
Variable architecture (nests, sheets, glands)
Choriocarcinoma
Malignant cytotrophoblasts (mononuclear) and Choriocarcinoma
syncytiotrophoblasts (multinucleated)
Abundant Hemorrhage
Teratoma
Composed of tissues from 2-3 germ layers.
Common elements: Skin (with adnexal structures), Cartilage,
GI, Brain, etc… Very good to excellent prognosis.
Mature→ exclusively mature (adult-type) tissues Teratoma
Immature→ has immature fetal/embryonic tissue
Germ Cell Tumor Immunohistochemistry:
IHC Stain Seminoma Embryonal Yolk Sac ChorioCA
Carcinoma Tumor
SALL4 + + + +
OCT 3/4 + + - -
D2-40 + +/- - -
CD117 + - - -
CD30 - + -/+ -
Glypican 3 - - + +/-
Soft Tissue Tumors
Thymolipoma
Encapsulated tumor with mature adipose tissue and
interspersed normal thymic tissue.
Benign→ cured with excision. Rare.
Lipoma: mature adipose tissue only (like elsewhere).
Rare in mediastinum.
Liposarcoma
Similar to liposarcomas in soft tissue.
Most common sarcomas of mediastinum, often well-differentiated
liposarcomas or dedifferentiated liposarcomas→ both have giant
marker and ring chromosomes that contain amplified regions of 12q
including MDM2 and CDK4 (detect with MDM2 FISH)
Well-differentiated liposarcoma: Range of appearances. Variable
lipoblasts and hyperchromatic atypical cells in a background of
adipocytes and fibrous tissue.
Dedifferentiated liposarcoma: Contain an WDL component, with an
abrupt transition to another component, which is usually an
undifferentiated pleomorphic sarcoma
Often poor prognosis.
Synovial Sarcoma
Malignant spindle cell neoplasm of uncertain histogenesis.
Poor prognosis.
Like in soft tissue, monophasic or biphasic proliferation of
spindled cells with stubby nuclei and frequent Stag-horn
vessels.
IHC: Patchy EMA and CK (particularly strong in epithelial
areas). Usu. CD99 (+). TLE-1 (+)
Molecular: SS18-SSX gene fusions t(X;18)
Solitary Fibrous Tumor

Usually benign.
branching vessels).
SMARCA4-deficient Thoracic Sarcomas
Malignant. Centered in thorax. Very aggressive.
Diffuse sheets of mildly discohesive, relatively monotonous,
and undifferentiated epithelioid cells with prominent nucleoli.
IHC: (+) CD34, SALL4, (+/-)CK
Molecular: SMARCA4 mutations (part of SWI/SNF chromatin
remodeling complex, like INI-1)
Schwannoma Antoni B
Benign. Often associated with nerve. Usu. adults.
Composed entirely of well-differentiated Schwann
cells. Very low risk of transformation.
Usually solitary and sporadic in posterior
mediastinum.
Typically encapsulated.
Alternating compact spindle cells (Antoni A) and
hypocellular less orderly areas (Antoni B) Antoni A
Rows of nuclear palisading → Verocay bodies.
Axons not present in lesion→ pushed to periphery.
Hyalinized blood vessels and lymphoid aggregates
common.
IHC: Strong, diffuse S100, scattered CD34, moderate
calretinin. Neurofilament highlights displaced axons
at periphery.
Malignant Peripheral Nerve Sheath Tumor (MPNST)

Malignant. Adults. Frequently in setting of NF1.
Must arise from a peripheral nerve or pre-existing
peripheral nerve sheath tumor or display histologic/IHC
evidence of nerve sheath differentiation.
Spindled cells arranged in sweeping fascicles.
Densely cellular areas alternate with less cellular areas
giving a “marble-like” effect.
Can have herringbone architecture.
Wavy, buckled nuclei.
Geographic necrosis and/or mitotic activity (often
greater than 10/10 HPFs).
IHC: Patchy S100 and SOX10.

Loss of H3K27me3 expression (associated with worse
prognosis. Not entirely specific—see with SUZ12 and
EED gene inactivation)
Neuroblastoma Maturing Ganglioneuroblastoma Maturing Ganglioneuroma
Most primitive/aggressive Intermediate differentiation. Malignant. Most mature; Benign
Malignant. Vast majority <5 years Neuroblastoma + Ganglion cells Ganglion cells set in
SRBCT +/- rosettes, neurofibrillary fibrillary stroma
matrix NO neuroblastoma
Peripheral neuroblastic tumors derive from the sympathetic nervous system (therefore develop anywhere
along the distribution of the sympathoadrenal neuroendocrine system), often in posterior mediastinum.
Stains: Schwann cells (+) S100, Ganglion cells (+) Synaptophysin, neurofilament
Ganglioneuroma: Although some likely represent matured neuroblastoma, it is thought that most are de
novo. Multiple/diffuse and/or syndrome-related (MEN 2b, Cowden, and NF1) → Ganglioneuromatosis
Angiosarcoma
Malignant. Very aggressive. Typically elderly.
Variable degrees of vascular differentiation.
Some areas show well-formed anastomosing
vessels, while other areas may show solid sheets of
high-grade cells. Can be epithelioid or spindled.
Often extensive hemorrhage.
Unlike benign lesions: significant cytologic atypia,
necrosis, endothelial cells piling up, and mitotic
figures (although mitoses can be seen in some
benign tumors)
IHC: CD31, ERG, FLI1, often CD34
Sclerosing (fibrosing) Mediastinitis

Non-neoplastic fibrosis of mediastinum compressing
and infiltrating normal structures.
Bland spindled cells with lymphoplasmacytic infiltrate
Sometimes dense (keloid-like) collagen.
May see dystrophic calcifications.
May be caused by:
- prior infection/response to Histoplasma or TB
- IgG4-related disease
- Autoimmune diseases
- Radiation
Thyroid & Parathyroid Tumors
Thyroid Tumors:
Often arise in an extension of the thyroid from the neck (as opposed to ectopic thyroid).
Identical appearance, IHC, and behavior to thyroid tumors in the neck (see separate guide).
General IHC:
Tumors derived from follicular epithelium (PTC, follicular carcinoma): (+) TTF1, PAX8, Thyroglobulin, CK
Medullary thyroid carcinoma: (+) TTF1, Synaptophysin, Calcitonin, CK, (-) Thyroglobulin, (+/-) PAX8
Parathyroid Tumors:
Ectopic. Up to 20% of all parathyroid neoplasms are located in the mediastinum (often near/in thymus as
share a common origin in 3rd branchial pouch). Often present with hyperparathyroidism and resulting
hypercalcemia (kidney stones, bone pain, etc..). Identical appearance, IHC, and behavior (see separate
guide). IHC: (+) CK, Synaptophysin, Chromogranin, GATA-3, PTH. (-) TTF1, Thyroglobulin, Calcitonin; (+/-)
PAX8
Lymphomas
Classical Hodgkin Lymphoma:
Most common type of primary mediastinal lymphoma! Peak incidence in late adolescence/young adult.
Reed-Sternberg cells (classically large binucleated cells with abundant cytoplasm and prominent nucleoli
with perinucleolar clearing) in a background of inflammatory cells. Lacunar RS cells are smaller with
hyperlobated nuclei. Often lots of eosinophils.
RS cell IHC: (+) CD30, CD15, MUM1. Characteristic weak PAX5. (-)CD20, CD45
Most common variant: Nodular Sclerosis Classical Hodgkin Lymphoma—cellular nodules separated by
dense fibrous bands. Often has lacunar RS cells.
Primary Mediastinal Large B-cell Lymphoma:
Aggressive large B-cell lymphoma arising in the mediastinum. Most often in young adults.
Presents with localized mass in thymic area and minimal associated distant lymphadenopathy.
Diffuse growth of large cells with abundant, often clear, cytoplasm.
IHC: (+) CD19, CD20, CD79a, PAX5.
Requires clinical exclusion of widespread extrathoracic disease as morphology and IHC identical to DLBCL.
T lymphoblastic leukemia/lymphoma:
Use lymphoma term when confined to a mass lesion, Leukemia when there is extensive peripheral blood
and bone marrow involvement. Most common in late childhood to early adulthood.
Typically present acutely with symptoms related to a large mediastinal mass such as airway compromise.
Mediastinal disease often centered around thymus, involving nearby lymph nodes too.
Medium-sized cells with scant cytoplasm and fine chromatin. Lots of mitoses.
IHC/Flow: (+)TdT, CD34, CD1a, CD99, CD3,
Germ Cell Tumors with associated Hematologic Malignancy:
Coexisting clonally related mediastinal germ cell tumor and a hematologic malignancy, which can be
systemic or localized. Can be any type of heme malignancy, often acute leukemia. Very poor prognosis.
Metastases Always a consideration!!

Most common = Lung.
Also consider: Breast, Esophageal, Stomach, etc…
Histiocytic and Dendritic Cell Neoplasms
Follicular Dendritic Cell Sarcoma
Intermediate-grade malignancy of follicular dendritic cells.
Spindled tumor cells with indistinct cell borders, lightly
eosinophilic cytoplasm, and associated lymphocytes.
Oval vesicular nuclei with small nucleoli.
Variable architecture. Usually only mild pleomorphism.
IHC: (+) CD21, CD23, D2-40. Variable, weak CD68 & S100.
Usually localized at time of Dx. Usually Adults. Rare.
May arise from hyaline-vascular Castleman’s disease.
Subset of patients have recurrences or metastases.
Interdigitating dendritic cell sarcoma: Rare. Very similar
to FDCS (above), but derived from interdigitating
dendritic cells. Plumper cells. IHC: (+) S100, (-)SOX10,
CD1a, CD21, CD23, (+/-) CD68, CD45
Fibroblastic reticular cell tumor: Also similar to FDCS

(above). IHC: (+) Vimentin, (-) S100, CD21, CD23. (+/-) CK,
CD68
Histiocytic Sarcoma
Rare. Wide age range.
Malignant proliferation of cells with histiocytic differentiation
(excluding acute monocytic leukemia associated cases).
Large, round, discohesive cells with abundant eosinophilic
cytoplasm. Often pleomorphic. Nuclei often eccentric and
vesicular.
IHC: Must express at least one histiocytic marker (e.g., CD68,
CD163, or lysozyme). (-)Langerhans cell, myeloid, and follicular
dendritic cell markers (in addition to epithelial and
melanocytic)
Langerhans Cell Histiocytosis

Neoplastic proliferation of Langerhans cells.
Discohesive cells with grooved/contorted nuclei, fine
chromatin, and eosinophilic cytoplasm.
Often admixed eosinophils and multinucleated giant
cells.
IHC: (+)S100, CD1a, Langerin (CD207)
Molecular: Frequent BRAF V600E
Electron Microscopy: Birbeck granules
Overtly malignant cytology→ Langerhans cell Sarcoma
Pleural & Peritoneal Tumors

Non-neoplastic Mesothelial markers: D2-40, Calretinin, WT-1, CK5/6 (Not entirely specific)
Pancytokeratin can be helpful to highlight invasion, but is not specific at all.
Reactive Mesothelial Hyperplasia

“Activated” reactive mesothelial cells, often responding to
inflammation/irritation, can look very scary and mimic
mesothelioma/carcinoma.
Common scary findings: High cellularity, mitotic figures,
cytologic atypia, papillary groups, and entrapment of
mesothelial cells in fibrous tissue mimicking invasion.
Can see “layering” as additional layers of
mesothelium and fibrous tissue organize over
one another. Think: sedimentary rock
Figure from: Churg and Galateau-Salle. Arch Pathol Lab Med (2012) 136 (10): 1217–1226
Reactive Mesothelial Hyperplasia Mesothelioma

Absence of stromal invasion (beware of entrapment Stromal invasion usually apparent (highlight with
and tangential sectioning) pancytokeratin staining)
Cellularity may be prominent but is confined to the Dense cellularity, including cells surrounded by stroma
mesothelial surface/pleural space and is not in the
stroma
Simple papillae; single cell layers Complex papillae; tubules and cellular stratification
Loose sheets of cells without stroma Cells surrounded by stroma (‘‘bulky tumor’’ may
involve the mesothelial space without obvious
invasion)
Necrosis rare Necrosis occasionally present
Inflammation common Minimal inflammation (usually)
Uniform growth (highlighted with cytokeratin staining) Expansile nodules; disorganized growth (highlighted on
cytokeratin staining)
Usually Not Helpful: Mitotic activity, Mild to moderate cellular atypia
Modified from: Husain AN et al. Guidelines for Pathologic Diagnosis of Malignant Mesothelioma 2017 Update of the Consensus Statement From the
International Mesothelioma Interest Group. Arch Pathol Lab Med. 2018 Jan;142(1):89-108.
Fibrous pleurisy
aka “Diffuse Pleural Fibrosis” or “Chronic fibrosing
pleuritis”
Deposition of bland, hypocellular fibrous tissue in the

pleura.
Often involves the visceral pleura and may produce

apical fibrous “capping.” Severe cases can obliterate
pleural space.
May be associated with connective tissue disorders,

such as lupus erythematosus or rheumatoid arthritis, as
well as chronic infections and asbestos exposure.
May mimic desmoplastic mesothelioma
Fibrous Pleurisy Desmoplastic Mesothelioma

Storiform pattern not prominent Storiform pattern often prominent
Absence of stromal invasion Stromal invasion present (highlight with
pancytokeratin staining)
Uniform thickness of the process Disorganized growth, with uneven thickness,
expansile nodules, and abrupt changes in cellularity
Perpendicularly oriented vessels Paucity of vessels. No orientation.
Hypercellularity at the surface with maturation and Lack of maturation from the surface to the depths of
decreased cellularity deep (so-called zonation) the process
Necrosis, if present, is at the surface epithelioid Bland necrosis of paucicellular, collagenized tissue
mesothelial cells (where there is often associated
acute inflammation)
Not helpful: Cellularity, Atypia (unless severe),
Mitotic activity (unless numerous atypical mitotic figures)
Modified from: Husain AN et al. Guidelines for Pathologic Diagnosis of Malignant Mesothelioma 2017 Update of the Consensus Statement From the
International Mesothelioma Interest Group. Arch Pathol Lab Med. 2018 Jan;142(1):89-108.
Pleural Plaque
aka “hyaline pleural plaque”
Hypocellular, dense bundles of hyalinized collagen,
often with a “basket weave” arrangement. Often
dystrophic calcifications. Variable chronic
inflammation.
Often on parietal pleura, particularly on diaphragm
Often a marker of asbestos exposure, but can be seen
with other sources of chronic pleural irritation.
Peritoneal Inclusion Cyst
Often discovered incidentally. More common in women
Single or multiple, small, thin-walled, translucent,
unilocular cysts attached or free in the peritoneal
cavity.
Lined by a single layer of flattened, benign-appearing
mesothelial cells
If large and
Benign Multicystic Peritoneal Mesothelioma multiloculated
aka “multilocular peritoneal inclusion cysts” (better name!)
Occurs most frequently in young to middle-aged women in
the peritoneum/pelvis.
Likely a hyperplastic reactive lesion (vs. a benign neoplasm).
Associated with previous abdominal surgery, pelvic
inflammatory disease, and endometriosis.
It has a strong tendency to recur.
Grossly: often large, multiple small, thin-walled, translucent,
unilocular cysts that may be attached or free floating. Often
fibrous tissue in septae with sparse inflammation.
Cysts are lined by a single layer of flattened to cuboidal
mesothelial cells which occasionally have a “hob-nail”
appearance.
Sclerosing Peritonitis
“Cocoon abdomen”
Rare. Encasement of the bowel by fibrous tissue
causes bowel obstruction.
Can be idiopathic, or seen with intraperitoneal dialysis,
VP shunts, and fibrothecomas of the ovary.
Sclerosing Mesenteritis
Rare. Idiopathic.
Varying degrees of fat necrosis, chronic inflammation,
and fibrosis, usually involving the mesentery of the
small bowel→ forms a distinct mass
Other lesions:
Splenosis
Melanosis
Infarcted epiploicae
Keratin granulomas
Benign/Indolent Mesothelial Tumors IHC identical to all other mesothelial tumors
Adenomatoid Tumor
Irregularly shaped gland-like microcystic spaces
composed of flattened or cuboidal cells with
associated fibrous stroma.
Bland cytologic features.
Helpful feature: "thread-like bridging strands“ (→)
Sometimes signet ring-like vacuolated cells.
Solitary, localized.
Most commonly in the female genital tract (e.g.,
uterine or adnexal surface) or genitourinary tract
(e.g., paratesticular), but can be pleural.
Well-Differentiated Papillary Mesothelioma

Rare. Grossly velvety appearance.
Prominent papillary architecture with myxoid
cores covered by a single layer of flattened to
cuboidal bland epithelioid cells.
Nuclei are bland, round, and small without atypia.
Generally NO invasion.
Indolent tumors. Most cases cured by excision.

Very long survival. May recur.
Characteristic Well-differentiated Papillary Malignant Mesothelioma with a

Mesothelioma Papillary Pattern
Growth feature- bulk Often incidental, solitary, focal area of Diffuse or multinodular, grossly apparent
of disease velvety appearance
Morphology of Fibrous and stout cores, single-cell Fibrous cores, lined by cells with
papillae layer stratification
Cytology Flat cuboidal, no anisocytosis Cuboidal cells with nucleoli and variable
anisocytosis
Mitoses Low Low
Other growth patterns Absent Tubular, solid, cribriform, complex papillae
Stroma invasion Predominantly exophytic growth, Present
Invasion usually absent or very
focal/superficial
Prognosis Good, with local recurrence Poor
Malignant Mesothelial Tumors
Epithelioid Mesothelioma
Malignant proliferation of mesothelial cells with epithelioid
morphology.
Usually diffuse (circumferential, rind-like)→ Poor prognosis.
Rarely, localized (solitary, well-circumscribed)→ Better prognosis
Most common in elderly, often male. Often unilateral at first.
Most common cause is asbestos exposure.
Often insidious onset with chest pain and/or dyspnea
Clinical information (either from imaging or intraoperative
findings) can be very helpful with Dx: Circumferential pleural
thickening is highly suggestive of malignancy, Nodular pleural
thickening is also often malignant.
Often relatively bland cytologically (but can be pleomorphic)
with eosinophilic cytoplasm in vesicular nuclei.
Demonstration of tissue invasion (e.g., into chest wall or lung) is

often key for diagnosis (see next page).
However, when a substantial amount of solid, malignant tumor
(i.e., a mass) is identified, the presence of invasion is not
required for diagnosis.
Common histologic patterns: solid, tubulopapillary, trabecular.
Rare patterns: micropapillary, clear cell, deciduoid,
adenomatoid, transitional, small cell, lymphochistiocytoid, etc..
Can see psammoma bodies.
Metastatic Mesothelial
Special studies: Can serve several purposes
Adenocarcinoma cells
1) Use IHC to confirm mesothelial (and not metastatic
carcinoma) (see tables→) Always use a panel! BerEP4 Calretinin
2) After mesothelial origin is confirmed, special studies can MOC31 D2-40
support the diagnosis of malignancy (if necessary)
B72.3 WT-1
Special Studies that support the diagnosis of
Claudin-4 CK5/6
mesothelioma with good specificity (not fantastic
sensitivity though): Squamous cell Mesothelial
IHC: BAP1 or MTAP loss carcinoma cells
FISH: CDKN2A (p16) deletion p40 & p63 Calretinin
Multigene expression profiling panels MOC31 D2-40
Molecular: Often multiple chromosomal alterations. Claudin-4 WT-1

Frequent loss of tumor suppressors CDKN2A, BAP1, Adeno stains that can also get mesos: PAX8, CK7,
and NF2. GATA-3, AE1/AE3
Meso stains that can also get carcinomas: WT-1, CK5/6
Stains that get both mesos and SCC: CK5/6
Is it really invasive?
Given that reactive mesothelial processes can Fat
look so atypical, demonstrating tissue invasion
is often required for the diagnosis of
mesothelioma, unless there is a significant solid
tumor mass.
Tip: Use of IHC stains (e.g., Pancytokeratin or
Calretinin) can highlight infiltrative cells, helping
confirm invasion.
Look for cytokeratin-positive malignant cells in

regions in which they would not normally be Invasive malignant cells
present: adipose tissue, skeletal muscle deep to
the parietal pleura, or lung tissue (or other
extrapleural structures).
Benign processes→ Tend to be well-circumscribed
Caution: Sometimes the biopsy process can (only a few glands evident beneath the pleural surface,
create fake empty fat-like spaces. When in or a sharp line beyond which no mesothelial cells are
doubt, do an S100 to see if it is real fat. Also, found)
vimentin will be negative as this fake fat does Malignant processes→ Poorly-circumscribed, invasive
not have any cellular lining.
Warning: On small biopsies, it can be very hard to evaluate for invasion. In such cases where invasion is
not definite, it is recommended that you simply say “atypical mesothelial hyperplasia” or “atypical
mesothelial proliferation,” with a comment that another larger biopsy (likely surgical), may be
appropriate if the clinician is suspicious for mesothelioma.
Mesothelial Hyperplasia Mesothelioma

Major criteria
Stromal invasion Absent Present (the deeper the more definitive)
Cellularity Confined to the pleural surface Dense, with stromal reaction
Papillae Simple, lined by a single layer of cells Complex, with cell stratification
Growth Pattern Surface growth Expansile nodules, complex, disorganized
Zonation Process becomes less cellular towards No zonation of process, often more cellular away
chest wall from effusion
Vascularity Capillaries perpendicular to surface Irregular, haphazard
Minor criteria
Cytologic atypia Confined to areas of organizing effusion Present in any area, but often deceptively bland
Necrosis Rare More common
Mitoses May be plentiful Often rare (but atypical favors malignancy)
Sarcomatoid, Desmoplastic, and Biphasic Mesothelioma
Sarcomatoid mesothelioma: Spindle cell appearance.
Arranged in fascicles or haphazard. Can see heterologous
elements (e.g., rhabdomyosarcoma).
Desmoplastic mesothelioma: Dense collagenized tissue with

malignant mesothelial cells. Either patternless or storiform
pattern. Must be ≥50% of tumor. Invasion into fat is most
helpful feature to differentiate from organizing pleuritis.
Biphasic mesothelioma: Contains BOTH epithelioid and

sarcomatoid patterns, each ≥10%. Sarcomatoid
Stromal invasion is often more difficult to recognize in these
spindle cell proliferations as the invasive malignant cells are
often deceptively bland→ Use IHC liberally.
IHC: Usually stain, at least focally, with a broad spectrum

pancytokeratin (can also help demonstrate invasion).
Loss of BAP1 is very uncommon in these types.
Poorer prognosis than epithelioid mesotheliomas.

Desmoplastic mesothelioma has a particularly dismal
prognosis (often <6 months).
Desmoplastic
Hmm… that looks pretty bland,

but the clinician said it’s a mass.
Yikes! A cytokeratin stain shows that all

of those bland spindled cells are actually
invasion!
Biphasic
Other Tumors
Synovial Sarcoma
Malignant. Usually young adults.
Monophasic SS→ Just spindled component.
Biphasic SS→ Spindled and epithelioid components.
Monophasic
Fairly uniform spindled cells with relatively little cytoplasm.
Ovoid, “stubby,” nuclei with hyperchromatic granular
chromatin and small nucleoli. Can see “Stag-horn” vessels.
Epithelial cells arranged in nests and glands with paler
cytoplasm and vesicular nuclei.
IHC: Patchy EMA and CK (particularly strong in epithelial
areas). Usu. CD99 (+). TLE-1 (+)
Molecular: SS18-SSX gene fusions t(X;18) Biphasic
Solitary Fibrous Tumor (“SFT”) Old name: Hemangiopericytoma

(referred to cellular tumors on a spectrum with SFT)
Usually benign.
Prominent “Staghorn vessels” (dilated, thin-walled, branching
vessels). Can be hyalinized or myxoid.
Factors associated with malignant behavior:
Numerous mitoses (esp. >4/10 HPF), Large size (esp. >15 cm),
and tumor necrosis.
Desmoplastic Small Round Cell Tumor

Malignant tumor of uncertain histogenesis often found in the
peritoneal cavity; often in young men.
Basaloid nests of small, round, uniform tumor cells that are
surrounded by desmoplastic stroma.
Tumor cells have hyperchromatic nuclei and scant cytoplasm.
Mitoses and apoptoses are frequent.
IHC: Express Cytokeratins, EMA, Desmin (perinuclear dot-like
pattern), WT-1 (but C-terminus—opposite of the WT-1 in
Wilms!), and NSE
Molecular: Characteristic EWSR1–WT-1 translocation
Poor prognosis (although may respond at first)
Calcifying Fibrous Tumor
Rare. Benign. Occurs on visceral pleura/peritoneum.
More common in women, often younger.
Paucicellular collagenized fibrous tissue with associated
psammomatous or dystrophic calcifications.
Scattered chronic inflammation.
Circumscribed, but not encapsulated.
Confined to pleura and does not invade underlying tissue.
IHC: CD34(+). STAT6, ALK1, β-catenin (-)
Desmoid-type Fibromatosis
Benign (never metastasize), but infiltrative with high-recurrence rate (>50%).
Infiltrative growth into surrounding structures (esp. skeletal muscle).
Broad, sweeping fascicles.
Uniform spindled cells with small, pale nuclei with pinpoint nucleoli.
Moderate amounts of collagen, surrounding cells, in slightly myxoid
background.
IHC: Nuclear β-catenin. Some actin (+)
Molecular: Associated with FAP and mutations in the APC/β-catenin
(CTNNB1) pathway
Angiosarcoma
Some areas show well-formed anastomosing vessels, while other areas may
show solid sheets of high-grade cells. Can be epithelioid or spindled.
Unlike benign lesions: significant cytologic atypia, necrosis, endothelial cells
piling up, and mitotic figures (although mitoses can be seen in some benign
tumors)
IHC: CD31, ERG, FLI1, often CD34
Lymphoproliferative Disorders
Primary Effusion Lymphoma:
Rare. Presents as an effusion without solid tumor masses. Usually in immunocompromised patients (e.g.,
HIV-positive). Proliferation of large, atypical B cells with an immunoblastic appearance. Positive for
HHV8, often with coinfection with EBV. IHC: CD45(+), but usually lack pan-B-cell markers like CD20,
CD19, PAX5, CD79a. Usually express CD30 CD138, CD38, EMA. Poor prognosis.
Diffuse Large B Cell Lymphoma associated with chronic inflammation:

Occurs in patients with long-standing pyothorax or other chronic inflammatory processes, usually in body
cavities. EBV-associated. Morphologically resembles other forms of DLBCL with large vesicular nuclei
with prominent nucleoli. Express B-cell markers. Aggressive.
Müllerian Lesions The pelvic and lower abdominal mesothelium can be primarily or
secondarily involved by many Müllerian lesions.
Müllerianosis
Endosalpingiosis: Glands lined by benign tubal-type
(ciliated) epithelium involving the peritoneum or pelvic or
para-aortic lymph nodes. Likely secondary as associated
with salpingitis. Can have associated psammoma bodies.
Endometriosis: Benign endometrial glands and stroma.

Often accompanying hemosiderin-laden macrophages.
Endocervicosis: Benign endocervical-type epithelium.
Deciduosis
Ectopic decidual cells (epithelioid cells with abundant
pale pink granular cytoplasm and bland nuclei) arranged
individually, in nodules, or in plaques.
Seen during pregnancy.
May have associated hemorrhage/inflammation.
Primary Peritoneal Serous Borderline Tumors

Morphologically identical to the noninvasive peritoneal implants of ovarian serous borderline tumors.
Diagnosis of exclusion: only when the ovaries are uninvolved or there only minimal surface involvement.
Likely arises from endosalpingiosis.
Generally good prognosis. Can get primary peritoneal low-grade serous carcinomas, so sample well!
Primary Peritoneal High-Grade Serous Carcinoma

Morphologically identical to the primary tuboovarian high-
grade serous carcinoma.
Diagnosis of exclusion: Both tubes and both ovaries grossly
and microscopically uninvolved (when examined entirely). Dx
can only be made at primary surgery prior to any
chemotherapy.
Otherwise, looks and behaves like peritoneal carcinomatosis
from high-grade serous carcinoma
Other lesions:
Walthard rests
Peritoneal leiomyomatosis
(and pretty much anything arising from Müllerianosis!)
CHAPTER 6
Head and Neck

Salivary Gland Tumors

Normal Salivary Gland
Normal components:
1) Ducts: Interlobar, to intercalated, and striated.
Cuboidal to columnar epithelium. Surrounded by
myoepithelial cells. 3 2
2) Acini: Serous (esp. in parotid, with zymogen
granules) to mucous (esp. sublingual), surrounded by
myoepithelial cells. Looks like grapes on cytology. 1
3) Fat (esp. in parotid)
Also: lymph nodes (esp. in parotid, where salivary
gland can be within benign lymph nodes).
If have symmetric enlargement of salivary glands with
no discrete mass, consider sialadenosis.
Oncocytic Pink cells, often because they contain abundant mitochondria. Often big,
polygonal, with well-defined borders, granular cytoplasm, with large round
nuclei with prominent nucleoli.
Oncocytic hyperplasia
Oncocytic metaplasia: Non-mass forming transformation of glandular epithelium to oncocytes
Oncocytic hyperplasia (aka Oncocytosis): Non-neoplastic, mass-forming proliferation of oncocytes, which
can be focal or diffuse. Unencapsulated. Often multifocal, admixed with normal salivary tissue.
Oncocytoma Oncocytic Carcinoma

Benign
Malignant
Circumscribed to encapsulated
Oncocytic lesion with
proliferation of oncocytes.
pleomorphism, mitoses,
and/or invasion.
Actually Biphasic
1. Inner oncocytes,
May or may not be
2. Outer myoepithelial cells
encapsulated.
Usually in parotid
No significant: pleomorphism,
mitotic activity, or invasive
growth
Warthin Tumor
Old name: Papillary cystadenoma lyphomatosum
Benign
Key elements:
1) Mature lymphoid tissue, surrounding
2) Bilayerd oncocytic epithelium, with
3) Cystic to papillary growth
Strongly linked to smoking, can be bilateral
Likely develops from transformation of salivary gland
tissue entrapped in a lymph node.
Almost exclusively in parotid, usually at angle of jaw.
Aspirated fluid often thick, dark “motor oil.”
Secretory Carcinoma
Formerly: “Mammary Analogue Secretory Carcinoma”
Eosinophilic, granular to vacuolated cytoplasm
Tubular, papillary and cystic growth.
Sometimes has distinctive eosinophilic secretions in
lumina.
No zymogens present.
ETV6-NTRK3 gene fusions.
Stains: Positive for S100 and mammaglobin.
Malignant, but relatively indolent.
Intraductal Carcinoma
Non-invasive carcinoma with retained myoepithelial
cells. Think of as like DCIS of the breast.
Can highlight myoepithelial cells with p63.
If totally non-invasive→ Excellent prognosis!
Usually in Parotid.
Intercalated duct type Apocrine type

Always low-grade Variable grade
S100+, mammaglobin+ AR+, GCDFP15+, S100 –, mammaglobin –
Most have RET fusion (with NCOA4 or TRIM27) Salivary duct carcinoma-like genetics
Only rarely associated with invasion Often associated with invasion
Basaloid Looks very cellular and blue at low-power
Basal Cell Adenoma / Basal Cell Adenocarcinoma

Monomorphic Adenoma Malignant
Benign, well-circumscribed, Usually Parotid Like a basal cell adenoma, but with invasion,
Solid, trabecular, or tubular growth necrosis, and numerous mitotic figures
Perpendicular basal cells on outside of nests
Epithelial cells on inside of nests
No significant stroma, aside from possibly a
“membrane” surrounding a nest
(Think of pleomorphic adenoma without the stroma
– hence the name monomorphic adenoma)
Polymorphous Carcinoma
Cytologically uniform cells (monophasic)
Bland, round to spindled cells with moderate amounts of
cytoplasm. Oval nuclei with vesicular chromatin.
Strong, diffuse staining with S100. p63+ but p40 -
Varied architecture (hence the “polymorphous”)
Concentric layering, “whorled,” Tubules to single file
Infiltrative with significant PNI
PRKD fusions/mutations
Always in MINOR salivary glands, often palate
Formerly called “Polymorphous Low-Grade Adenocarcinoma” → “PLGA”
Canalicular Adenoma
Almost always upper lip
Encapsulated
Monophasic
Characteristic “canalicular” pattern of cords and
ribbons of basaloid tumor cells with occasional
interconnecting.
Cords separated by loose fibrillar stroma

Benign
Acinic Cell Carcinoma
Composed of acinar cells with variable cytoplasm
(vacuolated, clear, oncocytic, to hobnailed) and
architecture (solid to cystic or follicular)
Classically, has cells that are cells large, polygonal with
basophilic granular cytoplasm (contains zymogens→
highlighted by PASD).
Sometimes prominent lymphoid infiltrate
Usually in parotid. Can see in kids.
NR4A3 Translocations common

Stains: Positive for DOG-1 and SOX-10
Malignant, but generally not aggressive
Adenoid Cystic Carcinoma

Cribriform, tubular or solid growth
2 cell types: 1) Myoepithelial and 2) Ducts
Low-grade: Mostly myoepithelial (small cells with

oval to angulated nuclei), stain with p40 and SMA
High-grade: Mostly ductal cells (larger cells with

more vesicular chromatin), stain with CD117 and CK
Ducts can be inconspicuous in low-grade

(See image →)
Grading: give % Solid (ductal) component
Myoepithelial cells form pseudocysts that contain

Ducts
blue glycosaminoglycans or pink basement
(Most of the cells
membrane material (which are visible on FNA, with
are myoepithelial
“stromal exclusion” of myoepithelial cells)
in this case!)
Cytogenetics: Fusions of MYB or MYBL1 to NFIB
Infiltrative→ Extensive PNI→ Pain → Paralysis
Persistent local spread. OK 5yr survival, but poor
long-term survival.
Additional Basaloid tumors
Lymphadenoma: Encapsulated tumor with anastomosing cords of basaloid cells with abundant tumor-
associated lymphoid tissue.
Small cell neuroendocrine carcinoma: Like in the lung!
Sialoblastoma: Primitive-appearing basaloid cells. Seen in kids.
Prominent Spindled Cells
Pleomorphic Adenoma
Benign, but can recur if not completely excised.
(aka Benign Mixed Tumor)
Most common tumor of salivary glands 1
Three components, encapsulated, well-circumscribed:
1) Ductular structures
2) Myoepithelial cells (can be spindled, epithelioid,
plasmacytoid, etc…), intimately admixed with stroma
3) Mesenchymal-like tissue (often myxoid stroma, but
can be chondroid, etc…) 3
Architecturally pleomorphic (cytologically bland!)
If ducts or myoepithelial cells dominate (but some
component is classic), can use the term “cellular” PA
Can see: tyrosine crystals, squamous metaplasia, cystic
degeneration
2
Cytogenetics: PLAG1-HMGA2 fusions very common
Cytology:
Prominent fibrillar, metachromatic stroma that
on a Diff-quick stain looks like “Troll Hair.”
Also visible ductal cells and myoepithelial cells

intimately admixed with the stroma
Metachromatic Stroma
Myoepithelioma Myoepithelial Carcinoma

Benign Malignant
Composed of entirely myoepithelial Composed of entirely myoepithelial
cells cells
Typically spindled to plasmacytoid
Presence of necrosis, atypical mitotic
Although may see some collagen, figures, invasion to surrounding
chondroid/myxochondroid stroma is parenchyma
absent
Also Consider
Carcinosarcoma Epithelial-myoepithelial carcinoma
Adenoid cystic carcinoma
Squamoid
Squamous metaplasia
Can see in normal salivary glands or tumors (e.g., PA)
Classic Mimic of SCC!
In minor salivary gland often called:
“Necrotizing Sialometaplasia”
Lobular architecture is maintained
Smooth, rounded contours
Often associated inflammation and reactive changes
Acinar coagulative necrosis
Mucoepidermoid Carcinoma
Three components:
1) Mucinous cells (stain with PASD/mucicarmine)
2) Squamous cells
3) “Intermediate cells” (neither squamous nor 3
mucinous, with scanter cytoplasm) 1
Oncocytic variant exists, but is rare.
Most common malignant salivary cancer.

Often in parotid, but can get anywhere.
Broad age range, including kids
Cytogenetics: MAML2 gene fusions almost

definitional now
Must grade. Several systems, but often graded 2

intuitively (see table) Low-Grade High-Grade
Mostly cystic More solid
Well-circumscribed Infiltrative
More mucinous cells More squamous cells
Cytologically bland More atypical cytologically
Low mitotic count High mitotic count, Necrosis

If it is entirely squamous (with no mucinous cells or intermediate cells, and esp. when there are keratin
pearls), a metastasis needs to be excluded clinically
→ Often actually a metastasis from a Head or Neck squamous cell carcinoma (e.g., to an intra parotid
lymph node). Also consider extensive SCC differentiation of another salivary gland carcinoma.
Of note, higher grade Mucoep’s often are more squamous, so make sure the tumor is well-sampled.
High-Grade
Salivary Duct Carcinoma
Resembles breast ductal carcinoma
(both invasive and in situ components)
Large ducts with comedonecrosis (like DCIS!)
Often apocrine/oncocytic
Stains: Androgen receptor (AR) and HER2 positive
Often in parotid, sometimes arising from a

pleomorphic adenoma (see below)
Very Aggressive
Carcinoma ex-pleomorphic adenoma

ex-PA
Carcinoma arising from a Pleomorphic Adenoma
May be a specific type of epithelial or myoepithelial
carcinoma→ most often Salivary Duct Carcinoma
Very pleomorphic, with lots of mitoses, necrosis and
destructive growth.
Cytogenetics: PLAG1-HMGA1 (in PA) and TP53 (in
carcinoma)
Usually older (time to de-differentiate) in parotid PA
Often long history of mass (i.e., a PA), now with rapid
enlargement.
Lymphoepithelial Carcinoma
Sheets and cords of polygonal large syncytial cells with
eosinophilic cytoplasm and vesicular nucleoli. Also, scattered
spindled cells.
Abundant lymphoplasmacytic infiltrate
Often EBV positive (like nasopharyngeal carcinoma, must
consider metastases!); Also stains with CK
Other High-grade
Carcinosarcoma→ Malignant epithelium and mesenchymal components
Metastases
Any other de-differentiated tumors
Clear Cell
Clear Cell Carcinoma
Aka: Hyalinizing clear cell carcinoma
Sheets and tests of polygonal clear cells

Hyalinized/sclerotic stroma
EWSR1-ATF1 fusion
Unencapsulated, infiltrative
Usually intraoral salivary glands
“Clear” b/c full of glycogen→ stains with PAS

Stains: CK and p63 positive, Neg. myoep
markers
Epithelial-Myoepithelial Carcinoma
1
Malignant “EMC”
Biphasic:
1) Inner luminal ductal cells, with eosinophilic cytoplasm 2
2) Outer myoepithelial cells, with clear cytoplasm
Usually in parotid gland and indolent
Other Clear Cell

Acinic Cell Carcinoma Pleomorphic adenoma
Secretory Carcinoma
Mucoepidermoid carcinoma
ABC’s Try Building a DDX from the ABC’s
A: Architecture Infiltrative (Malignant, usually)
Adenoid cystic
How are the nests of tumor arranged?
Acinic cell carcinoma
Encapsulated (Benign, usually) Circumscribed Basal cell adenocarcinoma
Pleomorphic adenoma Pretty much anything Mucoepidermoid carcinoma
Basal cell adenoma (Benign or Malignant) Oncocytic carcinoma
Myoepithelioma Intraductal carcinoma
Oncocytoma Clear cell carcinoma
Warthin tumor Epithelial-myoepithelial carcinoma
Epithelial-Myoepithelial carcinoma Carcinosarcoma
Carcinoma ex-PA
Myoepithelial carcinoma
Secretory carcinoma
Lymphoepithelial carcinoma
B: Bi-Phasic (Phases)
How many different types of cells are present?
Monophasic Biphasic Triphasic (or More!)

Myoepithelioma Adenoid cystic Pleomorphic adenoma
Myoepithelial carcinoma Basal cell adenoma/CA Mucoepidermoid carcinoma
Clear cell carcinoma Epithelial-Myoepithelial CA Acinic cell carcinoma
Polymorphous adenocarcinoma Warthin tumor Carcinosarcoma
Small cell neuroendocrine carcinoma Oncocytoma/CA Carcinoma ex-PA
Salivary duct carcinoma Intraductal carcinoma Secretory carcinoma
Canalicular adenoma Lymphoepithelial carcinoma
C: Cytology
Which types of cells are present? Ductal cells
PA
Acinar cells Clear cells Adenoid cystic
Acinic cell carcinoma Clear cell carcinoma Basal cell adenoma/CA
Acinic cell carcinoma Canalicular adenoma
Basal cells Secretory carcinoma Epithelial-myoepithelial carcinoma
Basal cell adenoma Salivary Duct carcinoma
Basal cell carcinoma Polymorphous Adenocarcinoma
Myoepithelial cells
Oncocytoma Secretory carcinoma
PA
Oncocytic carcinoma Carcinoma ex-PA
Adenoid cystic
Myoepithelioma/CA
Tumor-Associated Lymphoid
Basal cell adenoma/CA
Proliferations Mucous cells
Epithelial-myoepithelial
Mucoepidermoid carcinoma Mucoepidermoid carcinoma
carcinoma
Intraductal carcinoma Oncocytes
Lymphoepithelial carcinoma
Carcinoma ex-PA Oncocytoma/CA
Lymphadenoma
Clear cell carcinoma
Secretory carcinoma
Note: Modified from a presentation by Joaquín J. García MD, Warthin tumor
Division of Anatomic Pathology, Mayo Clinic Rochester
Stains/Studies Warning: Morphology is still King!
Note: Many salivary gland tumors have at least some myoepithelial component
Myoepithelial markers: p63, p40, Calponin, SMA, GFAP, S100, SOX10
(but somewhat unpredictable!)
High-grade Salivary Tumors

p63/p40 SMA, CK8/18 CK5/6 Mucin AR Synaptophysin
Calponin
Mucoepidermoid, + - Focal + + - -
High-grade
Squamous cell carcinoma + - - + - - -
Salivary Duct Carcinoma - - + - - + -
Poorly-differentiated -/+ - Dot-like - - - +

neuroendocrine
carcinoma
Basaloid Salivary Tumors

p63 p40 SMA/ S100 CD117 LEF-1 PLAG1 MYB
Calponin
Pleomorphic adenoma + + + + +/- +/- + -
Basal cell + + + -/+ +/- + - -

adenoma/carcinoma
Adenoid cystic carcinoma +/- +/- + + + - - +
Myoepithelioma/carcinoma + + + + - - -/+ -
EMEC + + + + -/+ - - -
PLGA + - - + +/- - +/- -
Myoepithelial markers in “Abluminal” (outside) cells

Stains/Studies
Clear Cell Salivary Tumors
p63/p40 S100 Sox10 DOG1
Myoepithelioma/carcinoma + + - -
EMEC + + - -
Acinic cell carcinoma - - + +
Mucoepidermoid carcinoma + - -/+ -/+
Oncocytic Salivary Tumors

P63 P40 S100 Mammaglobin Sox10 DOG1 GATA3 AR
Warthin & + - - - - - - -
Oncocytoma
Acinic cell - - - - + + - -
carcinoma
Secretory - - + + + - + -
carcinoma
Mucoepidermoid + + - - -/+ -/+ - -
carcinoma
Salivary duct - - - -/+ - - + +

carcinoma
Molecular testing
Tumor Most common molecular alteration
Adenoid cystic carcinoma MYB fusions
Clear cell carcinoma EWSR1-ATF1 Fusion
Intraductal carcinoma NCOA4-RET fusions
Mucoepidermoid carcinoma MAML2 fusions
Pleomorphic adenoma PLAG1-HMGA2 fusions
Polymorphous low-grade adenocarcinoma PRKD fusions/mutations
Secretory carcinoma ETV6 Fusions
Acinic cell carcinoma NR4A3 translocations
Epithelial-Myoepithelial Carcinoma PLAG1/HMGA2 translocations or HRAS mutations
Myoepithelial Carcinoma PLAG1/HMGA2 translocations or EWSR1 translocations
Basal cell adenoma/adenocarcinoma CTNNB1 or CYLD mutations
Tables Adapted from:

The Milan System for Reporting Salivary Gland Cytopathology. Faquin and Rossi. 2018.
Quick Reference Handbook for Surgical Pathologists. Rekhtman et al. 2019.
Grading Salivary Gland Tumors
Some tumors have “intrinsic” grade. Others have a variable grade and must be specifically graded.
Intrinsically graded tumors can still be up/down-graded (usually up) based on atypia, etc…
Low-grade Intermediate High-grade Variable grade

(Treated surgically like (Treated (Treated aggressively)
benign tumors) variably)
Acinic Cell Carcinoma Myoepithelial Salivary Duct Carcinoma Mucoepidermoid
Polymorphous Adenocarcinoma Carcinoma Neuroendocrine carcinomas Carcinoma
Basal Cell Adenocarcinoma Lymphoepithelial carcinoma Adenoid Cystic Carcinoma
Epithelial-Myoepithelial Primary squamous cell Adenocarcinoma, NOS
Carcinoma carcinoma Intraductal Carcinoma
Secretory carcinoma Carcinoma-ex Pleomorphic
Clear Cell Carcinoma Adenoma
High-grade Transformation
Low/intermediate grade tumors can undergo “High-grade Transformation” (i.e., De-differentiation)
• Lose recognizable conventional histomorphology, with increased mitotic activity and pleomorphism
• Transformed component usually high-grade carcinoma NOS or squamous cell carcinoma
• Tends to occur in patients older than the median age for individual neoplasms
• (Time for tumors to de-differentiate)
• More aggressive behavior→ Worse prognosis
Adapted from a presentation from Justin A. Bishop, MD Chief of Anatomic Pathology UT Southwestern Medical Center
Milan System On FNA’s, try to use the Milan system to guide clinical management and whenever
possible subtype the tumor and, if malignant, give a grade (high vs low).
Category Explanation Risk of Clinical

Malignancy Management
1. Non-diagnostic Insufficient material for Dx 25% Clinical and radiologic
correlation/repeat FNA
2. Non-Neoplastic Inflammatory/reactive changes (e.g., 10% Clinical follow-up and
reactive lymph node, infection) radiologic correlation
3. Atypia of Undetermined Indefinite for neoplasm (often 20% FNA or surgery
Significance inadequately sampled neoplasm) (e.g.,
rare atypical cells, abundant mucin)
4. Neoplasm: Benign E.g., Pleomorphic adenoma, Warthin <5% Surgery or follow-up
Tumor
4. Neoplasm: Uncertain E.g., “Basaloid neoplasm” (Favor 35% Surgery
Malignant Potential Monomorphic adenoma, cannot rule
out adenoid cystic)
5. Suspicious for Features suspicious for malignancy but 60% Surgery
Malignancy not unequivocal
6. Malignant Clearly malignant (e.g., Mucoep, 90% Surgery
Adenoid cystic, etc…). Try to subtype
and grade if possible.
Squamous Mucosa Prepared by
Kurt Schaberg
(of the Upper Aerodigestive Tract)
Benign/Reactive Dysplastic
“Think Eggs” “Think Boulders”
Cytology: Although they may enlarge, they are Cytology: Nuclei are big, irregular, jagged,
still rounded with smooth nuclear contours. rough, and dark.
Low N:C ratios (More cytoplasm) High N:C ratios (mostly nucleus!)
Nuclei are smooth Nuclei are Dark

Round/oval, often with with Irregular
speckled chromatin crinkled contours
Sometimes have a Dyskeratotic cells

prominent nucleolus
(think Yolk) Usually no nucleoli
(unless perhaps
invasive)
Lots of inflammation? If so, raise your threshold

to account for reactive changes!
Maturating
Architecture: No maturation in traditional High-

grade dysplasia. Many cells don’t know which way
is up.
Architecture: Often matures towards surface, with
Can see maturation in low-grade dysplasia and
highest N:C ratio cells confined to the base
keratinizing dysplasia.
Cells seem to “Know which way is up”
Grading Squamous Dysplasia
Low-Grade Dysplasia
(previously mild dysplasia)
Low Malignant Potential (may regress or not advance)
Limited to LOWER half of epithelium, with surface maturation
Architectural criteria Stratification preserved with retained orientation
Cytologic Criteria At most minimal cellular atypia

Rare mitoses
Few dyskeratotic cells
(previously moderate to severe dysplasia or CIS)
Pre-malignant Lesion
Involves at least half of the epithelium, and may be full thickness
Architectural criteria Abnormal maturation
Altered cells involve ≥1/2 of the epithelium
Disordered stratification
Can be keratinizing or non-keratinizing
No stromal alterations
Cytologic Criteria Conspicuous cellular atypia
Increased N:C ratio
Increased mitoses at or above basal layer
Dyskeratotic or apoptotic cells throughout
Adapted from: WHO Classification of Head and Neck Tumors. 2017.
Sinonasal/Nasopharyngeal Tumors
Benign
Sinonasal Papillomas aka Schneiderian papilloma
Morphology Location Risk of Molecular
transformation
Exophytic Exophytic growth; Nasal Very low risk Low-risk HPV
immature squamous epithelium septum subtypes
Inverted Inverted ‘‘ribbonlike’’ growth; Lateral Low to EGFR

immature squamous epithelium; wall and Intermediate risk mutations or
transmigrating intraepithelial sinuses low-risk HPV
neutrophilic inflammation subtypes
Oncocytic Exophytic and endophytic growth; Lateral Low to KRAS
multilayered oncocytic epithelium; wall and intermediate
microcysts and intraepithelial sinuses
neutrophilic microabscesses
Modified from: Weindorf et al. Arch Pathol Lab Med—Vol 143, November 2019
Oncocytic Sinonasal Papilloma

Note the abundant oncocytic epithelium with
numerous neutrophils
Inverted Sinonasal Papilloma

Note the inverted, “ribbon-like” growth
Respiratory Epithelial Adenomatoid Hamartoma aka “REAH”
Sinonasal glandular proliferation arising
from the surface epithelium (i.e., in
continuity with the surface).
Invaginations of small to medium-sized
glands surrounded by hyalinized stroma
with characteristic thickened, eosinophilic
basement membrane
Exists on a spectrum with seromucinous

hamartoma, which has smaller glands.
Should be able to draw a circle around all

of the glands though, if too confluent
→ consider a low-grade adenocarcinoma
Inflammatory Polyp
Surface ciliated, sinonasal mucosa,
possibly with squamous metaplasia.
Edematous stroma (without a

proliferation of seromucinous glands).
Mixed inflammation (usu. Lymphocytes,

plasma cells, and eosinophils)
Pituitary adenoma
Benign anterior pituitary tumor
Although usually primary to sphenoid bone, can erode into
nasopharynx or be ectopic
Can result in endocrine disorders, such as Cushing’s disease
or acromegaly.
Solid, nested, or trabecular growth of epithelioid cells with

round nuclei and speckled chromatin and eosinophilic,
granular chromatin.
Express CK, and neuroendocrine markers.
NO S100 sustentacular pattern
Can stain with hormone-specific markers (e.g., prolactin)
Can recur
Small Round Cell DDX: MR. SLEEP’N
Malignant M: Melanoma, Mesenchymal chondrosarcoma
R: Rhabdomyosarcoma
S: SNUC, SCC, SMARCB1-deficient sinonasal carcinoma
L: Lymphoma
E: Esthesioneuroblastoma
E: Ewing sarcoma
P: Pituitary adenoma, Plasmacytoma
N: NUT Carcinoma, Nasopharyngeal Carcinoma, NEC,
Squamous cell carcinoma

Most common carcinoma!
Can be Keratinizing or Non-keratinizing
Associated with tobacco exposure.
High-risk HPV subtypes in a subset of tumors;

EGFR or KRAS mutations if papilloma–associated
Sinonasal Undifferentiated Carcinoma (SNUC)

Poorly differentiated carcinoma without squamous,
glandular, or neuroendocrine differentiation
(Dx of exclusion!).
Open to hyperchromatic nuclei. Somewhat monotonous.
Often prominent nucleoli.
CK+, but squamous markers negative
IDH2 codon R172 mutations in most tumors
Aggressive high-grade malignancy→ poor outcome
NUT (Midline) Carcinoma

Poorly-differentiated carcinoma (often small-round
blue cells), with often “abrupt keratinization” or
squamous differentiation.
Often younger patients, in the midline, often in the

head and neck.
NUT gene rearrangement→ stain with NUT IHC!
Aggressive high-grade malignancy→ poor outcome

SMARCB1(INI-1)–deficient sinonasal carcinoma
Poorly-differentiated carcinoma with high N:C ratios
Similar morphology to SNUC but may show
prominent plasmacytoid/rhabdoid features
Biallelic inactivation of SMARCB1 (loss of INI-1
staining by IHC)
Poor long-term outcomes
HPV-related multiphenotypic sinonasal carcinoma

High-grade carcinoma with morphologic and
immunohistochemical evidence of myoepithelial
differentiation → often Adenoid cystic-like
Shows associated surface squamous dysplasia
Positive for HPV: High-risk subtypes (especially type
33)→ P16 IHC block positive, but must do
additional, more specific testing.
Although typically advanced disease at presentation,
clinical course is relatively indolent
Lymphoepithelial Carcinoma
Essentially non-keratinizing nasopharyngeal
carcinoma, undifferentiated type (if in the sinonasal
cavity, just call it NPC if in nasopharynx)
Sheets of malignant cells with vesicular chromatin,
indististinct cytoplasm, and abundant tumor-
infiltrating lymphocytes.
EBV-positive. Positive for CK, CK5/6, p40, p63
More common in Asians.
Teratocarcinosarcoma
Malignant tumor with features of teratoma (e.g.,
squamous or glandular epithelium, often including
immatures fetal-appearing squamous epithelium,
and immature neuroepithelium, sometimes with
rosette formation) and carcinosarcoma (with
spindled cells, possibly with rhabdomyoblastic, or
other differentiation) without germ cell components
Like Poorly-differentiated neuroendocrine
carcinomas of the lung.
Divided into: 1) Small cell neuroendocrine carcinoma
2) Large cell neuroendocrine carcinoma
Strong staining with a neuroendocrine stain (e.g..,
synaptophysin or chromogranin). Often perinuclear
“dot-like” keratin expression.
Mucosal Melanoma
Distinct from cutaneous melanomas biologically
(but must exclude metastatic melanoma clinically!)
Epithelioid to spindled cells with pleomorphic nuclei
and often prominent nucleoli.
Intracytoplasmic melanin
Melanoma markers: S100, SOX10, HMB45, MelanA,
MITF, Tyrosinase. Do many (as can be loss)!
Poor prognosis: Staging starts at T3-4.
No need for Clark/Breslow depth.
Adenocarcinoma
Salivary gland adenocarcinomas are the most common (particularly adenoid cystic→ see separate guide)
Sinonasal Adenocarcinomas
Intestinal type
Causal relationship with wood dust and leather dust (so, mostly men)
Morphology and IHC identical to colonic adenocarcinoma
(CK7-, CK20+, CDX2+)
Non-intestinal type
(CK7+, CK20-, CDX2-)
Low-grade:
Very bland cytologically (to the point where you wonder if it is malignant!)
Excellent prognosis
High-grade
Cytologically malignant. Diagnosis of exclusion (must exclude metastasis, etc…)
Poor prognosis
Nasopharyngeal papillary adenocarcinoma
Low-grade adenocarcinoma of the nasopharynx with predominantly papillary architecture
Papillae are lined by a single layer of bland cuboidal cells with scant cytoplasm
Complex, arborizing papillae (sort of looks like ovarian micropapillary serous borderline tumor)
Rhabdomyosarcoma Malignant tumor with primary skeletal muscle differentiation, several types
Stain with Desmin, MyoD1, Myogenin
Embryonal Rhabdo:
Variable numbers of round (“rhabdoid”), strap-, or tadpole-shaped
eosinophilic rhabdomyoblasts in a myxoid stroma
Can see cytoplasmic cross striations
Alveolar Rhabdo:
Larger, more rounded undifferentiated cells with only occasional
rhabdomyoblasts
Often arranged in an alveolar (nested) pattern
Distinctively strong and diffuse myogenin positivity
Characteristic FOXO1 translocations
Olfactory Neuroblastoma aka “Esthesioneuroblastoma”

Malignant neuroectodermal neoplasm
Confined to the cribriform plate (and
surrounding region)
Lobulated, nests to sheets of cells with
speckled chromatin. High N:C ratio
Fibrillary cytoplasm→ Neuropil!
Can see pseudorosettes.
IHC: Diffuse Synaptophysin/Chromogranin
S100→ Sustentacular pattern. CK negative.
Ewing Sarcoma aka Primitive Neuroectodermal Tumor (PNET)

Malignant tumor of neuroectodermal differentiation
Often have EWSR1 translocation (with FLI-1 or ERG) t(11;22)
Usually uniform, small, round, blue cells with sheet-like to lobular,
growth pattern with variable necrosis
Strong, membranous CD99 staining
(Sensitive, but not Specific staining)
Cytoplasmic glycogen stains with PAS
“Adamantinoma-like” variant can show diffuse staining with CK Can see

and p40! pseudorosettes
Lymphoma Plasmacytoma
Extranodal NK/T-cell lymphoma IHC: CD138+ with light chain restriction
IHC: CD3, CD56, EBER + May or may not be associated with multiple myeloma
Most common in Asians
Unique (not benign) Mesenchymal Tumors
Glomangiopericytoma
Patternless proliferation of regular, syncytial spindled cells
with ovoid nuclei.
Prominent vascularity with perivascular hyalinization.
Can see “staghorn” vessels (hemangiopericytoma-like,
hence the name, in part)
Perivascular myoid phenotype (like a glomus tumor, hence
the name)
IHC: SMA+, Nuclear ẞ-catenin (CTNNB1 mutations)
Relatively indolent with good survival
Biphenotypic Sinonasal Sarcoma

Low-grade spindle cell sarcoma.
Cellular, submucosal spindle-cell proliferation.
Arranged in intersection fascicles, often herringbone.
Infiltrate into bone often.
Can induce epithelial proliferation.
“Biphenotypic” because has evidence of both neural
and muscular differentiation.
Neural→ S100 (focal to diffuse)
Muscle→ SMA (focal to diffuse)
PAX3-MAML3 translocations.
Slow, continuous growth, but no metastases.
Nasopharyngeal Angiofibroma
Richly vascular tumor with variably sized blood vessels set
in fibrotic stroma.
Vessels are usu. thin-walled and often dilated with
variable smooth muscle.
Stroma is myxoid to dense with stellate fibroblasts.
Almost exclusively young to adolescent boys (“Juvenile
angiofibroma”)→ classically causes epistaxis &
obstruction
Nuclear expression of ẞ-catenin and AR in stromal cells
Locally aggressive and can recur.
Treat with embolization and surgery
HPV-related multiphenotypic sinonasal

Sinonasal Undifferentiated Carcinoma
SMARCB1(INI-1)–deficient sinonasal
Nasopharyngeal carcinoma
Squamous cell carcinoma
Olfactory Neuroblastoma
Rhabdomyosarcoma
Mucosal melanoma
NUT carcinoma
Ewing Sarcoma
Lymphoma
carcinoma
carcinoma
(SNUC)
CK
(AE1/AE3) + + + + + + + - - - - ±
CK5/6
+ - ± + + + - - - - - ±
P63 and
p40
+ - ± + + + - - - - - ±
Synapto/
Chromo
- - - - - - + - ± - + ±
CD56
- - - - - - + - ± ± + ±
CD99
- - - - - - - - - ± - +
P16
± ± - - + - ± - - - - -
S100
SOX10
- - - - + - - + - - + -
CD45
- - - - - - - - - + - -
Myogenin/
Desmin
- - - - - - - - + - - -
NUT
- - - + - - - - - - - -
INI-1
+ + - + + + + + + + + +
EBER
- - - - - + - - - ± - -
Note: Weak/focal staining with synaptophysin, CD56, and CK can be seen with many tumors and
should be taken in context. Look for strong, diffuse staining (think Christmas tree).
Algorithm for Nasal Small Round Blue Cell Tumors
Starting IHC Panel: 1) AE1/AE3, 2) p40, 3) synaptophysin, 4) SOX10, 5) CD45, 6) CD99, and 7) Desmin
Adapted from a presentation from Justin A. Bishop, MD Chief of Anatomic Pathology UT Southwestern Medical Center
CK
- or F ++
Desmin/myogenin SMARCB1
- or F ++ lost intact
CD99/NKX2.2 Alveolar SMARCB1-deficient
P40
- or F
Rhabdomyosarcoma sinonasal carcinoma ++
++ - or F
Melanoma Ewing Sarcoma Synaptophysin/Chromogranin NUT
markers
+ - - or F + + -
Melanoma Lymphoid Multilineage Differentiation Pituitary hormones/ NUT carcinoma EBER
+ markers sphenoid location
- - + + -
Lymphoma Synaptophysin/ - Lymphoepithelial Myoepithelial
Chromogranin Pituitary Neuroendocrine Carcinoma markers
SNUC
+ adenoma carcinoma +
Olfactory + Solid adenoid -
neuroblastoma cystic carcinoma
Teratocarcinosarcoma
CD99/NKX2.2
Start with the whole panel, and

-
then work through the ++
Non-keratinizing
algorithm and get additional squamous cell
stains/studies if necessary. carcinoma Adimantimoma-
like Ewing
sarcoma
Thyroid & Parathyroid Lesions

Thyroid Tumors
Papillary Thyroid Carcinoma “PTC”
Malignant tumor with follicular epithelial cell differentiation and distinct nuclear features.
Most common form of thyroid cancer in both adults and children. More common in women.
Risk factor: Ionizing radiation. Often relatively indolent cancer.
Often presents with a painless thyroid mass.
Nuclear Features: (Definitional)
- Nuclear enlargement and elongation
- Nuclear overlapping
- Irregular nuclear contours
- Intranuclear pseudoinclusions (→)
- Longitudinal nuclear grooves
- Nuclear chromatin clearing
Conventional (classic) PTC: Papillary architecture (hence the name!).
May have mixed in other architectures like follicles. Frequent
psammoma bodies. Occasional squamous metaplasia. Often cystic
degeneration. Densely eosinophilic colloid.
Papillary microcarcinoma: Tumor variant ≤ 1 cm. Often missed
grossly/incidental. Malignant, but excellent prognosis.
Encapsulated variant: Totally surrounded by a fibrous capsule (intact or
focally infiltrated). Excellent prognosis.
Follicular variant: Exclusively (or almost exclusively) follicular
architecture. Can be infiltrative or encapsulated with invasion.
Tall Cell variant: Cells 2-3x as tall as they are wide with abundant
eosinophilic cytoplasm. Must account for ≥30% of tumor. More
aggressive behavior.
Columnar cell variant: Rare. Columnar cells with prominent
pseudostratification. Lack conventional nuclear features. Resembles
endometrioid/intestinal adenocarcinoma morphologically. IHC: CDX2+!
Diffuse sclerosing variant: Rare. Diffuse involvement with sclerosis and
solid nests of tumor cells. Also background lymphocytic inflammation
and psammoma bodies.
Cribriform-morular variant: Mixture of cribriform, follicular, papillary,
trabecular, and solid growth with round squamoid structures (morules).
Frequent vascular invasion. Almost exclusively in females. Association
with FAP→ nuclear β-catenin. IHC: LEF-1 positive.
Other variants: Hobnail, solid/trabecular, oncocytic, spindle cell, clear
cell, Warthin-like, and PTC with fibromatosis/fasciitis-like stroma
IHC: (+)TTF-1, PAX8, Thyroglobulin, CK7,
Molecular alterations: BRAF (most common by far, often V600E), RET,
RAS, TERT promoter→ often mutually exclusive→ MAPK activation
Follicular Adenoma
Benign neoplasm with thyroid epithelial differentiation
Completely surrounded by a fibrous capsule (→).
Variety of architectural patterns: normo-, micro-, or
macrofollicular, solid, and/or trabecular, but different than
surrounding parenchyma
Cells are cuboidal with round, basally located nuclei.
Smooth nuclear contours and uniform chromatin.
ABSENT: capsular/vascular invasion, PTC-like nuclei
(Must submit entire capsule to exclude invasion)
Molecular: Most frequently RAS mutations.
Associated with Cowden syndrome and Carney complex
Variants:
Hyperfunctioning—hyperthyroidism. Papillary projections.
Lipoadenoma—mature adipose tissue is sprinkled throughout
Signet-ring cell—cells with cytoplasmic vacuoles Capsular and/or
Other variants: clear cell, spindle cell, black
Vascular Invasion
Follicular Carcinoma
Malignant. Nuclear features of PTC are absent.
Risk factors: insufficient iodine, ionizing radiation
Often present with painless mass.
Requires either capsular or vascular invasion!
Otherwise, cytology and architecture is identical to
follicular adenoma
Often surrounded by thick fibrous capsule.
Most require that tumor penetrate the entire capsule→
classically has a “mushroom” appearance.
For vascular invasion, tumor cells should be adherent to
the vessel wall either with covering endothelium or in a
thrombus with fibrin (this is to distinguish from artifactual Thrombus
tumor “misplacement”). Controversial (see next page)
Invasion must occur in the capsule or beyond
Subclassified into 3 groups: Tumor
1) Minimally invasive → capsular invasion only →
excellent prognosis
2) Encapsulated angioinvasive→ risk of hematogenous
metastasis (often bone/lung)
3) Widely invasive → extensive involvement of thyroid
and soft tissues, often with prominent vascular invasion
Molecular: RAS point mutations and PAX8-PPARγ gene fusions most common.
Associated with Cowden syndrome
IHC: (+)TTF-1, PAX8, Thyroglobulin, CK7, (More on next page!)
Is that “good enough” for capsular invasion?
Most require complete transgression of the capsule
(labeled “Yes”→)
Some pathologists are more lenient, and may accept
those labeled “Not yet”
When in doubt, get multiple deeper histologic levels.
Remember, a prior FNA may disrupt the capsule.
Also, as the tumor grows and extends into the
parenchyma, it can induce a new stromal reaction
forming a secondary fibrous band (example D). So,
instead of just the fibrous capsule itself, look at the
gland contour. If the invasive tongue of tumor
extends outside of the usual contour (even if there is
a thin capsule), many would consider this invasive.
From the CAP Protocol for the Examination of Specimens From Patients With Carcinomas of the Thyroid Gland
Is that “good enough” for vascular invasion?

PTC→ usually spreads via lymphatics (no RBCs, stain with D2-40) to lymph nodes.
Follicular Carcinoma→ spreads via veins (luminal RBCs, stain with CD31) hematogenously to lungs/bones
Vascular invasion must be outside of the tumor—either in the capsule or beyond.
According to the WHO, tumor cells should be adherent to the vessel wall either with covering
endothelium or in a thrombus with fibrin.
However, newer data suggests tumor cells within vascular lumina unassociated with thrombus and tumor
cells underlying intact endothelium could represent “pseudoinvasion” given the fenestrated endothelial
network of endocrine organs.
Stricter CAP unequivocal definition: invasion of tumor through a vessel wall accompanied by fibrin
thrombus→ correlates more closely with aggressive disease.
These examples have fibrin associated with tumor,

so they are unequivocal vascular invasion
Controversial, WHO would say Yes. Stricter CAP would say NO.
Consider “Uncertain Malignant Potential” (next page)
May represent tangential

example B, get deeper levels
Tumor bulging and indenting

the vessel wall does not count
(Blue = endothelium) →
(Red = fibrin)
From the CAP Protocol for the Examination of Specimens From Patients With Carcinomas of the Thyroid Gland
Hürthle (Oncocytic) Cell Tumors
Neoplasms composed of oncocytic cells with abundant
eosinophilic granular cytoplasm.
Hürthle cell adenoma→ essentially a follicular adenoma
composed of Hürthle cells. Encapsulated. Benign.
Hürthle cell carcinoma→ contains vascular and/or capsular
invasion (essentially a follicular carcinoma with Hürthle cells)
Most use term only if “majority” (greater than 75%) of

tumor has this morphology (otherwise use term “Hürthle
cell features”)
Hürthle cells are large with abundant eosinophilic granular
cytoplasm and large central nuclei with prominent nucleoli.
Full of mitochondria.
Variable architecture: follicular, trabecular, or solid
Larger tumors are more likely to be malignant.
Tumors of “Uncertain Malignant Potential”

Some encapsulated neoplasms with a follicular architecture can have questionable capsular/vascular
invasion or nuclear changes that are mild, where it is unclear if they are sufficient to justify a diagnosis
of papillary thyroid carcinoma→ In such diagnostically uncertain cases, one can use the diagnosis of
“Uncertain Malignant Potential” (UMP)
For example: Tumor cells invade into, but not completely across the capsule, or, Tumor cells are in a
blood vessel, but are not covered by endothelium or thrombus.
Follicular Tumor of Uncertain Malignant Potential→ encapsulated or well-circumscribed follicular-
patterned tumor lacking nuclear features of PTC with equivocal vascular or capsular invasion (and no
PTC-like nuclear features). Essentially between follicular adenoma and carcinoma.
Well-differentiated Tumor of Uncertain Malignant Potential → Encapsulated or well-circumscribed

follicular-patterned tumor well-developed or partially developed PTC-type nuclear changes and with
questionable capsular or vascular invasion. If invasion is totally excluded→ NIFTP (next page)
Capsular or Vascular Invasion

Present Questionable Absent
Invasive Encapsulated Non-invasive
Present Follicular Variant of Well-differentiated Follicular Thyroid
Nuclear PTC Tumor of Uncertain Neoplasm with
features Well-Differentiated Malignant Potential Papillary-like nuclear
of PTC Questionable features (NIFTP)
Carcinoma, NOS
Follicular Tumor of
Absent Follicular Carcinoma Uncertain Malignant Follicular Adenoma
Potential
Modified from: WHO Classification of Tumors of the Endocrine Organs. 2017.
Non-invasive Follicular Thyroid Neoplasm
with Papillary-like Nuclear Features (“NIFTP”)
Diagnostic Requirements:
1) Encapsulated or Clear demarcation
2) Follicular pattern of growth with:
- No true papillae
- No psammoma bodies
- <30% solid, trabecular, or insular growth pattern
3) Nuclear features of papillary carcinoma (nuclear score 2-3)
4) No lymphovascular or capsular invasion
5) No tumor necrosis
6) No significant mitotic activity (<3 mitoses/10 HPF)
Score nuclear features using table below. If present +1, if absent

= 0. Need a score of 2-3 to qualify. May be patchy/focal.
However, nuclear features of PTC are usually only partially

developed in NIFTP. So, if they are very well-developed,
reconsider the diagnosis and consider testing for BRAF
mutations (present in PTC, not in NIFTP)
The entire tumor (or at least the Nuclear Alteration Findings
entire capsule) should be submitted
Size and Shape nuclear enlargement, overlapping,
for histologic evaluation
crowding, elongation
Molecular: RAS mutations (like Nuclear membrane irregular contours, grooves,
follicular adenomas/carcinomas). irregularities pseudoinclusions
BRAF mutations (like in PTC) are
notably absent, which can be useful Chromatin clearing with margination, glassy
diagnostically with challenging cases. characteristics nuclei
Prognosis: Very low risk of

progressive disease. Can be treated Encapsulated Follicular Tumor Algorithm
with lobectomy alone.
Invasive?
Yes Questionable
Carcinoma No Uncertain
Malignant
Potential
Papillary Carcinoma Nuclear Features?
Yes No Questionable
NIFTP Follicular Use Nuclear Assessment

Adenoma Guide
Score: 2-3 Score: 0-1

Poorly-Differentiated Thyroid Carcinoma
Thyroid carcinoma with morphology, genetics, and behavior
between differentiated carcinomas (i.e., papillary and follicular)
and anaplastic carcinoma. Applies to Hürthle cell tumors also.
Turin Criteria:
1) Carcinoma of follicular cell origin
2) Solid, trabecular, or insular growth pattern
3) Absence of conventional nuclear features of papillary thyroid
carcinoma
4) At least of one of the following:
- Convoluted nuclei (dedifferentiated PTC nuclear features)
- ≥3 mitoses per 10 high-power fields
- Tumor necrosis
Tumor cells are small and uniform with round hyperchromatic
nuclei or convoluted nuclei. Mitoses are common. Extensive
tumor necrosis can give a peritheliomatous pattern.
Some arise from via dedifferentiation of PTC or follicular
carcinoma (which may be visible in the lesion), while others
appear to be de novo.
Often widely invasive into soft tissue and vessels
IHC: (+)TTF1, PAX8, Thyroglobulin, often express HMW-CKs
Prognosis: Intermediate prognosis
Malignant thyroid tumor

of follicular cells
Follicular Carcinoma Solid, Trabecular, or

Papillary Carcinoma, Etc.. No Insular Pattern
Yes
Solid Variant of Typical PTC nuclei

Yes
Papillary Carcinoma throughout
No
Presence of one of the following:

Follicular Variant 1) Convoluted nuclei,
No
(solid growth pattern) 2) Necrosis, 3) Mitoses
Yes
Poorly Differentiated Thyroid

Carcinoma
Anaplastic Thyroid Carcinoma
Highly aggressive thyroid malignancy composed of
undifferentiated follicular epithelial cells.
Classically older women with rapidly growing firm, fixed, highly
infiltrative neck mass→ Pain, hoarseness, dysphagia
Can occlude airway!
Many cases seem to arise from dedifferentiation of a pre-existing
thyroid tumor (may have history of long-standing nodule)
Variable morphology with 3 main patterns:
Sarcomatoid→ spindled cells resembling pleomorphic sarcoma,
Giant cell→ highly pleomorphic cells some of which have multiple
nuclei, Epithelial→ Squamoid nests
Common findings: Necrosis, mitoses, invasive growth.
Often inflammatory cells.
IHC: PAX8 often maintained. Frequent loss of TTF1, CK
Molecular: Frequent TP53 mutations. Also, BRAF, RAS, PTEN
Prognosis: Very aggressive with often <1 yr survival

Malignant epithelial tumor with entirely squamous differentiation.
Clinical features and prognosis similar to anaplastic carcinoma
Notably, both PTC and Anaplastic carcinoma can have squamous
areas, so the tumor should be sampled well to exclude squamous
differentiation of another tumor.
Often extensive infiltration of soft tissue/vessels.
Thyroid Carcinoma Immunohistochemistry

CK Thyroglobulin TTF1 PAX8 Ki67 P53 Calcitonin,
synaptophysin
Normal Thyroid + + + + <3% Wt -
Follicular cells
Well-differentiated + + + + <10% Wt -
thyroid carcinoma
Poorly-differentiated + -/+ + + 10-30% + -
thyroid carcinoma
Anaplastic thyroid +/- - -/+ +/- >30% + -
carcinoma
Medullary carcinoma + - + -/+ Wt +
Medullary Thyroid Carcinoma
Malignant tumor of the thyroid with parafollicular C-cells
differentiation.
Uncommon. Although mostly sporadic, associated with
Multiple Endocrine Neoplasia (MEN) type 2 (germline RET
Inclusion
mutations).
Often present with painless mass. Frequent LN metastases
at presentation with elevated serum calcitonin.
Wide morphologic spectrum! Common patterns of growth
include: solid, lobular, trabecular, and/or insular.
Tumor cells can appear: round, polygonal, plasmacytoid, or
spindled. Nuclei are “Neuroendocrine” (round, speckled
“salt and pepper”) with occasional pseudoinclusions.
Cytoplasm is eosinophilic to amphophilic and granular. Amyloid
Although scattered markedly atypical cells may be present

(“Endocrine atypia”), generally not too pleomorphic.
Frequent stromal amyloid.
In familial tumors (e.g., MEN 2b) → more frequently
multifocal with C-cell hyperplasia.
IHC: (+) Calcitonin (most specific), Neuroendocrine
markers (synaptophysin, chromogranin), TTF-1. (+/-) PAX8.
(-) thyroglobulin.
Molecular: Frequent RET mutations. Occasional RAS mutations.
Prognosis: Intermediate aggressive behavior.
Rare variant: “Mixed medullary and follicular thyroid carcinoma”
Hyalinizing Trabecular Tumor

Extremely good prognosis. Follicular-derived neoplasm. Rare.
Solid, well-circumscribed nodule.
NO capsular, vascular, or thyroid parenchymal invasion.
Wide trabeculae and nests separated into bundles by stroma.
Cells may be enveloped by hyalinized PAS-d positive basement
membrane material.
Large polygonal/elongated cells. Eosinophilic finely granular
cytoplasm. Occasional perinuclear yellow bodies.
Nuclei are vesicular and mostly round, but with frequent
grooves, inclusions (→), and membrane irregularities.
(Can be mistaken for PTC, particularly on FNA!!!)
IHC: (+)TTF-1, thyroglobulin; (-) Calcitonin
Unique membranous staining with MIB1 (Ki67 clone)
Mucoepidermoid Carcinoma
Low-grade malignant/indolent. Very rare.
Unclear origin, but favored to represent metaplastic
differentiation of follicular derived carcinoma in most
cases. Associated with PTC in ~1/2 of cases
Two required cell types: 1) Squamoid cells ,
2) Mucin-producing goblet cells.
IHC: Most cases express PAX8, TTF-1, thyroglobulin
Molecular: Occasional MAML2 rearrangements.
Sclerosing Mucoepidermoid Carcinoma with Eosinophilia

Malignant with sometimes aggressive behavior.
Rare. Strong female predominance.
Consistently associated with fibrosing Hashimoto’s thyroiditis.
Small nests and strands of epidermoid cells infiltrating sclerotic
stroma. With interspersed mucous-secreting cells.
Rich inflammatory infiltrate with lymphocytes, plasma cells, and
prominent eosinophils.
Frequent PNI and LVI.
IHC: (+/-)TTF1, (-/+) Thyroglobulin.
Mucinous Carcinoma
Malignant. Extremely Rare.
Unknown origin/etiology.
Abundant pools of mucin with floating trabeculae/
tumor clusters. Cells have large nuclei with nucleoli.
Other typical carcinomas should be absent.
Must clinically exclude a metastasis.
IHC: Focal staining with thyroglobulin, TTF-1, PAX8
Ectopic Thymoma
Very Rare. Typical mediastinal thymoma histology, but
located ectopically within the thyroid gland.
Arises from ectopic thymus tissue.
Jigsaw puzzle-like lobules separated by sclerotic septae.
Intimate admixture of ovoid to spindled epithelial cells
with a variable amount of small lymphocytes.
IHC: Epithelium—cytokeratins, p63, PAX8
Lymphocytes—immature T cells (TdT+, CD1a, CD99)
Spindle Epithelial Tumor with Thymus-like Differentiation (“SETTLE”)
Malignant. Intermediate behavior. Rare.
Highly cellular. Lobulated architecture.
Spindled epithelial cells that merge into glandular
structures.
May have glomeruloid glands/papillae, reticulated
fascicles, or be exclusively spindled.
IHC: Both cell types stain with HMWCK and CK7.
Spindled cells rarely show myoepithelial staining.
Intrathyroid Thymic Carcinoma

Old name: Carcinoma showing thymus-like
differentiation (“CASTLE”)
Very Rare. Malignant tumor with thymic epithelial
differentiation (malignant counterpart of intrathyroidal
thymoma).
Appears identical to thymic carcinoma of mediastinum:
essentially a squamous cell carcinoma with
lymphocyte-rich stroma.
IHC: (+) CD5, p63, CD117, Cytokeratins, PAX8, calretinin
(-) TTF-1, Thyroglobulin; Ki67 10-30%
Other Thyroid Tumors

Paraganglioma Langerhans Cell Histiocytosis
Peripheral Nerve Sheath Tumors Rosai-Dorfman Disease
Hemangioma Follicular Dendritic Cell Sarcoma
Angiosarcoma Diffuse Large B-cell Lymphoma
Smooth Muscle Tumors MALT lymphoma
Solitary Fibrous Tumors Teratoma
Metastases
Parathyroid Tumors IHC: These are (+) PTH, GATA3, Synaptophysin, Chromogranin
(-) TTF1, Thyroglobulin, Calcitonin; (+/-) PAX8
Normal Parathyroid
Regulates calcium levels with parathyroid hormone PTH 3 1
Three main components:
1- Chief cells: main cell type, round central nucleus, clear to
amphophilic cytoplasm
2-Oxyphil cells: large cells with abundant pink cytoplasm 2
3-Fat (and fibrous tissue) dividing cells into lobules
Parathyroid Adenoma
Benign parathyroid neoplasm. Relatively common.
Often present with primary hyperparathyroidism→ hypercalcemia
(metabolic bone disease, kidney stones, fatigue, etc.)
Can arise in any of the 4 glands, or be ectopic.
A minority of cases are associated with MEN1/2A
Well-circumscribed, often encapsulated
Composed of chief cells (most common), oncocytes, or a mixture.
Cells have round, central nuclei with dense chromatin.
Unlike normal parathyroid, there is typically NO FAT
Occasional mitoses acceptable. Sometimes follicular architecture.
Many variants: Oncocytic, water-clear cell, lipoadenomas (contain
fat and other parenchymal elements)
Remember, the surgeon often wants a weight!
Parathyroid Carcinoma
Rare. Malignant neoplasm derived from parathyroid cells.
Usually presents with hyperparathyroidism.
Requires evidence of one of the following:
- Invasive growth involving adjacent structures (e.g., thyroid or soft tissue)
- Invasion of vessels in capsule or beyond (attached to wall)
- Metastases
Usually subdivided by broad fibrous bands. Variable pleomorphism/mitoses.
Ki67 usually 6-8% (vs <4% in adenomas)
“Atypical Parathyroid Adenoma”
Adenomas that exhibit some features of parathyroid carcinoma but lack
unequivocal invasive growth→ essentially “Uncertain Malignant Potential.”
Frequent findings: bands of fibrosis, adherence to other structures, tumor in
capsule, solid/trabecular growth, nuclear atypia, increased mitotes.
Usually benign clinical course with close clinical follow-up.
Fibrous bands
CHAPTER 7
Soft Tissue and Bone

Soft Tissue Tumors

Adipocytic
Lipoma
Benign adipocytic tumor

Most are mature “white fat” with a single large lipid droplet.
Common. Usually superficial/subcutaneous.
May recur.
Although clinically form a mass, may be indistinguishable
histologically from normal fat (so can sign out as “Mature adipose
tissue, compatible with lipoma”)
Molecular: Various chromosomal aberrations
Specific types:
Angiolipoma—Fat + prominent branching network of vessels, often with
fibrin thrombi. Usu. Tender nodule on forearm.
Spindle Cell Lipoma—Fat + bland spindle cells with a variably myxoid
background. Can be fat-poor.
Note, these two subtypes (↑↓) exist on a spectrum. Classically, they
are seen in older men in a “cape-like” distribution (neck, shoulder, back).
Spindled and floret cells stain with CD34.
Pleomorphic Lipoma—Spindle cell lipoma + scattered, bizarre giant cells
that frequently with floret-like arrangement of multiple hyperchromatic
nuclei
Chondroid Lipoma—Fat + round cells in a myxochondroid background.
Neural fibrolipoma—Fat+ fibrous tissue growing in nerves. Usu. in arms.

Myelolipoma—Fat + bone marrow elements. Most common in adrenal
medulla.
Lipoblastoma—Occurs in infants and resembles fetal adipose tissue.

Lobules of immature fat cells separated by connective tissue septa with
a loose myxoid appearance.
Myolipoma—Fat + smooth muscle bundles
Hibernoma—Brown fat (multiple small vacuoles within polygonal cells

with distinct cell membranes).
Atypical Lipomatous Tumor/Well-Differentiated Liposarcoma
Most common adult sarcoma. Usually elderly.
Non-metastasizing (but recur/grow).
Deep soft tissue, most common in extremity, use ALT term, easier
to excise, curable and less likely to recur).
In retroperitoneum, use WDL term, harder to excise, basically
incurable.
Variable amount of lipoblasts (cytoplasmic lipid-rich droplets with a

hyperchromatic, indented/scalloped nucleus).
Can be lipoma-like (resembling mature fat), sclerotic (fibrous areas,

often with scattered hyperchromatic atypical cells), or
inflammatory (with associated brisk inflammatory infiltrate).
Molecular: Giant marker and ring chromosomes that contain
amplified regions of 12q including MDM2 and CDK4 → Test for
with MDM2 or CDK4 IHC, or, more commonly, MDM2 FISH for gene
amplification. P16 is a sensitive (but not specific) marker as it is
downstream from CDK4, so it is overexpressed.
Can De-differentiate (see below).
Fatty Tumors to FISH for MDM2

Lipomatous tumors with equivocal cytologic atypia
Recurrent lipomas
Deep lipomas without atypia that exceed 15 cm
Retroperitoneal or intra-abdominal lipomatous tumors lacking
cytologic atypia (Although retroperitoneal lipomas DO exist,
they are very rare and a diagnosis of exclusion)
(No need to FISH classic cases with lipoblasts and/or atypia)

Can
Dedifferentiated Liposarcoma Dedifferentiate
Contain an ALT/WDL component, with an abrupt transition to another
component, which is usually an undifferentiated pleomorphic sarcoma
(sometimes fibrosarcoma, or lower grade sarcoma).
Some say de-differentiated area should have a mitotic count of at least

5 mitotic figures per 10 high-power fields.
Molecular: Same 12q amplifications as in ALT/WDL (but with more

superimposed), so can use same FISH.
Has Metastatic potential in addition to being more locally aggressive.

Myxoid Liposarcoma
Usu. younger and on the lower extremity
Resemble developing fat:

Multinodular proliferation of round cells
Abundant myxoid matrix,
Chicken-wire vasculature,
multivacuolar and univacuolar lipoblasts
As get higher grade→ lose myxoid

component → composed of primarily round
cells → “Round cell liposarcoma”
Molecular: FUS-DDIT3 fusions
(do FUS break apart FISH)
Higher
Outcome: Higher round cell component→
worse outcome. Grade
Can metastasize.
Pleomorphic Liposarcoma
Least common liposarcoma.
Essentially, an undifferentiated pleomorphic
sarcoma, but with scattered lipoblasts.
Extreme pleomorphism including bizarre giant cells.
Malignant with frequent metastases.
Molecular: Complex structural chromosomal
rearrangements.
Fibroblastic/Myofibroblastic
Nodular Fasciitis
Benign, self-limited, “transient neoplasia.”
Rapidly growing, mass-forming subcutaneous lesion,
sometimes after trauma, that self-regresses. Often upper
extremity or head and neck of kids or young adults.
Can be misdiagnosed as a sarcoma because of rapid growth
and mitotic activity. Previously thought to be reactive.
Bland spindled to stellate cells with variably cellular “tissue
culture-like” pattern.
“Torn stroma” resembling “S” and “C” shapes.
Extravasated RBCs.
Pale nuclei with prominent nucleoli.
Older lesions may be scarred/collagenous.
Molecular: MYH9-USP6 gene fusions (do USP6 break apart
FISH).
IHC: Actin (+) (as myofibroblastic), but desmin (-).
Specific variants: Ossifying fasciitis (with metaplastic bone),
Cranial fasciitis (on scalp of infants), and intravascular
fasciitis (in vessels).
Proliferative Fasciitis/Myositis
Benign. Subcutaneous soft tissue of adults usu. on arm.
Like nodular fasciitis (tissue culture-like)
Prominent large, basophilic ganglion-like cells with one or
two vesicular nuclei and prominent nucleoli.
IHC: Similar to Nodular fasciitis. Not true ganglion cells

(negative S100, etc…)
If in muscle, use “Proliferative myositis.”
Ischemic Fasciitis
“Pseudosarcomatous” (Benign/reactive) proliferation overlying bony prominences of elderly and/or
immobile patients.
Often shoulder or sacral site→ intermittent ischemia with breakdown/regenerative changes.
Zonal growth with central necrosis surrounded by proliferating blood vessels and
fibroblasts/myofibroblasts.
Can see scattered hyperchromatic atypical cells and mitoses, but no atypical mitoses.
Elastofibroma EVG
Benign (likely reactive/degenerative pseudotumor).
Usually under scapula of elderly patient.
Eosinophilic collagen and Elastin.

Occasional fibroblasts, myxoid material, and fat.
Elastic fibers have a degenerative, “beaded” appearance
that can fragment into flower-like disks
Stains: Can highlight Elastin with EVG.
Nuchal-type Fibroma
Benign. Usu. Posterior neck of adults. Painless mass.
Almost acellular densely collagenized with rare
fibroblasts. Somewhat ill-defined entrapping adjacent
structures.
IHC: Spindled cells usu. (+) CD34 and CD99. (-) actin.
Gardner-associated Fibroma
Benign. Usually back of younger patient.
Strong association with FAP and desmoid tumors (Gardner
syndrome).
Histologic overlap with nuchal-type fibroma.
Densely collagenized with sparse spindled cells with interspersed
lobules of fat.
Can entrap other structures at periphery.
IHC: Spindled cells usu. (+) CD34 and CD99. Often nuclear β-
catenin (like desmoids!)
Fibrous Hamartoma of Infancy

Benign superficial fibrous lesion occurring during first 2
years of life
3 components in organoid growth pattern: 3

1)Intersecting bands of mature fibrous tissue, comprising
spindle-shaped myofibroblasts and fibroblasts
2
2) Nests of immature round, ovoid, or spindle cells within
loose stroma
3) Interspersed mature fat
1
Molecular: EGFR exon 20 insertion/duplication
Fibroma of Tendon Sheath
Benign. Slowly growing mass on tendon sheath or
aponeuroses.
Usu. adults, under 2 cm, and on extremities, often hand.
Well-circumscribed, lobulated.
Mostly hypocellular with spindled cells in densely
collagenized stroma.
Characteristic cleft-like areas spaces, possibly vascular.
IHC: variable actin and CD68
Calcifying Aponeurotic Fibroma

Benign. Primarily in Children. Can recur.
Slow-growing, painless mass on hands or feet attached
to aponeurosis, tendons, or fascia
Variable cellularity throughout lesion.
Plump, bland fibroblasts with dense collagen.
Distinct areas of calcification and cartilage formation.
Infiltrative growth.
Molecular: FN1-EGF fusions
Fibromatosis
Benign (never metastasize), but infiltrative with strong tendency to
recur.
2 Major Divisions:
Superficial: E.g., Palmar, plantar, penile. Small. Slowly-growing. Usu.
older.
Deep (“Desmoid-type”): E.g., Abdominal, mesenteric. More
aggressive. High-recurrence rate (>50%). Involve deep structures.
Usu. younger. Interestingly, microscopic margins do NOT predict
recurrence.
background.
With age, less cellular and more collagen.
Microhemorrhages and scattered chronic inflammation.
IHC: Nuclear β-catenin (more cells with deep than superficial).
Some actin (+)
Molecular: Deep fibromatosis is associated with FAP and mutations in
the APC/β-catenin (CTNNB1) pathway
Inflammatory Myofibroblastic Tumor
Borderline malignancy (tend to recur, rarely metastasize).
Most common sites: Lung, mesentery, omentum.
Any age, but more common in children.
Bland spindled to stellate cells in myxoid to hyalinize
stroma. Can have loose, fascicular, or storiform growth.
Prominent lymphoplasmacytic infiltrate.
Most cells bland, but sometimes large cells with
prominent nucleoli.
IHC: Variable staining with actin/desmin. ALK (+) in ~50%
Molecular: ~50% have ALK gene rearrangements.
Fibrosarcoma (Adult)
“Almost defined out of existence” – Dr. Richard Kempson
(Many tumors previously called fibrosarcoma have been re-
classified as synovial sarcoma, UPS, fibromatosis, or MPNST)
Now a diagnosis of exclusion! Must do work up to exclude
other diagnoses (IHC and FISH).
Uniform spindled cells with fascicular to herringbone growth.
Interwoven collagen fibers.
No specific IHC of molecular.

Can get Fibrosarcomatous transformation of DFSP→ Loses
storiform pattern and CD34 to become herringbone
fibrosarcoma.
Infantile Fibrosarcoma
Malignant. Newborns (congenital) or infants. Usu.

extremities.
Sheets of tightly packed spindled cells with herringbone

appearance. Little pleomorphism. Mitoses present.
Often lymphocytic infiltrate.
Molecular: ETV6-NTRK3 fusions (also seen in cellular

mesoblastic nephroma)
Myxofibrosarcoma Old name: Myxoid Malignant Fibrous Histiocytoma (MFH)
Malignant. Slow-growing mass on extremity
of elderly.
Multinodular growth.
Myxoid background with varying cellularity
(usually low).
Stellate to spindled cells with
hyperchromatic, pleomorphic nuclei with
indistinct pink cytoplasm.
Characteristic curvilinear vessels that the
tumor cells attach to like “melting wax.”
IHC: focal actin
Molecular: Complex karyotype
Low-grade Fibromyxoid Sarcoma Old/alternative name: Hyalinizing Spindle Cell

Tumor with Giant Rosettes
Malignant. Deep soft tissues of extremity of
young to middle-aged adults.
Recur and can have late metastases.
Varying fibrous and myxoid areas, mostly
fibrous though.
Bland spindled cells with small hyperchromatic
nuclei.
Myxoid areas have curvilinear, branching
capillaries.
Can have large collagenous rosettes.
IHC: (+) MUC4, often EMA

Molecular: FUS-CREB3L2 fusions (do FUS FISH)
Sclerosing Epithelioid Fibrosarcoma

Malignant. Deep soft tissue of limbs.
Densely hyalinized stroma with epithelioid cells arranged in

cords and nests.
Cells have scant clear cytoplasm and angulated nuclei.
IHC: (+) MUC4, often EMA
Molecular: Somewhat diverse—many cases have FUS or

EWSR1 and CREB fusions
Nerve Sheath Tumors
Schwannoma
Benign. Often associated with nerve. Usu. adults. Composed entirely of well-differentiated Schwann cells.
Very low risk of transformation.
Usually solitary and sporadic. NF2 associated with bilateral vestibular schwannomas.
Typically encapsulated.
Alternating compact spindle cells (Antoni A) and hypocellular less orderly areas (Antoni B)
Rows of nuclear palisading → Verocay bodies.
Axons not present in lesion→ pushed to periphery. Antoni B
Hyalinized blood vessels and lymphoid aggregates
common.
IHC: Strong, diffuse S100, scattered CD34,
moderate calretinin. Neurofilament highlights
displaced axons at periphery.
Subtypes: Antoni A
“Ancient change”- Degenerative atypia with
large, hyperchromatic nuclei, but no mitoses
Cellular – Exclusively Antoni A areas.
Melanotic – contain melanosomes, so stain with

melanocytic markers. Often epithelioid. Higher
risk of transformation.
Neurofibroma
Benign. Most commonly solitary and sporadic.
Multiple NF is a hallmark of neurofibromatosis type 1 (NF1), also
known as von Recklinghausen disease.
Higher, but still low, risk of transformation.
Can be cutaneous (most common), intraneural, or diffuse.
Plexiform NF→ almost exclusively in NF1; higher risk of MPNST.
Mixture of Schwann cells, perineurial-like cells, fibroblastic cells,
and entrapped axons.
Randomly oriented spindled cells with wavy, hyperchromatic nuclei.
Often hypocellular and variably myxoid
Thin and thick collagen strands (“shredded carrot collagen”)
Entrapped axons are overrun by lesion and scattered throughout.
IHC: Diffuse S100 (+) (but less so than schwannoma). Moderate
CD34. Neurofilament shows entrapped axons within lesion.
Types: Can be pigmented or show ancient change.
Perineurioma
Benign. Can be intraneural or soft tissue. Sporadic.
Spindle cell proliferation with characteristic long,
thin, delicate, bipolar processes.
Wavy/tapering nuclei. Perivascular whorls.
IHC: EMA , Claudin-1, and GLUT-1 (+), Occasional
CD34. S100 (-)
Granular Cell Tumor

Benign neoplasm with neuroectodermal differentiation.
Epithelioid to spindled cells with abundant eosinophilic granular
cytoplasm highlighted by PASd
Full of lysosomes due to inactivating mutations in ATP6AP1 or 2
(makes it so can’t break down lysosomes)→ granular appearance
Stains: (+) S100, CD68, Inhibin, Calretinin
Congenital (Gingival) Granular Cell Tumor (Congenital Epulis):
Although looks similar, S-100 (-), located on gingiva at birth.
Ganglioneuroma
Benign. Usually posterior mediastinum or
retroperitoneum. No immature neuroblastic
element (unlike ganglioneuroblastoma).
Although some likely represent matured
neuroblastoma, it is thought that most are de novo.
Mature ganglion cells in neuromatous stroma
(unmyelinated axons with Schwann cells).
When multiple/diffuse and/or syndrome-related
(MEN 2b, Cowden, and NF1)→ Ganglioneuromatosis
Stains: Schwann cells (+) S100, Ganglion cells (+)

Synaptophysin, neurofilament
Traumatic (Amputation) Neuroma

Non-neoplastic nerve proliferation after
trauma (nerve is growing to try to
reestablish connection).
Haphazard proliferation of nerve fascicles

including axons and perineurial cells.
Damaged nerve often easily identified.
Malignant Peripheral Nerve Sheath Tumor (MPNST)
Malignant. Adults. Frequently in setting of NF1.
Must arise from a peripheral nerve or pre-existing

peripheral nerve sheath tumor or display histologic/IHC
evidence of nerve sheath differentiation.
Variable appearance, can resemble undifferentiated

pleomorphic sarcoma or fibrosarcoma.
Spindled cells arranged in sweeping fascicles.

Densely cellular areas alternate with less cellular areas
giving a “marble-like” effect.
Can have herringbone architecture.
Wavy, buckled nuclei.
Geographic necrosis and/or mitotic activity (often
greater than 10/10 HPFs)
IHC: Patchy S100 and SOX10.

Loss of H3K27me3 expression (associated with worse
prognosis. Not entirely specific—see with SUZ12 and
EED gene inactivation)
Subtypes:
MPNST with rhabdomyoblastic differentiation
(“Malignant triton tumor”)
MPNST with glandular differentiation
Epithelioid MPNST—composed of polygonal, epithelioid

cells. Unique strong, diffuse S100 staining
Other Nerve Sheath Tumors

Nerve Sheath Myxoma: Benign. Superficial, myxoid. Irregular, slow-growing nodules separated by
fibrous bands containing spindled cells in myxoid matrix. S100 (+)
Ectopic Meningioma: Benign. Essentially a meningioma in soft tissue. Whorled architecture. Oval
nuclei. Occasional nuclear pseudoinclusions. IHC: EMA, PR, and SSTR2A (+)
Palisaded encapsulated neuroma (Solitary circumscribed neuroma): Benign. Dermal tumor, often on
head/neck. Lobular with sharply demarcated borders. Composed of axons, Schwann cells, and
perineural fibroblasts.
Perivascular Tumors
Glomus
Benign. Tumor derived from glomus body (specialized AV
anastomosis that regulates heat).
Often red-blue nodules in the deep dermis of extremities.
fingers/toes. Often painful.
Very richly vascular network separating tumor cell nests.

Distinctive cells with round nuclei and eosinophilic cytoplasm.
IHC: Actin (+) other smooth muscle markers variable.
Myopericytoma/Myofibroma
Benign. Exist on a spectrum.
Myofibroma: Usu. Head/neck in first year of life.

Multinodular, well-circumscribed.
Biphasic: 1) immature-appearing plump spindled cells with
staghorn vessels, 2) areas of more mature spindled cells in
bundles and whorls.
Myopericytoma: Superficial mass in adults.
Nodular, well-circumscribed.
Concentric, multilayered growth of spindled cells around
vessels.
Very richly vascular
IHC: Actin (+) other smooth muscle markers variable.
Perivascular Epithelioid Cell Tumor (PEComa)

Benign.
Often areas of epithelioid tumor cells with abundant
granular eosinophilic to clear cytoplasm with round
nuclei.
Associated with vessel walls in radial arrangement.
IHC: Express melanocytic (usu. HMB45, variable MelanA),
and smooth muscle (Actins, desmin, etc..) markers.
A subset of cases are associated with Tuberous Sclerosis.
Can see in many sites/organs.
Includes Angiomyolipoma, Clear cell “sugar” tumor, and
lymphangioleimyomatosis.
Smooth Muscle IHC: SMA, Desmin, H-Caldesmon, Calponin (+)
Leiomyoma
Benign.
Can see commonly in dermis (derived from pilar muscles
and vessels).
Very uncommon in deep soft tissue.
Cytologically bland spindled cells with cigar-shaped

nuclei. Fascicular architecture.
No nuclear atypia. At most very rare mitoses (<1/50 HPF)
Pilar Leiomyoma
Ill-defined, dermal nodule composed of haphazardly
arranged smooth muscle bundles/fascicles
Fascicles often dissect between dermal collagen
Often painful.
Angioleiomyoma
Well-circumscribed neoplasm composed of mature
smooth muscle cells arranged around prominent blood
vessels
Leiomyosarcoma
Malignant. Poor prognosis.
Often in retroperitoneum of adults.
Often arise from veins.
Similar appearance to leiomyoma (fascicular
architecture)
But often notable pleomorphism.
Mitotic activity, often atypical mitoses.
Necrosis.
Molecular: Complex karyotype
EBV-associated Smooth Muscle Tumor

Benign, but patients can get multiple primaries.
Seen in setting of immunodeficiency (e.g., HIV, post-transplant, etc…)
Mostly typical smooth muscle appearance (fascicular architecture,

blunt-ended nuclei). Can see tumor-infiltrating lymphs and more
“round cell” areas.
Molecular/IHC: Need to confirm EBV in tumor with EBER

Skeletal Muscle Tumors IHC: Most specific Myogenin, MyoD1
Also smooth muscle markers (e.g., Desmin, Actin)
Rhabdomyoma
Benign. But location/growth may cause problems (especially in
heart)
Cardiac-type Rhabdomyoma:
Occur in hearts of infants and young children, often in the
setting of Tuberous sclerosis.
Large, polygonal, vacuolated, cleared out, “spider cells”
Adult-type Rhabdomyoma:
Mature skeletal muscle differentiation.
Usu. Head and neck. Often pharynx or tongue.
Large, polygonal cells with abundant granular eosinophilic
cytoplasm. Some spider cells
Unencapsulated, lobular growth.
Fetal-type Rhabdomyoma:
Usu. Head and neck. Any age.
Irregular bundles of immature skeletal muscle.
Myxoid background.
Embryonal Rhabdomyosarcoma
Malignant.
Most common soft tissue sarcoma in kids.
Occasional adult.
Usu. Head/Neck (e.g., nasal, tongue, etc..) or
Genitourinary (e.g., bladder, prostate, etc…)
Resembles embryonic skeletal muscle cells.

Some areas are hypercellular “small round blue cells.”
Other areas maturing with rhabdoid cells with abundant,
eccentric eosinophilic cytoplasm, “tadpole cells,” and
“strap cells” (with cross striations)
Set in myxoid stroma
Botryoid type: Densely cellular layer below epithelial

surface (“cambium layer”) separated by hypocellular
area. Polypoid surface nodules (“grape-like”). Usually
projecting into mucosa-lined spaces (like vagina or nasal
cavity)
Alveolar Rhabdomyosarcoma
Malignant. More aggressive than Embryonal
Rhabdo.
Often adolescents and young adults in deep soft
tissue of extremities and sinuses.
Highly cellular “small round blue cell” tumor.
Monomorphous round nuclei.
Often nest-like arrangement (hence “alveolar”).
Notable absence of strap cells, tadpole cells,
etc…
Molecular: FOXO1 fusions with either PAX3 or
PAX7
IHC: Strong, diffuse Myogenin suggests this Dx

(often patchier in embryonal). Often patchy
neuroendocrine staining.
Pleomorphic Rhabdomyosarcoma
Malignant. Adults. Deep soft tissue.
High-grade cytologically: sheets of large, atypical cells.

Eosinophilic polygonal cells to tadpole-like.
No embryonal or alveolar component. Resembles

heterologous differentiation in carcinosarcomas.
Spindle Cell Rhabdomyosarcoma

Malignant. Likely a variant of embryonal.
Usu. Young boys, esp. paratesticular.
Exclusively spindled cells with cigar-shaped nuclei.
Better prognosis than other Rhabdomyosarcomas.
Sclerosing Rhabdomyosarcoma
Malignant. Usually adults in soft tissue.
Nests of small round blue cells in nests and single file.

Abundantly hyalinized, eosinophilic to basophilic
matrix.
IHC: Of note, MyoD1 is strongly positive, while

Myogenin and desmin are only focal often.
Fibrohistiocytic Tumors
Tenosynovial Giant Cell Tumor
Benign, but can be locally destructive. 4
Mixture of 1) bland mononuclear cells, 2) foamy macrophages, 3)
hemosiderin-laden macrophages, and 4) osteoclast-like giant cells.
Mononuclear cells are spindled to round with reniform/grooved
nuclei. Mitoses common. 2
IHC: Mononuclear cells CD68, CD163 (+), scattered desmin.
Molecular: CSF1 gene rearrangements 1
Localized-type:
L
Discrete, rounded proliferation. Usually occurs in digits. Less

aggressive. Often cure with excision.
Diffuse-type:
Grows in expansive sheets. Often in or around knee. Often
intraarticular. Large. Destructive.
Aka “Pigmented Villonodular Synovitis” (PVNS)
Need to treat more aggressively.
3
Fibrous Histiocytoma
Benign (generally). Neoplasm or Neoplasm-like (some seem to
occur after trauma)
Fibroblastic and histiocytic cells arranged in short fascicles.
Dermatofibroma
In Dermis (most common site by far)
Looks like a “blue haze” in the dermis
Tumors are grossly circumscribed but microscopically have
irregular, often jagged borders Collagen trapping at periphery
Overlying epithelial basilar induction with hyperpigmentation
(may mimic BCC)
Lots of variants: Epithelioid, Cellular, Aneurysmal, etc…
IHC: FXIIIA(+), CD163(+), CD68(+), CD34(-)
“Deep Benign Fibrous Histiocytoma:” If in deep soft tissue.

Very rare.
Plexiform Fibrohistiocytic tumor: Plexiform architecture in

deep soft tissue/dermis
Vascular Tumors Endothelial cells stain with: CD31, ERG, FLI1,
often CD34
Vascular Malformations
Developmental abnormalities (occur during embryogenesis in
utero), that grow with the host. Static. Do not regress.
Arteriovenous Malformation (AVM)
Large, tortuous arteries with fragmented elastic lamina and
associated with thick-walled veins. Variable small vessel
component.
Most common in head/neck and brain.
Venous Malformations (Venous Hemangiomas)
Poorly-circumscribed collection of abnormal veins
Vary in size/proportion.
Often abnormally thick or thin walls for size.
Includes: Cavernous hemangiomas (collection of large, dilated
veins with thin walls)
Cutaneous Capillovenous Malformation
E.g. Telangiectasia. Often diagnosed clinically.
Associated with a variety of conditions (e.g., Osler-Weber-
Rendu)
Intramuscular hemangioma
Small vessels within muscle. Often parallel.
Papillary Endothelial Hyperplasia aka Mason’s Tumor
Intravascular exuberant proliferation of endothelial cells

with fibrin.
Small papillae covered by a single layer of endothelium
with a collagenized fibrin core. No atypia or mitoses.
Papillae can fuse, forming anastomotic channels.
Main importance is that it can mimic angiosarcoma
histologically. However, can be distinguished by exclusively
intravascular growth and lack of mitoses/atypia.
Bacillary Angiomatosis
Pseudo-neoplastic vascular proliferation caused by Bartonella
(Gram-negative bacilli, also causes Cat scratch disease).
Almost exclusively in immunocompromised adults, often AIDs.
Often in skin/soft tissue.
Lobules of capillary-sized vessels with plump endothelium with
clear cytoplasm. Associated neutrophilic infiltrate.
Stains: Warthin-starry highlights organisms
Hemangiomas
Benign vascular neoplasms. Often grow faster than patient.
Categorized by vessels size/appearance.
Lobular Capillary Hemangioma (“Pyogenic granuloma”)

Polypoid, exophytic on skin and mucosal surfaces.
Unclear if truly neoplastic.
Lobular arrangement of small capillaries with larger “feeder”
vessel.
Myxoid stroma with inflammatory cells.
Infantile (Juvenile) Hemangioma

Starts as flat, red mark soon after birth→ grows to look like
“strawberry” over several months → regress over several years.
Multinodular masses fed by single arteriole.
Appearance varies depending on phase.
IHC: Unique expression of GLUT1 (not in other hemangiomas)
Rarer subtypes
Hobnail hemangioma
Anastomosing hemangioma
Spindle cell hemangioma
Epithelioid Hemangioma aka Angiolymphoid hyperplasia with eosinophils

Benign.
Often young adults in superficial head and neck.
Circumscribed, subcutis. Large and deep.
Lobules of capillaries centered around larger vessel.
Endothelial cells are plump (“epithelioid”), projecting
like tombstones into vessels. Round nuclei. Abundant
eosinophilic cytoplasm. Associated inflammatory
infiltrate rich in eosinophils.
Lymphangioma
Benign. Often in kids during the first year of life.
Associated with Turner syndrome (XO).
Thin-walled, dilated lymphatic vessels of different
sizes, lined by flattened endothelium. Frequently
surrounded by lymphoid aggregates.
Contain grossly “milky” lymphatic fluid.
IHC: Endothelium expresses D2-40 and PROX1
(specific for lymphatics). Also CD31.
Kaposiform Hemangioendothelioma
Locally aggressive vascular tumor.
Exclusively in children.
Often associated with Kasabach-Merrit
phenomenon (consumption of
platelets→ thrombocytopenia)
Infiltrate soft tissue in “cannon-ball

fashion.” Different areas have features of
both capillary hemangioma and Kaposi
sarcoma (spindled cells).
Tightly coiled glomeruloid-like areas.
Malignant (but less aggressive than angiosarcoma).
In soft tissue, often angiocentric, expanding wall and obliterating
lumen. Also common in liver.
Cords of epithelioid endothelial cells in myxohyaline stroma.
Eosinophilic cells with vacuoles containing erythrocytes (“Blister
cells”).
IHC: CAMTA1 stain specific
Molecular: recurrent CAMTA1-WWTR1 fusions
Kaposi Sarcoma
Locally aggressive. Often multiple cutaneous lesions
Caused by Human Herpes Virus 8 (HHV8) in all cases.
Can be Classic/Endemic, which are usually indolent, or
associated with immunosuppression (either
iatrogenically for organ transplantation or by AIDs),
which is more aggressive often.
Proliferation of bland spindled cells with slit-like
vascular spaces containing erythrocytes.
Often associated inflammatory infiltrate and hyaline
globules.
IHC: HHV8
Pseudomyogenic Hemangioendothelioma
Rarely metastasize. Often develop additional nodules in
same anatomic region. Often young men on leg.
Infiltrative sheets and fascicles of plump spindled cells.
Abundant brightly eosinophilic cytoplasm (resembling
rhabdomyoblasts, hence the name!). Vesicular nuclei.
IHC: CK AE1/AE3 (+), ERG(+), FOSB (+). CD31 (+/-),
INI1 intact.
Molecular: SERPINE1 and FOSB genes fusion
Atypical Vascular Lesion

Benign. Occur in irradiated skin (often of breast).
Often small/multiple.
Irregularly-shaped thin-walled vessels with branching and
anastomosing growth. Lined by a single layer of endothelium
with some hobnailing and hyperchromasia.
NO endothelial cell multilayering or true cytologic atypia
IHC/Molecular: No MYC overexpression/amplification.
Angiosarcoma

vessels, while other areas may show solid sheets
of high-grade cells.
Can be epithelioid or spindled.

necrosis, endothelial cells piling up, and mitotic
figures (although mitoses can be seen in some
benign tumors)
Grade does not predict prognosis (all aggressive)
Post-radiation angiosarcoma of the breast:

Occurs after radiation (usu. ~5yrs).
High-level amplification of MYC (by IHC or FISH) is
a hallmark of this lesion.
Tumors of Uncertain Differentiation
Myxoma
Benign. Adults.
Uniform, cytologically bland, small spindled to stellate cells in
abundant myxoid stroma.
Can show cystic change and/or have more slightly more cellular
areas. Grossly look like jelly.
Notably: No atypia or mitoses (otherwise consider
myxofibrosarcoma)
Intramuscular:
Within muscle. Frequent GNAS mutations.
Intramuscular myxoma + fibrous dysplasia = Mazabraud
syndrome (both have GNAS mutations)
Juxta-articular:
Vicinity of a large joint (usu. Knee)
Lacks GNAS mutations.
Deep (“Aggressive”) Angiomyxoma

Benign (despite name!), but frequent recurrences
Adult women in pelvicoperineal region.
Small spindled to stellate cells in a loosely collagenized,
myxoid stroma. Scattered vessels of varying size.
Scant eosinophilic cytoplasm.
Larger spindled myoid cells congregate around larger
vessels and nerves.
IHC: ER, PR (+), Variable desmin and actin.

Molecular: HMGA2 rearrangements frequently.
Extrarenal Rhabdoid Tumor

Malignant. Very aggressive! Mainly infants and children.
Characteristic “rhabdoid” cells (Large, round/polygonal
cells with abundant, eccentric, glassy eosinophilic
cytoplasmic inclusions and vesicular nuclei with prominent
nucleoli)
Morphologically/genetically identical to Rhabdoid tumors
in kidney and brain of kids.
IHC/Molecular: SMARCB1 (INI1) loss/inactivation
CAM5.2 (+) in inclusions.
Ossifying Fibromyxoid Tumor
Usually benign with potential with recurrence.
Lobules of uniform, monomorphous round to
spindled cells arranged in cords surrounded by
fibromyxoid stroma.
Circumscribed mass with peripheral zones of
metaplastic bone.
IHC: S100 (+), Desmin (+/-)
Molecular: PHF1 rearrangements
Angiomatoid Fibrous Histiocytoma

Indolent with very rare recurrence. Most commonly young.
Often pericapsular cuffing of lymphocytes (mimicking a lymph node)

Nodules of spindled/histiocytoid cells with syncytial growth.
Pseudoangiomatoid spaces full of blood. Thick fibrous capsule.
IHC: Variable desmin and EMA.
Molecular: EWSR1-CREB1 fusions.
Ectopic Hamartomatous Thymoma

Benign. Exclusively in the lower neck region. Often adults.
Despite name, no evidence of thymic origin/differentiation.
Haphazard blending of spindle cells, epithelial islands and
adipocytes.
Some spindled cells show “lattice-like” growth. Islands of often
squamous epithelium blend with spindled cells.
IHC: Epithelium stains with keratins. Plump spindled cells express
actin. Delicate spindled cells express CD34.
Phosphaturic Mesenchymal Tumor

Most tumors are benign (but cause significant side-effects!).
Produce FGF23 → causes tumor-induced osteomalacia by
inhibiting renal proximal tubule phosphate reuptake.
Bland spindled to stellate cells with produce unusual

hyalinized “smudgy” matrix with “grungy” or flocculent
calcifications.
FGF23 can be demonstrated by testing blood or by IHC.

Clear Cell Sarcoma of Soft Tissue aka Malignant Melanoma of Soft Parts
Malignant. Typically young adults.
Characteristic nested growth with dividing collagenous
bands.
Epithelioid (mostly) to spindled cells with palely eosinophilic
to amphophilic (despite name) with vesicular nuclei and
prominent nucleoli. Scattered multinucleated giant cells.
IHC: Expresses melanocytic markers (S100, HMB45, MITF,

etc..)
Molecular: EWSR1-ATF1 fusions
Extraskeletal Myxoid Chondrosarcoma

Malignant. Prolonged survival, but frequent, metastases.
Despite name, no overt cartilaginous differentiation!
Abundant myxoid matrix with cords, clusters, networks, and
nests of cells with modest amounts of eosinophilic cytoplasm
and round/oval nuclei.
“AT&T tumor”→ “reach out and touch someone” → cells are
often reaching out to touch each other.
Molecular: NR4A3 fusions, often with EWSR1 or TAF15
Pleomorphic Hyalinizing Angiectatic Tumor/ Think: PHAT

Hemosiderotic Fibrolipomatous Tumor
Malignant. Usually adults in soft tissue. Often on foot.
PHAT:
Prominent thin-walled ectatic blood vessels lined by fibrin.
Embedded in spindled to pleomorphic cells with
intranuclear inclusions and fine hemosiderin granules.
Hemosiderotic Fibrolipomatous Tumor:

Thought to represent early PHAT. Can be by itself or at
periphery of PHAT.
Adipocytes with admixed hemosiderin-laden spindled
cells, hemosiderin-laden macrophages, and scattered
inflammation.
IHC: CD34 (+)
Molecular: Both have recurrent TGFBR3 and/or MGEA5

rearrangements
Synovial Sarcoma
Malignant. Usually young adults.
Often soft tissue, but also common in Thorax and
Head/Neck.
Monophasic SS→ Just spindled component.
Biphasic SS→ Spindled and epithelioid component.
Fairly uniform spindled cells with relatively little

cytoplasm.
Ovoid, “stubby,” nuclei with hyperchromatic granular
chromatin and small nucleoli. Can see “Stag-horn”
vessels.
Epithelial cells arranged in nests and glands with
paler cytoplasm and vesicular nuclei.
IHC: Patchy EMA and CK (particularly strong in
epithelial areas). Usu. CD99 (+). TLE-1 (+)
Molecular: SS18-SSX gene fusions t(X;18)
Epithelioid Sarcoma
Malignant. Often youngish adults.
Classic/conventional type:
Cellular nodules of epithelioid to spindled cells with central
degeneration/necrosis→ looks vaguely granulomatous.
Vesicular chromatin and eosinophilic cytoplasm.
Proximal type:
Multinodular and sheet-like growth of large pleomorphic cells large
vesicular nuclei and prominent nucleoli. Often Rhabdoid-appearing.
IHC: INI1 loss; Cytokeratin/EMA and CD34 (+)
Molecular: Complex, but SMARCB1 (INI1) deletions/loss.
Alveolar Soft Part Sarcoma

Malignant. Often young adults.
Organoid nests of large, uniform, epithelioid cells with
abundant, eosinophilic, granular cytoplasm. Round
nuclei with prominent nucleoli.
PAS demonstrates rhomboid or rod-shaped
intracytoplasmic inclusions.
IHC: TFE3 (+), S100 and Desmin (-/+)
Molecular: ASPSCR1-TFE3 Fusion

Ewing Sarcoma
Malignant. Variable neuroectodermal differentiation.
Often arises in the bone of young (but can see in many
organs; Chest wall = Askin tumor).
Usually uniform, small, round, blue cells with sheet-like
to lobular, growth pattern with variable necrosis
IHC: Strong, membranous CD99 staining (Sensitive, but

not specific staining)
Molecular: EWSR1 fusion (with FLI-1 or ERG) t(11;22)
Can see pseudorossettes
CIC-rearranged Sarcomas
Malignant. More aggressive the Ewing.
Often young adults in soft tissue.
Solid proliferation of small round cells (like

Ewing sarcoma).
Scant eosinophilic to clear cytoplasm.
Geographic necrosis usually present.
IHC: WT1 (+), variable CD99
Molecular: CIC-DUX4 fusions
BCOR-rearranged Sarcomas
Malignant. Outcome similar to Ewing.
Often in bone or soft tissue of young.
Solid proliferation of mostly small round cells with

monomorphic round nuclei, fine chromatin, and
delicate capillary network.
Sometimes partially spindled.
Molecular: BCOR fusion with either CCNB3 or MAML3

or a BCOR internal tandem duplication.
IHC: SATB2
Solitary Fibrous Tumor (“SFT”) Old name: Hemangiopericytoma
(referred to cellular tumors on a spectrum with SFT)
Usually benign.
Adults in deep soft tissue or serosal surfaces (classically
lung/pleura).
“Patternless pattern” of varying cellularity of bland

spindled cells with varying amounts of collagenized
stroma.
branching vessels).
Factors associated with malignant behavior:

Numerous mitoses (esp. >4/10 HPF), Large size (esp. >15
cm), and tumor necrosis.
Intimal Sarcoma
Malignant.
Arises in large blood vessels of systemic and pulmonary circulation. Characteristic predominantly
intraluminal growth with obstruction of blood flow and seeding tumor emboli.
Mild to severely pleomorphic spindled cells with necrosis, nuclear pleomorphism, and mitoses. Can have
myxoid or fascicular areas.
IHC: MDM2 (+)
Molecular: Amplification of MDM2/CDK4 (like in ALT/WDL)
Undifferentiated Sarcoma
A sarcoma with no identifiable line of differentiation.
Heterogeneous group and diagnosis of exclusion.
Subclassify based on histologic appearance.
Undifferentiated Pleomorphic Sarcoma

(aka Malignant Fibrous Histiocytoma (MFH)
Wildly pleomorphic cells.
Complex karyotypes
Undifferentiated Spindle Cell Sarcoma
Undifferentiated Round Cell Sarcoma
Undifferentiated Epithelioid Sarcoma
Pattern-Based Approach Modified from/inspired by: “Practical Soft Tissue Pathology”
by Jason Hornick
General Comments: Although a pattern-based approach is very useful, in many cases you might have a
good idea of the Dx via “instant pattern recognition.” Nevertheless, it can be helpful to judiciously
consider mimickers and other diagnoses based on a pattern-based approach.
Myxoid IHC to consider: S100, Desmin, CK AE1/AE3
Myxoma Low-grad fibromyxoid sarcoma

Neurofibroma Myoepithelioma
Perineurioma Myoepithelial carcinoma
Neurothekeoma Myxoinflammatory fibroblastic sarcoma
Spindle cell lipoma Aggressive angiomyxoma
Nodular fasciitis Chordoma
Ossifying fibromyxoid tumor
Myxoid liposarcoma
Myxofibrosarcoma
Extraskeletal myxoid chondrosarcoma
Note: Some people prefer SOX10 over S100
Pleomorphic IHC to consider: S100, Desmin, CD45, CK AE1/AE3, MDM2, ERG
Undifferentiated pleomorphic sarcoma Extraskeletal osteosarcoma

Pleomorphic leiomyosarcoma Pleomorphic fibroma
Pleomorphic liposarcoma Pleomorphic dermal sarcoma
Pleomorphic rhabdomyosarcoma Atypical fibroxanthoma
Dedifferentiated liposarcoma Schwannoma/Neurofibroma with ancient change
Myxoinflammatory fibroblastic sarcoma Metastatic carcinoma
Pleomorphic angiectatic tumor
Myxofibrosarcoma
Angiosarcoma
Round cell IHC to consider: S100, Desmin, CK AE1/AE3, CD45, CD99, TdT, WT-1, Synaptophysin,
Ewing sarcoma BCOR-rearranged sarcomas

Alveolar rhabdomyosarcoma Lymphoma/Leukemia
Round cell liposarcoma Wilm’s tumor
Desmoplastic small round cell tumor Neuroblastoma
Synovial sarcoma
Mesenchymal chondrosarcoma
CIC-rearranged sarcomas
Spindled Cells IHC to consider: S100, Desmin, SMA, CK AE1/AE3, p40, β-catenin,
MUC4, CD34, CD31, CD117
Nodular fasciitis Low-grade fibroblastic sarcoma
Inflammatory myofibroblastic tumor Embryonal/Spindled rhabdomyosarcoma
Myofibroma/myopericytoma Kaposi sarcoma
Fibrous hamartoma of infancy Angiosarcoma
Calcifying aponeurotic fibroma Fibrous histiocytoma
Fibromatosis Dedifferentiated liposarcoma
Schwannoma Follicular dendritic cell sarcoma
Neurofibroma Solitary fibrous tumor
Perineurioma Aggressive angiomyxoma
Ganglioneuroma Myxofibrosarcoma
Spindle cell lipoma Fibroma (several kinds)
Leiomyoma Myofibroblastoma (mammary-type)
Leiomyosarcoma Hemosiderotic fibrolipomatous tumor
GIST
MPNST
Synovial sarcoma
Biphenotypic sinonsasal sarcoma
DFSP
Epithelioid IHC to consider: S100, Desmin, CD45, CK AE1/AE3, ERG, CD68,

INI1,
Epithelioid schwannoma Clear cell sarcoma
Epithelioid hemangioma Alveolar soft part sarcoma
Epithelioid sarcoma Ossifying fibromyxoid tumor
Extrarenal rhabdoid tumor Granular cell tumor
Epithelioid MPNST Juvenile xanthogranuloma
Tenosynovial giant cell tumor Glomus tumor
Myoepithelioma/carcinoma Epithelioid angiosarcoma
GIST Metastatic carcinoma
PEComa Metastatic melanoma
Meningioma
Biphasic IHC to consider: S100, CK AE1/AE3, MDM2, SMA, H3K27me3
Carcinosarcoma
Biphasic synovial sarcoma
MPNST (with heterologous differentiation)
Ectopic hamartomatous thymoma
Dedifferentiated liposarcoma
Myoepithelioma/carcinoma
Tumor Behavior “Beyond Benign and Malignant”
Soft tissue tumors can have varied behavior that often exits more on a spectrum than carcinomas
making specific subtyping (if possible) of considerable clinical importance. While some tumors (e.g.,
fibromatosis) are benign (meaning that they do not metastasize), they can nevertheless be locally
destructive and recurrent.
For sarcomas, which are by definition malignant, histologic type alone often does not provide sufficient
information for predicting clinical behavior and treatment planning. As such, the tumors must also be
graded, most often using the French Federation of Cancer Centers Sarcoma Group (FNCLCC) system.
French Grading System (FNCLCC) Histologic Type Score

Tumor Differentiation ALT/WDL 1
Score 1 Sarcomas closely resemble normal adult tissue Myxoid liposarcoma 2

Round cell liposarcoma 3
Score 2 Sarcomas for which histologic typing is certain
Pleomorphic liposarcoma 3
(e.g., myxoid liposarcoma)
Dedifferentiated liposarcoma 3
Score 3 Embryonal or undifferentiated sarcomas,
sarcomas of doubtful subtype Fibrosarcoma 2
Mitotic Count (per 40x field) Myxofibrosarcoma 2
Score 1 0-9 mitoses per 10 HPF Undifferentiated Pleomorphic Sarcoma 3

Well-differentiated leiomyosarcoma 1
Score 2 10-19 mitoses per 10 HPF
Conventional leiomyosarcoma 2
Score 3 ≥20 mitoses per 10 HPF
Poorly-differentiated leiomyosarcoma 3
Tumor Necrosis
Low-grade fibromyxoid sarcoma 3
Score 0 No necrosis
Sclerosing epithelioid sarcoma 2
Score 1 <50% necrosis
Synovial sarcoma 3
Score 2 ≥50% N
DFSP 1
Pleomorphic rhabdomyosarcoma 3
Mesenchymal chondrosarcoma 3
Extra-skeletal osteosarcoma 3
Total Score Grade
Ewing sarcoma 3
2-3 Grade 1 Malignant rhabdoid tumor 3
4-5 Grade 2 Undifferentiated sarcoma, NOS 3
The following tumors are not graded: GIST, alveolar

6-8 Grade 3 and embryonal rhabdomyosarcoma, MPNST,
angiosarcoma, extraskeletal myxoid
chondrosarcoma, clear cell sarcoma, alveolar soft
part sarcoma, and epithelioid sarcoma.
Bone Tumors
Normal Bone
Two main types of bone organization:
(highlighted by polarization)
Woven bone (Immature): collagen fibers are haphazardly arranged
feltwork. Formed during ossification and rapid bone growth/repair
(e.g, fracture callus). Relatively hypercellular with large cells.
Lamellar bone (Mature): collagen fibers are organized in parallel
arrays. Formed through gradual remodeling of woven bone. In
adults, almost all bone is lamellar. Hypocellular with small cells.
Two main types of mature lamellar bone architecture:

Cortical (Compact) Bone: Dense lamellar bone with Haversian
canals surrounded by concentric lamellar units.
Trabecular (Cancellous) Bone: Connecting plates of lamellar bone
Tumor Bone: Typically, Woven bone. Mineralized or unmineralized.
Is that bone? It can sometimes be challenging to differentiate

osteoid (unmineralized bone) from other collagen and extracellular
material.
Some helpful hints:
- “Cement lines” (reversal lines)→ thin, dark, linear lines are seen
in osteoid, but not other substances (specific, but not sensitive)
- SATB2→Expression supports osteoblastic differentiation
Epidemiology
Overall primary clinically significant bone tumors are rare.
Benign, incidental benign tumors (like non-ossifying fibroma) are relatively common, but are often
clinically insignificant.
Primary Bone Sarcomas have a Bimodal distribution:
First peak in second decade (teens with actively growing skeleton): 1) Osteosarcoma, 2) Ewing
Sarcoma
Second peak after age 60: 1) Chondrosarcoma, 2) Osteosarcoma
Although varies by tumor, for most, the most common location is near the knee, which is the site of
the fastest growing growth plate.
Although most often de novo, conditions that predispose to osteosarcomas include: Radiation,
Paget’s Disease, Chronic Osteomyelitis, Bone infarcts, and prosthetic joints.
Presenting symptoms: Often pain, which is classically worse at night, and a mass
Can have pathologic fractures, swelling, tenderness,
Anatomic Sites Radiology is Essential for bone tumors!
<30 years old >30 years old
Fibrous
Dysplasia
Metastases
Myeloma
Ewing Lymphoma
LCH
Diaphysis
Leukemia Osteoid osteoma
Non-ossifying Fibroma
ABC
Osteochondroma
Enchondroma
Chondrosarcoma
Metaphysis
Enchondroma
Simple cyst
Giant Cell
Tumor of
Bone
Epiphysis
Infection Chondroblastoma Infection
Skeleton < 30 years > 30 years

Axial Osteoblastoma Metastases
(skull, vertebrae, pelvis) Langerhans cell histiocytosis Plasmacytoma
ABC Hemangioma
Hemangioma Chordoma
Appendicular Most tumors. Most tumors,
(arms and legs) Osteosarcoma, Ewing sarcoma Chondrosarcoma,
Osteosarcoma
Acral Enchondroma Enchondroma
(hands and feet)
Classic Specific Locations:

Anterior Cortex of Tibia→ Adamantinoma and Osteofibrous dysplasia
Posterior Cortex of Distal Femur→ Parosteal Osteosarcoma
Clivus, Vertebral bodies, Sacrum→ Chordoma
Posterior Elements of Spine→ Osteoblastoma
Osteogenic Tumors generating neoplastic bone.
Wondering if something you’re seeing is true bone? SATB2 stains osteoblasts and can be helpful
Osteoid Osteoma
Benign. Often in the cortex of long bones.
<2 cm central nidus composed of microtrabecular woven
bone rimmed by plump, bland osteoblasts in vascularized
stroma. Often surrounded by sclerosis with circumscribed,
abrupt transition to normal bone at edge of nidus.
NO nuclear pleomorphism or cartilage
FOS gene rearrangements.
Often recognized radiographically and ablated.

Classically present with night pain relieved by NSAIDs.
Osteoblastoma
Benign. Often in the spine, particularly the neural arch.
Morphologically similar to osteoid osteoma (interconnecting
delicate woven bone rimmed by a layer of plump osteoblasts)
But have growth potential and generally >2 cm.
Well-circumscribed without destructive invasion of bone (if
see infiltration, consider osteoblastoma-like osteosarcoma)
FOS gene rearrangements.
Often recognized radiographically and ablated also.
Often present with pain/nerve compression symptoms, but
not relieved by NSAIDs
Osteoma
Benign. Usually on face or jaw bones (sites of
membranous ossification)
Often on the surface.
Composed of lamellar/cortical-type bone
Osteoblasts are inconspicuous
When develops in medullary cavity→ use the
term “Bone Island”
Multiple osteomas→ seen in Gardner’s
syndrome (subset of FAP)
Generally require no treatment unless
symptomatic
Conventional Osteosarcoma
High-grade sarcoma in which the tumor cells produce bone. Most common primary bone sarcoma.
Most commonly metaphysis of long bones near the knee (site of most proliferative growth plates).
Imaging shows permeative bone destruction with fluffy immature mineralization and tumor ossification.
Cortical disruption→ Periosteal response→ sunburst-like production of new bone→ “Codman’s Triangle”
Histologic spectrum, but requires neoplastic bone
formation (any amount is sufficient for Dx)
Bone is often intimately associated with the tumor
cells and is woven with disorganized trabeculae
Bone matrix is eosinophilic (on H&E), often with
purple mineralized “cement lines”
Infiltrative growth→ replacing marrow space and
eroding pre-existing bone
Often high-grade cytologic atypia, but tumor cells
“normalize” (become less pleomorphic) when they
are surrounded by bone matrix
Brisk mitotic activity. Atypical mitoses often present.
May have varying components including cartilaginous (“Chondroblastic osteosarcoma”), spindled cells
(“Fiboblastic osteosarcoma”), Giant cells-rich, etc… → may only see this component on a small biopsy!
IHC: SATB2 can help identify osteoblasts. Frequently express EMA, cytokeratins, CD99, S100, and
actins.
Molecular: Chromosomal instability (highly complex aneuploidy) due to chromothripsis and
chromoplexy
Frequent TP53 and RB1 mutations→ Increased risk in Li-Fraumeni and Hereditary retinoblastoma
Sometimes MDM2 amplifications→ indicates likely arose from prior low-grade central osteosarcoma.
Aggressive tumors with local growth and rapid hematogenous dissemination, most frequently to the
lungs. Often treated with pre-operative chemo→ Resection → post-operative chemo
Histologic response to neoadjuvant chemotherapy is one of the most important prognosticators of
survival (good response is >90% necrosis)→ requires careful/extensive grossing and sampling
Low-grade Central Osteosarcoma

Low-grade malignant. Arises in the intramedullary cavity,
most often in the metaphysis of long bones at the knee.
Moderately cellular fascicles of spindled cells with only
mild nuclear atypia with admixed (usually woven)
neoplastic bone, which is composed of long and thick
boney trabeculae, often in parallel arrangement.
Permeates host bone.
MDM2 amplifications.
Good prognosis if widely resected, but can dedifferentiate
into conventional osteosarcoma.
Telangiectatic Osteosarcoma
Closely resembles aneurysmal bone cyst (ABC)
Similar distribution to conventional osteosarcoma.
Blood-filled or empty cystic spaces separated by fibrous
septae of variable thickness with pleomorphic cells with
significant nuclear atypia and hyperchromasia and
osteoclast-like giant cells
Frequent atypical mitoses. Often infiltrative.

Osteoid production is often focal (may be absent on biopsy).
Parosteal osteosarcoma
Parosteal location. Often posterior metaphysis of distal femur.
Exophytic, lobular mass on bone surface.
Low-grade spindle cell tumor with woven bone formation
Often hypocellular with minimal atypia and mitoses
Bone is often arranged in parallel, ±osteoblastic rimming
~1/2 contain cartilage (either nodules or cap)
Molecular: MDM2 amplifications (from supernumerary ring
chromosomes) (just like low-grade central osteosarcoma!)
Excellent prognosis. Can dedifferentiate.
Periosteal osteosarcoma
Malignant, predominantly chondroblastic, intermediate-grade
bone-forming sarcoma arising from the bone surface, usually
under periosteum.
Often diaphysis of long bones, especially femur and tibia.
Most of the tumor is composed of irregular lobules of cartilage
with cytologic atypia. Intervening bands of primitive sarcoma
show bone formation.
Better prognosis than conventional osteosarcoma.
Other Osteosarcoma Variants

Small Cell osteosarcoma— a subtype of conventional
osteosarcoma with small round blue cell morphology
with focal neoplastic bone formation. Tumor cells
have scant cytoplasm and fine to course chromatin.
Similar distribution to conventional osteosarcoma.
High-grade surface osteosarcoma—histologically

high-grade osteosarcoma, but arising on the surface of
the bone, without substantial intraosseous
involvement.
Chondroblastic Tumors with cartilage production.
Cartilage stains with S100.
Osteochondroma
Benign. Cartilage cap with growth plate-like architecture
and an underlying stalk with medullary and cortical bone.
Continuous with medullary cavity and cortex of bone.
No significant nuclear atypia or mitotic activity.
Often on the metaphysis of long bones near the knee.
Molecular: Biallelic inactivation of EXT1 or EXT2
Germline mutations in EXT1 are present in hereditary
multiple osteochondroma syndrome
Enchondroma
Benign, relatively common. Hyaline cartilage neoplasm arising within the
medullary cavity. Most frequently in short tubular bones of the hands,
often in the metaphysis.
Abundant hyaline cartilaginous matrix. Hypocellular. Chondrocytes in
sharp-edged lacunae with bland lymphocyte-like nuclei.
No significant cytologic atypia, mitoses, cortical invasion (destroying or
entrapping cortical bone), or soft tissue extension (otherwise consider
chondrosarcoma)
In small bones of hand and enchondromatosis, there is some leniency and
tumors can have increased cellularity, myxoid cartilage, mild atypia (e.g.,
small nucleoli), and binucleation.
Molecular: Frequent IDH1 and IDH2 mutations
Endchondromatosis (includes Ollier disease and Maffucci syndrome)→
germline IDH1 or IDH2 mutations→ multiple symptomatic enchondromas
Often treated with curettage if symptomatic.
Bizarre parosteal osteochondromatous proliferation “Nora Lesion”

Benign surface lesion composed of spindled
cells, cartilage, and bone.
Most common in small bones of the hand and
feet, often phalanges. Not contiguous with
medullary cavity
Surrounded by cartilaginous cap with central
trabecular bone (via endochondral ossification)
and hypervascular bland spindled cells.
Between the cartilage and bone is characteristic
“Blue bone” with basophilia
The chondrocytes can show moderate atypia
Unclear if it is a reactive process or neoplasm.
Synovial chondromatosis
Locally aggressive. Involves large joints, most commonly the
knee.
Multiple hyaline cartilage nodules within synovium or loose
in joint space. Chondrocytes cluster together in groups.
Minimal atypia.
If significant atypia, loss of chondrocyte clustering, bone
invasion, lots of mitoses→ malignant
Molecular: FN1-ACVR2A fusions
Chondromyxoid fibroma
Benign. Occurs in many sites, but often long bones
near the knee.
Lobulated lesion with sharp margins and zonal
architecture.
Chondroid and stellate cells embedded in a chondroid
to myxoid matrix in the center of each lobule.
Peripheral spindled cells and admixed giant cells.
IHC: Diffuse S100 positivity (like all cartilage)
Molecular: GRM1 fusions/upregulation
Chondroblastoma
Benign. Involve the epiphysis of long bones, most
commonly the femur.
Sheets of ovoid to polygonal cells with a single grooved
nucleus and eosinophilic cytoplasm and interspersed
multinucleated giant cells.
Characteristic “lace-like” or “chicken wire-like”
calcification
Islands of eosinophilic chondroid matrix.
Can have cystic degeneration, nuclear atypia, and mitoses.
Molecular: H3.3 p.Lys36Met substitution (same as giant
cell tumor of bone, can detect with IHC or molecular)
Subungual exostosis
Benign osteocartilaginous surface lesion in the distal
pharyngeal bone underneath the nail bed. Most often big toe.
Often young adults.
Sometimes cartilage is mildly atypical with mitoses.
No continuity with medullary cavity (as is seen in
osteochondromas)
Recurrent cytogenetic breakpoint resulting in increased IRS4
expression.
Chondrosarcoma
Atypical Cartilaginous Tumor/Chondrosarcoma Grade 1:
Locally aggressive and can progress, but don’t metastasize
Appendicular skeleton (easier to resect)→ ACT
Axial skeleton (harder to resect)→ Chondrosarcoma, grade 1
Abundant cartilaginous matrix (usually hyaline, but sometimes
partially myxoid), with lobular growth and entrapment of pre-
existing bone. Increased cellularity, but bland condensed nuclei.
Binucleated cells common. No significant nuclear atypia or
mitotic activity.
Chondrosarcoma Grade 2/3:
Malignant with metastatic potential.
Same as above, but increased cellularity, more myxoid matrix,
and mitoses. Grade as below. No osteoid production by tumor
cells.
Grade:
Molecular: ~1/2 have IDH1 or 2
mutations (likely progressed from 1 2 3
enchondroma). Higher grade tumors
may also have TP53, RB1, and CDKN2A
mutations.
Central: arising in the medulla of the bone
Central Primary: no pre-existing precursor
Central Secondary: arising from an
enchondroma
Secondary Peripheral: arising in the pre-
existing cartilaginous cap of an
osteochondroma (cap > 2 cm)
Grade Cellularity Cytology

Radiographically,
lobulations looks 1 Hypocellular Nuclei are small and dark with fine chromatin (lymphocyte-like)
like “Popcorn”
calcifications 2 More cellular Nuclei are larger, irregular, and have coarse chromatin; mitoses
infrequent
3 Hypercellular Severe pleomorphism and mitoses. Cells often more spindled.
Dedifferentiated chondrosarcoma
Conventional chondrosarcoma with an abrupt transition
to a high-grade non-cartilaginous sarcoma.
Most commonly located in the femur of elderly.
Molecular: Complex karyotypes with frequent IDH1/2 and
TP53 mutations.
Very poor prognosis.
Mesenchymal Chondrosarcoma
Biphasic tumor with 1)Islands of organized 1
hyaline cartilage in 2)an undifferentiated
component with high N:C ratios.
Frequent staghorn vessels (3).
Varied locations, but often craniofacial
Molecular: HEY1-NCOA2 fusions.

3
Aggressive behavior. 2
Clear cell chondrosarcoma

Clear cells with abundant cytoplasm, centrally placed
nuclei, and distinct cell membranes.
Woven bone and osteoclast-like giant cells
Minimal atypia and low mitotic activity
~1/2 of cases have a conventional low-grade
chondrosarcoma component
Frequently in the epiphysis, particularly the femoral
head.
IHC: Strong S100 in clear cells.
Low-grade malignant.
Periosteal chondrosarcoma
Cartilaginous tumor arising on the surface of a bone
in close association with the periosteum with either:
1) Invasion of the underlying bone, or
2) Size > 5.0 cm
Located on the surface of long tubular bones, usually

the distal femur.
Molecular: Comparatively low IDH1/2 mutation rate
Low metastatic rate, grading not predictive.
Vs. “Periosteal Chondroma”

Well-marginated, lobulated cartilaginous tumor arising on the bone surface, with elevation of the
periosteum and erosion, but no invasion of the underlying bone cortex. Low to moderate cellularity, and
relatively uniform chondrocytes. Usually < 5 cm. Also frequently has IDH1 mutations. Benign and treated
with curettage.
Hematopoietic Neoplasms
Plasma cell neoplasms
Sheets of neoplastic plasma cells.
Often characteristic morphology with perinuclear hof and
“soccer ball” nuclei. Plasma cells may be small and mature,
or large, immature, and atypical.
May see associated amyloid or crystal-storing histiocytosis.
IHC/Flow cytometry demonstrates CD138+, CD45 – or dim,

with monotypic Ig light chain expression.
If solitary→ Solitary plasmacytoma
If systemic→ often “CRAB” symptoms (hyperCalcemia, Renal insufficiency, Anemia, Bone involvement)
→ Plasma cell myeloma
Leukemia/Lymphoma
Always a consideration for cellular tumors with scant
cytoplasm and no significant extracellular matrix.
May be primary to the bone or bone involvement by a
systemic process.
Consider sending for flow cytometry if a sample is received
for frozen section or FNA adequacy and/or doing multiple
heme stains.
Consider at least:
CD45 (“LCA,” a good broad marker)
TdT and/or CD34 (for lymphoblastic leukemias)
CD138 (for plasmacytoid things)
Langerhans cell histiocytosis “LCH”

Clonal neoplasm resembling Langerhans cells:
Characteristic grooved or folded nuclei
Moderate amounts of eosinophilic cytoplasm
Lots of associated eosinophils, histiocytes, and giant cells.
No prominent nucleoli or significant atypia
IHC: cells express S100, CD1a, Langerin (CD207), and CD68
Molecular: MAPK pathway activation (e.g., BRAF V600E)
If “single system”→ often impacts skull
If “multisystem”→ can impact many bones and organs
Most common in kids.
Prognosis depends on stage, but is generally good (and

excellent in single system disease)
Erdheim-Chester Disease
A clonal systemic histiocytosis with inflammation and fibrosis.
Infiltration by foamy, lipid-laden histiocytes.
Variable amounts of Touton giant cells, small lymphocytes,
and other inflammatory cells.
Fibrosis is usually present and can be extensive.
Usually involves long bones, but multisystem disease.
IHC: Foamy histiocytes stain with CD68, CD163, and CD14
Molecular: Activations of MAPK pathway (e.g., BRAF)
Rosai-Dorfman Disease
Histiocytic proliferation composed of large, S100-positive
histiocytes with emperipolesis.
Cells have abundant eosinophilic to foamy cytoplasm.
Round to reniform nuclei with vesicular chromatin.
Associated fibrosis and inflammatory cells.
IHC: (+) S100, (-)CD1a, Langerin
Molecular: Probably RAS/MAPK pathway activation
Good prognosis.
Osteoclastic Giant Cell Rich Tumors

Non-Ossifying Fibroma
Benign, generally self-limited.
Storiform proliferation of plump spindled cells with
intermingled giant cells.
Scattered hemosiderophages and foamy macrophages.
Skeletally immature patients in cortex of metaphysis in
long bones, often near knee.
Molecular: KRAS or FGFR1 mutations→ MAPK pathway
activation
Aneurysmal Bone Cyst

Benign. Multiloculated blood-filled cystic spaces.
Cyst wall is composed of fibroblasts, osteoclast-like giant cells,
hemosiderin pigment, and new bone formation. Well-circumscribed.
Mitoses are common. Can be solid.
Most often in the metaphysis of long bones and posterior vertebrae

Most common in kids, but all ages can get.
Molecular: USP6 gene rearrangements (same as nodular fasciitis)

Giant Cell Tumor of Bone
Locally aggressive with rare metastases (often to lung)
Proliferation of numerous (reactive) large osteoclasts together
with a mononuclear neoplastic component without atypia.
Generally skeletally mature individuals, involving the epiphysis
Mononuclear cells have oval nuclei with even chromatin and ill-
defined cytoplasm. Often associated hemorrhage, hemosiderin,
and macrophages.
Molecular: H3.3 gene mutations, most commonly H3.3
pGly34Trp (chondrosarcoma has same mutation, but is usually
in the epiphysis of kids)
IHC: (+)H3.3 pGly34Trp, often p63,
Can be treated with the RANK ligand inhibitor Denosumab→
giant cells disappear→ bland spindled cells with new bone
deposition
Malignant Giant Cell Tumor of Bone:
Uncommon. Sarcomatous transformation of pre-existing Giant cell tumor. Can resemble any high-grade
sarcoma. Often retained H3.3 mutation.
Also Chondroblastoma Some osteosarcomas Paget’s disease
Fibrogenic Tumors
Desmoplastic Fibroma
Locally aggressive proliferation of spindled cells resembling
desmoid-type fibromatosis.
Infiltrative growth. Low cellularity proliferation of bland
spindled cells set in collagenous stroma.
IHC: Variable SMA; nuclear β-catenin in a subset.
Most common in mandible of children.
Must exclude low-grade central osteosarcoma and fibrous
dysplasia.
Fibrosarcoma
Malignant. Diagnosis of exclusion.
Monomorphic spindle cell proliferation with fascicular architecture.
Lacks morphologic, IHC, and genetic features suggesting an alternative Dx.
Classically, “herringbone fascicles”
Vascular Lesions Tumors showing vascular/endothelial differentiation.
Endothelial markers include: ERG, CD31, CD34, FLI-1, and Factor VIII
Hemangioma
Benign tumor composed of small or large
caliber thin-walled blood vessels.
Single layer of non-atypical endothelial cells.
Most common in vertebral bodies.
Often asymptomatic.
Unknown if neoplasm or developmental
abnormality
Epithelioid Hemangioma
Locally aggressive vascular neoplasm.
Large, epithelioid endothelial cells with densely
eosinophilic cytoplasm. Distinct vasoformation.
Lobular architecture. Can have solid areas.
Mitoses are infrequent and not atypical.
Often rich inflammatory infiltrate with eosinophils.
Most common in long bones. Can be multifocal.
IHC: Vascular markers, Keratins, EMA, ±FOS/B
Molecular: Rearrangements of FOS or FOSB
Low to intermediate-grade malignancy.
Cords and nests of epithelioid endothelial cells within
myxohyaline stroma. NO lobular architecture.
Large cells with abundant eosinophilic cytoplasm, some
of which have intracytoplasmic lumina with RBCs.
IHCs: Vascular markers, Keratins, EMA, CAMTA1
Molecular: WWTR1-CAMTA1 fusion (majority of cases),
or YAP1-TFE3 fusion (minority of cases)
Angiosarcoma
High-grade malignant neoplasm with endothelial differentiation.
Vasoformative architecture and/or expression of endothelial
markers.
Often epithelioid in bone with frequent solid growth.
Numerous extravasated RBCs and variable inflammation
Prominent nuclear atypia and readily observed mitoses.
IHC: Vascular markers, frequent keratins (if epithelioid)

Notochordal Tumors Tumors derived from/showing notochordal differentiation
Both stain with Brachyury, Cytokeratin, EMA and (variable) S100
Benign Notochordal Tumor

Benign. Often incidentally found.
Axial skeleton: Usually skull base, vertebral bodies, or sacrum.
Solid sheets of adipocyte-like vacuolated cells and eosinophilic

less vacuolated cells.
Bland nuclei. No mitoses. Sometimes cystic areas.
Unlike Chordoma, there should be NO: extracellular myxoid
matrix, tumor vasculature, fibrous septae, or lobular
architecture
Chordoma
Malignant. Usually in the axial skeleton, equally distributed
between skull base (esp. clivus), vertebrae, and sacrum.
Large epithelioid cells with eosinophilic to clear cytoplasm
separated into lobules by fibrous septae.
Some cells have bubbly “physaliphorous” cytoplasm
Arranged in cords and nests embedded in abundant myxoid
matrix or more cellular packets.
Variable pleomorphism and mitotic activity.
IHC: Expresses Brachyury and cytokeratin
Molecular: A subset of cases have Brachyury (TBXT) copy
number variations
Intermediate aggressiveness, but can dedifferentiate.
“Poorly differentiated chordoma:” Cohesive nests of epithelioid cells with abundant eosinophilic cytoplasm.
Scattered signet ring-like cells. Often rhabdoid areas. Loss of SMARCB1 (INI1) expression. Poor prognosis.
Miscellaneous Tumors
Simple Bone Cyst
Benign. Intramedullary, usually unilocular.
Often in the proximal humerus or femur. Usually in younger pts.
Simple cyst, lacking a true lining, with a thin wall of fibrous

tissue.
Often with fibrin deposition within cyst, which can calcify.
May have foci of chronic inflammation, histiocytes,

multinucleated giant cells, hemosiderin, cholesterol, and
reactive bone.
Fibrous Dysplasia 骨病理很棒
Benign. Often medullary in the craniofacial bones or femur.
Can be monostotic (one bone, more common) or polyostotic
(multiple bones, often presenting younger)
Fibro-osseous lesion with: 1)Irregular, curvilinear woven bone

(“Chinese letters”) without conspicuous osteoblastic rimming,
and 2)fibrous tissue composed of bland fibroblastic cells.
Molecular: GNAS activating missense mutations

Both Mazabraud syndrome (FD + Intramuscular myxomas) and
McCune-Albright syndrome (FD + Café-au-lait macules +
endocrinopathies) have GNAS mutations
Osteofibrous Dysplasia
Benign. Almost exclusively in Tibia or Fibula anterior
cortex during childhood.
Woven bone with prominent osteoblastic rimming with
intervening bland fibrous tissue.
IHC: Cytokeratin highlights scattered SINGLE cells.

If CK highlights clusters of cells, consider: Osteofibrous
dysplasia-like adamantinoma
Lipoma/Hibernoma
Benign. Often calcaneus or metaphysis of long bones.
Lipoma: Lobules of mature-appearing adipocytes with a
single large vacuole that displaces the nucleus. There may
be woven bone present.
Hibernoma: Composed of brown fat, with large cells with
eosinophilic cytoplasm with numerous small clear
vacuoles and a central nucleus.
Chondromesenchymal Hamartoma of Chest Wall

Benign. Well-circumscribed mass arising from the rib,
present at birth.
Composed of: nodules of hyaline cartilage, admixed

with blood-filled cystic spaces, reactive bone, bland
spindled cells, and osteoclast-like giant cells.
Leiomyosarcoma
Malignant. Often lower extremity near knee.
Intersecting fascicles of uniform cells with eosinophilic
fibrillar cytoplasm and elongated cigar-like nuclei and
variable pleomorphism demonstrating smooth muscle
differentiation.
IHC: SMA, Desmin, and/or H-caldesmon
Must exclude a metastasis!!
Ewing Sarcoma
Malignant. Most common in the diaphysis of long bones (but can be in any
bone and soft tissue).
On imaging causes a mulitlaminated periosteal reaction→ “onion skinning”
Most common in children and young adults.
Small round blue cell morphology. Uniform. Stippled chromatin and scant
clear to eosinophilic cytoplasm. Can form rosettes.
IHC: CD99 diffuse strong membranous staining (not specific though)
NKX2-2 (much more specific). FLI1 and ERG in cases with corresponding
fusions. Occasional keratin expression.
Molecular: EWSR1 fusions, most commonly with FL1, sometimes with ERG,
or rarely other combinations.
Adamantinoma
Locally aggressive to Malignant. Often youngish adult.
Located in cortex of anterior Tibia or Fibula
Biphasic with a variety of morphologic patterns with variable
epithelial component within a bland osteofibrous component.
Classic adamantinoma: obvious epithelial element in fibro-osseos
stroma. Epithelium can be squamous, basaloid, tubular, or spindled.
Malignant.
Osteofibrous dysplasia-like adamantinoma: Inconspicuous
epithelial cells (see clusters on CK IHC), primarily osteofibrous lesion.
Locally aggressive.
Dedifferentiated adamantinoma: epithelial component progressed
to high-grade sarcoma.
Other Small Round Blue Cell Sarcomas
CIC-rearranged sarcoma: High-grade round cell undifferentiated sarcomas
with CIC gene fusions, most commonly CIC-DUX4. Most commonly in soft
tissue, rarely bone. Common in young adults. By IHC: CD99 variable,
frequent WT1, ERG, and calretinin staining. Significantly worse prognosis
than Ewing Sarcoma.
Sarcoma with BCOR genetic alterations: Primitive round to spindled cells

arranged in nests, sheets, or fascicles. Variably myxoid stroma with
delicate vasculature. Can see either BCOR gene fusions (e.g., BCOR-
CCNB3) or BCOR internal tandem duplications. By IHC: (+) BCOR, SATB2,
TLE1, and CyclinD1. CD99 variable. Survival similar to Ewing sarcoma.
Round cell sarcoma with EWSR1-non-ETS fusions (“Ewing-like Sarcoma”):

Like the name says, round cell sarcomas with a fusion of EWSR1 to a non-
traditional fusion partner (i.e., not FLI, ERG, or FUS). Most often in the
bone (like Ewing sarcoma). Most common fusions: EWSR1-NFATC2 and
FUS-NFATC2. IHC very variable.
Undifferentiated Pleomorphic Sarcoma

Malignant. Diagnosis of exclusion!
Often in the long tubular bones near the knee of adults

(often older).
A pleomorphic malignant neoplasm with no identifiable line

of differentiation.
Diffusely composed of spindled to epithelioid cells with

marked pleomorphism in various growth patterns (often
storiform to fascicular)
Brisk mitotic activity and frequent necrosis.
Collagenous stroma, but NO osteoid or cartilage production.
IHC: Do at least S100, SMA, Desmin, CK AE1/AE3

Can see focal keratin staining, but if extensive consider
metastatic carcinoma.
Can see focal staining with one muscle marker (e.g., SMA),
but if more markers also positive (e.g., Desmin)→ consider
leiomyosarcoma.
SATB2 can be positive
H3.3 p.Gly34Trp expression suggests derived from giant cell
tumor of bone.
IDH1/2 mutations can suggest dedifferentiated
chondrosarcoma
Genetics/Molecular
Alteration Tumors
EWSR1 Ewing sarcoma (and MANY other tumors, including clear cell sarcoma,
angiomatoid fibrous histiocytoma, desmoplastic small round cell tumor,
extraskeletal myxoid chondrosarcoma, etc...)
FOS rearrangements Osteoid Osteoma, Osteoblastoma, Epithelioid hemangioma
MDM2 amplifications Low-grade central osteosarcoma, Parosteal osteosarcoma, Conventional

osteosarcomas derived from either of these (and Well-differentiated
liposarcoma and Intimal sarcoma)
EXT1 or EXT2 biallelic inactivation Osteochondroma
IDH1 or IDH2 Enchondroma, Chondrosarcoma or Dedifferentiated chondrosarcoma

derived from an enchondroma
GNAS Fibrous dysplasia, (also intramuscular myxoma)
H3.3 p.Lys36Met substitution Chondroblastoma, Giant cell tumor of bone
HEY1-NCOA2 fusions Mesenchymal chondrosarcoma
USP6 rearrangements Aneurysmal bone cyst (also nodular fasciitis)
MAPK pathway activation Non-ossifying fibroma, Langerhans cell histiocytosis, Erdheim-Chester

disease, Rosai-Dorfman disease
GRM1 fusions/upregulation Chondromyxoid fibroma
FN1-ACVR2A fusions Synovial chondromatosis
WWTR1-CAMTA1 fusion Epithelioid hemangioma
Syndrome Gene Manifestations
Li-Fraumeni Syndrome TP53 Early onset of a broad spectrum of cancers, most commonly breast
cancer, followed by soft tissue sarcomas, brain tumors, and
osteosarcomas
Enchondromatosis IDH1/2 Ollier disease: Multiple enchondromas in multiple bones

Maffucci syndrome: Multiple enchondromas + hemangiomas
McCune—Albright GNAS Fibrous dysplasia (monostotic or polyostotic), hyperfunctioning

syndrome endocrinopathies (precocious puberty, hyperthyroid, hypercortisolism,
etc..), various GI polyps, and intramuscular myxomas (FD + myxoma =
Mazabraud syndrome)
Multiple EXT1/2 Multiple osteochondromas during early life that stop growing when
Osteochondromas growth plates close. May be asymptomatic.
CHAPTER 8
Breast
In Situ Lesions of the Breast

Normal Anatomy
Lobule
Terminal Duct Lobular Unit (TDLU)
Increasingly small branching ducts terminate in
clusters of acini called lobules. Terminal Duct
Milk flow: Acini→ ducts→ collecting ducts → Nipple

Set in fibrous stroma with varying amounts of
adipose tissue
Two cell layers:

1) Inner Epithelial cell
Cuboidal to columnar cells with eosinophilic
cytoplasm and oval nuclei.
Stain with LMW cytokeratins (e.g., CK7)
2) Outer myoepithelial cell
Flat (sometimes barely visible) to plump with
abundant clear cytoplasm. Stain with Actin,
calponin, SMMHC, p63, CK5/6, S100
In Situ Lesions
Usual Ductal Hyperplasia (UDH)
Benign epithelial proliferation that is architecturally,
cytologically, and molecularly heterogeneous.
Think: “Polyclonal”
Cohesive proliferation with haphazard architecture
Irregular, slit-like lumina, often peripherally located
Streaming, syncytial pattern
Variably sized cells with indistinct borders
Overlapping nuclei
Frequent nuclear grooves, some pseudoinclusions
Any bridges are thin and stretched
Any micropapillae have broad bases and narrow tips with
small pyknotic nuclei
Cells stain with a mixture of low-molecular weight
cytokeratins (e.g., CK7) and high-molecular with CKs (e.g.,
CK5/6). Heterogeneous ER staining.
~2x Relative Risk of Developing Cancer
Treatment: None needed
UDH Low-grade DCIS
Think: “Polyclonal” Think: “Monoclonal”
Irregular, Slit-like lumina, often peripheral Regular, punched out lumina, often central
Streaming architecture, minimal polarization Prominent polarization
Variation in cell size/shape Monomorphic cells/shape
Indistinct cell margins Distinct cell margins
Admixture of cell types (epithelial, Proliferating cells are epithelial. Myoepithelial

myoepithelial and/or apocrine): Stain with cells are against the basement membrane:
high and low-molecular weight cytokeratins Epithelium stains with low-molecular weight
cytokeratins only
Heterogeneous ER staining Strong, diffuse ER staining
UDH Low-grade DCIS
CK5/6
ER
Ductal Carcinoma In Situ (DCIS)
Non-invasive neoplastic epithelial proliferation
Often detected on mammography (e.g., linear
calcifications)
Often limited to one duct system, but can involve
lobules (“Cancerization of the lobule”) and/or can
“skip” around in duct
Graded based on nuclear morphology, but can be
varying grades within one case due to tumor
heterogeneity (Grade NOT architecture based)
Low-Grade
Low-grade DCIS
Think: “Monoclonal”
Small, monomorphic cells
Uniform size and shape
Regular chromatin; small nucleoli
1.5-2x size of RBC
Few mitoses
Often cribriform or micropapillary growth
Often forms microrosettes/glands with
polarization around the gland
Sometimes solid growth
Calcifications common. Necrosis uncommon.
Size requirement: >2mm and involving more than
two complete spaces
High-grade DCIS:
Think: “Pleomorphic, Ugly”
Large, ugly cells Intermediate-Grade
Irregular contours, course chromatin
Often prominent nucleoli
>2.5-3x the size of an RBC
Lots of mitoses
Often solid architecture
Minimal/no polarization
Comedo necrosis common
Sometimes single layer of cells (“Clinging
carcinoma”). Uncommonly cribriform or
micropapillary
Size requirement: None!!
High-Grade
Intermediate-grade DCIS:
In between low and high-grade
~10x Relative Risk of Cancer in ipsilateral breast
Moderate variability, size, polarization
May have necrosis and/or calcifications Treatment: Excision with “wide” negative margins
Possibly +/- radiation and/or hormone therapy
Low-grade DCIS High-grade DCIS
Small, monomorphic cells Large, pleomorphic cells
1.5-2x size of RBC >2.5x size of RBC
Regular nuclear contours Irregular nuclear contours
Even chromatin Course chromatin
Inconspicuous nucleoli Prominent nucleoli
Usually cribriform or micropapillary growth Usually solid growth, but any architecture can
be present
Polarization around lumina No polarization around lumina
Necrosis uncommon Necrosis common
Must be >2mm No size requirement
ER and PR positive frequently ER and PR negative more frequently
HER2 negative frequently HER2 positive frequently
Few mitoses Many mitoses
Low-grade associated cancers High-grade associated cancers
Atypical Ductal Hyperplasia (ADH)

Non-invasive neoplastic epithelial proliferation
resembling DCIS (similar cytology and architecture),
BUT less developed in architecture or extent
Similarly genetically to low-grade DCIS→ clonally
related, just smaller or questionable architecture
Size: ≤2mm and <2 duct spaces

Cells (same as low-grade DCIS):
• Evenly spaced monotonous cells
• Round nuclei with dense chromatin
Architecture:
• Cribriform
• Rigid bridges, arcades, and bars
• Bulbous micropapillae (with narrow bases and
wide tips)
~4-5x relative risk of breast cancer

Treatment: if on Bx→ surgical excision to exclude
DCIS/carcinoma; On excision→ Nothing more
Step-wise Diagnosis Evaluate Cytology: Is it High-grade or
Intermediate-grade?
No Unsure Yes
Cytology low-grade (bland)
Consider UDH vs Consider intermediate or
Intermediate-grade high-grade DCIS (and its
Is the cytology
DCIS mimics)
monotonous/clonal
appearing?
CK5/6 and
No Unsure Yes ER stains
Polymorphous Unsure if Monotonous/ Negative CK5/6

/polyclonal cytology Clonal “Mosaic pattern” result and uniform
appearing is clonal appearing CK5/6 result and strong ER staining =
variable ER staining = Support a neoplastic
Supports UDH (non- process like DCIS
neoplastic)
Evaluate Architecture: Are there
neoplastic architectural features present? Yes
No or Unsure
Cytology Unsure if Monotonous/ Cytology Unsure if Monotonous/

Polyclonal cytology is Clonal Polyclonal cytology is Clonal
clonal cytology clonal cytology
UDH
UDH Solid or Flat
vs ADH UDH Evaluate Extent
Subtle process vs ADH
architecture
Modified from a presentation by
Dr. Kimberly Allison. Stanford University
FEA
ADH or < 2 mm 2-3 mm > 3mm
ALH/LCIS
ADH Non-uniform Uniform

Throughout
Lesion
Borderline
Distinguishing DCIS from LCIS: Lesion (ADH
Low-grade
DCIS
Feature LCIS DCIS vs DCIS)
Loss of cohesion Present Absent

Intracytoplasmic vacuoles More common Less common
Pagetoid ductal involvement More common Less common
Microacini Absent Present
Polarization at duct periphery Absent Present
Columnar Cell Change
Clonal alterations of the TDLU characterized by
enlarged, variably dilated acini lined by columnar
epithelial cells arranged perpendicular to the
basement membrane; 1-2 cells thick
Apical snouts, secretions and calcification are
often present
Earliest step in low-grade carcinoma pathway
Not infrequently associated with ADH, low grade
DCIS, or invasive carcinoma, but risk of developing More than 2 cell layers thick?
a subsequent carcinoma is negligible, so excision is → Columnar cell hyperplasia
not indicated More complex architecture? → ADH
Flat Epithelial Atypia (FEA)

Similar to columnar cell change (in dilated TDLUs),
but lined by 1-2 layers of cells with enlarged round
to oval nuclei
(same cells as in ADH/low grade DCIS!)
Complex architecture of the type seen in ADH/low
grade DCIS is not allowed
Apical snouts, secretions and calcification may be
present
Frequently associated with DCIS/cancer, so if found
on core biopsy, it is an indication for excision (to
exclude a worse lesion nearby). No further
treatment on excision.
Radial Scar / Complex Sclerosing Lesion

Benign lesion with fibroelastosis with entrapped
glandular structures, ± Proliferative epithelial
lesions (e.g., UDH)
Radial scar→ smaller with stellate configuration
Complex sclerosing lesion→ larger and more
disorganized
Dense, hyalinized, elastotic stroma
Two cell layers maintained throughout
Excision somewhat controversial, often excised
Often may want to do myoepithelial stains to confirm no invasive component given complexity
Lobular Neoplasia In Situ
Epithelial proliferations originating in the TDLU
characterized by:
• Small, discohesive monomorphic cells
• E-cadherin inactivation → Loss of
membranous E-cadherin staining → cellular
discohesion
• Note: Up to 15% of lobular lesions
retain E-cad, but with an aberrant
staining pattern
• CDH1 mutations common (same gene as
hereditary diffuse gastric cancer) LCIS
Atypical Lobular Hyperplasia (ALH)

Solid proliferation of discohesive, monomorphic
epithelial cells expanding <50% of the acini in a
TDLU
If incidental on a biopsy, no need to excise
LCIS
Lobular Carcinoma In Situ (LCIS)
>50% of the acini are filled and expanded
Often >8 cells thick
Non-obligate precursor to invasive lobular
carcinoma
~8-10x Relative Risk of Cancer
If incidental on a biopsy, no need to excise
On excision, margins don’t matter
Pleomorphic LCIS
LCIS Subtypes:
Pleomorphic LCIS—composed of large cells
(>4x size of a lymphocyte) with marked nuclear
IHC Stain Normal Lobular DCIS
pleomorphism Epithelium Neoplasia
E-Cadherin Membrane Negative Membrane
Florid LCIS—classic LCIS cells, but forming a
staining staining
confluent mass-like lesion with little to no
intervening stroma between distended TDLUs P120 Membrane Cytoplasmic Membrane
catenin staining staining
(often ~50 cells in diameter)
β-catenin Membrane Absence of Membrane
Both of these subtypes exhibit greater genomic staining membrane staining
staining
instability→ behave more aggressively→ excise
with negative margins
Sclerosing Adenosis
Very common
Lobulocentric proliferation of acini and tubules
accompanied by compressing fibrosis
Epithelial cells are often cuboidal, small, and bland
Myoepithelial cells have spindled, hyperchromatic nuclei and
inconspicuous to prominent clear cytoplasm
Can highlight myoep’s with IHC stains if necessary
Microcalcifications are common
Can extend into fat occasionally
Can be involved by epithelial proliferations (e.g., UDH)
Primarily significant as it can be confused with carcinoma
Lactating Adenoma
Benign breast nodule diagnosed during pregnancy
or breast feeding, that is composed of an aggregate
of glands with lactational change
Well-circumscribed proliferation of closely packed
hyperplastic secretory lobules separated by delicate
connective tissue
Cuboidal to hobnailed epithelial cells are bland with
vacuolated to granular cytoplasm and small,
uniform, pinpoint nuclei
Spontaneously regress when done lactating
Microglandular adenosis
Haphazard proliferation of small, round, uniform,
tubular glands composed of a single layer of
epithelium (without associated myoepithelial cells!)
Luminal spaces are open and often contain an

eosinophilic colloid-like secretion
Small bland nuclei with amphophilic cytoplasm
IHC: Cells stain with CKs and S100,

Negative for ER, PR, and HER2
Myoepithelial stains negative
Benign, but thought to be a non-obligate precursor DDX:

to basal-type breast cancer Sclerosing adenosis→ S100 Neg, Myoep intact
Tubular carcinoma → ER pos, S100 Neg
Tubular Adenoma
Benign. Usually Younger women. Uncommon.
Well-circumscribed, sharply demarcated, dense
proliferation of closely approximated round to
oval tubular structures with little background
stroma
Glands have usual two layers: Epithelium and
myoepithelium
May be related to fibroadenomas histogenetically
(but just stroma poor)
Apocrine Adenosis
= Apocrine metaplasia + Sclerosing adenosis
Lobulocentric proliferation of benign glandular
structures composed of cells with abundant granular
cytoplasm distorted by fibrosis
Enlarged, round nuclei with prominent nucleoli
Often have apical “snouts”
Intact myoepithelial cells→ can highlight with IHC
Cells typically ER-negative, AR-positive, and positive
for GCDFP-15
If significant cytologic atypia (>3:1 size variation,
mitotic activity)→ Atypical Apocrine Adenosis
If complex architecture (e.g., cribriform growth) or

very marked pleomorphism, → Apocrine DCIS
Collagenous Spherulosis
Intraductal deposits of basement membrane: Appear
as hyaline, acellular, eosinophilic spherules or
fibropapillary, amorphous eosinophilic to mucoid
material
Myoepithelial cells surround the lumina and are often
compressed and spindle-shaped.
Can be calcified. Commonly seen with papillomas, UDH,
or sclerosing lesions.
Main importance is to recognize that it is benign and
NOT DCIS or adenoid cystic carcinoma
Gynecomastia Male breast histology:
Bilateral, diffuse or discrete retroareolar masses. Contains fibrous stroma and branching ducts and
Most common lesion of the male breast. terminal ductules, but extremely few (if any) acini.
Caused by androgen/estrogen imbalance.

Physiologic in infants, children, and adolescents.
In a minority, often older age, it is pathologic and
associated with endocrine abnormalities
(Klinefelter syndrome, obesity, cirrhosis) and
certain drugs (e.g., spironolactone and marijuana).
Histologic appearance varies with duration/stage:

Early
Loose periductal stroma
Mixed chronic inflammatory infiltrate
Extensive epithelial hyperplasia with tapering tufts
(pyramid-shaped micropapillae) and protrusion
into lumen (like what is seen in juvenile
fibroadenomas), so have a high threshold for
calling DCIS/ADH
Late
Fibrosis and hyalinization of periductal stroma
Atrophy of epithelium
Can se pseudoangiomatous hyperplasia (PASH)
Not associated with any risk of cancer

Usually no treatment necessary
Invasive Breast Carcinoma

General Background
Most common cancer in women and leading cause of female cancer death worldwide.
Presenting signs and symptoms:
Unscreened populations—mass, skin erythema and edema due to cancer in dermal lymphatics.
Screened populations—spiculated mass, architectural distortion, MRI enhancement
Three pillars of diagnosis: physical exam, imaging, needle biopsy/cytology
When these are concordant, the risk of missing cancer is extremely low, but must do careful correlation.
General Risk factors:
Increased estrogen—seen with early menarche, fewer children, less lactation, and obesity.
Increased Alcohol
Pathogenesis/Molecular
Two main pathways separated by Estrogen Receptor (ER) status:
ER-Positive: ER+, HER2-, Diploid with specific chromosomal gains/losses (e.g., gain 1q, loss of
16q)→ usually low to intermediate-grade cancers
ER-Negative: ER-, HER2+/-, Aneuploid with complex karyotypes, Frequent TP53 mutations →
frequently high-grade tumors with high proliferation
Both pathways show PIK3CA mutations, but it is more common in ER-positive tumors.
Molecular classification: (based on hierarchical cluster analysis of gene expression)
Lumina A Luminal B HER2-Positive Basal type
Percent of all ~50% ~20% ~15% ~15%

tumors
Classic ER/HER2 ER+, HER2- ER+, HER2- ER-, HER2+ ER-, HER2-
status
Ki67 Low Intermediate High High
Actual ER/HER2
ER+ HER2+ Triple Negative
Grade High
Low
Recurrence Risk High, but short term
Low, but long term
Therapies used
Hormone Rx HER2 Rx Chemotherapy
Note: Other molecular classifications exist and include additional/alternate groupings. This is
just the most well-established frequently utilized.
General Considerations
Precursor lesions:
ER(+) cancers→ FEA, ADH, Low-grade DCIS are non-obligate precursors
ER(-) cancers→ Microglandular adenosis and High-grade DCIS are non-obligate precursors
Grading
Grade using the Nottingham system (see below) with its 3 characteristics.
Tubules formation: Assessed throughout the whole tumor at low magnification. Only structures with
central lumina surrounded by polarized tumor cells are counted.
Nuclear pleomorphism: Assessed in the area showing the worst cytologic atypia
Mitotic count: Assessed in mitotic “hot spot.” Remember to factor in your field area!
Feature Score
Add the scores for gland
Tubule formation formation, nuclear pleomorphism,
Majority of tumor (>75%) 1 and mitotic count:
Moderate degree (10-75%) 2 Total Score Final Grade

Little or none (<10%) 3 3-5 Grade 1
Nuclear pleomorphism 6 or 7 Grade 2
Small, regular, uniform 8 or 9 Grade 3
1
(<1.5x the size of normal nucleus)
Moderate increase in size and
2
variability (1.5-2x cell size)
NOTE: Remember, the size of an HPF varies
Marked variation (>2x cell size)
depending on your scope/magnification, so be
vesicular chromatin, 3 sure to factor this in when counting mitoses!
often prominent nucleoli
Mitotic Count (per 10 HPF) Olympus, 10x Mitotic Count (per 10 HPF) Olympus, 15x oculars
oculars [most attending scopes], 40x objective [most resident scopes], 40x objective
0-8 1 0-3 1
9-17 2 4-7 2
≥18 183 ≥8 3
General Immunohistochemistry
Invasive cancers usually stain with low-molecular weight cytokeratins (including CK7 and CK19), EMA,
and GATA-3.
Some cancers (often the well-differentiated ones) stain with GCDFP-15 (BRST2) and mammaglobin.
Some cancers (often the higher-grade triple-negative ones) stain with basal markers including high-
molecular weight cytokeratins (e.g., CK5/6).
A subset of cancers express S100 and/or p63.
Is it invasive?
Invasive breast cancer is defined by the absence of peripheral myoepithelial cells.
Stains for myoepithelial cells (see below) should be employed as part of a panel or cocktail with at least
one nuclear and one cytoplasmic stain (e.g., p63 and SMMHC).
However, do not rely solely on negative myoepithelial stains to diagnose invasion. The H&E findings must
be concordant. Nests of in situ carcinoma may well be surrounded by reduced numbers of myoepithelial
cells and those present may stain weakly.
From: Liu H. Application of Immunohistochemistry in Breast Pathology: A Review and Update. Archives of Pathology & Laboratory Medicine:
December 2014, Vol. 138, No. 12, pp. 1629-1642.
Morphologic features of Cancer vs Mimics:

Feature Invasive cancer Complex sclerosing DCIS involving
lesions sclerosing adenosis
Stroma Desmoplastic Dense Dense

Cytology Atypical Bland Atypical
Gland profile Angulated Compressed Solid/cribriform
Architecture Infiltrative Lobulated Lobulated

Myoepithelial cells Absent Present Present
Modified From: Peng et al. Update on Immunohistochemical Analysis in Breast Lesions. Archives of Pathology & Laboratory Medicine: August 2017,
Vol. 141, No. 8, pp. 1033-1051.
Subtypes Tumors showing a special histologic pattern in ≥90% of the tumor are designated
as pure special tumor. Otherwise, they are designated as NST, which accounts for
the majority of cases, including mixed patterns.
“No Special Type” (“NST”)

Older name: Invasive Ductal Carcinoma (IDC);
Now say: “Invasive Breast Carcinoma (IBC) of no special type (NST)”
A large and heterogeneous group that is essentially a “waste basket” including all cancers that don’t fit
into one of the specific groups.
When a special type makes up 10-90% of tumor: report as “mixed” IBC-NST and special subtype
Special morphologic patterns (as opposed to subtypes):

Medullary pattern: Well-circumscribed, high-grade,
pushing margins, syncytial architecture, and prominent
tumor infiltrating lymphocytes (TIL). Better outcome than
other stage-matched high-grade cancers (likely due to
TILs). Usually triple-negative (Basal-like). Associated with
BRCA1-related tumors.
Invasive carcinoma with Neuroendocrine differentiation:

Some degree of neuroendocrine differentiation by
immunohistochemistry. Not currently of any clinical
significance. More common in mucinous and solid papillary
carcinomas. Must be sure to consider a much rarer primary
neuroendocrine tumor/carcinoma and metastasis
Other rare subtypes: Carcinoma with Osteoclast-like giant cells, Pleomorphic pattern,
Choriocarcinomatous pattern, Melanotic pattern, Oncocytic pattern, Lipid-rich pattern, Glycogen-rich
clear cell pattern, and Sebaceous pattern
Microinvasive Carcinoma
Invasive breast carcinoma ≤1mm in size
Usually adjacent to an areas of DCIS, often
high-grade.
Earliest recognizable form of invasive
carcinoma
• Invasion beyond myoepithelium
• Small, angulated clusters of tumor cells
infiltrating stroma
• Often desmoplastic stromal changes
Better prognosis than larger invasive tumors
Often multifocal→ if any single invasive focus is larger than 1 mm→ invasive carcinoma (not micro)
Be cautious diagnosing this on core biopsy, as could be more invasion on excision. Often good to get
levels to exclude larger foci of invasion
Invasive Lobular Carcinoma
Invasive breast carcinoma composed of discohesive cells
that are often individually dispersed or arranged in a single-
file linear pattern.
~10% of all invasive breast carcinomas
Most are Luminal A (ER and PR positive, HER2 negative)
CDH1 mutations→ Loss of E-cadherin function→ cellular
discohesion.
Often little host reaction or disturbance of background
architecture.
Occasional intracytoplasmic lumina.
Can have signet-ring cells.
Often low-grade nuclei.
Pleomorphic lobular carcinoma: Same discohesive growth,
but with marked nuclear pleomorphism (>4x size of
lymphocyte = high-grade DCIS cytology)
Immunohistochemical stains can confirm loss of E-cadherin
and are therefore helpful in confirming the diagnosis, but
morphology is most important
IHC Stain Normal Epithelium Lobular Carcinoma No Special Type

E-Cadherin Membrane staining Negative Membrane staining
P120 catenin Membrane staining Cytoplasmic Membrane staining
β-catenin Membrane staining Absence of membrane staining Membrane staining
Tubular Carcinoma
Low-grade invasive carcinoma composed of
well-formed tubules with open lumina lined
by a single layer of neoplastic cells.
Often old women. ~1.5% of Invasive

carcinomas.
Luminal A subtype (ER and PR positive, HER
negative)
Small, angulated to ovoid glands and tubules
with open lumina set in fibrous, desmoplastic
stroma.
Relatively low-grade nuclei.
>90% of tumor must have this morphology (as
is the rule for all special types)
Good prognosis.
Cribriform Carcinoma
Low-grade invasive carcinoma composed of islands of
tumor cells with well-defined cribriform spaces.
Luminal A subtype (ER and PR positive, HER negative)
Well-defined rounded to angulated cribriform spaces
(like cribriform DCIS), but without surrounding
myoepithelial cells, set in desmoplastic stroma.
Low nuclear grade.
Good prognosis. Very rare
Mucinous Carcinoma
Invasive breast cancer characterized by clusters of
epithelial cells suspended in pools of abundant
extracellular mucin.
Well-circumscribed grossly (mimicking benign process).
Uncommon. Luminal A molecular type (ER & PR +, HER -)
Low to intermediate nuclear grade.
Frequent neuroendocrine differentiation.
Good prognosis.
Mucinous cystadenocarcinoma: Invasive breast cancer
characterized by cystic structures lined by tall columnar
cells with intracytoplasmic and intracystic mucin, like
pancreatic IPMNs or ovarian mucinous carcinomas
Invasive Micropapillary Carcinoma

Invasive breast carcinoma composed of small, hollow, or morula-like
clusters of malignant cells, surrounded by clear spaces with inside-out
growth pattern.
Pure form is uncommon, often mixed with other patterns.
Luminal A or B (ER and PR +, HER – usually)
No fibrovascular cores (as is the case with all micropapillary tumors!)
Characteristic empty spaces around cells with delicate stromal framework.
Show reverse polarity→ Apical surface faces outward stroma (can see on
EMA stain where it stains the outside more strongly)
Often eosinophilic, granular cytoplasm and intermediate to high-grade
nuclei. Cuboidal to columnar cells.
Significantly more lymphovascular invasion and positive lymph nodes, but
when stage-matched with NST tumors, not significantly worse survival.
EMA
Metaplastic Carcinoma
Invasive Breast Cancers with differentiation of epithelium
towards squamous or mesenchymal-looking elements.
Usually present as a mass; Rare, <1% of all breast cancers.
Several distinct patterns (with some overlap, often mixed):
Low-grade Adenosquamous Carcinoma

Well-developed, rounded glands and tubules associated
with solid squamous nests infiltrating through desmoplastic
stroma. Sometimes associated “cannon ball” lymphoid
aggregates. Good prognosis.
Fibromatosis-like Metaplastic Carcinoma

Bland spindled cells with pale eosinophilic cytoplasm and
slender nuclei in stroma with variable collagen. Only mild
nuclear atypia. Often arranged in fascicles. Some cells may
be plumper/epithelioid. Good prognosis.
Spindle Cell Carcinoma

Atypical spindle cells with a variety of architectural patterns
(e.g., fascicles, herringbone, etc…). Elongate to plump
spindled cells with moderate to high-grade cytologic atypia.
Often associated inflammation. Includes a spectrum of
tumors from sarcomatoid SCC to myoepithelial carcinoma.
Worse prognosis.

Pure squamous cell carcinoma. Often cystic. Must exclude
a metastasis. Worse prognosis.
Metaplastic Carcinoma with Heterologous Mesenchymal

Differentiation
Essentially a carcinosarcoma. Heterologous elements may
include chondroid, osseous, and rhabdoid components.
Epithelial and mesenchymal components can have variable
atypia. Sometimes extensive sampling is necessary to find
the epithelial component (and exclude a primary sarcoma).
IHC: Vast majority do not express ER, PR, or HER2 (Triple

Negative). However, they do express some epithelial
markers:
(+) p63, HMWCKs (e.g., CK5/6), CK AE1/AE3
(-) CK7, CD34,
(+/-) SMA, CD10, Desmin, β-catenin
Molecular: Frequent TP53, PIK3CA, and WNT pathway

mutations. May be derived from late dedifferentiation or
basal-like stem cells.
Clinical: Much fewer LN metastases.

Carcinoma with Apocrine Differentiation
An invasive carcinoma with large cells with abundant
eosinophilic, granular cytoplasm and large nuclei with prominent
nucleoli (resembling apocrine sweat glands)
Androgen receptor (AR)-positive; ER/PR-negative.

~50% HER2 positive.
Often mostly solid growth with high mitotic index→ Grade 2 or 3
Rare Types
Tall Cell Carcinoma with Reverse Polarity:
Rare subtype of breast carcinoma with tall
columnar cells with reverse nuclear polarity,
arranged in solid and solid papillary patterns,
most commonly associated with IDH2
mutations. (Resembles tall cell papillary
thyroid carcinoma). Express both high and
low molecular weight cytokeratins (e.g., CK7
+ CK5/6). Triple negative. Indolent.
Salivary gland tumors

Most salivary gland tumors can occur in the breast, where there are usually relatively more indolent
than their head and neck counterparts. They are often triple-negative.
Acinic Cell Carcinoma: Clear to granular epithelial cells containing zymogen granules arranged in glands
and solid sheets. Triple negative. Intermediate behavior.
Adenoid Cystic Carcinoma: An invasive carcinoma composed of epithelial and myoepithelial cells
arranged in tubules, cribriform, and solid patterns associated with basophilic matrix and basement
membrane material. Frequent MYB-NFIB fusions. Triple negative, but generally good prognosis (unlike
in head and neck), cured by surgery alone.
Secretory Carcinoma: Epithelial cells with intracytoplasmic secretory vacuoles and extracellular,
eosinophilic, bubbly secretions, arranged in a variable architecture. Frequent ETV6-NTRK3 fusions.
Triple negative. Generally indolent.
Mucoepidermoid Carcinoma: Composed of a mixture of 1) mucinous cells, 2) squamous cells, and 3)

“intermediate” cells, arranged in a solid and cystic pattern. Frequent MAML2 fusions. Triple negative.
Good prognosis if low-grade.
Polymorphous Adenocarcinoma: Monotonous neoplastic cells with a variety of architectures, including

large nests surrounded by cords and single-file growth. Triple negative.
Familial Syndromes Breast cancer shows more familial clustering than most tumors.
BRCA1/2
BRCA-genes are tumor suppressors involved in the homologous recombination repair pathway (repairs
DNA breaks using sister chromatids as a template) → mutations in BRCA → genomic instability →
oncogenesis
Highest risks: Breast and ovarian cancer
~3.5% of all breast cancers; More common in certain populations, like Ashkenazi Jews
Treatment: patients may opt for prophylactic bilateral mastectomy and salpingo-oophorectomy
before 40 yrs → Must submit entire FT and ovary looking for STIC
Carcinomas can be treated with PARP inhibitors (PARP helps with single-strand DNA breaks, so when
combined with BRCA mutations → cancer cells can’t repair breaks at all→ “synthetic lethality”)
Characteristic BRCA1 BRCA2

Risk of breast cancer 40-90% 45-85%
Risk of ovarian/fallopian tube 40-50% 10-20%
high-grade serous carcinoma
Male breast cancer risk Lower Higher
Other Cancer risk Possibly pancreatic and colon Pancreatic cancer, prostate
cancer
Morphology Circumscribed growth pattern with Variable morphology and
pushing borders, dense grade
lymphocytic infiltrate. High-grade.
Molecular cancer type Basal-like (triple-negative) Luminal A (ER/PR +; HER2 -)
Li Fraumeni Syndrome
TP53-associated:
Autosomal dominant TP53 mutation (one of the most prominent tumor suppressors)
Early onset of a broad spectrum of cancers. Most common is breast(>90% lifetime risk), but also soft
tissue, brain (esp. choroid plexus carcinoma), adrenal cortical, bone, etc…
CHEK2-associated:
Germline mutations in CHECK2, moderately penetrant. CHECK2 is a tumor suppressor activated by
double strand DNA breaks (upstream of TP53 and BRCA1). Mutation→ disrupt DNA repair→ more
errors → carcinogenesis. ~30% lifetime risk of breast cancer. Also increased risk of a variety of cancers.
Peutz-Jeghers Syndrome
Autosomal dominant polyp and cancer syndrome. Germline mutations in tumor suppressor STK11.
Characteristic hamartomatous polyps in >95% of patients, often in small bowel.
Also frequent mucocutaneous melanin pigmentation.
Increased risk of many cancers including Breast, colon, stomach, pancreas, ovary (SCTATs), etc…
CDH1-associated Breast Cancer
Inactivating germline mutations in CDH1 (gene for E-cadherin) resulting in
characteristic lobular carcinoma of the breast.
Most (but not all) CDH1 mutations are associated with Hereditary diffuse
gastric cancer (HDGC), which also has germline mutations in CDH1 and can
have lobular carcinoma of the breast also.
E-cadherin is important for cell adhesion and tumor suppression
Classic HDGC finding: Signet ring carcinoma in situ

Signet ring cells above basement membrane
Pagetoid spread
Can then progress to invasive, diffuse gastric cancer
Often Multifocal
Ataxia-Telangiectasia
Autosomal recessive disorder with progressive cerebellar ataxia, oculocutaneous telangiectasia, variable
immunodeficiency, sterility, and sinopulmonary infections.
Mutations in ATM gene (tumor suppressor→ phosphorylates p53 and BRCA1 in response to DNA double-
strand breaks
High risk of malignancy and sensitivity to ionizing radiation
Homozygotes have full disorder
Heterozygotes have a risk of breast cancer at a young age.
COWden’s Syndrome Uterine Cancer

Think of this cow (because of the bow… get it?
PTEN mutation. Autosomal dominant

Tumor suppressor → lots of different tumors
Other PTEN syndromes include: Bannayan-Riley
Ruvalcaba syndrome and Lhermitte-Duclos disease
At risk for:
Breast Cancer (highest risk)
Thyroid carcinoma (usually Follicular) Thyroid Cancer
Endometrial Cancer
TrichileMMOOOOOmas
Breast CA
Lipomas
Esophagus: Glycogen acanthosis
Stomach: Polyps that often resemble HP’s
Colon: Stroma-rich polyps with cystically dilated glands
Can mimic JP’s.
Can contain Adipocytes in lamina propria (relatively unique)
Can get ganlgioneuromatous polyps
Prognostic Markers Testing
Estrogen Receptor (ER)
From: Allison KH et al. Estrogen and Progesterone Receptor Testing in Breast Cancer: American Society of Clinical Oncology/College of American Pathologists Guideline Update. Arch
Pathol Lab Med. 2020 May;144(5):545-563.
From: Allison KH et al. Estrogen and Progesterone Receptor Testing in Breast Cancer: American Society of Clinical Oncology/College of American Pathologists Guideline Update. Arch
Pathol Lab Med. 2020 May;144(5):545-563.
HER2
Wolf et al. Human Epidermal Growth Factor Receptor 2 Testing in Breast Cancer: American Society of Clinical Oncology/College of American Pathologists Clinical
Practice Guideline Focused Update. Arch Pathol Lab Med. 2018 Nov;142(11):1364-1382.
HER2 Grading:
Score Interpretation Staining Pattern Think
Negative No staining is Essentially

0 observed, or noting, like an
membrane staining eraser
is observed in <10%
of tumor cells
Negative A faint/barely Slight pencil

1+ perceptible tracing
membrane staining
is detected in >10%
of tumor cells. The
cells exhibit
incomplete
membrane staining
Equivocal A weak to moderate Ballpoint pen

2+ (order FISH) complete,
circumfirential
membrane staining
is observed in >10%
of tumor cells.
Positive A strong complete Sharpie

3+ membrane staining marker
is observed in >10%
of tumor cells.
Modified from: HercepTest Interpretation Manual Breast Cancer. Dako.

Papillary Lesions of the Breast

Intraductal Papilloma Papillary Encapsulated Solid Invasive
Papilloma with DCIS DCIS Papillary Papillary Papillary
Carcinoma Carcinoma Carcinoma
Papillary Broad, blunt Broad, blunt Slender Numerous slender Solid with Infiltrative
Architecture fronds fronds fronds, fronds; inconspicuous carcinoma
sometimes sometimes fibrous septae with papillary
branching branching, morphology,
typically well- including
developed and fibrovascular
peripheral. cores
Fibrous capsule
Epithelial Heterogeneous Focal areas Entirely Entirely occupied Entire lesion Low,
Cells non-neoplastic with cytologic occupied by a cell occupied by a intermediate,
cells. features of by a cell population with population of or, rarely,
Sometimes DCIS (usually population features of DCIS cells with low to high-grade
UDH. low-grade) with (often low-grade); intermediate- nuclei
features of Cribriform, grade nuclei;
DCIS (often micropapillary, Often spindled
low-grade) and solid patterns or
may be present, neuroendocrine
with fusion of morphology.
papillae
Myoeps in Positive Positive in Negative Negative Negative or Negative

Papillae papilloma, positive
but may be
scant in DCIS
component
Myoeps at Positive Positive Positive Negative (usually) Negative or Negative

Periphery positive
CK5/6 Positive in Positive in Positive in Negative Negative Negative

myoeps and myoeps and peripheral
UDH UDH; myoeps;
Negative in Negative in
DCIS lesion
ER & PR Positive, but Strong, Strong, Strong, diffuse Strong, diffuse Positive
Heterogeneous diffuse in diffuse
DCIS
Other stains None None None None Frequent None

synaptophysin
and
chromogranin
expression
Modified from: WHO Classification of Tumors: Breast Tumors. 5th Edition. 2019
Intraductal Papilloma
Benign intraductal proliferation composed of
papillary projections with fibrovascular cores,
covered by epithelial and myoepithelial layers.
Can be central (Solitary) or peripheral (Multiple)
Often present with serosanguinous discharge.
May have superimposed UDH, apocrine metaplasia,
sclerosing adenosis, duct ectasia, etc..
Molecular: Monoclonal with frequent PIK3CA
mutations.
Management: Variable, but likely don’t need re-
excision after core biopsy
Papilloma with DCIS

Foci of DCIS (or ADH) superimposed on
an intraductal papilloma.
Focal monotonous cells with cytologic

and architectural features of low-grade
ductal neoplasia.
For low-grade lesions, use same size

criteria cut-off for ADH (<3mm) vs DCIS
(≥3mm).
For intermediate and high-grade

lesions, there is no size criteria.
Papillary DCIS
DCIS lining filiform, arborizing
fibrovascular cores devoid of
myoepithelial cells, but contained
in a duct with preserved
surrounding myoepithelial cells.
May be deceptively bland with

stratified spindled cells, compact
columnar cells, or clear cells.
Often accompanied by other

patterns of DCIS.
Grade based on nuclei.

Encapsulated Papillary Carcinoma
Carcinoma with fine fibrovascular stalks covered by
neoplastic epithelial cells of low to intermediate
nuclear grade, typically present within a cystic
space, and surrounded by a fibrous capsule.
No myoepithelial cells are present in the papillae or
at the periphery.
Circumscribed, round masses. Typically old women.
Pushing border with fibrous capsule.
Very favorable prognosis→ Stage as pTIS

If invasion beyond the capsule with an infiltrative
appearance→ then invasive carcinoma (likely of
NST), so one must sample the wall thoroughly
Solid Papillary Carcinoma

Solid, expansile, nodular growth with delicate
fibrovascular cores.
Monotonous, round to spindled-shaped epithelial
cells with mild to moderate nuclear atypia and
eosinophilic, granular cytoplasm.
Frequently show neuroendocrine differentiation.
If entirely rounded, well-circumscribed nodules

(regardless of if there are myoepithelial cells) →
Solid papillary carcinoma in situ
If infiltrating strands or ragged borders→ Solid
papillary carcinoma with invasion. Frequently
mucinous.
Good prognosis.
Invasive Papillary Carcinoma

Invasive carcinoma with fibrovascular cores covered
by neoplastic epithelium.
Frankly invasive, infiltrating growth.
No myoepithelial cells anywhere in lesion.
Very rare.
Must exclude metastasis (e.g., Ovarian or lung)

Algorithmic Approach
From: Tse GM et al. The role of immunohistochemistry in the differential diagnosis of papillary lesions of the breast.
J Clin Pathol. 2009 May;62(5):407-13.
Fibroepithelial and Mesenchymal/Spindle Cell Lesions

Fibroepithelial Lesions
Fibroadenoma
Circumscribed, benign neoplasm of the Terminal
Duct Lobular Unit (TDLU) with a biphasic proliferation
of epithelial and stromal cells.
Painless, solitary, slow-growing mobile masses.
Most common in younger women.
Hormone-sensitive, can grow during pregnancy.
Molecular: Not usually monoclonal, but frequent
MED12 mutations in stromal cells
Intracanalicular pattern→ expansion of stroma
compresses ducts into slit-like spaces
Pericanalicular pattern→ stroma grows around open
ducts
NO stromal overgrowth, cytologic atypia, significant
mitotic activity or well-developed fronds (otherwise
consider Phyllodes tumor!)
Can have lipomatous or smooth muscle metaplasia.
Can have superimposed DCIS, etc..
Juvenile Fibroadenoma:
More common in adolescents. Large and grow
rapidly. Pericanalicular growth with increased stromal
cellularity. Intraductal gynecomastoid UDH
Most FA do not recur after complete surgical excision
Hamartoma
Well-demarcated, generally encapsulated mass composed
of normal breast tissue components.
Lobulated and show ducts, lobules, fibrous tissue, and
adipose tissue in varying proportions (normal
components). Sometimes called “adenolipoma.”
Requires clinical and/or imaging correlation to distinguish
from normal breast→ Round and well-circumscribed lesion
Phyllodes Tumor
Fibroepithelial neoplasm with prominent
intracanalicular growth and stromal hypercellularity
Exaggerated intracanalicular growth→ “Leaf-like”
projections into variably dilated lumina
Increased stromal cellularity, particularly accentuated
adjacent to the epithelium. Sometimes heterogeneous.
Malignant phyllodes show:
• Stromal overgrowth (4x field without epithelium)
• Increased mitoses (≥10 per 10 HPFs)
• Increased stromal cellularity (Often diffuse)
• Infiltrative borders
• Malignant heterologous elements (except well-differentiated liposarcoma,
as it has a low metastatic risk)
When a Tumor has some but not all the features of malignancy, consider
“Borderline.”
Molecular: Recurrent MED12 mutations support a shared pathogenesis with
fibroadenomas. Additional mutations include: TERT, TP53, PTEN, RB1, and
EGFR
Risk of recurrence can also be calculated using the Singapore General Hospital
Nomogram
If unsure FA vs Phyllodes on core biopsy→ consider “fibroepithelial tumor,”
with a DDX.
Histologic Feature Fibroadenoma Benign Phyllodes Borderline Phyllodes Malignant

Phyllodes
Tumor Border Well-defined Well-defined Well-defined, maybe Permeative
focally infiltrative
Stromal Cellularity Variable, usually Cellular, usually mild, Cellular, usually Cellular, usually
uniform and scant may be non-uniform moderate, may be non- marked and diffuse
of diffuse uniform or diffuse
Stromal Atypia None Mild or none Mild or moderate Marked
Mitotic Activity Usually none (<2 Usually low (<5 per 10 Frequent (5-9 per 10 Abundant (≥10 per
per 10 HPF) HPFs) HPFs) 10 HPFs)
Stromal Overgrowth Absent Absent Absent (or very focal) Often present
Malignant heterologous Absent Absent Absent Maybe present
elements
Frequency Common Uncommon Rare Rare
Proportion of all N/A 60-75% 15-26% 8-20%
Phyllodes tumors
Behavior Benign. Recurrence Benign. Recurrence Benign. Recurrence even Malignant.
rare more common more common.
Modified from: WHO Classification of Breast Tumors. 2019.
Spindle Cell Lesions
Pseudoangiomatous Stromal Overgrowth aka “PASH”
Proliferation of myofibroblasts amongst
collagenous stroma forming anastomosing slit-
like channels (resembling blood vessels, but not
actually vascular, hence the “pseudo”).
PASH is non-neoplastic and is thought to be an
aberrant stromal response to hormones and
typically presents as an incidental mass-forming
lesion.
It is benign and needs no treatment.
Myofibroblastoma
Benign tumor of mammary stroma composed of fibroblasts
and myofibroblasts. Often presents as slow-growing painless
mass. Cured by local excision
Purely mesenchymal (no epithelium or myoepithelial cells)
Well-circumscribed, unencapsulated
Bland, spindled cells; rarely epithelioid
Short, haphazardly intersecting fascicles
Interspersed thick collagen bundles
Minimal mitoses and atypia
IHC: (+) Desmin, CD34, ER/PR/AR; Loss of RB1
Molecular: 13q14 deletions by FISH in majority of cases
(contains RB1)
Desmoid Fibromatosis
Benign (never metastasize), but infiltrative with strong tendency to
recur (>25%). Interestingly, microscopic margins do NOT predict
recurrence.
background.
Microhemorrhages and scattered chronic inflammation.
IHC: Nuclear β-catenin (more cells with deep than superficial).
Some actin (+)
Molecular: Associated with FAP and mutations in the APC/β-catenin
(CTNNB1) pathway
Metaplastic Carcinoma
Invasive Breast Cancers with differentiation of epithelium
towards squamous or mesenchymal-looking elements.
Usually present as a mass; Rare, <1% of all breast cancers.
Several distinct patterns (with some overlap, often mixed):
Low-grade Adenosquamous Carcinoma

Well-developed, rounded glands and tubules associated
with solid squamous nests infiltrating through desmoplastic
stroma. Sometimes associated “cannon ball” lymphoid
aggregates. Good prognosis.
Fibromatosis-like Metaplastic Carcinoma

Bland spindled cells with pale eosinophilic cytoplasm and
slender nuclei in stroma with variable collagen. Only mild
nuclear atypia. Often arranged in fascicles. Some cells may
be plumper/epithelioid. Good prognosis.
Spindle Cell Carcinoma

Atypical spindle cells with a variety of architectural patterns
(e.g., fascicles, herringbone, etc…). Elongate to plump
spindled cells with moderate to high-grade cytologic atypia.
Often associated inflammation. Includes a spectrum of
tumors from sarcomatoid SCC to myoepithelial carcinoma.
Worse prognosis.

Pure squamous cell carcinoma. Often cystic. Must exclude
a metastasis. Worse prognosis.
Metaplastic Carcinoma with Heterologous Mesenchymal

Differentiation
Essentially a carcinosarcoma. Heterologous elements may
include chondroid, osseous, and rhabdoid components.
Epithelial and mesenchymal components can have variable
atypia. Sometimes extensive sampling is necessary to find
the epithelial component (and exclude a primary sarcoma).
IHC: Vast majority do not express ER, PR, or HER2 (Triple

Negative). However, they do express some epithelial
markers:
(+) p63, HMWCKs (e.g., CK5/6), CK AE1/AE3
(-) CK7, CD34,
(+/-) SMA, CD10, Desmin, β-catenin
Molecular: Frequent TP53, PIK3CA, and WNT pathway

mutations. May be derived from late dedifferentiation or
basal-like stem cells.
Clinical: Much fewer LN metastases.

Hemangioma
Benign proliferation of mature blood vessels.
Usually non-palpable, found on imaging.
Most likely non-neoplastic.
Well-differentiated vessels of varying size.

Often non-anastomosing.
Endothelium without nuclear atypia
(hyperchromasia or pleomorphism), mitoses, or
multi-layering.
Excision is not necessary.
Atypical Vascular Lesion

Benign. Occur in irradiated skin (often of breast).
Often small/multiple.
Irregularly-shaped thin-walled vessels with branching and
anastomosing growth. Lined by a single layer of endothelium
with some hobnailing and hyperchromasia.
NO endothelial cell multilayering or true cytologic atypia
IHC/Molecular: No MYC overexpression/amplification.
Angiosarcoma
vessels, while other areas may show solid sheets
of high-grade cells.
Can be epithelioid or spindled.

necrosis, endothelial cells piling up, and/or
mitotic figures (although mitoses can be seen in
some benign tumors)
Grade does not predict prognosis (all aggressive)
Post-radiation angiosarcoma:
Occurs after radiation (usu. ~5yrs).
High-level amplification of MYC (by IHC or FISH) is
a hallmark of this lesion.
Adenomyoepithelioma
Biphasic proliferation of inner ductal cells
and outer myoepithelial cells.
Essentially like Epithelial-Myoepithelial
Carcinoma of the salivary gland.
Various patterns, but can be tubular with
prominent myoeps with clear cytoplasm; or
have more spindled myoeps with admixed
ducts
Typically older women with palpable mass.
Usually benign but can de-differentiate into
a carcinoma.
Molecular: Frequent PIK3CA, ATK1, and
HRAS mutations
Other Lesions Schwannoma Leiomyosarcoma

Neurofibroma Lipoma
Nodular fasciitis Granular cell tumor Angiolipoma
Inflammatory myofibroblastic tumor Leiomyoma Liposarcoma
Immunohistochemical Staining
A panel should include some combination of: Multiple Cytokeratins (CK AE1/AE3, CK5/6, CK34βE12),
p63, SMA, CD34, desmin, S100, ERG
For spindle cell lesions, always
consider metaplastic carcinoma
and/or stromal overgrowth in a
Phyllodes tumor. Sample the
lesion well, looking for an
epithelial component and stain
it with multiple epithelial
markers.
Indeed, given the limitations of

sampling, be particularly careful
(and perhaps descriptive) on
core biopsy!
Always be weary diagnosing a

primary sarcoma in the breast.
From: Liu H. Application of immunohistochemistry in breast pathology: a review and update. Arch Pathol Lab Med. 2014 Dec;138(12):1629-42.
Reactive and Non-Proliferative Lesions

Non-Proliferative Lesions
Fibrocystic Change
Most common non-proliferative lesion of the breast!
No significant increased risk of cancer.
Cysts = fluid filled, dilated terminal duct lobular units.

Still have inner epithelial and outer myoepithelial cells.
Epithelium may be markedly attenuated.
Frequent apocrine metaplasia. Rarely squamous
metaplasia
May contain calcifications
Cyst walls often contain areas of fibrosis
Apocrine metaplasia = enlarged epithelial cells with

abundant, granular, eosinophilic cytoplasm and apical
luminal blebbing. Round nuclei with prominent
nucleoli. Can sometimes be papillary. Can enhance on
MRI. ER (-), AR (+). Sometimes fewer myoeps.
Inflammatory/Reactive Lesions
Biopsy Site Changes
Changes after a biopsy/prior surgery.
Frequent changes include:
Organizing hemorrhage (with hemosiderin laden
macrophages and blood)
Fat necrosis (with foamy macrophages)
Foreign body giant cells and/or foreign material
Granulation tissue
Scarring/fibrosis
Acute and chronic inflammation
Squamous metaplasia
Pitfall Warning: After a biopsy, there can be “epithelial displacement” where epithelium (benign or
atypical) can be found within the stroma and/or vascular spaces! This is particularly common with
papillary lesions. This can result in the erroneous diagnosis of invasive carcinoma. When the epithelial
fragments are confined to biopsy site, a diagnosis of epithelial displacement should be favored! A
diagnosis of invasive carcinoma should only be made if epithelium is found in the stroma away from
the biopsy site or if there are other characteristic findings.
Fat Necrosis
After injury (surgery, biopsy, or trauma).
However, sometimes incident is not
remarkable.
Can mimic malignancy clinically and/or
radiographically
Cystic spaces surrounded by lipid-laden
(“foamy”) macrophages
Variable acute and chronic inflammation
Early→ hemorrhage
Late→ fibroblastic proliferation and collagen
deposition
Reactions to Foreign Material

Silicone granuloma:
Silicone leakage can be seen even without frank implant
rupture. Oval cystic spaces that appear empty or have
amorphous pale material with histiocytes and giant cells.
Can be present in capsule or in draining axillary lymph
nodes.
Synovial Metaplasia:
Implant capsules can develop a lining essentially identical
to synovium
Duct Ectasia
aka Periductal Mastitis
Primarily perimenopausal and post-menopausal
women. Can present with pain, discharge, mass,
or calcifications
Varying amounts of:

• Periductal inflammation
• Periductal fibrosis
• Duct dilation
• Inspissated lipid-rich material, with foamy
macrophages that often infiltrate the wall
• Squamous metaplasia
Diabetic Mastopathy
aka Lymphocytic Mastopathy
Typically young to middle-aged women, most
often with type 1 diabetes, but can be seen
with other autoimmune disorders, presenting
with a mass.
Characteristic findings:
1. Dense, keloid-like fibrosis
2. Periductal, perivascular, and perilobular
lymphocytic infiltrates (mostly B cells)
3. Epithelioid myofibroblasts in the stroma
IgG-4 Related Mastitis

Discrete painless masses.
Classic findings of IgG-4 related disease:

1. Dense lymphoplasmacytic infiltrate,
2. Storiform pattern of fibrosis,
3. Obliterative phlebitis.
IHC: Increased IgG-4 positive plasma cells
Often accompanying lobular atrophy
Granulomatous Mastitis
Granulomas can be seen with a variety of conditions
including sarcoidosis, prior biopsy, duct ectasia, and
infections (e.g., mycobacteria and fungi). So, one must
do bug stains!
Sometimes it can be idiopathic.
Corynebacterium causes a granulomatous infection

with abundant neutrophils and central lipid vacuole.
Diseases of the Nipple

Paget Disease of the Breast
Intraepidermal proliferation of malignant
glandular epithelial cells in the nipple areolar
region.
Clinically, nipple is often erythematous,
crusted, and eroded.
Most cases are a cutaneous extension of DCIS
or invasive carcinoma. If not present, may
derive from Toker cells.
Tumor cells have abundant pale cytoplasm
with large nucleoli and prominent nucleoli.
May form glandular structures and contain
mucin.
May secondarily invade the dermis.
IHC: (+) CK7, HER2 in most cases. Usu. ER (-)
DDX: SCCIS, Melanoma in situ, Toker cell
hyperplasia
Nipple Adenoma
Benign epithelial proliferation of the
superficial duct orifices. Very rare.
Clinically can mimic Paget’s as often
erythematous and crusted.
Nodular mass directly under the surface
of the nipple, often in continuity with the
surface.
Overall, relatively well circumscribed
Composed of a mixture of simple ducts,
areas resembling sclerosing adenosis,
papilloma, and sometimes florid UDH
Myoepithelial cells surround the ducts.
Stromal fibrosis may entrap ducts in a
pattern resembling invasive carcinoma
Molecular: Frequent PIK3CA mutations
Main significance is to not confuse it with
invasive carcinoma!
Syringomatous Tumor
Benign infiltrative tumor resembling a cutaneous
syringoma.
Locally infiltrative tumor in the dermis and
smooth muscle of the nipple and areola,
composed of bland cells with glandular and
squamous morphology.
No destructive invasion into ducts or epidermis.
Poorly-circumscribed.
Often has keratin-filled cysts near the surface.
Like the cutaneous counterpart, many of the nests
are “tadpole” shaped with comma-like tails
IHC: Given both glandular and squamous cells,
staining is variable, but dominant cell type stains
with p63 and HMWCKs, with variable
myoepithelial marker staining.
ER (mostly -); HER2 (-)
Squamous Metaplasia of the Lactiferous Ducts “SMOLD”

Squamous metaplasia of
lactiferous ducts, with abundant
keratin in the lumen→ clogging.
Surrounded mixed stromal
inflammatory infiltrate with
foreign body giant cell reaction,
extruded keratin, and possible
abscess formation.
May occur at any age.
Highly associated with smoking
Also known as “Recurrent
subareolar abscess” and “Zuska
disease”
Requires excision of duct to resolve
CHAPTER 9
Gynecologic
Lesions of the Vulva

Non-Neoplastic Lesions
Lichen Sclerosus (formerly lichen sclerosus et atrophicus)
Most common in postmenopausal women. 4
Autoimmune disease. 4
Clinically appears as white to red plaques with 1
wrinkling and hypopigmentation resembling 1
“tissue paper.”
Causes pruritis and pain.
Sclerosis of papillary dermis and atrophy of
overlying epithelium.
3
1) Hyalinization and edema in papillary dermis
(“homogenization”)
2) Some degree of vacuolar degeneration of
basal keratinocytes
3) Band-like lymphocytic infiltrate beneath 3
2
homogenized collagen.
4) Epidermal atrophy
Increases risk of differentiated VIN.
Lichen Simplex Chronicus

Non-specific pattern in response to chronic rubbing/scratching.
Can be seen in association with other disorder (e.g., Candida
infection, contact dermatitis) or due to clothing or other
irritation.
Clinically looks thickened, leathery, scaled (“Lichenification”)
Marked hyperkeratosis (sometimes parakeratosis)
Hypergranulosis
Irregular epidermal hyperplasia
Papillary dermis is thickened with vertical dense collagen
between papillae
Lots of spongiosis? → consider contact dermatitis
Neutrophils in stratum corneum? → consider fungal → PAS/GMS
Bartholin’s Cyst Bartholin Glands

(can be seen in wall of Bartholin cyst)
Vulvar cyst due to Bartholin gland duct outlet
obstruction with subsequent retention of mucinous
secretions (Duct→ Cyst).
Located in posterior vestibule.
Unilocular with smooth inner lining of nonkeratinizing
squamous, transitional, or mucinous epithelium.
CHAPTER 10
Skin
CHAPTER 11
Pediatrics
CHAPTER 12
Genitourinary
CHAPTER 13
Tumors in the Epithelium
Seborrheic Keratosis
Benign. Clinically, “Stuck-on” look
Varying degrees of: Acanthosis, hyperkeratosis,

interlacing pigmented epidermal strands,
papillomatosis, and horn cysts
Hidradenoma Papilliferum
Benign. Often presents as an
asymptomatic nodule.
Virtually identical to intraductal
papilloma of the breast
Well-circumscribed subepithelial nodule
Papillary proliferation with tubular glands
Apocrine differentiation with apical snouts
Two cell layers (inner epithelial and outer
myoepithelial) can be seen on IHC.
Squamous Intraepithelial Lesion (SIL)

Intraepithelial (in situ, non-invasive), squamous dysplasia due to HPV infection.
Clinically, can be flat or plaque-like, white to reddish-brown in color, and asymptomatic or pruritic
Vulvar Intraepithelial Neoplasia grade 1 (VIN1)
Can be due to High or Low-risk HPV. Most common during
reproductive age. Low risk of progression to cancer.
Proliferation of hyperchromatic basal-like cells that extends no
more than 1/3 of the way up the epithelium
Cells differentiate (gain cytoplasm) in upper epithelium
Mitoses confined to lower zone. Epithelium often thickened.
Many nuclei are hyperchromatic with irregular nuclear contours
(at all levels)
Koilocytes = large superficial cells

with perinuclear halos and large,
irregular, “Rasinoid” nuclei.
Sometimes binucleated.
Often spontaneously regresses, so

just observed clinically with repeat
cytology
Condyloma acuminatum→ grossly evident variant of LSIL. Often composed of papillary fronds.
Squamous Intraepithelial Lesion (SIL) (Continued…)
Associated with High-risk HPV (usually type 16). Higher risk
of progression to invasive carcinoma if left untreated
compared to LSIL, but not super high absolute risk.
Proliferation of hyperchromatic basal-like cells that extend
2/3 of the way up (VIN2) or full-thickness (VIN3/CIS) of the
epithelium
Cells have enlarged, hyperchromatic nuclei with irregular
nuclear contours and increased N:C ratios.
Little to no superficial maturation.
Mitoses common at all levels, including atypical mitoses
Nucleoli are unusual→ raise the possibility of inadequately
sampled invasive carcinoma (p16+) or metaplasia (p16-)
Can colonize skin appendages→ mimicking invasion!
Treatment includes: excision, laser ablation, topical

chemotherapy
When to use P16 Immunohistochemistry
Used as surrogate marker of High-risk HPV infection
• When the morphologic DDX is between HSIL (P16 +) and a mimic (P16 -)
• When you are considering a Dx of VIN2, which should be P16+ (vs. LSIL,
which should be P16 -)
• When there is disagreement between pathologists
• When there is a high-risk for missed HSIL disease (e.g., HPV +)

negative.
Differentiated-type Vulvar Intraepithelial Neoplasia
HPV-negative squamous dysplasia.
Predominantly in elderly women, associated with
lichen planus and lichen sclerosus.
Basal cell atypia with nuclear hyperchromasia.
Anastomosing of rete ridges.
Atypical basal mitoses. Prominent nucleoli.
Superficial terminal differentiation
(cornification) with hyperkeratosis and
dyskeratosis
IHC: p16 negative (non-block positive), p53
mutant with strong staining of all basal cells (see
example), Ki67 profoundly increased.
Higher risk/quicker progression to invasive SCC
than normal VIN3, so treat with excision.
p53 IHC→
(Extramammary) Paget Disease

Intraepithelial proliferation of apocrine-like cells.
Often old Caucasian women. Often red, pruritic lesion.
Large, round “Paget” cells with prominent pale
cytoplasm and nucleoli spreading throughout
epithelium. Can be single cells or in groups/glands.
Can extend down adnexal structures.
Important to rule out cutaneous pagetoid spread of
urothelial or GI cancer with IHC (see below)
Treatment: Resection, but high rates of recurrence.

Can progress to invasive adenocarcinoma.
CK7 CK20 GCDFP-15 CDX2 CEA S100, MelanA, UPK III HER2 GATA-3
etc…
Primary
Paget Disease + - + - + - - + +
Urothelial
carcinoma + + - - - - + - +
Anorectal
carcinoma +/- + - + + - - - -
Melanoma - - - - - + - - -
An invasive epithelial tumor composed of squamous cells with varying degrees of differentiation.
Derived from HSIL (HPV-related) or Differentiated VIN (not HPV-related)
Most common vulvar malignancy. Most common in elderly.
Most important factor determining outcome→ Lymph node status
Most important factor determining Lymph node metastases→ depth of invasion
Femoral and inguinal lymph nodes are the sites of regional spread
Sheet-like growth with infiltrating bands and single cells
Often desmoplastic/inflammatory stroma
Two main morphologic types:
Keratinizing Basaloid
Squamous Squamous
Carcinoma Carcinoma
High-risk HPV No Yes (Type 16>18)
association
Associated Differentiated-type VIN Classic VIN

precursor lesion
Basaloid SCC Keratinizing SCC
Association with Common. Often Lichen Rare
inflammatory sclerosus
condition
Morphology Keratinizing Warty, Basaloid
Age Older females Younger females
Distribution Usually unifocal Often multifocal

Verrucous Carcinoma: Highly-differentiated,
Prevalence More common Less common exophytic SCC variant with prominent acanthosis,
(approximately 80%) (approximately 20%) minimal nuclear atypia, superficial cells with
IHC p53: Some cases positive p53: Negative abundant eosinophilic cytoplasm, and broad
p16: Negative p16: Positive “pushing” invasion (non-infiltrative) with an
associated inflammatory infiltrate. Lymph node
Modified from: CAP Cancer Protocol Template: Vulva. 2020. metastases are very rare.
Other Tumors
Melanocytic nevi—Like nevi elsewhere on the skin, but remember the vulva is a “special site.” As
such, there can be concerning (but benign) changes including Pagetoid spread, moderate cytologic
atypia, an adnexal spread. There should be dermal maturation and no dermal mitoses.
Melanoma—Malignant. Variable appearances (epithelioid to spindled). Large nuclei, prominent
nucleoli. Absence of maturation. Lots of mitoses. Extensive pagetoid spread.
Basal Cell Carcinoma—Like elsewhere on the skin. Basaloid cells with peripheral palisading.
Bartholin Gland Carcinomas—can be SCC, adenocarcinomas, transitional cell, etc…
Mammary-type Adenocarcinoma—like breast cancers in the breast, thought to arise from anogenital
mammary-like glands. Notably, you can get phyllodes tumors too!
Adenocarcinoma of Skene glands—resembles prostate cancer. Stains with PSA
Unique Vulvar Mesenchymal Lesions
Fibroepithelial Stromal Polyp
Benign.
Polypoid growth with variably cellular central
fibrovascular core covered in squamous epithelium.
Stroma contains predominantly bland spindled cells. Can
see multinucleated stroma cells with degenerative-type
atypia including significant pleomorphism.
Most common in reproductive age women.
Can grow during pregnancy.
Massive Vulvar Edema

Also called “Vulvar hypertrophy with lymphedema”
(or other, similar, names)
Reactive (non-neoplastic), likely due to lymphatic
obstruction.
Associated with obesity and immobilization.
May present with generalized vulvar enlargement,
papillomatous plaques, polyps, or pedunculated
masses.
Dermal edema with uniformly distributed cells.

Dilated lymphatics (arrows).
Perivascular inflammation.
Aggressive Angiomyxoma
Benign (despite name!), but with a tendency to
recur after incomplete recurrence.
Often presents as a “cyst” in reproductive age
Large (>5 cm), poorly-circumscribed, infiltrative.
Gelatinous consistency.
Low-grade, hypocellular. Composed of small,
bland spindled cells with scant cytoplasm.
Numerous blood vessels of varying sizes,
including thin-walled capillary-like and thick-
walled arteries with radiating perivascular
smooth muscle.
Invades fat and muscle. Extravasated RBCs.
No mitotic activity of atypia.
IHC: (+)ER, PR, desmin. (+/-)CD34
Molecular: HMGA2 rearrangements
Treatment: Complete surgical resection. Most
people treated with first surgery.
Superficial Angiomyxoma
Benign with localized recurrences.
Small (<5 cm), exophytic polypoid mass centered in skin
and subcutaneous tissue (“Superficial”!!). Multilobulated.
Well-dermarcated, but unencapsulated.
Hypocellular myxoid nodules in dermis.
Bland stellate and spindled cells and inflammatory cells
(classically neutrophils) and numerous delicate vessels.
Can envelope skin adnexal structures/epithelium
Cellular Angiofibroma
Benign. Usually painless superficial mass or polyp.
Small (<5 cm). Rare.
Circumscribed, but unencapsulated. Often traps fat at edges.
Composed of uniform bland spindled cells in fibrous stroma.
Small to medium-sized blood vessels with thick hyalinized
walls.
Sort of resembles a spindle-cell lipoma, but with wispy
collagen.
Superficial Myofibroblastoma
Benign.
Discrete, unencapsulated. Usually small (< 5 cm)
Oval to spindled cells with wavy nuclei and scant
cytoplasm
Fine collagenous stroma. Varied architecture.
Thin-walled vessels, which might be dilated and
“Stag-horn”
IHC: (+) Desmin, ER/PR; (+/-) CD34
Angiomyofibroblastoma
Benign. Non-recurring.
Small (<5 cm), circumscribed.
Alternating hypocellular and
hypercellular areas
Spindle and plump epithelioid or
plasmacytoid cells
IHC: (+) Desmin, ER/PR; (-) CD34

Tumors of the Cervix

Squamous Lesions
Squamous Metaplasia
The process where glandular endocervical cells are replaced with squamous epithelium
The primary importance of this lesion is that it can closely resemble HSIL
In contrast to SIL, metaplasia:
- has uniform chromatin
- has minimal nuclear contour irregularities
- is more likely to have residual mucinous epithelium
- is p16 negative
Squamous Intraepithelial Lesion (SIL)

Intraepithelial (in situ, non-invasive), squamous dysplasia due to HPV infection.

Proliferation of hyperchromatic basal-like cells that extends
no more than 1/3 of the way up the epithelium
Cells differentiate (gain cytoplasm) in upper epithelium
Mitoses confined to lower zone
Many nuclei are hyperchromatic with irregular nuclear
contours (at all levels)
Koilocytes = large superficial cells
with perinuclear halos and large,
irregular, “Rasinoid” nuclei.
Sometimes binucleated.
Often spontaneously regresses, so

just observed clinically with repeat
cytology
Condyloma → grossly evident morphological variant of LSIL. Often composed of papillary fronds.
Human Papilloma Virus (HPV)

Sexually Transmitted Disease
Serotypes: 16 &18 → Most associated with HSIL/SCC
6 &11 → Most associated with LSIL/Condylomas
Usually infects transition zone between squamous and glandular mucosa.
HPV can infect epithelium without integrating into the nucleus, creating LSIL/Condyloma (often
transient, self-limited) or integrate, where viral oncogene overexpression drives a clonal production of
undifferentiated cells causing HSIL (precancerous)
HPV-associated oncoprotein E6 inactivates p53, E7 inactivates Rb
Squamous Intraepithelial Lesion (SIL) (Continued…)
Proliferation of hyperchromatic basal-like cells that extend
2/3 of the way up (CIN2) or full-thickness (CIN3/CIS) of the
epithelium
Cells have enlarged, hyperchromatic nuclei with irregular
nuclear contours and increased N:C ratios.
Little to no superficial maturation.
Mitoses common at all levels, including atypical mitoses
Nucleoli are unusual→ raise the possibility of inadequately
sampled invasive carcinoma (p16+) or metaplasia (p16-)
Variants:
Keratinizing—abnormal surface keratinization
Papillary—papillomatous architecture
Treatment: Given risk of progression to SCC, often treated

with LEEP, laser ablation, cryotherapy, or surgical conization.
When to use P16 Immunohistochemistry

Used as surrogate marker of High-risk HPV infection
• When the morphologic DDX is between HSIL (P16 +) and a mimic,
such as squamous metaplasia (P16 -)
• When you are considering a Dx of CIN2, which should be P16+ (vs.
LSIL, which should be P16 -)
• When there is disagreement between pathologists
• When there is a high-risk for missed HSIL disease (e.g., HPV +)

negative.
An invasive epithelial tumor composed of squamous cells of varying degrees of differentiation.
Virtually all associated with HPV infection, most commonly types 16 or 18, and arise from HSIL
World-wide, 2nd or 3rd most common cancer in women, mostly in low resource countries without
cervical cancer screening programs (Pap smears) and programs to manage precursor lesions.
In the US, rates have dropped dramatically in recent history due first to screening, and now to HPV
immunizations.
Morphologically, most are non-keratinizing and

basaloid
Sheet-like growth with infiltrating bands and single cells

Often desmoplastic/inflammatory stroma
Can be keratinizing or non-keratinizing
With invasion can see “paradoxical maturation” with
increased cytoplasmic eosinophilia
Several subtypes including, keratinizing, non-
keratinizing, basaloid, Verrucous, papillary, and
lymphoepithelioma-like
Treatment depends on stage, but often involves
chemoradiation.
Tumor depth of invasion must be calculated for all
Stage 1 carcinomas. This is measured from the base of
the HSIL origin (or nearest dysplastic epithelium if the
site of origin is not apparent) to the deepest point of
invasion.
Note: if tumors are severely ulcerated or largely
exophytic, measuring depth of invasion may be
hard/impossible.
Invasive Squamous Cell Carcinoma HSIL colonization of endocervical glands

Paradoxical maturation of cells from high N:C ratio Paradoxical maturation absent.
HSIL to invasive cells with more abundant Same cells throughout lesion
eosinophilic cytoplasm
Stromal reaction present with edema, desmoplasia, No stromal reaction
and/or inflammation
Irregular contours of nests: angulated, wavy, or Regular, rounded nests
bulging, resulting in unusual shapes
Anastomosing nests of atypical cells (after tangential Anastomosing absent
sectioning is excluded)
No nearby uninvolved glands Often residual uninvolved glands nearby
Glandular Lesions
Endocervical Polyp
Benign. Most common growth of cervix
Focal hyperplastic protrusions of benign
endocervical glands and loose fibrous stroma
May have cystic change of glands
Frequently associated inflammation.
May have surface squamous metaplasia
Napothian Cyst
Common. Non-neoplastic. Usually incidental and asymptomatic.
Endocervical gland dilation after outlet obstruction
Grossly dilated cysts filled with translucent mucoid material

Lined by a single layer of columnar mucinous endocervical
epithelium, but may be flattened due to atrophy.
Microglandular Hyperplasia
Benign. Very common.
Tightly packed glands/tubules lined by
flattened to cuboidal cells with eosinophilic
cytoplasm sometimes a small mucin vacuole.
Uniform small nuclei with rare mitoses.
In florid cases, can have reticular (“net-like”)
or solid growth with increased atypia.
No invasive growth.
Often associated inflammation
p63 highlights a subset of the cells.
Usually vimentin negative and ER/PR positive
Arias Stella Reaction

Benign change seen during pregnancy
Glandular cells are markedly enlarged with irregular,
hyperchromatic nuclei and abundant vacuolated cytoplasm.
Hobnail and papillary architecture with nuclear pseudostratification
Often only focal within cervix. Does not form a mass.
Main importance is that it can be confused with clear cell
carcinoma. In contrast though, this reactive condition lacks mitotic
figures, does not form a mass, and is seen only during pregnancy.
Tunnel Clusters
Benign. Common. Incidental.
Clusters of benign endocervical glands often near
the surface. Can be cystically dilated.
Main importance—can be confused with minimal
deviation adenocarcinoma (but in contrast, tunnel
clusters are superficial and have no atypia or mitotic
activity)
Endocervical Glandular Hyperplasia

Both confined to the inner 1/3–1/2 of the cervical wall with no mitoses or atypia.
Lobular Endocervical Glandular Hyperplasia (LEGH)
Rare. Proliferation of tightly packed small endocervical glands in a lobular pattern, resembling gastric
pyloric gland epithelium.
Thought to be the precursor lesion to Gastric-type/Minimal deviation adenocarcinoma
Diffuse Laminar Endocervical Glandular Hyperplasia (DLEG)
Rare. Proliferation of tightly packed small to medium-sized endocervical glands. No lobular architecture,
but has a clearly defined base.
Tubal Metaplasia
Benign. Non-neoplastic. Incidental.
Endocervical glandular epithelium is replaced by tubal
epithelium, which is ciliated with intercalated “peg”
cells
Main significance—can be confused with AIS. However,
tubal metaplasia shouldn’t have mitoses, has no
significant atypia, and should be 1 cell layer thick.
Can also have endometrioid or tuboendometrioid
metaplasia (with varying resemblance to normal
endometrium)
Mesonephric Remnants
Benign vestigial embryologic remnants from the
mesonephric duct.
Most common in lateral aspect of the cervix
Small tubules/cysts deep within the wall of the
cervix, often arranged in clusters.
Tubules lined by cuboidal cells and have central
characteristic pink PAS-positive secretions.
IHC: GATA-3 and TTF-1 frequently +
P16, ER negative
If large collection→ Mesonephric hyperplasia (still
maintains lobular growth though)
Adenocarcinoma In Situ (AIS)
Non-invasive adenocarcinoma, so confined to normal, pre-existing glandular epithelium on surface and in
endocervical glands. Maintained lobular architecture. Caused by High-risk HPV, classically type 18
Often nearby HSIL.
Cell crowding, pseudo-stratification, mucin-depletion
Enlarged nuclei with variable size/shape
Hyperchromasia. Sometimes large nucleoli
“Floating” mitoses (near surface, see arrows).
Atypical mitoses
Apoptotic debris
IHC: P16 diffuse/strong positive. Loss of ER/PR staining
Ki67 higher than adjacent normal endocervix
Uncommon features:
Cribriform growth, Goblet cells
Intraglandular tufting, branching, papillary
Unique Variant:
Stratified Mucin-producing Intraepithelial Lesion
(SMILE)—Stratified epithelium with nuclear atypia,
hyperchromasia, and mitotic figures. Has mucin
vacuoles at all cell layers.
Endocervical Adenocarcinoma, Usual type

An invasive adenocarcinoma of the cervix with relative mucin-depletion. HPV-mediated (P16-positive).
Most common type of endocervical adenocarcinoma by far (~90%)
Often presents with vaginal bleeding and a mass. May be exophytic or ulcerated.
Most tumors are well- to moderately-differentiated

Cribriform to papillary architecture
Characteristic morphology with mucin-poor glands
and pseudostratified, enlarged, hyperchromatic
nuclei. Must have <50% of cells with mucin.
Frequent floating mitotic figures and apoptoses.
Hints for invasion (beyond “infiltrating” growth):
• Very complex architecture
• Haphazard growth
• Extension of glands beyond the depth of normal
endocervical glands, esp. if near thick-walled
blood vessels
• Stromal reaction (edema, chronic inflammation,
or desmoplasia)
• Increased eosinophilic cytoplasm and prominent Site of Origin Immunohistochemical stain
nucleoli Endocervical P16+, ER/PR-, Vimentin-
• Exophytic villoglandular surface growth
Endometrial ER/PR+, Vimentin+ (cup-like), P16-
IHC: P16 block positive. PAX8+. HPV ISH+
Both PAX8
Patterns of Invasion (Silva system):
A B C
Silva Morphology Risk Treatme

Group nt
Well-demarcated glands with rounded contours, usually forming groups. Low No need
No destructive stromal invasion, single cells, or lymphovascular invasion. (No LN for nodal
A Complex intraglandular growth acceptable (cribriform, papillae), but no solid mets) sampling
growth. May be hard to separate from AIS. THINK:“AIS-like”
Localized (limited, early) destructive stromal invasion arising from pattern A Middle Sentinel
glands (well-demarcated glands). Individual or small groups of tumor cells, (Rare LN lymph
B separated from pattern A-type glands, frequently in desmoplastic or inflamed mets) node
stroma. LVI acceptable. Lack of solid growth (well-moderately differentiated). sampling
Diffuse destructive stromal invasion, characterized by: Diffusely infiltrative High Need
glands, with associated extensive desmoplastic response. Glands often (Frequent nodal
C angulated or with canalicular pattern, with interspersed open glands LN mets) resection
Confluent growth filling a 4x field (5 mm).
Solid, poorly differentiated component (architecturally high grade)
Modified from: Roma AA, et al. New pattern-based personalized risk stratification system for endocervical adenocarcinoma with important clinical
implications and surgical outcome. Gynecol Oncol. 2016;141(1):36-42.
Gastric Type
NOT related to high-risk HPV.
Diffuse infiltration (without a distinct mass) of stroma
Infiltrating glands lined by cells with abundant pale to
eosinophilic cytoplasm and distinct cell borders.
Malignant cytologic features: Round, vesicular nuclei,
often with prominent nucleoli
Glands show marked variation in size and shape.
Tumor is usually deeply invasive, often with a
desmoplastic response.
Typical presentation: profuse watery discharge and
“barrel-shaped” cervix
IHC: p16 usually negative. P53 is sometimes mutated.

Loss of hormone receptor expression.
Often express: PAX8, CK7, HNF-1β, and NapsinA.
Putative precursor lesion: LEGH.
Prognosis: Significantly WORSE than usual-type

adenocarcinoma
Minimal Deviation (“Adenoma Malignum”)
Highly differentiated form of gastric-type adenocarcinoma
Numerous deceptively bland glands, which often lack
surrounding stromal desmoplasia.
Deeply invasive with haphazard distribution
Architectural abnormalities: intraglandular papillary
protrusions and irregular profiles.
At least focally, some glands display malignant cytologic
features (vesicular nuclei with distinct/prominent red
nucleoli) and are associated with stromal desmoplasia
Associated with Peutz-Jegher’s syndrome
Mucinous Carcinoma
HPV-associated.
Typical HPV-morphology: “floating” mitoses, frequent
apoptoses, but with >50% of cells with intracytoplasmic
mucin, often in a background of usual-type
adenocarcinoma.
Subtypes: NOS, Signet ring cell type, Intestinal, and iSMILE
(Invasive stratified mucin-producing carcinoma, which has
peripheral palisading)
Mesonephric Carcinoma
Rare. Develop from mesonephric remnants.
Often located deep in lateral cervical stroma.
Characteristic glandular spaces with eosinophilic PAS-D
positive secretions.
Variable architectural patterns: tubular, papillary, etc…
Often small, tightly-packed glands with low-cuboidal cells.
Relatively bland, uniform cytology
IHC: Similar to mesonephric remnants, express CK7, PAX8,
TTF-1, GATA3, apical CD10. Patchy P16. Negative ER/PR
Villoglandular Carcinoma
Well-differentiated variant of usual-type.
Often occurs in young women.
Exophytic surface component of papillae lined by
epithelium that has only mild atypia.
Papillae can be thin or thick.
Similar staining pattern to usual-type endocervical
adenocarcinoma (p16-positive)
Excellent prognosis.
NOT associated with high-risk HPV. Associated with DES.
Cells with abundant clear to granular eosinophilic cytoplasm
Large, hyperchromatic, pleomorphic nuclei
Solid, cystic, or papillary architecture.
Frequent “hobnail” appearance
IHC: Positive HNF-1β, and NapsinA (but not all that specific!)
P16 +/-, p53 wild-type, ER/PR -
Other Subtypes
Adenoid basal carcinoma—Rare. Composed of small, well-differentiated rounded nests of basaloid cells
that have scant cytoplasm and which resemble basal cell carcinoma. Only focal gland formation. Good
prognosis.
Adenoid cystic carcinoma—Rare. Resemble salivary gland tumor: cribriform and tubular patterns of
growth with basement membrane-like material.
Serous carcinoma—Rare. Resembles Serous carcinoma of the uterus/ovary. Must exclude secondary
involvement/metastasis.
Endometrioid—Rare. Resembles uterine endometrioid adenocarcinoma. Must consider secondary
involvement/metastasis. May arise from endometriosis.
Adenosquamous carcinoma—Rare. Contains malignant squamous and glandular components. Must
have good gland formation. May arise from SIL or AIS. Similar behavior to usual-type adenocarcinoma.
Glassy Cell carcinoma—Rare. Variant of adenosquamous carcinoma characterized by cells with sharp
cytoplasmic margins, “ground glass” appearing eosinophilic cytoplasm, and large round nuclei with
prominent nucleoli. Often in young women. Aggressive with frequent metastases at presentation.
Frequently eosinophilic inflammation.
Neuroendocrine Tumors/Carcinomas
Use same classification system as GI tract (see separate GI guide with more info).
Cervical Neuroendocrine Tumors (NETs) are extremely rare.
Neuroendocrine carcinomas (NECs) may be seen in association with other in situ of invasive
carcinomas.
Cervical Adenocarcinoma Typing Algorithm
Cytoplasmic mucin?
Limited cytoplasmic
Cytoplasmic mucin
mucin
Positive HPV-ISH HPV-ISH

Positive
Negative
Usual-type
Negative
adenocarcinoma Mucinous
Positive ER
Carcinoma
ER
Positive
Endometrioid Negative
Adenocarcinoma Negative
GATA3 Mucinous
Positive adenocarcinoma Gastric-type
of the adenocarcinoma
Negative endometrium
Mesonephric
Carcinoma
Clear Cell
carcinoma
Modified from: Stolnicu S, Barsan I, Hoang L, et al. Am J Surg Pathol. 2018;42(8):989-1000.

NOTE: This journal article also contains great IHC tables with % staining of each tumor for each marker.
HPV-status Unifying morphology Tumors included

Apical mitotic figures and
Usual-type
apoptotic bodies easily
HPV-Positive appreciable at scanning
Mucinous
Villoglandular
magnification
Gastric
Clear Cell
Absence of usual findings
HPV-Negative (Diverse histology)
Endometrioid
Serous
Mesonephric
IHC Endocervical Endocervical Endometrial Serous carcinoma

adenocarcinoma, adenocarcinoma, endometrioid
usual type gastric type carcinoma
p16 Block positive Negative or patchy Patchy, variable Block positive
P53 Wild-type Some mutated Wild-type (usually) Mutated
ER/PR Negative Negative Positive Negative (usually)

High-risk HPV Positive Negative Negative Negative
Non-Epithelial/Mesenchymal Lesions
Rhabdomyoma
Benign. Non-recurring.
Haphazardly-arranged, interlacing, mature, bland-
appearing rhabdomyoblasts with oval or tubular
shape.
Cytoplasmic striations. No mitoses or necrosis.
IHC: +Desmin, Myogenin, MyoD1
Rhabdomyosarcoma
Malignant tumor with skeletal muscle differentiation.
Most commonly Embryonal subtype.

Polypoid tumors of small, round or spindled
hyperchromatic cells.
Subepithelial condensation→ “Cambrium layer”
Variable skeletal muscle differentiation (e.g., strap
cells, rhabdomyoblasts). Frequent cartilage nodules.
IHC: +Desmin, Myogenin, MyoD1
Blue Nevus
Benign, melanocytic lesion.
Grossly appear as blue/black flat nodules, often 2-3mm.
Markedly elongated spindle cells in submucosa.

Often heavily pigmented dendritic projections.
Often organized parallel to surface
IHC: +S100, SOX10, HMB45, MelanA, MiTF
Leiomyoma
Benign tumor with smooth muscle differentiation.
Resemble uterine leiomyomas.

Well-circumscribed.
Intersecting fascicles of spindled cells.
“Cigar-shaped” nuclei.
No significant mitoses, atypia, or necrosis.
Can also get leiomyosarcomas.

Always think Broadly!

Consider the 4 main families
Ovarian
of ovarian tumors
Tumors
Sex Cord-
Germ Cell Epithelial/Surface Metastasis
Stromal
~10% ~70% ~15% Always a possibility,
often from GI tract
~5%
Dysgerminoma
Teratoma Remembering the “pentagons” can help

Choriocarcinoma
you remember that there are 5 of each
Sometimes
“Mixed”
Yolk Sac Embryonal

Nests of cells resembling
Bladder in fibrous stroma
Brenner Mucinous epithelium

Cells resembling fallopian tube
(must consider GI
2 pathways:
source if carcinoma)
1)Low-grade (KRAS/BRAF mt)
2) High-grade (p53 mt and
genetically unstable) Serous Mucinous
Endometrioid Clear Cell
Resembles endometrial glands

Large, clear cells with pleomorphic nuclei
Associated with Endometriosis
Associated with Endometriosis
Epithelial/Surface Subclassification:
Three levels of biologic potential
Borderline/
Cystadenoma &
Low Malignant Carcinoma
Adenofibroma
Potential
Benign Malignant
Borderline Tumors:
aka: “Atypical proliferative serous tumor” or “Low Malignant Potential (LMP)”
Neither clinically benign or malignant: Peritoneal dissemination and recurrence, but rarely death
Neither morphologically benign or malignant: Architectural complexity, but no invasion or high-
grade cytology
Serous and seromucinous borderline tumors are morphologically and clinically borderline.
Mucinous, endometrioid, and clear cell borderline tumors are morphologically borderline, but
clinically benign.
Given the differences in outcome between borderline and carcinoma, these tumors must be well
sampled (>1 section / cm) to appropriately exclude a carcinomatous component.
Distribution of each Epithelium type by biologic potential:

Serous Mucinous Endometrioid Clear Cell Brenner/ Seromucinous
Transitional
Benign 50% 80% 5% <1% 99% <1%
Borderline 15% 15% 20% <1% <1% 99%
Carcinoma 35% 5% 75% 99% <1% <1%
Common mixtures of Epithelial tumors:

• Brenner + Mucinous Cystadenoma or Borderline
• Serous + Seromucinous Borderline
• Endometrioid + Clear Cell Carcinoma Histologically exists, but likely
not a true histomolecular entity
that will eventually disappear as
likely composed of serous and
endometrioid tumors
Epithelial/Surface
Serous Fallopian Tube-like Thought to arise from either tubal metaplasia of cortical inclusion cysts
(likely derived from surface mesothelium) or tubal implant
Serous Cystadenoma/Adenofibroma
Benign. Often incidental and asymptomatic in
reproductive age.
Epithelium resembles fallopian tube
• Cuboidal to columnar cells; Simple architecture
• Ciliated
• Sometimes stratified; No hierarchical branching
Can be cystic → Serous cystadenoma
>1 cm in size (if < 1cm considered a cortical
inclusion cyst)
Can have a prominent exophytic fibrous component →
Serous adenofibroma
Can have BOTH → Serous cystadenofibroma
Molecular: Typically polyclonal (not neoplasms→
hyperplastic expansion of epithelial inclusions)
Serous Borderline Tumor

Typically middle-aged women (mean 40s)
Grossly, cystic with a papillary proliferation that resemble

cauliflower; Often bilateral
Non-invasive tumors with greater epithelial proliferation
and atypia
• Hierarchical branching: papillae branch into
progressively smaller papillae
• Epithelial tufting of columnar to cuboidal cells
• Minimal to moderate cytologic atypia
Proliferative area must be >10% of epithelial volume →
otherwise call it “Serous cystadenoma/fibroma with focal
epithelial proliferation”
Molecular: KRAS and BRAF most common
IHC: Express ER, PR, PAX8, WT-1;
p53 wild-type; P16 non-diffuse
Can spread to peritoneum through “implants”
Prognosis depends on stage:
• If limited to ovary→ very good prognosis Can progress to low-grade serous
• If peritoneal implants→ risk of recurrence and carcinoma→ so must be sampled well!
potentially progression to low-grade serous carcinoma
Implants: Peritoneal spread of a Serous Borderline Tumor
Non-invasive implant: Are there small, solid nests of cells
No infiltration of fat or muscle, high- surrounded by a cleft-like space,
grade cytology, or micropapillary micropapillae, and/or cribriform
architecture growth? If so→ best to just call
Can have desmoplasia→ low-grade serous carcinoma as it
“desmoplastic implant” behaves the same
Diffuse high-grade cytology→
Invasive implant:
High-grade serous carcinoma
Fat or muscle invasion.
Serous Borderline Tumor-Micropapillary Variant

Aka: “non-invasive serous carcinoma”
Non-hierarchical branching architecture
Fine micropapillae, 5x taller than they are wide, coming off larger
fibrotic papillae
Sometimes micropapillae fuse→ cribriform growth
Cells are cuboidal with high N:C ratios with often prominent nucleoli
This component must be lager than 5mm to make Dx
When low stage→ same outcome as SBT; Higher stage →
comparatively worse outcome
Low-Grade Serous Carcinoma

Patients about one decade younger than High-grade
Often bilateral and advanced stage
Most often arise in Serous Borderline Tumors
Several patterns of invasion:
• Single, infiltrating pink cells
• Irregularly-shaped infiltrative nests
• Micropapillae and macropapillae surrounded by
cleft-like spaces
Frequent psammoma bodies→ sometimes can even
obscure tumor → “psammocarcinoma”
Cells often have often moderate cytologic atypia
Fairly uniform population of cells and low mitotic
activity (<2-3/HPF) compared to High-grade serous
carcinoma
Mutations and IHC like Serous Borderline Tumor
Prognosis depends on stage.
Does not respond as well to Platinum-based therapy (as
less proliferative compared to High-grade) Microinvasion: < 5mm
High-Grade Serous Carcinoma
Usually older women (60s), presenting with
nonspecific symptoms at advanced stage→
responsible for most ovarian cancer deaths
Often bilateral and exophytic
Most commonly solid areas with slit-like spaces.
Sometimes papillary or cribriform.
Lots of necrosis and mitoses.
Large, hyperchromatic, pleomorphic nuclei. Often
prominent nucleoli.
Molecular: TP53 nearly always; about half have
inactivating (germline or somatic) BRCA mutations.
Lots of chromosomal and copy number changes.
IHC: WT-1 and PAX8 positive; Variable ER, PR,
p53 overexpressed or null; P16 “Block” positive
BRCA1&2→ Very high risk → often get prophylactic salpingo-oophorectomy (entirely submitted for
histologic eval, esp. fimbriae)
BRCA-related cancers often have Solid, pseudo-Endometrioid, and Transitional morphology (“SET”)
and lots of tumor-infiltrating lymphocytes
Most originate in fallopian tube: Normal tube → P53 mutation → Serous tubal intraepithelial
carcinoma (STIC) → Invasive High-grade serous carcinoma of tube → spreads to ovary
(Essentially, tubal origin until proven otherwise. Only consider primary ovarian if both tubes are
completely histologically examined and free of disease. If both tubes and ovaries negative→ primary
peritoneal)
Treat with cytotoxic chemotherapy and often debulking staging surgery
Low-Grade Serous Carcinoma High-Grade Serous Carcinoma

Cytology Uniform round to oval nuclei Pleomorphic nuclei (>3:1)
Chromatin Even Irregular
Mitoses ≤12 /HPF >12 /HPF
P53 Wild-type Mutated
P16 Patchy Block-positive
Mutations BRAF, KRAS P53, BRCA
Precursor Serous Borderline Tumor Serous Tubal Intraepithelial Carcinoma
lesion (STIC), usually
Architecture Papillary, with hierarchical branching Solid to papillary with slit-like spaces
Response to Minimal (not proliferative) Good

Chemo
Mucinous Mucinous epithelium like GI tract
Mucinous Cystadenoma/Adenofibroma
Benign. Usually unilateral.
Wide age range (average 50)
Grossly cystic/multicystic with a smooth surface
Single layer of mucinous epithelium either resembling
gastric (foveolar-type) or intestinal (with goblet cells)
Minimal atypia; Only very rare mitoses.
No epithelial tufting or broad papillae
Molecular: Frequent KRAS mutations
Adenofibromas are uncommon
Can have a clonally related Brenner or dermoid cyst
component
Mucinous Borderline Tumor

Wide age range.
Usually Unilateral, multicystic, with a smooth surface
Lined by mucinous epithelium with mild to moderate
nuclear atypia (not high-grade)
Varying degrees of epithelial tufting, stratification, villi,
and papillae.
Proliferative area must be >10% of epithelial volume
If there is high-grade cytologic atypia→ “Intraepithelial
carcinoma”
Can rupture→ leak mucin into stroma →
“pseudomyxoma ovarii”
Can have nodules in wall with atypical spindled cells and
lots of mitoses, but CK-negative→ “Sarcoma-like mural
nodules” → Benign clinical course
Molecular: Frequent KRAS Mutations
Can progress to mucinous
Prognosis is generally very good, even with intraepithelial carcinoma→ must be sampled well to
carcinoma. And still not bad with microinvasive exclude an invasive component!
carcinoma.
If it is truly just borderline, subsequent
transformation to carcinoma is rare.
Mucinous Carcinoma
Malignant. Average age ~45
Most tumors confined to ovary at presentation. Unilateral.
Large, complex solid and cystic mases without surface
involvement.
Two main patterns of growth:
1. Confluent/expansile glandular growth with little stroma
2. Destructive stromal invasion with infiltrating irregular
glands, nests, and single cells in desmoplastic stroma
(This pattern is less common and should prompt
consideration for a metastasis)
Increased cytologic atypia and mitoses
Often exist on a spectrum with concurrent cystadenoma and
borderline components
Can have mural nodules with large atypical spindled to
rhabdoid cells that react with cytokeratin→ “Anaplastic
carcinoma” (in contrast to sarcoma-like nodules in borderline
tumors)
If destructive invasive component is <5mm in greatest
dimension→ microinvasion
Molecular: KRAS mutations frequent
Prognosis: Since disease is usually confined to the ovary, often
good prognosis. However, if advances stage, then poor
prognosis.
Primary Ovarian Metastatic Mucinous Tumors

Laterality Unilateral Bilateral more often
Size Large (usually > 20 cm) Smaller (usually <10 cm)
Gross Multicystic ± solid component with Nodular with cystic component
smooth capsule
Location Within stroma Within surface and stroma
within ovary
Microscopic Well-differentiated mucinous Infiltrative mucinous glands
epithelium forming organized cysts
(borderline) or confluent glands
(carcinoma)
Extraovarian Usually absent (Stage 1) Often present
disease
Adapted from a presentation by Dr. Anne Folkins, Stanford University

Mucinous Tumor Immunohistochemistry:
CK7 CK20 ER/PR CDX2 SATB2 PAX8
Ovarian mucinous borderline and + -/+ - + - +/-

carcinoma
Ovarian seromucinous borderline and + - + - - +
carcinoma
Metastatic Colon Cancer -/+ + - + + -
Metastatic Gastric Cancer + -/+ - + - -
Metastatic low-grade appendiceal -/+ + - + + -

mucinous neoplasm (LAMN)
Likely best panel: CK7 (strong positive in ovarian) and SATB2 (strong positive in lower GI).
Pax8 is helpful if positive but isn’t always positive in primary ovarian (specific, but not sensitive).
Mucinous Borderline Tumors vs. Low-grade Appendiceal Mucinous Neoplasm

I remember that the appendix often has mucinous neoplasms, could this cytologically low-
grade tumor be a metastasis from the appendix?
Primary Ovarian Mucinous Secondary involvement by a

Borderline Tumor Low-grade Appendiceal
Mucinous Neoplasm (LAMN)
Size Large (>20 cm) Variable (usually <20 cm)
Laterality Unilateral Bilateral
Location of Tumor Within stroma, rarely on surface Surface and stromal involvement
Pseudomyxoma Usually absent Prominent
Ovarii
Amount and Abundant; organized cysts Scant; haphazard
Pattern of
Epithelium
Appendiceal Absent Present
Tumor
Adapted from a presentation by Dr. Anne Folkins, Stanford University
Clear Cell Clear cells (the name says it all!), with no normal counterpart
Clear Cell Cystadenoma/Adenofibroma

Benign. Extremely RARE! Associated with endometriosis.
Widely spaced simple glands in fibrous stroma. Cells clear to eosinophilic with bland nuclei.
No mitoses.
Clear Cell Borderline Tumor

Extremely RARE! Associated with endometriosis.
Round to oval glands in fibrous stroma. Clear to eosinophilic cells with Moderate nuclear pleomorphism.
Mild epithelial layering. NO invasion or stromal reaction. Infrequent mitoses. Good prognosis.

Malignant. Older middle age.
Usually unilateral, solid to cystic
Associated with endometriosis
Considered High-grade (but no need to grade).
Clear cell morphology:
• Clear or eosinophilic granular cytoplasm
• Angulated, pleomorphic, hyperchromatic nuclei,
with prominent nucleoli
• Hobnail cells
• Varied architecture: Papillary, tubulocystic,
glandular, or solid sheets
• Hyaline globules
Low mitotic index
Molecular: ARID1A mts most common. Also PIK3CA.
IHC: CK7, HNF-1β, and Napsin A positive (none of
these are specific though, so rely on morphology most)
WT-1 and ER/PR negative; Usually wild-type p53
Glycogen-rich cytoplasm is PAS positive, diastase
sensitive
Prognosis: Depends on stage (low stage behaves well).
Can be associated with vascular thrombosis and
paraneoplastic hypercalcemia
DDX: Yolk sac tumor→ Positive Glypican-3, AFP, SALL4; Negative CK7
Dysgerminoma→ Positive Oct3/4, SALL4 ; Negative CK7
Serous carcinoma→ Positive WT-1, often ER; Diffuse or Null p53
Endometrioid carcinoma→ Positive ER (usually)
Endometrioid Endometrial glands, like in the uterus
Endometriotic Cyst Aka: Endometrioma

Benign. Common, usually middle aged. Cystic form of endometriosis. Non-neoplastic.
Frequently associated with endometriosis elsewhere in pelvis.
Grossly hemorrhagic/dark brown → “chocolate cyst”
Endometrial glands + Endometrial stroma (often with hemorrhage + hemosiderin-laden macrophages)
Can undergo malignant transformation → Endometrioid, Clear cell, and Seromucinous carcinoma
Endometrioid Cystadenoma/Adenofibroma
Benign. Uncommon. Cystic lesion lined by endometrial glands without any endometrial stroma.
When dense fibrous component→ adenofibroma.
Likely just endometriomas in which stroma is indistinct.
Associated with endometriosis
Endometrioid Borderline Tumor

Uncommon. Middle-aged. Associated with endometriosis.
Unilateral, solid or cystic. Hemorrhagic.
Crowded or back to back endometrial glands lined by cells
with mild to moderate cytologic atypia→ resembles atypical
hyperplasia / Endometrial Intraepithelial Neoplasia (EIN)
Can be papillary, protruding into cystic lumen
No destructive stromal invasion and/or confluent/expansile
glandular growth > 5mm
If severe enough atypia → Intraepithelial carcinoma
Prognosis: Excellent
Endometrioid Carcinoma Malignant. Late middle-age. Often unilateral, low-stage.

Often associated with endometriosis.
Resembles endometrial cavity endometrioid adenocarcinoma
→ Back-to-back glands with confluent or cribriform growth
→ Complex villoglandular, papillary, or Labyrinthine glands
Less commonly destructive growth
Squamous morules/differentiation common.
Occasional mucinous metaplasia
Molecular: β-Catenin/Wnt pathway dysregulation, PTEN
inactivation, PIK3CA, ARID1A, and TP53 (in high-grade)
IHC: Usually ER/PR positive; WT-1 negative; P53 can be
positive in high-grade endometrioid
Prognosis: Good if low-stage. Bad if high-stage.
Transitional/Brenner Transitional epithelium, resembling urothelium of GU tract
Brenner Tumor
Benign. Often older adults, but can get at any
age.
Usually small, unilateral, solid, firm mass with
small cysts
Nests of Transitional epithelium/urothelium
(resembling Walthard’s rests) set in dense
fibrous stroma
Mucinous differentiation can be common and
extensive
Calcifications common
IHC: Urothelial immunophenotype (+p63, p40,
CK7, GATA-3, uroplakin III, thrombomodulin)
Borderline Brenner Tumor

Brenner tumor with papillary areas resembling non-
invasive, low-grade papillary urothelial carcinoma
No destructive stromal invasion
Often large, cystic tumors
Prognosis: Generally benign with some local recurrences
Malignant Brenner Tumor

Brenner tumor with papillary areas resembling
invasive, high-grade papillary urothelial carcinoma
Stromal invasion: Irregular nests, confluent growth,
Marked cytologic atypia
Need to see underlying Brenner tumor!
Otherwise, likely serous carcinoma (sometimes can
have a Transitional look) or metastatic urothelial
carcinoma
Seromucinous Epithelium with both serous and mucinous appearance
Although this exists histologically, it is likely not a true histomolecular entity and will eventually disappear
as likely composed of serous and endometrioid tumors. Nevertheless, it is in the WHO (for now).
Seromucinous Cystadenoma/Adenofibroma
Benign. Very RARE.
Cystic with two or more Müllerian cell types including mucinous and serous.
Less often also endometrioid, transitional, and/or squamous
Seromucinous Borderline Tumor

Usually younger (~30s), and Unilateral.
Cystic tumor with smooth surface and inside papillary
excrescences
Non-invasive, proliferative epithelial tumor containing at
least 2 types of epithelium. Most often: 1) Serous and 2)
Endocervical-type mucinous
Can also include endometrioid, clear cell, transitional. If

these are present, use term “Müllerian Borderline Tumor”
Complex papillary growth. Stroma often edematous.

Often lots of neutrophilic inflammation.
Similarities with serous borderline tumor:
• Hierarchical and papillary growth
• Dissemination of peritoneal implants
• Can (rarely) progress to carcinoma
Differences from serous borderline tumor:
• Strong association with endometriosis
• Malignant potential lower
• Morphologically resembles endometrioid tumors with
mucinous metaplasia
• Little/no WT-1 staining
• ARID1A mutations in many (like some endometrial)
Prognosis: Generally good, even with implants
Seromucinous Carcinoma
Rare.
Carcinoma containing predominantly serous and endocervical-type mucinous epithelium
Sex Cord-Stromal A little variable, but often stain with some combination of: Inhibin,
calretinin, SF-1, FOXL2, Melan A
Fibroma/Thecoma
Fibroma:
Benign stromal tumor composed of spindled cells with abundant collagen.
Grossly solid, firm, chalky white.
Bland nuclear features. Varying patterns including storiform to bundled.
Usually middle-aged and unilateral. If young/bilateral, and esp. if lots of calcifications → consider Gorlin
syndrome (Nevoid Basal Cell Carcinoma Syndrome)
Meig’s syndrome = fibroma + ascites + pleural effusion; relatively rare
“Cellular Fibroma:” Cellular with scant collagen, only mild atypia, increased mitoses
Thecoma:
Benign stromal tumors composed of sheets of uniform cells with pale greyish-pink cytoplasm.
Cytologically bland. Reticulin surrounds individual cells.
Usually unilateral, post-menopausal women. Often Estrogen producing!
Grossly solid and yellow (as full of lipid/fat)
Fibroma Fibrothecoma Thecoma
Less Less
Collagen; Collagen;
More More
Cells; Cells;
More More
cytoplasm cytoplasm
Sclerosing Stromal Tumor

Benign. Rare! Young women. Unilateral.
Bland rounded and spindled cells with eosinophilic

to vacuolated cytoplasm
Pseudolobular architecture: arranged in cellular

nodules in a hypocellular, edematous to
collagenous background
Dilated, thin-walled, branching, Stag-horn vessels

Sex Cord Tumor with Annular Tubules (SCTAT)
Composed of aggregates of simple or complex annular tubules
Cells are columnar with clear cytoplasm with an “antipodal”
arrangement of the nuclei (at opposite ends)
Hyaline cores within nests
Occur in Two Settings. Generally, broad age range. Often

younger.
1) Sporadic: Can have a low-grade malignant course. Often
unilateral, larger. Set in fibrous stroma. More complex growth
2) Peutz-Jeghers Syndrome: Benign, often incidental finding.

Often multiple, small, bilateral tumors. Set in normal ovarian
stroma.
Granulosa Cell Tumors

Two types, occurring in different settings with different prognoses:
Adult Granulosa Cell Tumors

Wide age range, but often middle-aged. Usually unilateral, low-stage.
Solid with some cystic, hemorrhagic areas
Secrete estrogen→ menorrhagia, post-menopausal bleeding, or
amenorrhea.
Cells: Scant pale architecture with grooved nuclei
Varied architecture: Sheet-like, trabecular, ribbon-like, microfolicular
(with “Call-Exner bodies” filled with pink secretions). Occasional
macrofollicular architecture.
Frequent mitoses
IHC: Usual sex-cord stromal stains, plus WT-1, some keratins, and
others
Molecular: Majority have FOXL2 point mutations
Low-grade malignant: can recur and even metastasize, even after long
intervals, but not very common
Juvenile Granulosa Cell Tumors

Occurs mainly in children and young adults. Less common.
Secrete estrogen→ precocious puberty, menorrhagia, or amenorrhea
Cells: Round, with abundant eosinophilic cytoplasm and NO
GROOVES
Architecture: Macrofollicular with usually basophilic secretions
Frequent mitoses.
Molecular: NO FOXL2 mutations
Prognosis: Good, with infrequent recurrences
Leydig Cell Tumor
Benign. Usually older middle-aged women. Unilateral
Secrete androgens → Masculinization
Changes include: hirsutism, amenorrhea, breast
atrophy, clitoral hypertrophy, and hoarseness
Cells with abundant pink, granular cytoplasm
Regular round nuclei with vesicular chromatin
May contain rod-like eosinophilic crystals (Reinke crystals)
Fibrinoid necrosis of vessels
Sertoli Cell Tumor

Any age, usually younger. Unilateral. Solid to cystic.
Can be estrogenic.
Very Varied architecture: Tubular (with or without
lumens), trabecular, diffuse, alveolar, pseudopapillary,
etc…
Cells with eosinophilic to pale cytoplasm and round

nuclei with visible nucleoli
Usually Benign, but can be malignant.
Sertoli-Leydig Cell Tumors

Any age, often younger. Solid. Unilateral.
Contain varying proportions of Sertoli and Leydig cells
Leydig cell component secretes androgens→
masculinization
Sertoli cell component can have very varied

architecture.
Varying degrees of differentiation.
Can have slit-like areas resembling rete testis→
“retiform”
Can have heterologous differentiation, including
mucinous epithelium
Molecular: DICER 1 mutations common

Germline DICER 1 mutations→ multinodular goiter,
Sertoli-Leydig cell tumors, pleuropulmonary blastoma
Prognosis: Well-differentiated→ very good

Worse is higher grade/stage
Steroid Cell Tumor
Middle-aged. Unilateral.
Secrete androgens (usually), estrogens, or
corticosteroids (rarely)
Polygonal cells with abundant cytoplasm that is

eosinophilic (lipid poor) to vacuolated (lipid rich).
Round nuclei.
NO Reinke crystals
Usually benign, but can be malignant (if large, lots of
mitoses, atypia, and/or necrosis)
Rare Types (Where the Name Says It All)

Signet-Ring Stromal Tumor
Microcystic Stromal Tumor
Leutinized thecoma-associated with sclerosing peritonitis
Metastasis
Spread from extraovarian sites→
most commonly GI tract
More often bilateral
Especially hard to discriminate from primary for

mucinous tumors (see previous
table/discussions)
Signet ring cells strongly favor a metastasis from

the stomach or breast
Colon cancer is the most common metastasis

and often has a distinctive look with “dirty
necrosis” and a “garland” pattern of growth
After GI, breast is the most common

Germ Cell Tumors Derived from Germ Cells. Rapidly growing→ Chemo-sensitive
Almost exclusively in young women and girls.
Dysgerminoma Think: Clear/White color
Most common germ cell tumor.
Large, solid, fleshy. Usually unilateral.
Large polygonal cells with clear to eosinophilic
cytoplasm, distinct cell membranes, vesicular chromatin,
and prominent nucleoli
Fibrous septae and nested architecture
Lymphocytic infiltrate; Sometimes granulomas
Elevated serum LDH, rarely hCG
Molecular: majority have isochrome 12p; ckit mutations

in many.
Prognosis: Good if treated.
Embryonal Carcinoma Think: Purple color
Rare.
Rudimentary epithelial differentiation
Large “Primitive” cells
Coarse, basophilic chromatin
Amphophilic cytoplasm
Variable architecture (nests, sheets, glands)
Molecular: Isochrome 12p
Aggressive, but respond to chemotherapy
Choriocarcinoma Think: Red color
In ovary, usually non-gestational

(Can get choriocarcinoma after a molar, ectopic,
or normal pregnancy)
Malignant cytotrophoblasts (mononuclear) and

syncytiotrophoblasts (multinucleated)
Abundant Hemorrhage
Very elevated Serum hCG → precocious puberty,

vaginal bleeding, or mimics pregnancy
Yolk Sac Tumor Think: Pink color
Aka: “Endodermal Sinus Tumor”
Large, white, soft with cystic degeneration
Many patterns/architecture
Can also be solid, papillary, etc…
Often hypocellular myxoid areas
Classic: Schiller-Duval Bodies
Hyaline globules
Elevated Serum AFP
Teratoma
Mature
Composed of tissues from 2-3 germ layers. Often cystic and unilateral.
Common elements: Skin (with adnexal structures), Cartilage, GI, Brain, etc..
Mature – exclusively mature tissue; Benign unless a secondary somatic
malignancy develops (usually carcinoma such as SCC or PTC)
Immature – contains immature tissues, typically
primitive/embryonal neuroectodermal tissues → Malignant
Often see neuroectodermal tubules and rosettes
Grade based on amount of immature neuroepithelium (below)
Immature elements can mature to look like cerebral tissue with
chemotherapy even if spread to peritoneum → “Gliomatosis
peritonei”
Generally good prognosis with treatment
Grade Criteria
1 Rare foci of immature neuroepithelium (<
1 in a 4x field on any slide)
2 1-3 foci per 4x field on any slide
3 > 3 foci per 4x field on any slice Immature
Germ Cell Tumor IHC:

IHC Stain Seminoma Embryonal Yolk Sac ChorioCA
Carcinoma Tumor
SALL4 + + + +
OCT 3/4 + + - -
D2-40 + +/- - -
CD117 + - - -
CD30 - + -/+ - Rosettes
Glypican 3 - - + +/-
Teratoma (continued)
“Monodermal” teratomas – composed of only/primarily one tissue type
Struma ovarii – mostly or all thyroid
Carcinoid – resemble well-differentiated neuroendocrine tumors of GI tract. Considered a type of
monodermal teratoma. When combined with struma ovarii→ “stromal carcinoid.” Benign
Miscellaneous
Small Cell Carcinoma, Hypercalcemic-type
Young women. Unilateral.
Associated with paraneoplastic hypercalcemia
Undifferentiated tumor with diffuse growth
Small, monotonous cells with scant cytoplasm
Often focal macrofollicle-like spaces
Often a component of larger cells with more
cytoplasm
IHC: Diffuse WT-1; Focal CK, EMA;
Very Aggressive!!
Small Cell Carcinoma, Pulmonary Type

As the name implies, it’s like the lung (so must exclude a metastasis)!
Older women. Often bilateral with extra-ovarian spread (Advanced, like in the lung!)
Diffuse growth of small cells with scant cytoplasm, “salt and pepper” chromatin, and moulding.
Lots of mitoses and apoptotic bodies. Poor prognosis.
Gonadoblastoma
Contains a mixture of immature sex cord cells and germ cells
Predominantly in young women with gonadal dysgenesis. Not uncommonly bilateral.
Sex cord component: SCTAT-like with nests with hyalinized basement-membrane material in lumens
Germ cell component: often dysgerminoma
Wolffian Tumor
Aka: “Female Adnexal Tumor of Probable Wolffian Origin” or
“FATWO”
Often unilateral, older women, and solid.
Often in adnexa, but distinct from ovary (esp. Broad ligament)
Variable patterns: Sieve-like, retiform tubules, or solid
Cuboidal to columnar cells, but lining cells may be flattened
Usually benign.
Tumors of the Endometrial Cavity

Endometrial Hyperplasia→ Carcinoma Pathway
Proliferative Endometrium
Straight or mildly tortuous tubular glands

Abundant stroma (Stroma ≥ Glands)
Columnar cells with pseudostratified
hyperchromatic cigar-like nuclei and mitoses
Unopposed
Estrogen
Disordered Proliferative Endometrium
Variably/haphazardly shaped glands (e.g, branching),
including cystically dilated
Abundant stroma (Gland : Stroma ratio <2:1)
Glands/cells identical to proliferative endometrium
Often due to anovulatory cycles Unopposed
Estrogen
Hyperplasia (without atypia)
Gland crowding (Gland : Stroma ratio >2:1)
Can be “simple” (normal tubular glands—lowest risk) or
“complex” (abnormal, irregular glands, with even less stroma—
higher risk).
Normal nuclei/cytology (elongate, dense, polarized, nuclei)
Unopposed
Estrogen
Hyperplasia with atypia/
Endometrial Intraepithelial Carcinoma
Crowded glands (Gland : Stroma ratio >2:1)
Typically “complex” architecture with irregular, often back-to-
to back glands
Cytologically altered nuclei: enlarged, rounded, pleomorphic,
loss of polarity, vesicular chromatin, nucleoli.
Unopposed
Estrogen
Endometrioid Carcinoma
Distinction from CAH/EIN is based on stromal invasion, which is
defined by one of the following
1- Loss of intervening stroma: confluent growth, cribriform
growth, or complex folded mazelike epithelium
2- Irregular infiltration of myometrium associated with an
altered fibroblastic stroma (desmoplastic response)
3- Solid nonsquamous epithelial growth
4- Papillary architecture or villoglandular growth
Complex Atypical Hyperplasia “CAH”
Gland crowding (Gland : Stroma ratio usually >2:1), often
densely crowded with only small amounts of intervening
stroma and back-to-back glands
Nuclear Atypia: relatively enlarged, rounded nuclei with loss
of polarization, chromatin abnormalities (often clearing or
vesicular) and variably prominent nucleoli
Often important to compare nuclei to non-hyperplastic glands
elsewhere in specimen to account for fixation artifact, etc..
If nuclear atypia is too much, consider other diagnoses like
endometroid adenocarcinoma, serous carcinoma, etc…
Although CAH and EIN are often

overlapping diagnoses, they
have slightly different diagnostic
criteria. EIN is likely more
specific, while CAH is more
sensitive.
Endometrial Intraepithelial Neoplasia (EIN) Both are acceptable by the
Conceived as a true carcinoma precursor based on WHO and usage often depends
architectural and genetic abnormalities interpreted on local practice.
as neoplastic.
Diagnostic criteria:
1- Crowded glands with a gland to stroma ratio >1:1
2- Altered cytology of the crowded glands from the
background epithelium (“cytologic demarcation”).
This can be nuclear or cytoplasmic.
- If no background epithelium is present, use same
criteria as for CAH (above)
3- Must be > 1mm within a single tissue fragment
EIN/CAH: Nuclei are enlarged Proliferative Endometrium: Cigar-

and rounded with chromatin like dense nuclei with basal, often
clearing and loss of polarity pseudostratified, arrangement
Endometrioid Carcinoma
Most common carcinoma of the endometrium.
Classically, in post-menopausal women and related to
increased levels of estrogen exposure (associated with
obesity, diabetes, PCOS, and certain medications) and
preceded by hyperplasia.
Often presents with vaginal bleeding (always a concerning
finding after menopause!)
Crowded, complex glandular or villoglandular
architecture.
Cells are often columnar and share an apical border with
Cribriform growth
eosinophilic granular cytoplasm. Nuclear atypia is often
mild to moderate.
Distinction from CAH/EIN is based on stromal invasion,
which is defined by one of the following
1- Loss of intervening stroma: confluent growth,
cribriform growth, or complex folded mazelike epithelium
2- Irregular infiltration of myometrium associated with an
altered fibroblastic stroma (desmoplastic response)
3- Solid nonsquamous epithelial growth
4- Papillary architecture or villoglandular growth Villoglandular growth
Some cut-off’s for the extent of “confluent growth” to be
more objective have been suggested:
Kurman & Norris = 2 mm
Longacre = 30% of total proliferation and should be able
to traverse a 10x field without hitting stroma
Sometimes the cutoff of carcinoma vs CAH cutoff can be
challenging. OK, to diagnose as “CAH bordering on well-
differentiated endometrioid adenocarcinoma” Squamous morules
Frequently see squamous differentiation with morules,
keratin pearls, and intercellular bridges.
Occasionally see secretory changes with glycogen vacuole
or bland spindled epithelial cell component.
Corded and Hyalinized: has cords, clusters, and/or
trabeculae of epithelioid to spindled cells embedded within
hyalinized to myxoid matrix. Often associated with grade 1-
2 glandular component. No prognostic significance, but
sometimes confused with carcinosarcoma, leading to
overtreatment.
IHC: (+)CK7, PAX8; (-)CK20; Cup-like vimentin staining.
Low-grade often ER/PR +;
FIGO grade % Solid Growth
Grade using the FIGO system: based on the amount of solid
growth. Be sure to exclude squamous morules from this 1 ≤5%
calculation. The grade can be increased by 1 based on severe
2 6-50%
nuclear atypia in the majority of the cells. A confluent
microacinar pattern is often counted as solid. 3 >50%
Endometrioid Carcinoma (continued)
Molecular Classification
Ultramutated (POLE mutated) subtype (~5%): Mutations of DNA polymerase ε result in an extremely high
tumor mutation rate→ lots of neoantigens in tumor cells→ recognized by immune system→ lots of tumor
infiltrating lymphocytes→ Excellent prognosis. Often younger patients. Often grade 3 with intratumoral
heterogeneity and giant tumor cells. Broad invasive front with low clinical stage.
Hypermutated/Microsatellite Instability (MSI) subtype (~25%): Mutations in mismatch repair proteins

result in a high mutation rate → lots of neoantigens in tumor cells→ recognized by immune system→ lots
of tumor infiltrating lymphocytes. Intermediate prognosis despite TILs. Often Grade 3, substantial LVI,
MELF-pattern of invasion. Often located in lower uterine segment. Associated with Lynch Syndrome.
Copy Number High/Serous-like subtype (~25%): Genomically unstable→ high somatic copy number
alterations. Very high rate of TP53 mutations. Often Grade 3 with diffuse high nuclear grade, slit-like
spaces, hobnailing, and destructive invasion. Often older patients and advanced stage. Poor prognosis.
Copy Number Low/Microsatellite Stable (MSS) subtype (~45%): Most common type. Often Grade 1-2,
ER/PR+ with squamous differentiation. Associated with unopposed estrogen exposure (as is seen in
obesity). Overall low mutation rate. Very frequent PTEN mutations. Intermediate prognosis (depends
largely on stage).
Generally, frequent mutations (can be seen all groups) in PTEN, PIK3CA, ARID1A, CTNNB1, and KRAS
In general:
Low-grade (FIGO 1/2): map to the copy number low and MSI-H categories
High-grade (FIGO 3): map to all 4 categories, but least to the copy number low group
Familial syndromes:
Lynch Syndrome: germline mutations in mismatch repair (MMR) proteins → MSI-subtype
~50% lifetime risk (similar to risk of colon cancer).
PTEN-hamartoma tumor syndrome/Cowden syndrome: Germline PTEN mutation→ no specific morphology
Molecular Classification Algorithm:

Endometrioid
POLE mutation Adenocarcinoma
POLE wild type
Ultramutated/
POLE-mutated MMR loss MMR intact
Hypermutated/MMR-deficient p53 overexpressed or null

p53 wild type
Copy number low

P53-mutated/ Serous-like
How do you separate serous carcinoma from serous-like endometrioid carcinoma?

Primarily by morphology (e.g., if there is squamous differentiation→ serous-like endometrioid).
However, both are TP53-mutated and are aggressive, and this can be morphologically challenging,
so this distinction is likely not too important at this time.
Myoinvasion
Endometrium
Can be very challenging to identify/measure! Tumor
Depth of Invasion
Measure from endomyometrial junction to the deepest point of
Myometrial Thickness
invasion.
Report as % (depth of invasion/total myometrial thickness).
Critical clinical cutoff point = 50% (inner vs outer ½)
Myometrial invasion often (but not always!) includes irregular angular

Myometrium
glands eliciting a desmoplastic response or loose granulation tissue
with inflamed edematous fibrous stroma
It can be helpful to look for compressed non-neoplastic glands to

determine the level of the endomyometrial junction.
Carcinoma involving adenomyosis or within vessels do not count as

invasion. So, look for surrounding benign glands and stroma to rule
out colonization of adenomyosis
Challenging patterns of myometrial invasion:

“Pushing” Invasion—broad, expansile front with a mild or absent
stromal reaction. Helpful to submit adjacent normal endometrium to
determine level of endomyometrial junction (if present).
“Microcystic, Elongated, and Fragmented” (MELF)— invasive glands

often lined by a single, flattened layer of epithelium with eosinophilic,
squamoid cytoplasm. Simulate vascular spaces. Associated
edematous, inflamed stroma. Very sneaky!! More aggressive.
Diffusely infiltrative “melter” pattern—individual well-formed glands

with mild to moderate atypia that diffusely infiltrate the myometrium
with minimal stromal reaction (sort of like “adenoma malignum” of
the cervix). Often wide-spread throughout uterus. Make Dx on low-
power from architecture. Can be extremely challenging to evaluate
for superficial invasion, but good prognosis if stage 1, so less
important.
Lymphovascular Invasion
Frequently seen with MELF pattern.
Sometimes intravascular cells can appear “histiocytoid,”
requiring stains to confirm that they are tumor.
Can see frequent vascular “pseudoinvasion” with
laparoscopic hysterectomy specimens, which is thought to
be artifactual/iatrogenic. So, if it is a low-grade, non-
invasive tumor that was removed laparoscopically, it’s
probably “pseudoinvasion.”
An Approach to Difficult Endometrial Lesions Modified from: Mills and Longacre. Surg
Pathol Clin. 2011 March
High-Grade Cytology?
No Yes
Architecture Adenocarcinoma
Be sure to consider:
Serous
Low-risk Intermediate-risk High-risk Clear cell
Note: If the proliferation has

CAH/EIN ≥30% a papillary or labyrinthine
<30% ≥30% <30% growth pattern, there is no %
CAH/EIN Borderline Carcinoma
Borderline requirement.
Architectural Patterns:
High-risk Patterns: Carcinoma
- Glandular confluence without intervening
stroma (10x field)
- Extreme, meandering or labyrinth pattern
- Macroglands with well-developed secondary
branching or multiple generations of bridging
forming a cribriform pattern
- Villous and nonvillous papillae containing
second and third degree branching and/ or
cribriform budding
Intermediate-risk Patterns: Borderline
Low-risk Patterns: Hyperplasia

- Simple budding into small glands
- Macroglands with simple, non-branching
nonvillous papillae or minimal bridging
- Simple non-branching villous and nonvillous
papillae
From: Longacre et al. Am J Surg Pathol. 1995 Apr;19(4):371-406.

Polyps
Benign Endometrial Polyp
Localized, disorganized altered glands and stroma.
Glands: tubules that may be simple, branched, or
cystically dilated. Lined by inactive epithelium.
Stroma: often collagen-rich containing
characteristic thick blood vessels
Often solitary. Can be anywhere in uterus.
Small polyps are often asymptomatic.
Large polyps may cause bleeding.
May have superimposed metaplasia, hyperplasia, or
carcinoma (particularly SEIC in postmenopausal)
Atypical Polypoid Adenomyoma “APA”

Three key features:
1) Endometrial glands with some architectural
complexity and cytologic atypia 2
2) Prominent squamous morules
3) Surrounding prominent cellular fibromuscular stroma 1
Often centered in lower uterine segment. ~2cm.
Associated with MLH-1 promoter methylation (~1/2)
Can be confused with myoinvasive endometrioid
adenocarcinoma, but APA fibromuscular stroma is P16+
(whereas desmoplastic stroma/myometrium is P16-)
Although benign, can progress or be associated with 3
atypical hyperplasia/EIN or endometrioid
adenocarcinoma
Adenosarcoma (Think: Phyllodes tumor)

Mixed epithelial and mesenchymal tumor with a benign
epithelial component and low-grade malignant stroma.
Papillary/polypoid projections of cellular stroma into dilated
gland lumens. Often with condensation, “collaring” around
benign surface glands. Stroma resembles endometrial stroma
but is often more fibroblastic.
Often post-menopausal but can be any age.
Can show heterologous elements and sarcomatous
overgrowth. When ≥25% of tumor is a high-grade sarcoma,
“Adenosarcoma with sarcomatous overgrowth”
IHC: Stroma (+) CD10, ER, PR.
Prognosis: Recurring potential. If sarcomatous overgrowth,
more aggressive→ can metastasize.
Other Endometrial Carcinomas
Serous Carcinoma
Epithelial cells with large atypical nuclei, prominent nucleoli, and
scant cytoplasm. Numerous mitoses.
Often complex papillary architecture. Can be solid or glandular.
Luminal surfaces often appear scalloped (no common apical
border as is seen in endometrioid). Grading not applicable.
Often infiltrates in “gaping” to slit-like (non-solid) glands
Typically post-menopausal women presenting with bleeding.
Often grossly inconspicuous on the surface of a polyp.
Background endometrium often atrophic.
Serous Endometrial Intraepithelial Carcinoma (“SEIC”)—non-
invasive precursor to serous carcinoma; confined to the
epithelium (e.g., surface of a polyp). Malignant: Can still undergo
transtubal metastasis to pelvis.
Molecular: Frequent TP53 mutations. Associated with BRCA1/2.
IHC: p53 mutant (either diffuse or null), P16 block positive.
Prognosis depends on stage (advanced = very bad).

Polygonal or hobnail-shaped cells with clear cytoplasm (or
sometimes eosinophilic) and prominent nuclear atypia
Tubulocystic, papillary, or solid architecture with hyalinized
stroma and eosinophilic extracellular hyaline globules.
Often atrophic background.
Often postmenopausal women with vaginal bleeding.
Grading not applicable.
Relatively poor prognosis.
Mucinous Carcinoma
An endometrial carcinoma in which > 50% of the neoplasm is mucinous. Very rare.
(Most tumors that are mucinous are endometrioid adenocarcinoma with mucinous differentiation)
Often low-grade with glandular or villoglandular architecture and uniform mucinous columnar cells
with minimal stratification/atypia. Frequent KRAS mutations. Can still grade using FIGO System.
Relatively good prognosis.
Be sure to consider endocervical origin on biopsy!
Mixed Carcinoma
The term mixed carcinoma should be used when two or more distinctive subtypes of endometrial
carcinoma are identified, each representing at least 5% of the tumor.
Undifferentiated Carcinoma
Malignant epithelial neoplasm with no differentiation.
Sheets of medium-sized relatively uniform, monotonous,
discohesive cells with often condensed chromatin.
No gland formation (resembles lymphoma). Numerous
mitoses. Often numerous tumor-infiltrating lymphocytes (TIL)
Often form large, polypoid masses within uterine cavity.
Molecular: Often MMR-deficient (some Lynch-associated);
Frequent mutations of SWF/SNF pathway (SMARCA4,
SMARCA1/INI-1, ARID1B de-activation)
IHC: Loss of MLH1/PMS2. Loss/focal Cytokeratins, EMA, ER,
PAX8. (+)CD34
Very aggressive.
Dedifferentiated Endometrial Carcinoma

Two distinct components: 2
1) Low-grade (FIGO 1-2) endometrioid carcinoma 1
2) High-grade undifferentiated carcinoma (see above)
Each component has the IHC/molecular of that component

(e.g., undifferentiated component has SWF/SNF mutations).
Very aggressive.
Carcinosarcoma
Biphasic tumor with two components:
1
1) High-grade carcinoma (epithelial) and
2) Sarcoma (mesenchymal)
Typically post-menopausal women presenting with
vaginal bleeding. Often a large pelvic mass that
prolapses out of the cervix in ~1/2 of cases.
Often intimate admixture of carcinoma and sarcoma
elements.
2
Carcinoma is often serous or endometrioid carcinoma
Sarcoma is often high-grade non-specific sarcoma, but
“heterologous” elements can be seen including:
rhabdomyosarcoma, chondrosarcoma, and
osteosarcoma (which look/stain like they do elsewhere)
Molecular: Frequent TP53 mutations.
Poor prognosis. Frequent pelvic recurrences and lymph
node metastases (of carcinomatous component)
Rhabdomyoblastic differentiation
Helpful Tables
Carcinoma Immunohistochemistry
Endometrioid Serous Clear Cell
(Low-grade)
ER/PR + -/+ -/+
p53 Wild-type Abnormal Wild-type, usually
P16 -/patchy Block-positive -/patchy
PTEN Loss Intact Intact
NapsinA - -/+ +
HNF1β - -/+ +
However, as always, there are exceptions. For example, grade 3 endometrioid carcinomas may exhibit
a “serous” immunophenotype with p53 mutations via dedifferentiation and rare clear cell carcinomas
may also stain with p53.
Endometrial Polyp Classification and Treatment

Diagnosis Epithelium Stroma Management
Benign Endometrial Polyp Benign Benign, Fibrous Polypectomy
Polypoid adenomyoma Benign Benign, Muscle Polypectomy
CAH/EIN in a polyp Atypical/Crowded Benign, Fibrous Hysterectomy or
Hormones
Atypical Polypoid Adenomyoma Atypical/Crowded Benign, Muscle Hysterectomy or
(APA) Hormones
Adenosarcoma Benign Malignant Hysterectomy
Carcinoma Malignant Benign Hysterectomy
Carcinosarcoma Malignant Malignant Hysterectomy
Mesenchymal Tumors of the Uterus
Smooth Muscle Tumors

Stain with: Desmin, SMA, Caldesmon
Leiomyoma
Benign smooth muscle tumor. Most common uterine tumor.
If tons, particularly at a young age, consider hereditary leiomyomatosis and renal cell carcinoma (HLRCC) syndrome.
Still have metastatic potential—“Benign metastasizing leiomyoma”
Variants:
Cellular leiomyoma—significantly increased cellularity compared to normal myometrium
Leiomyoma with bizarre nuclei—bizarre nuclei (smudged, hyperchromatic, pleomorphic) in an otherwise normal
leiomyoma (no mitoses or tumor necrosis)
Mitotically active leiomyoma—increased mitoses, but no atypia or tumor necrosis
Smooth Muscle Tumor of Uncertain Malignant Potential (“STUMP”)

Smooth muscle tumor whose features preclude a definitive diagnosis of leiomyoma vs. leiomyosarcoma
(Either equivocal mitoses or necrosis often; Many IMT’s were previously mistakenly Dx'd as this!)
Relatively low risk of recurrence
Leiomyosarcoma
Malignant smooth muscle tumor. Typically spindle cell, but can be epithelioid.
Want to see: 1) High-grade cytologic atypia, 2) Increased mitoses (typically >2/10 HPF), and 3) Tumor-type necrosis
Genetically complex chromosomal aberrations
Very poor prognosis
Endometrial Stromal Tumors

Low-grade/benign tumors stain like normal endometrial stroma with CD10 and ER/PR; High-grade stains with Cyclin-D1
Endometrial Stromal Nodule

Benign tumor resembling proliferative endometrial stroma with a relatively well-circumscribed margin
Low-grade Endometrial Stromal Sarcoma

Malignant tumor composed of cells resembling proliferative endometrial stroma with infiltrative growth into
myometrium and/or lymphovascular invasion—Often have “tongue-like” growth
Fusion of JAZF1 and SUZ12 (think “Jazzy Suzie”)
Intermediate prognosis, mostly depending on stage
High-grade Endometrial Stromal Sarcoma

Malignant tumor derived from endometrial stromal cells with high-grade round cell morphology.
Typically confluent, permeative, destructive growth. Usually high mitotic activity, necrosis, and LVI.
Fusion: YWHAE-FAM22.
Other Tumors
Undifferentiated Uterine Sarcoma
Malignant tumor arising in the endomyometrium with high-grade cytologic atypia and no specific line of differentiation.
Destructive invasion. Marked cytologic atypia and brisk mitotic activity.
IHC: Variable CD10, Often Cyclin-D1 (+). May see focal SMA.
Complex genetically
Most patients present at high stage. Poor prognosis.
Uterine Tumor Resembling Ovarian Sex Cord Tumor (“UTROSCT”)
Neoplasms resembling ovarian sex cord tumors without endometrial stromal component
Usually well-circumscribed.
IHC: Frequently WT-1 positive, variable expression of Inhibin, calretinin, and Melan-A
Benign course typically.
Rhabdomyosarcoma
Malignant tumor showing skeletal muscle differentiation (like rhabdomyosarcomas elsewhere)
IHC: (+) desmin, myogenin, MyoD1
Perivascular Epithelioid Cell Tumor (PEComa)

Mesenchymal tumor containing epithelioid cells with clear to eosinophilic, granular cytoplasm demonstrating
melanocytic and smooth muscle differentiation, thought to be derived from so-called “Perivascular Epithelioid Cells.”
Mixture of spindled and epithelioid cells, many with granular cytoplasm.
IHC: (+) HMB45 and Melan-A; Variable smooth muscle markers
Inflammatory Myofibroblastic Tumor (IMT)

Spindled to polygonal cells growing in fascicles. Often have myxoid stroma.
IHC: ALK1 positive; variable smooth muscle markers
ALK molecular rearrangements.
Recurring potential.
Tumors with a Glandular Component

Carcinosarcoma
Biphasic tumor with malignant carcinomatous and sarcomatous elements.
Usually old women with a mass prolapsing out of the cervix
Carcinoma: Often serous, sometimes endometrioid
Sarcoma: Often high-grade non-specific sarcoma, but can make heterologous elements (osteosarcoma,
chondrosarcoma, rhabdosarcoma, etc…)
Often advanced stage and poor prognosis
Adenosarcoma
Mixed epithelial and mesenchymal tumor with a benign epithelial component and stroma is low-grade malignant.
(Think phyllodes tumor)
Papillary/polypoid projections of cellular stroma (often with condensation, “cuffing” around glands).
Can show heterologous elements and sarcomatous overgrowth.
MDM2/CDK4 and TERT gene amplifications.
Misc.
Adenomatoid tumor
Benign tumor of mesothelial origin.
Inter-anastomosing pseudo glands with variably sized tubules (sometimes with a signet ring appearance) with associated
smooth muscle hypertrophy (so can be mistaken for a mesenchymal tumor!)
IHC: Tumor cells express CK AE1/AE3 and Mesothelial markers (D2-40, WT-1, Calretinin)
Intraoperative Evaluation of a Hysterectomy for Suspected Endometrial Carcinoma
WHAT TO REPORT INTRAOPERATIVELY:

The following variables should be reported in every case because of their ability to predict
outcome and guide the type of surgery.
- *Histologic subtype (histotype)
- *Grade
- *Myometrial invasion (stage IA/IB) – estimate % involved, not just whether >/< 50%
- *Lymphovascular invasion
- Involvement of cervical stroma (stage II)
- Involvement of adnexa or uterine serosa (stage III)
Indicate whether the reported variables are based on microscopic or gross evaluation.
Grade endometrioid tumors. (FIGO grade 1 or 2 (low grade) vs. FIGO grade 3 (high grade))
Also note whether tumor is exclusively fundal (more likely to skip pelvic lymph nodes and go
right to para-aortic nodes).
REASON FOR INTRAOP EVALUATION:

To guide the type of surgery. There are four options:
1. Hysterectomy alone
2. Hysterectomy with pelvic lymph node dissection (Hyst+Pelvic LND)
3. Hyst + Pelvic LND + Para-aortic LND
4. Hyst + Pelvic LND + Para-aortic LND + omentectomy
The decision is influenced by the aforementioned variables reported intraoperatively. The pre-
operative biopsy/curettage provides only histotype and grade is usually not enough
information to decide on extent of surgery. Thus, the intraoperative evaluation provides the
missing variables that are needed to define how much more surgery should be performed
immediately. The surgeon will integrate this intraoperative path data with intraop surgical
findings and other clinical data (e.g. patient comorbidities) to make an immediate decision
regarding the surgical plan.
OVERVIEW OF PROCEDURE:
1. Review Beaker for pre-operative biopsy diagnosis.
2. Gross evaluation of the unopened uterus for serosal tumor (including surface of
ovaries/tubes, if present).
3. Standardized gross dissection (including Photos prior to slicing).
4. Gross evaluation for endometrial tumor and involvement of myometrium / cervix /
adnexa.
5. When appropriate: Frozen section evaluation of are of most extensive growth beyond
endometrium.
6. Render intraoperative diagnosis.
7. Documentation of relevant gross pathology and details of frozen section sampling on Gross
Template.
8. Pin and fix specimen.
DETAILED PROCEDURE
Step 1: Review Beaker biopsy report. Sometimes biopsy findings may be too limited to
confidently assign a subtype or a grade; conversely, sometimes there may be findings
suggestive of >stage1A growth, such as necrosis or desmoplasia. This info helps guide what to
look for in Hyst.
Step 2: Document presence or absence of grossly visible serosal tumor on uterus (and/or
ovaries/tubes if present). Do FS if suspicious for tumor.
Step 3: Ink paracervical/radial surgical margin and cervical/vaginal cuff. Bivalve uterus. If time
allows, it is strongly advised to take a photo of the bivalved uterus before bread loafing.
Evaluate gross appearance of endometrium, endocervix, ectocervix, and myometrium.
Document presence/absence of abnormalities. Using long bread knife, bread-loaf uterine
body (not endocervix/ectocervix) in thin slices (about 0.5 cm) that run parallel to the right/left
axis. Slice almost entirely all the way deep down to the serosa, but leave serosa intact. If
fibroids are present, do not dissect these using separate slices; simply include them in the
overall parallel bread-loaf slices and ensure that they are fully sliced down to nearly the
serosa. If there is no gross mass/nodule in the endocervix, leave the uterus intact from the top
of the endocervix to the ectocervix. If there is an endocervical lesion suspicious for stage II
cancer, dissect using slices that are parallel to the length of the endocervical canal since this
will allow you to better see the relationship of the lesion to endocervix versus lower uterine
segment. Leave the ovaries/tubes intact without dissecting unless there is suspicion for stage
IIIA cancer.
Step 4: Examine dissected specimen for the location of the endometrial mass, depth of
myoinvasion (if any), cervical invasion, adnexal invasion, serosal involvement. Document on
gross template.
Step 5: Determine if FS needed. Especially in the early phase of gaining experience, it is better
to perform FS to confirm gross impression of tumor stage and to evaluate for more aggressive
component of tumor subtype or higher grade (particularly if suggested by biopsy). Also, if
outside biopsy not reviewed at UC Davis and not strongly supported by either the microscopic
comment or IHC, lean toward doing a frozen section. Select tissue for FS from the uterine
body at the area most suspicious for deepest myoinvasion plus any areas suspicious for
cervical/adnexal involvement.
Step 6: The intraoperative diagnosis should attempt to report all of the following variables.
Indicate whether based on gross only or on FS. When uncertain, being descriptive with details
or providing a differential diagnosis when uncertain is extremely helpful, to at least give the
surgeon an idea of the range of possibilities. Communicating your uncertainty is important
(sometimes it’s hard to determine histotype or extent of myoinvasion).
Report these variables in the intraop diagnosis: (see top of document)
Step 7: Document relevant gross findings on the gross template (remember Step 2) so that
the person completing the grossing knows what you saw freshly before and after dissection
and knows exactly where you took FS samples from. Remember that tissue is hard to evaluate
after fixation, so all the help that you can give by documentation is appreciated by the person
who ultimately receives this specimen for completion, as well as the attending who is
ultimately responsible for the case, medically and legally.
Step 8: Pin the bivalved uterus out, with careful attention to orienting and pinning the
cervical/vaginal cuff margins. Fix in formalin immediately. As a final step, review the Gross
Template and verify that you’ve written down all the relevant gross findings to help out the
final gross on this case.
Intraoperative Evaluation of a Hysterectomy for Ovarian Tumors
WHAT TO REPORT INTRAOPERATIVELY

The following variables should be noted and reported in every case, when applicable, because
of their ability to predict outcome and guide the type of surgery. The evaluation of ovaries can
be very challenging because of the wide spectrum of primary ovarian tumors and the unusual
propensity of ovaries to harbor metastatic carcinomas (especially from the GI tract, lung, and
breast – beware!). This also makes it difficult to generate general guidelines for frozen section
reporting.
Pathology is usually asked to evaluate an adnexal mass for suspected carcinoma. Other times,
we receive a more complex specimen (hysterectomy with bilateral adnexa). And sometimes,
we just receive a peritoneal/pelvic implant (e.g. omentum). Masses in pediatric or young adult
women are much less common. Therefore, the discussion below focuses on primary ovarian
carcinomas and borderline tumors since these are the tumors we encounter most often.
- *Histotype – primary epithelial, sex cord-stromal, and germ cell tumors; metastases
- *Grade – benign/borderline/malignant; histotype of carcinomas
- *Capsule status (stage IA vs. IC)
- Laterality (stage IA vs. IB)
- Pelvic involvement (stage II) – uterine serosa, fallopian tubes, pelvic sidewall
- Abdominal/extra-pelvic involvement (stage III) – omentum
- Presence of concurrent endometrial tumor
Indicate whether the reported variables are based on microscopic or gross evaluation.
Most intraoperative evaluations will only deal with histotype, grade, and capsule status of
an adnexal mass, since the surgeon usually knows the other variables from their operative
findings. If the contralateral ovary, pelvis, or abdomen are part of the sample and may have
tumor, freeze the sample(s) that will provide the highest possible stage.
EPITHELIAL LESION CATEGORIES

Most commonly encountered frozen sections that fall into 3 main categories.
- Benign – simple cysts or complex cysts with bland lining, usually serous or mucinous
o No staging
- Borderline – usually serous or mucinous
o Extent of staging depends on histotype (serous more likely to be advanced stage)
- Malignant/carcinoma – either primary or metastasis (see below)
o Full staging, port placement for IP chemo if HGSC
OVARIAN CARCINOMA HISTOTYPES
5 major histotypes: High-grade serous carcinoma (HGSC, 70%), endometrioid and clear cell CA
(each 10-25%), low-grade serous carcinoma (LGSC, 5%), mucinous CA (<5%)
Specify histotype because of staging and other immediate surgical implications.
HGSC: port placement for intraperitoneal (IP) chemotherapy. Usually stage III with bilateral
ovarian involvement (bad cancer). Papillary/micropapillary, slit-like glands, solid, transitional
patterns. G2-G3 nuclei. High mitotic activity (>12/10 HPF), often atypical mitotic figures.
Endometrioid carcinoma (EC) and clear cell carcinomas (CCC): Commonly discussed together
because of similar risk factors (endometriosis) and genetics. Usually unilateral (stage IA). EC
looks like its endometrial counterpart (glandular, solid, often squamous differentiation. CCC
has papillary, tubulocystic, solid patterns, hobnail growth, hyalinized pink stroma, cytoplasmic
hyaline globules.) High incidence of concurrent endometrial carcinoma, so open the uterus!
LGSC: Hierarchical branching of serous borderline tumor precursor, destructive stromal
invasion, broad expanses of papillary and micropapillary buds, cribriform growth, often
abundant psammoma bodies (not specific but helpful). G1-G2 nuclei. Low mitotic activity
(<12/10 HPF), normal mitotic figures.
Mucinous CA: CAN REPRESENT METASTASES. Gross features can help.
- Favoring primary: larger (>10-13 cm), unilateral, smooth capsule, multiloculated cut
surface
- Favoring metastasis: smaller (<10-13 cm), bilateral, tumor on capsule, lobular cut surface,
signet ring cells, extensive destructive stromal invasion
Two patterns of stromal invasion define mucinous carcinoma (vs. mucinous borderline tumor)
- Expansile (confluent) invasion
o Complex glands with minimal intervening stroma, circumscribed periphery
o ~4x field (variable size criteria: 3 mm, 5 mm, 10 cm2)
- Destructive stromal invasion / infiltrative invasion
o Looks like it sounds (infiltrative pattern, desmoplasia), worse prognosis
o Also observed in metastases to the ovary
BORDERLINE TUMORS
Serous borderline tumor (SBT): Hierarchical, tree-like, arborizing, multilevel (>3) branching.
Stubby, less complex branching (1-2 branches of the tree) = serous cystadenofibroma. More
likely than other borderline tumors to have extraovarian disease – staging implications.
Mucinous borderline tumor (MBT): Cytological atypia and architectural complexity (vs.
mucinous cystadenoma). Usually intestinal type (endocervical type much less common).
Endometrioid borderline tumor (EMBT): Looks like EIN/complex atypical hyperplasia
(crowded endometrioid glands).
Clear cell borderline tumor (CCBT): Very rare as pure tumor, usually coexists with clear cell
carcinoma
GERM CELL TUMORS

Age helps – usually young women/teens, though yolk sac tumor can occur in older age group
Usually dysgerminoma (similar to seminoma), yolk sac tumor, embryonal carcinoma.
Ovarian choriocarcinoma is very rare. Sufficient to tell surgeon “germ cell tumor, favor X.”
GYN Oncologists will usually take lymph nodes regardless of which type. Pediatric surgeons
tend to be more conservative. Mixed germ cell tumours (dysgerminoma + X) tend to be more
aggressive, so they will be more extensive in their sampling.
SEX CORD-STROMAL TUMORS

Most common benign = fibroma/fibrothecoma
- White or white/yellow, firm, whorled, sometimes gritty/calcified
- Bland spindle cells (fibroma), occasional plump spindle cells (theca-like)
Most common malignant/LMP = adult granulosa cell tumor (AGCT)
- Microfollicular, corded, diffuse/solid, insular/nested, other patterns (often combined)
- Intermediate grade, monomorphic, coffee bean nuclei (nuclear grooves) typical
- Surgical implication – staging performed
CAPSULE STATUS: intact vs. disrupted, smooth vs. tumor on surface.

Our main role is to determine whether there is tumor on the surface (stage IC2, freeze to
confirm if this would be the most advanced stage of the tumor).
For capsules received disrupted in pathology, we must know when it happened. This is not
important for us to know for intraoperative evaluation (the surgeon knows what happened)
but it is a common clinical issue attendings have to chase down to stage the patient.
- intraop rupture into the surgical field (surgical spill, stage IC1)
- preop rupture (stage IC2)
- deflated by surgeon, e.g. in a capture bag or ex vivo (staged as capsule intact).
Therefore, if you receive a tumor with a disrupted capsule, record the size of the disruption,
ask the surgeon when the disruption happened, and record the source on the frozen section
grossing sheet and in the gross description. Sample gross descriptions include:
“The tumor capsule was received disrupted prior to receipt in Pathology. According to Dr. X,
the tumor was removed intact, and the tumor capsule was incised on the counter after
removal from the patient.” (inconsequential)
Or “…the tumor was decompressed in the Endocatch bag without spillage.” (inconsequential)
Or “…the tumor capsule was disrupted during removal from the patient.” (stage IC1)
Or “…tumor spillage was noted upon entering the abdomen.” (stage IC2)
CONCURRENT ENDOMETRIAL TUMOR – often endometrioid carcinoma

Up to half of ovarian endometrioid carcinomas have a concurrent endometrial counterpart.
Adult granulosa cell tumor (AGCT) sometimes presents with bleeding from a low grade
endometrial endometrioid carcinoma by virtue of the ability of AGCT to express aromatase
and synthesize estradiol.
CHAPTER 10
Skin
Keratinocyte tumors
Actinic Keratosis
Precancerous, risk of malignancy ~8-20% per year
(progresses to SCC); Due to chronic sun exposure
Rough scaly plaque; typically due to sun exposure
Tx: liquid nitrogen, 5-FU, shave, curettage
• Atypical keratinocytes in lower third of epidermis
• Alternating orthokeratosis and parakeratosis
• Sparing of cutaneous adnexa
• Solar elastosis in dermis
Squamous cell carcinoma in situ (aka Bowen’s disease)

• No epidermal maturation
• Atypical cells at all levels of the epidermis Loss of granular layer
• Epidermis appears disorganized

Second most common form of skin cancer (20% of cutaneous malignancies)
Locally destructive; metastatic potential
Tx: Depends on size, location and depth of invasion: Excision, Mohs micrographic surgery, Radiation
• Nests of atypical squamous cells arise from the epidermis and invade the dermis
• Evidence of squamous differentiation (keratinization and intercellular bridges)
• Dyskeratotic cells = squamous differentiation
Risk factors for metastasis (high risk):
• Often associated with AK or SCCIS - location (ear, lip)
• Findings that suggest invasion - size (>2 cm)
• Jagged interface with dermis - depth
• Aberrant deep keratinization - evidence of perineural invasion
- evidence of desmoplastic
• Single cells invasion
features
Variants:
Keratoacanthoma - well-differentiated variant of SCC that spontaneously regresses in most cases.
Typically composed of large, crateriform (cup-like) lesion filled with abundant keratin debris
Acantholytic SCC – acantholysis with large epithelioid cells with dense eosinophilic cytoplasm and
scattered dyskeratotic (apoptotic) cells
Verrucous SCC – Extremely well-differentiated, low-risk with pushing border and acanthotic papilla.
NO infiltrative growth. Associated inflammation at base.
Desmoplastic SCC – tumor cells become spindled/sarcomatoid
HMWCKs, p63, and p40 are most sensitive markers for poorly differentiated and spindle
cell/sarcomatoid SCC (Pankeratin can be lost in poorly differentiated and spindle cell tumors)
Basal Cell Carcinoma Most common malignancy in humans
Locally aggressive and destructive behavior
Very low metastatic potential (< 0.1%)
Pediatric BCC?  consider Gorlin’s Syndrome
• Basaloid cells with increased N/C ratio
• Nests with peripheral palisading
• Cleft formation between the tumor and surrounding stroma
Note: Some focal keratinization may be present!
May mimic adnexal structures, making margins challenging.
However, basal cell carcinoma tumor cells should have darker
chromatin, more apoptosis and mitoses, and paler cytoplasm than
the hair follicles.
Subtypes:
Nodular – Large, rounded nests Stains: BerEP4 will stain BCC but not SCC
Micronodular* – smaller nests
Superficial – superficial nests separated by uninvolved areas
Infiltrative*- small infiltrative cords
Sclerosing/morpheic* - infiltrative nests with desmoplastic stroma
Basosquamous* - Prominent areas of squamous differentiation
Infundibulocystic – resemble hair follicle
Fibroepithelioma of Pincus – anastomosing cords
* more aggressive variants Infiltrative
Seborrheic Keratosis
• Horn cysts
• Interlacing pigmented epidermal strands
• Acanthosis
• Hyperkeratosis
Solar lentigo aka lentigo senilis, age spot

“Dirty feet”
Finger-like proliferation of hyperpigmented rete growing down
from the epidermis. Keratinocytes, not melanocytes, are the
pigmented cells
Verruca vulgaris aka Wart

HPV-induced, circumscribed lesion
Cup-like rete ridges
Papillomatosis (“church spires”)
Hyperkeratosis often with parakeratosis
Koilocytes may be variably present
Verruca plana = flat wart
More Skin Tumors
Epithelial Cysts Epidermal Inclusion Cyst (EIC)
Acquired unilocular cyst due to trauma, etc..
Lined by squamous epithelium with granular layer
Contains laminated (basket weave) keratin
May rupture and become inflamed
Dermoid Cyst
Present at birth
Like EIC, but with hair follicles and sebaceous glands
Pilar (Trichilemmal) Cyst

Filled with dense, “wet” eosinophilic keratin
Stratified squamous epithelium
Granular layer generally absent
Sebaceous Tumors Ectopic sebaceous glands

Not associated with hair follicles
Sebaceous hyperplasia
Overgrowth of Sebaceous glands. Lobules of sebocytes
arranged around infundibulum of central hair follicle. 1 layer
of basaloid cells compressed at periphery of sebocytes. No
cytologic atypia
Sebaceous Adenoma
May have similar low-power architecture to sebaceous hyperplasia, but
typically larger nodular aggregates. Lobular downgrowth from epidermis.
Predominance (> 50%) of sebocytes. Cytologic atypia not prominent
Composed of > 50% germinative/basaloid cells Sebaceoma
Sebaceous Carcinoma
Aggressive tumors with high incidence of metastasis (> 30%)
Strong association with Muir-Torre syndrome if patients have multiple
sebaceous tumors (Genes implicated include MLH1, MSH2, MSH6, PMS2)
Eyelids are most common site (~ 75% of cases)
Clear cells often present but vary greatly in number
Show prominent cytologic atypia and pleomorphism
Mitotic figures, including atypical forms, are usually abundant
Stains: May stain with AR, EMA, and Factor XIIa
(Eccrine) Spiroadenoma “blue cannonballs in the dermis”
Basophilic tumor nodules in dermis
Tumor lobules may be partially encapsulated
Biphasic appearance with 2 cell types:
1) Peripheral small cells with scant cytoplasm and small
hyperchromatic nuclei
2) Central larger cells with eosinophilic cytoplasm and oval,
vesicular nuclei
Tumor lobules sometimes surrounded by thickened basement
membrane, similar to cylindroma
Cylindroma
“jigsaw puzzle”
Also has basaloid (blue) nests in the dermis, also with
two cell populations and basement membrane
matrix.
Multiple nodules/lobules of basaloid cells
surrounded by dense eosinophilic basement
membrane
Tumor lobules have complex pattern, where tumor
lobules appear to fit together in irregular jigsaw
puzzle-like pattern
Chondroid Syringoma aka Cutaneous mixed tumor
Essentially a pleomorphic adenoma, but primary to the skin

Epithelial cells embedded in myxoid, chondroid, or fibrous stroma
Tumor shows eccrine and apocrine differentiation
Ductal structures of variable size and shape present
Ducts lined by 2 layers of cuboidal cells and peripheral layer of
myoepithelial cells
Small ducts, nests, cords, and cysts in superficial dermis Syringoma

Ducts and cysts lined by 1 or 2 layers of small, bland-
appearing cuboidal cells
Some ducts have tadpole-like appearance with comma-
like tails (like paisley)
Dilated ducts may have eosinophilic contents
Most common in head/neck, esp. eyelids
If deep/perineural invasion  consider Microcystic
Adenexal Carcinoma (MAC)
Pilomatrixoma
Well-circumscribed with mixture of 1) basaloid and
2) shadow/ghost cells (abundant pink cytoplasm and open
space at their center where nucleus was)
Dystrophic calcification is frequently seen
Foreign-body giant cell reaction surrounding tumor is common
Infiltrative, prominent nucleoli, necrosis, mitoses? 
Pilomatrical Carcinoma
Trichofoliculoma
Cystic tumor that communicates to overlying epidermis
Cystic space filled with keratinous debris and hair shafts
Lined by squamous epithelium with thin granular layer
Numerous small, primitive follicles radiate around
periphery of tumor and communicate with central
cystic space
Trichilemmoma
Lobular proliferation of mature squamoid cells with pale-
to clear-staining cytoplasm
Peripheral palisading of basaloid cells
Cells are surrounded by thickened, glassy-appearing
basement membrane
Multiple broad connections to epidermis and follicles
Associated with Cowden’s Syndrome
COWden’s Syndrome Macrocephaly

& Uterine Cancer
PTEN mutation (tumor suppressor)

Thyroid carcinoma (usually Follicular)
Breast Cancer (very high risk)
Endometrial Cancer
Macrocephaly
trichileMMOOOOmas Thyroid Cancer
Breast CA
Dermal tumors
Dermatofibroma aka Benign Fibrous Histiocytoma
Dermal-based proliferation of typically bland, spindled to

histiocytoid-appearing cells—can appear like a blue haze
Tumors are grossly circumscribed but microscopically have
irregular, often jagged borders
Collagen trapping at periphery
Overlying epithelial basilar induction with hyperpigmentation
(may mimic BCC)
Evidence supports both neoplastic & reactive etiologies
Many variants: Epithelioid, Cellular, with “monster cells” etc…
Stains: FXIIIA(+), CD163(+), CD68(+), CD34(-)
Dermatofibrosarcoma Protuberans (DFSP)

Spindle cell tumor Proliferation of monomorphic spindle-
shaped cells with deep dermal and subcutaneous involvement
Arrayed in storiform or cartwheel patterns
Lesional cells typically lack significant atypia and pleomorphism
Subcutaneous areas typically show honeycombing fat
entrapment (“pearls on a string”)
Defined by t(17;22): Rearrangement of COL1A1 with PDGFB
If loses storiform pattern herringbone pattern consider
malignant transformation to fibrosarcoma
Stains: Strong, diffuse CD34, Factor XIIIA (-)
Neurofibroma
Benign peripheral nerve sheath tumor composed of
Schwann cells, fibroblasts, perineurial-like cells, and residual
nerve axons within extracellular matrix
Sporadic in ~ 90% of cases; others are syndromic in
association with NF1
Loosely arranged spindle cells in haphazard arrangement
Poorly defined cytoplasmic borders/processes–Small,
hyperchromatic, wavy or buckled nuclei
Stains: S100(+) in ~ 50% of total cells (Schwann cells); CD34(+)
admixed spindled fibroblasts; Neurofilament protein
highlights intratumoral axons
Fibrous Papule Type of Angiofibroma
Solitary, dome-shaped, flesh-colored papules on nose or
central face
Scattered bland, spindled to stellate, and multinucleated
fibroblasts
Dense collagenous stroma
Ectatic thin-walled blood vessels
If show enlarged, hyperchromatic-staining nuclei with small
nucleoli, scant amounts of eosinophilic cytoplasm 
consider Pleomorphic Fibroma
Fibrous Hamartoma of Infancy
Benign superficial fibrous lesion occurring during first 2
years of life
3 components in organoid growth pattern
1) Intersecting bands of mature fibrous tissue, comprising
spindle-shaped myofibroblasts and fibroblasts
2) Nests of immature round, ovoid, or spindle cells within
loose stroma
3) Interspersed mature fat
Atypical Fibroxanthoma (AFX)

Mesenchymal neoplasm showing no specific lineage of differentiation
Highly atypical and pleomorphic dermal-based proliferation of
spindled to epithelioid-appearing cells
Scattered large, bizarre-appearing multinucleated cells often seen
Numerous mitoses, including highly atypical forms, easily found
Subcutaneous invasion, PNI, LVI, and tumor necrosis implies more
aggressive behavior, and such cases are typically diagnosed as
pleomorphic dermal sarcoma
Stains: Essential to exclude more specific diagnoses:
Negative for melanocytic markers, cytokeratins (especially HMWCKs),
p63, muscle (except for SMA), and vascular markers
Positive for nonspecific markers like CD10, CD68, CD99, and vimentin
Additional DX: Fibroepithelial polyp (Acrochordon)  aka Skin Tag

Fibrovascular core is composed of loose to dense connective
tissue devoid of adnexal structures
Sclerotic Fibroma  Circumscribed, unencapsulated dermal nodule composed of
thickened, hyalinized-appearing collagen bundles in storiform/whorled pattern with
prominent clefts
Neurothekeoma
Rare dermal tumor of uncertain histogenesis composed of
epithelioid cells in multiple nests divided by fibrous septa
Epithelioid to spindled cells with abundant pale eosinophilic
cytoplasm arranged in nests divided by dense fibrous septa
Stains: Often positive for variety of nonspecific markers,
including NKI/C3, NSE, PGP9.5
Granular Cell Tumor

Benign tumor of putative schwannian origin composed of
cells with abundant granular cytoplasm
Overlying pseudoepitheliomatous hyperplasia
Stains: PAS-D(+) granules; Strong, diffuse S100(+),
SOX10(+), Calretinin, CD68
Leiomyoma Benign Smooth Muscle Tumors;

Both often painful (esp. pilar)
Pilar Leiomyoma
Ill-defined, dermal nodule composed of haphazardly
arranged smooth muscle bundles/fascicles
Fascicles often dissect between dermal collagen
Angioleiomyoma
Well-circumscribed neoplasm composed of mature
smooth muscle cells arranged around prominent
blood vessels
Numerous mitoses, diffuse/marked atypia, necrosis  Leiomyosarcoma
Scars
Scar
Dense collagen fibers run parallel to the surface
Small, perpendicularly oriented vessels
Loss of adnexal structures
Keloid
Dense proliferation of thickened, hyalinized
collagen bundles in dermis
Decreased vessels compared to conventional and
hypertrophic scars
Classically on ear
Hemangiomas Benign vascular tumors composed of blood vessels lined by plump to flattened
endothelial cells with no atypia
Lobular Capillary Hemangioma (aka Pyogenic Granuloma)
Exophytic with collarette
Numerous small capillaries radiating out from larger
central vessels; May be ulcerated
Cavernous Hemangioma
Non-lobular, poorly demarcated proliferation of large,
cystically dilated vessels filled with blood
Infantile (Juvenile) Hemangioma
Characterized by onset during infancy, rapid growth, and
spontaneous involution
Appearance changes over time; Tightly packed small- to
medium-sized vessels; Unique immunoprofile of placental
vasculature Glut 1 expression
Glomus tumor
Solid nests of round cells with round, uniform, central
nuclei closely associated with variably sized blood vessels
Most common in distal extremities, particularly nail bed
Typically small, red, painful nodule
Stains: SMA (+)
Angiosarcoma
Malignant neoplasm showing morphologic and/or immunophenotypic
evidence of vascular/endothelial differentiation
Most often scalp/face in elderly (sun exposed) or breast s/p radiation
Aggressive tumor treated surgically
Infiltrative, poorly circumscribed
Variable vascular formation
Often cytologic atypia (hyperchromasia, nuclear pleomorphism) and mitoses
Stains: CD31 (+); CD34 (+); ERG (+); FlI-1 (+); Epithelioid angiosarcomas may be CK (+)!
Additional DX: Kaposi Sarcoma  Vascular neoplasm caused by HHV8; often

AIDS-associated; Jagged interconnected vascular channels in
reticular dermis; grows into normal vessels (promontory sign)
Papillary Endothelial Hyperplasia (Mason’s Tumor)  Reactive intravascular endothelial
proliferation; circumscribed, intravascular; Fibrin thrombus with associated papillary
structures lined by endothelial cells in single layer; may form anastomosing network;
Introduction to Inflammatory Dermpath

Spongiotic Dermatitis intraepidermal intercellular edema (spongiosis)
- presence of widened intercellular spaces between

keratinocytes, with elongation of the intercellular
bridges
- may be associated inflammation
- with chronic disease, there can be progressive
psoriasiform hyperplasia, usually accompanied by
diminishing spongiosis (lichenification)
Atopic Dermatitis Aka Eczema

Dx: “spongiotic dermatitis consistent with eczematous dermatitis”
“Atopic Triad:” 1) Atopic dermatitis, 2) Seasonal allergies, 3) Asthma
Acutely Edema can form vesicles
Chronically Lichenification
Can appear similar histologically: Contact dermatitis and Nummular
or Id reactions
Stasis Dermatitis
Begins on medial aspect on lower legs but can
become circumferential;
Clinically mimics cellulitis
Micro: Spongiotic dermatitis, vascular

proliferation, dilated, thickened blood vessels in
papillary dermis, hemosiderin, chronic
inflammation
Pityriasis Rosea
First“ Herald patch”
Followed by secondary lesions 1-2 weeks later, Self-resolving ~1 month
Christmas tree pattern
Clinical DDX: secondary syphilis, cutaneous T cell lymphoma
Micro: Spongiotic dermatitis with mounds of parakeratosis.
Extravasated RBCs. Some exocytosis of lymphocytes.
Lichenoid Dermatitis Interface Dermatitis
Band-like infiltrate that hugs the Basal keratinocyte hydropic change with
dermoepidermal junction vacuolization and variable lymphocytic
inflammation
Lichen Planus Common entity, unknown

etiology; Pruritic, purple, papules
Micro: Compact hyperkeratosis (lack of paraker.)
Band-like inflammatory Infiltrate
Civatte bodies
Wedge-shaped hypergranulosis
“Saw-tooth” rete ridges
Single lesion on trunk? Consider Lichen Planus-like Keratosis (LPLK)
Lichen Sclerosus
Predilection for anogenital skin
Glans penis = “balanitis xerotica obliterans”
Micro: Homogenization of dermal collagen

Variable band of chronic inflammation BELOW
edema and homogenization
Vacuolar change
Atrophic epidermis
Fixed Drug Reaction

Take Drug One or few circumscribed
erythematous to violaceous/brown plaques
Lesions recur at same site with rechallenge
Micro: Vacuolar change
Lymphs along DEJ and in dermis
Necrotic keratinocytes
Usually Eos, some Neuts
Prominent pigmentary incontinence
Erythema Multiforme Acute, self-limited disease.
Reactive in nature (usu. HSV, Mycoplasma, or Drug).
Targetoid, dusky lesions which tend to be distributed
symmetrically in acral locations
On spectrum with Stephen-Johnson Syndrome and Toxic
Epidermal Necrolysis
Micro:
Erythema multiforme Interface dermatitis with necrotic
keratinocytes
SJS/TEN Severe to full-thickness epidermal necrosis with
variable inflammation
Graft-vs-host Disease (GVHD)

Usually post-stem cell transplant
(transplanted immunocompetent T-cells
attack new host)
Involves skin, liver, GI tract  rash,

↑LFTs, diarrhea, and vomiting
Acute GVHD
Acute: Interface dermatitis with necrotic/dyskeratotic keratinocytes;
“Satellite cell necrosis”- association of lymphs to necrotic keratinocytes
Chronic: Sclerosis of the dermis, Compact hyperkeratosis, Lichenoid reaction
Lupus Erythematosus Subacute cutaneous lupus (SCLE)- may be

associated with mild systemic disease
Chronic cutaneous lupus/discoid lupus (arthralgias, etc.) but must r/o SLE
erythematosus (DLE)- usually only limited to
the skin Micro: Epidermal atrophy
Intense basal vacuolar change
Micro: epidermal atrophy, Necrotic keratinocytes
basal vacuolization, Patchy to moderate chronic inflammation
thickened basement membrane zone Dermal mucin usually prominent
Immunofluorescence: IgM, IgG, C3  granular BM deposition

Psoriasiform Dermatitis marked, uniform elongation of the rete ridges
Psoriasis
Clinical Findings:
Erythematous plaques and silvery white scale
Extensor surfaces
Scale is micaceous (oyster-like)
Microscopic Findings:
Psoriasiform hyperplasia
Confluent parakeratosis
Hypogranulosis
Neutrophils in the stratum corneum/epidermis
Thinning of supra-papillary plates
Dilated BV in dermal papillae
Other Psoriasiform Disorders
Reactive arthritis (Reiter’s disease)

Pityriasis rubra pilaris
Lichen simplex chronicus/Chronic spong. derm.
Psoriasiform drug eruptions
Herald patch of pityriasis rosea
Secondary syphilis (sometimes)
Granulomatous Reaction
Discrete collections of histiocytes with variable
numbers of multinucleated cells and lymphocytes
Characterized by:
Arrangement of granulomas
Presence or absence of necrosis, suppuration, or
necrobiosis
Presence of foreign material or organisms
Must evaluate any granulomatous process for infection

 FITE, GMS
Polarized light examination for foreign material

Sarcoidal Granulomas
Granuloma annulare
Self-limited dermatosis; Unknown etiology

Rashes are often annular (round)
Micro: Areas of necrobiosis in superficial or mid dermis
Surrounding palisaded histiocytes and lymphocytes
Central mucin collection
Necrobiosis lipoidica
Associated with diabetes; Often bilateral shins
Micro: Normal epidermis (unless ulcerated)

Linear palisading of chronic inflammation with some
aggregates resembling germinal centers
“layer cake” appearance
Necrobiosis of collagen between
Plasma cells
May extend to septae of fat
Other Granulomatous Processes Sarcoidosis - “Naked” non-caseating granulomas

Granulomatous Rosacea - Persistent erythema Foreign body reaction – Foreign body giant cells
and telangiectasia; Usually on cheeks, chin, and and polarizable (foreign) material
nose; Perifollicular and perivascular granulomas
with chronic inflammation Rheumatoid nodule - Subcutaneous/deep,
Extensive necrobiosis with fibrin deposition
Tuberculosis – Caseating granulomas; +FITE/AFB centrally, often multi-focal
Vesiculobullous Reaction
Vesicles or bullae at any level within the epidermis/DEJ
Specific diagnosis depends on: 1)anatomical level of the
split, 2)the underlying mechanism, 3)pattern of other
inflammation
Pemphigus Vulgaris Bullous Pemphigoid
Autoantibody to desmosomes Autoantibody to hemidesmosomes at DEJ
Intraepidermal vesicle Subepidermal cleft with abundant
Suprabasilar acantholysis (“tombstoning”) Eosinophils
Dermatitis Herpetiformis
Subepidermal split with numerous neutrophils
in dermal papillae and microabscesses
Granular IgA staining on IF
Highly associated with Celiac disease
Vasculopathic Reaction Pathological changes in blood vessels

Includes vasculitis and vascular occlusive diseases
Leukocytoclastic vasculitis Thrombotic Vasculopathy
Histologic reaction pattern due to immune

complex deposition
Micro: Fibrinoid necrosis of blood vessel walls Histologic reaction pattern denoting
Endothelial cell swelling presence of noninflammatory small
Perivascular neutrophilic infiltrate vessel fibrin thrombi
Karyorrhexis (nuclear dust) Many possible etiologies (e.g., DIC,
RBC extravasation hypercoagulable state, etc..)
Panniculitis = Inflammation of the Fat
NO Vasculitis YES Vasculitis
Septal Erythema Nodosum Polyarteritis Nodosa
Lobular Others: Histiocytic cytophagic panniculitis, α1-

antitrypsin deficiency, pancreatic, sclerema
Erythema Induratum
neonatorum, subQ fat necrosis of the

newborn,
Erythema Nodosum Red, tender nodules, on shins

Associated fever, malaise, arthralgias
Micro: Thickening of fibrous septae
Lymphohistiocytic infiltrate
Some “spill over” into adjacent fat
lobules
NO vasculitis
Multi-nucleate giant cells, granulomas
Polyarteritis Nodosa
May be systemic or cutaneous-only
Tender painful nodules on the legs with livedo
reticularis
Vasculitis of small and medium sized arteries
Overlap with microscopic polyangiitis
May have fever, malaise, arthralgias, and myalgias,
peripheral nerve involvement
Other Common Diagnoses:

Arthropod Bite Reaction
Various degrees of:
wedge-shaped perivascular lymphocytic
infiltrate with eosinophils
Spongiosis, Ulceration, blister formation
Dermal edema, necrosis
Insect tissue fragments,
Spiders more neutrophils
Dermatophyte reaction Superficial fungal infection secondary to dermatophytes
(Trichophyton, Epidermophyton, Microsporum)
Helpful Clue = Neutrophils in stratum corneum
Fungal stains (GMS, PAS-D) highlight hyphae
Sandwich sign = Parakeratosis or compact

orthokeratosis underlying basket-woven
stratum corneum (dermatophytes located in
between)
Morbilliform Drug Reaction
Histologic findings are nonspecific and

clinical correlation is essential
“SPD with Eos”
Superficial perivascular and interstitial
dermal infiltrate
Most often polymorphous infiltrate of
lymphocytes, neutrophils, and eosinophils
Subset have vacuolar interface change
Pernio (aka Chilblains)

Caused by exposure to cold, damp
conditions
Micro: Superficial and deep perivascular

infiltrate of lymphocytes
Prominent perieccrine inflammatory
infiltrates
Chondrodermatitis nodularis helicis (CNH)

Lesion of outer helix of ear that is usually result
of trauma; Clinically concerning for malignancy
Micro: Ulceration
Central fibrin deposition
Granulation tissue in base
Adjacent telangiectatic vessels & parakeratosis
Cartilage usu. uninvolved
CHAPTER 11
Pediatrics
“Small Round Blue Cell Tumors”
(in kids) Prepared by Kurt Schaberg
Leukemia/Lymphoma Always a consideration! Do several heme markers and show a

hematopathologist.
Ewing Sarcoma
Malignant tumor of neuroectodermal differentiation that is often
arises in the bone (but can see in many organs; Chest wall = Askin
tumor)
Often have EWSR1 translocation (with FLI-1 or ERG) t(11;22)
Usually uniform, small, round, blue cells with sheet-like to lobular,
growth pattern with variable necrosis
Strong, membranous CD99 staining
(Sensitive, but not Specific staining)
Can see
pseudorossettes
Rhabdomyosarcoma Malignant tumor with primary skeletal muscle differentiation, several types
Stain with Desmin, MyoD1, Myogenin
Embryonal Rhabdo:
Variable numbers of round (“rhabdoid”), strap-, or tadpole-shaped
eosinophilic rhabdomyoblasts in a myxoid stroma
Can see cytoplasmic cross striations
Alveolar Rhabdo:
Larger, more rounded undifferentiated cells with only occasional
rhabdomyoblasts
Often arranged in an alveolar (nested) pattern
Distinctively strong and diffuse myogenin positivity
Characteristic FOXO1 translocations
Wilms Tumor aka nephroblastoma

Malignant tumor originating in Kidney
3 key elements: 1)Primitive epithelial tubules, 2)Blastema
(sheets of small high N:C ratio cells), 3)Stroma
In some cases may only see 2 (or possibly even 1) element
3 component stain differently with IHC stains
Epithelium: ⊕ WT-1, CK
Blastema: ⊕ WT-1, Desmin
Stroma: Weak WT-1, (plus heterologous elements)
Most primitive/aggressive Intermediate differentiation Most mature; Benign
Malignant Neuroblastoma + Ganglion cells Ganglion cells set in
SRBCT +/- rosettes, fibrillary stroma
neurofibrillary matrix NO neuroblastoma
Peripheral neuroblastic tumors derive from the sympathetic nervous system (therefore develop anywhere
along the distribution of the sympathoadrenal neuroendocrine system)
Positive stains: synaptophysin, chromogranin, CD56, NB84, and neuron-specific enolase
staining for S-100 protein has been used to identify cytodifferentiated cells such as Schwann cells
MYCN amplification  Poor prognosis!
Desmoplastic Round Cell Tumor

Malignant tumor of uncertain histogenesis often found in the peritoneal
cavity; often in young men
Characteristic EWSR1 – WT-1 translocation
Basaloid nests of tumor that are surrounded by cellular desmoplastic
stroma
Stains: Positive CK, Desmin, WT-1 (but C-terminus—opposite of Wilms!)
For all pediatric tumors, consider in addition to Formalin-Fixed Tissue:

1) Flow cytometry, 2) Cytogenetics, 3) Freezing some (depends on quantity, etc..)
CD45 TdT CK Desmin MyoD1 Synapto. CD99 WT-1

AE1/AE3 Myogenin Chromo
Leukemia/ + +/- - - - - -/+ -
Lymphoma
Ewing Sarcoma - - Usu. - - - - + -
Rhabdomyosarcoma - - -/+ + + Rare -/+ -
Wilms’ Tumor - - + -/+ - -/+ - +
Neuroblastoma - - - - - + - -
Desmoplastic Round - - + + - - -/+ C-terminus

Cell Tumor
CHAPTER 12
Genitourinary
Kidney Tumors
Eosinophilic
CK7 CD117 CA-IX Vimentin AMACR SDH FH
Racemase
Oncocytoma
- + - - - + +
(rare)
Chromophobe RCC
+ + - - - + +
Papillary RCC
(Type 2)
+/- - +/- + + + +
HLRCC-associated
RCC
- - - - - + -!
SDH-deficient RCC
- - - - +/- -! +
Acquired Cystic
Disease-associated
- + + +
RCC
Clear Cell RCC
(sometimes pinkish)
- - ++ + - + +
Oncocytoma
Benign
Abundant eosinophilic, mitochondria-rich cytoplasm
Round, regular nuclei throughout
Tight nests and alveoli surrounded by myxoid or hyalinized
hypocellular stroma. Some solid areas acceptable.
Grossly: Circumscribed, mahogany brown
NOT allowed: Necrosis, Sheet-like or papillary growth, clear
or sarcomatoid cells
Stains: Only rare CK7 + cells

(Most CK7 Negative!)
Chromophobe Renal Cell Carcinoma
Clear to Eosinophilic cytoplasm
Prominent “Plant-like” cell membranes
Perinuclear clearing
Round to Koilocytic nuclei
(hyperchromatic, crinkled, and/or binucleated)
Stains: CK7+, Hale’s colloidal iron +
Better prognosis than clear cell RCC.

No need to grade.
Chromophobe/oncocytoma hybrid tumors may be seen

in Birt-Hogg-Dubé syndrome
Papillary RCC (Type 2)

Predominantly papillary architecture
Type 2 is lined by large cells with
abundant eosinophilic cytoplasm
Higher nuclear grade→ Prominent
Nucleoli (consider HLRCC though!)
Macrophages, edema, psammoma
bodies
Hereditary Leiomyomatosis and Renal Cell Carcinoma-associated RCC

Abbreviated: HLRCC-associated RCC
Prominent, eosinophilic, inclusion-like nucleoli with
perinucleolar clearing
Usu. Papillary to tubular architecture
Loss of Fumarate Hydratatse (FH) expression
(Germline FH mutations)
Usually younger patients. Cutaneous and uterine leiomyomas.
Aggressive tumors!
Succinate Dehydrogenase Deficient RCC
Eosinophilic cytoplasm with “flocculent”
cytoplasm/inclusions (see arrows)
Neuroendocrine-like nuclei (round, evenly
dispersed chromatin
Solid to nested architecture
Defined by loss of Succinate Dehydrogenase B
(SDH-B)→ Majority of patients have germline
mutations.
Young age, good prognosis
SDH-deficient tumor syndrome: SDH-deficient
RCC, paraganglioma/pheochromocytoma, SDH-
deficient GISTs
Acquired Cystic Disease-associated RCC
Occurs only in patients with ESRD with cystic disease
Abundant granular eosinophilic cytoplasm
Microcribriform appearance due to frequent

intracytoplasmic and intercellular microlumens
Large nuclei with prominent nucleoli
Frequent oxalate crystals and calcifications
Clear Cell RCC

Although it is called “Clear Cell” RCC, some cases
can have relatively eosinophilic cytoplasm.
More common with higher grades
Can have “Rhabdoid” areas
Look for classic clear cell areas as a clue

Clear
CK7 CD10 CA-IX Keratins/ Melanocytic TFEB/
EMA Markers TPF3
Clear Cell RCC
- + + + - -
(diffuse)
Clear Cell Papillary

RCC
+ - + (basal + - -
cup-like)
Multilocular cystic
renal cell neoplasm
- + + + - -
of LMP
MiTF translocation-
associated RCC
- + - - (weak to neg) +/- +
Clear Cell RCC
Predominantly clear cells (contains lipid and glycogen)

with sharp cell borders
Sheets and nests of cells surrounded by extensive

capillary network
Frequent alveolar lumens
Grossly: Yellow, with frequent hemorrhage and

necrosis
Associated with von Hippel Lindau Syndrome (VHL

gene)—Along with: Hemangioblastomas,
pheochromocytoma, pancreatic serous cystadenomas,
and endolymphatic sac tumor
WHO/ISUP grading system for clear cell and papillary renal cell carcinomas
Grade Findings
1 Nucleoli are absent or inconspicuous and basophilic at 400x magnification
2 Nucleoli are conspicuous and eosinophilic at 400x and visible but not prominent at 100x
3 Nucleoli are conspicuous and eosinophilic at 100x
4 Extreme nuclear pleomorphism, multinucleate giant cells, and/or rhabdoid and/or

sarcomatoid differentiation
Multilocular Renal Cell Neoplasm of Low Malignant Potential
Cysts lined by single layer of low-grade clear cells
(grade 1-2 only)
Groups of low-grade clear cells are permitted within the

septa, but must not be expansile nodules or show
infiltrative growth
Features not allowed: Necrosis, Vascular invasion,

Sarcomatous differentiation
NOTE: No longer called a carcinoma as act so indolently
Clear Cell Papillary RCC

Mixture of tubular, cystic, acinar and papillary patterns
Lined by a single layer of cuboidal to low columnar cells
Scant eosinophilic to clear cytoplasm
Nuclei apical to mid-cytoplasmic orientation
(“pseudoendometrial” appearance)
Low-grade and Low-stage
Unique immunophenotype
(CK7 +, CA-IX basolateral cuplike)
Very indolent (no reported metastases!)
MiT Family Translocation RCC

Gene fusions in MiT family transcription factors TFE3 or TFEB
(Demonstrate with cytogenetics, FISH, or IHC)
Composed of cells with abundant to voluminous cytoplasm
Clear to granular eosinophilic cytoplasm
Sharp cell borders
Frequent papillary, pseudopapillary, alveolar and nested
patterns
Most often recognized in younger patients
Variable outcomes
Basaloid
CK7 CD10 CA-IX AMACR WT-1 CD57
Racemase
+ + -/+ + - -
(luminal)
Metanephric Adenoma
- + - - + +
Wilms Tumor
-/+ (in - - + -
epithelium) (diffuse)
Mucinous Tubular and
Spindle Cell RCC
+ -/+ - + - -
Tubulocystic RCC
+/- + -/+ + - -

Predominantly papillary architecture
Often some tubular or solid growth also
Type 1 is lined by small cells with scant
amphophilic cytoplasm
Lower nuclear grade than type 2
Macrophages, edema, psammoma bodies
Papillary Adenoma
Same thing, but < 1.5 cm
Nuclear grade 1 or 2
Benign
Metanephric Adenoma
Benign
Composed of small, primitive tubules.
Cells have minimal cytoplasm with uniform, small nuclei
Minimal mitoses.
Grossly: well-circumscribed, unencapsulated, tan nodule.
Very cellular with minimal stroma.
May appear papillary or glomeruloid
Often incidental, but associated with polycythemia
Tubulocystic RCC
Closely packed variably sized tubules and cysts
No solid component→ Grossly looks like a sponge
Lined by cuboidal to flattened and hobnail cells
High grade nuclear features with prominent round nucleoli
Good Prognosis
Grossly
looks like a
sponge
Wilms Tumor (Nephroblastoma)
Vast majority in Children 1

Triphasic (recapitulating nephrogenesis):
1) Blastema
(small, undifferentiated, overlapping cells)
2) Epithelium 2
(Tubules, rosette-like to well-formed)
3) Stroma
(Nondescript spindled cells, occasional 3
heterologous elements)
Special reporting (amount of Anaplasia, etc…)

Anaplasia = increased nuclear size (>3x size), hyperchromasia, and mitotic figures → Chemo resistant
Malignant, but often good survival
Mucinous Tubular and Spindle Cell Carcinoma

Like the name says:
1) Elongate tubules that blend into 2)
Bland spindle cells, set in 3) Mucinous 2
stroma
Cytologically bland with small oval nuclei
Very indolent/benign course

1
3
Spindled (Adult)
Angiomyolipoma
Benign
Member of “PEComa” family
(Perivascular Epithelioid Cell)
Generally 3 components (like the name):
1) Blood vessels (“Angio”)
2) Smooth muscle (“Myo”)—often blending with vessels
3) Fat (“Lipoma”)—often seen radiographically
Stains with Melanocytic Markers:
HMB45 +, MelanA +/-, Desmin + (in muscle)
Associated with Tuberous sclerosis
Renomedullary Interstitial Cell Tumor
Benign
Usually incidental, small, well-circumscribed
Located in renal medulla
Composed of bland stellate cells set in loose to
dense fibrocollagenous stroma with entrapped
tubules at the periphery
Sarcomatoid RCC
Renal cell carcinoma of any type exhibiting at least

focal sarcomatoid/spindle cell differentiation
Represents a form of high-grade transformation,
not a distinct subtype of renal cell carcinoma
Requires evidence of epithelial differentiation
(either conventional component or CK expression)
Automatically WHO/ISUP grade 4
Poor prognosis
Other Spindled Tumors
Mixed-Epithelial Stromal Tumor—Benign tumor. Cystic and solid. Ovarian-type stroma and smooth
muscle with bland epithelial cysts (conceptually sort of like a mucinous cystic neoplasm of the
pancreas, but epithelium is hobnailed and bland). Stroma stains with desmin and ER.
Juxtaglomeurlar Cell Tumor—Benign tumor that originates from smooth muscle cells in the walls of
the glomerular afferent arteriole (juxtaglomerular apparatus)→ secretes renin→ Hypertension,
Hyperaldosteronism, hypokalemia! Monotonous eosinophilic spindled to epithelioid cells with oval
nuclei.
Mucinous tubular and spindle cell carcinoma
Sarcomatoid clear cell RCC
Renomedullary interstitial cell tumor
(And any other sarcoma pretty much)
High-Grade
Collecting Duct Carcinoma
High-grade renal carcinoma arising in medulla of the
kidney, with a predominantly invasive tubular growth
pattern.
Diagnosis of exclusion. Requires:

1) No other RCC, Urothelial carcinoma, or Metastasis
2) Predominantly tubular growth
3) Firm mass centered in Medulla
4) Prominent stromal desmoplasia
5) Infiltrative growth
6) High nuclear grade
Poor Prognosis
Urothelial carcinoma
Always consider as a possibility if doesn’t fit well into
one of the RCC diagnoses.
Sample and examine the renal pelvis for urothelial CIS
Stains: GATA-3 +, p63+, HMWCK+, CK7+, CK20+,
Pitfalls: PAX8+, CA-IX +
Other Renal Medullary Carcinoma—Like collecting duct carcinoma, but associated with
sickle cell disease, INI-1 loss
Sarcomatoid clear cell RCC, RCC NOS, Metastases, Sarcomas
Papillary Papillary adenoma Urothelial carcinoma
Papillary RCC HLRCC-associated RCC
Clear cell papillary RCC
MiTF translocation-associated RCC
Spindled (Kids)
Clear Cell Sarcoma
Aggressive→ Old name “bone metastasizing renal tumor
of childhood”
Nests or cords of uniform cells with clear cytoplasm and
fine chromatin and a delicate vascular network
Some areas may be sarcomatous/anaplastic
No good stains
Rhabdoid Tumor
Aggressive
Sheets and trabeculae of cells with:

Eccentric nuclei with vesicular chromatin and prominent
nucleoli
Eosinophilic cytoplasm with pink hyaline inclusions (looks
“rhabdoid”)
Stains: CK+, INI-1 loss, Myogenin/MyoD1 -
Congenital Mesoblastic Nephroma

Classic Variant
Fibromatosis-like: intersecting bundles of bland spindled cells, infrequent mitoses
Infiltrates adjacent kidney and structures
Cellular Variant
Recurrent ETV6-NTRK3 fusions (Same as infantile fibrosarcoma, secretory carcinoma)
Pushing border, dense cellularity, numerous mitoses
Biopsy/FNA Algorithm
Bladder Tumors
Normal Anatomy
Urothelium: Thickness depends on distention of bladder.
Normal thickness = 2-7 cells.
Distended Non-distended
Basal and intermediate layer are often cuboidal to columnar
(2-3 cells) (5-7 cells)
Normal urothelial nucleus is about the size of 2 lymphocyte nuclei
Top Umbrella/Superficial layer are large, sometimes binucleate
with abundant eosinophilic, sometimes vacuolated cytoplasm
Lamina Propria: Contains vessels, connective tissue, nerves, and

thin, wispy, haphazard, scattered muscularis mucosae
Muscularis propria (Detrusor muscle): More organized, thick

bundles of muscle
Adventitia: Connective Tissue outside muscle. Serosa at dome.
Normal Variations
von Brunn Nests:
Invaginations of the surface urothelium into underlying
lamina propria. Normal urothelium thickness & cytology.
Round shape (not infiltrative), uniform size.
If lots of small nests, irregular size, stacked on top of each
other→ consider nested variant of urothelial carcinoma
Cystitis Cystica:
Name used when these nests become cystically dilated
Cystitis Glandularis:
Name used when lining undergoes glandular metaplasia
Urothelial Tumors
Most common in older males. Risk factors include smoking, occupational exposures (e.g., paints and
exhaust), radiation, and Schistosoma. Most commonly present with hematuria
Location: 90% in Urinary bladder; 10% upper tract;
Can often be multifocal (often attributed to a “field defect”)
Molecular: Very high mutational rate (second only to lung!). Two main pathways
1. Large chromosomal alterations: loss/gain of large chromosomal fragments occur, corresponding to
higher grade tumors
2. Recurrent mutations: Frequent mutations include deactivating TP53 and activating FGFR3. Very
common, TERT promoter mutations→ lengthens telomeres. Others include PIK3CA, RB1, and HRAS
Lynch Syndrome→ increased risk of urothelial neoplasms (esp. MSH2), particularly upper tract
Two main categories: 1) Flat, 2)Papillary
Carcinoma In Situ (CIS) Flat lesion (No papillary structures!)

Often erythematous on cystoscopy
High-grade cytology (Pleomorphism):
• Frequent nucleomegaly (usually >5x lymphocyte nucleus)
• Hyperchromasia
Disorder: Loss of polarity; Nuclear crowding;
Increased cytoplasmic eosinophilia
Does NOT need to be full-thickness (can show Pagetoid spread)
Can be discohesive → shed into urine → remaining cells =
“Clinging carcinoma”
IHC to help distinguish CIS from Reactive:

CK20 P53 Ki67
Normal/Reactive Umbrella cells only Wild-type Low (usually)
CIS All cells (full-thickness) Diffuse or Null High
Prognosis: ~25% progress to invasive disease

Treatment: Cystoscopic observation, Intravesical BCG Therapy
Urothelial Dysplasia
Flat urothelium with appreciable cytologic and architectural features that are believed to be
preneoplastic, but do not reach the threshold of CIS.
No consensus criteria. Tremendous inter-oberserver variability.
Not diagnosed routinely in clinical practice as a result
Some use terms like: “Atypia of unknown significance” or “Urothelial atypia, cannot exclude dysplasia”
as are treated clinically similar
Given lack of consensus in diagnosis, prognosis not well-established
Papillary Neoplasms Fibrovascular cores covered in urothelium.
Hierarchical branching
At medium magnification, overall predominant impression?
Order of architecture and cytology? Disorder of architecture and cytology?
Variation of architecture and cytology?

Papillary Urothelial Carcinoma, High-grade
No Yes
Modified from: WHO Classification of Tumours of the
Urinary System and Male Genital Organs. 2016.
PUNLMP Papillary urothelial carcinoma, Low-grade
Papilloma PUNLMP Low-grade, High-grade,

Papillary Papillary
carcinoma carcinoma
Architecture of Delicate Delicate Fused to Fused to
papillae branching branching
Architecture of Normal Polarity like Ordered, but with Disorder!
cells normal; Ordered, variation
no variation
Nuclear size Normal Normal to slightly Enlarged with Enlarged with
enlarged variation variation
Nuclear shape Normal Oval-round; Round-oval; Moderate to
uniform slight variation marked
pleomorphism
Umbrella cells Uniformly present Present +/- +/-
Mitoses Absent Rare, basal Occasional, any Frequent, at any

level level
Modified from: Epstein et al. Biopsy Interpretation of the Bladder. Wolters Kluwer, 2017.
Papilloma
Papillary urothelial neoplasm with delicate
fibrovascular cores covered by urothelium of
normal appearance and thickness
Relatively rare
Prognosis: Recurrence rate ~10%;
Progression to carcinoma ~1%
Treat with TURBT
Papillary Urothelial Neoplasm of
Low Malignant Potential (PUNLMP)
Papillary urothelial neoplasm with minimal atypia
Epithelial thickness usually exceeds normal (>7 cells)
Lots of order, little variation → every high-power
field should look the same One HPF should
Overall, monotonous appearance. look like the next!
Maintained cell polarity (little variation)
Often hard to distinguish from Low-grade papillary

urothelial carcinoma→ sometimes low interobserver
agreement→ for both, treatment is TURBT and
observation
Lower risk of recurrence/progression than carcinoma
Non-Invasive Papillary Urothelial Carcinoma, Low-Grade

Relatively delicate papillae with extensive branching
Relatively orderly, but with some variation at high-power
Mild to moderate nuclear pleomorphism
Any thickness, but often thicker than normal
Cell polarity maintained (cells know which way is “up”)
Inconspicuous nucleoli.
Grade based on highest-grade component (at least if >5%)
Recurrence rate ~30%; Treat with TURBT & surveillance
Non-Invasive Papillary Urothelial Carcinoma, High-grade

Disordered appearance: Architectural and cytologic
abnormalities
Loss of cell polarity. Irregular spacing and nuclear
overlap. Often discohesive.
Nuclear pleomorphism, hyperchromasia, clumped
chromatin. Sometimes prominent nucleoli.
Often fusion of papillae
Recurrence rate ~50%; Treat with TURBT &
surveillance
Urothelial Proliferation of Uncertain Malignant Potential (UPUMP)
Markedly thickened urothelium (> 10 cells)
No or minimal atypia
Increased cell density
No true papillary fronds with fibrovascular
cores
Undulating mucosal folds
Clonal. May be early pre-cursor to low-

grade papillary urothelial carcinoma (often
at “shoulder”).
Followed clinically.
Inverted Urothelial Lesions

• Complex, branching, anastomosing inverted
growth cords of urothelium
• Peripheral basal cells in nests
• Smooth stromal-epithelial interface (no
infiltrative growth)
• No stromal reaction
• Do not involve muscularis propria
• May have cystic areas (like cystitis cystica)
Inverted Urothelial Papilloma

• 5-10 cells layers thick
• No significant atypia
• Benign with low recurrence risk
Inverted Papillary Urothelial Carcinoma

• More than 10 cell layers thick
• More nodular, expansile growth
• More mitoses
• More significant cytologic atypia
• Irregular chromatin
• Enlarged, irregular nucleoli
Invasive (Infiltrating) Urothelial Carcinoma
Invasive beyond the basement membrane
Usually, cytologically High-Grade (Nuclear
pleomorphism, Hyperchromasia, Numerous mitoses)
Moderate amounts of eosinophilic cytoplasm
Various architectures (nests, single cells, etc…), but often
elicits a desmoplastic stromal response
Diversity in morphologic manifestations, including
specific variants and divergent differentiation.
IHC: GATA3, Uroplakin III, Thrombomodulin, High-
Molecular Weight Cytokeratin (e.g., CK5/6), p63, p40,
CK7, CK20, S100-P
Divergent differentiation:
Squamous—intercellular bridges and/or keratinization.
Very common (up to almost 50% of urothelial cancers)
Glandular—presence of gland formation (up to 20%).
Often has enteric appearance and immunophenotype
Trophoblastic—giant cells resembling
syncytiotrophoblasts. Can secrete βhCG.
Specific Variants:
Plasmacytoid—Bland cells resembling plasma cells. E-
cadherin loss (like lobular breast). Express CD138.
Aggressive. Poor prognosis.
Micropapillary—Nests surrounded by lacunae.
Peripherally located nuclei. Aggressive. Often high stage.
Plasmacytoid
Nested—Cytologically bland discrete to crowded
infiltrating nests. Can be hard to dx on biopsy unless into
muscle.
Lymphoepithelial-like—High-grade syncytial cells with
prominent inflammatory infiltrate. EBV negative.
Sarcomatoid—Resembles a sarcoma, possibly including
heterologous differentiation (e.g., osteosarcoma).
Micropapillary (And others!)
Squamous differentiation Nested

Diagnosis of Lamina propria invasion:
Can be challenging→ Look especially hard in high-grade tumors
Pattern of invasion: single cell infiltration, irregularly shaped, jagged, haphazard nests, finger-like
projections, architecturally complex proliferations not conforming to normal papillary neoplasms
Paradoxical maturation: invading cells have more abundant cytoplasm and more pleomorphism
Stromal response: desmoplastic stroma, retraction artifact, inflamed stroma, myxoid stroma
(although sometimes there is no response!)
Potential pitfalls:
Tangential sectioning/von Brunn’s nests→ Smooth, round, regular contours of cells that look like the
surface favors non-invasive/benign
Thermal injury→ don’t over interpret burned tissue
Muscularis propria invasion:

A big decision clinically, if stage T ≥2 (into musclularis propria), then often proceed with “definitive
therapy” (chemo then cystectomy). If T <2, then often conservative treatment with TURBT
For muscularis propria invasion, look for thick, organized smoot muscle bundles
Thin, wispy muscle with associated vessels→ favors muscularis mucosae
Some use smoothelin (stronger in muscularis propria) and vimentin (stronger is musclaris mucosae)
IHC to distinguish the two, but this can be problematic and is not recommended routinely
Other Epithelial Tumors

Pure SCC has no urothelial component (otherwise just squamous differentiation in urothelial
carcinoma—which is much more common!)
Uncommon in US, but predominates in some parts of Africa and Middle-east, largely related to
prevalence of Schistosoma haematobium
Other risk factors: Smoking, occupational, chronic UTI’s
Chronic inflammation → Increased proliferation and oxidative stress → Squamous metaplasia →
keratinizing dysplasia → SCC
Keratin pearls and intercellular bridges. No urothelial CIS or traditional urothelial component.
Neuroendocrine Tumors
Small cell neuroendocrine carcinoma—same has pulmonary (and other organ) small cell carcinoma.
Frequently associated with traditional urothelial carcinoma (that then de/transdifferentiates). Can
express TTF1. Aggressive.
Large cell neuroendocrine carcinoma—Very rare. Aggressive.
Well-differentiated neuroendocrine tumors—resemble those of the GI tract. Often have prominent
pseudoglandular pattern (resembling cystitis cystica/glandularis). Often mucosal and excellent
prognosis.
Nephrogenic Adenoma
Benign
Often arise in the setting of prior urothelial injury
Histologic spectrum:
Tubules lined by cuboidal to columnar cells
Papillary structures
Fibromyxoid variant has spindled cells surrounded
by fibromyxoid stroma Papillary
Cells can be hobnailed

Often thick basement membrane
No significant nuclear atypia
Histogenesis is a little controversial.
Possibly derived from shed renal
tubule cells→ Stain with Pax8 by
IHC Fibromyxoid Tubules
Villous Adenoma
Histologically identical to colonic adenomas
(Hyperchromatic, pencillate nuclei)
Papillary architecture. Rare.
Can progress
Adenocarcinoma
Purely glandular malignant tumor (as opposed to
divergent glandular differentiation in a urothelial
carcinoma)
Can be hard to distinguish from a GI metastasis.
IHC: β-Catenin strong nuclear reactivity in most colon
cancers, but not in bladder adenocarcinomas. Other
markers (e.g., CDX2) can be positive in both
Urachal Carcinoma
Arise from urachal remnants. Often adenocarcinomas.
Frequently intestinal-type and/or mucinous appearing
Criteria:
1) Location in bladder dome or anterior wall (midline)
2) Epicenter in bladder wall (not mucosal)
3) Absence of widespread cystitis cystica near tumor
4) Absence of other known primaries
Derived from pre-existing Müllerian precursors
(Accordingly more common in women, can also get
endometrioid carcinomas)
Most common in urethra, bladder neck, and trigone.
Characteristic morphology:
Abundant clear to eosinophilic cytoplasm.
Severe cytologic atypia. Hyperchromatic nuclei.
Varied architecture: Tubules, papillary, diffuse, etc..
IHC: Positive CAM5.2, CK7, PAX8, HNF1β, AMCAR
Negative PSA, PSAP, p63, HMWCK, ER, PR, GATA3
Often advanced with poor prognosis.
Paraganglioma
Present with symptoms of catecholamine secretion
Urinate→ Hypertension or loss of consciousness
Derived from paraganglion cells of the bladder, so
submucosal
Typical architecture: “Zellballen” with nests
separated with a rich vascular network of
sustentacular cells.
Cell have amphophilic to acidophilic cytoplasm
IHC: Synaptophysin/Chromogranin positive in tumor
cells; S100/Sox10 positive in sustentacular cells. CK
negative. GATA3 positive.
Germline SDH mutations present in some cases (Carney-Stathakis syndrome) with familial GIST
Often benign behavior if low stage, but can metastasize.
Polypoid cystitis
Benign. Reaction to any inflammatory insult
(most commonly an indwelling catheter)
Submucosal edema, fibrosis, and inflammation

→ broad bulbous projections covered with
reactive urothelium
(No epithelial branching, epithelial thickening,

atypia or delicate cores, like in papillary
neoplasms)
Mesenchymal Lesions
Inflammatory Myofibroblastic Tumor
Fibroblastic/myofibroblastic origin
Most common in children and young adults
Loose stellate to spindled cells in a myxoid background
Admixed inflammatory cells
Mild amounts of collagen
Infiltrative, often into muscle
Mitoses, but no atypical ones
Delicate vascular network
NO significant hyperchromasia
IHC: Positive SMA; Sometimes aberrant CK; ALK positive in ~60% (FISH or IHC) Neoplastic (clonal)
May recur, but very rarely metastasize.
Usually treated with TURBT or partial cystectomy
Myofibroblastic
Proliferations
Pseudosarcomatous Myofibroblastic Proliferation Reactive (after
instrumentation)
Aka: “inflammatory pseudotumor,” or “Post-operative spindle
cell nodule”
Can get what are thought to be reactive spindle cell lesions
after instrumentation.
A little controversial if this is the same entity as inflammatory
myofibroblastic tumor (IMT)
• Identical appearance (nodular fasciitis-like with
inflammatory cells and myxoid background)
• Identical IHC in many cases
• Some people use a single combined Dx (IMT/PMP)
Leiomyosarcoma
Malignant tumor arising from or differentiating along
the lines of smooth muscle.
Most common urinary bladder sarcoma
Infiltrative. Intersecting fascicles.
Eosinophilic spindled cells with cigar-shaped nuclei
Cytologic atypia, high cellularity, mitotic activity, tumor
necrosis.
IHC: Positive SMA, desmin, h-caldesmon, calponin
Poor prognosis
Rhabdomyosarcoma
Malignant tumor with skeletal muscle differentiation
Often Children and Embryonal subtype
Composed of primitive spindled to rhabdoid cells in a
myxoid background. Numerous rhabdomyoblasts and/or
strap cells. Can see cross-striations.
Botryoid type forms multiple grape-like polypoid
projections with characteristic cellular cambium layer
below mucosa
IHC: Positive Desmin, MyoD1, Myogenin. Sometimes patchy CK or neuroendocrine markers.
(Very rare in adults, more commonly sarcomatoid urothelial carcinoma with heterologous differentiation)
Other Mesenchymal Tumors

PEComa Hemangioma
Angiosarcoma Granular cell tumor
Solitary Fibrous Tumor Neurofibroma
Leiomyoma
Immunohistochemistry for Spindle Cell Lesions of the Bladder

Recommended First Panel: ALK1, SMA, desmin, cytokeratin (AE1/AE3), GATA3, and p63 with
a HMWCK (e.g., CK5/6) (with possible second panel with myogenin, S100, etc..)
IHC Stain IMT/PMP Sarcomatoid Leiomyosarcoma Rhabdomyosarcoma

Carcinoma
ALK1 +/- - - -
SMA +/- +/- + -/+
Desmin & -/+ - + +
h-caldesmon
Myogenin & - - - ++
MyoD1
CK AE1/AE3 -/+ +/- - -
p63 & p40 - + - -
HMWCK - + - -
(e.g., CK5/6)
GATA3 - +/- - -
Last updated: 9/22/2020 Prepared by Kurt Schaberg MD
Prostate Tumors
Acinar Adenocarcinoma (The most common/default type of “Prostate Cancer”)
An invasive adenocarcinoma consisting of neoplastic prostatic epithelial cells with secretory

differentiation arranged in a variety of patterns, typically without basal cells.
Most common cancer in men and second leading cause of cancer death in the U.S.A.
Prevalence is strongly correlated with age (older = higher prevalence)

Majority are multifocal, often with 2-3 separate tumors in each prostate.
Most commonly located in posterior/posterolateral peripheral gland.
Early tumors are often asymptomatic. Locally advanced prostate cancer mimics BPH with urinary
symptoms. Bone very common site of metastasis → bone pain and pathologic fractures
Morphology: Always use multiple features (there is no single feature to Dx!)
Nuclear Features:
Benign
• Prominent nucleoli
• Nuclear enlargement
• Nuclear hyperchromasia
• Mitotic figures
• Apoptotic bodies
Cytoplasmic features:
• Amphophilic cytoplasm
• Sharp luminal borders
Luminal contents:
• Blue-tinged mucin
• Pink amorphous secretions
• Crystalloids
Benign
Architecture:
• Crowded small glands
• Linear row of atypical glands spanning the width of a core
• Small glands on both sides of a benign gland
• Haphazard, infiltrative pattern
Absent basal cell layer (can highlight with IHC, as fibroblasts may mimic basal cells)
Usually lack desmoplastic stroma. When present, often associated with high-grade carcinoma.
Findings more common in benign glands:

• Atrophic cytoplasm
• Merging with benign glands
• Corpora amylacea
• Inflammation
• Lipofuscin
Cancer
Features Specific To Malignancy Mucinous Fibroplasia
(collagenous micronodules)
Glomerulations Perineural Invasion
Dense nodules of collagen (hyalinized
Cribriform formations To Dx malignancy, tumor must
mucin) surrounded and encased by
attached only to one edge completely encircle nerve. (Benign
epithelium
of the surrounding gland glands may abut, but not encircle)
Specific Variants (Same prognosis, unless

otherwise mentioned)
Atrophic variant
Cytoplasmic volume loss (like atrophy), Often absent
nuclear enlargement and nucleoli→ mimicking benign
atrophy!
Luckily, conventional carcinoma often present nearby.
Can be sporadic or after therapy.
Often Gleason pattern 3 (small infiltrative glands)
Pseudohyperplastic variant
Simulates luminal cell hyperplasia→ papillary
infoldings, luminal undulations, and branching.
Round nuclei, not pseudo stratified, with prominent
nucleoli.
Often relatively pure and well-circumscribed.
Foamy gland variant

Abundant foamy/xanthomatous cytoplasm
and small, pyknotic nuceli
Usually combined with usual type (rare to be
pure)
Rare Variants (continued)
Microcystic variant
Large, dilated round glands with flattened luminal
cells→ mimic benign atrophy.
Mucinous (colloid) variant

≥25% of tumor has extracellular mucin pools
Can only be Dx’d on prostatectomy (on Bx say
“mucinous features”)
Mentally subtract mucin for grading.
Signet ring-like variant

≥25% of tumor is composed of infiltrative single
cells with large vacuoles (that do not actually
contain mucin). Gleason pattern 5.
Poor prognosis. Must consider GI metastasis.
Notably, vacuoles can be seen in any grade
prostatic cancer (vacuoles ≠ Signet ring-like)!
Sarcomatoid variant (Carcinosarcoma)

Biphasic with both epithelial and mesenchymal
differentiation. Poor prognosis.
Can see various heterologous elements.
Hypernephroid variant (vanishing variant)

Sheets of cells with abundant clear cytoplasm.
Gleason pattern 4
Pleomorphic giant cell variant (not pictured)

Giant bizarre anaplastic cells with pleomorphic
nuclei and without a spindle cell component.
Poor prognosis.
Gleason Grading Based on architecture at low power (using 4x or 10x objective).
Circumscribed nodule of closely packed but

separate, uniform, rounded to oval, medium-
1
sized acini
Should not be diagnosed regardless of the type

of specimen, with extremely rare exceptions
Fairly circumscribed, yet at the edge of the

tumor nodule there may be minimal infiltration
2
Do not diagnose on biopsy, rarely diagnosed
regardless of specimen.
Glands are more loosely arranged and not quite
as uniform as Gleason pattern 1
Well-formed glands (with lumina)
3
Separate, discrete, Non-fused
Infiltration
Ill-defined, poorly formed glands

Gland fusion
4
ALL cribriform glands
Hypernephromatoid
Glomerulations
Ductal Adenocarcinoma (without necrosis)
Often Disqualifies from Active Surveillance
Essentially no glandular differentiation:

• Solid sheets
5 • Cords
• Single cells
• Linear arrays
Comedocarcinoma with central necrosis
Notes: Given the importance of distinguishing between patterns 3 and 4 for active surveillance, getting
levels can be helpful to differentiate tangential sectioning of small well-formed glands (pattern 3) from
poorly-formed glands (pattern 4).
Gleason Scoring
Biopsies:
Most common pattern + Second most common pattern = Score
• If the tumor has only one pattern, then add the same pattern twice.
• No tertiary pattern assigned.
• In the setting of high-grade cancer one should ignore lower-grade patterns if they occupy less
than 5% of the area of the tumor. (e.g., 98% pattern 4 and 2% pattern 3 → 4+4=8)
• High-grade tumor of any quantity, as long as it was identified at low to medium magnification
should be included. (e.g., 98% pattern 3 and 2% pattern 4 → 3+4=7)
• On needle biopsies with patterns 3, 4, and 5, both the primary pattern and the highest grade
should be recorded. Consequently, tumors with Gleason score 3 + 4 and a tertiary pattern 5
would be recorded as Gleason score 3 + 5 = 8.
Prostatectomies:
Most common + Second most common = Score, with tertiary pattern if present
than 5% of the area of the tumor.
Grade Groups
Grade Group Gleason Score
1 ≤6 Only individual discrete well-formed glands
2 3+4=7 Predominantly well-formed glands with a lesser

component of poorly formed/fused/cribriform
glands
3 4+3=7 Predominantly poorly formed/fused/cribriform
glands with a lesser component of well-formed
glands
4 8 - Only poorly formed/fused/cribriform glands

- Predominantly well-formed gland and lesser
component lacking glands
- Predominantly lacking glands and lesser
component of well-formed glands
5 9-10 Lack gland formation (or with necrosis) with or
without poorly formed/fused/cribriform glands
For cases with >95% poorly formed/fused/cribriform glands or lack of glands on a core or at radical
prostatectomy, the component of <5% well-formed glands is not factored into the grade.
Immunohistochemical Stains
Markers of Prostatic Origin
Prostate Specific Antigen (PSA), Prostatic Acid Phosphatase (PSAP), NKX3.1, Prostein
Each marker ~95% sensitive. NKX3.1 is the most specific.
PSA & PSAP can decrease after androgen deprivation therapy and are less specific (e.g., also get some
salivary gland tumors).
Markers of limited utility due to poor sensitivity or specificity: ERG, AR, AMACR.
Cancer vs Benign Glands Most useful for the confirmation of a small quantity of tumor.
Basal cells are absent in invasive prostatic adenocarcinoma (usually).
Stains for basal cells
Cytoplasm: High-molecular weight cytokeratins (HMWCK) (e.g., 34βE12, CK5/6)
Nuclear: p63, p40
AMACR (aka P504S or Racemase): frequently overexpressed in glandular neoplasia of the prostate
(~90%) with granular cytoplasmic staining. Needs to be done in combination with basal markers as
HGPIN is often positive.
ERG: expression is highly specific for neoplastic prostate glands, but has a low sensitivity (~50%), so
doesn’t have much value over AMACR.
Notable Pitfalls:
Loss of basal cells is not specific for cancer and
may be observed in benign mimics like atrophy,
partial atrophy, and adenosis.
Rare cases of adenocarcinoma can stain for
basal markers (even though they don’t have
basal cells) in a non-basal distribution.
AMACR expression can be seen in benign
mimics such as atrophy, adenosis, and
nephrogenic adenoma.
Common triple stain:

HMWCK + p63 → Brown cytoplasmic and
nuclear, respectively, staining of basal cells in
benign glands
AMACR → Red cytoplasmic staining in

neoplastic glands (that in this case are also
lacking basal cells, supporting the diagnosis of
cancer)
Diagnosing Limited Cancer
Major Criteria for diagnosing prostate cancer (no single criteria is diagnostic):
1) Infiltrative growth
2) Absence of basal cells
3) Nuclear atypia (nuclear enlargement with prominent nucleoli)
How many glands do you need?

There is no absolute number, but many urologic
pathologists like to see at least 3 glands with
cytologic/architectural features of cancer.
Atypical Small Acinar Proliferation (“ASAP”)

A descriptive term (not an entity) designed to be
used when you have a collection of small glands
suspicious for cancer but lack definitive diagnostic
features or are too small to be certain that they do
not represent the edge of a benign lesion.
IHC in ASAP: Basal cells may be missing in benign
small glands, so, immunohistochemistry is primarily
useful to disprove cancer, not to prove cancer.
Detection of even rare basal cells in any of the
glands of the suspicious population essentially
excludes carcinoma for the entire population.
Clinical follow-up for ASAP: Repeat biopsy
What to do with these 4 glands?

This is potentially a borderline case. If this is all
you had, it’d probably safest to go “ASAP” given
how limited they are and the absence of
prominent nucleoli, but some might call it 3+3
Benign Glands Prostatic Adenocarcinoma

Big, regularly spaced glands Small, infiltrative glands with haphazard and
variable spacing
Papillary infoldings Sharp luminal contours
Small nuclei without nucleoli Large nuclei with prominent nucleoli and
frequent hyperchromasia
Abundant pale, clear apical cytoplasm Amphophilic cytoplasm
Corpora amylacea Eosinophilic or blue mucin secretions
Biopsy Reporting
For each biopsy specimen/location report:
• Gleason Score and Grade Group
• Number of cores with cancer ( or for TURPs the number of positive chips and total number of chips)
• Linear extent of cancer in each core (percentage and/or length)
• Perineural invasion or extraprostatic extension (if present)
• Percentage of pattern 4 should be recorded in cases with a Gleason score 7 (with very limited
pattern 4, the patient may still be eligible for active surveillance)
PROSTATE, LEFT MEDIAL TRANSITION ZONE, BIOPSY

- Prostatic adenocarcinoma, Gleason Score 3+4=7 (Grade Group 2), 10% Pattern 4, Involving 1 of
1 cores, 5% of tissue
Discontinuous Cancer
5% Additive Total = 10% 5%
Controversial! Several studies have shown that
the linear total (“end to end”) method
correlates better with prostatectomy findings
as they often represent portions of the same
tumor. However, there is no consensus so Linear Total = 95%
consider reporting both for now.
Extraprostatic Extension
Presence of tumor beyond the confines of the
prostate gland. Including:
• Invading fat
• Involving loose connective tissue beyond the plane of the
prostate (does not need to be directly touching adipocytes)
• Involving perineural spaces in the neurovascular bundles
• In the apex and base, EPE is determined when the tumor
extends beyond the confines of the normal glandular
prostate (can be hard to clearly define)
Invasion of the urinary bladder neck: neoplastic glands involve the thick intersecting smooth muscle
bundles characteristic of the bladder neck region in the absence of associated benign prostate tissue.
Seminal vesicle involvement: invasion of the muscular wall of seminal vesicle (must be Extraprostatic)
Genetics
Recurrent mutations in the ETS family of transcription factors: most commonly TMPRSS2-ERG fusion
Other frequent mutations: TP53, PTEN
Prostate cancer is one of the most heritable cancer types, driven by numerous common mutations
(and some rare germline mutations). This risk is mostly associated with many SNPs with each having
relatively low risk/penetrance (but the effect can be multiplicative).
BRACA2→ significantly increased risk of prostate cancer
Treatment effect
Can show minimal or extensive changes in both benign and
malignant glands. Use stains liberally.
Do not grade if significant treatment effect (behave better
than grade would suggest). Benign Gland with
Radiation atypia
Radiation therapy:
Benign glands: atrophic, basal cell immunophenotype, may
show marked radiation atypia.
Adenocarcinoma: often inconspicuous with vacuolated
cytoplasm and inconspicuous nuclei/nucleoli
Hormonal therapy:
Tumor with
Benign glands: diffuse atrophy with prominent basal cells
Treatment
Adenocarcinoma: atrophic with vacuolated cytoplasm and
effect
small inconspicuous nuclei/nucleoli
Active Surveillance
Management strategy where patients diagnosed with prostate cancer undergo regular follow-up with
serum PSA tests and repeat biopsies (looking for progression), rather than receiving immediate
definitive treatment with curative intent. Focus on low and very low risk patients
NCCN Inclusion Criteria:

Absolute (Low risk):
• Gleason Score ≤6
• PSA <10 ng/mL
• Clinical stage <T2a (Tumor involves one-half of one lobe or less)
Especially if (Very low risk):
• Fewer than 3 prostate biopsy cores positive, all ≤50%
• PSA density <0.15 ng/mL/g
PNI allowed
NCCN Progression Criteria: (initiates transition to curative therapy)

• Gleason grade 4 or 5 on repeat biopsy
• Prostate cancer found in a greater number of biopsies or greater extent of biopsies
Excluded if: any variant other than acinar adenocarcinoma (e.g., ductal, sarcomatoid, small cell),
intraductal carcinoma
Active Surveillance Protocol: Serum PSA monitoring, Digital rectal exam, repeat prostate biopsies (6-12
months after initial) yearly for up to 10 years.
Intraductal Tumors Non-invasive tumors growing within ducts
High-grade Prostatic Intraepithelial Neoplasia (“HGPIN”)

Pre-invasive neoplastic proliferation.
Often multifocal.
Cytologic changes resembling cancer:
• Nuclear enlargement
• Prominent nucleoli
• Hyperchromasia
• Clumped chromatin
Although non-invasive, basal cells may

be patchy (so be careful interpreting
IHC!)
Four main architectures: tufting,
micropapillary, cribriform, and flat
Often cytoplasmic AMACR staining
Clinical importance: associated with subsequent detection of cancer (more HGHPIN→ higher risk)
Intraductal Carcinoma
Diagnostic requirement:
Malignant epithelial cells filling large acini and
prostatic ducts, with preservation of basal cells
with either:
- Solid or dense cribriform pattern, or
- A loose cribriform or micropapillary pattern
with either:
- Marked nuclear atypia (nuclei 6x
normal or larger)
- Comedonecrosis Comedonecrosis
Can be seen in two scenarios:
1) Intraductal spread of a high-grade invasive
cancer (majority of cases)
2) Distinct precursor lesion (separate from
HGPIN) with high risk of progression to cancer
IHC often required for diagnosis to demonstrate

basal cells. Can show loss of PTEN (rarely seen in
HGPIN)
If seen on biopsy→ often treat with radical prostatectomy as highly associated with cancer and multiple
adverse factors (high Gleason grade, high tumor volume, etc..). Sometimes repeat biopsy immediately.
If a lumen-spanning atypical lesion morphologically falls short of Intraductal Carcinoma, best to call
“Atypical Intraductal Proliferation” and recommend immediate repeat biopsy.
Other Tumors
Ductal Adenocarcinoma
Subtype of prostatic adenocarcinoma with
tall, columnar, pseudostratified epithelium
Cytoplasm is usually amphophilic.
Often elongate nuclei with more cytologic
atypia that acinar type.
Prominent nucleoli, coarse chromatin, and
lots of mitotic figures.
Frequent necrosis.
Combination of papillary and cribriform
architecture in dilated glands
Old name: “endometrioid” (looks like
endometrioid adenocarcinoma of uterus)
Typically periurethral location
Similar IHC to acinar type: no basal cells,
AMACR positive.
More aggressive than average acinar
adenocarcinoma.
Grade as pattern 4, but if necrosis as 5
Basal Cell Carcinoma

Malignant neoplasm composed of basal cells
Most cases show various proportions of:

• adenoid cystic/cribriform pattern with
inspissated secretions, and a
• basaloid pattern with small solid nests of
basal cells
Desmoplastic stroma. Can have hyaline rim.
IHC: basal cell markers usually label

outermost layers (sparing luminal cells),
while luminal cells stain with CK7.
HER2/neu overexpressed.
Some cases with Adenoid cystic morphology
have MYB-rearrangements (like elsewhere)
Normal PSA
Can be aggressive.
Urothelial Carcinoma
Most often secondarily involving the prostate
from the bladder and/or prostatic urethra.
Note: Determining which site the urothelial
carcinoma is coming from is very important for
staging!! Bladder→ Prostate stroma =T4, while
Prostatic urethra→ Prostate stroma = T2
Morphology similar to urothelial carcinoma of

bladder (often pleomorphic epithelioid cells
with frequent squamous differentiation).
Frequent spread of CIS or pagetoid spread into

ducts. Invasion elicits desmoplastic stroma.
IHC: p63, HMWCK, GATA-3 (+), NKX3.1 & PSA (-)

Pagetoid Spread of CIS
Squamous Neoplasms
Very Rare. Arise through either divergent differentiation of basal cells or transdifferentiation of usual
adenocarcinoma following hormone therapy.
Squamous Cell Carcinoma: Pure squamous morphology. Similar morphology/IHC to SCC elsewhere. Must
be distinguished from secondary involvement of a bladder/urethral SCC or TCC.
Adenosquamous Carcinoma: Both glandular (acinar) and squamous morphology.
Neuroendocrine Tumors
Adenocarcinoma with neuroendocrine cells
Neuroendocrine cells can be seen on IHC in
many usual prostate cancers, does not seem
to be clinically significant, so no need to stain
routinely
Some cases show “Paneth cell-like
neuroendocrine differentiation” with
eosinophilic granules. Can see similar changes
in benign glands.
Well-differentiated Neuroendocrine Tumor

Very rare. Must exclude adenocarcinoma with
neuroendocrine differentiation (with more
typical areas).
Small Cell Neuroendocrine Carcinoma. Morphologically identical to in the lung (small cells with scan
cytoplasm and stippled, hyperchromatic nuclei). May be admixed with acinar adenocarcinoma or
pure. Do not Gleason grade. Stains with at least 1 neuroendocrine marker usually. May be TTF-1
positive. Ki67 near 100%. Very aggressive.
Mesenchymal Tumors
Stromal Tumor of Uncertain Malignant Potential (“STUMP”)
Tumor of specialized prostatic stroma.
Often present with urinary symptoms.
Several growth patterns:
• Hypercellular stroma with scattered degenerative-
appearing cells admixed with benign glands.
• Phyllodes subtype with leaf-like branching
• Also: myxoid, epithelioid, hypercellular bland stroma
IHC: Express CD34 and PR
Usually good prognosis. My recur or progress
Stromal Sarcoma
Malignant tumor of specialized prostatic stroma.
Phyllodes-like growth pattern with malignant,
pleomorphic stroma or fascicular growth similar to a
leiomyosarcoma
IHC: Express CD34 and PR
Can behave aggressively.
Other Tumors Synovial Sarcoma

Leiomyoma Inflammatory Myofibroblastic Tumor (IMT)
Leiomyosarcoma Solitary Fibrous tumor (SFT)
Rhabdomyosarcoma Hemangioma
Angiosarcoma Granular cell tumor
Immunohistochemistry of Mesenchymal Lesions:

STUMP Stromal Sarcoma Leiomyosarcoma Rhabdomyosarcoma IMT SFT GIST
CD34 + + - - - + +
SMA +/- - + + + - -
Desmin +/- - + + -/+ - -
Myogenin - - - + - - -
CD117 - - - - -/+ - +
ALK1 - - - - +/- - -
PR + + +/- - - +/- -
Modified from: Epstein and Netto. Biopsy Interpretation of the Prostate. 5th Edition
Seminal Vesicle
Normal Anatomy
Complex papillary folds lined with pseudostratified tall
columnar epithelium with microvesicular lipid-filled
cytoplasm and prominent lipofuscin pigment (golden-
brown and refractile granules, which help distinguish it
from prostate).
Moderate to severe cytologic atypia with large irregular
hyperchromatic nuclei with coarse chromatin and
prominent nucleoli. Likely degenerative.
Stains with GATA-3
Amyloidosis
Linear or massive nodular subepithelial deposits of
amorphous eosinophilic fibrillar material.
Relatively common benign incidental finding. Not
associated with systemic amyloidosis.
Highlighted with Congo Red with “Apple-green”
birefringence
Adenocarcinoma
Always first consider secondary involvement, most
commonly by prostatic acinar adenocarcinoma.
Primary adenocarcinoma is RARE. It has a variety of
patterns. Most often a papillary clear cell tumor,
but can be hobnail, etc..
IHC: CK7(+), CK20(+/-), Prostate maker (-).
Mixed Epithelial and Stromal Tumors (“MEST”)

Biphasic tumors with stromal and benign
epithelial components. Cystic to solid masses.
Cystadenoma→ Lobular pattern. Branching
lumens and cysts of various sizes.
Fibroadenoma→ Spindle cell component is more
pronounced.
Adenosarcoma→ Stroma is densely cellular and
condenses around distorted gland spaces (like
Phyllodes tumors or adenosarcoma of uterus)
Mimics of Cancer
Basal Cell Hyperplasia
Proliferation of basal cells piling up and filling
tubules/glands→ may form solid nests
Appear very blue due to crowded nuclei with scant
cytoplasm.
Retains lobular architecture and smooth borders.
Nuclei are very bland with very small nucleoli
Basal cell markers very strongly positive.
Central Zone Sampling

Anatomic zone with characteristic complex architecture.
Stratified eosinophilic cytoplasm and prominent basal
cell layer.
Intra-luminal bridges ("Roman arches")
Can mimic HG-PIN, so in biopsies from the mid-base,
have higher threshold for HGPIN & r/o normal anatomy!
Verumontanum mucosal gland hyperplasia

Crowded glands near verumontanum. Often nearby
urothelium. Corpora amylacea often present
Adenosis
(aka Atypical Adenomatous Hyperplasia)
Well-circumscribed tightly packed, largely
uniform glands. Lobular architecture. Pale to
clear cytoplasm. Admixture of small and larger
glands.
Occurs in the transition zone (mostly seen in
TURPs and Prostatectomies)
Some features suggestive of carcinoma may be
seen such as prominent nucleoli and
crystalloids/mucin, but often merge with
benign glands.
Principal differential diagnosis is Gleason grade
2 carcinoma. This distinction requires IHC for
basal cells:
• Basal cells may be decreased in Adenosis
• Demonstration of any basal cells indicates
adenosis in this context
• Carcinoma must lack basal cells completely
Atrophy
“Simple” Atrophy
Basophilic glands with scant cytoplasm (both
apically and laterally).
Normal caliber glands with normal spacing.
Postatrophic Hyperplasia (“PAH”)

Tightly packed very small cytologically bland
glands. Very blue at low-power.
Usually clustered around a larger dilated “feeder”
duct (Think: TDLU of breast)
Bland nuclei without prominent nucleoli
Basal cells present
Stroma often sclerotic
Partial Atrophy
Retain moderately abundant pale/clear cytoplasm
lateral to the nuclei (with reduced apical
cytoplasm), which may produce pale glands that
lack the blue appearance of atrophy.
Frequently merges with nearby atrophy.
Bland nucleoli without prominent nucleoli.
No infiltrative growth.
Undulating luminal surfaces.
Retained (but possibly decreased) basal cell
markers.
Cowper’s Glands
Periurethral, near apex
Lobular architecture with central duct
Abundant mucin-filled cytoplasm (PASd+)
No nuclear atypia or prominent nucleoli.
Basal cells markers positive, frequently muscle-
specific actin positive (unlike in prostate)
IHC: PSAP negative (PSA may be positive)
Clear Cell Hyperplasia
Big nodules of clear cells with cribriform pattern.
Smooth gland borders and lobular pattern.
Uniform bland nuclei without prominent nucleoli
Intact basal cell markers.
Most often seen in central zone on TURP in setting
of BPH.
Sclerosing Adenosis
Dense spindled stroma with compressed and
distorted epithelial elements
Entrapped epithelium ranges from small acini to
cords and single cells. No cytologic atypia.
Can have surrounding hyaline sheath
Basal cells present with unique immunologic profile
Usual markers positive (p63, HMWCK)
Also express myoepithelial markers (smooth muscle
actin, S100)
Other Mimics
Nephrogenic adenoma
Malakoplakia
Seminal Vesicle
Mesonephric hyperplasia
Colonic mucosa
Urothelial metaplasia
Granulomatous prostatitis
Signet-ring lymphocytes
Paraganglia
Prostate Acinar Adenocarcinoma
Gleason Grading
Circumscribed nodule of closely packed but
separate, uniform, rounded to oval, medium-
1
sized acini
Should not be diagnosed regardless of the type

of specimen, with extremely rare exceptions
Fairly circumscribed, yet at the edge of the

tumor nodule there may be minimal infiltration
2 Glands are more loosely arranged and not quite

as uniform as Gleason pattern 1
Very rarely diagnosed
Well-formed glands (with lumina)
3
Separate, Non-fused
Infiltration
Ill-defined, poorly formed glands

Gland fusion
4
ALL cribriform glands
Hypernephromatoid
Glomerulations (possibly)
Ductal Adenocarcinoma
Often Disqualifies from Active Surveillance
Essentially no glandular differentiation:

• solid sheets
5 • cords
• single cells
Comedocarcinoma with central necrosis

Biopsies:
Gleason Scoring
Most common + Second most common = Score
• No tertiary pattern assigned
than 5% of the area of the tumor. (e.g., 98% pattern 4 and 2% pattern 3 → 4+4=8)
• High-grade tumor of any quantity, as long as it was identified at low to medium magnification
should be included. (e.g., 98% pattern 3 and 2% pattern 4 → 3+4=7)
• On needle biopsies with patterns 3, 4, and 5, both the primary pattern and the highest grade
should be recorded. Consequently, tumors with Gleason score 3 + 4 and a tertiary pattern 5
would be recorded as Gleason score 3 + 5 = 8.
Prostatectomies:
Most common + Second most common = Score, with tertiary pattern if present
than 5% of the area of the tumor.
Grade Groups
Grade Group Gleason Score
1 ≤6
2 3+4=7
3 4+3=7
4 8
5 9-10
Active Surveillance
NCCN Inclusion Criteria:
Absolute (Low risk):
• Gleason Score ≤6
• PSA <10 ng/mL
• Clinical stage <T2a (Tumor involves one-half of one lobe or less)
Especially if (Very low risk):
• Fewer than 3 prostate biopsy cores positive, all ≤50%
• PSA density <0.15 ng/mL/g
NCCN Progression Criteria: (initiates transition to curative therapy)

• Gleason grade 4 or 5 on repeat biopsy
• Prostate cancer found in a greater number of biopsies or greater extent of biopsies
Last updated: 10/12/2020 Prepared by Kurt Schaberg MD
Testicular Tumors
Germ Cell Tumors
3 main subtypes depending on age and if they are derived from germ cell neoplasia in situ (GCNIS).
Most common: Germ cell tumors derived from GCNIS (Post-pubertal type) (Type 2, below), which is
often sub-grouped into seminoma and non-seminoma germ cell tumors
Although only 1% of all male cancers, they are the most common cancers among young men between
puberty and 40s.
Risk factors: Family history, cryptorchidism, subfertility, pesticides, marijuana, microlithiasis.
Although can be aggressive tumors, with current treatments can often be cured as very responsive to
chemoradiation.
Type Tumors Age Derived Genotype Behavior
from GCNIS
1 Teratoma (prepubertal) Usually < 6 yrs No Diploid or Very good.
Yolk sac tumor (prepubertal) aneuploid. Mostly
Dermoid cyst No i12p gains benign.
2 Seminoma Post-pubertal Yes Aneuploid Malignant,
Embryonal carcinoma Usually 20s-30s Frequent gains but
Choriocarcinoma and losses. responsive to
Yolk sac tumor Overexpression of therapy
Mixed Germ cell tumor isochrome 12p
3 Spermatocytic Tumor Usually > 50 yrs No Aneuploid Excellent
No i12p gains
Germ Cell Neoplasia In situ (“GCNIS”)

Proliferation of atypical germ cells within seminiferous
tubules
Large, angulated nuclei with coarse chromatin
(resemble seminoma cells)
Often located at base of tubules with prominent halos
Often present in nearby parenchyma adjacent to most
associated germ cell tumors.
Often absent spermatogenesis.
Identical IHC profile to seminoma: OCT3/4, cKit (+)
Precursor lesion: ~50% progresses to overt Germ Cell
Tumor within 5yrs.
Intermediate stages between GCNIS and invasion:

Intratubular seminoma→ complete filling of expanded Intratubular non-seminoma→ Same concept,
seminiferous tubule by neoplastic cells with obliteration but almost exclusively embryonal carcinoma.
of normal components. Thought to be reprogrammed GCNIS cells.
Seminoma Think: Clear/White color
Most common germ cell tumor (~50%).
Present with mass. Usually unilateral.
Grossly solid, fleshy, lobulated, cream-colored.
Large polygonal cells with clear to eosinophilic cytoplasm
(full of glycogen), distinct cell membranes, vesicular
chromatin, and prominent nucleoli
Fibrous septae and nested architecture
Lymphocytic infiltrate; Sometimes granulomas.
GCNIS usually in residual tubules. Rare syncytiotrophoblasts.
IHC: (+) OCT3/4, CD117, D2-40, SALL4
Elevated serum LDH, rarely hCG.
First site of metastases often retroperitoneal lymph nodes.
Molecular: majority have isochrome 12p; ckit mutations in
many.
Prognosis: Good if treated.
Embryonal Carcinoma Think: Purple color

Second-most common testicular GCT.
Usually part of a mixed GCT
Rudimentary epithelial differentiation
Large, crowded, “Primitive” pleomorphic cells
Vesicular nuclei with prominent nucleoli.
Coarse, basophilic chromatin. Amphophilic cytoplasm.
Variable architecture (nests, sheets, papillae, glands)
Prominent mitoses and apoptotic bodies.
IHC: (+)CD30, OCT3/4, AE1/AE3, SALL4
Molecular: Isochrome 12p amplification
Aggressive, but often responds to chemotherapy
Choriocarcinoma Think: Red color

Usually part of a mixed GCT.
Malignant cytotrophoblasts and trophoblasts
(mononuclear with light cytoplasm) and
syncytiotrophoblasts (multinucleated with deeply
eosinophilic cytoplasm). Abundant Hemorrhage
IHC: (+) hCG. Syncytiotrophoblasts: (+) inhibin, glypican-3.
Cytotrophoblasts: (+) SALL4, p63, GATA3
Very elevated Serum hCG → (similar to LH and TSH)→
gynecomastia, thyrotoxicosis
Most aggressive GCT. Frequent hemorrhagic metastases.
Less responsive to treatment.
Yolk Sac Tumor, Postpubertal-type Think: Pink color
aka: “Endodermal Sinus Tumor” or “YST”

Almost always a component of mixed GCT
Many patterns/architecture (often combined)
(Honeycomb meshwork)
Can also be solid, papillary, glandular, etc…
Often hypocellular myxoid areas
Schiller-Duval Bodies (endodermal sinus)(→)
Refractile eosinophilic hyaline globules (→)
Band-like intercellular basement membrane
material
Can have “hepatoid” areas resembling liver that
stains with liver markers.
IHC: (+)AFP, Glypican-3, SALL4, AE1/AE3,
Elevated Serum AFP
Post-chemo can get sarcomatoid YST
Teratoma, Postpubertal-type
Composed of tissues from one or more germinal layers.
May be composed of differentiated mature tissue or immature,
embryonic-type tissue. Often part of a mixed GCT.
In contrast to ovary, pretty much all teratomas in postpubertal testis

are malignant!
Can see virtually all tissue types including epithelial and mesenchymal.
Often multiple cysts lined by glandular or squamous epithelium.
Frequent immature neuroectodermal structures.
IHC: Differentiated elements express profile of that tissue type.
Often areas of cytologic atypia, including primitive mitotically active
stroma cuffing glands.
If a dysplastic component forms a nodule that is larger than a 4X field (5
mm)→ somatic-type malignancy arising in a teratoma. Usually a
sarcoma, most commonly rhabdomyosarcoma.
Most common component in a treated GCT.
Rare situation where can be benign teratoma in an adult: Dermoid

cysts, or, organoid morphology with prominent components of ciliated
epithelium and smooth muscle and no GCNIS, isochrome 12p, or
testicular scarring.
Mixed Germ Cell Tumor
Malignant tumors with more than one germ cell tumor component.
Clinically regarded as “non-seminoma” (even if seminoma present).
Majority of all non-seminomatous GCT are mixed.
Must report approximate % of each component.
Note: Syncytiotrophoblasts ≠ choriocarcinoma (can see in other
tumors, like seminoma)
Special subtypes:
Polyembryoma→ combination of embryonal carcinoma and YST
resembling an embryo
Diffuse embryoma→ orderly combination of embryonal carcinoma
and YST in parallel flat layers (pictured→).
Regressed Germ Cell Tumors

Germ cell tumors that have undergone either partial
or complete regression (“burnt-out”), leaving behind
a well-delineated nodular focus of scaring fibrosis in
the testis.
Can present with metastatic disease, but primary has
completely regressed. Can be seminoma or Non-
seminoma.
Scar findings: Well-demarcated scar, Coarse
calcifications within tubules, chronic inflammation,
hyalinized tubular ghosts.
Nearby findings: GCNIS, tubular atrophy, microliths
Spermatocytic tumor
Relatively rare. Generally excellent prognosis.
NOT associated with GCNIS or cryptorchidism
NOT a component of mixed GCT
Usually occurs in OLDer men (>50yo)
Polymorphous cell population (3 cell types: small,
medium, and large)
Poorly-defined cell membranes. Dense cytoplasm.
Round nuclei with dense to granular chromatin.
Diffuse to multinodular pattern of growth.
Frequent cystic change/edema.
No significant inflammation/granulomas
IHC: Negative for usual seminoma markers (e.g.,
OCT3/4). (+) cKit and SALL4
Can undergo sarcomatous transformation.
Teratoma, Prepubertal-type
Composed of elements resembling somatic tissues from one or more
germ cell layers.
Primarily occurs in prepubertal males <6 years old
(but can see in older)
In contrast with Postpubertal-type:
Benign behavior. Do not recur or metastasize.
NO association with GCNIS or isochrome 12p amplification.
NO cytologic atypia. NO association with mixed GCT.
As such, they are most akin to the mature cystic teratomas seen in the
ovary.
Frequently include skin structures, ciliated epithelium, fat, cartilage,
bone, and muscle in organoid structures. No significant cytologic atypia.
Normal surrounding testicle: No GCNIS, tubular atrophy, scars,
microlithiasis, necrosis, or impaired spermatogenesis (which might
suggest a GCNIS-derived GCT)
Specialized variants:
Dermoid Cyst: replicate skin in an organoid arrangement. Squamous
epithelium with adnexal structures. Cured by excision.
Epidermoid Cyst: Unilocular cyst with squamous lining and keratinaceous
debris. No adnexal structures or other elements. Cured by excision.
Well-differentiated Neuroendocrine Tumor: Similar morphology to
elsewhere. Often pure. Usually good behavior. Only variant that can
behave aggressively.
Yolk Sac Tumor, Prepubertal-type

Rare. Usually in young boys <6 years old
Identical morphology and IHC profile to postpubertal-type.
Secretes AFP
However, unlike postpubertal YST:
NOT associated with GCNIS. NO isochrome 12p amplification.
Excellent survival, even with advanced stage.
Usually pure, but can see in combination: Mixed teratoma and

yolk sac tumor, prepubertal-type
Immunohistochemistry of Germ Cell Tumors
Embryonal Carcinoma
Metastatic Carcinoma
Spermatocytic Tumor
Choriocarcinoma
Yolk Sac Tumor
Other Tumors
Seminoma
Teratoma
GCNIS
AE1/AE3 - ± + + + + - + Many!
OCT3/4 + + + - - - - - Rare NSCLC and RCC and large cell

lymphoma
CD30 - - + - - - - ± Lymphomas, melanoma,
nasopharyngeal carcinoma,
mesenchymal tumors
Glypcian-3 - - - + + ± ± HCC, gastric cancers,
syncytiotrophoblasts
D2-40 + + ± - - ± - ± Gliomas, meningiomas, mesothelial
tumors, lymphatic tumors,
PLAP + + + ± + - - ± Numerous adenocarcinomas (colon,
endometrium, etc..)
SALL4 + + + + ± ± + ± Hematologic malignancies, rhabdoid
tumors, Wilms tumor, lots of GI
adenocarcinomas among others
βhCG - - - - + - - ± Other trophoblastic tumors,
syncytiotrophoblasts
cKIT + + - ± - - ± ± Lots of tumors
(CD117)
AFP - - ± + - ± - ± Hepatocellular tumors, etc..
CK7 ± ± + - + + ± Many carcinomas
Modified from: WHO classification of Tumors of the Urinary System and Male Genital Organs. 4th ed.
Sex Cord-Stromal Rare. More common in kids. Vast majority are benign.
A little variable, but often stain with some combination of: Inhibin, calretinin, SF-1, FOXL2, Melan A
Leydig Cell Tumor

Abundant, eosinophilic granular cytoplasm.
Diffuse growth. Uniform round cells.
Round, central nuclei with prominent nucleoli.
Frequent Reinke crystals (→)
Usually asymptomatic, but children can present with
precocious puberty as the tumor can secrete steroid
hormones (e.g., testosterone).
Most common testicular sex cord-stromal tumor.
Vast majority are benign.
Sertoli Cell Tumor

Often shows at least focal tubular differentiation.
Usually moderate pale cytoplasm.
Rarely diffuse growth.
Unique IHC: Frequent nuclear β-catenin, WT-1, CK
AE1/AE3, and neuroendocrine markers.
Vast majority are benign.
Variant:
Sclerosing Sertoli Cell Tumor—extensively hyalinized
stroma with cells arranged in tight cords and clusters
Factors associated with Malignant behavior in Sex Cord-Stromal Tumors:

Cytologic Atypia, Abundant Mitoses, Large size, Vascular Invasion, Necrosis, Infiltrative growth
(Pretty common-sense bad findings ;-)
Granulosa Cell Tumors
Similar to the more common ovarian counterpart
Adult Granulosa Cell Tumors
Rare.
Often asymptomatic, but can secrete estrogen
Cells: Scant pale architecture with grooved nuclei
Varied architecture: Sheet-like, trabecular, ribbon-like,
microfolicular (with “Call-Exner bodies” filled with pink secretions).
Molecular: Frequent FOXL2 point mutations
Juvenile Granulosa Cell Tumors
Rare. Almost all in first decade, often before 6 months old.
Usually presents as a mass.
Macrofollicles with mucinous secretions
Round nuclei with NO GROOVES
Large Cell Calcifying Sertoli Cell Tumor

Large Sertoli cells with abundant granular
eosinophilic cytoplasm
Calcifications (focal, psammomatous to
large, plaque-like)
Often prominent neutrophilic infiltrate.
NO nuclear β-catenin
Frequently associated with Carney complex
Frequent PRKAR1A mutations
Other Tumors
Intratubular Large Cell Hyalinizing Sertoli Cell Neoplasia:
Expanded seminiferous tubules with large Sertoli cells with pale
cytoplasm accompanied by prominent basement membrane
deposits around and within tubules (→).
Almost exclusively in Peutz-Jegher’s syndrome (think: like SCTATs!).
Often present as prepubertal males with gynecomastia (aromatases
made by tumor convert androgens→ estrogen).
Always benign.
Fibroma/Thecoma:
Resemble ovarian counterparts. Benign. Rare.
Unencapsulated proliferation of spindled cells with scant
eosinophilic cytoplasm.
Miscellaneous Tumors
Gonadoblastoma
Germ cells resembling GCNIS cells and spermatogonium
Sex cord cells resembling immature granulosa cells
Arranged in round nests with round deposits of
eosinophilic basement membrane
Frequent calcifications
Develop in individuals with gonadal dysgenesis.
Can progress to a germ cell tumor, often seminoma.
Hematolymphoid Tumors
Most common testicular tumor in men over 50 years old.
Can be primary or part of systemic involvement.
Often obliterate the seminiferous tubules centrally with peripheral
intertubular spread.
Diffuse Large B-Cell Lymphoma comprises ~90% of primary
testicular lymphomas.
Same stains as elsewhere.
Other Tumors
Ovarian-type Epithelial Tumors:
Resemble entire spectrum of ovarian type epithelial tumors. Most commonly Serous and Mucinous,
with most being Serous Borderline Tumors, which do not recur or metastasize.
Rete Testis Adenoma:

Very rare. Benign tumor of rete epithelium that spans the spectrum from packed tubules (adenoma) to
tumors with a cystic component (cystadenoma), papillary architecture (papillary cystadenoma), or
glands with prominent fibrous tissue (adenofibroma).
Rete Testis Adenocarcinoma:

Very Rare. Malignant. Diagnosis of exclusion. Malignant gland forming tumor of rete epithelium. Must
be centered in hilum of testis, patient must have no other similar primary, and other Dx’s (e.g.,
mesothelioma), must be excluded. Poor prognosis.
Myoid Gonadal Stromal Tumor:

Spindle cell tumor near rete testis with features of gonadal stroma and smooth muscle. Circumscribed
with densely packed spindled cells arranged in short fascicles. IHC: (+)SF1, FOXL2, SMA, S100.
Paratesticular Tumors
Adenomatoid Tumor
Benign Mesothelial tumor.
Most common neoplasm of paratesticular region
Often based in the epididymis and < 2cm.
Irregularly shaped gland-like microcystic spaces
composed of flattened or cuboidal cells with
associated fibrous stroma and lymphoid aggregates.
Bland cytologic features.
Helpful feature: "thread-like bridging strands“ (→)
Sometimes signet ring-like vacuolated cells.
Solitary, localized.
IHC: Mesothelial markers: D2-40, Calretinin, WT-1,
CK5/6 , CK AE1/AE3.
Mesothelioma
Rare. Malignant proliferation of mesothelial cells arising
from tunica vaginalis.
Mass envelops testicle, often invading it.
Like in the pleura, variable appearance. Often epithelioid
with papillary or tubulopapillary architecture.
Less associated with asbestos.
IHC: Usual mesothelial markers (see above)
Papillary Cystadenoma of the Epididymis

Rare. Benign Tumor of Epididymal ducts.
Associated with von Hippel-Lindau syndrome (but is more often
sporadic)
Cystic structures that are focally papillary.
Clear columnar/cuboidal cells with abundant clear cytoplasm.
Frequent reverse nuclear polarity.
Colloid-like secretions.
Morphologically (and immunophenotypically) resembles
papillary clear cell RCC (see separate Kidney guide)
Adipocytic Tumors
Lipoma:
Benign. Most common mesenchymal tumor of region.
Consist of entirely mature adipocytes.
Well-differentiated Liposarcoma:
Common paratesticular sarcoma. Recur, but won’t
metastasize unless dedifferentiate.
Varying proportion of adipocytes, fibrous bands with
enlarged, hyperchromatic stromal cells, and occasional
lipoblasts. Can see inflammation/myxoid change.
Giant marker and/or ring chromosomes→ MDM2
amplification.
If large or questionable atypia→ consider getting FISH

to help differentiate.
Smooth Muscle Tumors

Leiomyoma:
Benign. Somewhat common.
Consist of entirely bland smooth muscle (like in other
locations).
Leiomyosarcoma:
Common paratesticular sarcoma.
Fascicles of spindled cells with brightly eosinophilic
cytoplasm and “cigar-like” blunt nuclei.
Significant atypia, mitoses, and/or tumor necrosis.
IHC: Desmin, SMA, H-Caldesmon, Calponin
Skeletal Muscle Tumors

Rhabdomyoma:
Benign. Very rare. Most often adolescents.
Rhabdomyosarcoma:
Often in children or young adults and Embryonal
subtype with primitive round or spindled cells and
variable eosinophilic rhabdomyoblasts with abundant
eccentric cytoplasm. Often good prognosis.
IHC: MyoD1, Myogenin, Desmin.

Algorithmic Diagnosis of Testicular Tumors
Algorithms modified from: Urologic Surgical Pathology. Liang Chen et al. 2020.
Clear Cytoplasm:
Start
Nests polygonal cells Yes GCNIS Present? No Predominantly
arranged with fibrous Intertubular
septae with Growth?
lymphocytes? Yes No
Yes No
3 Distinct Cell
Seminoma Large, Focal Types?
irregular Glandular
[Oct3/4+, partially clear Architecture?
CD30-, nuclei? No
Yes Yes Yes
Glypican3-] No
No
Yolk Sac Sertoli Cell

Embryonal Metastatic Lymphoma Tumor Spermatocytic
Tumor Adenocarcinoma Tumor
[Oct3/4+, [CD45+, [Inhibin+,
CD30+, [Oct3/4-, [CK+, SALL4-,
CD30-, Oct3/4-, SF1+, [Oct3/4-, CD30,
Glypican3-] Oct3/4-, CD30-, inhibin-] Nuclear β- Glypican3-]
Glypican3+, Glypican3-]
AFP+] catenin]
Glandular and/or Tubular growth:

Start Predominantly
Cells with large Yes GCNIS Present? No intertubular and
crowded, irregular intralymphatic
nuclei lining gland-like growth??
spaces? Yes
No
Yes No
Metastatic Tubular growth
Embryonal Variably sized cells, Adenocarcinoma with solid tubules?
hyaline globules,
[Oct3/4+, variable patterns? [CK+, SALL4-,
CD30+, Oct3/4-, CD30-, Yes No
Glypican3-] Glypican3-]
Yes No
Rete Testis
Sertoli Cell
Neoplasm
Tumor
Yolk Sac Tumor Seminoma [centered in
[Inhibin+,
hilum, CK+,
[Oct3/4-, CD30-, SF1+,
[Oct3/4+, CD30-, PAX8-, CEA+,
Glypican3+, AFP+] Nuclear β-
Glypican3-] EMA+]
catenin]
Microcystic:
Start Prominent cords of
Yes GCNIS Present? No tumor cells, Lipid
Variably sized nuclei and
flattened nuclei linin rich cells, and
cysts? Sertoli Cell Yes hyalinized stroma?
Tumor No
Yes No
Yes Neonate?
[Inhibin+,
Yolk Sac Tumor SF1+,
Seminoma No
(post-pubertal) Nuclear β- Juvenile Granulosa
[Oct3/4+, CD30-, catenin] Cell Tumor
[CK+, Oct3/4-, Abundant
Glypican3-, CK-] eosinophilic
CD30-, Glypican3+,
[Inhibin+, AFP-, cytoplasm?
AFP+, PLAP+]
Glypican3-]
Yes No
Yolk Sac
Leydig Cell Tumor: Oct3/4+, CD30+, Glypican3- Tumor (pre-
Adenomatoid Tumor: CK+, Calretinin+ pubertal)
[CK+, Oct3/4-,
CD30-,
Glypican3+,
AFP+, PLAP+]
Pink Cells with Abundant cytoplasm (Oxyphil):
Start
Leydig Cell Tumor No Fibromyxoid stroma with
Yes Round nuclei
with prominent neutrophils and calcifications?
[Inhibin+]
nucleoli, ±
Yes No
lipofuscin or
Reinke Crystals? Presence of other patterns,
Large Cell
Lots of mitoses, and
Calcifying Sertoli
associated GCNIS?
Cell Tumor
Yes
Consider: [Inhibin+]
Metastatic Carcinoma, Melanoma,
Hematolymphoid tumors No
Hepatoid Yolk Sac Tumor
Yes [CK+, Glypican3+, AFP+, Oct3/4,

CD30-, Inhibin-]
Highly pleomorphic
nuclei, Prominent
intratubular No Insular and trabecular
Adenomatoid growth? patterns, coarse chromatin,
Tumor ± teratomatous elements?
No Well-differentiated
[CK+, Calretinin-] Neuroendocrine Tumor Yes
[CK+, Synaptophysin+, Inhibin-]
Spindle Cells: Start
Round nuclei
with prominent
nucleoli, ±
lipofuscin or
Leydig Cell Tumor Yes Reinke Crystals? No Bland Nuclear
[Inhibin+] Cytology with no
Mitoses?
Yes
No
Fibrothecoma
Smooth Muscle Actin Keratin, S100,
[SMA-, S100-] and S100 staining? Desmin staining?
Myoid Gonadal Stromal Tumor
[SMA+, S100+]
Sarcomatoid MPNST,
Melanoma, Leiomyosarcoma,
Carcinoma or Rhabdomyosarcoma
Mesothelioma Liposarcoma
[S100+ at least [Desmin+]

[CK+]
partial]
Adrenal and Paraganglia Tumors

Adrenal Cortical Tumors IHC: (+) SF1, Inhibin, Melan-A, Calretinin, Synaptophysin,
(-) Chromogranin, Cytokeratin, S100. Often variable!!
Adrenal Cortical Adenoma
Benign. Very common. Often incidentally identified.
Usually unilateral solitary masses with atrophic
background adrenal gland.
Tumor cells can be lipid-rich (clearer) or lipid-poor
(pinker) arranged in nests and cords separated by
abundant vasculature. Occasional lipofuscin pigment.
Nuclei generally small and round (occasional extreme
“endocrine atypia” is common).
Low/no mitotic activity.
Intact reticulin framework.
On a spectrum with and may hard to differentiate from
hyperplastic nodules, which is more often multinodular
(background hyperplasia) and bilateral.
Can be non-functional (85%) or functional (15%).
Associated with MEN1, FAP, Carney Complex, among Aldosterone-producing→ “Conn syndrome”→
others… hypertension and hypokalemia
If aldosterone-secreting adenoma is treated with Cortisol-producing→ (ACTH-independent)
spironolactone→ “spironolactone bodies” (below) “Cushing Syndrome” → central obesity, moon
face, hirsutism, poor healing, striae
Sex-hormone-producing→ Rare (more common
in carcinomas). Symptoms depend on
hormone/sex (virilization or feminization)
Adrenal Cortical Carcinoma

Malignant.
Most common in older adults.
Can present with an incidental unilateral mass or
with an endocrinopathy (see above).
Solid, broad trabeculae, or large nested growth
(more diffuse, and larger groups than in adenomas)
Thick fibrous capsule with occasional fibrous bands.
Frequent tumor necrosis.
Frequent vascular or capsular invasion.
Increased mitotic activity.
Variants: Oncocytic, Myxoid, Sarcomatoid
Mostly sporadic, but can be associated with Lynch
Syndrome and Li-Fraumeni Syndrome
Distinguishing between an Adrenal Cortical Adenoma vs Carcinoma
Weiss Criteria: Weiss Criteria (≥3 = Malignant)
Most widely used system, but doesn’t work as well High nuclear grade (based of Fuhrman criteria)
in borderline cases or variants.
Mitotic rate of >5 mitoses per 50 HPF
The presence of ≥3 of these of these criteria
correlates with malignant behavior. Atypical mitotic figures
Cannot be used on oncocytic adrenal cortical <25% Clear cells
neoplasms or pediatric adrenal tumors (refer to
separate specific grading schemes) Diffuse architecture
Features only seen in metastasizing tumors: ≥6 Tumor necrosis
mitoses per 50 HPF, atypical mitoses, invasion of
Venous invasion
venous structures.
[PMID: 6703192] Sinusoidal invasion
Capsular invasion
“Modified” Weiss Criteria Points
“Modified” Weiss Criteria: Mitotic rate (≥6 mitotic figures/50 HPF) 2

Designed to be more reproducible. Cytoplasm characteristics, clear vs. compact 2
Total score of 3 or greater correlates with (compact >75% of cells)
subsequent malignant behavior Abnormal mitoses 1
[PMID: 12459628]
Tumor necrosis 1
Invasion of capsule 1
≥3 = Malignant
Reticulin Algorithm:
1) Look to see if reticulin framework is intact. If intact throughout→ adenoma, if disrupted, move to step 2.
2) Malignancy is defined by at least one of the following: tumor necrosis, high mitotic rate (>5/50HPF), and
venous invasion. [PMID: 23774167]
Intact framework in an adenoma Disrupted framework in a carcinoma
Loss of Reticulin
Although this distinction is often straightforward, some borderline cases are likely best categorized as
having “Uncertain Malignant Potential”.
Although it doesn’t fit into the above systems, Ki-67 can also be helpful with this distinction. The
proliferation index in adenomas generally <5%, whereas carcinomas have a proliferation index >5%
Oncocytic Adrenocortical Neoplasms
Cells with abundant granular eosinophilic cytoplasm.
Many require >90% of tumor to be oncocytic.
Mostly non-functional.
Often show areas of nuclear pleomorphism, intranuclear

pseudoinclusions, and prominent nucleoli.
Cannot use Weiss Criteria (use LWB system below).

Lin-Weiss-Bisceglia Criteria:
Mitotic rate >5 per 50 HPF
Major Criteria Atypical mitotic figures Lin-Weiss-Bisceglia Criteria:
Venous invasion Used for Oncocytic Adrenal Neoplasms
1 major criteria → Malignant→ carcinoma
Size >10 cm and/or weight >200 g 1-4 minor criteria →Uncertain Malignant Potential
Tumor necrosis No minor or major → Benign → adenoma
Minor Criteria [PMID: 15306935]
Sinusoidal invasion
Capsular invasion
Myelolipoma
Benign. Composed of mature fat and bone marrow elements.
Second most common adrenal neoplasm.
Often older adults presenting with incidental asymptomatic mass.
Can often Dx on imaging due to fat content.
Rare outside of adrenal, can see in pre-sacral region.
Ectopic Adrenal Tissue

Frequent ectopic rests, sometimes fused/embedded with
other organs→ Don’t mistake for invasion/metastases!!
Common locations: Kidney (adrenal-renal fusion/adhesion),
spermatic cord, fallopian tube, liver (hepatoadrenal fusion).
Schwannoma: Benign nerve sheath tumor. Spindled cells with cellular (Antoni A) and hypocellular
(Antoni B) areas. Frequent findings: Verocay bodies, lymphoid aggregates, hyalinized vessels. IHC: (+)
S100 and SOX10)
Adenomatoid Tumor: Benign mesothelial tumor, as frequently seen associated with GYN/GU tracts.
Variably sized tubules in fibromuscular stroma. Express mesothelial markers (D2-40, WT-1, Calretinin).
Sex cord-Stromal Tumors: Rare reports of primary granulosa cell tumors and Leydig cell tumors. All in
post-menopausal women.
Adrenal Medulla and Extra-adrenal Paraganglia Tumors
Pheochromocytoma
Tumor of chromaffin cells that arises in the adrenal medulla.
All malignant, but only ~10% metastasize
Can occur at any age, but usually older adults.
~1/2 are incidentally identified (asymptomatic)
Can make catecholamines→ hypertension→ sustained or
paroxysmal symptoms→ headache, tachycardia,
palpitations, sweating
Can detect with urine or serum metanephrine testing
Classically, nested (“Zellballen”) architecture

Can have trabecular or diffuse growth
Polygonal tumor cells with amphophilic to purple cytoplasm
Variable small to large nuclei
Rich vascularity→ often hemorrhage and hemosiderin
Frequent intranuclear pseudoinclusions and intracytoplasmic
hyaline globules (PASD+)
Nuclear pleomorphism can be prominent, but mitoses are rare.
IHC: (+) Diffuse Chromogranin and Synaptophysin,

Sustentacular S100 and SOX10
(-) Cytokeratins, SF1, Inhibin, Melan-A, Calretinin,
No current standardized system to assess tumor risk.
At least 30% familial due to germline mutations

The most strongly hereditary human tumor!!
Genetic testing is recommended for all patients
Common mutations: SDH, RET, NF1
SDHB mutations→ higher risk of metastases
Complete resection is only cure. S100: Stains peripheral nest Sustentacular cells,
Can have metastases years later. highlighting Zellballen pattern
Paragangliomas
Arise from Extra-adrenal paraganglia, but morphologically and functionally like pheochromocytomas.
Also frequently hereditary!
Head and Neck paragangliomas: arise from parasympathetic nerves.
Most common sites: carotid body and jugulotympanicum. Generally non-functional.
Generally good prognosis (<5% risk of metastasis)
Sympathetic paragangliomas: arise from prevertebral and paravertebral sympathetic chains and
sympathetic nerves, mainly in the abdomen. Frequently functional.
Risk similar to pheochromocytomas, SDHB associated with higher risk of metastasis.
Neuroblastic Tumors
Most primitive/aggressive Intermediate differentiation. Most mature; Benign
Malignant. Malignant. Ganglion cells set in abundant
Small round blue cell tumor Neuroblastoma with Schwannian fibrillary Schwannian stroma
+/- rosettes, neurofibrillary stroma, including ganglion cells NO neuroblastoma or neuropil
matrix. NO Schwannian stroma
Derive from neural crest cells→ sites reflect path of migration→ Most commonly in adrenal gland,
followed by abdominal ganglia, thoracic ganglia, and pelvic ganglia.
Neuroblastoma is the 3rd most common pediatric tumor (after leukemia and brain tumors)
Most common neoplasm in the first year of life. ~90% are before age 5.
Neuroblastoma IHC: (+) Synaptophysin, chromogranin, PGP9.5, CD56, NB84, PHOX2B
Ganglioneuroma IHC: Schwann cells (+) S100; Ganglion cells (+) Synaptophysin, neurofilament
Favorable vs Unfavorable histology is determined by age, degree of neuroblast differentiation, nodular
pattern, degree of Schwannian stromal development, and mitosis-karyorrhexis- index (MKI)
Genetics: MYCN is a major oncogenic driver. Amplification→ higher risk
Tumors with whole-chromosome copy-number gains without structural abnormalities (hyperploidy) have
an excellent prognosis
Composite Pheochromocytoma/Paraganglioma
A pheochromocytoma or paraganglioma Ganglioneuroma
combined with a developmentally related
neurogenic tumor such as a ganglioneuroma,
ganglioneuroblastoma, neuroblastoma, or
peripheral nerve sheath tumor.
Each component stains/looks like it would

usually.
Can occur in the setting of NF1.
If surgically resected, usually good prognosis.
Pheochromocytoma
Related Tumor Syndromes
Multiple Endocrine Neoplasia 1&2 (MEN)
MEN 1 MEN 2A MEN 2B
Gene MEN1, RET, RET,

autosomal dominant autosomal dominant autosomal dominant
Most Parathyroid hyperplasia Medullary thyroid carcinoma Medullary thyroid carcinoma
common Pituitary adenoma Parathyroid hyperplasia Pheochromocytoma
conditions Pancreatic/duodenal Pheochromocytoma Mucosal neuromas
neuroendocrine tumors Marfanoid features
Think “2 P’s, 1 M”
Think “3 P’s” Think “1 P, 3 M’s”
Other Adrenal cortex, Thymus, Hirschsprung disease Ganglioneuromas
conditions lungs, stomach tumors
Often multiple tumors in each organ (e.g., diffuse pancreatic microadenomatosis with several
dominant larger nodules)
Familial Paraganglioma-Pheochromocytoma Syndromes

Caused by mutations in genes encoding subunits of Succinate dehydrogenase (SDH).
Autosomal dominant. Can see mutations in SDHA, SDHB (most common), SDHC, SDHD, or SDHAF2.
Most common tumor: Paraganglioma/pheochromocytoma. Can be multifocal.

Tumors associated with SDHB mutations are often more aggressive and present younger.
Other specific tumors:

SDH-deficient Gastrointestinal Stromal Tumors (GIST)—Usually occur in kids or young adults. Epithelioid
morphology and can be multifocal or plexiform. Metastasize to lymph nodes, don’t respond to RTK
inhibitor therapy (no Ckit mutations!), but overall more indolent.
SDH-deficient Renal Cell Carcinoma (RCC)—Eosinophilic cytoplasm with “flocculent”

cytoplasm/inclusions. Neuroendocrine-like nuclei (round, evenly dispersed chromatin solid to nested
architecture). Young age, good prognosis.
IHC: Immunoreactivity for SDHB is lost in SDH-deficient tumors caused by mutations in any of the
subunits→ can be used to screen for SDH mutations in paragangliomas, pheochromocytomas, and
unusual GISTS and RCC’s.
Carney Triad→ generally non-hereditary SDHC promoter hypermethylation→ Paraganglioma + SDH-

deficient GIST + Pulmonary chondroma
Carney-Stratakis syndrome→ Paraganglioma + SDH-deficient GIST

CHAPTER 13
Applications of immunohistology to non-heme tumor differential diagnosis
R V Rouse 7/22/2014 http://surgpathcriteria.stanford.edu
Table of Contents Page

Undifferentiated panel 1
CK7/20 table 2
Breast carcinoma 2
Lung adenocarcinoma 3
Mesothelioma 4
GYN 5
GI 6
GU and germ cell 6
Misc carcinomas (liver, kidney, adrenal) 7
Squamous and sarcomatoid carcinoma 8
Sustentacular cells 8
Derm 9
Soft tissue keratin+ 9
Soft tissue CD34+ 10
Soft tissue other markers 11
Soft tissue no good markers 12
Undifferentiated panel: Ca vs Mel vs La

Keratin AE1/3 mix, 90%+ of Ca
Not CK7 or 20 or 5/6 to start with
EMA, CEA as backups
S100
95%+ of Mel, but 10% of Ca are +
SOX10 may be better, more sensitive and specific
HMB45, MelanA less sensitive, very specific
LCA or CD20 90% of lymphomas
Things that might be negative

Anaplastic large cell lymphoma - use CD30, ALK, CD3
Plasmacytoma – use CD138, kappa, lambda
Sarcomas – use various markers, esp vascular CD31, CD34
Spindled/sarcomatoid carcinoma – use CK5/6 and p63
Liver – use HepPar1
Adrenal – use Inhibin, MelanA, SF1
Seminoma/germinoma – use OCT3/4 or SALL4
Non-heme IPOX 7/22/2014 Rouse http://surgpathcriteria.stanford.edu p 2
Carcinoma – primary site

What is the DDx? Choose complementary antibodies (check the history first)
CK7/20: USE THE TABLES

Most use is for ADENOCARCINOMAS, Little data for undifferentiated Ca
UNKNOWN PRIMARY: immunohistochemistry

CK7+20+ CK7-20+
Ovary mucinous 90% Colorectal adeno 80%
Transitional cell 65% Merkel cell 70%
Pancreas adeno 65% Gastric adeno 35%
Cholangio 65% Excluded tumors ≤ 5%
Gastric adeno 40% Breast; Carcinoid lung;
Excluded tumors ≤ 5% Cholangio; Esoph squam;
Carcinoid; Germ cell; Esoph Germ cell; Lung all types;
squam; Head/neck squam; Hepatocellular; Ovary;
Hepatocellular; Lung small Pancreas adeno; Renal
cell & squam; Ovary non- adeno; Transitional cell;
mucinous; Renal adeno Uterus endometrioid
CK7+20- CK7-20-
Ovary non-mucinous 100% Adrenal 100%
Thyroid (all 3 types) 100% Seminoma & YST 95%
Breast 90% Prostate 85%
Lung adeno 90% Hepatocellular 80%
Uterus endometrioid 85% Renal adeno 80%
Embryonal 80% Carcinoid GI & lung 80%
Mesothelioma 65% Lung small cell & squam 75%
Transitional cell 35% Esoph squam 70%
Pancreas adeno 30% Head/neck squam 70%
Cholangio 30% Mesothelioma 35%
Excluded tumors ≤ 5% Excluded tumors ≤ 5%
Colorectal adeno; Ovary Breast; Cholangio; Lung
mucinous, Seminoma, Yolk adeno; Ovary; Pancreas
sac tumor adeno; Transitional cell
Breast Carcinoma
GATA3 90%, BRST2 (GCDFP15) 60%+, quite specific (salivary and skin adnexal tumors pos)
ER 75%+, PR 60%+ (lung most neg to focal/weak but up to 5% strong pos in one report)
S100 15%+, (lung neg)
CK7+20- 90% (lung is also 7+20-)
Mammaglobulin breast 85%, cholangio, GI, lung adenoca 10-20%
ER, PR +
Breast
Ovary
Endometrium
Papillary thyroid
Skin adnexal tumors
Sarcomas
Meningioma (PR only)
Solid-pseudopapillary neoplasm of pancreas (PR only)
Breast carcinoma type

E cadherin
Ductal positive, Lobular negative
Works for invasive and in situ
Breast vs Lung Panel

BRST2 (60%) or GATA3 (90%) Breast pos Lung neg
ER, PR favor breast but not sensitive
TTF1 (70%) or Napsin (80%) - Lung pos Breast neg
Metaplastic/Sarcomatoid Carcinoma
CK5/6 about 50%
P63 60%
AE1/3 40%
Smooth muscle actin 70%
Breast invasive vs in situ

Myoepithelial cells absent in invasion
Smooth muscle actin stains myoepithelial cells; myofibroblasts frequently confusing
Calponin cytoplasmic, a bit more specific than actin, easier to interpret at low power than p63
P63 nuclear, most specific but may be harder to see at low power if not strong
Calponin vs p63: personal preference or use both
Occasionally get divergent results
Usually go with the positive
Breast papilloma vs in situ

Calponin and/or p63
Are myoepithelial cells present throughout the lesion?
Lung Adenocarcinoma
CK7+20- 90%, TTF1 70% (also thyroid +), Napsin 80% (also some RCCa +)
CD56 5%, CK5/6 10%, p63 0-25% focal, PAX8 neg
Lung squamous Ca, both basaloid and usual types

CK7-20- 70% (CK7+20- 25%)
TTF1/Napsin neg, CD56 0-10%, PAX8 neg
P63, 34BE12 and CK5/6+ 100%
Lung small cell (oat cell) Ca

CK7-20- 90%, CK20 rare
TTF1 90%, CD56 95%
P63 neg, CK5/6 neg, 34BE12 scattered pos cells 12%, no confluent positive cases
Synaptophysin 50%, Chromogranin 40%
Keratin usually absent to patchy or dot like
Oat vs Merkel cell

TTF1 Oat 90%, Merkel neg
CK20 Oat neg, Merkel 90%
Keratin may be dot like for both
Chromogranin and synaptophysin variable in both
Merkel 35-75% pos for TdT, do not confuse with ALL
Mesothelioma
Reactive vs neoplastic mesothelium:
EMA, IMP3, Glut1, p53: favor mesothelioma if positive
Desmin favors reactive if positive
Pleural Mesothelioma Lung Adenoca
Calretinin 90% (nuclear) 15%
CK5/6 90% (Benign mesos freq neg) 10%
D2-40 (podoplanin) 90% 0-7%
WT1 90% 25%
TTF1 (nucl) / Napsin (cytopl) neg 70-80%
CD15 very rare 95%
CEA very rare 90%
BerEp4 15% 95%
MOC31 10% 100%
B72.3 (TAG72) 5-15% 85%
Lung vs Mesothelioma Panel

Two or three of each of meso pos and lung pos markers should be enough
WT1 not useful vs lung
D2-40
Kaposi sarcoma 100%
Angiosarcoma 72%
Seminoma 100%
Nonseminomatous germ cell negative
Mesothelioma 90%
Lung adenocarcinoma 0-7%
Various carcinomas 20-40%
Dermatofibroma 100%
Ovary serous Peritoneal mesothelioma

Calretinin 7-34%, rare in our studies 100% (nuclear)
CK5/6 17% 100%
Thrombomodulin 30% 74%
PAX8 75-90% 9% (weak)
BerEp4 100% 9%
CD15 60% neg
S100 27% neg
B72.3 (TAG72) 80% neg
MOC31 97% 3%
WT1 stains both (but good for ovary vs breast)
Ovary serous vs mesothelioma panel

BerEp4 Ovary+
MOC31 Ovary+
PAX8 Ovary+
Calretinin Mesothelioma+
GYN
Ovary vs Breast PAX8
Ovary surface epithelial carcinomas 70-100%
Only mucinous 10-59%
Breast negative
Ovary Serous Ca
CK7+20- 100%
WT1 90%
90% mesotheliomas, 25% lung adenoca, 5% breast
Neg: colorectal, endometrial (incl pap serous), panc, bile duct, ovary mucinous
WT1 other reactivity

90% DSRCT
75% Wilms
55% Rhabdo
12% Neuroblastoma
0% PNET
30% Burkitt and lymphoblastic
Pos AML
Angiosarcoma (cytoplasmic)
Ovary Mucinous
CK7+20+ 95%
MUC2 and MUC5AC various mucinous tumors +
Ovary, appendix, colon, breast, stomach, endocervix
CDX2 mucinous ovary and GI tract all sites, pancreas +
Ovary CK7/20
Serous 7+20- 100%
Mucinous 7+20+ 95% (rule out stomach, pancreas, bile duct)
Colorectum 7-20+ 90%
Endometrial vs Endocervical (applies to glandular areas only)

Endometrial Endocervical
ER and vimentin Usually diffuse pos Usually neg or focal
P16 and CEA Usually neg or focal usually positive
Endometrial stromal vs Smooth muscle

Muscle Stromal
Caldesmon 70% 5%
CD10 35% 95%
Desmin 90% only in areas of muscle differentiation
B-catenin neg 50-100%
Complete mole p57 neg vs partial mole and hydropic change p57 pos
MUC4 may be useful for identifying implantation site trophoblast
GI Tract
Colorectum
CK7-20+ 90%
MUC2 and MUC5AC various mucinous tumors +
Ovary, appendix, colon, breast, stomach, endocervix
CDX2
Colorectal >90%
Mucinous carcinomas of all organs including ovary, pancreas positive from 40-100%
<5% lung, prostate, breast, ovarian serous
Carcinoids: ileum and appendix >90%, other sites variable but frequently negative, lung negative
TTF1 stains 50% of pulmonary and 0% of GI.
Stomach, Pancreas, Bile Duct
No great markers
Wide range of CK7&20
Stomach 50%+ HepPar1
CA19-9 not specific for pancreas
Pos: Colon, ovary, lung, cholangio
0-5%: Liver, breast, mesothelioma
Esophageal adenocarcinoma frequently TTF1 and napsin +
GU & Germ Cell

Prostate – well/mod diff
PSA or NKX3.1 and PSAP (prost acid phos) 95% pos
All very specific, one is usually enough if untreated, mod diff carcinoma
ERG very specific but 50% sensitive
Prostate vs TCCa (high grade or treated Ca)
For poorly diff TCCa: GATA3 may be most sensitive and specific
Backups p63 (85%) and HMWCK (CK5/6 or 34BE12 60%)
Uroplakin and thrombomodulin do not work for poorly diff TCCa
For poorly diff prostate ca, NKX3.1 more sensitive (>90%) than PSA (may be neg in 10%)
Both very specific
Prostate Ca vs benign
In general, for small foci, IPOX can prove benignancy but not prove malignancy
Small foci that stain as cancer are usually best left at ASAP (see surgpathcriteria)
Basal epithelial cells (not myoepithelial cells) absent in carcinoma
High molecular weight keratin - 34BE12 or CK5/6 cytoplasmic, p63 nuclear
Basal cells may be patchy
Presence of a basal layer virtually rules out invasive Ca (Gold standard?)
Intraductal carcinoma is an exception (see surgpathcriteria)
Rare cases of prostate carcinoma reported as p63 positive
Not a basal layer, but single layer glands
HMWCK negative, Racemase positive
P504S (Racemase, AMACR)
Positive in Ca and PIN, negative in benign
At least moderate, circumlumenal stain
Faint or patchy stain may be seen in benign
Lots of other carcinomas stain – this is not specific for prostate origin
PIN2-PIN4 cocktails
P504S (cytoplasmic), p63 (nuclear) +/- high molecular weight keratin
Especially useful if only one slide
P504S helps highlight the area of interest – go down and look for basal cells
For small foci, destain H&E instead of recutting block
Germ cell tumors

General
EMA neg
SALL4, OCT3/4 and CD30 are quite specific for germ cell
PLAP and ckit stain many other carcinomas also
Seminoma - Keratin dots, focal or negative, rarely strong and diffuse
Embryonal Ca - HCG, AFP 20-30%, serum test may be better
Yolk sac Ca - AFP may be scant, serum test may be better
Germ cell tumors differential, % positive

Sem. EmbCa YST ChorioCa
CD117, ckit 90 0 0 0 few cases
D2-40, podoplanin 100 diffuse 30 focal 0 0 few cases
OCT3/4, POU5F1 100 100 0 0
SALL4 100 100 100 100 few cases
NANOG 100 100 9
SOX2 0 100 0
CD30 5 90 20 0
CK7 5 80 0 + few cases
Glypican 3 0 0-8 100 30-100
EMA 2 5 3 50
Miscellaneous
Renal cell carcinoma
CK7-20- 80%neg for both
Keratin, EMA, CD10 90% but not specific
PAX8 >80% (best for mets)
SF1, CDX2, P63 negative
RCCma 85%? (not in our hands)
Major types of RCCa (see surgpathcriteria for details and other types)
Vimentin CD117 CK7 CAIX
Clear cell >85% <5% neg/focal 100%
Papillary >90 <20 20-80 50%
Chromophobe 0 >80% >70 neg
Oncocytoma 0 >90% neg/scat neg
Hepatocellular Ca
70-90% HepPar1
50% gastric
Occasional adrenal, yolk sac, colon, lung, ovary, endocervix
CholangioCa and pancreatic Ca can be + in up to 15%
85-100% Arginase1
CholangioCa and pancreatic Ca 0-8%
<20% EMA, CD15, mCEA, MOC31
80% mets and cholangiocarcinoma are positive for these markers
<50% Canalicular staining: CD10 & pCEA, quite specific if branching
88% Glypican 3
Hepatic adenoma, FNH, cirrhosis negative
Other carcinomas 3%
CD34 stains sinusoidal lining in HCC but not normal sinusoid lining cells
Keratin and EMA

Keratin+ EMA-
Hepatocellular Ca
Germ cell tumors
Granulosa cell tumor (keratin 30-50%)
Keratin- EMA+
Meningioma
Pulmonary sclerosing hemangioma (keratin+/-)
Small cell ca and renal cell ca frequently EMA strong, keratin weak
Adrenal cortical carcinoma

SF1 85%, PAX8 negative
MelanA, Inhibin 90% - less in carcinomas than adenomas?
Calretinin, Synaptophysin 60-90%
Keratin, EMA 0-15%
CD10
RCCa 90%
Endometrioid ovary, prostate, HCCa, TCCa, SqCC 50-60%
Melanoma, oat cell, pancreas 30-50%%
Lung adeno, colorectal, breast, serous ovary, stomach 10-20%
Several sarcomas may stain (MFH, fibrosarcoma, MPNST…)
Thyroid Ca
Follicular or papillary - TTF1, thyroglobulin+
Medullary - TTF1, calcitonin, chromogranin +
Thymus
Thymoma PAX8+, p63+, CD5 neg except B3 may be positive
Thymic carcinoma PAX8+, p63+, CD5+
Lymphocytes of normal thymus and thymoma have immature T phenotype
Squamous Ca – all sites

Can’t separate sites by IPOX
P63, CK5/6 and 34BE12 more sensitive than AE1 or CAM5.2
Majority are CK7-20-, PAX8-
Cutaneous CEA-
Spindled/sarcomatoid Ca
CK5/6 and p63 frequently better than AE1
About half are keratin negative
About half may be smooth muscle actin positive
Sustentacular cells (S100+. quite specific if definite)

Paraganglioma
Esthesioneuroblastoma
Neuroblastoma
Carcinoid (infrequent)
R/O interdigitating cells
Derm IPOX - selected topics

DF vs DFSP
Factor 13a, increased in DF, not in DFSP
Not easy to interpret
Lesional cells or reactive cells? Entrapped around edges in some cases?
CD34 - 75% DFSP
Occasional cases seem to have a bit of both F13a and CD34
D2-40 DF positive, DFSP negative/weak (one report)
Nestin DFSP positive, DF neg/focal
Desmoplastic melanoma
S100, SOX10 95-100%
Both stain nerve sheath tumors
Interdigitating cells S100+, SOX10 neg
HMB45, MelanA neg or almost always neg
Literature mixes desmoplastic with spindled
Spindled melanomas usually pos for HMB45 and MelanA
May have SMA+ myofibroblasts
Intraepidermal melanocytic processes

MelanA, MITF and SOX10 are better than S100
CK5/6 is a good complementary stain
Use a red chromogen to avoid mistaking melanin pigment for positive stain
Some reports of MelanA nonspecificity in actinic keratoses
Dermal nevus vs invasive melanoma

Dermal nevus HMB45 neg, Ki67 <5%
Melanoma frequently HMB45 pos, Ki67 >10%
Ki67 may stain reactive lymphocytes etc
Atypical fibroxanthoma
Defined as keratin, S100 negative
Should also be p63, SOX10 neg
Spindled, not desmoplastic, melanoma usually the differential
Spindled carcinomas 50% keratin negative
CD68 50% (Histiocyte marker, nonspecific – also in carcinoma, melanoma)
CD163 better
Smooth muscle actin 40%
Leiomyosarcoma, some spindled SCC +
CD10 and Procollagen 1 >90%, strong reactions appear relatively specific
BerEp4 BCC and sebaceous carcinoma +, SCC neg
Soft tissue tumors Keratin+

Synovial sarcoma
Keratin, EMA: Biphasic 100%, Monophasic 50%
S100 30%
TLE1 95%, occasionally in schwannoma, sft/hpc
Temperamental IPOX stain, FISH is better
CD99 50% (not specific, see CD99 and bcl2 notes below)
bcl2 >90% (not specific, see CD99 and bcl2 notes below)
Epithelioid sarcoma (both proximal and distal)

Keratin, EMA essentially 100%, INI1 negative
CD34 50%, Carcinomas are negative
(Intra-abdominal) desmoplastic small round cell tumor (DSRCT)

Co-expresses desmin and keratin >90%
WT1 90%, CD15, BerEp4 70%
Calretinin, CK5/6 0-15%
CD99 35% (not specific, see CD99 and bcl2 notes below)
Other keratin+ soft tissue tumors

Inflammatory myofibroblastic tumor 30-77%
Extra-renal rhabdoid tumor 100% (INI1 loss in 85%)
Epithelioid angiosarcoma 0-50%
May also be seen in nerve sheath sarcomas (35%)
Occasionally seen in MFH (up to 17%) and smooth muscle tumors (dot-like)
Rhabdomyosarcoma reported 5-50%
Soft tissue – CD34+

Vascular
ERG new marker, may be most sensitive and specific
CD31 does well on high grade tumors
Also stains histiocytes
CD34 does better on lower grade tumors
Stains various other tumors
D2-40 lymphatic marker, stains 100% of Kaposi and 70% of angiosarcomas
Frequently use multiple markers
Epithelioid hemangioendothelioma – frequently only the lumens stain
Keratin 30-50% esp epithelioid tumors
GIST
DOG1 appears to be more sensitive and specific than CD117 or CD34
CD117 (c-kit) 90%
Quite specific among spindle cell tumors
Stains lots of carcinomas, melanomas
CD34 75%
Quite specific vs carcinoma, melanoma (better for epithelioid tumors)
Stains lots of spindle cell tumors
Epithelioid sarcoma CD34 50% (see above under Soft Tissue Keratin+)
DFSP CD34 75% (see above, Derm lesions)
Solitary fibrous tumor / HPC

CD34 SFT 90%, HPC 75%
STAT6 appears to be very sensitive and specific
CD99, bcl2 90% (not specific, see below)
Neg: keratin, actin, desmin, S100
Spindle cell lipoma / Pleomorphic Lipoma

CD34 100%
Other fatty tumors only scattered dendritic cells
Some dediff liposarcs positive
CD99, bcl2 >90% (not specific, see below)
Pleomorphic hyalinizing angiectatic tumor (PHAT)

CD34 80% large cells+
Factor 13a many pos small spindle cells
S100, keratin, actin neg
Mammary type myofibroblastoma

CD34 90%+
Desmin pos
Smooth muscle actin variable
Keratin, S100 negative
Soft tissue tumors - other markers +

Rhabdomyosarcoma
Desmin, muscle specific actin 50-100%
Myogenin more specific, less sensitive
SMA occasional + cells
CD56 50-100%
Keratin 5-50%
CD99 0-50%
Nerve sheath
S100, SOX10
Benign virtually 100%, Malignant 30-50%
HMB45, MelanA pos indicates spindled melanoma
(Pigmented nerve sheath tumors also positive)
Negative result is indeterminate
CD34 stains some dendritic cells but not typically the neoplastic cells
True S100+ CD34+ is unusual phenotype
Perineurioma: CD34+, EMA+(may be focal, faint), GLUT1+, S100 neg
PNET/Ewing
CD99 >90% (Not specific)
Keratin 15%
S100, synaptophysin 0-50%, chromogranin neg
Actin, desmin very rare
INI1: PNET/Ewing, Wilms, DSRCT 100%; Rhabdoid tumor 0%
FLI1 specific but not sensitive
CD99: soft tissue tumors

>90%: SFT, Sp cell lipoma, PNET/Ewing
20-60%: Synovial sarc, HPC, MFH, Osteosarc, Fibrosarc, Leiomyosarc, DSRCT
Before you use CD99, be sure it distinguishes between your candidates
bcl2: soft tissue tumors

>90%: Kaposi, Leiomyosarc, Spindle cell lipoma, GIST, SFT, Synovial sarc, Melanoma,
Nerve sheath tumors, PNET
50%: DFSP, MFH, Fibrosarc
Before you use bcl2, be sure it distinguishes between your candidates
Angiomyolipoma/PEComa (Perivascular Epithelioid Cell – oma)

HMB45, SMA definitional
MelanA, MITF pos
S100 variable
Atypical lipomatous tumor and dedifferentiated liposarcoma

MDM2 & CDK4 95-100% but difficult to interpret
FISH is better for MDM2
Myxofibrosarcoma 40%, MFH 10%, Spindle cell lipoma 10%, Myxoid liposarcoma 4%
Pleomorphic liposarcoma neg
p16 reported as sensitive and more specific than MDM2 staining
Fibromatosis beta catenin 80-90% (nuclear), smooth muscle actin variable

Most others in ddx negative except SFT and synovial sarcoma
S100, CD34, CD117 neg
Desmoplastic small round cell tumor

Desmin and keratin pos, see above under Soft Tissue Keratin+
Alveolar soft part sarcoma

TFE3 strong nuclear +, muscle markers variably positive
Low grade fibromyxoid sarcoma & sclerosing epithelioid fibrosarcoma

MUC4 relatively sensitive and specific, except for 30% of monophasic synovial sarcoma
Soft tissue – No good markers

MFH - CD68 stains cells with lysosomes, not specific
CD163 stains only 4%
Fibrosarcoma
IPOX mostly to rule out things in the differential dx of this group
Robert V Rouse MD
Department of Pathology
Stanford University School of Medicine
http://surgpathcriteria.stanford.edu

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KURT'S NOTES

By Dr. Kurt Schaberg

Inflammatory Patterns of the GI tract

Gastrointestinal Tract: Tumors

Head and Neck

NOTE: There is also now a convenient shorter

My suggestions on wording for streamlined, user-friendly

Patterns of GI Tract Injury

Acute Esophagitis Intraepithelial Neutrophils with Erosion/Ulceration

Eosinophilic Esophagitis Increased intraepithelial Eosinophils (report per HPF)

Lymphocytic Pattern Intraepithelial Lymphocytes

Acute Gastritis Intraepithelial Neutrophils often with Erosion/Ulceration

Lymphocytic Gastritis Intraepithelial Lymphocytes

Collagenous Gastritis Increased subepithelial collagen band with Intraepithelial

Although there is no strict cut-off, >30/HPF is likely too many and

Innumerable or Dysplastic? Consider a Syndrome:

Foveolar Hyperplasia “Corkscrew glands”, Mucin depletion, Edema

Innumerable or Dysplastic? Consider a Syndrome:

Acute Duodenitis Neutrophils in duodenal epithelium

Acute Ileitis Neutrophils in Ileal epithelium

Eosinophilic Gastroenteritis Increased Eosinophils

Ischemia Severe pain. Coagulative necrosis. Crypt withering.

Radiation Most sensitive to damage. Endothelial injury → edema,

Graft Rejection Host T-lymphocytes attack donor bowel. Grade Findings

Causes Diarrhea clinically often with weight loss.

Gluten Sensitive Enteropathy (Celiac Disease)

Focal Active Colitis Rare collections of neutrophils in crypt epithelium

Infection Usu. acute bacterial or viral infections

Medications Esp. NSAIDs. Also Resins

Ischemic Colitis Superficial epithelial damage, Crypt withering, Lamina propria

Although there is no strict cut-off, >60/HPF is likely too many and

Lymphocytic Colitis Increased intraepithelial lymphocytes

Lymphocytic Colitis Watery diarrhea with normal endoscopic

Crohn’s Disease Loose, non-necrotizing. Seen in less than ½ of

Sevelamer: Used to treat hyperphosphatemia in renal failure

Bile Acid Sequestrants: (e.g., cholestyramine) Binds bile acids

Calcium Appears dark purple and often cracked on

Tattoo Very black, coarse granules in

Presumably cleaning up after epithelial injury and

Air “Pseudolipomatosis” Pneumatosis Cystoides Intestinalis

Inflammatory Bowel Disease

Some architectural distortion and muciphages in the rectum is considered normal.

Patterns of Damage in IBD

Typical appearance IBD in recent

Can see deeper inflammation with severe

Can have increased inflammation in cecum

Can have inflammation in terminal ileum

Crohn’s Disease Patchy Transmural chronic active

Indeterminate Colitis aka: IBD, type unclassified

Focal Active Colitis FOCAL Neutrophilic Cryptitis

Microscopic Colitis Increased Intraepithelial Lymphocytes (IELs)

Cancer Risk and Screening Cancer Risk:

Management: Complete endoscopic resection if visible.

P53 staining often highlights both grades:

Non-Conventional Dysplasia May be present with conventional dysplasia in ~50%

Hypermucinous—Villous architecture with prominent

Compared to Sporadic, IBD-associated CRC is:

Medication Injury in the GI tract