Abstract
Celiac disease (CD) is a risk factor for developing small-bowel carcinoma with a 14-fold higher risk compared with general population. As small-bowel carcinomas associated with CD (CD-SBCs) are extremely rare, very few molecular data are available about their pathogenesis, and information about their transcriptomic profiling is lacking. We generated RNA-seq data on 13 CD-SBCs, taken from the largest well-characterized series published so far, collected by the Small Bowel Cancer Italian Consortium, and compared the tumor transcriptional signatures with the four Consensus Molecular Subtypes (CMS) of colorectal carcinoma by applying the “CMS classifier.” CpG Island Methylator Phenotype (CIMP) was evaluated using methylation-sensitive multiple ligation-dependent probe amplification. Up to 12 of 13 cancers fell within the two main subtypes exhibiting high immune and inflammatory signatures, i.e., subtypes 1 and 4. The first and predominant subset was commonly microsatellite unstable, and exhibited CIMP and high CD3+ and CD8+ T cell infiltration. Moreover, it showed increased expression of genes associated with T helper 1 and natural killer cell infiltration, as well as upregulation of apoptosis, cell cycle progression, and proteasome pathways. By contrast, cancers falling in subtype 4 showed prominent transforming growth factor-β activation and were characterized by complement-associated inflammation, matrix remodeling, cancer-associated stroma production, and angiogenesis. Parallel histologic and histochemical analysis confirmed such tumor subtyping. In conclusion, two molecular subtypes have been consistently identified in our series of CD-SBCs, a microsatellite instability-immune and a mesenchymal subtype, the former likely associated with an indolent and the latter with a worse tumor behavior.
Similar content being viewed by others
References
Di Sabatino A, Corazza GR (2009) Coeliac disease. Lancet 373:1480–1493. https://doi.org/10.1016/S0140-6736(09)60254-3
Dube C, Rostom A, Sy R, Cranney A, Saloojee N, Garritty C, Sampson M, Zhang L, Yazdi F, Mamaladze V, Pan I, Macneil J, Mack D, Patel D, Moher D (2005) The prevalence of celiac disease in average-risk and at-risk Western European populations: a systematic review. Gastroenterology 128:S57–S67. https://doi.org/10.1053/j.gastro.2005.02.014
Aparicio T, Zaanan A, Svrcek M, Laurent-Puig P, Carrere N, Manfredi S, Locher C, Afchain P (2014) Small bowel adenocarcinoma: epidemiology, risk factors, diagnosis and treatment. Dig Liver Dis 46:97–104. https://doi.org/10.1016/j.dld.2013.04.013
Han Y, Chen W, Li P, Ye J (2015) Association between coeliac disease and risk of any malignancy and gastrointestinal malignancy: a meta-analysis. Medicine (Baltimore) 94:e1612. https://doi.org/10.1097/MD.0000000000001612
Howdle PD, Jalal PK, Holmes GK, Houlston RS (2003) Primary small-bowel malignancy in the UK and its association with coeliac disease. QJM 96:345–353. https://doi.org/10.1093/qjmed/hcg058
Bruno CJ, Batts KP, Ahlquist DA (1997) Evidence against flat dysplasia as a regional field defect in small bowel adenocarcinoma associated with celiac sprue. Mayo Clin Proc 72:320–322. https://doi.org/10.1016/S0025-6196(11)63330-2
Rampertab SD, Forde KA, Green PH (2003) Small bowel neoplasia in coeliac disease. Gut 52:1211–1214. https://doi.org/10.1136/gut.52.8.1211
Potter DD, Murray JA, Donohue JH, Burgart LJ, Nagorney DM, van Heerden JA, Plevak MF, Zinsmeister AR, Thibodeau SN (2004) The role of defective mismatch repair in small bowel adenocarcinoma in celiac disease. Cancer Res 64:7073–7077. https://doi.org/10.1158/0008-5472.CAN-04-1096
Diosdado B, Buffart TE, Watkins R, Carvalho B, Ylstra B, Tijssen M, Bolijn AS, Lewis F, Maude K, Verbeke C, Nagtegaal ID, Grabsch H, Mulder CJ, Quirke P, Howdle P, Meijer GA (2010) High-resolution array comparative genomic hybridization in sporadic and celiac disease-related small bowel adenocarcinomas. Clin Cancer Res 16:1391–1401. https://doi.org/10.1158/1078-0432.CCR-09-1773
Alvi MA, McArt DG, Kelly P, Fuchs MA, Alderdice M, McCabe CM, Bingham V, McGready C, Tripathi S, Emmert-Streib F, Loughrey MB, McQuaid S, Maxwell P, Hamilton PW, Turkington R, James JA, Wilson RH, Salto-Tellez M (2015) Comprehensive molecular pathology analysis of small bowel adenocarcinoma reveals novel targets with potential for clinical utility. Oncotarget 6:20863–20874. https://doi.org/10.18632/oncotarget.4576
Vanoli A, Di Sabatino A, Furlan D, Klersy C, Grillo F, Fiocca R, Mescoli C, Rugge M, Nesi G, Fociani P, Sampietro G, Ardizzone S, Luinetti O, Calabro A, Tonelli F, Volta U, Santini D, Caio G, Giuffrida P, Elli L, Ferrero S, Latella G, Ciardi A, Caronna R, Solina G, Rizzo A, Ciacci C, D’Armiento FP, Salemme M, Villanacci V, Cannizzaro R, Canzonieri V, Reggiani Bonetti L, Biancone L, Monteleone G, Orlandi A, Santeusanio G, Macciomei MC, D’Inca R, Perfetti V, Sandri G, Silano M, Florena AM, Giannone AG, Papi C, Coppola L, Usai P, Maccioni A, Astegiano M, Migliora P, Manca R, Martino M, Trapani D, Cerutti R, Alberizzi P, Riboni R, Sessa F, Paulli M, Solcia E, Corazza GR (2017) Small bowel carcinomas in coeliac or Crohn’s disease: clinico-pathological, molecular, and prognostic features. A Study From the Small Bowel Cancer Italian Consortium. J Crohns Colitis 11:942–953. https://doi.org/10.1093/ecco-jcc/jjx031
Vanoli A, Di Sabatino A, Martino M, Klersy C, Grillo F, Mescoli C, Nesi G, Volta U, Fornino D, Luinetti O, Fociani P, Villanacci V, D’Armiento FP, Cannizzaro R, Latella G, Ciacci C, Biancone L, Paulli M, Sessa F, Rugge M, Fiocca R, Corazza GR, Solcia E (2017) Small bowel carcinomas in celiac or Crohn’s disease: distinctive histophenotypic, molecular and histogenetic patterns. Mod Pathol 30:1453–1466. https://doi.org/10.1038/modpathol.2017.40
Bijlsma MF, Sadanandam A, Tan P, Vermeulen L (2017) Molecular subtypes in cancers of the gastrointestinal tract. Nat Rev Gastroenterol Hepatol 14:333–342. https://doi.org/10.1038/nrgastro.2017.33
Network CGAR (2014) Comprehensive molecular characterization of gastric adenocarcinoma. Nature 513:202–209. https://doi.org/10.1038/nature13480
Guinney J, Dienstmann R, Wang X, de Reynies A, Schlicker A, Soneson C, Marisa L, Roepman P, Nyamundanda G, Angelino P, Bot BM, Morris JS, Simon IM, Gerster S, Fessler E, De Sousa EMF, Missiaglia E, Ramay H, Barras D, Homicsko K, Maru D, Manyam GC, Broom B, Boige V, Perez-Villamil B, Laderas T, Salazar R, Gray JW, Hanahan D, Tabernero J, Bernards R, Friend SH, Laurent-Puig P, Medema JP, Sadanandam A, Wessels L, Delorenzi M, Kopetz S, Vermeulen L, Tejpar S (2015) The consensus molecular subtypes of colorectal cancer. Nat Med 21:1350–1356. https://doi.org/10.1038/nm.3967
Becht E, Giraldo NA, Lacroix L, Buttard B, Elarouci N, Petitprez F, Selves J, Laurent-Puig P, Sautes-Fridman C, Fridman WH, de Reynies A (2016) Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression. Genome Biol 17:218. https://doi.org/10.1186/s13059-016-1070-5
Trinh A, Trumpi K, De Sousa EMF, Wang X, de Jong JH, Fessler E, Kuppen PJ, Reimers MS, Swets M, Koopman M, Nagtegaal ID, Jansen M, Hooijer GK, Offerhaus GJ, Kranenburg O, Punt CJ, Medema JP, Markowetz F, Vermeulen L (2017) Practical and robust identification of molecular subtypes in colorectal cancer by immunohistochemistry. Clin Cancer Res 23:387–398. https://doi.org/10.1158/1078-0432.CCR-16-0680
Tarallo R, Giurato G, Bruno G, Ravo M, Rizzo F, Salvati A, Ricciardi L, Marchese G, Cordella A, Rocco T, Gigantino V, Pierri B, Cimmino G, Milanesi L, Ambrosino C, Nyman TA, Nassa G, Weisz A (2017) The nuclear receptor ERbeta engages AGO2 in regulation of gene transcription, RNA splicing and RISC loading. Genome Biol 18:189. https://doi.org/10.1186/s13059-017-1321-0
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29:15–21. https://doi.org/10.1093/bioinformatics/bts635
Anders S, Pyl PT, Huber W (2015) HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics 31:166–169. https://doi.org/10.1093/bioinformatics/btu638
Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:550. https://doi.org/10.1186/s13059-014-0550-8
Ogino S, Kawasaki T, Kirkner GJ, Kraft P, Loda M, Fuchs CS (2007) Evaluation of markers for CpG island methylator phenotype (CIMP) in colorectal cancer by a large population-based sample. J Mol Diagn 9:305–314. https://doi.org/10.2353/jmoldx.2007.060170
Furlan D, Sahnane N, Mazzoni M, Pastorino R, Carnevali I, Stefanoli M, Ferretti A, Chiaravalli AM, La Rosa S, Capella C (2013) Diagnostic utility of MS-MLPA in DNA methylation profiling of adenocarcinomas and neuroendocrine carcinomas of the colon-rectum. Virchows Arch 462:47–56. https://doi.org/10.1007/s00428-012-1348-2
Satow R, Inagaki S, Kato C, Shimozawa M, Fukami K (2017) Identification of zinc finger protein of the cerebellum 5 as a survival factor of prostate and colorectal cancer cells. Cancer Sci 108:2405–2412. https://doi.org/10.1111/cas.13419
Li L, Yan LH, Manoj S, Li Y, Lu L (2017) Central role of CEMIP in tumorigenesis and its potential as therapeutic target. J Cancer 8:2238–2246. https://doi.org/10.7150/jca.19295
Matheu A, Collado M, Wise C, Manterola L, Cekaite L, Tye AJ, Canamero M, Bujanda L, Schedl A, Cheah KS, Skotheim RI, Lothe RA, Lopez de Munain A, Briscoe J, Serrano M, Lovell-Badge R (2012) Oncogenicity of the developmental transcription factor Sox9. Cancer Res 72:1301–1315. https://doi.org/10.1158/0008-5472.CAN-11-3660
Roche KC, Gracz AD, Liu XF, Newton V, Akiyama H, Magness ST (2015) SOX9 maintains reserve stem cells and preserves radioresistance in mouse small intestine. Gastroenterology 149(1553-1563):e1510. https://doi.org/10.1053/j.gastro.2015.07.004
Panarelli NC, Vaughn CP, Samowitz WS, Yantiss RK (2015) Sporadic microsatellite instability-high colon cancers rarely display immunohistochemical evidence of Wnt signaling activation. Am J Surg Pathol 39:313–317. https://doi.org/10.1097/PAS.0000000000000380
Senger S, Sapone A, Fiorentino MR, Mazzarella G, Lauwers GY, Fasano A (2015) Celiac disease histopathology recapitulates hedgehog downregulation, consistent with wound healing processes activation. PLoS One 10:e0144634. https://doi.org/10.1371/journal.pone.0144634
Ma F, Ye H, He HH, Gerrin SJ, Chen S, Tanenbaum BA, Cai C, Sowalsky AG, He L, Wang H, Balk SP, Yuan X (2016) SOX9 drives WNT pathway activation in prostate cancer. J Clin Invest 126:1745–1758. https://doi.org/10.1172/JCI78815
Sun L, Mathews LA, Cabarcas SM, Zhang X, Yang A, Zhang Y, Young MR, Klarmann KD, Keller JR, Farrar WL (2013) Epigenetic regulation of SOX9 by the NF-kappaB signaling pathway in pancreatic cancer stem cells. Stem Cells 31:1454–1466. https://doi.org/10.1002/stem.1394
Fernandez-Jimenez N, Castellanos-Rubio A, Plaza-Izurieta L, Irastorza I, Elcoroaristizabal X, Jauregi-Miguel A, Lopez-Euba T, Tutau C, de Pancorbo MM, Vitoria JC, Bilbao JR (2014) Coregulation and modulation of NFkappaB-related genes in celiac disease: uncovered aspects of gut mucosal inflammation. Hum Mol Genet 23:1298–1310. https://doi.org/10.1093/hmg/ddt520
Maiuri MC, De Stefano D, Mele G, Fecarotta S, Greco L, Troncone R, Carnuccio R (2003) Nuclear factor kappa B is activated in small intestinal mucosa of celiac patients. J Mol Med (Berl) 81:373–379. https://doi.org/10.1007/s00109-003-0440-0
Castellanos-Rubio A, Santin I, Martin-Pagola A, Irastorza I, Castano L, Vitoria JC, Bilbao JR (2010) Long-term and acute effects of gliadin on small intestine of patients on potentially pathogenic networks in celiac disease. Autoimmunity 43:131–139. https://doi.org/10.3109/08916930903225229
Di Sabatino A, Lenti MV, Giuffrida P, Vanoli A, Corazza GR (2015) New insights into immune mechanisms underlying autoimmune diseases of the gastrointestinal tract. Autoimmun Rev 14:1161–1169. https://doi.org/10.1016/j.autrev.2015.08.004
Calon A, Lonardo E, Berenguer-Llergo A, Espinet E, Hernando-Momblona X, Iglesias M, Sevillano M, Palomo-Ponce S, Tauriello DV, Byrom D, Cortina C, Morral C, Barcelo C, Tosi S, Riera A, Attolini CS, Rossell D, Sancho E, Batlle E (2015) Stromal gene expression defines poor-prognosis subtypes in colorectal cancer. Nat Genet 47:320–329. https://doi.org/10.1038/ng.3225
Isella C, Terrasi A, Bellomo SE, Petti C, Galatola G, Muratore A, Mellano A, Senetta R, Cassenti A, Sonetto C, Inghirami G, Trusolino L, Fekete Z, De Ridder M, Cassoni P, Storme G, Bertotti A, Medico E (2015) Stromal contribution to the colorectal cancer transcriptome. Nat Genet 47:312–319. https://doi.org/10.1038/ng.3224
Bergmann F, Singh S, Michel S, Kahlert C, Schirmacher P, Helmke B, Von Knebel DM, Kloor M, Blaker H (2010) Small bowel adenocarcinomas in celiac disease follow the CIM-MSI pathway. Oncol Rep 24:1535–1539. https://doi.org/10.3892/or_00001015
Giuffrida P, Vanoli A, Arpa G, Bonometti A, Luinetti O, Solcia E, Corazza GR, Paulli M, Di Sabatino A (2018) Small bowel carcinomas associated with immune-mediated intestinal disorders: the current knowledge. Cancers (Basel):11. https://doi.org/10.3390/cancers11010031
Herbst RS, Soria JC, Kowanetz M, Fine GD, Hamid O, Gordon MS, Sosman JA, McDermott DF, Powderly JD, Gettinger SN, Kohrt HE, Horn L, Lawrence DP, Rost S, Leabman M, Xiao Y, Mokatrin A, Koeppen H, Hegde PS, Mellman I, Chen DS, Hodi FS (2014) Predictive correlates of response to the anti-PD-L1 antibody MPDL3280A in cancer patients. Nature 515:563–567. https://doi.org/10.1038/nature14011
Le DT, Durham JN, Smith KN, Wang H, Bartlett BR, Aulakh LK, Lu S, Kemberling H, Wilt C, Luber BS, Wong F, Azad NS, Rucki AA, Laheru D, Donehower R, Zaheer A, Fisher GA, Crocenzi TS, Lee JJ, Greten TF, Duffy AG, Ciombor KK, Eyring AD, Lam BH, Joe A, Kang SP, Holdhoff M, Danilova L, Cope L, Meyer C, Zhou S, Goldberg RM, Armstrong DK, Bever KM, Fader AN, Taube J, Housseau F, Spetzler D, Xiao N, Pardoll DM, Papadopoulos N, Kinzler KW, Eshleman JR, Vogelstein B, Anders RA, Diaz LA Jr (2017) Mismatch repair deficiency predicts response of solid tumors to PD-1 blockade. Science 357:409–413. https://doi.org/10.1126/science.aan6733
Acknowledgments
We thank all the Collaborators of the “Small Bowel Cancer Italian Consortium.”
Funding
This study was supported by the University of Insubria (to Prof. Furlan, FAR project 2016-2017), the Italian Association for Cancer Research (AIRC Grant: IG-17426), and Regione Campania (“La Campania lotta contro il cancro” project Rare-Plat-Net, CUP: B63D18000380007; and project GENOMAeSALUTE, CUP: B41C17000080007) and Genomix4Life to Prof. Weisz. This research was also supported by a grant of the Italian Ministry of Education, University and Research (MIUR), to the Department of Molecular Medicine of the University of Pavia under the initiative “Dipartimenti di Eccellenza” (2018–2022) to Prof. Marco Paulli and by Fondazione IRCCS Policlinico San Matteo to Dr. Ombretta Luinetti. A.S. is a PhD student of the Research Doctorate in “Sciences and Biomedical Technologies–XXXI Cycle,” University Roma 3.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Declaration of Helsinki and its revision and was approved by the Ethics Committee of the IRCCS San Matteo Hospital Foundation, Italy (no. 20140018113, on 22nd September 2014).
Conflict of interest
The authors have no conflicts of interest
Ethical responsibilities of authors section
Study design: DF, FR, AV, ES; acquisition, analysis, or interpretation of data: all authors
Drafting the work or revising it critically: all authors
Final approval of the version to be published: all authors
Agreement to be accountable for all aspects of the work: all authors
Additional information
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
This article is part of the Topical Collection on Quality in Pathology
Rights and permissions
About this article
Cite this article
Rizzo, F., Vanoli, A., Sahnane, N. et al. Small-bowel carcinomas associated with celiac disease: transcriptomic profiling shows predominance of microsatellite instability-immune and mesenchymal subtypes. Virchows Arch 476, 711–723 (2020). https://doi.org/10.1007/s00428-019-02675-w
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00428-019-02675-w