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Epigenetic remodelling licences adult cholangiocytes for organoid formation and liver regeneration

Aloia, Luigi and McKie, Mikel Alexander and Vernaz, Grégoire and Cordero-Espinoza, Lucía and Aleksieva, Niya and van den Ameele, Jelle and Antonica, Francesco and Font-Cunill, Berta and Raven, Alexander and Cigliano, Riccardo Aiese and Belenguer, German and Mort, Richard L. and Brand, Andrea H. and Zernicka-Goetz, Magdalena and Forbes, Stuart J. and Miska, Eric A. and Huch, Meritxell (2019) Epigenetic remodelling licences adult cholangiocytes for organoid formation and liver regeneration. Nature Cell Biology, 21 (11). pp. 1321-1333. ISSN 1465-7392. PMCID PMC6940196 . https://resolver.caltech.edu/CaltechAUTHORS:20191111-124015897

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Abstract

Following severe or chronic liver injury, adult ductal cells (cholangiocytes) contribute to regeneration by restoring both hepatocytes and cholangiocytes. We recently showed that ductal cells clonally expand as self-renewing liver organoids that retain their differentiation capacity into both hepatocytes and ductal cells. However, the molecular mechanisms by which adult ductal-committed cells acquire cellular plasticity, initiate organoids and regenerate the damaged tissue remain largely unknown. Here, we describe that ductal cells undergo a transient, genome-wide, remodelling of their transcriptome and epigenome during organoid initiation and in vivo following tissue damage. TET1-mediated hydroxymethylation licences differentiated ductal cells to initiate organoids and activate the regenerative programme through the transcriptional regulation of stem-cell genes and regenerative pathways including the YAP–Hippo signalling. Our results argue in favour of the remodelling of genomic methylome/hydroxymethylome landscapes as a general mechanism by which differentiated cells exit a committed state in response to tissue damage.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1038/s41556-019-0402-6DOIArticle
https://rdcu.be/bWBU1PublisherFree ReadCube access
http://www.ncbi.nlm.nih.gov/pmc/articles/pmc6940196/PubMed CentralArticle
ORCID:
AuthorORCID
Aloia, Luigi0000-0003-4509-2730
McKie, Mikel Alexander0000-0002-1711-4034
Vernaz, Grégoire0000-0001-8942-2370
van den Ameele, Jelle0000-0002-2744-0810
Antonica, Francesco0000-0001-9359-9689
Mort, Richard L.0000-0002-3566-8217
Zernicka-Goetz, Magdalena0000-0002-7004-2471
Additional Information:© 2019 Springer Nature Limited. Received 05 April 2019; Accepted 11 September 2019; Published 04 November 2019. Data availability: The RNA, ChIP, DamID, WGBS and RRHP sequencing data that support the findings of this study have been deposited in the Gene Expression Omnibus under the accession code GSE123133. All other data supporting the findings of this study are available from the corresponding author on reasonable request. Code availability: All codes used are available on request. M.H. is a Wellcome Trust Sir Henry Dale Fellow and is jointly funded by the Wellcome Trust and the Royal Society (grant no. 104151/Z/14/Z). A.H.B. was funded by the Wellcome Trust Senior Investigator Award 103792 and a Royal Society Darwin Trust Research Professorship. S.J.F. is supported by a Medical Research Council (MRC) grant (grant no. MR/P016839/1). L.A. was supported by a Marie Skłodowska-Curie Postdoctoral fellowship (grant no.702585-EPILIPRO-H2020-MSCA-IF-2015) and a NC3Rs grant awarded to M.H. (grant no. NC/R001162/1). M.A.M. was supported by a MRC doctoral training grant (grant no. MR/K50127X/1). L.C.-E. was jointly funded by a Wellcome Trust Four-Year PhD Studentship with the Stem Cell Biology and Medicine Programme and a Wellcome Cambridge Trust Scholarship. J.v.d.A. was supported by a EMBO Long-term Fellowship (grant no. ALTF 1600_2014) and Wellcome Trust Postdoctoral Training Fellowship for Clinicians (grant no. 105839). F.A. was supported by an ERC advanced research grant to M.Z.-G. M.Z.-G. is a Wellcome Trust Senior Research Fellow. This work was partially funded by a H2020 LSMF4LIFE (grant no. ECH2020-668350) awarded to M.H., a ERC advanced grant to M.Z.G., a Wellcome Trust Senior Investigator Award awarded to E.A.M. (grant nos 104640/Z/14/Z and 092096/Z/10/Z) and a Cancer Research Programme Grant awarded to E.A.M. (grant nos C13474/A18583 and C6946/A14492). G.V. would like to thank Wolfson College at the University of Cambridge and the Genetics Society, London for financial help. The authors acknowledge core funding to the Gurdon Institute from the Wellcome Trust (grant no. 092096) and CRUK (grant no. C6946/A14492). The authors thank R. Krautz and W. Sanseverino for their advice on bioinformatic analyses, R. Arnes-Benito and A. A. Malcom for assistance with histological and immunostaining analyses, W. Reik and J. Silva for sharing TET1 plasmids, R. Butler for developing macro scripts, K. Harnish and C. Bradshaw of the Gurdon Institute’s genomic and bioinformatic facility for high-throughput sequencing, the Gurdon Institute facilities for assistance with imaging, animal care and bioinformatics analysis, A. Riddell and M. Paramor (Cambridge Stem Cell Institute) for assistance with FACS sorting and library preparation, respectively, the CRUK CI genomic facility for sequencing of the WGBS and RRHP libraries and M. Keighren (MRC Human Genetics Unit, University of Edinburgh) for technical support. M.H. would like to thank “Life Science Editors” for assistance during manuscript preparation and B. Simons and H. Clevers for their critical comments on the manuscript. Author Contributions: M.H. and L.A. conceived and designed the project and interpreted the results. L.A., M.A.M., L.C.-E., G.B., G.V., N.A., J.v.d.A., A.R. and M.H. designed and performed experiments and interpreted results. L.A. designed and performed the in vitro experiments involving molecular biology techniques and organoid cultures, M.A.M. designed and performed the in vivo experiments and related stainings, L.C.-E. performed the hydroxymethylation and EdU stainings, G.B. performed the experiments with small molecule inhibitors. G.V. and E.A.M. prepared and analysed the WGBS and RRHP libraries, analysed the RNA sequencing and interpreted the corresponding bioinformatic analyses. N.A., A.R. and S.J.F. performed experiments with the β1-integrin model and interpreted the results of the p21 models. J.v.d.A. and A.H.B. performed the DamID-seq experiments. B.F.-C. helped with the in vivo analyses. R.A.C. helped with the bioinformatics analyses. R.L.M. provided the R26Fucci2a line. F.A. and M.Z.-G. performed the live imaging of ductal cells. L.A. and M.H. wrote the manuscript. All of the authors commented on the manuscript. The authors declare no competing interests.
Funders:
Funding AgencyGrant Number
Wellcome Trust103792
Wellcome Trust104151/Z/14/Z
Medical Research Council (UK)MR/P016839/1
Marie Curie FellowshipH2020-MSCA-IF-2015
European Research Council (ERC)702585-EPILIPRO
National Centre for the Replacement, Refinement and Reduction of Animals in Research (NC3Rs)NC/R001162/1
Medical Research Council (UK)MR/K50127X/1
European Molecular Biology Organization (EMBO)ALTF 1600_2014
Wellcome Trust105839
European Research Council (ERC)UNSPECIFIED
European Research Council (ERC)ECH2020-668350
Wellcome Trust104640/Z/14/Z
Wellcome Trust092096/Z/10/Z
Cancer Research ProgrammeC13474/A18583
Cancer Research ProgrammeC6946/A14492
University of CambridgeUNSPECIFIED
Genetics SocietyUNSPECIFIED
Wellcome Trust092096
Cancer Research UKC6946/A14492
Subject Keywords:Regeneration; Stem cells
Issue or Number:11
PubMed Central ID:PMC6940196
Record Number:CaltechAUTHORS:20191111-124015897
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20191111-124015897
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:99779
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:12 Nov 2019 17:40
Last Modified:08 Apr 2020 17:31

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