{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,4]],"date-time":"2026-05-04T12:12:43Z","timestamp":1777896763836,"version":"3.51.4"},"reference-count":71,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2021,3,4]],"date-time":"2021-03-04T00:00:00Z","timestamp":1614816000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Coeliac disease (CD) is a clinically heterogeneous autoimmune disease with variable presentation and progression triggered by gluten intake. Molecular or genetic factors contribute to disease heterogeneity, but the reasons for different outcomes are poorly understood. Transcriptome studies of tissue biopsies from CD patients are scarce. Here, we present a high-resolution analysis of the transcriptomes extracted from duodenal biopsies of 24 children and adolescents with active CD and 21 individuals without CD but with intestinal afflictions as controls. The transcriptomes of CD patients divide into three groups\u2014a mixed group presenting the control cases, and CD-low and CD-high groups referring to lower and higher levels of CD severity. Persistence of symptoms was weakly associated with subgroup, but the highest marsh stages were present in subgroup CD-high, together with the highest cell cycle rates as an indicator of virtually complete villous atrophy. Considerable variation in inflammation-level between subgroups was further deciphered into immune cell types using cell type de-convolution. Self-organizing maps portrayal was applied to provide high-resolution landscapes of the CD-transcriptome. We find asymmetric patterns of miRNA and long non-coding RNA and discuss the effect of epigenetic regulation. Expression of genes involved in interferon gamma signaling represent suitable markers to distinguish CD from non-CD cases. Multiple pathways overlay in CD biopsies in different ways, giving rise to heterogeneous transcriptional patterns, which potentially provide information about etiology and the course of the disease.<\/jats:p>","DOI":"10.3390\/ijms22052551","type":"journal-article","created":{"date-parts":[[2021,3,4]],"date-time":"2021-03-04T21:58:07Z","timestamp":1614895087000},"page":"2551","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["Deciphering the Transcriptomic Heterogeneity of Duodenal Coeliac Disease Biopsies"],"prefix":"10.3390","volume":"22","author":[{"given":"Johannes","family":"Wolf","sequence":"first","affiliation":[{"name":"Department of Laboratory Medicine at Hospital \u201cSt. Georg\u201d Leipzig, 04129 Leipzig, Germany"},{"name":"Immuno Deficiency Centre Leipzig (IDCL) at Hospital St. Georg Leipzig, Jeffrey Modell Diagnostic and Research Centre for Primary Immunodeficiency Diseases, 04129 Leipzig, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Edith","family":"Willscher","sequence":"additional","affiliation":[{"name":"IZBI, Interdisciplinary Centre for Bioinformatics, University Leipzig, H\u00e4rtelstr. 16\u201318, 04107 Leipzig, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Henry","family":"Loeffler-Wirth","sequence":"additional","affiliation":[{"name":"IZBI, Interdisciplinary Centre for Bioinformatics, University Leipzig, H\u00e4rtelstr. 16\u201318, 04107 Leipzig, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5317-3920","authenticated-orcid":false,"given":"Maria","family":"Schmidt","sequence":"additional","affiliation":[{"name":"IZBI, Interdisciplinary Centre for Bioinformatics, University Leipzig, H\u00e4rtelstr. 16\u201318, 04107 Leipzig, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gunter","family":"Flemming","sequence":"additional","affiliation":[{"name":"Paediatric Gastroenterology Unit, University Hospital for Children and Adolescents, 04103 Leipzig, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marlen","family":"Zurek","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of the Clinical Centre \u201cSankt Georg\u201d, 04129 Leipzig, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6111-7355","authenticated-orcid":false,"given":"Holm H.","family":"Uhlig","sequence":"additional","affiliation":[{"name":"Translational Gastroenterology Unit, Oxford NIHR Biomedical Research Centre, Experimental Medicine, Department of Paediatrics, University of Oxford, John Radcliffe Hospital, Oxford OX4 2PG, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Norman","family":"H\u00e4ndel","sequence":"additional","affiliation":[{"name":"Children\u2019s Hospital of the Clinical Centre \u201cSankt Georg\u201d, 04129 Leipzig, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2242-4678","authenticated-orcid":false,"given":"Hans","family":"Binder","sequence":"additional","affiliation":[{"name":"IZBI, Interdisciplinary Centre for Bioinformatics, University Leipzig, H\u00e4rtelstr. 16\u201318, 04107 Leipzig, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2021,3,4]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"26","DOI":"10.1016\/j.jaut.2015.07.003","article-title":"The genetics of celiac disease: A comprehensive review of clinical implications","volume":"64","year":"2015","journal-title":"J. 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