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Ban M, Bredikhin D, Huang Y, Bonder MJ, Katarzyna K, Oliver AJ, Wilson NK, Coupland P, Hadfield J, Göttgens B, Madissoon E, Stegle O, Sawcer S. Expression profiling of cerebrospinal fluid identifies dysregulated antiviral mechanisms in multiple sclerosis. Brain 2024; 147:554-565. [PMID: 38038362 PMCID: PMC10834244 DOI: 10.1093/brain/awad404] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 08/04/2023] [Revised: 11/06/2023] [Accepted: 11/18/2023] [Indexed: 12/02/2023] Open
Abstract
Despite the overwhelming evidence that multiple sclerosis is an autoimmune disease, relatively little is known about the precise nature of the immune dysregulation underlying the development of the disease. Reasoning that the CSF from patients might be enriched for cells relevant in pathogenesis, we have completed a high-resolution single-cell analysis of 96 732 CSF cells collected from 33 patients with multiple sclerosis (n = 48 675) and 48 patients with other neurological diseases (n = 48 057). Completing comprehensive cell type annotation, we identified a rare population of CD8+ T cells, characterized by the upregulation of inhibitory receptors, increased in patients with multiple sclerosis. Applying a Multi-Omics Factor Analysis to these single-cell data further revealed that activity in pathways responsible for controlling inflammatory and type 1 interferon responses are altered in multiple sclerosis in both T cells and myeloid cells. We also undertook a systematic search for expression quantitative trait loci in the CSF cells. Of particular interest were two expression quantitative trait loci in CD8+ T cells that were fine mapped to multiple sclerosis susceptibility variants in the viral control genes ZC3HAV1 (rs10271373) and IFITM2 (rs1059091). Further analysis suggests that these associations likely reflect genetic effects on RNA splicing and cell-type specific gene expression respectively. Collectively, our study suggests that alterations in viral control mechanisms might be important in the development of multiple sclerosis.
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Affiliation(s)
- Maria Ban
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Danila Bredikhin
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Yuanhua Huang
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge CB10 1SD, UK
| | - Marc Jan Bonder
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Kania Katarzyna
- University of Cambridge, CRUK Cambridge Institute, Cambridge CB2 0RE, UK
| | - Amanda J Oliver
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Nicola K Wilson
- Department of Haematology, University of Cambridge, Cambridge CB2 0AW, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Paul Coupland
- University of Cambridge, CRUK Cambridge Institute, Cambridge CB2 0RE, UK
| | - James Hadfield
- University of Cambridge, CRUK Cambridge Institute, Cambridge CB2 0RE, UK
| | - Berthold Göttgens
- Department of Haematology, University of Cambridge, Cambridge CB2 0AW, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Elo Madissoon
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge CB10 1SD, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Oliver Stegle
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge CB10 1SD, UK
| | - Stephen Sawcer
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
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2
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Barmada A, Handfield LF, Godoy-Tena G, de la Calle-Fabregat C, Ciudad L, Arutyunyan A, Andrés-León E, Hoo R, Porter T, Oszlanczi A, Richardson L, Calero-Nieto FJ, Wilson NK, Marchese D, Sancho-Serra C, Carrillo J, Presas-Rodríguez S, Ramo-Tello C, Ruiz-Sanmartin A, Ferrer R, Ruiz-Rodriguez JC, Martínez-Gallo M, Munera-Campos M, Carrascosa JM, Göttgens B, Heyn H, Prigmore E, Casafont-Solé I, Solanich X, Sánchez-Cerrillo I, González-Álvaro I, Raimondo MG, Ramming A, Martin J, Martínez-Cáceres E, Ballestar E, Vento-Tormo R, Rodríguez-Ubreva J. Single-cell multi-omics analysis of COVID-19 patients with pre-existing autoimmune diseases shows aberrant immune responses to infection. Eur J Immunol 2024; 54:e2350633. [PMID: 37799110 DOI: 10.1002/eji.202350633] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 06/28/2023] [Revised: 09/29/2023] [Accepted: 10/03/2023] [Indexed: 10/07/2023]
Abstract
In COVID-19, hyperinflammatory and dysregulated immune responses contribute to severity. Patients with pre-existing autoimmune conditions can therefore be at increased risk of severe COVID-19 and/or associated sequelae, yet SARS-CoV-2 infection in this group has been little studied. Here, we performed single-cell analysis of peripheral blood mononuclear cells from patients with three major autoimmune diseases (rheumatoid arthritis, psoriasis, or multiple sclerosis) during SARS-CoV-2 infection. We observed compositional differences between the autoimmune disease groups coupled with altered patterns of gene expression, transcription factor activity, and cell-cell communication that substantially shape the immune response under SARS-CoV-2 infection. While enrichment of HLA-DRlow CD14+ monocytes was observed in all three autoimmune disease groups, type-I interferon signaling as well as inflammatory T cell and monocyte responses varied widely between the three groups of patients. Our results reveal disturbed immune responses to SARS-CoV-2 in patients with pre-existing autoimmunity, highlighting important considerations for disease treatment and follow-up.
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Affiliation(s)
- Anis Barmada
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
- Department of Medical Genetics, University of Cambridge, Cambridge, United Kingdom
| | | | - Gerard Godoy-Tena
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Barcelona, Spain
| | | | - Laura Ciudad
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Barcelona, Spain
| | - Anna Arutyunyan
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Eduardo Andrés-León
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Regina Hoo
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Tarryn Porter
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Agnes Oszlanczi
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Laura Richardson
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Fernando J Calero-Nieto
- Department of Haematology and Wellcome & MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Nicola K Wilson
- Department of Haematology and Wellcome & MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Domenica Marchese
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Carmen Sancho-Serra
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Jorge Carrillo
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, Badalona, Spain
| | - Silvia Presas-Rodríguez
- MS Unit, Department of Neurology, Germans Trias i Pujol University Hospital, Barcelona, Spain
| | - Cristina Ramo-Tello
- MS Unit, Department of Neurology, Germans Trias i Pujol University Hospital, Barcelona, Spain
| | - Adolfo Ruiz-Sanmartin
- Department of Intensive Care, Hospital Universitari Vall d'Hebron, Shock, Organ Dysfunction and Resuscitation Research Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Ricard Ferrer
- Department of Intensive Care, Hospital Universitari Vall d'Hebron, Shock, Organ Dysfunction and Resuscitation Research Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Juan Carlos Ruiz-Rodriguez
- Department of Intensive Care, Hospital Universitari Vall d'Hebron, Shock, Organ Dysfunction and Resuscitation Research Group, Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Mónica Martínez-Gallo
- Division of Immunology, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Mónica Munera-Campos
- Dermatology Service, Germans Trias i Pujol University Hospital, LCMN, Germans Trias i Pujol Research Institute (IGTP), Barcelona, Spain
| | - Jose Manuel Carrascosa
- Dermatology Service, Germans Trias i Pujol University Hospital, LCMN, Germans Trias i Pujol Research Institute (IGTP), Barcelona, Spain
| | - Berthold Göttgens
- Department of Haematology and Wellcome & MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Holger Heyn
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Elena Prigmore
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Ivette Casafont-Solé
- Department of Rheumatology, Germans Trias i Pujol University Hospital, LCMN, Germans Trias i Pujol Research Institute (IGTP), Barcelona, Spain
- Department of Infectious Diseases, Germans Trias i Pujol University Hospital, Barcelona, Spain
| | - Xavier Solanich
- Department of Internal Medicine, Hospital Universitari de Bellvitge, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | | | | | - Maria Gabriella Raimondo
- Department of Internal Medicine 3, Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Andreas Ramming
- Department of Internal Medicine 3, Friedrich-Alexander-University Erlangen-Nürnberg (FAU) and Universitätsklinikum Erlangen, Erlangen, Germany
- Deutsches Zentrum Immuntherapie (DZI), Friedrich-Alexander-University Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Javier Martin
- Instituto de Parasitología y Biomedicina López-Neyra, Consejo Superior de Investigaciones Científicas (IPBLN-CSIC), Granada, Spain
| | - Eva Martínez-Cáceres
- Division of Immunology, Germans Trias i Pujol University Hospital, LCMN, Germans Trias i Pujol Research Institute (IGTP), Barcelona, Spain
- Department of Cell Biology, Physiology, and Immunology, Universitat Autònoma, Barcelona, Spain
| | - Esteban Ballestar
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Barcelona, Spain
| | - Roser Vento-Tormo
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Javier Rodríguez-Ubreva
- Epigenetics and Immune Disease Group, Josep Carreras Research Institute (IJC), Barcelona, Spain
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3
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Isobe T, Kucinski I, Barile M, Wang X, Hannah R, Bastos HP, Chabra S, Vijayabaskar M, Sturgess KH, Williams MJ, Giotopoulos G, Marando L, Li J, Rak J, Gozdecka M, Prins D, Shepherd MS, Watcham S, Green AR, Kent DG, Vassiliou GS, Huntly BJ, Wilson NK, Göttgens B. Preleukemic single-cell landscapes reveal mutation-specific mechanisms and gene programs predictive of AML patient outcomes. Cell Genom 2023; 3:100426. [PMID: 38116120 PMCID: PMC10726426 DOI: 10.1016/j.xgen.2023.100426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 07/13/2023] [Accepted: 09/29/2023] [Indexed: 12/21/2023]
Abstract
Acute myeloid leukemia (AML) and myeloid neoplasms develop through acquisition of somatic mutations that confer mutation-specific fitness advantages to hematopoietic stem and progenitor cells. However, our understanding of mutational effects remains limited to the resolution attainable within immunophenotypically and clinically accessible bulk cell populations. To decipher heterogeneous cellular fitness to preleukemic mutational perturbations, we performed single-cell RNA sequencing of eight different mouse models with driver mutations of myeloid malignancies, generating 269,048 single-cell profiles. Our analysis infers mutation-driven perturbations in cell abundance, cellular lineage fate, cellular metabolism, and gene expression at the continuous resolution, pinpointing cell populations with transcriptional alterations associated with differentiation bias. We further develop an 11-gene scoring system (Stem11) on the basis of preleukemic transcriptional signatures that predicts AML patient outcomes. Our results demonstrate that a single-cell-resolution deep characterization of preleukemic biology has the potential to enhance our understanding of AML heterogeneity and inform more effective risk stratification strategies.
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Affiliation(s)
- Tomoya Isobe
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Iwo Kucinski
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Melania Barile
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Xiaonan Wang
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Rebecca Hannah
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Hugo P. Bastos
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Shirom Chabra
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - M.S. Vijayabaskar
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Katherine H.M. Sturgess
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Matthew J. Williams
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - George Giotopoulos
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Ludovica Marando
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Juan Li
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Justyna Rak
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
- Hematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Malgorzata Gozdecka
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
- Hematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Daniel Prins
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Mairi S. Shepherd
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Sam Watcham
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Anthony R. Green
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - David G. Kent
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
- York Biomedical Research Institute, Department of Biology, University of York, York, UK
| | - George S. Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
- Hematological Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Brian J.P. Huntly
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Nicola K. Wilson
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
| | - Berthold Göttgens
- Wellcome-MRC Cambridge Stem Cell Institute, Department of Hematology, University of Cambridge, Cambridge, UK
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4
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Sturgess K, Yankova E, Vijayabaskar MS, Isobe T, Rak J, Kucinski I, Barile M, Webster NA, Eleftheriou M, Hannah R, Gozdecka M, Vassiliou G, Rausch O, Wilson NK, Göttgens B, Tzelepis K. Pharmacological inhibition of METTL3 impacts specific haematopoietic lineages. Leukemia 2023; 37:2133-2137. [PMID: 37464070 PMCID: PMC10539174 DOI: 10.1038/s41375-023-01965-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/21/2023] [Accepted: 06/29/2023] [Indexed: 07/20/2023]
Affiliation(s)
- Katherine Sturgess
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW, UK
- Department of Haematology, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Eliza Yankova
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW, UK
- Department of Haematology, University of Cambridge, Cambridge, CB2 0AW, UK
- Milner Therapeutics Institute, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - M S Vijayabaskar
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW, UK
- Department of Haematology, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Tomoya Isobe
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW, UK
- Department of Haematology, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Justyna Rak
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW, UK
- Department of Haematology, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Iwo Kucinski
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW, UK
- Department of Haematology, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Melania Barile
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW, UK
- Department of Haematology, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Natalie A Webster
- Storm Therapeutics Ltd, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Maria Eleftheriou
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW, UK
- Department of Haematology, University of Cambridge, Cambridge, CB2 0AW, UK
- Milner Therapeutics Institute, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK
| | - Rebecca Hannah
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW, UK
- Department of Haematology, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Malgorzata Gozdecka
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW, UK
- Department of Haematology, University of Cambridge, Cambridge, CB2 0AW, UK
| | - George Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW, UK
- Department of Haematology, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Oliver Rausch
- Storm Therapeutics Ltd, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Nicola K Wilson
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW, UK
- Department of Haematology, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Berthold Göttgens
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW, UK.
- Department of Haematology, University of Cambridge, Cambridge, CB2 0AW, UK.
| | - Konstantinos Tzelepis
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW, UK.
- Department of Haematology, University of Cambridge, Cambridge, CB2 0AW, UK.
- Milner Therapeutics Institute, University of Cambridge, Puddicombe Way, Cambridge, CB2 0AW, UK.
- Experimental Cancer Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.
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5
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Goh I, Botting RA, Rose A, Webb S, Engelbert J, Gitton Y, Stephenson E, Londoño MQ, Mather M, Mende N, Imaz-Rosshandler I, Yang L, Horsfall D, Basurto-Lozada D, Chipampe NJ, Rook V, Lee JTH, Ton ML, Keitley D, Mazin P, Vijayabaskar M, Hannah R, Gambardella L, Green K, Ballereau S, Inoue M, Tuck E, Lorenzi V, Kwakwa K, Alsinet C, Olabi B, Miah M, Admane C, Popescu DM, Acres M, Dixon D, Ness T, Coulthard R, Lisgo S, Henderson DJ, Dann E, Suo C, Kinston SJ, Park JE, Polanski K, Marioni J, van Dongen S, Meyer KB, de Bruijn M, Palis J, Behjati S, Laurenti E, Wilson NK, Vento-Tormo R, Chédotal A, Bayraktar O, Roberts I, Jardine L, Göttgens B, Teichmann SA, Haniffa M. Yolk sac cell atlas reveals multiorgan functions during human early development. Science 2023; 381:eadd7564. [PMID: 37590359 PMCID: PMC7614978 DOI: 10.1126/science.add7564] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 07/03/2023] [Indexed: 08/19/2023]
Abstract
The extraembryonic yolk sac (YS) ensures delivery of nutritional support and oxygen to the developing embryo but remains ill-defined in humans. We therefore assembled a comprehensive multiomic reference of the human YS from 3 to 8 postconception weeks by integrating single-cell protein and gene expression data. Beyond its recognized role as a site of hematopoiesis, we highlight roles in metabolism, coagulation, vascular development, and hematopoietic regulation. We reconstructed the emergence and decline of YS hematopoietic stem and progenitor cells from hemogenic endothelium and revealed a YS-specific accelerated route to macrophage production that seeds developing organs. The multiorgan functions of the YS are superseded as intraembryonic organs develop, effecting a multifaceted relay of vital functions as pregnancy proceeds.
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Affiliation(s)
- Issac Goh
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | - Rachel A. Botting
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | - Antony Rose
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | - Simone Webb
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | | | - Yorick Gitton
- Sorbonne Université, INSERM, CNRS, Institut de la Vision,
Paris, France
| | - Emily Stephenson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | | | - Michael Mather
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | - Nicole Mende
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell
Institute, CB2 0AW, UK
| | - Ivan Imaz-Rosshandler
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell
Institute, CB2 0AW, UK
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus,
CD2 0QH, UK
| | - Lu Yang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Dave Horsfall
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | - Daniela Basurto-Lozada
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | - Nana-Jane Chipampe
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Victoria Rook
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Jimmy Tsz Hang Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Mai-Linh Ton
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell
Institute, CB2 0AW, UK
| | - Daniel Keitley
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Department of Zoology, University of Cambridge, Cambridge UK
| | - Pavel Mazin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - M.S. Vijayabaskar
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell
Institute, CB2 0AW, UK
| | - Rebecca Hannah
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell
Institute, CB2 0AW, UK
| | - Laure Gambardella
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Kile Green
- Translational and Clinical Research Institute, Newcastle University,
NE2 4HH, UK
| | - Stephane Ballereau
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Megumi Inoue
- Sorbonne Université, INSERM, CNRS, Institut de la Vision,
Paris, France
| | - Elizabeth Tuck
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Valentina Lorenzi
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Kwasi Kwakwa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Clara Alsinet
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Centre Nacional d’Analisi Genomica-Centre de Regulacio
Genomica (CNAG-CRG), Barcelona Institute of Science and Technology (BIST),
Barcelona, Spain
| | - Bayanne Olabi
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | - Mohi Miah
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | - Chloe Admane
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | | | - Meghan Acres
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | - David Dixon
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | - Thomas Ness
- NovoPath, Department of Pathology, Newcastle Hospitals NHS
Foundation Trust, Newcastle upon Tyne, UK
| | - Rowen Coulthard
- NovoPath, Department of Pathology, Newcastle Hospitals NHS
Foundation Trust, Newcastle upon Tyne, UK
| | - Steven Lisgo
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | | | - Emma Dann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Chenqu Suo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Sarah J. Kinston
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell
Institute, CB2 0AW, UK
| | - Jong-eun Park
- Korea Advanced Institute of Science and Technology, Daejeon, South
Korea
| | - Krzysztof Polanski
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - John Marioni
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- EMBL-EBI, Wellcome Genome Campus, Cambridge, UK
- CRUK Cambridge Institute, University of Cambridge, Cambridge,
UK
| | - Stijn van Dongen
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Kerstin B. Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Marella de Bruijn
- MRC Molecular Haematology Unit, MRC Weatherall Institute of
Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, OX3 9DS,
UK
| | - James Palis
- Department of Pediatrics, University of Rochester Medical Center,
Rochester, 14642, NY, USA
| | - Sam Behjati
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Department of Paediatrics, University of Cambridge, Cambridge,
UK
| | - Elisa Laurenti
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell
Institute, CB2 0AW, UK
| | - Nicola K. Wilson
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell
Institute, CB2 0AW, UK
| | - Roser Vento-Tormo
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Alain Chédotal
- Sorbonne Université, INSERM, CNRS, Institut de la Vision,
Paris, France
| | - Omer Bayraktar
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
| | - Irene Roberts
- Department of Paediatrics, University of Oxford, OX3 9DS, UK
| | - Laura Jardine
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Biosciences Institute, Newcastle University, NE2 4HH, UK
| | - Berthold Göttgens
- Department of Haematology, Wellcome-MRC Cambridge Stem Cell
Institute, CB2 0AW, UK
| | - Sarah A. Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Theory of Condensed Matter Group, Cavendish Laboratory/Department
of Physics, University of Cambridge, Cambridge, UK
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton,
Cambridge CB10 1SA, UK
- Biosciences Institute, Newcastle University, NE2 4HH, UK
- Department of Dermatology and NIHR Newcastle Biomedical Research
Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE1 4LP,
UK
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6
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Wang M, Brandt LTL, Wang X, Russell H, Mitchell E, Kamimae-Lanning AN, Brown JM, Dingler FA, Garaycoechea JI, Isobe T, Kinston SJ, Gu M, Vassiliou GS, Wilson NK, Göttgens B, Patel KJ. Genotoxic aldehyde stress prematurely ages hematopoietic stem cells in a p53-driven manner. Mol Cell 2023; 83:2417-2433.e7. [PMID: 37348497 PMCID: PMC7614878 DOI: 10.1016/j.molcel.2023.05.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 08/01/2022] [Revised: 04/18/2023] [Accepted: 05/25/2023] [Indexed: 06/24/2023]
Abstract
Aged hematopoietic stem cells (HSCs) display diminished self-renewal and a myeloid differentiation bias. However, the drivers and mechanisms that underpin this fundamental switch are not understood. HSCs produce genotoxic formaldehyde that requires protection by the detoxification enzymes ALDH2 and ADH5 and the Fanconi anemia (FA) DNA repair pathway. We find that the HSCs in young Aldh2-/-Fancd2-/- mice harbor a transcriptomic signature equivalent to aged wild-type HSCs, along with increased epigenetic age, telomere attrition, and myeloid-biased differentiation quantified by single HSC transplantation. In addition, the p53 response is vigorously activated in Aldh2-/-Fancd2-/- HSCs, while p53 deletion rescued this aged HSC phenotype. To further define the origins of the myeloid differentiation bias, we use a GFP genetic reporter to find a striking enrichment of Vwf+ myeloid and megakaryocyte-lineage-biased HSCs. These results indicate that metabolism-derived formaldehyde-DNA damage stimulates the p53 response in HSCs to drive accelerated aging.
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Affiliation(s)
- Meng Wang
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA; Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK; MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK.
| | - Laura T L Brandt
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
| | - Xiaonan Wang
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK; School of Public Health, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Holly Russell
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Emily Mitchell
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK; Wellcome Sanger Institute, Hinxton, UK
| | - Ashley N Kamimae-Lanning
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Jill M Brown
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Felix A Dingler
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Juan I Garaycoechea
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center, Utrecht, the Netherlands
| | - Tomoya Isobe
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Sarah J Kinston
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Muxin Gu
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - George S Vassiliou
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Nicola K Wilson
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Berthold Göttgens
- Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Ketan J Patel
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK.
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7
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Li J, Williams MJ, Park HJ, Bastos HP, Wang X, Prins D, Wilson NK, Johnson C, Sham K, Wantoch M, Watcham S, Kinston SJ, Pask DC, Hamilton TL, Sneade R, Waller AK, Ghevaert C, Vassiliou GS, Laurenti E, Kent DG, Göttgens B, Green AR. STAT1 is essential for HSC function and maintains MHCIIhi stem cells that resist myeloablation and neoplastic expansion. Blood 2022; 140:1592-1606. [PMID: 35767701 PMCID: PMC7614316 DOI: 10.1182/blood.2021014009] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 04/21/2022] [Indexed: 02/02/2023] Open
Abstract
Adult hematopoietic stem cells (HSCs) are predominantly quiescent and can be activated in response to acute stress such as infection or cytotoxic insults. STAT1 is a pivotal downstream mediator of interferon (IFN) signaling and is required for IFN-induced HSC proliferation, but little is known about the role of STAT1 in regulating homeostatic hematopoietic stem/progenitor cells (HSPCs). Here, we show that loss of STAT1 altered the steady state HSPC landscape, impaired HSC function in transplantation assays, delayed blood cell regeneration following myeloablation, and disrupted molecular programs that protect HSCs, including control of quiescence. Our results also reveal STAT1-dependent functional HSC heterogeneity. A previously unrecognized subset of homeostatic HSCs with elevated major histocompatibility complex class II (MHCII) expression (MHCIIhi) displayed molecular features of reduced cycling and apoptosis and was refractory to 5-fluorouracil-induced myeloablation. Conversely, MHCIIlo HSCs displayed increased megakaryocytic potential and were preferentially expanded in CALR mutant mice with thrombocytosis. Similar to mice, high MHCII expression is a feature of human HSCs residing in a deeper quiescent state. Our results therefore position STAT1 at the interface of stem cell heterogeneity and the interplay between stem cells and the adaptive immune system, areas of broad interest in the wider stem cell field.
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Affiliation(s)
- Juan Li
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Matthew J. Williams
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Hyun Jung Park
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Hugo P. Bastos
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Xiaonan Wang
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Daniel Prins
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Nicola K. Wilson
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Carys Johnson
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Kendig Sham
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Michelle Wantoch
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Sam Watcham
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Sarah J. Kinston
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Dean C. Pask
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Tina L. Hamilton
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Rachel Sneade
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Amie K. Waller
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Cedric Ghevaert
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - George S. Vassiliou
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Elisa Laurenti
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - David G. Kent
- Department of Biology, University of York, York, United Kingdom
| | - Berthold Göttgens
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Anthony R. Green
- Wellcome–Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
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8
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Wu C, Boey D, Bril O, Grootens J, Vijayabaskar M, Sorini C, Ekoff M, Wilson NK, Ungerstedt JS, Nilsson G, Dahlin JS. Single-cell transcriptomics reveals the identity and regulators of human mast cell progenitors. Blood Adv 2022; 6:4439-4449. [PMID: 35500226 PMCID: PMC9636317 DOI: 10.1182/bloodadvances.2022006969] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 01/03/2022] [Accepted: 04/15/2022] [Indexed: 11/20/2022] Open
Abstract
Mast cell accumulation is a hallmark of a number of diseases, including allergic asthma and systemic mastocytosis. Immunoglobulin E-mediated crosslinking of the FcεRI receptors causes mast cell activation and contributes to disease pathogenesis. The mast cell lineage is one of the least studied among the hematopoietic cell lineages, and controversies remain about whether FcεRI expression appears during the mast cell progenitor stage or during terminal mast cell maturation. Here, we used single-cell transcriptomics analysis to reveal a temporal association between the appearance of FcεRI and the mast cell gene signature in CD34+ hematopoietic progenitors in adult peripheral blood. In agreement with these data, the FcεRI+ hematopoietic progenitors formed morphologically, phenotypically, and functionally mature mast cells in long-term culture assays. Single-cell transcriptomics analysis further revealed the expression patterns of prospective cytokine receptors regulating development of mast cell progenitors. Culture assays showed that interleukin-3 (IL-3) and IL-5 promoted disparate effects on progenitor cell proliferation and survival, respectively, whereas IL-33 caused robust FcεRI downregulation. Taken together, we showed that FcεRI expression appears at the progenitor stage of mast cell differentiation in peripheral blood. We also showed that external stimuli regulate FcεRI expression of mast cell progenitors, providing a possible explanation for the variable FcεRI expression levels during mast cell development.
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Affiliation(s)
- Chenyan Wu
- Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Daryl Boey
- Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Oscar Bril
- Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Jennine Grootens
- Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - M.S. Vijayabaskar
- Department of Haematology, Jeffrey Cheah Biomedical Centre, Wellcome–MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Chiara Sorini
- Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Maria Ekoff
- Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Nicola K. Wilson
- Department of Haematology, Jeffrey Cheah Biomedical Centre, Wellcome–MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Johanna S. Ungerstedt
- Hematology and Regenerative Medicine, HERM, Department of Medicine Huddinge, Karolinska Institutet and ME Hematology, Karolinska University Hospital, Stockholm, Sweden
| | - Gunnar Nilsson
- Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Joakim S. Dahlin
- Department of Medicine Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
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9
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Zaidan N, Nitsche L, Diamanti E, Hannah R, Fidanza A, Wilson NK, Forrester LM, Göttgens B, Ottersbach K. Endothelial-specific Gata3 expression is required for hematopoietic stem cell generation. Stem Cell Reports 2022; 17:1788-1798. [PMID: 35905741 PMCID: PMC9391417 DOI: 10.1016/j.stemcr.2022.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 11/01/2021] [Revised: 06/23/2022] [Accepted: 06/27/2022] [Indexed: 11/23/2022] Open
Abstract
To generate sufficient numbers of transplantable hematopoietic stem cells (HSCs) in vitro, a detailed understanding of how this process takes place in vivo is essential. The endothelial-to-hematopoietic transition (EHT), which culminates in the production of the first HSCs, is a highly complex process during which key regulators are switched on and off at precise moments, and that is embedded into a myriad of microenvironmental signals from surrounding cells and tissues. We have previously demonstrated an HSC-supportive function for GATA3 within the sympathetic nervous system and the sub-aortic mesenchyme, but show here that it also plays a cell-intrinsic role during the EHT. It is expressed in hemogenic endothelial cells and early HSC precursors, where its expression correlates with a more quiescent state. Importantly, endothelial-specific deletion of Gata3 shows that it is functionally required for these cells to mature into HSCs, placing GATA3 at the core of the EHT regulatory network.
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Affiliation(s)
- Nada Zaidan
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK; Department of Haematology, Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Leslie Nitsche
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Evangelia Diamanti
- Department of Haematology, Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Rebecca Hannah
- Department of Haematology, Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Antonella Fidanza
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Nicola K Wilson
- Department of Haematology, Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Lesley M Forrester
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK
| | - Berthold Göttgens
- Department of Haematology, Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Katrin Ottersbach
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh EH16 4UU, UK.
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10
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Kapeni C, Nitsche L, Kilpatrick AM, Wilson NK, Xia K, Mirshekar-Syahkal B, Chandrakanthan V, Malouf C, Pimanda JE, Göttgens B, Kirschner K, Tomlinson SR, Ottersbach K. p57Kip2 regulates embryonic blood stem cells by controlling sympathoadrenal progenitor expansion. Blood 2022; 140:464-477. [PMID: 35653588 PMCID: PMC9353151 DOI: 10.1182/blood.2021014853] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 11/15/2021] [Accepted: 05/13/2022] [Indexed: 11/20/2022] Open
Abstract
Hematopoietic stem cells (HSCs) are of major clinical importance, and finding methods for their in vitro generation is a prime research focus. We show here that the cell cycle inhibitor p57Kip2/Cdkn1c limits the number of emerging HSCs by restricting the size of the sympathetic nervous system (SNS) and the amount of HSC-supportive catecholamines secreted by these cells. This regulation occurs at the SNS progenitor level and is in contrast to the cell-intrinsic function of p57Kip2 in maintaining adult HSCs, highlighting profound differences in cell cycle requirements of adult HSCs compared with their embryonic counterparts. Furthermore, this effect is specific to the aorta-gonad-mesonephros (AGM) region and shows that the AGM is the main contributor to early fetal liver colonization, as early fetal liver HSC numbers are equally affected. Using a range of antagonists in vivo, we show a requirement for intact β2-adrenergic signaling for SNS-dependent HSC expansion. To gain further molecular insights, we have generated a single-cell RNA-sequencing data set of all Ngfr+ sympathoadrenal cells around the dorsal aorta to dissect their differentiation pathway. Importantly, this not only defined the relevant p57Kip2-expressing SNS progenitor stage but also revealed that some neural crest cells, upon arrival at the aorta, are able to take an alternative differentiation pathway, giving rise to a subset of ventrally restricted mesenchymal cells that express important HSC-supportive factors. Neural crest cells thus appear to contribute to the AGM HSC niche via 2 different mechanisms: SNS-mediated catecholamine secretion and HSC-supportive mesenchymal cell production.
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Affiliation(s)
- Chrysa Kapeni
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, United Kingdom
| | - Leslie Nitsche
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, United Kingdom
| | - Alastair M Kilpatrick
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, United Kingdom
| | - Nicola K Wilson
- Department of Haematology, Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Kankan Xia
- Department of Haematology, Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Bahar Mirshekar-Syahkal
- Department of Haematology, Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Vashe Chandrakanthan
- School of Medical Sciences, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia
| | - Camille Malouf
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, United Kingdom
| | - John E Pimanda
- School of Medical Sciences, Lowy Cancer Research Centre, UNSW, Sydney, NSW, Australia
- Department of Haematology, The Prince of Wales Hospital, Sydney, NSW, Australia
| | - Berthold Göttgens
- Department of Haematology, Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Kristina Kirschner
- Institute of Cancer Sciences and
- CRUK Beatson Institute for Cancer Research, University of Glasgow, Glasgow, United Kingdom
| | - Simon R Tomlinson
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, United Kingdom
| | - Katrin Ottersbach
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, Edinburgh, United Kingdom
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11
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Mende N, Bastos HP, Santoro A, Mahbubani KT, Ciaurro V, Calderbank EF, Londoño MQ, Sham K, Mantica G, Morishima T, Mitchell E, Lidonnici MR, Meier-Abt F, Hayler D, Jardine L, Curd A, Haniffa M, Ferrari G, Takizawa H, Wilson NK, Göttgens B, Saeb-Parsy K, Frontini M, Laurenti E. Unique molecular and functional features of extramedullary hematopoietic stem and progenitor cell reservoirs in humans. Blood 2022; 139:3387-3401. [PMID: 35073399 PMCID: PMC7612845 DOI: 10.1182/blood.2021013450] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [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: 07/23/2021] [Accepted: 01/05/2022] [Indexed: 02/02/2023] Open
Abstract
Rare hematopoietic stem and progenitor cell (HSPC) pools outside the bone marrow (BM) contribute to blood production in stress and disease but remain ill-defined. Although nonmobilized peripheral blood (PB) is routinely sampled for clinical management, the diagnosis and monitoring potential of PB HSPCs remain untapped, as no healthy PB HSPC baseline has been reported. Here we comprehensively delineate human extramedullary HSPC compartments comparing spleen, PB, and mobilized PB to BM using single-cell RNA-sequencing and/or functional assays. We uncovered HSPC features shared by extramedullary tissues and others unique to PB. First, in contrast to actively dividing BM HSPCs, we found no evidence of substantial ongoing hematopoiesis in extramedullary tissues at steady state but report increased splenic HSPC proliferative output during stress erythropoiesis. Second, extramedullary hematopoietic stem cells/multipotent progenitors (HSCs/MPPs) from spleen, PB, and mobilized PB share a common transcriptional signature and increased abundance of lineage-primed subsets compared with BM. Third, healthy PB HSPCs display a unique bias toward erythroid-megakaryocytic differentiation. At the HSC/MPP level, this is functionally imparted by a subset of phenotypic CD71+ HSCs/MPPs, exclusively producing erythrocytes and megakaryocytes, highly abundant in PB but rare in other adult tissues. Finally, the unique erythroid-megakaryocytic-skewing of PB is perturbed with age in essential thrombocythemia and β-thalassemia. Collectively, we identify extramedullary lineage-primed HSPC reservoirs that are nonproliferative in situ and report involvement of splenic HSPCs during demand-adapted hematopoiesis. Our data also establish aberrant composition and function of circulating HSPCs as potential clinical indicators of BM dysfunction.
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Affiliation(s)
- Nicole Mende
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Hugo P. Bastos
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Antonella Santoro
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Krishnaa T. Mahbubani
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Haematology and Cambridge NIHR Biomedical Research Centre, Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Valerio Ciaurro
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Emily F. Calderbank
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Mariana Quiroga Londoño
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Kendig Sham
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Giovanna Mantica
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Tatsuya Morishima
- Laboratory of Stem Cell Stress, International Research Centre for Medical Sciences, and Centre for Metabolic Regulation of Healthy Aging, Kumamoto University, Kumamoto, Japan
- Laboratory of Hematopoietic Stem Cell Engineering, International Research Center for Medical Sciences, Kumamoto University, 860-0811 Kumamoto, Japan
| | - Emily Mitchell
- Cancer, Ageing and Somatic Mutation Group, Wellcome Sanger Institute, Hinxton, UK
| | - Maria Rosa Lidonnici
- San Raffaele-Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Fabienne Meier-Abt
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
- Institute of Molecular Systems Biology (IMSB), ETH Zurich, Zurich, Switzerland
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Daniel Hayler
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Laura Jardine
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
- Haematology Department, Freeman Hospital, Newcastle-upon-Tyne Hospitals NHS Foundation Trust, Newcastle-upon-Tyne, NE7 7DN, UK
| | - Abbie Curd
- Department of Surgery and Cambridge NIHR Biomedical Research Centre, Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Muzlifah Haniffa
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
- Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
| | - Giuliana Ferrari
- San Raffaele-Telethon Institute for Gene Therapy (SR-TIGET), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Hitoshi Takizawa
- Laboratory of Stem Cell Stress, International Research Centre for Medical Sciences, and Centre for Metabolic Regulation of Healthy Aging, Kumamoto University, Kumamoto, Japan
| | - Nicola K. Wilson
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Berthold Göttgens
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Kourosh Saeb-Parsy
- Department of Surgery and Cambridge NIHR Biomedical Research Centre, Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Mattia Frontini
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Institute of Biomedical & Clinical Science, College of Medicine and Health, University of Exeter Medical School, Exeter, UK
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- British Heart Foundation Centre of Excellence, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Elisa Laurenti
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
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12
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Wang J, Kotagiri P, Lyons PA, Al-Lamki RS, Mescia F, Bergamaschi L, Turner L, Morgan MD, Calero-Nieto FJ, Bach K, Mende N, Wilson NK, Watts ER, Maxwell PH, Chinnery PF, Kingston N, Papadia S, Stirrups KE, Walker N, Gupta RK, Menon DK, Allinson K, Aitken SJ, Toshner M, Weekes MP, Nathan JA, Walmsley SR, Ouwehand WH, Kasanicki M, Göttgens B, Marioni JC, Smith KG, Pober JS, Bradley JR. Coagulation factor V is a T-cell inhibitor expressed by leukocytes in COVID-19. iScience 2022; 25:103971. [PMID: 35224470 PMCID: PMC8863325 DOI: 10.1016/j.isci.2022.103971] [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] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/24/2022] [Accepted: 02/17/2022] [Indexed: 12/21/2022] Open
Abstract
Clotting Factor V (FV) is primarily synthesized in the liver and when cleaved by thrombin forms pro-coagulant Factor Va (FVa). Using whole blood RNAseq and scRNAseq of peripheral blood mononuclear cells, we find that FV mRNA is expressed in leukocytes, and identify neutrophils, monocytes, and T regulatory cells as sources of increased FV in hospitalized patients with COVID-19. Proteomic analysis confirms increased FV in circulating neutrophils in severe COVID-19, and immunofluorescence microscopy identifies FV in lung-infiltrating leukocytes in COVID-19 lung disease. Increased leukocyte FV expression in severe disease correlates with T-cell lymphopenia. Both plasma-derived and a cleavage resistant recombinant FV, but not thrombin cleaved FVa, suppress T-cell proliferation in vitro. Anticoagulants that reduce FV conversion to FVa, including heparin, may have the unintended consequence of suppressing the adaptive immune system.
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Affiliation(s)
- Jun Wang
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Box 157, Hills Rd, Cambridge CB2 0QQ, UK
| | - Prasanti Kotagiri
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Box 157, Hills Rd, Cambridge CB2 0QQ, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | - Paul A. Lyons
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Box 157, Hills Rd, Cambridge CB2 0QQ, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | - Rafia S. Al-Lamki
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Box 157, Hills Rd, Cambridge CB2 0QQ, UK
- Cambridge University Hospitals NHS Foundation Trust, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK
| | - Federica Mescia
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Box 157, Hills Rd, Cambridge CB2 0QQ, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | - Laura Bergamaschi
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Box 157, Hills Rd, Cambridge CB2 0QQ, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | - Lorinda Turner
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Box 157, Hills Rd, Cambridge CB2 0QQ, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | - Michael D. Morgan
- Cancer Research UK –Cambridge Institute, Robinson Way, Cambridge CB2 0RE, UK
- Department of Haematology, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Fernando J. Calero-Nieto
- Department of Haematology, Wellcome and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, Cambridgeshire CB2 0AW, UK
| | - Karsten Bach
- Cancer Research UK –Cambridge Institute, Robinson Way, Cambridge CB2 0RE, UK
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK
| | - Nicole Mende
- Department of Haematology, Wellcome and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, Cambridgeshire CB2 0AW, UK
| | - Nicola K. Wilson
- Department of Haematology, Wellcome and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, Cambridgeshire CB2 0AW, UK
| | - Emily R. Watts
- Centre for Inflammation Research, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Cambridge Institute of Therapeutic Immunology and Infectious Disease-National Institute of Health Research (CITIID-NIHR) Covid BioResource Collaboration
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Box 157, Hills Rd, Cambridge CB2 0QQ, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
- Cambridge University Hospitals NHS Foundation Trust, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Cancer Research UK –Cambridge Institute, Robinson Way, Cambridge CB2 0RE, UK
- Department of Haematology, Wellcome and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, Cambridgeshire CB2 0AW, UK
- Department of Pharmacology, University of Cambridge, Cambridge CB2 1PD, UK
- Centre for Inflammation Research, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
- NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
- Department of Haematology, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- Department of Public Health and Primary Care, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Medical Research Council Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR, UK
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
- Royal Papworth Hospital NHS Foundation Trust, Papworth Road, Cambridge CB2 0AY, UK
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
- EMBL-EBI, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Patrick H. Maxwell
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Box 157, Hills Rd, Cambridge CB2 0QQ, UK
| | - Patrick F. Chinnery
- NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0XY, UK
| | - Nathalie Kingston
- NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- Department of Haematology, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Sofia Papadia
- NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- Department of Public Health and Primary Care, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Kathleen E. Stirrups
- NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- Department of Haematology, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Neil Walker
- NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- Department of Haematology, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Ravindra K. Gupta
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Box 157, Hills Rd, Cambridge CB2 0QQ, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | - David K. Menon
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Kieren Allinson
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Sarah J. Aitken
- Cancer Research UK –Cambridge Institute, Robinson Way, Cambridge CB2 0RE, UK
- Department of Histopathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
- Medical Research Council Toxicology Unit, University of Cambridge, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR, UK
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Mark Toshner
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Box 157, Hills Rd, Cambridge CB2 0QQ, UK
- Royal Papworth Hospital NHS Foundation Trust, Papworth Road, Cambridge CB2 0AY, UK
| | - Michael P. Weekes
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Box 157, Hills Rd, Cambridge CB2 0QQ, UK
| | - James A. Nathan
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Box 157, Hills Rd, Cambridge CB2 0QQ, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | - Sarah R. Walmsley
- Centre for Inflammation Research, Queen’s Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Willem H. Ouwehand
- Department of Haematology, Wellcome and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, Cambridgeshire CB2 0AW, UK
- NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
| | - Mary Kasanicki
- Cambridge University Hospitals NHS Foundation Trust, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK
| | - Berthold Göttgens
- Department of Haematology, Wellcome and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, Cambridgeshire CB2 0AW, UK
| | - John C. Marioni
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Cancer Research UK –Cambridge Institute, Robinson Way, Cambridge CB2 0RE, UK
- EMBL-EBI, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Kenneth G.C. Smith
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Box 157, Hills Rd, Cambridge CB2 0QQ, UK
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge CB2 0AW, UK
| | - Jordan S. Pober
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Box 157, Hills Rd, Cambridge CB2 0QQ, UK
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - John R. Bradley
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Box 157, Hills Rd, Cambridge CB2 0QQ, UK
- Cambridge University Hospitals NHS Foundation Trust, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK
- NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
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13
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Mende N, Laurenti E, Göttgens B, Wilson NK. Simultaneous Analysis of Single-Cell Transcriptomes and Cell Surface Protein Expression of Human Hematopoietic Stem Cells and Progenitors Using the 10x Genomics Platform. Methods Mol Biol 2022; 2386:189-201. [PMID: 34766273 DOI: 10.1007/978-1-0716-1771-7_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Indexed: 02/15/2024]
Abstract
The CITE-seq workflow combines conventional single-cell transcriptomic analysis with simultaneous analysis of cell surface protein expression using oligonucleotide-conjugated antibodies. This addition of immunophenotyping to mRNA data allows for a more detailed characterization of single-cell heterogeneity and can help to identify markers for the prospective isolation of transcriptionally defined novel cell subsets. Here, we describe the workflow for the preparation of human cord blood mononuclear cells and CD34+-enriched hematopoietic progenitors for the simultaneous characterization of protein and RNA using the commercially available TotalSeq™ antibodies from BioLegend and the droplet-based single-cell RNA-seq commercial platform from 10x Genomics.
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Affiliation(s)
- Nicole Mende
- Department of Haematology, Wellcome and MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Elisa Laurenti
- Department of Haematology, Wellcome and MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Berthold Göttgens
- Department of Haematology, Wellcome and MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Nicola K Wilson
- Department of Haematology, Wellcome and MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK.
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14
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Hamey FK, Lau WW, Kucinski I, Wang X, Diamanti E, Wilson NK, Göttgens B, Dahlin JS. Single-cell molecular profiling provides a high-resolution map of basophil and mast cell development. Allergy 2021; 76:1731-1742. [PMID: 33078414 PMCID: PMC8246912 DOI: 10.1111/all.14633] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [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: 07/20/2020] [Revised: 09/11/2020] [Accepted: 09/30/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND Basophils and mast cells contribute to the development of allergic reactions. Whereas these mature effector cells are extensively studied, the differentiation trajectories from hematopoietic progenitors to basophils and mast cells are largely uncharted at the single-cell level. METHODS We performed multicolor flow cytometry, high-coverage single-cell RNA sequencing analyses, and cell fate assays to chart basophil and mast cell differentiation at single-cell resolution in mouse. RESULTS Analysis of flow cytometry data reconstructed a detailed map of basophil and mast cell differentiation, including a bifurcation of progenitors into two specific trajectories. Molecular profiling and pseudotime ordering of the single cells revealed gene expression changes during differentiation. Cell fate assays showed that multicolor flow cytometry and transcriptional profiling successfully predict the bipotent phenotype of a previously uncharacterized population of peritoneal basophil-mast cell progenitors. CONCLUSIONS A combination of molecular and functional profiling of bone marrow and peritoneal cells provided a detailed road map of basophil and mast cell development. An interactive web resource was created to enable the wider research community to explore the expression dynamics for any gene of interest.
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Affiliation(s)
- Fiona K. Hamey
- Department of HaematologyWellcome–Medical Research Council Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUK
- Present address: JDRF/Wellcome Diabetes and Inflammation LaboratoryWellcome Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Winnie W.Y. Lau
- Department of HaematologyWellcome–Medical Research Council Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUK
| | - Iwo Kucinski
- Department of HaematologyWellcome–Medical Research Council Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUK
| | - Xiaonan Wang
- Department of HaematologyWellcome–Medical Research Council Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUK
| | - Evangelia Diamanti
- Department of HaematologyWellcome–Medical Research Council Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUK
| | - Nicola K. Wilson
- Department of HaematologyWellcome–Medical Research Council Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUK
| | - Berthold Göttgens
- Department of HaematologyWellcome–Medical Research Council Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUK
| | - Joakim S. Dahlin
- Department of HaematologyWellcome–Medical Research Council Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUK
- Department of MedicineKarolinska Institutet and Karolinska University HospitalStockholmSweden
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15
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Stephenson E, Reynolds G, Botting RA, Calero-Nieto FJ, Morgan MD, Tuong ZK, Bach K, Sungnak W, Worlock KB, Yoshida M, Kumasaka N, Kania K, Engelbert J, Olabi B, Spegarova JS, Wilson NK, Mende N, Jardine L, Gardner LCS, Goh I, Horsfall D, McGrath J, Webb S, Mather MW, Lindeboom RGH, Dann E, Huang N, Polanski K, Prigmore E, Gothe F, Scott J, Payne RP, Baker KF, Hanrath AT, Schim van der Loeff ICD, Barr AS, Sanchez-Gonzalez A, Bergamaschi L, Mescia F, Barnes JL, Kilich E, de Wilton A, Saigal A, Saleh A, Janes SM, Smith CM, Gopee N, Wilson C, Coupland P, Coxhead JM, Kiselev VY, van Dongen S, Bacardit J, King HW, Rostron AJ, Simpson AJ, Hambleton S, Laurenti E, Lyons PA, Meyer KB, Nikolić MZ, Duncan CJA, Smith KGC, Teichmann SA, Clatworthy MR, Marioni JC, Göttgens B, Haniffa M. Single-cell multi-omics analysis of the immune response in COVID-19. Nat Med 2021; 27:904-916. [PMID: 33879890 PMCID: PMC8121667 DOI: 10.1038/s41591-021-01329-2] [Citation(s) in RCA: 317] [Impact Index Per Article: 105.7] [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: 01/15/2021] [Accepted: 03/23/2021] [Indexed: 02/07/2023]
Abstract
Analysis of human blood immune cells provides insights into the coordinated response to viral infections such as severe acute respiratory syndrome coronavirus 2, which causes coronavirus disease 2019 (COVID-19). We performed single-cell transcriptome, surface proteome and T and B lymphocyte antigen receptor analyses of over 780,000 peripheral blood mononuclear cells from a cross-sectional cohort of 130 patients with varying severities of COVID-19. We identified expansion of nonclassical monocytes expressing complement transcripts (CD16+C1QA/B/C+) that sequester platelets and were predicted to replenish the alveolar macrophage pool in COVID-19. Early, uncommitted CD34+ hematopoietic stem/progenitor cells were primed toward megakaryopoiesis, accompanied by expanded megakaryocyte-committed progenitors and increased platelet activation. Clonally expanded CD8+ T cells and an increased ratio of CD8+ effector T cells to effector memory T cells characterized severe disease, while circulating follicular helper T cells accompanied mild disease. We observed a relative loss of IgA2 in symptomatic disease despite an overall expansion of plasmablasts and plasma cells. Our study highlights the coordinated immune response that contributes to COVID-19 pathogenesis and reveals discrete cellular components that can be targeted for therapy.
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Affiliation(s)
- Emily Stephenson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Gary Reynolds
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Rachel A Botting
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | - Michael D Morgan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Zewen Kelvin Tuong
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Karsten Bach
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Waradon Sungnak
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Kaylee B Worlock
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Masahiro Yoshida
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | | | - Katarzyna Kania
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Justin Engelbert
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Bayanne Olabi
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | - Nicola K Wilson
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Nicole Mende
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Laura Jardine
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Louis C S Gardner
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Issac Goh
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Dave Horsfall
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Jim McGrath
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Simone Webb
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Michael W Mather
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | | | - Emma Dann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Ni Huang
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | | | - Elena Prigmore
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Florian Gothe
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Jonathan Scott
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Rebecca P Payne
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Kenneth F Baker
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Aidan T Hanrath
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Infection and Tropical Medicine, Newcastle upon Tyne Hospitals NHS Foundation, Newcastle upon Tyne, UK
| | | | - Andrew S Barr
- Department of Infection and Tropical Medicine, Newcastle upon Tyne Hospitals NHS Foundation, Newcastle upon Tyne, UK
| | - Amada Sanchez-Gonzalez
- Department of Infection and Tropical Medicine, Newcastle upon Tyne Hospitals NHS Foundation, Newcastle upon Tyne, UK
| | - Laura Bergamaschi
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Federica Mescia
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Josephine L Barnes
- UCL Respiratory, Division of Medicine, University College London, London, UK
| | - Eliz Kilich
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Angus de Wilton
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Anita Saigal
- Royal Free Hospital NHS Foundation Trust, London, UK
| | - Aarash Saleh
- Royal Free Hospital NHS Foundation Trust, London, UK
| | - Sam M Janes
- UCL Respiratory, Division of Medicine, University College London, London, UK
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Claire M Smith
- UCL Great Ormond Street Institute of Child Health, London, UK
| | - Nusayhah Gopee
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Dermatology, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Caroline Wilson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
- The Innovation Lab Integrated COVID Hub North East, Newcastle Upon Tyne, UK
| | - Paul Coupland
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | | | | | - Stijn van Dongen
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Jaume Bacardit
- School of Computing, Newcastle University, Newcastle Upon Tyne, UK
| | - Hamish W King
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
- Centre for Immunobiology, Blizard Institute, Queen Mary University of London, London, UK
| | - Anthony J Rostron
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Integrated Critical Care Unit, Sunderland Royal Hospital, South Tyneside and Sunderland NHS Foundation Trust, Sunderland, UK
| | - A John Simpson
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Sophie Hambleton
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Elisa Laurenti
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Paul A Lyons
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Kerstin B Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK
| | - Marko Z Nikolić
- UCL Respiratory, Division of Medicine, University College London, London, UK
- University College London Hospitals NHS Foundation Trust, London, UK
| | - Christopher J A Duncan
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
- Department of Infection and Tropical Medicine, Newcastle upon Tyne Hospitals NHS Foundation, Newcastle upon Tyne, UK
| | - Kenneth G C Smith
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Theory of Condensed Matter Group, Cavendish Laboratory/Department of Physics, University of Cambridge, Cambridge, UK.
| | - Menna R Clatworthy
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Cambridge Biomedical Campus, Cambridge, UK.
- NIHR Cambridge Biomedical Research Centre, Cambridge, UK.
| | - John C Marioni
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK.
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
| | - Berthold Göttgens
- Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
| | - Muzlifah Haniffa
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, UK.
- NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
- Department of Dermatology, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK.
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16
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Sturgess KHM, Calero-Nieto FJ, Göttgens B, Wilson NK. Single-Cell Analysis of Hematopoietic Stem Cells. Methods Mol Biol 2021; 2308:301-337. [PMID: 34057731 DOI: 10.1007/978-1-0716-1425-9_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 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] [Indexed: 12/03/2022]
Abstract
The study of hematopoiesis has been revolutionized in recent years by the application of single-cell RNA sequencing technologies. The technique coupled with rapidly developing bioinformatic analysis has provided great insight into the cell type compositions of many populations previously defined by their cell surface phenotype. Moreover, transcriptomic information enables the identification of individual molecules and pathways which define novel cell populations and their transitions including cell lineage decisions. Combining single-cell transcriptional profiling with molecular perturbations allows functional analysis of individual factors in gene regulatory networks and better understanding of the earliest stages of malignant transformation. In this chapter we describe a comprehensive protocol for scRNA-Seq analysis of the mouse bone marrow, using both plate-based (low throughput) and droplet-based (high throughput) methods. The protocol includes instructions for sample preparation, an antibody panel for flow cytometric purification of hematopoietic progenitors with index sorting for plate-based analysis or in bulk for droplet-based methods. The plate-based protocol described in this chapter is a combination of the Smart-Seq2 and mcSCRB-Seq protocols, optimized in our laboratory. It utilizes off-the-shelf reagents for cDNA preparation, is amenable to automation using a liquid handler, and takes 4 days from preparation of the cells for sorting to producing a sequencing-ready library. The droplet-based method (using for instance the 10× Genomics platform) relies on the manufacturer's user guide and commercial reagents, and takes 3 days from isolation of the cells to the production of a library ready for sequencing.
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Affiliation(s)
- Katherine H M Sturgess
- Department of Haematology, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Fernando J Calero-Nieto
- Department of Haematology, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Berthold Göttgens
- Department of Haematology, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Nicola K Wilson
- Department of Haematology, Jeffrey Cheah Biomedical Centre, Puddicombe Way, Wellcome - MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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17
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Dingler FA, Wang M, Mu A, Millington CL, Oberbeck N, Watcham S, Pontel LB, Kamimae-Lanning AN, Langevin F, Nadler C, Cordell RL, Monks PS, Yu R, Wilson NK, Hira A, Yoshida K, Mori M, Okamoto Y, Okuno Y, Muramatsu H, Shiraishi Y, Kobayashi M, Moriguchi T, Osumi T, Kato M, Miyano S, Ito E, Kojima S, Yabe H, Yabe M, Matsuo K, Ogawa S, Göttgens B, Hodskinson MRG, Takata M, Patel KJ. Two Aldehyde Clearance Systems Are Essential to Prevent Lethal Formaldehyde Accumulation in Mice and Humans. Mol Cell 2020; 80:996-1012.e9. [PMID: 33147438 PMCID: PMC7758861 DOI: 10.1016/j.molcel.2020.10.012] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [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: 06/15/2020] [Revised: 08/20/2020] [Accepted: 10/08/2020] [Indexed: 01/04/2023]
Abstract
Reactive aldehydes arise as by-products of metabolism and are normally cleared by multiple families of enzymes. We find that mice lacking two aldehyde detoxifying enzymes, mitochondrial ALDH2 and cytoplasmic ADH5, have greatly shortened lifespans and develop leukemia. Hematopoiesis is disrupted profoundly, with a reduction of hematopoietic stem cells and common lymphoid progenitors causing a severely depleted acquired immune system. We show that formaldehyde is a common substrate of ALDH2 and ADH5 and establish methods to quantify elevated blood formaldehyde and formaldehyde-DNA adducts in tissues. Bone-marrow-derived progenitors actively engage DNA repair but also imprint a formaldehyde-driven mutation signature similar to aging-associated human cancer mutation signatures. Furthermore, we identify analogous genetic defects in children causing a previously uncharacterized inherited bone marrow failure and pre-leukemic syndrome. Endogenous formaldehyde clearance alone is therefore critical for hematopoiesis and in limiting mutagenesis in somatic tissues.
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Affiliation(s)
- Felix A Dingler
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Meng Wang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Department of Haematology, University of Cambridge, Cambridge, UK
| | - Anfeng Mu
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Kyoto University, Kyoto, Japan; Department of Genome Biology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan; Department of Clinical Application, Center for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | | | - Nina Oberbeck
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Sam Watcham
- Department of Haematology, University of Cambridge, Cambridge, UK; Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Lucas B Pontel
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET, Polo Científico Tecnológico, Godoy Cruz 2390, C1425FQD Buenos Aires, Argentina
| | | | - Frederic Langevin
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Camille Nadler
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Rebecca L Cordell
- Department of Chemistry, University of Leicester, Leicester LE1 7RH, UK
| | - Paul S Monks
- Department of Chemistry, University of Leicester, Leicester LE1 7RH, UK
| | - Rui Yu
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Nicola K Wilson
- Department of Haematology, University of Cambridge, Cambridge, UK; Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | - Asuka Hira
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Kyoto University, Kyoto, Japan; Department of Genome Biology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Minako Mori
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Kyoto University, Kyoto, Japan; Department of Genome Biology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan; Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yusuke Okamoto
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Kyoto University, Kyoto, Japan; Department of Genome Biology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan; Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yusuke Okuno
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hideki Muramatsu
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuichi Shiraishi
- Section of Genome Analysis Platform, Center for Cancer Genomic and Advanced Therapeutics, National Cancer Center, Tokyo, Japan
| | - Masayuki Kobayashi
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan; Department of Hematology, Kyoto Katsura Hospital, Kyoto, Japan
| | | | - Tomoo Osumi
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Motohiro Kato
- Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, The Institute of Medical Science, University of Tokyo, Tokyo Japan
| | - Etsuro Ito
- Department of Pediatrics, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Seiji Kojima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiromasa Yabe
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Japan
| | - Miharu Yabe
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Japan
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Aichi Cancer Center Research Institute, Nagoya, Japan; Division of Analytical Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan; Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institute, Sweden; Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Berthold Göttgens
- Department of Haematology, University of Cambridge, Cambridge, UK; Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
| | | | - Minoru Takata
- Laboratory of DNA Damage Signaling, Department of Late Effects Studies, Radiation Biology Center, Kyoto University, Kyoto, Japan; Department of Genome Biology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan.
| | - Ketan J Patel
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 2QQ, UK; MRC Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK.
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18
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Kucinski I, Wilson NK, Hannah R, Kinston SJ, Cauchy P, Lenaerts A, Grosschedl R, Göttgens B. Interactions between lineage-associated transcription factors govern haematopoietic progenitor states. EMBO J 2020; 39:e104983. [PMID: 33103827 PMCID: PMC7737608 DOI: 10.15252/embj.2020104983|] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Recent advances in molecular profiling provide descriptive datasets of complex differentiation landscapes including the haematopoietic system, but the molecular mechanisms defining progenitor states and lineage choice remain ill-defined. Here, we employed a cellular model of murine multipotent haematopoietic progenitors (Hoxb8-FL) to knock out 39 transcription factors (TFs) followed by RNA-Seq analysis, to functionally define a regulatory network of 16,992 regulator/target gene links. Focussed analysis of the subnetworks regulated by the B-lymphoid TF Ebf1 and T-lymphoid TF Gata3 revealed a surprising role in common activation of an early myeloid programme. Moreover, Gata3-mediated repression of Pax5 emerges as a mechanism to prevent precocious B-lymphoid differentiation, while Hox-mediated activation of Meis1 suppresses myeloid differentiation. To aid interpretation of large transcriptomics datasets, we also report a new method that visualises likely transitions that a progenitor will undergo following regulatory network perturbations. Taken together, this study reveals how molecular network wiring helps to establish a multipotent progenitor state, with experimental approaches and analysis tools applicable to dissecting a broad range of both normal and perturbed cellular differentiation landscapes.
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Affiliation(s)
- Iwo Kucinski
- Wellcome–MRC Cambridge Stem Cell InstituteDepartment of HaematologyJeffrey Cheah Biomedical CentreUniversity of CambridgeCambridgeUK
| | - Nicola K Wilson
- Wellcome–MRC Cambridge Stem Cell InstituteDepartment of HaematologyJeffrey Cheah Biomedical CentreUniversity of CambridgeCambridgeUK
| | - Rebecca Hannah
- Wellcome–MRC Cambridge Stem Cell InstituteDepartment of HaematologyJeffrey Cheah Biomedical CentreUniversity of CambridgeCambridgeUK
| | - Sarah J Kinston
- Wellcome–MRC Cambridge Stem Cell InstituteDepartment of HaematologyJeffrey Cheah Biomedical CentreUniversity of CambridgeCambridgeUK
| | - Pierre Cauchy
- Department of Cellular and Molecular ImmunologyMax Planck Institute of Immunobiology and EpigeneticsFreiburgGermany
| | - Aurelie Lenaerts
- Department of Cellular and Molecular ImmunologyMax Planck Institute of Immunobiology and EpigeneticsFreiburgGermany,International Max Planck Research School for Molecular and Cellular BiologyMax Planck Institute of Immunobiology and EpigeneticsFreiburgGermany
| | - Rudolf Grosschedl
- Department of Cellular and Molecular ImmunologyMax Planck Institute of Immunobiology and EpigeneticsFreiburgGermany
| | - Berthold Göttgens
- Wellcome–MRC Cambridge Stem Cell InstituteDepartment of HaematologyJeffrey Cheah Biomedical CentreUniversity of CambridgeCambridgeUK
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19
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Kucinski I, Wilson NK, Hannah R, Kinston SJ, Cauchy P, Lenaerts A, Grosschedl R, Göttgens B. Interactions between lineage-associated transcription factors govern haematopoietic progenitor states. EMBO J 2020; 39:e104983. [PMID: 33103827 PMCID: PMC7737608 DOI: 10.15252/embj.2020104983] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 03/12/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 12/26/2022] Open
Abstract
Recent advances in molecular profiling provide descriptive datasets of complex differentiation landscapes including the haematopoietic system, but the molecular mechanisms defining progenitor states and lineage choice remain ill-defined. Here, we employed a cellular model of murine multipotent haematopoietic progenitors (Hoxb8-FL) to knock out 39 transcription factors (TFs) followed by RNA-Seq analysis, to functionally define a regulatory network of 16,992 regulator/target gene links. Focussed analysis of the subnetworks regulated by the B-lymphoid TF Ebf1 and T-lymphoid TF Gata3 revealed a surprising role in common activation of an early myeloid programme. Moreover, Gata3-mediated repression of Pax5 emerges as a mechanism to prevent precocious B-lymphoid differentiation, while Hox-mediated activation of Meis1 suppresses myeloid differentiation. To aid interpretation of large transcriptomics datasets, we also report a new method that visualises likely transitions that a progenitor will undergo following regulatory network perturbations. Taken together, this study reveals how molecular network wiring helps to establish a multipotent progenitor state, with experimental approaches and analysis tools applicable to dissecting a broad range of both normal and perturbed cellular differentiation landscapes.
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Affiliation(s)
- Iwo Kucinski
- Wellcome–MRC Cambridge Stem Cell InstituteDepartment of HaematologyJeffrey Cheah Biomedical CentreUniversity of CambridgeCambridgeUK
| | - Nicola K Wilson
- Wellcome–MRC Cambridge Stem Cell InstituteDepartment of HaematologyJeffrey Cheah Biomedical CentreUniversity of CambridgeCambridgeUK
| | - Rebecca Hannah
- Wellcome–MRC Cambridge Stem Cell InstituteDepartment of HaematologyJeffrey Cheah Biomedical CentreUniversity of CambridgeCambridgeUK
| | - Sarah J Kinston
- Wellcome–MRC Cambridge Stem Cell InstituteDepartment of HaematologyJeffrey Cheah Biomedical CentreUniversity of CambridgeCambridgeUK
| | - Pierre Cauchy
- Department of Cellular and Molecular ImmunologyMax Planck Institute of Immunobiology and EpigeneticsFreiburgGermany
| | - Aurelie Lenaerts
- Department of Cellular and Molecular ImmunologyMax Planck Institute of Immunobiology and EpigeneticsFreiburgGermany
- International Max Planck Research School for Molecular and Cellular BiologyMax Planck Institute of Immunobiology and EpigeneticsFreiburgGermany
| | - Rudolf Grosschedl
- Department of Cellular and Molecular ImmunologyMax Planck Institute of Immunobiology and EpigeneticsFreiburgGermany
| | - Berthold Göttgens
- Wellcome–MRC Cambridge Stem Cell InstituteDepartment of HaematologyJeffrey Cheah Biomedical CentreUniversity of CambridgeCambridgeUK
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20
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Haltalli MLR, Watcham S, Wilson NK, Eilers K, Lipien A, Ang H, Birch F, Anton SG, Pirillo C, Ruivo N, Vainieri ML, Pospori C, Sinden RE, Luis TC, Langhorne J, Duffy KR, Göttgens B, Blagborough AM, Lo Celso C. Manipulating niche composition limits damage to haematopoietic stem cells during Plasmodium infection. Nat Cell Biol 2020; 22:1399-1410. [PMID: 33230302 PMCID: PMC7611033 DOI: 10.1038/s41556-020-00601-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 10/06/2020] [Indexed: 12/17/2022]
Abstract
Severe infections are a major stress on haematopoiesis, where the consequences for haematopoietic stem cells (HSCs) have only recently started to emerge. HSC function critically depends on the integrity of complex bone marrow (BM) niches; however, what role the BM microenvironment plays in mediating the effects of infection on HSCs remains an open question. Here, using a murine model of malaria and combining single-cell RNA sequencing, mathematical modelling, transplantation assays and intravital microscopy, we show that haematopoiesis is reprogrammed upon infection, whereby the HSC compartment turns over substantially faster than at steady-state and HSC function is drastically affected. Interferon is found to affect both haematopoietic and mesenchymal BM cells and we specifically identify a dramatic loss of osteoblasts and alterations in endothelial cell function. Osteo-active parathyroid hormone treatment abolishes infection-triggered HSC proliferation and-coupled with reactive oxygen species quenching-enables partial rescuing of HSC function.
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Affiliation(s)
- Myriam L R Haltalli
- Department of Life Sciences, Imperial College London, London, UK
- The Francis Crick Institute, London, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Haematology, Cambridge Institute for Medical Research, Cambridge, UK
| | - Samuel Watcham
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Haematology, Cambridge Institute for Medical Research, Cambridge, UK
| | - Nicola K Wilson
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Haematology, Cambridge Institute for Medical Research, Cambridge, UK
| | - Kira Eilers
- Department of Life Sciences, Imperial College London, London, UK
| | - Alexander Lipien
- Department of Life Sciences, Imperial College London, London, UK
| | - Heather Ang
- Department of Life Sciences, Imperial College London, London, UK
| | - Flora Birch
- Department of Life Sciences, Imperial College London, London, UK
- The Francis Crick Institute, London, UK
| | - Sara Gonzalez Anton
- Department of Life Sciences, Imperial College London, London, UK
- The Francis Crick Institute, London, UK
| | - Chiara Pirillo
- Department of Life Sciences, Imperial College London, London, UK
- The Francis Crick Institute, London, UK
| | - Nicola Ruivo
- Department of Life Sciences, Imperial College London, London, UK
| | - Maria L Vainieri
- Department of Life Sciences, Imperial College London, London, UK
- AO Research Institute, Davos Platz, Switzerland
| | - Constandina Pospori
- Department of Life Sciences, Imperial College London, London, UK
- The Francis Crick Institute, London, UK
| | - Robert E Sinden
- Department of Life Sciences, Imperial College London, London, UK
| | - Tiago C Luis
- Department of Life Sciences, Imperial College London, London, UK
| | | | - Ken R Duffy
- Hamilton Institute, Maynooth University, Maynooth, Ireland
| | - Berthold Göttgens
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, UK
- Department of Haematology, Cambridge Institute for Medical Research, Cambridge, UK
| | | | - Cristina Lo Celso
- Department of Life Sciences, Imperial College London, London, UK.
- The Francis Crick Institute, London, UK.
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21
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Hsu J, Huang HT, Lee CT, Choudhuri A, Wilson NK, Abraham BJ, Moignard V, Kucinski I, Yu S, Hyde RK, Tober J, Cai X, Li Y, Guo Y, Yang S, Superdock M, Trompouki E, Calero-Nieto FJ, Ghamari A, Jiang J, Gao P, Gao L, Nguyen V, Robertson AL, Durand EM, Kathrein KL, Aifantis I, Gerber SA, Tong W, Tan K, Cantor AB, Zhou Y, Liu PP, Young RA, Göttgens B, Speck NA, Zon LI. CHD7 and Runx1 interaction provides a braking mechanism for hematopoietic differentiation. Proc Natl Acad Sci U S A 2020; 117:23626-23635. [PMID: 32883883 PMCID: PMC7519295 DOI: 10.1073/pnas.2003228117] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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] [Indexed: 12/24/2022] Open
Abstract
Hematopoietic stem and progenitor cell (HSPC) formation and lineage differentiation involve gene expression programs orchestrated by transcription factors and epigenetic regulators. Genetic disruption of the chromatin remodeler chromodomain-helicase-DNA-binding protein 7 (CHD7) expanded phenotypic HSPCs, erythroid, and myeloid lineages in zebrafish and mouse embryos. CHD7 acts to suppress hematopoietic differentiation. Binding motifs for RUNX and other hematopoietic transcription factors are enriched at sites occupied by CHD7, and decreased RUNX1 occupancy correlated with loss of CHD7 localization. CHD7 physically interacts with RUNX1 and suppresses RUNX1-induced expansion of HSPCs during development through modulation of RUNX1 activity. Consequently, the RUNX1:CHD7 axis provides proper timing and function of HSPCs as they emerge during hematopoietic development or mature in adults, representing a distinct and evolutionarily conserved control mechanism to ensure accurate hematopoietic lineage differentiation.
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Affiliation(s)
- Jingmei Hsu
- Division of Hematology/Oncology, Department of Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA 19104
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Hsuan-Ting Huang
- Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - Chung-Tsai Lee
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Avik Choudhuri
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138
| | - Nicola K Wilson
- Cambridge Institute for Medical Research, Department of Haematology, Wellcome Trust/Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom CB2 OXY
| | - Brian J Abraham
- Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Victoria Moignard
- Cambridge Institute for Medical Research, Department of Haematology, Wellcome Trust/Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom CB2 OXY
| | - Iwo Kucinski
- Cambridge Institute for Medical Research, Department of Haematology, Wellcome Trust/Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom CB2 OXY
| | - Shuqian Yu
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104
| | - R Katherine Hyde
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
| | - Joanna Tober
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Xiongwei Cai
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Yan Li
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Yalin Guo
- Department of Microbiology and Immunology, Geisel School of Medicine, Lebanon, NH 03756
| | - Song Yang
- Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - Michael Superdock
- Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - Eirini Trompouki
- Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - Fernando J Calero-Nieto
- Cambridge Institute for Medical Research, Department of Haematology, Wellcome Trust/Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom CB2 OXY
| | - Alireza Ghamari
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - Jing Jiang
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Peng Gao
- Division of Oncology and Center for Childhood Cancer Research, Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Long Gao
- Division of Oncology and Center for Childhood Cancer Research, Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Vy Nguyen
- Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - Anne L Robertson
- Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - Ellen M Durand
- Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - Katie L Kathrein
- Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - Iannis Aifantis
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016
| | - Scott A Gerber
- Department of Genetics, Geisel School of Medicine, Lebanon, NH 03756
| | - Wei Tong
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA 19104
| | - Kai Tan
- Division of Oncology and Center for Childhood Cancer Research, Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA 19104
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Alan B Cantor
- Division of Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - Yi Zhou
- Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115
| | - P Paul Liu
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142
| | - Berthold Göttgens
- Cambridge Institute for Medical Research, Department of Haematology, Wellcome Trust/Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom CB2 OXY
| | - Nancy A Speck
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104;
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104
| | - Leonard I Zon
- Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital and Dana Farber Cancer Institute, Harvard Medical School, Boston, MA 02115;
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138
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22
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Pijuan-Sala B, Wilson NK, Xia J, Hou X, Hannah RL, Kinston S, Calero-Nieto FJ, Poirion O, Preissl S, Liu F, Göttgens B. Single-cell chromatin accessibility maps reveal regulatory programs driving early mouse organogenesis. Nat Cell Biol 2020; 22:487-497. [PMID: 32231307 PMCID: PMC7145456 DOI: 10.1038/s41556-020-0489-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [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: 07/25/2019] [Accepted: 02/20/2020] [Indexed: 11/29/2022]
Abstract
During mouse embryonic development, pluripotent cells rapidly divide and diversify, yet the regulatory programs that define the cell repertoire for each organ remain ill-defined. To delineate comprehensive chromatin landscapes during early organogenesis, we mapped chromatin accessibility in 19,453 single nuclei from mouse embryos at 8.25 days post-fertilization. Identification of cell-type-specific regions of open chromatin pinpointed two TAL1-bound endothelial enhancers, which we validated using transgenic mouse assays. Integrated gene expression and transcription factor motif enrichment analyses highlighted cell-type-specific transcriptional regulators. Subsequent in vivo experiments in zebrafish revealed a role for the ETS factor FEV in endothelial identity downstream of ETV2 (Etsrp in zebrafish). Concerted in vivo validation experiments in mouse and zebrafish thus illustrate how single-cell open chromatin maps, representative of a mammalian embryo, provide access to the regulatory blueprint for mammalian organogenesis.
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Affiliation(s)
- Blanca Pijuan-Sala
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Nicola K Wilson
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Jun Xia
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Xiaomeng Hou
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, School of Medicine, La Jolla, CA, USA
| | - Rebecca L Hannah
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Sarah Kinston
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Fernando J Calero-Nieto
- Department of Haematology, University of Cambridge, Cambridge, UK
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Olivier Poirion
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, School of Medicine, La Jolla, CA, USA
| | - Sebastian Preissl
- Center for Epigenomics, Department of Cellular and Molecular Medicine, University of California, San Diego, School of Medicine, La Jolla, CA, USA
| | - Feng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Berthold Göttgens
- Department of Haematology, University of Cambridge, Cambridge, UK.
- Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
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23
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Fitch SR, Kapeni C, Tsitsopoulou A, Wilson NK, Göttgens B, de Bruijn MF, Ottersbach K. Gata3 targets Runx1 in the embryonic haematopoietic stem cell niche. IUBMB Life 2020; 72:45-52. [PMID: 31634421 PMCID: PMC6973286 DOI: 10.1002/iub.2184] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 08/09/2019] [Accepted: 10/01/2019] [Indexed: 02/02/2023]
Abstract
Runx1 is an important haematopoietic transcription factor as stressed by its involvement in a number of haematological malignancies. Furthermore, it is a key regulator of the emergence of the first haematopoietic stem cells (HSCs) during development. The transcription factor Gata3 has also been linked to haematological disease and was shown to promote HSC production in the embryo by inducing the secretion of important niche factors. Both proteins are expressed in several different cell types within the aorta-gonads-mesonephros (AGM) region, in which the first HSCs are generated; however, a direct interaction between these two key transcription factors in the context of embryonic HSC production has not formally been demonstrated. In this current study, we have detected co-localisation of Runx1 and Gata3 in rare sub-aortic mesenchymal cells in the AGM. Furthermore, the expression of Runx1 is reduced in Gata3 -/- embryos, which also display a shift in HSC emergence. Using an AGM-derived cell line as a model for the stromal microenvironment in the AGM and performing ChIP-Seq and ChIP-on-chip experiments, we demonstrate that Runx1, together with other key niche factors, is a direct target gene of Gata3. In addition, we can pinpoint Gata3 binding to the Runx1 locus at specific enhancer elements which are active in the microenvironment. These results reveal a direct interaction between Gata3 and Runx1 in the niche that supports embryonic HSCs and highlight a dual role for Runx1 in driving the transdifferentiation of haemogenic endothelial cells into HSCs as well as in the stromal cells that support this process.
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Affiliation(s)
- Simon R. Fitch
- Cambridge Institute for Medical Research and Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUK
| | - Chrysa Kapeni
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUK
- Cambridge Institute for Medical Research and Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUK
| | | | - Nicola K. Wilson
- Cambridge Institute for Medical Research and Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUK
| | - Berthold Göttgens
- Cambridge Institute for Medical Research and Cambridge Stem Cell InstituteUniversity of CambridgeCambridgeUK
| | - Marella F. de Bruijn
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
| | - Katrin Ottersbach
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUK
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24
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Sasca D, Yun H, Giotopoulos G, Szybinski J, Evan T, Wilson NK, Gerstung M, Gallipoli P, Green AR, Hills R, Russell N, Osborne CS, Papaemmanuil E, Göttgens B, Campbell P, Huntly BJP. Cohesin-dependent regulation of gene expression during differentiation is lost in cohesin-mutated myeloid malignancies. Blood 2019; 134:2195-2208. [PMID: 31515253 PMCID: PMC7484777 DOI: 10.1182/blood.2019001553] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 09/04/2019] [Indexed: 02/06/2023] Open
Abstract
Cohesin complex disruption alters gene expression, and cohesin mutations are common in myeloid neoplasia, suggesting a critical role in hematopoiesis. Here, we explore cohesin dynamics and regulation of hematopoietic stem cell homeostasis and differentiation. Cohesin binding increases at active regulatory elements only during erythroid differentiation. Prior binding of the repressive Ets transcription factor Etv6 predicts cohesin binding at these elements and Etv6 interacts with cohesin at chromatin. Depletion of cohesin severely impairs erythroid differentiation, particularly at Etv6-prebound loci, but augments self-renewal programs. Together with corroborative findings in acute myeloid leukemia and myelodysplastic syndrome patient samples, these data suggest cohesin-mediated alleviation of Etv6 repression is required for dynamic expression at critical erythroid genes during differentiation and how this may be perturbed in myeloid malignancies.
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Affiliation(s)
- Daniel Sasca
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Department of Hematology, Oncology and Pneumology, University Medical Center Mainz, Mainz, Germany
| | - Haiyang Yun
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - George Giotopoulos
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Jakub Szybinski
- Department of Hematology, Oncology and Pneumology, University Medical Center Mainz, Mainz, Germany
| | - Theo Evan
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Nicola K Wilson
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Moritz Gerstung
- European Bioinformatic Institute, Genome Campus, Hinxton, United Kingdom
| | - Paolo Gallipoli
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Anthony R Green
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Robert Hills
- Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Nigel Russell
- Department of Haematology, University of Nottingham, Nottingham, United Kingdom
| | - Cameron S Osborne
- Department of Medical and Molecular Genetics, Kings College London, United Kingdom
| | - Elli Papaemmanuil
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY; and
| | - Berthold Göttgens
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Peter Campbell
- Cancer, Ageing and Somatic Mutation Programme, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, United Kingdom
| | - Brian J P Huntly
- Wellcome Trust-MRC Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
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25
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Shepherd MS, Li J, Wilson NK, Oedekoven CA, Li J, Belmonte M, Fink J, Prick JCM, Pask DC, Hamilton TL, Loeffler D, Rao A, Schröder T, Göttgens B, Green AR, Kent DG. Single-cell approaches identify the molecular network driving malignant hematopoietic stem cell self-renewal. Blood 2018; 132:791-803. [PMID: 29991556 PMCID: PMC6107881 DOI: 10.1182/blood-2017-12-821066] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 07/03/2018] [Indexed: 12/24/2022] Open
Abstract
Recent advances in single-cell technologies have permitted the investigation of heterogeneous cell populations at previously unattainable resolution. Here we apply such approaches to resolve the molecular mechanisms driving disease in mouse hematopoietic stem cells (HSCs), using JAK2V617F mutant myeloproliferative neoplasms (MPNs) as a model. Single-cell gene expression and functional assays identified a subset of JAK2V617F mutant HSCs that display defective self-renewal. This defect is rescued at the single HSC level by crossing JAK2V617F mice with mice lacking TET2, the most commonly comutated gene in patients with MPN. Single-cell gene expression profiling of JAK2V617F-mutant HSCs revealed a loss of specific regulator genes, some of which were restored to normal levels in single TET2/JAK2 mutant HSCs. Of these, Bmi1 and, to a lesser extent, Pbx1 and Meis1 overexpression in JAK2-mutant HSCs could drive a disease phenotype and retain durable stem cell self-renewal in functional assays. Together, these single-cell approaches refine the molecules involved in clonal expansion of MPNs and have broad implications for deconstructing the molecular network of normal and malignant stem cells.
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Affiliation(s)
- Mairi S Shepherd
- Wellcome MRC Cambridge Stem Cell Institute and
- Department of Haematology, University of Cambridge, United Kingdom
| | - Juan Li
- Wellcome MRC Cambridge Stem Cell Institute and
- Department of Haematology, University of Cambridge, United Kingdom
| | - Nicola K Wilson
- Wellcome MRC Cambridge Stem Cell Institute and
- Department of Haematology, University of Cambridge, United Kingdom
| | - Caroline A Oedekoven
- Wellcome MRC Cambridge Stem Cell Institute and
- Department of Haematology, University of Cambridge, United Kingdom
| | - Jiangbing Li
- Wellcome MRC Cambridge Stem Cell Institute and
- Department of Haematology, University of Cambridge, United Kingdom
| | - Miriam Belmonte
- Wellcome MRC Cambridge Stem Cell Institute and
- Department of Haematology, University of Cambridge, United Kingdom
| | - Juergen Fink
- Wellcome MRC Cambridge Stem Cell Institute and
- Department of Haematology, University of Cambridge, United Kingdom
| | - Janine C M Prick
- Wellcome MRC Cambridge Stem Cell Institute and
- Department of Haematology, University of Cambridge, United Kingdom
| | - Dean C Pask
- Wellcome MRC Cambridge Stem Cell Institute and
- Department of Haematology, University of Cambridge, United Kingdom
| | - Tina L Hamilton
- Wellcome MRC Cambridge Stem Cell Institute and
- Department of Haematology, University of Cambridge, United Kingdom
| | - Dirk Loeffler
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; and
| | - Anjana Rao
- La Jolla Institute and Department of Pharmacology, University of California, San Diego, La Jolla, CA
| | - Timm Schröder
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland; and
| | - Berthold Göttgens
- Wellcome MRC Cambridge Stem Cell Institute and
- Department of Haematology, University of Cambridge, United Kingdom
| | - Anthony R Green
- Wellcome MRC Cambridge Stem Cell Institute and
- Department of Haematology, University of Cambridge, United Kingdom
- Department of Haematology, Addenbrooke's Hospital, Hills Road, Cambridge, United Kingdom
| | - David G Kent
- Wellcome MRC Cambridge Stem Cell Institute and
- Department of Haematology, University of Cambridge, United Kingdom
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26
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Dahlin JS, Hamey FK, Pijuan-Sala B, Shepherd M, Lau WWY, Nestorowa S, Weinreb C, Wolock S, Hannah R, Diamanti E, Kent DG, Göttgens B, Wilson NK. A single-cell hematopoietic landscape resolves 8 lineage trajectories and defects in Kit mutant mice. Blood 2018; 131:e1-e11. [PMID: 29588278 PMCID: PMC5969381 DOI: 10.1182/blood-2017-12-821413] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 03/16/2018] [Indexed: 12/19/2022] Open
Abstract
Hematopoietic stem and progenitor cells (HSPCs) maintain the adult blood system, and their dysregulation causes a multitude of diseases. However, the differentiation journeys toward specific hematopoietic lineages remain ill defined, and system-wide disease interpretation remains challenging. Here, we have profiled 44 802 mouse bone marrow HSPCs using single-cell RNA sequencing to provide a comprehensive transcriptional landscape with entry points to 8 different blood lineages (lymphoid, megakaryocyte, erythroid, neutrophil, monocyte, eosinophil, mast cell, and basophil progenitors). We identified a common basophil/mast cell bone marrow progenitor and characterized its molecular profile at the single-cell level. Transcriptional profiling of 13 815 HSPCs from the c-Kit mutant (W41/W41) mouse model revealed the absence of a distinct mast cell lineage entry point, together with global shifts in cell type abundance. Proliferative defects were accompanied by reduced Myc expression. Potential compensatory processes included upregulation of the integrated stress response pathway and downregulation of proapoptotic gene expression in erythroid progenitors, thus providing a template of how large-scale single-cell transcriptomic studies can bridge between molecular phenotypes and quantitative population changes.
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Affiliation(s)
- Joakim S Dahlin
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research and Wellcome-Medical Research Council Cambridge Stem Cell Institute, Cambridge, United Kingdom
- Department of Medicine, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Fiona K Hamey
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research and Wellcome-Medical Research Council Cambridge Stem Cell Institute, Cambridge, United Kingdom
| | - Blanca Pijuan-Sala
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research and Wellcome-Medical Research Council Cambridge Stem Cell Institute, Cambridge, United Kingdom
| | - Mairi Shepherd
- Department of Haematology, University of Cambridge, Wellcome-Medical Research Council Cambridge Stem Cell Institute, Cambridge, United Kingdom; and
| | - Winnie W Y Lau
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research and Wellcome-Medical Research Council Cambridge Stem Cell Institute, Cambridge, United Kingdom
| | - Sonia Nestorowa
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research and Wellcome-Medical Research Council Cambridge Stem Cell Institute, Cambridge, United Kingdom
| | - Caleb Weinreb
- Department of Systems Biology, Harvard Medical School, Boston, MA
| | - Samuel Wolock
- Department of Systems Biology, Harvard Medical School, Boston, MA
| | - Rebecca Hannah
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research and Wellcome-Medical Research Council Cambridge Stem Cell Institute, Cambridge, United Kingdom
| | - Evangelia Diamanti
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research and Wellcome-Medical Research Council Cambridge Stem Cell Institute, Cambridge, United Kingdom
| | - David G Kent
- Department of Haematology, University of Cambridge, Wellcome-Medical Research Council Cambridge Stem Cell Institute, Cambridge, United Kingdom; and
| | - Berthold Göttgens
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research and Wellcome-Medical Research Council Cambridge Stem Cell Institute, Cambridge, United Kingdom
| | - Nicola K Wilson
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research and Wellcome-Medical Research Council Cambridge Stem Cell Institute, Cambridge, United Kingdom
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27
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Hamey FK, Nestorowa S, Kinston SJ, Kent DG, Wilson NK, Göttgens B. Reconstructing blood stem cell regulatory network models from single-cell molecular profiles. Proc Natl Acad Sci U S A 2017; 114:5822-5829. [PMID: 28584094 PMCID: PMC5468644 DOI: 10.1073/pnas.1610609114] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [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] [Indexed: 01/18/2023] Open
Abstract
Adult blood contains a mixture of mature cell types, each with specialized functions. Single hematopoietic stem cells (HSCs) have been functionally shown to generate all mature cell types for the lifetime of the organism. Differentiation of HSCs toward alternative lineages must be balanced at the population level by the fate decisions made by individual cells. Transcription factors play a key role in regulating these decisions and operate within organized regulatory programs that can be modeled as transcriptional regulatory networks. As dysregulation of single HSC fate decisions is linked to fatal malignancies such as leukemia, it is important to understand how these decisions are controlled on a cell-by-cell basis. Here we developed and applied a network inference method, exploiting the ability to infer dynamic information from single-cell snapshot expression data based on expression profiles of 48 genes in 2,167 blood stem and progenitor cells. This approach allowed us to infer transcriptional regulatory network models that recapitulated differentiation of HSCs into progenitor cell types, focusing on trajectories toward megakaryocyte-erythrocyte progenitors and lymphoid-primed multipotent progenitors. By comparing these two models, we identified and subsequently experimentally validated a difference in the regulation of nuclear factor, erythroid 2 (Nfe2) and core-binding factor, runt domain, alpha subunit 2, translocated to, 3 homolog (Cbfa2t3h) by the transcription factor Gata2. Our approach confirms known aspects of hematopoiesis, provides hypotheses about regulation of HSC differentiation, and is widely applicable to other hierarchical biological systems to uncover regulatory relationships.
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Affiliation(s)
- Fiona K Hamey
- Department of Haematology, Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge Institute for Medical Research, Cambridge CB2 0XY, United Kingdom
| | - Sonia Nestorowa
- Department of Haematology, Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge Institute for Medical Research, Cambridge CB2 0XY, United Kingdom
| | - Sarah J Kinston
- Department of Haematology, Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge Institute for Medical Research, Cambridge CB2 0XY, United Kingdom
| | - David G Kent
- Department of Haematology, Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge Institute for Medical Research, Cambridge CB2 0XY, United Kingdom
| | - Nicola K Wilson
- Department of Haematology, Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge Institute for Medical Research, Cambridge CB2 0XY, United Kingdom
| | - Berthold Göttgens
- Department of Haematology, Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge Institute for Medical Research, Cambridge CB2 0XY, United Kingdom
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28
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Scialdone A, Tanaka Y, Jawaid W, Moignard V, Wilson NK, Macaulay IC, Marioni JC, Göttgens B. Resolving early mesoderm diversification through single-cell expression profiling. Nature 2016; 535:289-293. [PMID: 27383781 PMCID: PMC4947525 DOI: 10.1038/nature18633] [Citation(s) in RCA: 226] [Impact Index Per Article: 28.3] [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: 03/14/2016] [Accepted: 06/09/2016] [Indexed: 12/21/2022]
Abstract
In mammals, specification of the three major germ layers occurs during gastrulation, when cells ingressing through the primitive streak differentiate into the precursor cells of major organ systems. However, the molecular mechanisms underlying this process remain unclear, as numbers of gastrulating cells are very limited. In the mouse embryo at embryonic day 6.5, cells located at the junction between the extra-embryonic region and the epiblast on the posterior side of the embryo undergo an epithelial-to-mesenchymal transition and ingress through the primitive streak. Subsequently, cells migrate, either surrounding the prospective ectoderm contributing to the embryo proper, or into the extra-embryonic region to form the yolk sac, umbilical cord and placenta. Fate mapping has shown that mature tissues such as blood and heart originate from specific regions of the pre-gastrula epiblast, but the plasticity of cells within the embryo and the function of key cell-type-specific transcription factors remain unclear. Here we analyse 1,205 cells from the epiblast and nascent Flk1(+) mesoderm of gastrulating mouse embryos using single-cell RNA sequencing, representing the first transcriptome-wide in vivo view of early mesoderm formation during mammalian gastrulation. Additionally, using knockout mice, we study the function of Tal1, a key haematopoietic transcription factor, and demonstrate, contrary to previous studies performed using retrospective assays, that Tal1 knockout does not immediately bias precursor cells towards a cardiac fate.
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Affiliation(s)
- Antonio Scialdone
- EMBL-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust
Genome Campus, Cambridge, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Yosuke Tanaka
- Department of Haematology, Cambridge Institute for Medical Research,
University of Cambridge, Cambridge, UK
- Wellcome Trust - Medical Research Council Cambridge Stem Cell
Institute, University of Cambridge, Cambridge, UK
| | - Wajid Jawaid
- Department of Haematology, Cambridge Institute for Medical Research,
University of Cambridge, Cambridge, UK
- Wellcome Trust - Medical Research Council Cambridge Stem Cell
Institute, University of Cambridge, Cambridge, UK
| | - Victoria Moignard
- Department of Haematology, Cambridge Institute for Medical Research,
University of Cambridge, Cambridge, UK
- Wellcome Trust - Medical Research Council Cambridge Stem Cell
Institute, University of Cambridge, Cambridge, UK
| | - Nicola K. Wilson
- Department of Haematology, Cambridge Institute for Medical Research,
University of Cambridge, Cambridge, UK
- Wellcome Trust - Medical Research Council Cambridge Stem Cell
Institute, University of Cambridge, Cambridge, UK
| | | | - John C. Marioni
- EMBL-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust
Genome Campus, Cambridge, UK
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
- CRUK Cambridge Institute, University of Cambridge, Cambridge,
UK
| | - Berthold Göttgens
- Department of Haematology, Cambridge Institute for Medical Research,
University of Cambridge, Cambridge, UK
- Wellcome Trust - Medical Research Council Cambridge Stem Cell
Institute, University of Cambridge, Cambridge, UK
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29
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Hamey FK, Nestorowa S, Wilson NK, Göttgens B. Advancing haematopoietic stem and progenitor cell biology through single-cell profiling. FEBS Lett 2016; 590:4052-4067. [PMID: 27259698 DOI: 10.1002/1873-3468.12231] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 05/27/2016] [Accepted: 05/31/2016] [Indexed: 12/25/2022]
Abstract
Haematopoietic stem and progenitor cells (HSPCs) sit at the top of the haematopoietic hierarchy, and their fate choices need to be carefully controlled to ensure balanced production of all mature blood cell types. As cell fate decisions are made at the level of the individual cells, recent technological advances in measuring gene and protein expression in increasingly large numbers of single cells have been rapidly adopted to study both normal and pathological HSPC function. In this review we emphasise the importance of combining the correct computational models with single-cell experimental techniques, and illustrate how such integrated approaches have been used to resolve heterogeneities in populations, reconstruct lineage differentiation, identify regulatory relationships and link molecular profiling to cellular function.
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Affiliation(s)
- Fiona K Hamey
- Department of Haematology and Wellcome Trust - MRC Cambridge Stem Cell Institute, University of Cambridge, UK
| | - Sonia Nestorowa
- Department of Haematology and Wellcome Trust - MRC Cambridge Stem Cell Institute, University of Cambridge, UK
| | - Nicola K Wilson
- Department of Haematology and Wellcome Trust - MRC Cambridge Stem Cell Institute, University of Cambridge, UK
| | - Berthold Göttgens
- Department of Haematology and Wellcome Trust - MRC Cambridge Stem Cell Institute, University of Cambridge, UK
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30
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Schütte J, Wang H, Antoniou S, Jarratt A, Wilson NK, Riepsaame J, Calero-Nieto FJ, Moignard V, Basilico S, Kinston SJ, Hannah RL, Chan MC, Nürnberg ST, Ouwehand WH, Bonzanni N, de Bruijn MF, Göttgens B. An experimentally validated network of nine haematopoietic transcription factors reveals mechanisms of cell state stability. eLife 2016; 5:e11469. [PMID: 26901438 PMCID: PMC4798972 DOI: 10.7554/elife.11469] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [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: 09/09/2015] [Accepted: 02/12/2016] [Indexed: 12/12/2022] Open
Abstract
Transcription factor (TF) networks determine cell-type identity by establishing and maintaining lineage-specific expression profiles, yet reconstruction of mammalian regulatory network models has been hampered by a lack of comprehensive functional validation of regulatory interactions. Here, we report comprehensive ChIP-Seq, transgenic and reporter gene experimental data that have allowed us to construct an experimentally validated regulatory network model for haematopoietic stem/progenitor cells (HSPCs). Model simulation coupled with subsequent experimental validation using single cell expression profiling revealed potential mechanisms for cell state stabilisation, and also how a leukaemogenic TF fusion protein perturbs key HSPC regulators. The approach presented here should help to improve our understanding of both normal physiological and disease processes.
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Affiliation(s)
- Judith Schütte
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.,Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Huange Wang
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.,Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Stella Antoniou
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Andrew Jarratt
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Nicola K Wilson
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.,Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Joey Riepsaame
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Fernando J Calero-Nieto
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.,Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Victoria Moignard
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.,Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Silvia Basilico
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.,Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Sarah J Kinston
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.,Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Rebecca L Hannah
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.,Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Mun Chiang Chan
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Sylvia T Nürnberg
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom.,NHS Blood and Transplant, Cambridge, United Kingdom
| | - Willem H Ouwehand
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom.,NHS Blood and Transplant, Cambridge, United Kingdom
| | - Nicola Bonzanni
- IBIVU Centre for Integrative Bioinformatics, VU University Amsterdam, Amsterdam, Netherlands.,Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Marella Ftr de Bruijn
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Berthold Göttgens
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom.,Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
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31
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Schulte R, Wilson NK, Prick JCM, Cossetti C, Maj MK, Gottgens B, Kent DG. Index sorting resolves heterogeneous murine hematopoietic stem cell populations. Exp Hematol 2015; 43:803-11. [PMID: 26051918 PMCID: PMC4571925 DOI: 10.1016/j.exphem.2015.05.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [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: 05/07/2015] [Accepted: 05/07/2015] [Indexed: 12/17/2022]
Abstract
Recent advances in the cellular and molecular biology of single stem cells have uncovered significant heterogeneity in the functional properties of stem cell populations. This has prompted the development of approaches to study single cells in isolation, often performed using multiparameter flow cytometry. However, many stem cell populations are too rare to test all possible cell surface marker combinations, and virtually nothing is known about functional differences associated with varying intensities of such markers. Here we describe the use of index sorting for further resolution of the flow cytometric isolation of single murine hematopoietic stem cells (HSCs). Specifically, we associate single-cell functional assay outcomes with distinct cell surface marker expression intensities. High levels of both CD150 and EPCR associate with delayed kinetics of cell division and low levels of differentiation. Moreover, cells that do not form single HSC-derived clones appear in the 7AAD(dim) fraction, suggesting that even low levels of 7AAD staining are indicative of less healthy cell populations. These data indicate that when used in combination with single-cell functional assays, index sorting is a powerful tool for refining cell isolation strategies. This approach can be broadly applied to other single-cell systems, both to improve isolation and to acquire additional cell surface marker information.
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Affiliation(s)
- Reiner Schulte
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Nicola K Wilson
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom; Department of Haematology, University of Cambridge, Cambridge, United Kingdom; Wellcome Trust/MRC Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Janine C M Prick
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom; Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Chiara Cossetti
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Michal K Maj
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Berthold Gottgens
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom; Department of Haematology, University of Cambridge, Cambridge, United Kingdom; Wellcome Trust/MRC Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - David G Kent
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom; Department of Haematology, University of Cambridge, Cambridge, United Kingdom; Wellcome Trust/MRC Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom.
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32
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Wilson NK, Kent DG, Buettner F, Shehata M, Macaulay IC, Calero-Nieto FJ, Sánchez Castillo M, Oedekoven CA, Diamanti E, Schulte R, Ponting CP, Voet T, Caldas C, Stingl J, Green AR, Theis FJ, Göttgens B. Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations. Cell Stem Cell 2015; 16:712-24. [PMID: 26004780 PMCID: PMC4460190 DOI: 10.1016/j.stem.2015.04.004] [Citation(s) in RCA: 315] [Impact Index Per Article: 35.0] [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: 10/09/2014] [Revised: 02/26/2015] [Accepted: 04/10/2015] [Indexed: 01/27/2023]
Abstract
Heterogeneity within the self-renewal durability of adult hematopoietic stem cells (HSCs) challenges our understanding of the molecular framework underlying HSC function. Gene expression studies have been hampered by the presence of multiple HSC subtypes and contaminating non-HSCs in bulk HSC populations. To gain deeper insight into the gene expression program of murine HSCs, we combined single-cell functional assays with flow cytometric index sorting and single-cell gene expression assays. Through bioinformatic integration of these datasets, we designed an unbiased sorting strategy that separates non-HSCs away from HSCs, and single-cell transplantation experiments using the enriched population were combined with RNA-seq data to identify key molecules that associate with long-term durable self-renewal, producing a single-cell molecular dataset that is linked to functional stem cell activity. Finally, we demonstrated the broader applicability of this approach for linking key molecules with defined cellular functions in another stem cell system.
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Affiliation(s)
- Nicola K Wilson
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute and Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - David G Kent
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute and Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - Florian Buettner
- Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Mona Shehata
- Department of Oncology and Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, UK
| | - Iain C Macaulay
- Single Cell Genomics Centre, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Fernando J Calero-Nieto
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute and Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - Manuel Sánchez Castillo
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute and Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - Caroline A Oedekoven
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute and Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - Evangelia Diamanti
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute and Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - Reiner Schulte
- Head of Flow Cytometry, Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - Chris P Ponting
- Single Cell Genomics Centre, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; MRC Computational Genomics Analysis and Training Programme, MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK
| | - Thierry Voet
- Single Cell Genomics Centre, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK; Laboratory of Reproductive Genomics, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Carlos Caldas
- Department of Oncology and Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, UK
| | - John Stingl
- Department of Oncology and Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 0RE, UK
| | - Anthony R Green
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute and Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany; Department of Mathematics, Technische Universität München, Boltzmannstraße 3, 85748 Garching, Germany
| | - Berthold Göttgens
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute and Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK.
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33
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Sánchez-Castillo M, Ruau D, Wilkinson AC, Ng FSL, Hannah R, Diamanti E, Lombard P, Wilson NK, Gottgens B. CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities. Nucleic Acids Res 2014; 43:D1117-23. [PMID: 25270877 PMCID: PMC4384009 DOI: 10.1093/nar/gku895] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
CODEX (http://codex.stemcells.cam.ac.uk/) is a user-friendly database for the direct access and interrogation of publicly available next-generation sequencing (NGS) data, specifically aimed at experimental biologists. In an era of multi-centre genomic dataset generation, CODEX provides a single database where these samples are collected, uniformly processed and vetted. The main drive of CODEX is to provide the wider scientific community with instant access to high-quality NGS data, which, irrespective of the publishing laboratory, is directly comparable. CODEX allows users to immediately visualize or download processed datasets, or compare user-generated data against the database's cumulative knowledge-base. CODEX contains four types of NGS experiments: transcription factor chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq), histone modification ChIP-Seq, DNase-Seq and RNA-Seq. These are largely encompassed within two specialized repositories, HAEMCODE and ESCODE, which are focused on haematopoiesis and embryonic stem cell samples, respectively. To date, CODEX contains over 1000 samples, including 221 unique TFs and 93 unique cell types. CODEX therefore provides one of the most complete resources of publicly available NGS data for the direct interrogation of transcriptional programmes that regulate cellular identity and fate in the context of mammalian development, homeostasis and disease.
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Affiliation(s)
- Manuel Sánchez-Castillo
- Department of Haematology, Wellcome Trust-MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - David Ruau
- Department of Haematology, Wellcome Trust-MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - Adam C Wilkinson
- Department of Haematology, Wellcome Trust-MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - Felicia S L Ng
- Department of Haematology, Wellcome Trust-MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - Rebecca Hannah
- Department of Haematology, Wellcome Trust-MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - Evangelia Diamanti
- Department of Haematology, Wellcome Trust-MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - Patrick Lombard
- Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Nicola K Wilson
- Department of Haematology, Wellcome Trust-MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
| | - Berthold Gottgens
- Department of Haematology, Wellcome Trust-MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK
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34
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Calero-Nieto FJ, Ng FS, Wilson NK, Hannah R, Moignard V, Leal-Cervantes AI, Jimenez-Madrid I, Diamanti E, Wernisch L, Göttgens B. Key regulators control distinct transcriptional programmes in blood progenitor and mast cells. EMBO J 2014; 33:1212-26. [PMID: 24760698 PMCID: PMC4168288 DOI: 10.1002/embj.201386825] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [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: 09/06/2013] [Revised: 02/27/2014] [Accepted: 03/20/2014] [Indexed: 12/21/2022] Open
Abstract
Despite major advances in the generation of genome-wide binding maps, the mechanisms by which transcription factors (TFs) regulate cell type identity have remained largely obscure. Through comparative analysis of 10 key haematopoietic TFs in both mast cells and blood progenitors, we demonstrate that the largely cell type-specific binding profiles are not opportunistic, but instead contribute to cell type-specific transcriptional control, because (i) mathematical modelling of differential binding of shared TFs can explain differential gene expression, (ii) consensus binding sites are important for cell type-specific binding and (iii) knock-down of blood stem cell regulators in mast cells reveals mast cell-specific genes as direct targets. Finally, we show that the known mast cell regulators Mitf and c-fos likely contribute to the global reorganisation of TF binding profiles. Taken together therefore, our study elucidates how key regulatory TFs contribute to transcriptional programmes in several distinct mammalian cell types.
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Affiliation(s)
- Fernando J Calero-Nieto
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, Cambridge University, Cambridge, UK
| | - Felicia S Ng
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, Cambridge University, Cambridge, UK
| | - Nicola K Wilson
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, Cambridge University, Cambridge, UK
| | - Rebecca Hannah
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, Cambridge University, Cambridge, UK
| | - Victoria Moignard
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, Cambridge University, Cambridge, UK
| | - Ana I Leal-Cervantes
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, Cambridge University, Cambridge, UK
| | - Isabel Jimenez-Madrid
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, Cambridge University, Cambridge, UK
| | - Evangelia Diamanti
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, Cambridge University, Cambridge, UK
| | - Lorenz Wernisch
- MRC Biostatistics Unit, Institute of Public Health, Cambridge, UK
| | - Berthold Göttgens
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, Cambridge University, Cambridge, UK
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35
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Ruau D, Ng FSL, Wilson NK, Hannah R, Diamanti E, Lombard P, Woodhouse S, Göttgens B. Building an ENCODE-style data compendium on a shoestring. Nat Methods 2013; 10:926. [PMID: 24076986 DOI: 10.1038/nmeth.2643] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- David Ruau
- 1] Department of Hematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK. [2] Wellcome Trust-Medical Research Council (MRC) Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
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36
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Lancrin C, Mazan M, Stefanska M, Patel R, Lichtinger M, Costa G, Vargel O, Wilson NK, Möröy T, Bonifer C, Göttgens B, Kouskoff V, Lacaud G. GFI1 and GFI1B control the loss of endothelial identity of hemogenic endothelium during hematopoietic commitment. Blood 2012; 120:314-22. [PMID: 22668850 DOI: 10.1182/blood-2011-10-386094] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Recent studies have established that during embryonic development, hematopoietic progenitors and stem cells are generated from hemogenic endothelium precursors through a process termed endothelial to hematopoietic transition (EHT). The transcription factor RUNX1 is essential for this process, but its main downstream effectors remain largely unknown. Here, we report the identification of Gfi1 and Gfi1b as direct targets of RUNX1 and critical regulators of EHT. GFI1 and GFI1B are able to trigger, in the absence of RUNX1, the down-regulation of endothelial markers and the formation of round cells, a morphologic change characteristic of EHT. Conversely, blood progenitors in Gfi1- and Gfi1b-deficient embryos maintain the expression of endothelial genes. Moreover, those cells are not released from the yolk sac and disseminated into embryonic tissues. Taken together, our findings demonstrate a critical and specific role of the GFI1 transcription factors in the first steps of the process leading to the generation of hematopoietic progenitors from hemogenic endothelium.
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Affiliation(s)
- Christophe Lancrin
- Cancer Research UK Stem Cell Biology Group, Paterson Institute for Cancer Research, University of Manchester, Manchester, United Kingdom
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37
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Tanaka Y, Joshi A, Wilson NK, Kinston S, Nishikawa S, Göttgens B. The transcriptional programme controlled by Runx1 during early embryonic blood development. Dev Biol 2012; 366:404-19. [PMID: 22554697 PMCID: PMC3430866 DOI: 10.1016/j.ydbio.2012.03.024] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Revised: 03/20/2012] [Accepted: 03/28/2012] [Indexed: 01/22/2023]
Abstract
Transcription factors have long been recognised as powerful regulators of mammalian development yet it is largely unknown how individual key regulators operate within wider regulatory networks. Here we have used a combination of global gene expression and chromatin-immunoprecipitation approaches during the early stages of haematopoietic development to define the transcriptional programme controlled by Runx1, an essential regulator of blood cell specification. Integrated analysis of these complementary genome-wide datasets allowed us to construct a global regulatory network model, which suggested that key regulators are activated sequentially during blood specification, but will ultimately collaborate to control many haematopoietically expressed genes. Using the CD41/integrin alpha 2b gene as a model, cellular and in vivo studies showed that CD41 is controlled by both Scl/Tal1 and Runx1 in fully specified blood cells, and initiation of CD41 expression in E7.5 embryos is severely compromised in the absence of Runx1. Taken together, this study represents the first global analysis of the transcriptional programme controlled by any key haematopoietic regulator during the process of early blood cell specification. Moreover, the concept of interplay between sequentially deployed core regulators is likely to represent a design principle widely applicable to the transcriptional control of mammalian development.
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Affiliation(s)
- Yosuke Tanaka
- Laboratory for Stem Cell Biology, RIKEN Center for Developmental Biology, Kobe, Japan
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38
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Davison LJ, Wallace C, Cooper JD, Cope NF, Wilson NK, Smyth DJ, Howson JM, Saleh N, Al-Jeffery A, Angus KL, Stevens HE, Nutland S, Duley S, Coulson RM, Walker NM, Burren OS, Rice CM, Cambien F, Zeller T, Munzel T, Lackner K, Blankenberg S, Fraser P, Gottgens B, Todd JA. Long-range DNA looping and gene expression analyses identify DEXI as an autoimmune disease candidate gene. Hum Mol Genet 2011; 21:322-33. [PMID: 21989056 PMCID: PMC3276289 DOI: 10.1093/hmg/ddr468] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [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] [Indexed: 01/13/2023] Open
Abstract
The chromosome 16p13 region has been associated with several autoimmune diseases, including type 1 diabetes (T1D) and multiple sclerosis (MS). CLEC16A has been reported as the most likely candidate gene in the region, since it contains the most disease-associated single-nucleotide polymorphisms (SNPs), as well as an imunoreceptor tyrosine-based activation motif. However, here we report that intron 19 of CLEC16A, containing the most autoimmune disease-associated SNPs, appears to behave as a regulatory sequence, affecting the expression of a neighbouring gene, DEXI. The CLEC16A alleles that are protective from T1D and MS are associated with increased expression of DEXI, and no other genes in the region, in two independent monocyte gene expression data sets. Critically, using chromosome conformation capture (3C), we identified physical proximity between the DEXI promoter region and intron 19 of CLEC16A, separated by a loop of >150 kb. In reciprocal experiments, a 20 kb fragment of intron 19 of CLEC16A, containing SNPs associated with T1D and MS, as well as with DEXI expression, interacted with the promotor region of DEXI but not with candidate DNA fragments containing other potential causal genes in the region, including CLEC16A. Intron 19 of CLEC16A is highly enriched for transcription-factor-binding events and markers associated with enhancer activity. Taken together, these data indicate that although the causal variants in the 16p13 region lie within CLEC16A, DEXI is an unappreciated autoimmune disease candidate gene, and illustrate the power of the 3C approach in progressing from genome-wide association studies results to candidate causal genes.
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Affiliation(s)
- Lucy J. Davison
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
- To whom correspondence should be addressed at: JDRF/WT Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, Hills Road, Cambridge CB2 0XY, UK. Tel: +44 1223762104; Fax: +44 1223762102;
| | - Chris Wallace
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Jason D. Cooper
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Nathan F. Cope
- Nuclear Dynamics Laboratory, Babraham Institute, Cambridge, UK
| | - Nicola K. Wilson
- Haematopoetic Stem Cell Lab, Cambridge Institute for Medical Research (CIMR), NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Deborah J. Smyth
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Joanna M.M. Howson
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Nada Saleh
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Abdullah Al-Jeffery
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Karen L. Angus
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Helen E. Stevens
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Sarah Nutland
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Simon Duley
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Richard M.R. Coulson
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Neil M. Walker
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Oliver S. Burren
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
| | - Catherine M. Rice
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Francois Cambien
- INSERM UMRS 937, Pierre and Marie Curie University and Medical School, Paris, France
| | - Tanja Zeller
- University Heart Center Hamburg, Clinical for General and Interventional Cardiology, 20246 Hamburg, Germany
| | - Thomas Munzel
- Medizinische Klinik und Poliklinik, Johannes-Gutenberg Universität Mainz, Germany and
| | - Karl Lackner
- Department of Clinical Chemistry and Laboratory Medicine, Johannes-Gutenberg Universität Mainz, Germany
| | - Stefan Blankenberg
- University Heart Center Hamburg, Clinical for General and Interventional Cardiology, 20246 Hamburg, Germany
| | | | - Peter Fraser
- Nuclear Dynamics Laboratory, Babraham Institute, Cambridge, UK
| | - Berthold Gottgens
- Haematopoetic Stem Cell Lab, Cambridge Institute for Medical Research (CIMR), NIHR Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - John A. Todd
- Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics and
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39
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Levantini E, Lee S, Radomska HS, Hetherington CJ, Alberich-Jorda M, Amabile G, Zhang P, Gonzalez DA, Zhang J, Basseres DS, Wilson NK, Koschmieder S, Huang G, Zhang DE, Ebralidze AK, Bonifer C, Okuno Y, Gottgens B, Tenen DG. RUNX1 regulates the CD34 gene in haematopoietic stem cells by mediating interactions with a distal regulatory element. EMBO J 2011; 30:4059-70. [PMID: 21873977 DOI: 10.1038/emboj.2011.285] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2011] [Accepted: 07/19/2011] [Indexed: 12/22/2022] Open
Abstract
The transcription factor RUNX1 is essential to establish the haematopoietic gene expression programme; however, the mechanism of how it activates transcription of haematopoietic stem cell (HSC) genes is still elusive. Here, we obtained novel insights into RUNX1 function by studying regulation of the human CD34 gene, which is expressed in HSCs. Using transgenic mice carrying human CD34 PAC constructs, we identified a novel downstream regulatory element (DRE), which is bound by RUNX1 and is necessary for human CD34 expression in long-term (LT)-HSCs. Conditional deletion of Runx1 in mice harbouring human CD34 promoter-DRE constructs abrogates human CD34 expression. We demonstrate by chromosome conformation capture assays in LT-HSCs that the DRE physically interacts with the human CD34 promoter. Targeted mutagenesis of RUNX binding sites leads to perturbation of this interaction and decreased human CD34 expression in LT-HSCs. Overall, our in vivo data provide novel evidence about the role of RUNX1 in mediating interactions between distal and proximal elements of the HSC gene CD34.
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Affiliation(s)
- Elena Levantini
- Division of Hematology/Oncology, Beth Israel Deaconess Medical Center, Center for Life Science, Boston, MA, USA.
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40
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Wilson NK, Tijssen MR, Göttgens B. Deciphering transcriptional control mechanisms in hematopoiesis:the impact of high-throughput sequencing technologies. Exp Hematol 2011; 39:961-8. [PMID: 21781948 DOI: 10.1016/j.exphem.2011.07.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Accepted: 07/07/2011] [Indexed: 12/18/2022]
Abstract
One of the key challenges facing biomedical research is to extract biologically meaningful information from the ever-increasing scale and complexity of datasets generated through high-throughput approaches. Hematopoiesis represents one of the most experimentally tractable mammalian organ systems and, therefore, has historically tended to be at the forefront of applying new technologies within biomedical research. The combination of massive parallel sequencing technologies with chromatin-immunoprecipitation (ChIP-Seq) permits genome-scale characterization of histone modification status and identification of the complete set of binding sites for transcription factors. Because transcription factors have long been recognized as essential regulators of cell fate choice in hematopoiesis, ChIP-Seq technology has rapidly entered the arena of modern experimental hematology. Here we review the biological insights gained from ChIP-Seq studies performed in the hematopoietic system since the earliest studies just 4 years ago. A surprisingly large number of different approaches have already been implemented to extract new biological knowledge from ChIP-Seq datasets. By focusing on successful insights from multiple different approaches, we hope to provide stimulating reading for anyone wanting to utilize ChIP-Seq technology within their particular research field.
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Affiliation(s)
- Nicola K Wilson
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, UK
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41
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Heuser M, Yun H, Berg T, Yung E, Argiropoulos B, Kuchenbauer F, Park G, Hamwi I, Palmqvist L, Lai CK, Leung M, Lin G, Chaturvedi A, Thakur BK, Iwasaki M, Bilenky M, Thiessen N, Robertson G, Hirst M, Kent D, Wilson NK, Göttgens B, Eaves C, Cleary ML, Marra M, Ganser A, Humphries RK. Cell of origin in AML: susceptibility to MN1-induced transformation is regulated by the MEIS1/AbdB-like HOX protein complex. Cancer Cell 2011; 20:39-52. [PMID: 21741595 PMCID: PMC3951989 DOI: 10.1016/j.ccr.2011.06.020] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Revised: 04/03/2011] [Accepted: 06/06/2011] [Indexed: 12/14/2022]
Abstract
Pathways defining susceptibility of normal cells to oncogenic transformation may be valuable therapeutic targets. We characterized the cell of origin and its critical pathways in MN1-induced leukemias. Common myeloid (CMP) but not granulocyte-macrophage progenitors (GMP) could be transformed by MN1. Complementation studies of CMP-signature genes in GMPs demonstrated that MN1-leukemogenicity required the MEIS1/AbdB-like HOX-protein complex. ChIP-sequencing identified common target genes of MN1 and MEIS1 and demonstrated identical binding sites for a large proportion of their chromatin targets. Transcriptional repression of MEIS1 targets in established MN1 leukemias demonstrated antileukemic activity. As MN1 relies on but cannot activate expression of MEIS1/AbdB-like HOX proteins, transcriptional activity of these genes determines cellular susceptibility to MN1-induced transformation and may represent a promising therapeutic target.
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MESH Headings
- Animals
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Gene Expression Profiling
- Gene Expression Regulation, Leukemic
- Genes, Dominant/genetics
- Granulocyte-Macrophage Progenitor Cells/metabolism
- Granulocyte-Macrophage Progenitor Cells/pathology
- Homeodomain Proteins/metabolism
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Mice
- Mice, Inbred C57BL
- Models, Biological
- Multiprotein Complexes/metabolism
- Myeloid Ecotropic Viral Integration Site 1 Protein
- Neoplasm Proteins/metabolism
- Promoter Regions, Genetic/genetics
- Protein Binding
- Tumor Suppressor Proteins/metabolism
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Affiliation(s)
- Michael Heuser
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, 30625 Hannover, Germany
| | - Haiyang Yun
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, 30625 Hannover, Germany
| | - Tobias Berg
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Eric Yung
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Bob Argiropoulos
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Florian Kuchenbauer
- Department of Internal Medicine III, University Hospital Medical Center, 89075 Ulm, Germany
| | - Gyeongsin Park
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Iyas Hamwi
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, 30625 Hannover, Germany
| | - Lars Palmqvist
- Institute of Biomedicine, Sahlgrenska University Hospital, 413 45 Göteborg, Sweden
| | - Courteney K. Lai
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Malina Leung
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Grace Lin
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Anuhar Chaturvedi
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, 30625 Hannover, Germany
| | - Basant Kumar Thakur
- Department of Pediatric Hematology and Oncology, Hannover Medical School, 30625 Hannover, Germany
| | - Masayuki Iwasaki
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Mikhail Bilenky
- Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Nina Thiessen
- Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Gordon Robertson
- Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Martin Hirst
- Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - David Kent
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Nicola K. Wilson
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Bertie Göttgens
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Connie Eaves
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Michael L. Cleary
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Marco Marra
- Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
| | - Arnold Ganser
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, 30625 Hannover, Germany
| | - R. Keith Humphries
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia V5Z 1L3, Canada
- Department of Medicine, University of British Columbia, Vancouver, British Columbia V5Z 1M9, Canada
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42
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Hannah R, Joshi A, Wilson NK, Kinston S, Göttgens B. A compendium of genome-wide hematopoietic transcription factor maps supports the identification of gene regulatory control mechanisms. Exp Hematol 2011; 39:531-41. [PMID: 21338655 DOI: 10.1016/j.exphem.2011.02.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Revised: 02/09/2011] [Accepted: 02/14/2011] [Indexed: 12/20/2022]
Abstract
OBJECTIVE Key regulators of blood stem cell differentiation into the various mature hematopoietic lineages are commonly encoded by transcription factor genes. Elucidation of transcriptional regulatory mechanisms therefore holds great promise in advancing our understanding of both normal and malignant hematopoiesis. Recent technological advances have enabled the generation of genome-wide transcription factor binding maps using chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq). However, transcription factors operate in a combinatorial fashion suggesting that integrated analysis of genome-wide maps for multiple transcription factors will be essential to fully exploit these new genome-scale data sets. MATERIALS AND METHODS Here we have generated a compendium that integrates 53 ChIP-Seq studies covering 30 factors across all major hematopoietic lineages with a total of 754,380 binding peaks. We also used transgenic mouse assays to validate a newly predicted transcriptional enhancer. RESULTS Integrated analysis of all 53 ChIP-Seq studies demonstrated that cell-type identity exerts a larger influence on global transcription factor binding patterns than the nature of the individual transcription factors. Furthermore, regions highlighted by multifactor binding within specific gene loci overlap with known regulatory elements and also provide a useful guide for identifying novel elements, as demonstrated by transgenic analysis of a previously unrecognized enhancer in the Maml3 gene locus. CONCLUSIONS The ChIP-Seq compendium described here provides a valuable resource for the wider research community by accelerating the discovery of transcriptional mechanisms operating in the hematopoietic system.
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Affiliation(s)
- Rebecca Hannah
- University of Cambridge, Department of Haematology, Cambridge Institute for Medical Research, Hills Road, Cambridge, UK
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43
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Wilson NK, Foster SD, Wang X, Knezevic K, Schütte J, Kaimakis P, Chilarska PM, Kinston S, Ouwehand WH, Dzierzak E, Pimanda JE, de Bruijn MFTR, Göttgens B. Combinatorial transcriptional control in blood stem/progenitor cells: genome-wide analysis of ten major transcriptional regulators. Cell Stem Cell 2011; 7:532-44. [PMID: 20887958 DOI: 10.1016/j.stem.2010.07.016] [Citation(s) in RCA: 531] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2010] [Revised: 06/10/2010] [Accepted: 07/21/2010] [Indexed: 11/16/2022]
Abstract
Combinatorial transcription factor (TF) interactions control cellular phenotypes and, therefore, underpin stem cell formation, maintenance, and differentiation. Here, we report the genome-wide binding patterns and combinatorial interactions for ten key regulators of blood stem/progenitor cells (SCL/TAL1, LYL1, LMO2, GATA2, RUNX1, MEIS1, PU.1, ERG, FLI-1, and GFI1B), thus providing the most comprehensive TF data set for any adult stem/progenitor cell type to date. Genome-wide computational analysis of complex binding patterns, followed by functional validation, revealed the following: first, a previously unrecognized combinatorial interaction between a heptad of TFs (SCL, LYL1, LMO2, GATA2, RUNX1, ERG, and FLI-1). Second, we implicate direct protein-protein interactions between four key regulators (RUNX1, GATA2, SCL, and ERG) in stabilizing complex binding to DNA. Third, Runx1(+/-)::Gata2(+/-) compound heterozygous mice are not viable with severe hematopoietic defects at midgestation. Taken together, this study demonstrates the power of genome-wide analysis in generating novel functional insights into the transcriptional control of stem and progenitor cells.
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Affiliation(s)
- Nicola K Wilson
- University of Cambridge Department of Haematology, Cambridge Institute for Medical Research, Hills Road, Cambridge, CB2 0XY, UK
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Abstract
The control of differential gene expression is central to all metazoan biology. Haematopoiesis represents one of the best understood developmental systems where multipotent blood stem cells give rise to a range of phenotypically distinct mature cell types, all characterised by their own distinctive gene expression profiles. Small combinations of lineage-determining transcription factors drive the development of specific mature lineages from multipotent precursors. Given their powerful regulatory nature, it is imperative that the expression of these lineage-determining transcription factors is under tight control, a fact underlined by the observation that their misexpression commonly leads to the development of leukaemia. Here we review recent studies on the transcriptional control of key haematopoietic transcription factors, which demonstrate that gene loci contain multiple modular regulatory regions within which specific regulatory codes can be identified, that some modular elements cooperate to mediate appropriate tissue-specific expression, and that long-range approaches will be necessary to capture all relevant regulatory elements. We also explore how changes in technology will impact on this area of research in the future.
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Affiliation(s)
- Nicola K Wilson
- University of Cambridge Department of Haematology, Cambridge Institute for Medical Research, Hills Road, Cambridge, CB2 0XY, UK.
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45
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Calero-Nieto FJ, Wood AD, Wilson NK, Kinston S, Landry JR, Göttgens B. Transcriptional regulation of Elf-1: locus-wide analysis reveals four distinct promoters, a tissue-specific enhancer, control by PU.1 and the importance of Elf-1 downregulation for erythroid maturation. Nucleic Acids Res 2010; 38:6363-74. [PMID: 20525788 PMCID: PMC2965225 DOI: 10.1093/nar/gkq490] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Ets transcription factors play important roles during the development and maintenance of the haematopoietic system. One such factor, Elf-1 (E74-like factor 1) controls the expression of multiple essential haematopoietic regulators including Scl/Tal1, Lmo2 and PU.1. However, to integrate Elf-1 into the wider regulatory hierarchies controlling haematopoietic development and differentiation, regulatory elements as well as upstream regulators of Elf-1 need to be identified. Here, we have used locus-wide comparative genomic analysis coupled with chromatin immunoprecipitation (ChIP-chip) assays which resulted in the identification of five distinct regulatory regions directing expression of Elf-1. Further, ChIP-chip assays followed by functional validation demonstrated that the key haematopoietic transcription factor PU.1 is a major upstream regulator of Elf-1. Finally, overexpression studies in a well-characterized erythroid differentiation assay from primary murine fetal liver cells demonstrated that Elf-1 downregulation is necessary for terminal erythroid differentiation. Given the known activation of PU.1 by Elf-1 and our newly identified reciprocal activation of Elf-1 by PU.1, identification of an inhibitory role for Elf-1 has significant implications for our understanding of how PU.1 controls myeloid-erythroid differentiation. Our findings therefore not only represent the first report of Elf-1 regulation but also enhance our understanding of the wider regulatory networks that control haematopoiesis.
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Affiliation(s)
- Fernando J Calero-Nieto
- Department of Haematology, Cambridge Institute for Medical Research, Cambridge University, Hills Road, Cambridge CB2 0XY, UK.
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46
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Abstract
Haematopoiesis (or blood formation) in general and haematopoietic stem cells more specifically represent some of the best studied mammalian developmental systems. Sophisticated purification protocols coupled with powerful biological assays permit functional analysis of highly purified cell populations both in vitro and in vivo. However, despite several decades of intensive research, the sheer complexity of the haematopoietic system means that many important questions remain unanswered or even unanswerable with current experimental tools. Scientists have therefore increasingly turned to modelling to tackle complexity at multiple levels ranging from networks of genes to the behaviour of cells and tissues. Early modelling attempts of gene regulatory networks have focused on core regulatory circuits but have more recently been extended to genome-wide datasets such as expression profiling and ChIP-sequencing data. Modelling of haematopoietic cells and tissues has provided insight into the importance of phenotypic heterogeneity for the differentiation of normal progenitor cells as well as a greater understanding of treatment response for particular pathologies such as chronic myeloid leukaemia. Here we will review recent progress in attempts to reconstruct segments of the haematopoietic system. A variety of modelling strategies will be covered from small-scale, protein-DNA or protein-protein interactions to large scale reconstructions. Also discussed will be examples of how stochastic modelling may be applied to multi cell systems such as those seen in normal and malignant haematopoiesis.
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Affiliation(s)
- Samuel D Foster
- Haematopoietic Stem Cell Laboratory, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Hills Rd, Cambridge, CB2 0XY
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47
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Wilson NK, Chuang JC, Lyu C. Levels of persistent organic pollutants in several child day care centers. J Expo Anal Environ Epidemiol 2001; 11:449-58. [PMID: 11791162 DOI: 10.1038/sj.jea.7500190] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2001] [Indexed: 04/17/2023]
Abstract
The concentrations of a suite of persistent organic chemicals were measured in multiple media in 10 child day care centers located in central North Carolina. Five centers served mainly children from low-income families, as defined by the federal Women, Infants, and Children (WIC) assistance program, and five served mainly children from middle-income families. The targeted chemicals were chosen because of their probable carcinogenicity, acute or chronic toxicity, or hypothesized potential for endocrine system disruption. Targeted compounds included polycyclic aromatic hydrocarbons (PAHs), pentachloro- and nonyl-phenol, bisphenol-A, dibutyl and butylbenzyl phthalate, polychlorinated biphenyls (PCBs), organochlorine pesticides, the organophosphate pesticides diazinon and chlorpyrifos, and the herbicide 2,4-dichlorophenoxyacetic acid (2,4D). Sampled media were indoor and outdoor air, food and beverages, indoor dust, and outdoor play area soil. Concentrations of the targeted compounds were determined using a combination of extraction and analysis methods, depending on the media. Analysis was predominantly by gas chromatography/mass spectrometry (GC/MS) or gas chromatography with electron capture detection (GC/ECD). Concentrations of the targeted pollutants were low and well below the levels generally considered to be of concern as possible health hazards. Potential exposures to the target compounds were estimated from the concentrations in the various media, the children's daily time-activity schedules at day care, and the best currently available estimates of the inhalation rates (8.3 m(3)/day) and soil ingestion rates (100 mg/day) of children ages 3-5. The potential exposures for the target compounds differed depending on the compound class and the sampled media. Potential exposures through dietary ingestion were greater than those through inhalation, which were greater than those through nondietary ingestion, for the total of all PAHs, the phenols, the organophosphate pesticides, and the organochlorine pesticides. Potential exposures through dietary ingestion were greater than those through nondietary ingestion, which were greater than those through inhalation, for those PAHs that are probable human carcinogens (B2 PAH), the phthalate esters, and 2,4D. For the PCBs, exposures through inhalation were greater than those through nondietary ingestion, and exposures through dietary ingestion were smallest. Differences in targeted compound levels between the centers that serve mainly low-income clients and those that serve mainly middle-income clients were small and depended on the compound class and the medium.
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48
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Morgan MK, Stout DM, Wilson NK. Feasibility study of the potential for human exposure to pet-borne diazinon residues following lawn applications. Bull Environ Contam Toxicol 2001; 66:295-300. [PMID: 11178642 DOI: 10.1007/s001280004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Affiliation(s)
- M K Morgan
- National Exposure Research Laboratory, MD-56, Research Triangle Park, NC 27711, USA
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49
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Chuang JC, Callahan PJ, Lyu CW, Wilson NK. Polycyclic aromatic hydrocarbon exposures of children in low-income families. J Expo Anal Environ Epidemiol 1999; 9:85-98. [PMID: 10321348 DOI: 10.1038/sj.jea.7500003] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Children in low-income families may have high exposures to polycyclic aromatic hydrocarbons (PAH). Such exposures could result from household proximity to heavy traffic or industrial sources, environmental tobacco smoke, contaminated house dust or soil, among others. The objectives of this study were: to establish methods for measuring total PAH exposure of children in low-income families, to estimate the PAH exposures of these children, and to estimate the relative importance of the environmental pathways for PAH exposure. Analytical methods to determine PAH in air, dust, soil, and food and to determine hydroxy-PAH in urine samples were evaluated and validated. A two-home pilot study was conducted in downtown Durham, North Carolina (NC) during February 1994. One smoker's and one nonsmoker's household, which had preschool children and income at or below the official U.S. poverty level, participated. A nine-home winter and a nine-home summer study were conducted in Durham and the NC Piedmont area during February 1995 and August 1995, respectively. A summer study in four smokers' homes was also conducted. In each of these studies, multimedia samples were collected and analyzed for PAH or hydroxy-PAH. Summary statistics, Pearson correlations, and analysis of variance were performed on the combined data from these four field studies. An effective screening method was established for recruiting low-income families. The field protocol involved measurements of three homes in 2-day periods. This protocol should be suitable for large-scale studies. The results showed that indoor PAH levels were generally higher than outdoor PAH levels. Higher indoor PAH levels were observed in the smokers' homes compared to nonsmokers' homes. Higher outdoor PAH levels were found in inner city as opposed to rural areas. The relative concentration trend for PAH in dust and soil was: house dust > entryway dust > pathway soil. The PAH concentrations in adults' food samples were generally higher than those in children's food samples. Children's potential daily doses of PAH were higher than those of adults in the same household, when intakes were normalized to body weights. Inhalation is an important pathway for children's exposure to total PAH because of the high levels of naphthalene present in both indoor and outdoor air. Dietary ingestion and nondietary ingestion pathways became more important for children's exposure to the B2 PAH (ranked as probable human carcinogens, B2 by the U.S. EPA's Integrated Risk System), most of which are of low volatility. The analysis of variance results showed that inner city participants had higher total exposure to B2 PAH than did rural participants.
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Affiliation(s)
- J C Chuang
- National Exposure Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina, USA.
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50
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Chuang JC, Pollard MA, Chou YL, Menton RG, Wilson NK. Evaluation of enzyme-linked immunosorbent assay for the determination of polycyclic aromatic hydrocarbons in house dust and residential soil. Sci Total Environ 1998; 224:189-199. [PMID: 9926435 DOI: 10.1016/s0048-9697(98)00351-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Two commercially available enzyme-linked immunosorbent assays (ELISA) for total polycyclic aromatic hydrocarbon (PAH) and carcinogenic PAH (C-PAH) were evaluated. The testing procedures were refined for application to screening PAH and C-PAH in house dust and soil samples for human exposure studies. The overall method precision expressed as percent relative standard deviation (%RSD) of triplicate real world dust and soil samples was within +/- 29% (12-29%) for PAH ELISA and +/- 21% (5.9-21%) for C-PAH ELISA. Spike recoveries from real world dust/soil samples were 114 +/- 30% for phenanthrene from PAH ELISA and 120 +/- 8.2% for benzo[a]pyrene from C-PAH ELISA. The overall method accuracy for PAH and C-PAH assays cannot be assessed for multiple PAH components in dust/soil samples (which represent real-world samples), because of the assays' cross reactivities with other PAH components. Over 100 dust/soil samples from 13 North Carolina homes and 22 Arizona homes were analyzed by PAH and C-PAH assays, as well as by the conventional gas chromatography/mass spectrometry (GC/MS) method. Statistical analysis showed that dust/soil PAH data from ELISA and GC/MS methods are significantly different. In general PAH ELISA responses were higher than PAH GC/MS responses. The regression analysis showed that the linear relationship between ELISA and GC/MS measurements is not strong in the combined data. The relationship became stronger for the data from the same type of dust/soil samples. The screening performance of ELISA was evaluated based on the frequency distribution of ELISA and GC/MS data. The results indicated that the ELISA PAH and C-PAH assays cannot be used as a quantitative analytical tool for determining PAH in real-world dust/soil samples. However, the ELISA is an effective screening tool for ranking PAH concentrations in similar types of real world dust/soil samples.
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