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Osnato A, Pasque V, David L. The human embryo selection arena is associated with transposable element activity. PLoS Biol 2023; 21:e3002153. [PMID: 37348048 DOI: 10.1371/journal.pbio.3002153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2023] Open
Abstract
Our current understanding of early human development is limited. A study in PLOS Biology found a previously undefined group of cells that diverges from the main lineages and undergo apoptosis through the activity of young transposable elements.
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Affiliation(s)
- Anna Osnato
- KU Leuven-University of Leuven, Department of Development and Regeneration, Leuven Stem Cell Institute, Leuven, Belgium
- KU Leuven Institute for Single Cell Omics (LISCO), Leuven, Belgium
| | - Vincent Pasque
- KU Leuven-University of Leuven, Department of Development and Regeneration, Leuven Stem Cell Institute, Leuven, Belgium
- KU Leuven Institute for Single Cell Omics (LISCO), Leuven, Belgium
| | - Laurent David
- Nantes Université, Inserm, CR2TI, Nantes, France
- Nantes Université, CHU Nantes, CNRS, Inserm, BioCore, Nantes, France
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2
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Madrigal P, Deng S, Feng Y, Militi S, Goh KJ, Nibhani R, Grandy R, Osnato A, Ortmann D, Brown S, Pauklin S. Epigenetic and transcriptional regulations prime cell fate before division during human pluripotent stem cell differentiation. Nat Commun 2023; 14:405. [PMID: 36697417 PMCID: PMC9876972 DOI: 10.1038/s41467-023-36116-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 01/17/2023] [Indexed: 01/26/2023] Open
Abstract
Stem cells undergo cellular division during their differentiation to produce daughter cells with a new cellular identity. However, the epigenetic events and molecular mechanisms occurring between consecutive cell divisions have been insufficiently studied due to technical limitations. Here, using the FUCCI reporter we developed a cell-cycle synchronised human pluripotent stem cell (hPSC) differentiation system for uncovering epigenome and transcriptome dynamics during the first two divisions leading to definitive endoderm. We observed that transcription of key differentiation markers occurs before cell division, while chromatin accessibility analyses revealed the early inhibition of alternative cell fates. We found that Activator protein-1 members controlled by p38/MAPK signalling are necessary for inducing endoderm while blocking cell fate shifting toward mesoderm, and that enhancers are rapidly established and decommissioned between different cell divisions. Our study has practical biomedical utility for producing hPSC-derived patient-specific cell types since p38/MAPK induction increased the differentiation efficiency of insulin-producing pancreatic beta-cells.
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Affiliation(s)
- Pedro Madrigal
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, UK
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0SZ, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Siwei Deng
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Headington, Oxford, OX3 7LD, UK
| | - Yuliang Feng
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Headington, Oxford, OX3 7LD, UK
| | - Stefania Militi
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Headington, Oxford, OX3 7LD, UK
| | - Kim Jee Goh
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
- The Francis Crick Institute, London, NW1 1AT, UK
| | - Reshma Nibhani
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Headington, Oxford, OX3 7LD, UK
| | - Rodrigo Grandy
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Anna Osnato
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Daniel Ortmann
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Stephanie Brown
- Department of Surgery, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Siim Pauklin
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, Old Road, University of Oxford, Headington, Oxford, OX3 7LD, UK.
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3
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Osnato A, Brown S, Krueger C, Andrews S, Collier AJ, Nakanoh S, Quiroga Londoño M, Wesley BT, Muraro D, Brumm AS, Niakan KK, Vallier L, Ortmann D, Rugg-Gunn PJ. TGFβ signalling is required to maintain pluripotency of human naïve pluripotent stem cells. eLife 2021; 10:e67259. [PMID: 34463252 PMCID: PMC8410071 DOI: 10.7554/elife.67259] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 07/26/2021] [Indexed: 12/30/2022] Open
Abstract
The signalling pathways that maintain primed human pluripotent stem cells (hPSCs) have been well characterised, revealing a critical role for TGFβ/Activin/Nodal signalling. In contrast, the signalling requirements of naive human pluripotency have not been fully established. Here, we demonstrate that TGFβ signalling is required to maintain naive hPSCs. The downstream effector proteins - SMAD2/3 - bind common sites in naive and primed hPSCs, including shared pluripotency genes. In naive hPSCs, SMAD2/3 additionally bind to active regulatory regions near to naive pluripotency genes. Inhibiting TGFβ signalling in naive hPSCs causes the downregulation of SMAD2/3-target genes and pluripotency exit. Single-cell analyses reveal that naive and primed hPSCs follow different transcriptional trajectories after inhibition of TGFβ signalling. Primed hPSCs differentiate into neuroectoderm cells, whereas naive hPSCs transition into trophectoderm. These results establish that there is a continuum for TGFβ pathway function in human pluripotency spanning a developmental window from naive to primed states.
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Affiliation(s)
- Anna Osnato
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
- Department of Surgery, University of CambridgeCambridgeUnited Kingdom
| | - Stephanie Brown
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
- Department of Surgery, University of CambridgeCambridgeUnited Kingdom
| | - Christel Krueger
- Bioinformatics Group, The Babraham InstituteCambridgeUnited Kingdom
| | - Simon Andrews
- Bioinformatics Group, The Babraham InstituteCambridgeUnited Kingdom
| | - Amanda J Collier
- Epigenetics Programme, The Babraham InstituteCambridgeUnited Kingdom
| | - Shota Nakanoh
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
- Department of Surgery, University of CambridgeCambridgeUnited Kingdom
- Division of Embryology, National Institute for Basic BiologyOkazakiJapan
| | - Mariana Quiroga Londoño
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
- Department of Surgery, University of CambridgeCambridgeUnited Kingdom
| | - Brandon T Wesley
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
- Department of Surgery, University of CambridgeCambridgeUnited Kingdom
| | - Daniele Muraro
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
- Department of Surgery, University of CambridgeCambridgeUnited Kingdom
- Wellcome Sanger Institute, HinxtonCambridgeUnited Kingdom
| | - A Sophie Brumm
- Human Embryo and Stem Cell Laboratory, The Francis Crick InstituteLondonUnited Kingdom
| | - Kathy K Niakan
- Human Embryo and Stem Cell Laboratory, The Francis Crick InstituteLondonUnited Kingdom
- Centre for Trophoblast Research, University of CambridgeCambridgeUnited Kingdom
| | - Ludovic Vallier
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
- Department of Surgery, University of CambridgeCambridgeUnited Kingdom
| | - Daniel Ortmann
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
- Department of Surgery, University of CambridgeCambridgeUnited Kingdom
| | - Peter J Rugg-Gunn
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of CambridgeCambridgeUnited Kingdom
- Epigenetics Programme, The Babraham InstituteCambridgeUnited Kingdom
- Centre for Trophoblast Research, University of CambridgeCambridgeUnited Kingdom
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4
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Sampaziotis F, Muraro D, Tysoe OC, Sawiak S, Beach TE, Godfrey EM, Upponi SS, Brevini T, Wesley BT, Garcia-Bernardo J, Mahbubani K, Canu G, Gieseck R, Berntsen NL, Mulcahy VL, Crick K, Fear C, Robinson S, Swift L, Gambardella L, Bargehr J, Ortmann D, Brown SE, Osnato A, Murphy MP, Corbett G, Gelson WTH, Mells GF, Humphreys P, Davies SE, Amin I, Gibbs P, Sinha S, Teichmann SA, Butler AJ, See TC, Melum E, Watson CJE, Saeb-Parsy K, Vallier L. Cholangiocyte organoids can repair bile ducts after transplantation in the human liver. Science 2021; 371:839-846. [PMID: 33602855 PMCID: PMC7610478 DOI: 10.1126/science.aaz6964] [Citation(s) in RCA: 138] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 05/01/2020] [Accepted: 12/09/2020] [Indexed: 02/02/2023]
Abstract
Organoid technology holds great promise for regenerative medicine but has not yet been applied to humans. We address this challenge using cholangiocyte organoids in the context of cholangiopathies, which represent a key reason for liver transplantation. Using single-cell RNA sequencing, we show that primary human cholangiocytes display transcriptional diversity that is lost in organoid culture. However, cholangiocyte organoids remain plastic and resume their in vivo signatures when transplanted back in the biliary tree. We then utilize a model of cell engraftment in human livers undergoing ex vivo normothermic perfusion to demonstrate that this property allows extrahepatic organoids to repair human intrahepatic ducts after transplantation. Our results provide proof of principle that cholangiocyte organoids can be used to repair human biliary epithelium.
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Affiliation(s)
- Fotios Sampaziotis
- Wellcome and MRC Cambridge Stem Cell Institute,Department of Medicine, University of Cambridge,Cambridge Liver Unit, Cambridge University Hospitals NHS Foundation Trust,Correspondence to: Fotios Sampaziotis, ; Ludovic Vallier,
| | | | - Olivia C. Tysoe
- Wellcome and MRC Cambridge Stem Cell Institute,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research centre, Cambridge, UK
| | - Stephen Sawiak
- University of Cambridge, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Timothy E. Beach
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research centre, Cambridge, UK
| | - Edmund M. Godfrey
- Department of Radiology, Cambridge University Hospitals NHS Foundation Trust
| | - Sara S. Upponi
- Department of Radiology, Cambridge University Hospitals NHS Foundation Trust
| | | | | | - Jose Garcia-Bernardo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Krishnaa Mahbubani
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research centre, Cambridge, UK
| | | | - Richard Gieseck
- Immunopathogenesis Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20852, USA
| | - Natalie L. Berntsen
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway,Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Victoria L. Mulcahy
- Department of Medicine, University of Cambridge,Academic Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Keziah Crick
- Department of Surgery, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Corrina Fear
- Department of Surgery, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Sharayne Robinson
- Department of Surgery, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Lisa Swift
- Department of Surgery, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Laure Gambardella
- Wellcome and MRC Cambridge Stem Cell Institute,Department of Medicine, University of Cambridge
| | - Johannes Bargehr
- Wellcome and MRC Cambridge Stem Cell Institute,Department of Medicine, University of Cambridge,Division of Cardiovascular Medicine, University of Cambridge, ACCI Level 6, Box 110, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | | | | | - Anna Osnato
- Wellcome and MRC Cambridge Stem Cell Institute
| | - Michael P. Murphy
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | | | - William T. H. Gelson
- Department of Medicine, University of Cambridge,Cambridge Liver Unit, Cambridge University Hospitals NHS Foundation Trust
| | - George F. Mells
- Department of Medicine, University of Cambridge,Cambridge Liver Unit, Cambridge University Hospitals NHS Foundation Trust,Academic Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | | | - Susan E. Davies
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Irum Amin
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research centre, Cambridge, UK,Department of Surgery, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Paul Gibbs
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research centre, Cambridge, UK,Department of Surgery, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Sanjay Sinha
- Wellcome and MRC Cambridge Stem Cell Institute,Department of Medicine, University of Cambridge
| | - Sarah A. Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK,Cavendish Laboratory, JJ Thomson Ave, Cambridge CB3 0HE, UK
| | - Andrew J Butler
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research centre, Cambridge, UK,Department of Surgery, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Teik Choon See
- Department of Radiology, Cambridge University Hospitals NHS Foundation Trust
| | - Espen Melum
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway,Research Institute of Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital, Oslo, Norway,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway,Section for Gastroenterology, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway,Hybrid Technology Hub-Centre of Excellence, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Christopher J. E. Watson
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research centre, Cambridge, UK,Department of Surgery, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK,National Institute of Health Research (NIHR) Cambridge Biomedical Research Centre, and the NIHR Blood and Transplant Research Unit (BTRU) at the,University of Cambridge in collaboration with Newcastle University and in partnership with NHS Blood and Transplant (NHSBT), Cambridge, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research centre, Cambridge, UK,Department of Surgery, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Ludovic Vallier
- Wellcome and MRC Cambridge Stem Cell Institute,Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research centre, Cambridge, UK,Correspondence to: Fotios Sampaziotis, ; Ludovic Vallier,
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5
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Ortmann D, Brown S, Czechanski A, Aydin S, Muraro D, Huang Y, Tomaz RA, Osnato A, Canu G, Wesley BT, Skelly DA, Stegle O, Choi T, Churchill GA, Baker CL, Rugg-Gunn PJ, Munger SC, Reinholdt LG, Vallier L. Naive Pluripotent Stem Cells Exhibit Phenotypic Variability that Is Driven by Genetic Variation. Cell Stem Cell 2020; 27:470-481.e6. [PMID: 32795399 PMCID: PMC7487768 DOI: 10.1016/j.stem.2020.07.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 04/10/2020] [Accepted: 07/24/2020] [Indexed: 12/11/2022]
Abstract
Variability among pluripotent stem cell (PSC) lines is a prevailing issue that hampers not only experimental reproducibility but also large-scale applications and personalized cell-based therapy. This variability could result from epigenetic and genetic factors that influence stem cell behavior. Naive culture conditions minimize epigenetic fluctuation, potentially overcoming differences in PSC line differentiation potential. Here we derived PSCs from distinct mouse strains under naive conditions and show that lines from distinct genetic backgrounds have divergent differentiation capacity, confirming a major role for genetics in PSC phenotypic variability. This is explained in part through inconsistent activity of extra-cellular signaling, including the Wnt pathway, which is modulated by specific genetic variants. Overall, this study shows that genetic background plays a dominant role in driving phenotypic variability of PSCs.
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Affiliation(s)
- Daniel Ortmann
- Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK; Department of Surgery, University of Cambridge, Cambridge, UK.
| | - Stephanie Brown
- Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK; Department of Surgery, University of Cambridge, Cambridge, UK
| | | | | | - Daniele Muraro
- Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK; Department of Surgery, University of Cambridge, Cambridge, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Yuanhua Huang
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
| | - Rute A Tomaz
- Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK; Department of Surgery, University of Cambridge, Cambridge, UK
| | - Anna Osnato
- Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK; Department of Surgery, University of Cambridge, Cambridge, UK
| | - Giovanni Canu
- Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK; Department of Surgery, University of Cambridge, Cambridge, UK
| | - Brandon T Wesley
- Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK; Department of Surgery, University of Cambridge, Cambridge, UK
| | | | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK; European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany; Division of Computational Genomics and Systems Genetics, German Cancer Research, Center (DKFZ), Heidelberg, Germany
| | - Ted Choi
- Jackson Laboratory, Bar Harbor, ME, USA
| | | | | | - Peter J Rugg-Gunn
- Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK; Epigenetics Programme, Babraham Institute, Cambridge, UK
| | | | | | - Ludovic Vallier
- Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK; Department of Surgery, University of Cambridge, Cambridge, UK.
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6
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Yiangou L, Grandy RA, Osnato A, Ortmann D, Sinha S, Vallier L. Cell cycle regulators control mesoderm specification in human pluripotent stem cells. J Biol Chem 2019; 294:17903-17914. [PMID: 31515269 PMCID: PMC6879335 DOI: 10.1074/jbc.ra119.008251] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 09/09/2019] [Indexed: 12/20/2022] Open
Abstract
The mesoderm is one of the three germ layers produced during gastrulation from which muscle, bones, kidneys, and the cardiovascular system originate. Understanding the mechanisms that control mesoderm specification could inform many applications, including the development of regenerative medicine therapies to manage diseases affecting these tissues. Here, we used human pluripotent stem cells to investigate the role of cell cycle in mesoderm formation. To this end, using small molecules or conditional gene knockdown, we inhibited proteins controlling G1 and G2/M cell cycle phases during the differentiation of human pluripotent stem cells into lateral plate, cardiac, and presomitic mesoderm. These loss-of-function experiments revealed that regulators of the G1 phase, such as cyclin-dependent kinases and pRb (retinoblastoma protein), are necessary for efficient mesoderm formation in a context-dependent manner. Further investigations disclosed that inhibition of the G2/M regulator cyclin-dependent kinase 1 decreases BMP (bone morphogenetic protein) signaling activity specifically during lateral plate mesoderm formation while reducing fibroblast growth factor/extracellular signaling-regulated kinase 1/2 activity in all mesoderm subtypes. Taken together, our findings reveal that cell cycle regulators direct mesoderm formation by controlling the activity of key developmental pathways.
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Affiliation(s)
- Loukia Yiangou
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge CB2 0SZ, United Kingdom
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
- Department of Medicine, Division of Cardiovascular Medicine, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
- Wellcome Sanger Institute, Hinxton CB10 1SA, United Kingdom
| | - Rodrigo A Grandy
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge CB2 0SZ, United Kingdom
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
| | - Anna Osnato
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge CB2 0SZ, United Kingdom
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
| | - Daniel Ortmann
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge CB2 0SZ, United Kingdom
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
| | - Sanjay Sinha
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge CB2 0SZ, United Kingdom
- Department of Medicine, Division of Cardiovascular Medicine, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
| | - Ludovic Vallier
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge CB2 0SZ, United Kingdom
- Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
- Wellcome Sanger Institute, Hinxton CB10 1SA, United Kingdom
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7
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Yiangou L, Grandy RA, Morell CM, Tomaz RA, Osnato A, Kadiwala J, Muraro D, Garcia-Bernardo J, Nakanoh S, Bernard WG, Ortmann D, McCarthy DJ, Simonic I, Sinha S, Vallier L. Method to Synchronize Cell Cycle of Human Pluripotent Stem Cells without Affecting Their Fundamental Characteristics. Stem Cell Reports 2018; 12:165-179. [PMID: 30595546 PMCID: PMC6335580 DOI: 10.1016/j.stemcr.2018.11.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 11/28/2018] [Accepted: 11/29/2018] [Indexed: 01/08/2023] Open
Abstract
Cell cycle progression and cell fate decisions are closely linked in human pluripotent stem cells (hPSCs). However, the study of these interplays at the molecular level remains challenging due to the lack of efficient methods allowing cell cycle synchronization of large quantities of cells. Here, we screened inhibitors of cell cycle progression and identified nocodazole as the most efficient small molecule to synchronize hPSCs in the G2/M phase. Following nocodazole treatment, hPSCs remain pluripotent, retain a normal karyotype and can successfully differentiate into the three germ layers and functional cell types. Moreover, genome-wide transcriptomic analyses on single cells synchronized for their cell cycle and differentiated toward the endoderm lineage validated our findings and showed that nocodazole treatment has no effect on gene expression during the differentiation process. Thus, our synchronization method provides a robust approach to study cell cycle mechanisms in hPSCs. Nocodazole can enrich cells in the G2/M, G1, and S phases of the cell cycle Treatment with nocodazole does not affect pluripotency maintenance hPSCs can efficiently form functional cell types after nocodazole treatment Nocodazole treatment allows genome-wide analyses of synchronous populations
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Affiliation(s)
- Loukia Yiangou
- Wellcome-MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge CB2 0SZ, UK; Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK; Department of Medicine, Division of Cardiovascular Medicine, University of Cambridge, Cambridge CB2 0QQ, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Rodrigo A Grandy
- Wellcome-MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge CB2 0SZ, UK; Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Carola M Morell
- Wellcome-MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge CB2 0SZ, UK; Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Rute A Tomaz
- Wellcome-MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge CB2 0SZ, UK; Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Anna Osnato
- Wellcome-MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge CB2 0SZ, UK; Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Juned Kadiwala
- Cambridge NIHR Biomedical Research Centre hIPSC Core Facility, University of Cambridge, Cambridge CB2 0SZ, UK
| | - Daniele Muraro
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | | | - Shota Nakanoh
- Wellcome-MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge CB2 0SZ, UK; Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK; Division of Embryology, National Institute for Basic Biology, Okazaki 444-8787, Japan
| | - William G Bernard
- Wellcome-MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge CB2 0SZ, UK; Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Daniel Ortmann
- Wellcome-MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge CB2 0SZ, UK; Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Davis J McCarthy
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK; St Vincent's Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Ingrid Simonic
- Medical Genetics Laboratories, Cambridge University Hospitals NHS Trust, Cambridge CB2 0QQ, UK
| | - Sanjay Sinha
- Wellcome-MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge CB2 0SZ, UK; Department of Medicine, Division of Cardiovascular Medicine, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Ludovic Vallier
- Wellcome-MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge CB2 0SZ, UK; Department of Surgery, University of Cambridge, Cambridge CB2 0QQ, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.
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8
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Bertero A, Brown S, Madrigal P, Osnato A, Ortmann D, Yiangou L, Kadiwala J, Hubner NC, de Los Mozos IR, Sadée C, Lenaerts AS, Nakanoh S, Grandy R, Farnell E, Ule J, Stunnenberg HG, Mendjan S, Vallier L. The SMAD2/3 interactome reveals that TGFβ controls m 6A mRNA methylation in pluripotency. Nature 2018; 555:256-259. [PMID: 29489750 PMCID: PMC5951268 DOI: 10.1038/nature25784] [Citation(s) in RCA: 245] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 01/22/2018] [Indexed: 12/17/2022]
Abstract
The TGFβ pathway has essential roles in embryonic development, organ homeostasis, tissue repair and disease. These diverse effects are mediated through the intracellular effectors SMAD2 and SMAD3 (hereafter SMAD2/3), whose canonical function is to control the activity of target genes by interacting with transcriptional regulators. Therefore, a complete description of the factors that interact with SMAD2/3 in a given cell type would have broad implications for many areas of cell biology. Here we describe the interactome of SMAD2/3 in human pluripotent stem cells. This analysis reveals that SMAD2/3 is involved in multiple molecular processes in addition to its role in transcription. In particular, we identify a functional interaction with the METTL3-METTL14-WTAP complex, which mediates the conversion of adenosine to N6-methyladenosine (m6A) on RNA. We show that SMAD2/3 promotes binding of the m6A methyltransferase complex to a subset of transcripts involved in early cell fate decisions. This mechanism destabilizes specific SMAD2/3 transcriptional targets, including the pluripotency factor gene NANOG, priming them for rapid downregulation upon differentiation to enable timely exit from pluripotency. Collectively, these findings reveal the mechanism by which extracellular signalling can induce rapid cellular responses through regulation of the epitranscriptome. These aspects of TGFβ signalling could have far-reaching implications in many other cell types and in diseases such as cancer.
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Affiliation(s)
- Alessandro Bertero
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory and Department of Surgery, University of Cambridge, Cambridge CB2 0SZ, UK
| | - Stephanie Brown
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory and Department of Surgery, University of Cambridge, Cambridge CB2 0SZ, UK
| | - Pedro Madrigal
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory and Department of Surgery, University of Cambridge, Cambridge CB2 0SZ, UK.,Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Anna Osnato
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory and Department of Surgery, University of Cambridge, Cambridge CB2 0SZ, UK
| | - Daniel Ortmann
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory and Department of Surgery, University of Cambridge, Cambridge CB2 0SZ, UK
| | - Loukia Yiangou
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory and Department of Surgery, University of Cambridge, Cambridge CB2 0SZ, UK
| | - Juned Kadiwala
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory and Department of Surgery, University of Cambridge, Cambridge CB2 0SZ, UK
| | - Nina C Hubner
- Department of Molecular Biology, Radboud University, Nijmegen 6525GA, The Netherlands
| | - Igor Ruiz de Los Mozos
- Francis Crick Institute and Department of Molecular Neuroscience, University College London, London NW1 1AT, UK
| | - Christoph Sadée
- Francis Crick Institute and Department of Molecular Neuroscience, University College London, London NW1 1AT, UK
| | - An-Sofie Lenaerts
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory and Department of Surgery, University of Cambridge, Cambridge CB2 0SZ, UK
| | - Shota Nakanoh
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory and Department of Surgery, University of Cambridge, Cambridge CB2 0SZ, UK
| | - Rodrigo Grandy
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory and Department of Surgery, University of Cambridge, Cambridge CB2 0SZ, UK
| | - Edward Farnell
- Department of Pathology, University of Cambridge, Cambridge CB2 1QP, UK
| | - Jernej Ule
- Francis Crick Institute and Department of Molecular Neuroscience, University College London, London NW1 1AT, UK
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Radboud University, Nijmegen 6525GA, The Netherlands
| | - Sasha Mendjan
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory and Department of Surgery, University of Cambridge, Cambridge CB2 0SZ, UK
| | - Ludovic Vallier
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Anne McLaren Laboratory and Department of Surgery, University of Cambridge, Cambridge CB2 0SZ, UK.,Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
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van der Woude AD, Angermayr SA, Puthan Veetil V, Osnato A, Hellingwerf KJ. Carbon sink removal: Increased photosynthetic production of lactic acid by Synechocystis sp. PCC6803 in a glycogen storage mutant. J Biotechnol 2014; 184:100-2. [DOI: 10.1016/j.jbiotec.2014.04.029] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 04/14/2014] [Accepted: 04/30/2014] [Indexed: 10/25/2022]
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