{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,20]],"date-time":"2026-10-20T00:49:59Z","timestamp":1792457399022,"version":"4.5.0"},"reference-count":42,"publisher":"Elsevier BV","issue":"6","license":[{"start":{"date-parts":[[2022,1,1]],"date-time":"2022-01-01T00:00:00Z","timestamp":1640995200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2022,1,1]],"date-time":"2022-01-01T00:00:00Z","timestamp":1640995200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2022,2,5]],"date-time":"2022-02-05T00:00:00Z","timestamp":1644019200000},"content-version":"vor","delay-in-days":35,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000062","name":"NIDDK","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007028","name":"Leona M and Harry B Helmsley Charitable Trust","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007028","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"NCI","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["clinicalkey.com","clinicalkey.com.au","clinicalkey.es","clinicalkey.fr","clinicalkey.jp","cmghjournal.org","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cellular and Molecular Gastroenterology and Hepatology"],"published-print":{"date-parts":[[2022]]},"DOI":"10.1016\/j.jcmgh.2022.02.005","type":"journal-article","created":{"date-parts":[[2022,2,12]],"date-time":"2022-02-12T02:45:04Z","timestamp":1644633904000},"page":"1717-1740","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":58,"title":["Single-Cell Analysis Reveals Unexpected Cellular Changes and Transposon Expression Signatures in the Colonic Epithelium of Treatment-Na\u00efve Adult Crohn\u2019s Disease Patients"],"prefix":"10.1016","volume":"13","author":[{"given":"Matt","family":"Kanke","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meaghan M.","family":"Kennedy Ng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sean","family":"Connelly","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manvendra","family":"Singh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew","family":"Schaner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael T.","family":"Shanahan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elizabeth A.","family":"Wolber","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Caroline","family":"Beasley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Grace","family":"Lian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Animesh","family":"Jain","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Millie D.","family":"Long","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Edward L.","family":"Barnes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hans H.","family":"Herfarth","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kim L.","family":"Isaacs","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jonathon J.","family":"Hansen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Muneera","family":"Kapadia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jose Gaston","family":"Guillem","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cedric","family":"Feschotte","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Terrence S.","family":"Furey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shehzad Z.","family":"Sheikh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Praveen","family":"Sethupathy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.jcmgh.2022.02.005_bib1","doi-asserted-by":"crossref","first-page":"771","DOI":"10.1016\/j.devcel.2020.11.010","article-title":"Single-cell sequencing of developing human gut reveals transcriptional links to childhood Crohn's disease","volume":"55","author":"Elmentaite","year":"2020","journal-title":"Dev Cell"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib2","doi-asserted-by":"crossref","first-page":"714","DOI":"10.1016\/j.cell.2019.06.029","article-title":"Intra- and inter-cellular rewiring of the human colon during ulcerative colitis","volume":"178","author":"Smillie","year":"2019","journal-title":"Cell"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib3","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1038\/s41586-019-0992-y","article-title":"Colonic epithelial cell diversity in health and inflammatory bowel disease","volume":"567","author":"Parikh","year":"2019","journal-title":"Nature"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib4","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1038\/nbt.4314","article-title":"Dimensionality reduction for visualizing single-cell data using UMAP","volume":"37","author":"Becht","year":"2018","journal-title":"Nat Biotechnol"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib5","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1186\/s12943-018-0874-1","article-title":"LINC01133 as ceRNA inhibits gastric cancer progression by sponging miR-106a-3p to regulate APC expression and the Wnt\/beta-catenin pathway","volume":"17","author":"Yang","year":"2018","journal-title":"Mol Cancer"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib6","doi-asserted-by":"crossref","first-page":"494","DOI":"10.1038\/s41586-018-0414-6","article-title":"RNA velocity of single cells","volume":"560","author":"La Manno","year":"2018","journal-title":"Nature"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib7","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1038\/nature10209","article-title":"Genetics and pathogenesis of inflammatory bowel disease","volume":"474","author":"Khor","year":"2011","journal-title":"Nature"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib8","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1053\/j.gastro.2013.04.040","article-title":"Association between variants of PRDM1 and NDP52 and Crohn's disease, based on exome sequencing and functional studies","volume":"145","author":"Ellinghaus","year":"2013","journal-title":"Gastroenterology"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib9","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1053\/gast.2002.31035","article-title":"Water transport by epithelia of the digestive tract","volume":"122","author":"Masyuk","year":"2002","journal-title":"Gastroenterology"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib10","doi-asserted-by":"crossref","first-page":"49","DOI":"10.2147\/CEG.S70119","article-title":"Reduced expression of aquaporins in human intestinal mucosa in early stage inflammatory bowel disease","volume":"8","author":"Ricanek","year":"2015","journal-title":"Clin Exp Gastroenterol"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib11","doi-asserted-by":"crossref","first-page":"962","DOI":"10.1093\/ecco-jcc\/jjaa020","article-title":"The water channel aquaporin 8 is a critical regulator of intestinal fluid homeostasis in collagenous colitis","volume":"14","author":"Escudero-Hernandez","year":"2020","journal-title":"J\u00a0Crohns Colitis"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib12","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1038\/nature17406","article-title":"Lypd8 promotes the segregation of flagellated microbiota and colonic epithelia","volume":"532","author":"Okumura","year":"2016","journal-title":"Nature"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib13","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1186\/s41232-017-0056-3","article-title":"Human LYPD8 protein inhibits motility of flagellated bacteria","volume":"37","author":"Hsu","year":"2017","journal-title":"Inflamm Regen"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib14","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1038\/s41385-019-0219-4","article-title":"Lypd8 inhibits attachment of pathogenic bacteria to colonic epithelia","volume":"13","author":"Okumura","year":"2020","journal-title":"Mucosal Immunol"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib15","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0090638","article-title":"Enteroendocrine cells are specifically marked by cell surface expression of claudin-4 in mouse small intestine","volume":"9","author":"Nagatake","year":"2014","journal-title":"PLoS One"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib16","doi-asserted-by":"crossref","first-page":"14514","DOI":"10.1038\/s41598-017-15108-y","article-title":"Identification of claudin-4 binder that attenuates tight junction barrier function by TR-FRET-based screening assay","volume":"7","author":"Watari","year":"2017","journal-title":"Sci Rep"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib17","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1016\/j.molmet.2018.07.011","article-title":"Co-storage and release of insulin-like peptide-5, glucagon-like peptide-1 and peptideYY from murine and human colonic enteroendocrine cells","volume":"16","author":"Billing","year":"2018","journal-title":"Mol Metab"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib18","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1038\/nrendo.2011.77","article-title":"GLP-1 and energy balance: an integrated model of short-term and long-term control","volume":"7","author":"Barrera","year":"2011","journal-title":"Nat Rev Endocrinol"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib19","doi-asserted-by":"crossref","first-page":"843","DOI":"10.1172\/JCI4217","article-title":"Neurotensin is a proinflammatory neuropeptide in colonic inflammation","volume":"103","author":"Castagliuolo","year":"1999","journal-title":"J\u00a0Clin Invest"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib20","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1186\/s13059-018-1577-z","article-title":"Ten things you should know about transposable elements","volume":"19","author":"Bourque","year":"2018","journal-title":"Genome Biol"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib21","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1146\/annurev-pathmechdis-012419-032633","article-title":"Our conflict with transposable elements and its implications for human disease","volume":"15","author":"Burns","year":"2020","journal-title":"Annu Rev Pathol"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib22","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1056\/NEJMra1510092","article-title":"Mobile DNA in health and disease","volume":"377","author":"Kazazian","year":"2017","journal-title":"N\u00a0Engl J Med"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib23","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1038\/s41586-021-03542-y","article-title":"The role of retrotransposable elements in ageing and age-associated diseases","volume":"596","author":"Gorbunova","year":"2021","journal-title":"Nature"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib24","doi-asserted-by":"crossref","first-page":"610","DOI":"10.1016\/j.tig.2020.05.004","article-title":"Transposable elements: a common feature of neurodevelopmental and neurodegenerative disorders","volume":"36","author":"J\u00f6nsson","year":"2020","journal-title":"Trends Genet"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib25","doi-asserted-by":"crossref","first-page":"1083","DOI":"10.1126\/science.aad5497","article-title":"Regulatory evolution of innate immunity through co-option of endogenous retroviruses","volume":"351","author":"Chuong","year":"2016","journal-title":"Science"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib26","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1016\/j.stem.2016.05.023","article-title":"Secreted phospholipases A2 are intestinal stem cell niche factors with distinct roles in homeostasis, inflammation, and cancer","volume":"19","author":"Schewe","year":"2016","journal-title":"Cell Stem Cell"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib27","doi-asserted-by":"crossref","first-page":"590","DOI":"10.1016\/j.stem.2020.07.003","article-title":"Regenerative reprogramming of the intestinal stem cell state via Hippo signaling suppresses metastatic colorectal cancer","volume":"27","author":"Cheung","year":"2020","journal-title":"Cell Stem Cell"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib28","doi-asserted-by":"crossref","first-page":"1003","DOI":"10.1038\/nature06196","article-title":"Identification of stem cells in small intestine and colon by marker gene Lgr5","volume":"449","author":"Barker","year":"2007","journal-title":"Nature"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib29","doi-asserted-by":"crossref","first-page":"3079","DOI":"10.1038\/emboj.2012.166","article-title":"The Lgr5 intestinal stem cell signature: robust expression of proposed quiescent '+4' cell markers","volume":"31","author":"Munoz","year":"2012","journal-title":"EMBO J"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib30","doi-asserted-by":"crossref","first-page":"1307","DOI":"10.1016\/j.cell.2018.10.008","article-title":"T\u00a0helper cell cytokines modulate intestinal stem cell renewal and differentiation","volume":"175","author":"Biton","year":"2018","journal-title":"Cell"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib31","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0079693","article-title":"Lineage-specific expression of bestrophin-2 and bestrophin-4 in human intestinal epithelial cells","volume":"8","author":"Ito","year":"2013","journal-title":"PLoS One"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib32","doi-asserted-by":"crossref","first-page":"476","DOI":"10.1016\/j.canlet.2016.07.015","article-title":"Long non-coding RNA LINC01133 inhibits epithelial-mesenchymal transition and metastasis in colorectal cancer by interacting with SRSF6","volume":"380","author":"Kong","year":"2016","journal-title":"Cancer Lett"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib33","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1038\/nature21683","article-title":"KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks","volume":"543","author":"Imbeault","year":"2017","journal-title":"Nature"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib34","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1146\/annurev-genet-112618-043717","article-title":"The arms race between KRAB-zinc finger proteins and endogenous retroelements and its impact on mammals","volume":"53","author":"Bruno","year":"2019","journal-title":"Annu Rev Genet"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib35","first-page":"366","article-title":"cDNA cloning and characterization of a novel 16 kDa protein located in zymogen granules of rat pancreas and goblet cells of the gut","volume":"65","author":"Cronshagen","year":"1994","journal-title":"Eur J Cell Biol"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib36","doi-asserted-by":"crossref","first-page":"5228","DOI":"10.1038\/s41467-019-13035-2","article-title":"Transposable element expression in tumors is associated with immune infiltration and increased antigenicity","volume":"10","author":"Kong","year":"2019","journal-title":"Nat Commun"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib37","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1158\/1541-7786.MCR-16-0247","article-title":"MYC mediates mRNA cap methylation of canonical Wnt\/beta-catenin signaling transcripts by recruiting CDK7 and RNA methyltransferase","volume":"15","author":"Posternak","year":"2017","journal-title":"Mol Cancer Res"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib38","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1136\/gutjnl-2016-312518","article-title":"Molecular classification of Crohn's disease reveals two clinically relevant subtypes","volume":"67","author":"Weiser","year":"2018","journal-title":"Gut"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib39","doi-asserted-by":"crossref","DOI":"10.1172\/jci.insight.122788","article-title":"Colonic epithelial miR-31 associates with the development of Crohn's phenotypes","volume":"3","author":"Keith","year":"2018","journal-title":"JCI Insight"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib40","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/j.jcmgh.2017.02.011","article-title":"Self-renewing monolayer of primary colonic or rectal epithelial cells","volume":"4","author":"Wang","year":"2017","journal-title":"Cell Mol Gastroenterol Hepatol"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib41","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1016\/j.jcmgh.2020.06.005","article-title":"Decreased colonic activin receptor-like kinase 1 disrupts epithelial barrier integrity in patients with Crohn's disease","volume":"10","author":"Toyonaga","year":"2020","journal-title":"Cell Mol Gastroenterol Hepatol"},{"key":"10.1016\/j.jcmgh.2022.02.005_bib42","doi-asserted-by":"crossref","first-page":"1504","DOI":"10.1101\/gr.165845.113","article-title":"Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape","volume":"24","author":"Camp","year":"2014","journal-title":"Genome Res"}],"container-title":["Cellular and Molecular Gastroenterology and Hepatology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2352345X22000327?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2352345X22000327?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,11,6]],"date-time":"2025-11-06T18:32:00Z","timestamp":1762453920000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2352345X22000327"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022]]},"references-count":42,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2022]]}},"alternative-id":["S2352345X22000327"],"URL":"https:\/\/doi.org\/10.1016\/j.jcmgh.2022.02.005","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.741645942.793596533","asserted-by":"object"}]},"ISSN":["2352-345X"],"issn-type":[{"value":"2352-345X","type":"print"}],"subject":[],"published":{"date-parts":[[2022]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Single-Cell Analysis Reveals Unexpected Cellular Changes and Transposon Expression Signatures in the Colonic Epithelium of Treatment-Na\u00efve Adult Crohn\u2019s Disease Patients","name":"articletitle","label":"Article Title"},{"value":"Cellular and Molecular Gastroenterology and Hepatology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jcmgh.2022.02.005","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2022 The Authors. Published by Elsevier Inc. on behalf of the AGA Institute.","name":"copyright","label":"Copyright"}]}}