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Kanemaru K, Cranley J, Muraro D, Miranda AMA, Ho SY, Wilbrey-Clark A, Patrick Pett J, Polanski K, Richardson L, Litvinukova M, Kumasaka N, Qin Y, Jablonska Z, Semprich CI, Mach L, Dabrowska M, Richoz N, Bolt L, Mamanova L, Kapuge R, Barnett SN, Perera S, Talavera-López C, Mulas I, Mahbubani KT, Tuck L, Wang L, Huang MM, Prete M, Pritchard S, Dark J, Saeb-Parsy K, Patel M, Clatworthy MR, Hübner N, Chowdhury RA, Noseda M, Teichmann SA. Spatially resolved multiomics of human cardiac niches. Nature 2023; 619:801-810. [PMID: 37438528 PMCID: PMC10371870 DOI: 10.1038/s41586-023-06311-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 06/12/2023] [Indexed: 07/14/2023]
Abstract
The function of a cell is defined by its intrinsic characteristics and its niche: the tissue microenvironment in which it dwells. Here we combine single-cell and spatial transcriptomics data to discover cellular niches within eight regions of the human heart. We map cells to microanatomical locations and integrate knowledge-based and unsupervised structural annotations. We also profile the cells of the human cardiac conduction system1. The results revealed their distinctive repertoire of ion channels, G-protein-coupled receptors (GPCRs) and regulatory networks, and implicated FOXP2 in the pacemaker phenotype. We show that the sinoatrial node is compartmentalized, with a core of pacemaker cells, fibroblasts and glial cells supporting glutamatergic signalling. Using a custom CellPhoneDB.org module, we identify trans-synaptic pacemaker cell interactions with glia. We introduce a druggable target prediction tool, drug2cell, which leverages single-cell profiles and drug-target interactions to provide mechanistic insights into the chronotropic effects of drugs, including GLP-1 analogues. In the epicardium, we show enrichment of both IgG+ and IgA+ plasma cells forming immune niches that may contribute to infection defence. Overall, we provide new clarity to cardiac electro-anatomy and immunology, and our suite of computational approaches can be applied to other tissues and organs.
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Affiliation(s)
- Kazumasa Kanemaru
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - James Cranley
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Daniele Muraro
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Siew Yen Ho
- Cardiac Morphology Unit, Royal Brompton Hospital and Imperial College London, London, UK
| | - Anna Wilbrey-Clark
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Jan Patrick Pett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Krzysztof Polanski
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Laura Richardson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Monika Litvinukova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Natsuhiko Kumasaka
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Yue Qin
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Zuzanna Jablonska
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Claudia I Semprich
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Lukas Mach
- National Heart and Lung Institute, Imperial College London, London, UK
- Royal Brompton Hospital, London, UK
| | - Monika Dabrowska
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Nathan Richoz
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Liam Bolt
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Lira Mamanova
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Rakeshlal Kapuge
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Sam N Barnett
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Shani Perera
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Carlos Talavera-López
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Würzburg Institute for Systems Immunology, Max Planck Research Group, Julius-Maximilian-Universität, Würzburg, Germany
| | - Ilaria Mulas
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Krishnaa T Mahbubani
- Department of Surgery, University of Cambridge, and Cambridge Biorepository for Translational Medicine, NIHR Cambridge Biomedical Centre, Cambridge, UK
| | - Liz Tuck
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Lu Wang
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Margaret M Huang
- Department of Surgery, University of Cambridge, and Cambridge Biorepository for Translational Medicine, NIHR Cambridge Biomedical Centre, Cambridge, UK
| | - Martin Prete
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Sophie Pritchard
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - John Dark
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery, University of Cambridge, and Cambridge Biorepository for Translational Medicine, NIHR Cambridge Biomedical Centre, Cambridge, UK
| | - Minal Patel
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Menna R Clatworthy
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Norbert Hübner
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité-Universitätsmedizin, Berlin, Germany
- German Centre for Cardiovascular Research (DZHK), Partner Site Berlin, Berlin, Germany
| | | | - Michela Noseda
- National Heart and Lung Institute, Imperial College London, London, UK.
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Department of Physics, Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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Semprich CI, Davidson L, Amorim Torres A, Patel H, Briscoe J, Metzis V, Storey KG. ERK1/2 signalling dynamics promote neural differentiation by regulating chromatin accessibility and the polycomb repressive complex. PLoS Biol 2022; 20:e3000221. [PMID: 36455041 PMCID: PMC9746999 DOI: 10.1371/journal.pbio.3000221] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 12/13/2022] [Accepted: 10/11/2022] [Indexed: 12/05/2022] Open
Abstract
Fibroblast growth factor (FGF) is a neural inducer in many vertebrate embryos, but how it regulates chromatin organization to coordinate the activation of neural genes is unclear. Moreover, for differentiation to progress, FGF signalling must decline. Why these signalling dynamics are required has not been determined. Here, we show that dephosphorylation of the FGF effector kinase ERK1/2 rapidly increases chromatin accessibility at neural genes in mouse embryos, and, using ATAC-seq in human embryonic stem cell derived spinal cord precursors, we demonstrate that this occurs genome-wide across neural genes. Importantly, ERK1/2 inhibition induces precocious neural gene transcription, and this involves dissociation of the polycomb repressive complex from key gene loci. This takes place independently of subsequent loss of the repressive histone mark H3K27me3 and transcriptional onset. Transient ERK1/2 inhibition is sufficient for the dissociation of the repressive complex, and this is not reversed on resumption of ERK1/2 signalling. Moreover, genomic footprinting of sites identified by ATAC-seq together with ChIP-seq for polycomb protein Ring1B revealed that ERK1/2 inhibition promotes the occupancy of neural transcription factors (TFs) at non-polycomb as well as polycomb associated sites. Together, these findings indicate that ERK1/2 signalling decline promotes global changes in chromatin accessibility and TF binding at neural genes by directing polycomb and other regulators and appears to serve as a gating mechanism that provides directionality to the process of differentiation.
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Affiliation(s)
- Claudia I. Semprich
- Division of Cell & Developmental Biology, School of Life Sciences, University of Dundee, Scotland, United Kingdom
| | - Lindsay Davidson
- Division of Cell & Developmental Biology, School of Life Sciences, University of Dundee, Scotland, United Kingdom
| | - Adriana Amorim Torres
- Division of Cell & Developmental Biology, School of Life Sciences, University of Dundee, Scotland, United Kingdom
| | | | | | - Vicki Metzis
- The Francis Crick Institute, London, United Kingdom
- Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
- * E-mail: (VM); (KGS)
| | - Kate G. Storey
- Division of Cell & Developmental Biology, School of Life Sciences, University of Dundee, Scotland, United Kingdom
- * E-mail: (VM); (KGS)
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Collier AJ, Bendall A, Fabian C, Malcolm AA, Tilgner K, Semprich CI, Wojdyla K, Nisi PS, Kishore K, Roamio Franklin VN, Mirshekar-Syahkal B, D’Santos C, Plath K, Yusa K, Rugg-Gunn PJ. Genome-wide screening identifies Polycomb repressive complex 1.3 as an essential regulator of human naïve pluripotent cell reprogramming. Sci Adv 2022; 8:eabk0013. [PMID: 35333572 PMCID: PMC8956265 DOI: 10.1126/sciadv.abk0013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
Uncovering the mechanisms that establish naïve pluripotency in humans is crucial for the future applications of pluripotent stem cells including the production of human blastoids. However, the regulatory pathways that control the establishment of naïve pluripotency by reprogramming are largely unknown. Here, we use genome-wide screening to identify essential regulators as well as major impediments of human primed to naïve pluripotent stem cell reprogramming. We discover that factors essential for cell state change do not typically undergo changes at the level of gene expression but rather are repurposed with new functions. Mechanistically, we establish that the variant Polycomb complex PRC1.3 and PRDM14 jointly repress developmental and gene regulatory factors to ensure naïve cell reprogramming. In addition, small-molecule inhibitors of reprogramming impediments improve naïve cell reprogramming beyond current methods. Collectively, this work defines the principles controlling the establishment of human naïve pluripotency and also provides new insights into mechanisms that destabilize and reconfigure cell identity during cell state transitions.
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Affiliation(s)
- Amanda J. Collier
- Epigenetics Programme, Babraham Institute, Cambridge, UK
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Adam Bendall
- Epigenetics Programme, Babraham Institute, Cambridge, UK
| | | | - Andrew A. Malcolm
- Epigenetics Programme, Babraham Institute, Cambridge, UK
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Katarzyna Tilgner
- Stem Cell Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | | | | | | | - Kamal Kishore
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | | | - Clive D’Santos
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Kathrin Plath
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Kosuke Yusa
- Stem Cell Genetics, Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Stem Cell Genetics, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Peter J. Rugg-Gunn
- Epigenetics Programme, Babraham Institute, Cambridge, UK
- Wellcome–MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
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Chovanec P, Collier AJ, Krueger C, Várnai C, Semprich CI, Schoenfelder S, Corcoran AE, Rugg-Gunn PJ. Widespread reorganisation of pluripotent factor binding and gene regulatory interactions between human pluripotent states. Nat Commun 2021; 12:2098. [PMID: 33828098 PMCID: PMC8026613 DOI: 10.1038/s41467-021-22201-4] [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: 05/25/2020] [Accepted: 03/05/2021] [Indexed: 01/10/2023] Open
Abstract
The transition from naive to primed pluripotency is accompanied by an extensive reorganisation of transcriptional and epigenetic programmes. However, the role of transcriptional enhancers and three-dimensional chromatin organisation in coordinating these developmental programmes remains incompletely understood. Here, we generate a high-resolution atlas of gene regulatory interactions, chromatin profiles and transcription factor occupancy in naive and primed human pluripotent stem cells, and develop a network-graph approach to examine the atlas at multiple spatial scales. We uncover highly connected promoter hubs that change substantially in interaction frequency and in transcriptional co-regulation between pluripotent states. Small hubs frequently merge to form larger networks in primed cells, often linked by newly-formed Polycomb-associated interactions. We identify widespread state-specific differences in enhancer activity and interactivity that correspond with an extensive reconfiguration of OCT4, SOX2 and NANOG binding and target gene expression. These findings provide multilayered insights into the chromatin-based gene regulatory control of human pluripotent states.
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Affiliation(s)
- Peter Chovanec
- Lymphocyte Signalling and Development Programme, Babraham Institute, Cambridge, UK
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
| | | | | | - Csilla Várnai
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
- Centre for Computational Biology, University of Birmingham, Birmingham, UK
| | | | - Stefan Schoenfelder
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
- Epigenetics Programme, Babraham Institute, Cambridge, UK
| | - Anne E Corcoran
- Lymphocyte Signalling and Development Programme, Babraham Institute, Cambridge, UK
- Nuclear Dynamics Programme, Babraham Institute, Cambridge, UK
| | - Peter J Rugg-Gunn
- Epigenetics Programme, Babraham Institute, Cambridge, UK.
- Wellcome - MRC Cambridge Stem Cell Institute, Cambridge, UK.
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Patel NS, Rhinn M, Semprich CI, Halley PA, Dollé P, Bickmore WA, Storey KG. FGF signalling regulates chromatin organisation during neural differentiation via mechanisms that can be uncoupled from transcription. PLoS Genet 2013; 9:e1003614. [PMID: 23874217 PMCID: PMC3715432 DOI: 10.1371/journal.pgen.1003614] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 05/21/2013] [Indexed: 01/08/2023] Open
Abstract
Changes in higher order chromatin organisation have been linked to transcriptional regulation; however, little is known about how such organisation alters during embryonic development or how it is regulated by extrinsic signals. Here we analyse changes in chromatin organisation as neural differentiation progresses, exploiting the clear spatial separation of the temporal events of differentiation along the elongating body axis of the mouse embryo. Combining fluorescence in situ hybridisation with super-resolution structured illumination microscopy, we show that chromatin around key differentiation gene loci Pax6 and Irx3 undergoes both decompaction and displacement towards the nuclear centre coincident with transcriptional onset. Conversely, down-regulation of Fgf8 as neural differentiation commences correlates with a more peripheral nuclear position of this locus. During normal neural differentiation, fibroblast growth factor (FGF) signalling is repressed by retinoic acid, and this vitamin A derivative is further required for transcription of neural genes. We show here that exposure to retinoic acid or inhibition of FGF signalling promotes precocious decompaction and central nuclear positioning of differentiation gene loci. Using the Raldh2 mutant as a model for retinoid deficiency, we further find that such changes in higher order chromatin organisation are dependent on retinoid signalling. In this retinoid deficient condition, FGF signalling persists ectopically in the elongating body, and importantly, we find that inhibiting FGF receptor (FGFR) signalling in Raldh2−/− embryos does not rescue differentiation gene transcription, but does elicit both chromatin decompaction and nuclear position change. These findings demonstrate that regulation of higher order chromatin organisation during differentiation in the embryo can be uncoupled from the machinery that promotes transcription and, for the first time, identify FGF as an extrinsic signal that can direct chromatin compaction and nuclear organisation of gene loci. Changes in the position of genes within the nucleus and in their local organisation frequently correlate with whether or not genes are turned on. However, little is known about how such nuclear organisation is controlled and whether this can be separated from the mechanisms that promote transcription. We show here that central nuclear position and chromatin de-compaction correlate with onset of expression at key neural differentiation gene loci in the mouse embryo. Conversely, the locus of a gene that is down-regulated as neural differentiation commences exhibits a shift towards the nuclear periphery as this takes place. Importantly, we show that signalling through the fibroblast growth factor (FGF) pathway regulates changes at this level of nuclear organisation. FGF represses differentiation gene transcription and keeps differentiation gene loci compact and at the nuclear periphery. By blocking FGF signalling in a retinoid deficient embryo in which differentiation genes are not expressed, we further show that control of nuclear organisation by FGF is not just a consequence of gene transcription. These findings are the first to demonstrate that such higher order nuclear organisation is regulated in the developing embryo, that this takes place downstream of FGF signaling, and can be uncoupled from the machinery of gene transcription.
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Affiliation(s)
- Nishal S. Patel
- Division of Cell & Developmental Biology, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Muriel Rhinn
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique (UMR 7104), Institut National de la Santé et de la Recherche Médicale (U 964), Université de Strasbourg, Illkirch-Strasbourg, France
| | - Claudia I. Semprich
- Division of Cell & Developmental Biology, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Pamela A. Halley
- Division of Cell & Developmental Biology, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Pascal Dollé
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique (UMR 7104), Institut National de la Santé et de la Recherche Médicale (U 964), Université de Strasbourg, Illkirch-Strasbourg, France
| | - Wendy A. Bickmore
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, United Kingdom
- * E-mail: (WAB); (KGS)
| | - Kate G. Storey
- Division of Cell & Developmental Biology, College of Life Sciences, University of Dundee, Dundee, United Kingdom
- * E-mail: (WAB); (KGS)
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