{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T15:29:57Z","timestamp":1791386997141,"version":"4.3.3"},"reference-count":48,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2021,7,7]],"date-time":"2021-07-07T00:00:00Z","timestamp":1625616000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002347","name":"Bundesministerium f\u00fcr Bildung und Forschung","doi-asserted-by":"publisher","award":["031A312"],"award-info":[{"award-number":["031A312"]}],"id":[{"id":"10.13039\/501100002347","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001663","name":"Volkswagen Foundation","doi-asserted-by":"publisher","award":["Lichtenberg program"],"award-info":[{"award-number":["Lichtenberg program"]}],"id":[{"id":"10.13039\/501100001663","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["KFO286"],"award-info":[{"award-number":["KFO286"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["SFB1399"],"award-info":[{"award-number":["SFB1399"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Cells"],"abstract":"<jats:p>Organoids retain the morphological and molecular patterns of their tissue of origin, are self-organizing, relatively simple to handle and accessible to genetic engineering. Thus, they represent an optimal tool for studying the mechanisms of tissue maintenance and aging. Long-term expansion under standard growth conditions, however, is accompanied by changes in the growth pattern and kinetics. As a potential explanation of these alterations, epigenetic drifts in organoid culture have been suggested. Here, we studied histone tri-methylation at lysine 4 (H3K4me3) and 27 (H3K27me3) and transcriptome profiles of intestinal organoids derived from mismatch repair (MMR)-deficient and control mice and cultured for 3 and 20 weeks and compared them with data on their tissue of origin. We found that, besides the expected changes in short-term culture, the organoids showed profound changes in their epigenomes also during the long-term culture. The most prominent were epigenetic gene activation by H3K4me3 recruitment to previously unmodified genes and by H3K27me3 loss from originally bivalent genes. We showed that a long-term culture is linked to broad transcriptional changes that indicate an ongoing maturation and metabolic adaptation process. This process was disturbed in MMR-deficient mice, resulting in endoplasmic reticulum (ER) stress and Wnt activation. Our results can be explained in terms of a mathematical model assuming that epigenetic changes during a long-term culture involve DNA demethylation that ceases if the metabolic adaptation is disturbed.<\/jats:p>","DOI":"10.3390\/cells10071718","type":"journal-article","created":{"date-parts":[[2021,7,7]],"date-time":"2021-07-07T02:00:17Z","timestamp":1625623217000},"page":"1718","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":30,"title":["Epigenetic Drifts during Long-Term Intestinal Organoid Culture"],"prefix":"10.3390","volume":"10","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5489-7405","authenticated-orcid":false,"given":"Torsten","family":"Thalheim","sequence":"first","affiliation":[{"name":"Interdisciplinary Center for Bioinformatics (IZBI), Leipzig University, 04107 Leipzig, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susann","family":"Siebert","sequence":"additional","affiliation":[{"name":"Laboratory for Translational Epigenetics and Tumor Genetics, University Hospital Cologne, 50931 Cologne, Germany"},{"name":"Center for Molecular Medicine Cologne (CMMC), 50931 Cologne, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marianne","family":"Quaas","sequence":"additional","affiliation":[{"name":"Research Laboratories, Department of Surgery, Leipzig University, 04103 Leipzig, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria","family":"Herberg","sequence":"additional","affiliation":[{"name":"Interdisciplinary Center for Bioinformatics (IZBI), Leipzig University, 04107 Leipzig, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michal R.","family":"Schweiger","sequence":"additional","affiliation":[{"name":"Laboratory for Translational Epigenetics and Tumor Genetics, University Hospital Cologne, 50931 Cologne, Germany"},{"name":"Center for Molecular Medicine Cologne (CMMC), 50931 Cologne, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabriela","family":"Aust","sequence":"additional","affiliation":[{"name":"Research Laboratories, Department of Surgery, Leipzig University, 04103 Leipzig, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joerg","family":"Galle","sequence":"additional","affiliation":[{"name":"Interdisciplinary Center for Bioinformatics (IZBI), Leipzig University, 04107 Leipzig, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2021,7,7]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1038\/nature07935","article-title":"Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche","volume":"459","author":"Sato","year":"2009","journal-title":"Nature"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1762","DOI":"10.1053\/j.gastro.2011.07.050","article-title":"Long-term expansion of epithelial organoids from human colon, adenoma, adenocarcinoma, and Barrett\u2019s epithelium","volume":"141","author":"Sato","year":"2011","journal-title":"Gastroenterology"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1190","DOI":"10.1126\/science.1234852","article-title":"Growing self-organizing mini-guts from a single intestinal stem cell: Mechanism and applications","volume":"340","author":"Sato","year":"2013","journal-title":"Science"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"2750","DOI":"10.1038\/onc.2016.429","article-title":"Different in vivo and in vitro transformation of intestinal stem cells in mismatch repair deficiency","volume":"36","author":"Keysselt","year":"2017","journal-title":"Oncogene"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"2608","DOI":"10.1016\/j.celrep.2017.02.056","article-title":"Canonical Wnt signaling ameliorates aging of intestinal stem cells","volume":"18","author":"Nalapareddy","year":"2017","journal-title":"Cell Rep."},{"key":"ref_6","first-page":"1","article-title":"Epigenetic silencing of Lgr5 induces senescence of intestinal epithelial organoids during the process of aging","volume":"5","author":"Uchida","year":"2018","journal-title":"NPJ Aging Mech. 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