{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T23:22:17Z","timestamp":1787008937569,"version":"build-2736575974"},"reference-count":22,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2021,12,20]],"date-time":"2021-12-20T00:00:00Z","timestamp":1639958400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,5,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Inflammatory bowel diseases (IBDs) are characterized by chronic inflammation and tissue damages in limited segments of the digestive tract. Pathogenesis in the tissue and mucosal inflammation probably differs according to disease location. Our aim was to further analyze transcriptomic profiles in different locations of IBD, differentiating ulcerative colitis (UC), colonic Crohn\u2019s disease (CD), ileal CD, and pouchitis, with respect to normal colonic and ileal mucosa. We thus performed a meta-analysis focusing on specific transcriptomic signatures of ileal and colonic diseases.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We identified 5 cohorts with available transcriptomic data in ileal or colonic samples from active IBD and non-IBD control samples. The meta-analysis was performed on 1047 samples. In each cohort separately, we compared gene expression in CD ileitis and normal ileum; in CD colitis, UC, and normal colon; and finally in pouchitis and normal ileum.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We identified specific markers of ileal (FOLH1, CA2) and colonic (REG3A) inflammation and showed that, with disease, some cells from the ileum start to express colonic markers. We confirmed by immunohistochemistry that these markers were specifically present in ileal or colonic diseases. We highlighted that, overall, colonic CD resembles UC and is distinct from ileal CD, which is in turn closer to pouchitis.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>We demonstrated that ileal and colonic diseases exhibit specific signatures, independent of their initial clinical classification. This supports molecular, rather than clinical, disease stratification, and may be used to design drugs specifically targeting ileal or colonic diseases.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/ibd\/izab311","type":"journal-article","created":{"date-parts":[[2021,12,20]],"date-time":"2021-12-20T09:41:24Z","timestamp":1639993284000},"page":"775-782","source":"Crossref","is-referenced-by-count":18,"title":["Meta-Analysis of IBD Gut Samples Gene Expression Identifies Specific Markers of Ileal and Colonic Diseases"],"prefix":"10.1093","volume":"28","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1802-185X","authenticated-orcid":false,"given":"Kevin","family":"Perez","sequence":"first","affiliation":[{"name":"EMily (INSERM U1160), Institut de Recherche Saint-Louis, Universit\u00e9 de Paris , Paris , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marjolaine","family":"Ngollo","sequence":"additional","affiliation":[{"name":"EMily (INSERM U1160), Institut de Recherche Saint-Louis, Universit\u00e9 de Paris , Paris , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keren","family":"Rabinowitz","sequence":"additional","affiliation":[{"name":"Division of Gastroenterology, Felsenstein Medical Research Center, Rabin Medical Center , Petah Tikva , Israel"},{"name":"Sackler Faculty of Medicine, Tel Aviv University , Tel Aviv , Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nassim","family":"Hammoudi","sequence":"additional","affiliation":[{"name":"EMily (INSERM U1160), Institut de Recherche Saint-Louis, Universit\u00e9 de Paris , Paris , France"},{"name":"Gastroenterology Department, H\u00f4pital Saint-Louis, Asisstance Publique-H\u00f4pitaux de Paris , Paris , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philippe","family":"Seksik","sequence":"additional","affiliation":[{"name":"Gastroenterology Department, H\u00f4pital Saint-Antoine, Universit\u00e9 de la Sorbonne, Asisstance Publique-H\u00f4pitaux de Paris , Paris , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ramnik J","family":"Xavier","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT and Harvard, Massachusetts General Hospital, Harvard Medical School , Boston, MA , USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark J","family":"Daly","sequence":"additional","affiliation":[{"name":"Broad Institute of MIT and Harvard, Massachusetts General Hospital, Harvard Medical School , Boston, MA , USA"},{"name":"Finnish Institute for Molecular Medicine , Helsinki , Finland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Iris","family":"Dotan","sequence":"additional","affiliation":[{"name":"Division of Gastroenterology, Felsenstein Medical Research Center, Rabin Medical Center , Petah Tikva , Israel"},{"name":"Sackler Faculty of Medicine, Tel Aviv University , Tel Aviv , Israel"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lionel","family":"Le Bourhis","sequence":"additional","affiliation":[{"name":"EMily (INSERM U1160), Institut de Recherche Saint-Louis, Universit\u00e9 de Paris , Paris , France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthieu","family":"Allez","sequence":"additional","affiliation":[{"name":"EMily (INSERM U1160), Institut de Recherche Saint-Louis, Universit\u00e9 de Paris , Paris , France"},{"name":"Gastroenterology Department, H\u00f4pital Saint-Louis, Asisstance Publique-H\u00f4pitaux de Paris , Paris , France"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,12,20]]},"reference":[{"key":"2022092311480825200_CIT0001","doi-asserted-by":"crossref","first-page":"2066","DOI":"10.1056\/NEJMra0804647","article-title":"Inflammatory bowel disease.","volume":"361","author":"Abraham","year":"2009","journal-title":"N Engl J Med."},{"key":"2022092311480825200_CIT0002","doi-asserted-by":"crossref","first-page":"749","DOI":"10.1136\/gut.2005.082909","article-title":"The Montreal classification of inflammatory bowel disease: controversies, consensus, and implications.","volume":"55","author":"Satsangi","year":"2006","journal-title":"Gut."},{"key":"2022092311480825200_CIT0003","doi-asserted-by":"crossref","DOI":"10.1016\/j.cgh.2019.04.040","article-title":"Should we divide Crohn\u2019s disease into ileum-dominant and isolated colonic diseases?","author":"Dulai","year":"2019","journal-title":"Clin Gastroenterol Hepatol."},{"key":"2022092311480825200_CIT0004","doi-asserted-by":"crossref","first-page":"2413","DOI":"10.1093\/ibd\/izy148","article-title":"Late-onset Crohn\u2019s disease is a subgroup distinct in genetic and behavioral risk factors with UC-like characteristics.","volume":"24","author":"Li","year":"2018","journal-title":"Inflamm Bowel Dis."},{"key":"2022092311480825200_CIT0005","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1136\/gutjnl-2016-312673","article-title":"Recent advances in clinical practice: a systematic review of isolated colonic Crohn\u2019s disease: the third IBD?","volume":"66","author":"Subramanian","year":"2017","journal-title":"Gut."},{"key":"2022092311480825200_CIT0006","doi-asserted-by":"crossref","first-page":"717","DOI":"10.1016\/j.crohns.2014.02.002","article-title":"Smoking in inflammatory bowel disease: impact on disease course and insights into the aetiology of its effect.","volume":"8","author":"Parkes","year":"2014","journal-title":"J Crohns Colitis."},{"key":"2022092311480825200_CIT0007","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1016\/S0140-6736(15)00465-1","article-title":"Inherited determinants of Crohn\u2019s disease and ulcerative colitis phenotypes: a genetic association study.","volume":"387","author":"Cleynen","year":"2016","journal-title":"Lancet."},{"key":"2022092311480825200_CIT0008","doi-asserted-by":"crossref","first-page":"2509","DOI":"10.1097\/01.MIB.0000437045.26036.00","article-title":"Gene expression profiles of ileal inflammatory bowel disease correlate with disease phenotype and advance understanding of its immunopathogenesis.","volume":"19","author":"Ben-Shachar","year":"2013","journal-title":"Inflamm Bowel Dis."},{"key":"2022092311480825200_CIT0009","doi-asserted-by":"crossref","first-page":"1710","DOI":"10.1016\/S0140-6736(17)30317-3","article-title":"Prediction of complicated disease course for children newly diagnosed with Crohn\u2019s disease: a multicentre inception cohort study.","volume":"389","author":"Kugathasan","year":"2017","journal-title":"Lancet."},{"key":"2022092311480825200_CIT0010","doi-asserted-by":"crossref","first-page":"3617","DOI":"10.1172\/JCI75436","article-title":"Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature.","volume":"124","author":"Haberman","year":"2014","journal-title":"J Clin Invest."},{"key":"2022092311480825200_CIT0011","doi-asserted-by":"crossref","first-page":"924","DOI":"10.1111\/apt.14944","article-title":"Male gender, active smoking and previous intestinal resection are risk factors for post-operative endoscopic recurrence in Crohn\u2019s disease: results from a prospective cohort study.","volume":"48","author":"Auzolle","year":"2018","journal-title":"Aliment Pharmacol Ther."},{"key":"2022092311480825200_CIT0012","doi-asserted-by":"crossref","first-page":"1718","DOI":"10.1097\/MIB.0000000000001246","article-title":"Genetic and transcriptomic bases of intestinal epithelial barrier dysfunction in inflammatory bowel disease.","volume":"23","author":"Vancamelbeke","year":"2017","journal-title":"Inflamm Bowel Dis."},{"key":"2022092311480825200_CIT0013","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1136\/gutjnl-2016-312293","article-title":"Effect of vedolizumab (anti-\u03b14\u03b27-integrin) therapy on histological healing and mucosal gene expression in patients with UC.","volume":"67","author":"Arijs","year":"2018","journal-title":"Gut."},{"key":"2022092311480825200_CIT0014","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1038\/s41467-018-07841-3","article-title":"Ulcerative colitis mucosal transcriptomes reveal mitochondriopathy and personalized mechanisms underlying disease severity and treatment response.","volume":"10","author":"Haberman","year":"2019","journal-title":"Nat Commun."},{"key":"2022092311480825200_CIT0015","doi-asserted-by":"crossref","first-page":"2509","DOI":"10.1097\/01.MIB.0000437045.26036.00","article-title":"Gene expression profiles of ileal inflammatory bowel disease correlate with disease phenotype and advance understanding of its immunopathogenesis.","volume":"19","author":"Ben-Shachar","year":"2013","journal-title":"Inflamm Bowel Dis."},{"key":"2022092311480825200_CIT0016","doi-asserted-by":"crossref","first-page":"517","DOI":"10.3389\/fmed.2020.00517","article-title":"Personalizing treatment in IBD: hype or reality in 2020? Can we predict response to anti-TNF?","volume":"7","author":"Atreya","year":"2020","journal-title":"Front Med (Lausanne)."},{"key":"2022092311480825200_CIT0017","doi-asserted-by":"crossref","first-page":"305","DOI":"10.1002\/pros.21065","article-title":"Expression of prostate-specific membrane antigen (PSMA), increases cell folate uptake and proliferation and suggests a novel role for PSMA in the uptake of the nonpolyglutamated folate, folic acid.","volume":"70","author":"Yao","year":"2010","journal-title":"Prostate."},{"key":"2022092311480825200_CIT0018","doi-asserted-by":"crossref","first-page":"e88634","DOI":"10.1172\/jci.insight.88634","article-title":"FOLH1\/GCPII is elevated in IBD patients, and its inhibition ameliorates murine IBD abnormalities.","volume":"1","author":"Rais","year":"2016","journal-title":"JCI insight."},{"key":"2022092311480825200_CIT0019","doi-asserted-by":"crossref","first-page":"E5399","DOI":"10.1073\/pnas.1607327113","article-title":"Reg4+ deep crypt secretory cells function as epithelial niche for Lgr5+ stem cells in colon.","volume":"113","author":"Sasaki","year":"2016","journal-title":"Proc Natl Acad Sci U S A."},{"key":"2022092311480825200_CIT0020","doi-asserted-by":"crossref","first-page":"1802","DOI":"10.1136\/gut.2005.068601","article-title":"Paneth cells: their role in innate immunity and inflammatory disease.","volume":"54","author":"Elphick","year":"2005","journal-title":"Gut."},{"key":"2022092311480825200_CIT0021","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1111\/j.1748-1716.1989.tb08659.x","article-title":"Carbonic anhydrase in the normal rat stomach and duodenum and after treatment with omeprazole and ranitidine.","volume":"136","author":"L\u00f6nnerholm","year":"1989","journal-title":"Acta Physiol Scand."},{"key":"2022092311480825200_CIT0022","doi-asserted-by":"crossref","first-page":"eaat0852","DOI":"10.1126\/scitranslmed.aat0852","article-title":"PAI-1 augments mucosal damage in colitis.","volume":"11","author":"Kaiko","year":"2019","journal-title":"Sci Transl Med."}],"container-title":["Inflammatory Bowel Diseases"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/ibdjournal\/article-pdf\/28\/5\/775\/45982238\/izab311.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ibdjournal\/article-pdf\/28\/5\/775\/45982238\/izab311.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,9,23]],"date-time":"2022-09-23T07:48:57Z","timestamp":1663919337000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/ibdjournal\/article\/28\/5\/775\/6470736"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,12,20]]},"references-count":22,"journal-issue":{"issue":"5","published-online":{"date-parts":[[2021,12,20]]},"published-print":{"date-parts":[[2022,5,4]]}},"URL":"https:\/\/doi.org\/10.1093\/ibd\/izab311","relation":{},"ISSN":["1078-0998","1536-4844"],"issn-type":[{"value":"1078-0998","type":"print"},{"value":"1536-4844","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,5,1]]},"published":{"date-parts":[[2021,12,20]]}}}