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DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development

OBJECTIVE: Human intestinal epithelial organoids (IEOs) are increasingly being recognised as a highly promising translational research tool. However, our understanding of their epigenetic molecular characteristics and behaviour in culture remains limited. DESIGN: We performed genome-wide DNA methyla...

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Autores principales: Kraiczy, Judith, Nayak, Komal M, Howell, Kate J, Ross, Alexander, Forbester, Jessica, Salvestrini, Camilla, Mustata, Roxana, Perkins, Sally, Andersson-Rolf, Amanda, Leenen, Esther, Liebert, Anke, Vallier, Ludovic, Rosenstiel, Philip C, Stegle, Oliver, Dougan, Gordon, Heuschkel, Robert, Koo, Bon-Kyoung, Zilbauer, Matthias
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BMJ Publishing Group 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6839835/
https://www.ncbi.nlm.nih.gov/pubmed/29141958
http://dx.doi.org/10.1136/gutjnl-2017-314817
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author Kraiczy, Judith
Nayak, Komal M
Howell, Kate J
Ross, Alexander
Forbester, Jessica
Salvestrini, Camilla
Mustata, Roxana
Perkins, Sally
Andersson-Rolf, Amanda
Leenen, Esther
Liebert, Anke
Vallier, Ludovic
Rosenstiel, Philip C
Stegle, Oliver
Dougan, Gordon
Heuschkel, Robert
Koo, Bon-Kyoung
Zilbauer, Matthias
author_facet Kraiczy, Judith
Nayak, Komal M
Howell, Kate J
Ross, Alexander
Forbester, Jessica
Salvestrini, Camilla
Mustata, Roxana
Perkins, Sally
Andersson-Rolf, Amanda
Leenen, Esther
Liebert, Anke
Vallier, Ludovic
Rosenstiel, Philip C
Stegle, Oliver
Dougan, Gordon
Heuschkel, Robert
Koo, Bon-Kyoung
Zilbauer, Matthias
author_sort Kraiczy, Judith
collection PubMed
description OBJECTIVE: Human intestinal epithelial organoids (IEOs) are increasingly being recognised as a highly promising translational research tool. However, our understanding of their epigenetic molecular characteristics and behaviour in culture remains limited. DESIGN: We performed genome-wide DNA methylation and transcriptomic profiling of human IEOs derived from paediatric/adult and fetal small and large bowel as well as matching purified human gut epithelium. Furthermore, organoids were subjected to in vitro differentiation and genome editing using CRISPR/Cas9 technology. RESULTS: We discovered stable epigenetic signatures which define regional differences in gut epithelial function, including induction of segment-specific genes during cellular differentiation. Established DNA methylation profiles were independent of cellular environment since organoids retained their regional DNA methylation over prolonged culture periods. In contrast to paediatric and adult organoids, fetal gut-derived organoids showed distinct dynamic changes of DNA methylation and gene expression in culture, indicative of an in vitro maturation. By applying CRISPR/Cas9 genome editing to fetal organoids, we demonstrate that this process is partly regulated by TET1, an enzyme involved in the DNA demethylation process. Lastly, generating IEOs from a child diagnosed with gastric heterotopia revealed persistent and distinct disease-associated DNA methylation differences, highlighting the use of organoids as disease-specific research models. CONCLUSIONS: Our study demonstrates striking similarities of epigenetic signatures in mucosa-derived IEOs with matching primary epithelium. Moreover, these results suggest that intestinal stem cell-intrinsic DNA methylation patterns establish and maintain regional gut specification and are involved in early epithelial development and disease.
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spelling pubmed-68398352019-11-20 DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development Kraiczy, Judith Nayak, Komal M Howell, Kate J Ross, Alexander Forbester, Jessica Salvestrini, Camilla Mustata, Roxana Perkins, Sally Andersson-Rolf, Amanda Leenen, Esther Liebert, Anke Vallier, Ludovic Rosenstiel, Philip C Stegle, Oliver Dougan, Gordon Heuschkel, Robert Koo, Bon-Kyoung Zilbauer, Matthias Gut Intestinal Inflammation OBJECTIVE: Human intestinal epithelial organoids (IEOs) are increasingly being recognised as a highly promising translational research tool. However, our understanding of their epigenetic molecular characteristics and behaviour in culture remains limited. DESIGN: We performed genome-wide DNA methylation and transcriptomic profiling of human IEOs derived from paediatric/adult and fetal small and large bowel as well as matching purified human gut epithelium. Furthermore, organoids were subjected to in vitro differentiation and genome editing using CRISPR/Cas9 technology. RESULTS: We discovered stable epigenetic signatures which define regional differences in gut epithelial function, including induction of segment-specific genes during cellular differentiation. Established DNA methylation profiles were independent of cellular environment since organoids retained their regional DNA methylation over prolonged culture periods. In contrast to paediatric and adult organoids, fetal gut-derived organoids showed distinct dynamic changes of DNA methylation and gene expression in culture, indicative of an in vitro maturation. By applying CRISPR/Cas9 genome editing to fetal organoids, we demonstrate that this process is partly regulated by TET1, an enzyme involved in the DNA demethylation process. Lastly, generating IEOs from a child diagnosed with gastric heterotopia revealed persistent and distinct disease-associated DNA methylation differences, highlighting the use of organoids as disease-specific research models. CONCLUSIONS: Our study demonstrates striking similarities of epigenetic signatures in mucosa-derived IEOs with matching primary epithelium. Moreover, these results suggest that intestinal stem cell-intrinsic DNA methylation patterns establish and maintain regional gut specification and are involved in early epithelial development and disease. BMJ Publishing Group 2019-01 2017-11-15 /pmc/articles/PMC6839835/ /pubmed/29141958 http://dx.doi.org/10.1136/gutjnl-2017-314817 Text en © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2019. All rights reserved. No commercial use is permitted unless otherwise expressly granted. This is an open access article distributed in accordance with the terms of the Creative Commons Attribution (CC BY 4.0) license, which permits others to distribute, remix, adapt and build upon this work, for commercial use, provided the original work is properly cited. See: http://creativecommons.org/licenses/by/4.0/
spellingShingle Intestinal Inflammation
Kraiczy, Judith
Nayak, Komal M
Howell, Kate J
Ross, Alexander
Forbester, Jessica
Salvestrini, Camilla
Mustata, Roxana
Perkins, Sally
Andersson-Rolf, Amanda
Leenen, Esther
Liebert, Anke
Vallier, Ludovic
Rosenstiel, Philip C
Stegle, Oliver
Dougan, Gordon
Heuschkel, Robert
Koo, Bon-Kyoung
Zilbauer, Matthias
DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development
title DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development
title_full DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development
title_fullStr DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development
title_full_unstemmed DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development
title_short DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development
title_sort dna methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development
topic Intestinal Inflammation
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6839835/
https://www.ncbi.nlm.nih.gov/pubmed/29141958
http://dx.doi.org/10.1136/gutjnl-2017-314817
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