PMID- 36038072
OWN - NLM
STAT- MEDLINE
DCOM- 20221122
LR  - 20230308
IS  - 2352-345X (Electronic)
IS  - 2352-345X (Linking)
VI  - 14
IP  - 6
DP  - 2022
TI  - Culture-Associated DNA Methylation Changes Impact on Cellular Function of Human 
      Intestinal Organoids.
PG  - 1295-1310
LID - S2352-345X(22)00186-2 [pii]
LID - 10.1016/j.jcmgh.2022.08.008 [doi]
AB  - 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.
CI  - Copyright (c) 2022 The Authors. Published by Elsevier Inc. All rights reserved.
FAU - Edgar, Rachel D
AU  - Edgar RD
AD  - European Molecular Biology Laboratory, European Bioinformatics Institute, 
      Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom.
FAU - Perrone, Francesca
AU  - Perrone F
AD  - Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, 
      Cambridge, United Kingdom.
FAU - Foster, April R
AU  - Foster AR
AD  - 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.
FAU - Payne, Felicity
AU  - Payne F
AD  - 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.
FAU - Lewis, Sophia
AU  - Lewis S
AD  - 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.
FAU - Nayak, Komal M
AU  - Nayak KM
AD  - Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, 
      Cambridge, United Kingdom.
FAU - Kraiczy, Judith
AU  - Kraiczy J
AD  - Department of Paediatrics, University of Cambridge, Addenbrooke's Hospital, 
      Cambridge, United Kingdom.
FAU - Cenier, Aurelie
AU  - Cenier A
AD  - 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.
FAU - Torrente, Franco
AU  - Torrente F
AD  - Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge 
      University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom.
FAU - Salvestrini, Camilla
AU  - Salvestrini C
AD  - Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge 
      University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom.
FAU - Heuschkel, Robert
AU  - Heuschkel R
AD  - Department of Paediatric Gastroenterology, Hepatology and Nutrition, Cambridge 
      University Hospitals, Addenbrooke's Hospital, Cambridge, United Kingdom.
FAU - Hensel, Kai O
AU  - Hensel KO
AD  - 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.
FAU - Harris, Rebecca
AU  - Harris R
AD  - Centre for Pathway Analysis, Milner Therapeutics Institute, University of 
      Cambridge, Cambridge, United Kingdom.
FAU - Jones, D Leanne
AU  - Jones DL
AD  - 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.
FAU - Zerbino, Daniel R
AU  - Zerbino DR
AD  - European Molecular Biology Laboratory, European Bioinformatics Institute, 
      Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom.
FAU - Zilbauer, Matthias
AU  - Zilbauer M
AD  - 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.
LA  - eng
GR  - MC_PC_17230/MRC_/Medical Research Council/United Kingdom
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
DEP - 20220828
PL  - United States
TA  - Cell Mol Gastroenterol Hepatol
JT  - Cellular and molecular gastroenterology and hepatology
JID - 101648302
SB  - IM
MH  - Humans
MH  - *Organoids
MH  - *DNA Methylation
MH  - Intestines
MH  - Epigenesis, Genetic
MH  - Intestinal Mucosa
PMC - PMC9703134
OTO - NOTNLM
OT  - Culture Conditions
OT  - Epigenetics
OT  - Intestinal Epithelium
OT  - Organoid
EDAT- 2022/08/30 06:00
MHDA- 2022/11/23 06:00
PMCR- 2022/08/28
CRDT- 2022/08/29 19:36
PHST- 2022/04/22 00:00 [received]
PHST- 2022/08/21 00:00 [revised]
PHST- 2022/08/22 00:00 [accepted]
PHST- 2022/08/30 06:00 [pubmed]
PHST- 2022/11/23 06:00 [medline]
PHST- 2022/08/29 19:36 [entrez]
PHST- 2022/08/28 00:00 [pmc-release]
AID - S2352-345X(22)00186-2 [pii]
AID - 10.1016/j.jcmgh.2022.08.008 [doi]
PST - ppublish
SO  - Cell Mol Gastroenterol Hepatol. 2022;14(6):1295-1310. doi: 
      10.1016/j.jcmgh.2022.08.008. Epub 2022 Aug 28.