Celiac Disease and Its Mimics

Rhonda K. Yantiss, M.D.

Professor of Pathology and Laboratory Medicine
Department of Pathology and Laboratory Medicine
Weill Cornell Medicine, New York, New York, USA
Who Gets a Duodenal Biopsy?
•Diarrhea
• With or without malabsorption
•Iron deficiency anemia
•GI hemorrhage
•Immunodeficiency
• HIV, bone marrow/solid organ transplant, others
•Inflammatory bowel disease
•Anyone getting upper endoscopy
• Reflux, gastritis, H. pylori, pain, dyspepsia
 Challenges to Duodenal Biopsy
Interpretation
•Clinical issues
•Not enough, if any, clinical information
• Rule out sprue, abdominal pain
•Technical issues
•Poor tissue orientation
•Small biopsy or too few tissue fragments
•Interpretive issues
•Difficulty understanding spectrum of normal
•Extensive differential diagnosis for non-
specific findings
•Normal villous:crypt
ratio is 3-5:1
•Easily identifiable
goblet cells and
Paneth cells
•One or two mitotic
figures per crypt
•Normal duodenum
•Lymphocytes
•Plasma cells
•Macrophages
•Eosinophils
•Acceptable as long as
they are not in
epithelium
•Neutrophils
•Acceptable as long as
they are not in
epithelium
Stripped villi look flat
Tangential sectioning simulates villous shortening
Duodenal Bulb Biopsies
•Prone to difficult interpretation
•Brunner gland hyperplasia
•Heterotopias
•Peptic injury is common (up to
80%)
Villi are broad and short overlying Brunner glands
Note intraepithelial lymphocytes over aggregate

Gastric heterotopia
Intraepithelial lymphocytes

Peptic duodenitis: Gastric mucous cell metaplasia

 Intraepithelial lymphocytes

Foveolar cell metaplasia

Peptic duodenitis: Neutrophils may be numerous

 Challenges to Biopsy Interpretation
Summary of Issues
•Artifacts simulate enteritis and villous abnormalities
•Small bowel histology is site dependent
•Villous morphology varies across populations
• Pediatric biopsies show more crypt crowding and more goblet cells
• Villous height varies with geography: shorter in tropics
•Brunner glands, gastric heterotopias, and lymphoid
follicles cause villous blunting
•Be careful interpreting changes limited to duodenal bulb-
they often don’t mean much
 Where Do We Biopsy…and How Many
Samples Do We Need?
•Most studies suggest at least 4 samples
•5 is probably better with 1 of the duodenal bulb
•10% of patients with celiac disease have
involvement of bulb only
•10% of patients with celiac disease have
normal duodenal bulb biopsies and
diagnostic changes more distally
•Probably best to biopsy bulb and more distal
duodenum, and submit samples in different
containers
Robert, et al. Am J Surg Pathol 2018; 42(9): e44-e58.
Case
•32-year-old woman
•Autoimmune
hepatitis and
cirrhosis Scalloped folds
•Underwent upper
endoscopy for
evaluation of
esophageal varices
Mosaic pattern
Summary of Findings
•Diffuse process similarly affecting all
tissue fragments
•Complete villous shortening with crypt
hyperplasia and marked plasma cell-
rich inflammation of the lamina propria
•Striking intraepithelial lymphocytosis of
surface and crypt epithelia
Differential Diagnosis
Villous Abnormalities with Lymphocytosis
• Peptic injury (mostly confined to duodenal bulb) Acid
• Celiac disease
• Protein intolerance (non-gluten)
• Food allergies (cereals, eggs, milk, etc)
• Autoimmune enteropathy Altered Immunity
• Common variable immunodeficiency
• Inflammatory bowel disease
• Eosinophilic gastroenteritis
• Targeted biologic agents (often immunomodulators for cancer)
Medications
• Olmesartan (and related agents)
• Bacterial overgrowth
• Tropical sprue
Infection
• Infection (viruses, coccidians, protozoa)
 Celiac Disease
•Genetic factors
•Familial clustering
•70% concordance between identical twins
•HLA associations (DQ2, DQ8) in almost all patients
• Corollary: celiac disease unlikely in patients without one of these HLA types
•Environmental factors
•Dietary gluten
•Probably triggered by viral exposure (adenovirus type 12)
•Emerging evidence for reovirus as a stimulus
 Wheat (and things like beer and ice cream)

Starch
Fat
Fiber
Protein
Water Soluble Fraction

Water Insoluble Fraction

Gluten

Alcohol Insoluble Alcohol Soluble

Glutenin Gliadin
 Serologic Markers of Celiac Disease
Marker Sensitivity Specificity

Anti-gliadin 31-100% 85-100%

Anti-reticulin 42-100% 95-100%
Anti-endomysium 60-100% 95-100%
Anti-tissue transglutaminase 85-100% 92-97%

• Serologic tests need to be done in patients who are not on gluten

restriction
• Sensitivities for all markers decrease among patients with mild/no
symptoms
• None are entirely specific for celiac disease; can be spuriously elevated in
other immune-mediated disorders
Celiac Disease

Scalloped folds Mosaic pattern

Flat: Complete villous blunting and marked crypt hyperplasia

Blue: Lamina propria expanded by chronic inflammation

Celiac disease
Celiac disease: Partial villous shortening
Tip: If there aren’t lots of IELs, then villous abnormalities aren’t due to celiac disease

Intraepithelial lymphocytes are universally present when villi are shortened

Neutrophils may be seen when mucosa is completely flat
 Celiac Disease
Findings After Treatment
•Marked clinical improvement within weeks
of gluten withdrawal
•Surface epithelium restored
•Gradual return of villous architecture
•Decrease in chronic inflammation of lamina
propria and epithelium
•Follow-up samples may be entirely normal
or show only patchy intraepithelial
lymphocytes with normal villous
architecture
Celiac disease: Normal villous architecture with increased intraepithelial lymphocytes
Celiac disease Normal

IELs evenly dispersed over villus IELs decrease from base to surface
Increased Intraepithelial Lymphocytes

•Diffuse (or tip-predominant)

distribution
•More than 20-25 IELs/100
enterocytes
•>12 IELs/20 enterocytes in tip of
villus
•>8 CD3+/CD8+ cells per 20
enterocytes in villous tip
Do I Need Immunostains to Detect IELs?

•No
•Only >25 IELs/100 enterocytes
pathologic
• No value to detecting fewer IELs
•Overestimate number
• Lymphocytes are numerous in lamina
propria
• Those near basement membrane
appear “intraepithelial” with
tangential sectioning
CD3 immunostain
The Significance of Intraepithelial
Lymphocytosis Affecting Normal Villi
• 2-3% of duodenal biopsy samples will show increased
intraepithelial lymphocytosis
• 9-40% of these prove to be related to gluten
depending on the population studied
• Early (Marsh 1) lesion or treated sprue
• Not clear whether all should be treated with gluten
withdrawal
• Other etiologies
• H. pylori infection (confined to bulb)
• Autoimmune conditions, IBD
• Post-infection
• Obesity
• Bacterial overgrowth
 DISEASES ASSOCIATED WITH DUODENAL
LYMPHOCYTOSIS
Miscellaneous
3% Celiac disease
NSAIDs
19%
17%

Crohn disease
7%

Bacterial
overgrowth
7%
Idiopathic 31%
H. pylori
7%
Irritable bowel
syndrome
9%
Extra-duodenal inflammation: Lymphocytic gastritis
Extraduodenal lymphocytosis: Increased intraepithelial lymphocytes in ileum
Extra-duodenal inflammation: Lymphocytic colitis or colonic lymphocytosis

Lymphocytic colitis Colonic lymphocytosis

Recurrent Symptoms After Initial
Response to Gluten Withdrawal
•Exposure to gluten (intentional or not)
•Other gastrointestinal lymphocytosis
(e.g. lymphocytic colitis)
•Collagenous sprue
•Refractory celiac disease
•Development of ulcerating disease or
lymphoma
Collagenous sprue
Collagenous sprue
Refractory Celiac Disease
•5% of patients with celiac disease
•Type I
•Non-clonal intraepithelial lymphocytes
(CD3+/CD8+)
•Better prognosis, but can progress to Type II
•Type II
•Clonal intraepithelial lymphocytes
• Aberrant phenotype (CD3+/CD8-)
• T-cell gene rearrangements
• Loss of staining for T-cell ab receptor
•50% mortality
 Celiac Disease
Summary of Features
•Intraepithelial lymphocytosis always present
•Variable villous abnormalities, crypt hyperplasia
•Lymphocytes and plasma cells predominate in lamina
propria
• Eosinophils and neutrophils present in small numbers
•Neutrophilic/eosinophilic cryptitis is not prominent
(especially distal to bulb)
•May be associated with generalized gastrointestinal
lymphocytosis
Autoimmune Enteropathy
• Severe protracted diarrhea that may result in hospitalization (very
unusual for celiac disease)
• No response to gluten withdrawal
• Extra-intestinal immune-mediated diseases
• Reported associations with thymoma
• Autoantibodies to enterocytes, goblet cells, and others (e.g. ANA)
• More common in young children, especially males
• Sporadic
• Immunodysregulation, polyendocrinopathy and enteropathy, X-linked
(IPEX) syndrome
• APECED syndrome (mucocutaneous candidiasis, ectodermal dystrophy)
 Autoimmune enteropathy

Diffuse, full-thickness plasma cell-rich inflammation with complete villous shortening

Intraepithelial lymphocytes not striking, especially in surface
Autoimmune enteropathy associated with variable villous abnormalities

Decreased goblet cells

More intraepithelial lymphocytes in crypts than surface; more inflammation in deep mucosa
Autoimmune enteropathy

Chromogranin immunostain confirms loss of endocrine cells

Tip: Think about autoimmune enteropathy if you see crypt abscesses and apoptosis

Apoptosis

Crypt abscesses

Decreased goblet cells and Paneth cells

Chronic gastritis with deep inflammation and gland destruction
Colon: crypt architectural distortion with plasma cell-rich infiltrates
 Histologic Features

•Celiac disease •Autoimmune enteropathy

• Surface more than crypt injury • Severe crypt injury with relative
• IELs uniformly present in sparing of surface
surface and crypts • IELs more prominent at crypt
• Granulocytes are infrequent bases
• Crypt abscesses rare • Neutrophils readily identified
• Apoptosis uncommon • Crypt abscesses frequent
• Duodenum and proximal • Apoptotic crypt cells common
jejunum most severely • Stomach and colon often
affected affected
Common Variable Immunodeficiency

•Immunodeficiency resulting from failed

plasma cell maturation
•Absent, or decreased plasma cells
•Plasma cells present, but non-functional
•Symptoms of malabsorption
•Chronic giardiasis and CMV
•Often affects entire gut
Common variable immunodeficiency: Complete villous shortening, crypt hyperplasia

Diffuse lamina propria inflammation

 Neutrophilic abscesses

Apoptosis
No plasma cells

Common variable immunodeficiency

 Apoptosis

Crypt abscesses

Cellular lamina propria with decreased, or absent, plasma cells

Common variable immunodeficiency: Normal villous architecture

Intraepithelial lymphocytes

Nearly normal cellularity of lamina propria, but no plasma cells

 Common variable immunodeficiency

Oops! Here is a viral inclusion

Intraepithelial inflammation more prominent in crypts than surface

Lymphoid hyperplasia of the duodenum
Tip: Look for plasma cells when you see duodenal lymphoid follicles and/or Giardia
Common variable immunodeficiency

Infiltrate does not contain plasma cells

Common variable immunodeficiency

Patchy inflammation simulates Crohn disease

Common variable immunodeficiency mimics Crohn disease

Pyloric metaplasia

Terminal ileum
Common variable immunodeficiency

Ulcers

Terminal ileum No plasma cells

Common variable immunodeficiency Crohn disease

Plasma cells

More plasma cells

Pericryptal granulomatous inflammation simulates Crohn disease

Common variable immunodeficiency: Prominent apoptosis is characteristic

Crypt cell apoptosis is not a striking feature of inflammatory bowel disease

 Histologic Features
•Celiac disease •Common variable immunodeficiency
• Surface more than crypt injury • Crypt more than surface injury
• IELs uniformly present in • IELs more prominent in crypts
surface and crypts • Lamina propria plasma cells are
• Numerous lamina propria decreased or absent
plasma cells • Neutrophils readily identified
• Granulocytes are infrequent • Crypt abscesses frequent
• Crypt abscesses rare • Apoptotic crypt cells common
• Apoptosis uncommon • Stomach and colon often affected
• Duodenum and proximal • CMV and/or Giardia
jejunum most severely affected
Crohn Disease

•Simulates celiac disease

• Increased intraepithelial lymphocytes
• Villous blunting
•Other features typical of Crohn disease
• Ulcers
• Active enteritis
• Granulomata and giant cells
• Metaplasia
• Most patients with duodenal disease also have ileal and colonic
involvement
Crohn disease

Patchy disease Severe mucosal injury and edema

Tip: Ulcers are not characteristic of celiac disease

Neutrophils often more prominent than intraepithelial lymphocytes

Eosinophilic Gastroenteritis

•75% of patients have peripheral eosinophilia

•Negative tissue transglutaminase
•No response to gluten withdrawal
•Infiltration of one, or more segments of the GI
tract, pancreas, or biliary tree
•Villous abnormalities, increased intraepithelial
lymphocytes
Tip: Celiac disease doesn’t feature lots of eosinophils, especially in the epithelium

Courtesy of Dr. Laura Lamps, University of Michigan

Case
• 60-year-old man with
unexplained, severe diarrhea
• Requisition
• Rule out IBD, microscopic colitis,
celiac disease, amyloid, Whipple
disease, etc.
• Endoscopic findings
• Mild congestion of colonic and
gastric mucosae
• Nodular duodenal mucosa with
some scalloping of folds
throughout Scalloped mucosal folds
Duodenum is flat and blue
Apoptotic debris
 Patchy IELs

Duodenal biopsy: Increased lamina propria plasma cells with blunt villi
Antral biopsy: Chronic gastritis, H. pylori-negative
Colon shows chronic colitis; crypt architecture mostly preserved
Patchy cryptitis

Crypt cell apoptosis

Summary of Findings
•Diffuse villous shortening with chronic
inflammation in jejunum and duodenum
•Chronic, focally active pan-gastritis with
deep inflammation
•Chronic, focally active colitis without crypt
architectural distortion
•Celiac serologies and HLA testing were
negative
Differential Diagnosis
Villous Abnormalities with Lymphocytosis
• Peptic injury (mostly confined to duodenal bulb) Acid
• Celiac disease
• Protein intolerance (non-gluten)
• Food allergies (cereals, eggs, milk, etc)
• Autoimmune enteropathy Altered Immunity
• Common variable immunodeficiency
• Inflammatory bowel disease
• Eosinophilic gastroenteritis
• Targeted biologic agents (often immunomodulators for cancer)
Medications
• Olmesartan (and related agents)
• Bacterial overgrowth
• Tropical sprue
Infection
• Infection (viruses, coccidians, protozoa)
Medications/Treatment-Related Injury
•NSAIDs
• Graft versus host disease
• Mycophenolate
• Chemotherapy/Radiation
• Targeted biologic agents (-ib, -ab)
• Idelalisib (inhibits PI3Kδ-mediated signaling)
• Ipilimumab (inhibits CTLA-4-mediated immune tolerance)
• Pembrolizumab (inhibits PD-L1-mediated immune
tolerance downstream to CTLA-4)
• Olmesartan (Benicar) and related compounds
Idelalisib-related injury

Completely flat mucosa

Idelalisib-related injury

Intraepithelial lymphocytes
Idelalisib-related injury

Intraepithelial lymphocytes

Apoptotic crypt cells

 Olmesartan Enteropathy
•Angiotensin II receptor antagonist (anti-
hypertensive)
•Severe chronic diarrhea; may require hospitalization
•Serologic studies generally normal
•Mimic of celiac disease and autoimmune
enteropathy
•May affect stomach and colon as well
•Culprit in collagenous “-itis” throughout GI tract
Sprue-like lesion

Olmesartan-induced enteropathy
Olmesartan-induced enteropathy

Photograph courtesy of Dr. Laura Lamps, University of Michigan

Tip: Think about olmesartan when you see collagenous “itis” anywhere in GI tract

Collagenous sprue
 Collagen deposits

Apoptosis

Olmesartan-induced gastropathy
Olmesartan-induced colonic injury mimics IBD
Back to the Case
• Multifocal involvement of GI tract
• Diffuse inflammation with neutrophils
and numerous apoptotic epithelial
cells
• Surface intraepithelial lymphocytosis
minimal
• HLA haplotypes don’t fit for celiac
disease
• Plenty of plasma cells
• Goblet cells and Paneth cells present
• Taking olmesartan
Olmesartan-Induced Enteropathy
Differential Diagnosis
Villous Abnormalities with Lymphocytosis
• Peptic injury (mostly confined to duodenal bulb) Acid
• Celiac disease
• Protein intolerance (non-gluten)
• Food allergies (cereals, eggs, milk, etc)
• Autoimmune enteropathy Altered Immunity
• Common variable immunodeficiency
• Inflammatory bowel disease
• Eosinophilic gastroenteritis
• Targeted biologic agents (often immunomodulators for cancer)
Medications
• Olmesartan (and related agents)
• Bacterial overgrowth
• Tropical sprue
Infection
• Infection (viruses, coccidians, protozoa)
 Stasis Syndrome
Bacterial Overgrowth
•Post-surgical
• Blind loops and pouches
• Entero-enterostomy
• Afferent loops
• Fistulae
• Adhesions and partial obstructions
•Pseudo-obstruction and dysmotility
• Small bowel diverticulosis
• Crohn disease
• Scleroderma
Bacterial overgrowth: Irregular villous abnormalities
Bacterial overgrowth: Injury doesn’t really fit any other pattern

Crypt hyperplasia with plasmacytosis Surface injury without IELs

Tropical Sprue
•Chronic malabsorption after episode of infectious
diarrhea
•Most common in tropical regions
•Bacterial overgrowth with B12 and folate deficiency
•Responds to antibiotic therapy and vitamin
supplements
•Variable biopsy changes
•Intraepithelial lymphocytosis
•Mild villous abnormalities
Tropical sprue generally causes duodenal lymphocytosis
Tropical sprue: More severe abnormalities in distal small bowel (ileum)
Case

•37-year-old woman
•Clinical history of candida
esophagitis and noldular duodenum
Intraepithelial lymphocytes
Chronic duodenitis with partial villous shortening and
increased intraepithelial lymphocytes

Note: The findings are compatible with a diagnosis of

celiac disease in the appropriate clinical setting.
Other diagnostic considerations include immune-
mediated disorders, infection, and a medication-
related injury.
 Oops

Subsequent conference review

At which time the gastroenterologist said, “Well you
know the patient has HIV and AIDS. I thought you would
guess that when I told you that she had candidal
esophagitis” (which, by the way, he didn’t biopsy)
 Intraepithelial Lymphocytosis
Differential Diagnosis
• Peptic injury/H. pylori gastritis
• Bacterial overgrowth
• Tropical sprue
• Infection (viral, coccidian, protozoa) Be very careful diagnosing any
• Celiac disease immune-mediated disorder in
• Protein intolerance (non-gluten) an immunodeficient patient
• Food allergies (cereals, eggs, milk, etc) (including HIV-infected
• Common variable immunodeficiency patients who don’t have AIDS)
• Autoimmune enteropathy
• Inflammatory bowel disease
• Eosinophilic gastroenteritis
• Idelalisib
• Olmesartan and related agents
Intraepithelial Lymphocytosis
HIV Infection/AIDS

•Giardiasis
•Cryptosporidiasis
•Cystoisosporiasis
•Microsporidiosis
•Cyclosporiasis
Giardia lamblia associated with minimal inflammation and no villous abnormalities
Giardia lamblia have teardrop or “falling leaves” appearance

Unassociated with substantial inflammation and easily overlooked

Mimics of Giardia

Mucin droplets

Degenerated epithelial cells

Cytospin of formalin fixative shows better preservation of Giardia organisms
 SAR Supergroup

Apicomplexa

Conoidasida

Gregarinasina Coccidiasina

Cryptosporidiidae Eucoccidiorida Sarcocystidae

Cryptosporidium Adeleorina Cystoisospora

C. parvum (previously Isospora)
C. hominis C. belli
Eimeriorina

Eimeriidae

Cyclospora
C. cayetanensis
Cryptosporidia Microsporidia

Cyclospora Cystisospora, courtesy L. Lamps

Features of Enteric “Coccidians”
Feature Cryptosporidia Cystoisospora Microsporidia Cyclospora
Size 2-5 µm 15-20 µm (largest) 2-3 µm 2-3 µm schizonts
(smallest) 5-6 µm
merozoites
Location Apical surface Epithelium Luminal aspect of Luminal aspect
Macrophages epithelial cells of epithelial cells
Morphologic “Blue beads on a Large, elliptoid, Multiple tiny round Multiple stages
Features string” at surface banana-shaped organisms in supranuclear of life cycle
vacuole
Ancillary Stains Giemsa Giemsa, Gram, PAS Modified trichrome, Acid fast
Gram Giemsa, Gram,
PAS,Warthin-Starry

• Self-limited disease in immunocompetent patients, but more severe in immunocompromised

• Cryptosporidia and Microsporidia can disseminate
• Microsporidia are now classified as fungi
• Cryptosporidia are still parasites, but gregarines, not coccidia
 Evaluating Small Bowel Biopsies
Take Home Points
• The most reliable change of celiac disease is intraepithelial lymphocytosis
• Most patients with negative serologies and no response to gluten withdrawal
do not have celiac disease
• Disorders of altered immunity show similar features
• Dense plasma cell-rich inflammation, cryptitis, and apoptosis suggest autoimmune
enteropathy; loss of goblet cells, Paneth cells, and endocrine cells, variably present
• Common variable immunodeficiency shows decreased or absent plasma cells
• Medications mimic immune-mediated disorders—get history
• Apoptosis, neutrophils, and lymphocytes are clues
• De novo immune-mediated disease in immunodeficiency is rare
• Be very careful with new diagnoses of celiac disease, ulcerative colitis, and Crohn
disease