Culture-Associated DNA Methylation Changes Impact on Cellular Function of Human Intestinal Organoids.

Autor:	Edgar RD; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom., Perrone F; Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom., Foster AR; Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom; Centre for Pathway Analysis, Milner Therapeutics Institute, University of Cambridge, Cambridge, United Kingdom., Payne F; Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom; Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom., Lewis S; Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California; Eli and Edythe Broad Stem Cell Research Center, University of California Los Angeles, Los Angeles, California., Nayak KM; Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom., Kraiczy J; Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom., Cenier A; Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom; Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom., Torrente F; Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom., Salvestrini C; Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom., Heuschkel R; Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom., Hensel KO; Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom; Witten/Herdecke University, Department of Paediatrics, Helios Medical Centre Wuppertal, Children's Hospital, Wuppertal, Germany., Harris R; Centre for Pathway Analysis, Milner Therapeutics Institute, University of Cambridge, Cambridge, United Kingdom., Jones DL; Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California; Eli and Edythe Broad Stem Cell Research Center, University of California Los Angeles, Los Angeles, California; Department of Anatomy and Medicine, Division of Geriatrics, University of California, San Francisco, San Francisco, California; Eli and Edythe Broad Center for Regeneration Medicine, University of California, San Francisco, San Francisco, California., Zerbino DR; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom., Zilbauer M; Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom; Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom; Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom. Electronic address: mz304@medschl.cam.ac.uk.
Jazyk:	angličtina
Zdroj:	Cellular and molecular gastroenterology and hepatology [Cell Mol Gastroenterol Hepatol] 2022; Vol. 14 (6), pp. 1295-1310. Date of Electronic Publication: 2022 Aug 28.
DOI:	10.1016/j.jcmgh.2022.08.008
Abstrakt:	Background & Aims: Human intestinal epithelial organoids (IEOs) are a powerful tool to model major aspects of intestinal development, health, and diseases because patient-derived cultures retain many features found in vivo. A necessary aspect of the organoid model is the requirement to expand cultures in vitro through several rounds of passaging. This is of concern because the passaging of cells has been shown to affect cell morphology, ploidy, and function. Methods: Here, we analyzed 173 human IEO lines derived from the small and large bowel and examined the effect of culture duration on DNA methylation (DNAm). Furthermore, we tested the potential impact of DNAm changes on gene expression and cellular function. Results: Our analyses show a reproducible effect of culture duration on DNAm in a large discovery cohort as well as 2 publicly available validation cohorts generated in different laboratories. Although methylation changes were seen in only approximately 8% of tested cytosine-phosphate-guanine dinucleotides (CpGs) and global cellular function remained stable, a subset of methylation changes correlated with altered gene expression at baseline as well as in response to inflammatory cytokine exposure and withdrawal of Wnt agonists. Importantly, epigenetic changes were found to be enriched in genomic regions associated with colonic cancer and distant to the site of replication, indicating similarities to malignant transformation. Conclusions: Our study shows distinct culture-associated epigenetic changes in mucosa-derived human IEOs, some of which appear to impact gene transcriptomic and cellular function. These findings highlight the need for future studies in this area and the importance of considering passage number as a potentially confounding factor. (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)
Databáze:	MEDLINE
Externí odkaz:	Zobrazit plný text záznamu