1
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Xiang G, He X, Giardine BM, Isaac KJ, Taylor DJ, McCoy RC, Jansen C, Keller CA, Wixom AQ, Cockburn A, Miller A, Qi Q, He Y, Li Y, Lichtenberg J, Heuston EF, Anderson SM, Luan J, Vermunt MW, Yue F, Sauria MEG, Schatz MC, Taylor J, Gottgens B, Hughes JR, Higgs DR, Weiss MJ, Cheng Y, Blobel GA, Bodine DM, Zhang Y, Li Q, Mahony S, Hardison RC. Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes. bioRxiv 2024:2023.04.02.535219. [PMID: 37066352 PMCID: PMC10103973 DOI: 10.1101/2023.04.02.535219] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Knowledge of locations and activities of cis-regulatory elements (CREs) is needed to decipher basic mechanisms of gene regulation and to understand the impact of genetic variants on complex traits. Previous studies identified candidate CREs (cCREs) using epigenetic features in one species, making comparisons difficult between species. In contrast, we conducted an interspecies study defining epigenetic states and identifying cCREs in blood cell types to generate regulatory maps that are comparable between species, using integrative modeling of eight epigenetic features jointly in human and mouse in our Validated Systematic Integration (VISION) Project. The resulting catalogs of cCREs are useful resources for further studies of gene regulation in blood cells, indicated by high overlap with known functional elements and strong enrichment for human genetic variants associated with blood cell phenotypes. The contribution of each epigenetic state in cCREs to gene regulation, inferred from a multivariate regression, was used to estimate epigenetic state Regulatory Potential (esRP) scores for each cCRE in each cell type, which were used to categorize dynamic changes in cCREs. Groups of cCREs displaying similar patterns of regulatory activity in human and mouse cell types, obtained by joint clustering on esRP scores, harbored distinctive transcription factor binding motifs that were similar between species. An interspecies comparison of cCREs revealed both conserved and species-specific patterns of epigenetic evolution. Finally, we showed that comparisons of the epigenetic landscape between species can reveal elements with similar roles in regulation, even in the absence of genomic sequence alignment.
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Jaffredo T, Balduini A, Bigas A, Bernardi R, Bonnet D, Canque B, Charbord P, Cumano A, Delwel R, Durand C, Fibbe W, Forrester L, de Franceschi L, Ghevaert C, Gjertsen B, Gottgens B, Graf T, Heidenreich O, Hermine O, Higgs D, Kleanthous M, Klump H, Kouskoff V, Krause D, Lacaud G, Celso CL, Martens JH, Méndez-Ferrer S, Menendez P, Oostendorp R, Philipsen S, Porse B, Raaijmakers M, Robin C, Stunnenberg H, Theilgaard-Mönch K, Touw I, Vainchenker W, Corrons JLV, Yvernogeau L, Schuringa JJ. The EHA Research Roadmap: Normal Hematopoiesis. Hemasphere 2021; 5:e669. [PMID: 34853826 PMCID: PMC8615310 DOI: 10.1097/hs9.0000000000000669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/02/2021] [Indexed: 01/01/2023] Open
Affiliation(s)
- Thierry Jaffredo
- Sorbonne Université, Institut de Biologie Paris Seine, Laboratoire de Biologie du Développement/UMR7622, Paris, France
| | | | - Anna Bigas
- Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
- Josep Carreras Leukemia Research Institute (IJC), Barcelona, Spain
- Centro de Investigación Biomedica en Red-Oncología (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Rosa Bernardi
- IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Bruno Canque
- INSERM U976, Universite de Paris, Ecole Pratique des Hautes Etudes/PSL Research University, Institut de Recherche Saint Louis, France
| | - Pierre Charbord
- Sorbonne Université, Institut de Biologie Paris Seine, Laboratoire de Biologie du Développement/UMR7622, Paris, France
| | - Anna Cumano
- Unité Lymphopoïèse, Département d’Immunologie, INSERM U1223, Institut Pasteur, Cellule Pasteur, Université de Paris, France
| | - Ruud Delwel
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Charles Durand
- Sorbonne Université, Institut de Biologie Paris Seine, Laboratoire de Biologie du Développement/UMR7622, Paris, France
| | - Willem Fibbe
- Leiden University Medical Center, The Netherlands
| | - Lesley Forrester
- Centre for Regenerative Medicine, Institute for Regeneration and Repair, University of Edinburgh, Scotland
| | | | | | - Bjørn Gjertsen
- Department of Medicine, Hematology Section, Haukeland University Hospital, Bergen, Norway
- Department of Clinical Science, Centre for Cancer Biomarkers CCBIO, University of Bergen, Norway
| | - Berthold Gottgens
- Wellcome - MRC Cambridge Stem Cell Institute and Department of Haematology, University of Cambridge, United Kingdom
| | - Thomas Graf
- Center for Genomic Regulation, Barcelona Institute for Science and Technology and Universitat Pompeu Fabra, Barcelona, Spain
| | - Olaf Heidenreich
- Prinses Máxima Centrum voor kinderoncologie, Utecht, The Netherlands
| | - Olivier Hermine
- Department of Hematology and Laboratory of Physiopathology and Treatment of Blood Disorders, Hôpital Necker, Imagine institute, University of Paris, France
| | - Douglas Higgs
- MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, United Kingdom
| | | | - Hannes Klump
- Institute for Transfusion Medicine, University Hospital Essen, Germany
| | | | - Daniela Krause
- Goethe University Frankfurt and Georg-Speyer-Haus, Frankfurt am Main, Germany
| | - George Lacaud
- Cancer Research UK Manchester Institute, The University of Manchester, United Kingdom
| | | | - Joost H.A. Martens
- Department of Molecular Biology, RIMLS, Radboud University, Nijmegen, The Netherlands
| | | | - Pablo Menendez
- Centro de Investigación Biomedica en Red-Oncología (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
- Josep Carreras Leukemia Research Institute, Barcelona, Spain
- RICORS-RETAV, Instituto de Salud Carlos III, Madrid, Spain
- Department of Biomedicine, School of Medicine, Universitat de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avancats (ICREA), Barcelona, Spain
| | - Robert Oostendorp
- Department of Internal Medicine III, Technical University of Munich, School of Medicine, Germany
| | - Sjaak Philipsen
- Department of Cell Biology, Erasmus University Medical Center Rotterdam, The Netherlands
| | - Bo Porse
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Denmark
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, Denmark
| | - Marc Raaijmakers
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Catherine Robin
- Hubrecht Institute-KNAW and University Medical Center Utrecht, The Netherlands
- Regenerative medicine center, University Medical Center Utrecht, The Netherlands
| | - Henk Stunnenberg
- Prinses Máxima Centrum voor kinderoncologie, Utecht, The Netherlands
| | - Kim Theilgaard-Mönch
- The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Denmark
- Biotech Research and Innovation Center (BRIC), University of Copenhagen, Denmark
- Novo Nordisk Foundation Center for Stem Cell Biology, DanStem, Faculty of Health Sciences, University of Copenhagen, Denmark
- Department of Hematology, Rigshospitalet/National University Hospital, University of Copenhagen, Denmark
| | - Ivo Touw
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Joan-Lluis Vives Corrons
- Red Blood Cell and Hematopoietic Disorders Research Unit, Institute for Leukaemia Research Josep Carreras, Badalona, Barcelona
| | - Laurent Yvernogeau
- Sorbonne Université, Institut de Biologie Paris Seine, Laboratoire de Biologie du Développement/UMR7622, Paris, France
| | - Jan Jacob Schuringa
- Department of Experimental Hematology, University Medical Center Groningen, The Netherlands
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3
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Che JLC, Bode D, Kucinski I, Cull A, Bain F, Barile M, Boyd G, Belmonte M, Rubio-Lara J, Shepherd M, Clay A, Wilkinson A, Yamazaki S, Gottgens B, Kent D. 3008 – A HIGHLY EFFICIENT REPORTER SYSTEM FOR IDENTIFYING AND CHARACTERIZING IN VITRO EXPANDED HEMATOPOIETIC STEM CELLS. Exp Hematol 2021. [DOI: 10.1016/j.exphem.2021.12.230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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4
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Wilson N, Watcham S, Sturgess K, Prins D, Shepherd M, Hannah R, Green A, Kent D, Gottgens B. 3145 – CHARACTERISATION OF PRE-LEUKEMIC TRANSCRIPTOMIC LANDSCAPES REVEALS RE-DISTRIBUTION OF THE EARLIEST STAGES OF THE HEMATOPOIETIC HIERARCHY AND THE PUTATIVE UNDERLYING TRANSCRIPTIONAL DRIVING PROCESSES. Exp Hematol 2020. [DOI: 10.1016/j.exphem.2020.09.152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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5
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Kucinski I, Wilson N, Hannah R, Kinston S, Cauchy P, Lenaerts A, Grosschedl R, Gottgens B. 3018 – FUNCTIONAL DISSECTION OF TRANSCRIPTION FACTOR NETWORKS GOVERNING MULTIPOTENT PROGENITOR STATES. Exp Hematol 2020. [DOI: 10.1016/j.exphem.2020.09.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Abstract
Technological advances play a key role in furthering our understanding of stem cell biology, and advancing the prospects of regenerative therapies. Highly parallelized methods, developed in the last decade, can profile DNA, RNA, or proteins in thousands of cells and even capture data across two or more modalities (multiomics). This allows unbiased and precise definition of molecular cell states, thus allowing classification of cell types, tracking of differentiation trajectories, and discovery of underlying mechanisms. Despite being based on destructive techniques, novel experimental and bioinformatic approaches enable embedding and extraction of temporal information, which is essential for deconvolution of complex data and establishing cause and effect relationships. Here, we provide an overview of recent studies pertinent to stem cell biology, followed by an outlook on how further advances in single-cell molecular profiling and computational analysis have the potential to shape the future of both basic and translational research.
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Affiliation(s)
- Iwo Kucinski
- Wellcome-MRC Cambridge Stem Cell Institute and Department of Haematology, University of Cambridge, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge CB2 0AW, United Kingdom
| | - Berthold Gottgens
- Wellcome-MRC Cambridge Stem Cell Institute and Department of Haematology, University of Cambridge, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge CB2 0AW, United Kingdom
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7
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Abstract
The blood and immune systems develop in parallel during early prenatal life. Waves of hematopoiesis separated in anatomical space and time give rise to circulating and tissue-resident immune cells. Previous observations have relied on animal models, which differ from humans in both their developmental timeline and exposure to microorganisms. Decoding the composition of the human immune system is now tractable using single-cell multi-omics approaches. Large-scale single-cell genomics, imaging technologies, and the Human Cell Atlas initiative have together enabled a systems-level mapping of the developing human immune system and its emergent properties. Although the precise roles of specific immune cells during development require further investigation, the system as a whole displays malleable and responsive properties according to developmental need and environmental challenge.
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Affiliation(s)
- Jong-Eun Park
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Laura Jardine
- Biosciences Institute, Newcastle University, Faculty of Medical Sciences, Newcastle upon Tyne NE2 4HH, UK
| | - Berthold Gottgens
- Department of Haematology, University of Cambridge, Cambridge CB2 2XY, UK.,Wellcome and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 2XY, UK
| | - Sarah A Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK. .,Department of Physics/Cavendish Laboratory, University of Cambridge, JJ Thomson Ave., Cambridge CB3 0HE, UK
| | - Muzlifah Haniffa
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK. .,Biosciences Institute, Newcastle University, Faculty of Medical Sciences, Newcastle upon Tyne NE2 4HH, UK.,Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4LP, UK
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8
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Vijayabaskar MS, Goode DK, Obier N, Lichtinger M, Emmett AML, Abidin FNZ, Shar N, Hannah R, Assi SA, Lie-A-Ling M, Gottgens B, Lacaud G, Kouskoff V, Bonifer C, Westhead DR. Identification of gene specific cis-regulatory elements during differentiation of mouse embryonic stem cells: An integrative approach using high-throughput datasets. PLoS Comput Biol 2019; 15:e1007337. [PMID: 31682597 PMCID: PMC6855567 DOI: 10.1371/journal.pcbi.1007337] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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] [Received: 12/11/2017] [Revised: 11/14/2019] [Accepted: 08/15/2019] [Indexed: 01/22/2023] Open
Abstract
Gene expression governs cell fate, and is regulated via a complex interplay of transcription factors and molecules that change chromatin structure. Advances in sequencing-based assays have enabled investigation of these processes genome-wide, leading to large datasets that combine information on the dynamics of gene expression, transcription factor binding and chromatin structure as cells differentiate. While numerous studies focus on the effects of these features on broader gene regulation, less work has been done on the mechanisms of gene-specific transcriptional control. In this study, we have focussed on the latter by integrating gene expression data for the in vitro differentiation of murine ES cells to macrophages and cardiomyocytes, with dynamic data on chromatin structure, epigenetics and transcription factor binding. Combining a novel strategy to identify communities of related control elements with a penalized regression approach, we developed individual models to identify the potential control elements predictive of the expression of each gene. Our models were compared to an existing method and evaluated using the existing literature and new experimental data from embryonic stem cell differentiation reporter assays. Our method is able to identify transcriptional control elements in a gene specific manner that reflect known regulatory relationships and to generate useful hypotheses for further testing.
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Affiliation(s)
- M. S. Vijayabaskar
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Debbie K. Goode
- Wellcome Trust & MRC Cambridge Stem Cell Institute and Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Nadine Obier
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham. Birmingham, United Kingdom
| | - Monika Lichtinger
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham. Birmingham, United Kingdom
| | - Amber M. L. Emmett
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Fatin N. Zainul Abidin
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Nisar Shar
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Rebecca Hannah
- Wellcome Trust & MRC Cambridge Stem Cell Institute and Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Salam A. Assi
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham. Birmingham, United Kingdom
| | - Michael Lie-A-Ling
- CRUK Manchester Institute, University of Manchester, Manchester, United Kingdom
| | - Berthold Gottgens
- Wellcome Trust & MRC Cambridge Stem Cell Institute and Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Georges Lacaud
- CRUK Manchester Institute, University of Manchester, Manchester, United Kingdom
| | - Valerie Kouskoff
- Division of Developmental Biology and Medicine, The University of Manchester, Manchester, United Kingdom
| | - Constanze Bonifer
- Institute for Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham. Birmingham, United Kingdom
| | - David R. Westhead
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
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9
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Wilkinson AC, Ryan DJ, Kucinski I, Wang W, Yang J, Nestorowa S, Diamanti E, Tsang JCH, Wang J, Campos LS, Yang F, Fu B, Wilson N, Liu P, Gottgens B. Expanded potential stem cell media as a tool to study human developmental hematopoiesis in vitro. Exp Hematol 2019; 76:1-12.e5. [PMID: 31326613 PMCID: PMC6859476 DOI: 10.1016/j.exphem.2019.07.003] [Citation(s) in RCA: 5] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Revised: 07/09/2019] [Accepted: 07/11/2019] [Indexed: 01/05/2023]
Abstract
Pluripotent stem cell (PSC) differentiation in vitro represents a powerful and tractable model to study mammalian development and an unlimited source of cells for regenerative medicine. Within hematology, in vitro PSC hematopoiesis affords novel insights into blood formation and represents an exciting potential approach to generate hematopoietic and immune cell types for transplantation and transfusion. Most studies to date have focused on in vitro hematopoiesis from mouse PSCs and human PSCs. However, differences in mouse and human PSC culture protocols have complicated the translation of discoveries between these systems. We recently developed a novel chemical media formulation, expanded potential stem cell medium (EPSCM), that maintains mouse PSCs in a unique cellular state and extraembryonic differentiation capacity. Herein, we describe how EPSCM can be directly used to stably maintain human PSCs. We further demonstrate that human PSCs maintained in EPSCM can spontaneously form embryoid bodies and undergo in vitro hematopoiesis using a simple differentiation protocol, similar to mouse PSC differentiation. EPSCM-maintained human PSCs generated at least two hematopoietic cell populations, which displayed distinct transcriptional profiles by RNA-sequencing (RNA-seq) analysis. EPSCM also supports gene targeting using homologous recombination, affording generation of an SPI1 (PU.1) reporter PSC line to study and track in vitro hematopoiesis. EPSCM therefore provides a useful tool not only to study pluripotency but also hematopoietic cell specification and developmental-lineage commitment.
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Affiliation(s)
- Adam C Wilkinson
- Department of Haematology, Wellcome & MRC Cambridge Stem Cell Institute, Cambridge, UK
| | - David J Ryan
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Iwo Kucinski
- Department of Haematology, Wellcome & MRC Cambridge Stem Cell Institute, Cambridge, UK
| | - Wei Wang
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Jian Yang
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Sonia Nestorowa
- Department of Haematology, Wellcome & MRC Cambridge Stem Cell Institute, Cambridge, UK
| | - Evangelia Diamanti
- Department of Haematology, Wellcome & MRC Cambridge Stem Cell Institute, Cambridge, UK
| | | | - Juexuan Wang
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Lia S Campos
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Fengtang Yang
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Beiyuan Fu
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Nicola Wilson
- Department of Haematology, Wellcome & MRC Cambridge Stem Cell Institute, Cambridge, UK
| | - Pentao Liu
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK; School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, Stem Cell and Regenerative Medicine Consortium, University of Hong Kong, Hong Kong, China
| | - Berthold Gottgens
- Department of Haematology, Wellcome & MRC Cambridge Stem Cell Institute, Cambridge, UK.
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10
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Ottersbach K, Zaidan N, Diamanti E, Shaw E, Wilson N, Gottgens B. 2005 - GATA3 PROMOTES THE ENDOTHELIAL-TO-HEMATOPOIETIC TRANSITION VIA REGULATION OF THE CELL CYCLE. Exp Hematol 2019. [DOI: 10.1016/j.exphem.2019.06.280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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11
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Watcham S, Kucinski I, Gottgens B. New insights into hematopoietic differentiation landscapes from single-cell RNA sequencing. Blood 2019; 133:1415-1426. [PMID: 30728144 PMCID: PMC6440294 DOI: 10.1182/blood-2018-08-835355] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [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: 08/15/2018] [Accepted: 10/22/2018] [Indexed: 12/20/2022] Open
Abstract
Single-cell transcriptomics has recently emerged as a powerful tool to analyze cellular heterogeneity, discover new cell types, and infer putative differentiation routes. The technique has been rapidly embraced by the hematopoiesis research community, and like other technologies before, single-cell molecular profiling is widely expected to make important contributions to our understanding of the hematopoietic hierarchy. Much of this new interpretation relies on inference of the transcriptomic landscape as a representation of existing cellular states and associated transitions among them. Here we review how this model allows, under certain assumptions, charting of time-resolved differentiation trajectories with unparalleled resolution and how the landscape of multipotent cells may be rather devoid of discrete structures, challenging our preconceptions about stem and progenitor cell types and their organization. Finally, we highlight how promising technological advances may convert static differentiation landscapes into a dynamic cell flux model and thus provide a more holistic understanding of normal hematopoiesis and blood disorders.
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Affiliation(s)
- Sam Watcham
- Department of Haematology and Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Iwo Kucinski
- Department of Haematology and Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Berthold Gottgens
- Department of Haematology and Wellcome-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
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12
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Jawaid W, Ibarra - Soria X, Pijuan - Sala B, Ladopoulo V, Calero-Nieto F, Scialdone A, Jorg D, Vallier L, Simons B, Gottgens B, Marioni J. Single cell census of early murine organogenesis reveals a novel pathway regulating generation of blood progenitors. Exp Hematol 2017. [DOI: 10.1016/j.exphem.2017.06.218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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13
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Silverbush D, Grosskurth S, Wang D, Powell F, Gottgens B, Dry J, Fisher J. Cell-Specific Computational Modeling of the PIM Pathway in Acute Myeloid Leukemia. Cancer Res 2017; 77:827-838. [PMID: 27965317 DOI: 10.1158/0008-5472.can-16-1578] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [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: 06/20/2016] [Revised: 11/09/2016] [Accepted: 11/30/2016] [Indexed: 11/16/2022]
Abstract
Personalized therapy is a major goal of modern oncology, as patient responses vary greatly even within a histologically defined cancer subtype. This is especially true in acute myeloid leukemia (AML), which exhibits striking heterogeneity in molecular segmentation. When calibrated to cell-specific data, executable network models can reveal subtle differences in signaling that help explain differences in drug response. Furthermore, they can suggest drug combinations to increase efficacy and combat acquired resistance. Here, we experimentally tested dynamic proteomic changes and phenotypic responses in diverse AML cell lines treated with pan-PIM kinase inhibitor and fms-related tyrosine kinase 3 (FLT3) inhibitor as single agents and in combination. We constructed cell-specific executable models of the signaling axis, connecting genetic aberrations in FLT3, tyrosine kinase 2 (TYK2), platelet-derived growth factor receptor alpha (PDGFRA), and fibroblast growth factor receptor 1 (FGFR1) to cell proliferation and apoptosis via the PIM and PI3K kinases. The models capture key differences in signaling that later enabled them to accurately predict the unique proteomic changes and phenotypic responses of each cell line. Furthermore, using cell-specific models, we tailored combination therapies to individual cell lines and successfully validated their efficacy experimentally. Specifically, we showed that cells mildly responsive to PIM inhibition exhibited increased sensitivity in combination with PIK3CA inhibition. We also used the model to infer the origin of PIM resistance engineered through prolonged drug treatment of MOLM16 cell lines and successfully validated experimentally our prediction that this resistance can be overcome with AKT1/2 inhibition. Cancer Res; 77(4); 827-38. ©2016 AACR.
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Affiliation(s)
- Dana Silverbush
- Department of Computer Science, Tel-Aviv University, Tel-Aviv, Israel
- Microsoft Research, Cambridge, UK
| | | | | | | | - Berthold Gottgens
- Department of Haematology, Cambridge Institute for Medical Research and Wellcome Trust and MRC Stem Cell Institute, University of Cambridge, UK
| | - Jonathan Dry
- AstraZeneca Oncology IMED, Waltham, Massachusetts.
| | - Jasmin Fisher
- Microsoft Research, Cambridge, UK.
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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14
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Basilico S, Nieto FC, Gottgens B. Characterization of leukaemogenic regulatory networks in acute myeloid leukaemia. Exp Hematol 2016. [DOI: 10.1016/j.exphem.2016.06.088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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15
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Yang L, Rodriguez B, Mayle A, Park HJ, Lin X, Luo M, Jeong M, Curry CV, Kim SB, Ruau D, Zhang X, Zhou T, Zhou M, Rebel VI, Challen GA, Gottgens B, Lee JS, Rau R, Li W, Goodell MA. DNMT3A Loss Drives Enhancer Hypomethylation in FLT3-ITD-Associated Leukemias. Cancer Cell 2016; 29:922-934. [PMID: 27300438 PMCID: PMC4908977 DOI: 10.1016/j.ccell.2016.05.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [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: 03/23/2015] [Revised: 02/29/2016] [Accepted: 05/10/2016] [Indexed: 10/21/2022]
Abstract
DNMT3A, the gene encoding the de novo DNA methyltransferase 3A, is among the most frequently mutated genes in hematologic malignancies. However, the mechanisms through which DNMT3A normally suppresses malignancy development are unknown. Here, we show that DNMT3A loss synergizes with the FLT3 internal tandem duplication in a dose-influenced fashion to generate rapid lethal lymphoid or myeloid leukemias similar to their human counterparts. Loss of DNMT3A leads to reduced DNA methylation, predominantly at hematopoietic enhancer regions in both mouse and human samples. Myeloid and lymphoid diseases arise from transformed murine hematopoietic stem cells. Broadly, our findings support a role for DNMT3A as a guardian of the epigenetic state at enhancer regions, critical for inhibition of leukemic transformation.
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Affiliation(s)
- Liubin Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Benjamin Rodriguez
- Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Allison Mayle
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Hyun Jung Park
- Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Xueqiu Lin
- Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Bioinformatics, School of Life sciences and Technology, Tongji University, Shanghai 20092, China
| | - Min Luo
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Mira Jeong
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Choladda V. Curry
- Department of Pathology and Immunology, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Sang-Bae Kim
- Department of Systems Biology, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - David Ruau
- Wellcome Trust/MRC Stem Cell Institute, Cambridge CB2 0XY, UK
| | - Xiaotian Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Ting Zhou
- Greehey Children's Cancer Research Institute and Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | | | - Vivienne I. Rebel
- Greehey Children's Cancer Research Institute and Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Grant A. Challen
- Division of Oncology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | | | - Ju-Seog Lee
- Department of Systems Biology, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Rachel Rau
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Wei Li
- Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Margaret A. Goodell
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Systems Biology, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
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16
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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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17
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Chuang R, Hall BA, Benque D, Cook B, Ishtiaq S, Piterman N, Taylor A, Vardi M, Koschmieder S, Gottgens B, Fisher J. Drug target optimization in chronic myeloid leukemia using innovative computational platform. Sci Rep 2015; 5:8190. [PMID: 25644994 PMCID: PMC4650822 DOI: 10.1038/srep08190] [Citation(s) in RCA: 9] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 01/08/2015] [Indexed: 11/09/2022] Open
Abstract
Chronic Myeloid Leukemia (CML) represents a paradigm for the wider cancer field. Despite the fact that tyrosine kinase inhibitors have established targeted molecular therapy in CML, patients often face the risk of developing drug resistance, caused by mutations and/or activation of alternative cellular pathways. To optimize drug development, one needs to systematically test all possible combinations of drug targets within the genetic network that regulates the disease. The BioModelAnalyzer (BMA) is a user-friendly computational tool that allows us to do exactly that. We used BMA to build a CML network-model composed of 54 nodes linked by 104 interactions that encapsulates experimental data collected from 160 publications. While previous studies were limited by their focus on a single pathway or cellular process, our executable model allowed us to probe dynamic interactions between multiple pathways and cellular outcomes, suggest new combinatorial therapeutic targets, and highlight previously unexplored sensitivities to Interleukin-3.
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Affiliation(s)
- Ryan Chuang
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge CB3 0WA, UK
| | - Benjamin A. Hall
- Microsoft Research, Cambridge CB1 2FB, UK
- MRC Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, UK
| | | | - Byron Cook
- Microsoft Research, Cambridge CB1 2FB, UK
- Department of Computer Science, University College London, London, WC1E 6BT, UK
| | | | - Nir Piterman
- Department of Computer Science, University of Leicester, Leicester, LE1 7RH, UK
| | | | - Moshe Vardi
- Department of Computer Science, Rice University, Huston 77005-1892, Texas
| | - Steffen Koschmieder
- Department of Medicine, University Hospital of Aachen, Aachen D-52074, Germany
| | - Berthold Gottgens
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0XY, UK
- Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge CB2 0XY, UK
| | - Jasmin Fisher
- Microsoft Research, Cambridge CB1 2FB, UK
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
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18
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Abstract
SUMMARY Unraveling transcriptional circuits controlling embryonic stem cell maintenance and fate has great potential for improving our understanding of normal development as well as disease. To facilitate this, we have developed a novel web tool called 'TRES' that predicts the likely upstream regulators for a given gene list. This is achieved by integrating transcription factor (TF) binding events from 187 ChIP-sequencing and ChIP-on-chip datasets in murine and human embryonic stem (ES) cells with over 1000 mammalian TF sequence motifs. Using 114 TF perturbation gene sets, as well as 115 co-expression clusters in ES cells, we validate the utility of this approach. AVAILABILITY AND IMPLEMENTATION TRES is freely available at http://www.tres.roslin.ed.ac.uk. CONTACT Anagha.Joshi@roslin.ed.ac.uk or bg200@cam.ac.uk SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Christopher Pooley
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Division of Developmental Biology, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 8GR, UK and Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, Cambridge University, Cambridge, UK
| | - David Ruau
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Division of Developmental Biology, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 8GR, UK and Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, Cambridge University, Cambridge, UK
| | - Patrick Lombard
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Division of Developmental Biology, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 8GR, UK and Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, Cambridge University, Cambridge, UK
| | - Berthold Gottgens
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Division of Developmental Biology, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 8GR, UK and Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, Cambridge University, Cambridge, UK
| | - Anagha Joshi
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Division of Developmental Biology, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 8GR, UK and Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, Cambridge University, Cambridge, UK
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19
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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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20
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Joshi A, Gottgens B. Concerted bioinformatic analysis of the genome-scale blood transcription factor compendium reveals new control mechanisms. Mol Biosyst 2014; 10:2935-41. [PMID: 25133983 PMCID: PMC4263230 DOI: 10.1039/c4mb00354c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Transcription control insights using blood ChIP sequencing compendium.
Transcription factors play a key role in the development of a disease. ChIP-sequencing has become a preferred technique to investigate genome-wide binding patterns of transcription factors in vivo. Although this technology has led to many important discoveries, the rapidly increasing number of publicly available ChIP-sequencing datasets still remains a largely unexplored resource. Using a compendium of 144 publicly available murine ChIP-sequencing datasets in blood, we show that systematic bioinformatic analysis can unravel diverse aspects of transcription regulation; from genome-wide binding preferences, finding regulatory partners and assembling regulatory complexes, to identifying novel functions of transcription factors and investigating transcription dynamics during development.
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Affiliation(s)
- Anagha Joshi
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK.
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21
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Nasrallah R, Knezevic K, Gottgens B, Lacaud G, Kouskoff V, Pimanda J. Endoglin modulates stage specific cell responses during lineage commitment from embryonic stem cells to blood and endothelium. Exp Hematol 2014. [DOI: 10.1016/j.exphem.2014.07.203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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22
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Moignard V, Woodhouse S, Haghverdi L, Lilly J, Tanaka Y, Wilkinson A, Buettner F, Nishikawa SI, Piterman N, Kouskoff V, Theis F, Fisher J, Gottgens B. Decoding the transcriptional program for blood development from whole tissue single-cell gene expression measurements. Exp Hematol 2014. [DOI: 10.1016/j.exphem.2014.07.195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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23
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Wyspiańska BS, Bannister AJ, Barbieri I, Nangalia J, Godfrey A, Calero-Nieto FJ, Robson S, Rioja I, Li J, Wiese M, Cannizzaro E, Dawson MA, Huntly B, Prinjha RK, Green AR, Gottgens B, Kouzarides T. BET protein inhibition shows efficacy against JAK2V617F-driven neoplasms. Leukemia 2014; 28:88-97. [PMID: 23929215 DOI: 10.1038/leu.2013.234] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [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: 07/26/2013] [Accepted: 08/06/2013] [Indexed: 12/17/2022]
Abstract
Small molecule inhibition of the BET family of proteins, which bind acetylated lysines within histones, has been shown to have a marked therapeutic benefit in pre-clinical models of mixed lineage leukemia (MLL) fusion protein-driven leukemias. Here, we report that I-BET151, a highly specific BET family bromodomain inhibitor, leads to growth inhibition in a human erythroleukemic (HEL) cell line as well as in erythroid precursors isolated from polycythemia vera patients. One of the genes most highly downregulated by I-BET151 was LMO2, an important oncogenic regulator of hematopoietic stem cell development and erythropoiesis. We previously reported that LMO2 transcription is dependent upon Janus kinase 2 (JAK2) kinase activity in HEL cells. Here, we show that the transcriptional changes induced by a JAK2 inhibitor (TG101209) and I-BET151 in HEL cells are significantly over-lapping, suggesting a common pathway of action. We generated JAK2 inhibitor resistant HEL cells and showed that these retain sensitivity to I-BET151. These data highlight I-BET151 as a potential alternative treatment against myeloproliferative neoplasms driven by constitutively active JAK2 kinase.
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Affiliation(s)
- B S Wyspiańska
- Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge, UK
| | - A J Bannister
- Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge, UK
| | - I Barbieri
- Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge, UK
| | - J Nangalia
- 1] Department of Haematology, Cambridge Institute for Medical Research and The Wellcome Trust and MRC Stem Cell Institute, University of Cambridge, Cambridge, UK [2] Addenbrooke's Hospital, Department of Haematology, University of Cambridge, Cambridge, UK
| | - A Godfrey
- 1] Department of Haematology, Cambridge Institute for Medical Research and The Wellcome Trust and MRC Stem Cell Institute, University of Cambridge, Cambridge, UK [2] Addenbrooke's Hospital, Department of Haematology, University of Cambridge, Cambridge, UK
| | - F J Calero-Nieto
- Department of Haematology, Cambridge Institute for Medical Research and The Wellcome Trust and MRC Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - S Robson
- Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge, UK
| | - I Rioja
- Epinova DPU, Immuno-Inflammation Centre of Excellence for Drug Discovery, GlaxoSmithKline, Medicines Research Centre, Stevenage, UK
| | - J Li
- 1] Department of Haematology, Cambridge Institute for Medical Research and The Wellcome Trust and MRC Stem Cell Institute, University of Cambridge, Cambridge, UK [2] Addenbrooke's Hospital, Department of Haematology, University of Cambridge, Cambridge, UK
| | - M Wiese
- 1] Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge, UK [2] Department of Haematology, Cambridge Institute for Medical Research and The Wellcome Trust and MRC Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - E Cannizzaro
- 1] Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge, UK [2] Department of Haematology, Cambridge Institute for Medical Research and The Wellcome Trust and MRC Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - M A Dawson
- 1] Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge, UK [2] Department of Haematology, Cambridge Institute for Medical Research and The Wellcome Trust and MRC Stem Cell Institute, University of Cambridge, Cambridge, UK [3] Addenbrooke's Hospital, Department of Haematology, University of Cambridge, Cambridge, UK
| | - B Huntly
- Department of Haematology, Cambridge Institute for Medical Research and The Wellcome Trust and MRC Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - R K Prinjha
- Epinova DPU, Immuno-Inflammation Centre of Excellence for Drug Discovery, GlaxoSmithKline, Medicines Research Centre, Stevenage, UK
| | - A R Green
- 1] Department of Haematology, Cambridge Institute for Medical Research and The Wellcome Trust and MRC Stem Cell Institute, University of Cambridge, Cambridge, UK [2] Addenbrooke's Hospital, Department of Haematology, University of Cambridge, Cambridge, UK
| | - B Gottgens
- Department of Haematology, Cambridge Institute for Medical Research and The Wellcome Trust and MRC Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - T Kouzarides
- Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge, UK
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24
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Xiang P, Wei W, Lo C, Rosten P, Hou J, Hoodless PA, Bilenky M, Bonifer C, Cockerill PN, Kirkpatrick A, Gottgens B, Hirst M, Humphries KR. Delineating MEIS1 cis-regulatory elements active in hematopoietic cells. Leukemia 2013; 28:433-6. [PMID: 24097337 DOI: 10.1038/leu.2013.287] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [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)
- P Xiang
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - W Wei
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - C Lo
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - P Rosten
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - J Hou
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - P A Hoodless
- 1] Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada [2] University of British Columbia, Medical Genetics, Vancouver, British Columbia, Canada
| | - M Bilenky
- BC Cancer Agency, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - C Bonifer
- School of Cancer Sciences, College of Medical and Dental Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, UK
| | - P N Cockerill
- School of Immunity and Infection, College of Medical and Dental Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, UK
| | - A Kirkpatrick
- Department of Haematology, Cambridge Institute for Medical Research and Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - B Gottgens
- Department of Haematology, Cambridge Institute for Medical Research and Wellcome Trust and MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - M Hirst
- BC Cancer Agency, Canada's Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - K R Humphries
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
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25
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Beck D, Thoms J, Perera D, Unnikrishnan A, Knezevic K, O'Brien T, Gottgens B, Wong J, Pimanda J. Genome-wide analysis of transcriptional regulators in human hscs reveals a densely interconnected network of coding and non-coding genes. Exp Hematol 2013. [DOI: 10.1016/j.exphem.2013.05.063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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26
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Lau W, Dominicus C, Hannah R, Jones A, Green A, Gottgens B. JAK/ stat signalling during normal and pathological myelopoiesis with focus on erythropoiesis and megakaryopoiesis. Exp Hematol 2013. [DOI: 10.1016/j.exphem.2013.05.275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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27
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Calero-Nieto F, Ng F, Wilson N, Hannah R, Diamanti E, Gottgens B. Genome scale transcriptional control of haematopoietic cell type identity. Exp Hematol 2013. [DOI: 10.1016/j.exphem.2013.05.269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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28
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Schütte J, Bonzanni N, Kinston S, Lelieveld S, Moignard V, Heringa J, Feenstra A, Gottgens B. Reconstructing a core regulatory network model for blood stem/progenitor cells. Exp Hematol 2013. [DOI: 10.1016/j.exphem.2013.05.266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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29
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Wilson N, Butter F, Calero-Nieto F, Vidal IF, Kinston S, Merkenschlager M, Mann M, Gottgens B. Interrogating the relationship between transcription factor complex binding and transcriptional activation. Exp Hematol 2013. [DOI: 10.1016/j.exphem.2013.05.073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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30
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Magnúsdóttir E, Dietmann S, Murakami K, Günesdogan U, Tang F, Bao S, Diamanti E, Lao K, Gottgens B, Azim Surani M. A tripartite transcription factor network regulates primordial germ cell specification in mice. Nat Cell Biol 2013; 15:905-15. [PMID: 23851488 DOI: 10.1038/ncb2798] [Citation(s) in RCA: 208] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 06/03/2013] [Indexed: 12/11/2022]
Abstract
Transitions in cell states are controlled by combinatorial actions of transcription factors. BLIMP1, the key regulator of primordial germ cell (PGC) specification, apparently acts together with PRDM14 and AP2γ. To investigate their individual and combinatorial functions, we first sought an in vitro system for transcriptional readouts and chromatin immunoprecipitation sequencing analysis. We then integrated this data with information from single-cell transcriptome analysis of normal and mutant PGCs. Here we show that BLIMP1 binds directly to repress somatic and cell proliferation genes. It also directly induces AP2γ, which together with PRDM14 initiates the PGC-specific fate. We determined the occupancy of critical genes by AP2γ-which, when computed altogether with those of BLIMP1 and PRDM14 (both individually and cooperatively), reveals a tripartite mutually interdependent transcriptional network for PGCs. We also demonstrate that, in principle, BLIMP1, AP2γ and PRDM14 are sufficient for PGC specification, and the unprecedented resetting of the epigenome towards a basal state.
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Affiliation(s)
- Erna Magnúsdóttir
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
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31
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Calero-Nieto FJ, Joshi A, Bonadies N, Kinston S, Chan WI, Gudgin E, Pridans C, Landry JR, Kikuchi J, Huntly BJ, Gottgens B. HOX-mediated LMO2 expression in embryonic mesoderm is recapitulated in acute leukaemias. Oncogene 2013; 32:5471-80. [PMID: 23708655 PMCID: PMC3898495 DOI: 10.1038/onc.2013.175] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [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] [Received: 10/04/2012] [Revised: 02/25/2013] [Accepted: 03/31/2013] [Indexed: 01/02/2023]
Abstract
The Lim Domain Only 2 (LMO2) leukaemia oncogene encodes an LIM domain transcriptional cofactor required for early haematopoiesis. During embryogenesis, LMO2 is also expressed in developing tail and limb buds, an expression pattern we now show to be recapitulated in transgenic mice by an enhancer in LMO2 intron 4. Limb bud expression depended on a cluster of HOX binding sites, while posterior tail expression required the HOX sites and two E-boxes. Given the importance of both LMO2 and HOX genes in acute leukaemias, we further demonstrated that the regulatory hierarchy of HOX control of LMO2 is activated in leukaemia mouse models as well as in patient samples. Moreover, Lmo2 knock-down impaired the growth of leukaemic cells, and high LMO2 expression at diagnosis correlated with poor survival in cytogenetically normal AML patients. Taken together, these results establish a regulatory hierarchy of HOX control of LMO2 in normal development, which can be resurrected during leukaemia development. Redeployment of embryonic regulatory hierarchies in an aberrant context is likely to be relevant in human pathologies beyond the specific example of ectopic activation of LMO2.
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Affiliation(s)
- F J Calero-Nieto
- Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute, Cambridge Institute for Medical Research, Cambridge University, Cambridge, UK
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32
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Birdsey GM, Dryden NH, Shah AV, Hannah R, Hall MD, Haskard DO, Parsons M, Mason JC, Zvelebil M, Gottgens B, Ridley AJ, Randi AM. The transcription factor Erg regulates expression of histone deacetylase 6 and multiple pathways involved in endothelial cell migration and angiogenesis. Blood 2012; 119:894-903. [PMID: 22117042 DOI: 10.1182/blood-2011-04-350025] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [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: 02/07/2023] Open
Abstract
The endothelial ETS transcription factor Erg plays an important role in homeostasis and angiogenesis by regulating many endothelial functions including survival and junction stability. Here we show that Erg regulates endothelial cell (EC) migration. Transcriptome profiling of Erg-deficient ECs identified ∼ 80 genes involved in cell migration as candidate Erg targets, including many regulators of Rho- GTPases. Inhibition of Erg expression in HUVECs resulted in decreased migration in vitro, while Erg overexpression using adenovirus caused increased migration. Live-cell imaging of Erg-deficient HUVECs showed a reduction in lamellipodia, in line with decreased motility. Both actin and tubulin cytoskeletons were disrupted in Erg-deficient ECs, with a dramatic increase in tubulin acetylation. Among the most significant microarray hits was the cytosolic histone deacetylase 6 (HDAC6), a regulator of cell migration. Chromatin immunoprecipitation (ChIP) and transactivation studies demonstrated that Erg regulates HDAC6 expression. Rescue experiments confirmed that HDAC6 mediates the Erg-dependent regulation of tubulin acetylation and actin localization. In vivo, inhibition of Erg expression in angiogenic ECs resulted in decreased HDAC6 expression with increased tubulin acetylation. Thus, we have identified a novel function for the transcription factor Erg in regulating HDAC6 and multiple pathways essential for EC migration and angiogenesis.
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Affiliation(s)
- Graeme M Birdsey
- Cardiovascular Sciences, National Heart and Lung Institute, Faculty of Medicine, Imperial College London, United Kingdom
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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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Garcia-Ortega A, Cañete A, Quintero C, Silberstein L, Gil MP, Alvarez-Dolado M, Dekel B, Gottgens B, Sanchez M. Enhanced Hemato-Vascular Contribution Of SCL-3′Enh Expressing Fetal Liver Cells Uncovers Their Potential To Integrate In Extra-Medullary Adult Niches. Stem Cells 2009; 28:100-12. [DOI: 10.1002/stem.228] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Follows GA, Janes ME, Vallier L, Green AR, Gottgens B. Real-time PCR mapping of DNaseI-hypersensitive sites using a novel ligation-mediated amplification technique. Nucleic Acids Res 2007; 35:e56. [PMID: 17389645 PMCID: PMC1885650 DOI: 10.1093/nar/gkm108] [Citation(s) in RCA: 17] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Mapping sites within the genome that are hypersensitive to digestion with DNaseI is an important method for identifying DNA elements that regulate transcription. The standard approach to locating these DNaseI-hypersensitive sites (DHSs) has been to use Southern blotting techniques, although we, and others, have recently published alternative methods using a range of technologies including high-throughput sequencing and genomic array tiling paths. In this article, we describe a novel protocol to use real-time PCR to map DHS. Advantages of the technique reported here include the small cell numbers required for each analysis, rapid, relatively low-cost experiments with minimal need for specialist equipment. Presented examples include comparative DHS mapping of known TAL1/SCL regulatory elements between human embryonic stem cells and K562 cells.
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Affiliation(s)
- George A Follows
- Department of Haematology, Cambridge Institute for Medical Research, Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 2XY, UK.
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Delabesse E, Ogilvy S, Chapman MA, Piltz SG, Gottgens B, Green AR. Transcriptional regulation of the SCL locus: identification of an enhancer that targets the primitive erythroid lineage in vivo. Mol Cell Biol 2005; 25:5215-25. [PMID: 15923636 PMCID: PMC1140604 DOI: 10.1128/mcb.25.12.5215-5225.2005] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [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: 12/06/2004] [Revised: 01/16/2005] [Accepted: 03/02/2005] [Indexed: 12/29/2022] Open
Abstract
The stem cell leukemia (SCL) gene, also known as TAL-1, encodes a basic helix-loop-helix protein that is essential for the formation of all hematopoietic lineages, including primitive erythropoiesis. Appropriate transcriptional regulation is essential for the biological functions of SCL, and we have previously identified five distinct enhancers which target different subdomains of the normal SCL expression pattern. However, it is not known whether these SCL enhancers also regulate neighboring genes within the SCL locus, and the erythroid expression of SCL remains unexplained. Here, we have quantitated transcripts from SCL and neighboring genes in multiple hematopoietic cell types. Our results show striking coexpression of SCL and its immediate downstream neighbor, MAP17, suggesting that they share regulatory elements. A systematic survey of histone H3 and H4 acetylation throughout the SCL locus in different hematopoietic cell types identified several peaks of histone acetylation between SIL and MAP17, all of which corresponded to previously characterized SCL enhancers or to the MAP17 promoter. Downstream of MAP17 (and 40 kb downstream of SCL exon 1a), an additional peak of acetylation was identified in hematopoietic cells and was found to correlate with expression of SCL but not other neighboring genes. This +40 region is conserved in human-dog-mouse-rat sequence comparisons, functions as an erythroid cell-restricted enhancer in vitro, and directs beta-galactosidase expression to primitive, but not definitive, erythroblasts in transgenic mice. The SCL +40 enhancer provides a powerful tool for studying the molecular and cellular biology of the primitive erythroid lineage.
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Affiliation(s)
- E Delabesse
- University of Cambridge, Department of Hematology, Cambridge Institute for Medical Research, Hills Road, Cambridge CB2 2XY, United Kingdom
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Huss R, Heil M, Moosmann S, Ziegelhoeffer T, Sagebiel S, Seliger C, Kinston S, Gottgens B. Improved Arteriogenesis with Simultaneous Skeletal Muscle Repair in Ischemic Tissue by SCL+ Multipotent Adult Progenitor Cell Clones from Peripheral Blood. J Vasc Res 2004; 41:422-31. [PMID: 15477694 DOI: 10.1159/000081441] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2004] [Accepted: 08/13/2004] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The CD34(-) murine stem cell line RM26 cloned from peripheral blood mononuclear cells has been shown to generate hematopoietic progeny in lethally irradiated animals. The peripheral blood-derived cell clones expresses a variety of mesodermal and erythroid/myeloid transcription factors suggesting a multipotent differentiation potential like the bone marrow-derived 'multipotent adult progenitor cells' (MAP-C). METHODS SCL(+) CD34(-) RM26 cells were transfused intravenously into mice suffering from chronic hind-limb ischemia, evaluating the effect of stem cells on collateral artery growth and simultaneous skeletal muscle repair. RESULTS RM26 cells are capable of differentiating in vitro into endothelial cells when cultured on the appropriate collagen matrix. Activation of the SCL stem cell enhancer (SCL(+)) is mediated through the binding to two Ets and one GATA site and cells start to express milieu- and growth condition-dependent levels of the endothelial markers CD31 (PECAM) and Flt-1 (VEGF-R1). Intravenously infused RM26 cells significantly improved the collateral blood flow (arteriogenesis) and neo-angiogenesis formation in a murine hind-limb ischemia transplant model. Although transplanted RM26 cells did not integrate into the growing collateral arteries, cells were found adjacent to local arteriogenesis, but instead integrated into the ischemic skeletal muscle exclusively in the affected limb for simultaneous tissue repair. CONCLUSION These data suggest that molecularly primed hem-/mesangioblast-type adult progenitor cells can circulate in the peripheral blood improving perfusion of tissues with chronic ischemia and extending beyond the vascular compartment.
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Affiliation(s)
- Ralf Huss
- Institute of Pathology, University of Munich, Munich, Germany.
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Conrad C, Gottgens B, Kinston S, Ellwart J, Huss R. GATA transcription in a small rhodamine 123(low)CD34(+) subpopulation of a peripheral blood-derived CD34(-)CD105(+) mesenchymal cell line. Exp Hematol 2002; 30:887-95. [PMID: 12160840 DOI: 10.1016/s0301-472x(02)00865-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
OBJECTIVE Based on previous animal experiments that suggest the plasticity of peripheral blood-derived, CD34(-) stem cell lines, the aim of this study was to isolate CD34(-) stem cell lines from human peripheral blood cells and obtain evidence of their multipotency and plasticity. MATERIALS AND METHODS Adherent growing cells were isolated from peripheral blood mononuclear cells from a healthy volunteer donor and different cell clones were established after SV40 large-T-antigen-mediated immortalization. The immunophenotype of the cell lines was investigated by flow cytometry. One particular cell clone, V54/2, was stained with rhodamine 123, and the Rh123(low) and Rh123(high) subpopulations were sorted for a reverse transcriptase polymerase chain reaction gene expression survey and distinct differences in morphology and biologic behavior. RESULTS The peripheral blood-derived and fibroblast-like cell line V54/2 expressed high levels of CD10 and CD105 and showed only a very low level expression of CD34 (<1.0%) and CD117 (c-kit). Among the entire CD34(-)CD105(+) cell population that transcribed factors such as Myb, Tie-1, and VEGF, there was a small Rh123(low)CD34(+) subpopulation that transcribed significant levels of several members of the GATA family of transcription factors. The morphology of the Rh123(low)CD34(+) (also expressing the P-glycoprotein) was different compared to the Rh123(high)CD34(-) population. Mesenchymal differentiation into glial fibrillary acidic protein (GFAP)(+) glial cells could be shown from the entire CD34(-)CD105(+) cell population. CONCLUSIONS The findings provide evidence that it is possible to isolate CD34(-)CD105(+) mesenchymal stem cell lines from human peripheral blood cells that contain a small subpopulation of CD34(+) and GATA-transcribing cells. Those cells are potential hematopoietic progenitors and can be recruited from the CD34(-) stem cell pool. The plasticity of stem cells seems to require essential molecular tools, such as a panel of transcription factors, to respond to the environmental demand within a biologic system.
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Barton LM, Gottgens B, Gering M, Gilbert JG, Grafham D, Rogers J, Bentley D, Patient R, Green AR. Regulation of the stem cell leukemia (SCL) gene: a tale of two fishes. Proc Natl Acad Sci U S A 2001; 98:6747-52. [PMID: 11381108 PMCID: PMC34424 DOI: 10.1073/pnas.101532998] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [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: 11/07/2000] [Indexed: 11/18/2022] Open
Abstract
The stem cell leukemia (SCL) gene encodes a tissue-specific basic helix-loop-helix (bHLH) protein with a pivotal role in hemopoiesis and vasculogenesis. Several enhancers have been identified within the murine SCL locus that direct reporter gene expression to subdomains of the normal SCL expression pattern, and long-range sequence comparisons of the human and murine SCL loci have identified additional candidate enhancers. To facilitate the characterization of regulatory elements, we have sequenced and analyzed 33 kb of the SCL genomic locus from the pufferfish Fugu rubripes, a species with a highly compact genome. Although the pattern of SCL expression is highly conserved from mammals to teleost fish, the genes flanking pufferfish SCL were unrelated to those known to flank both avian and mammalian SCL genes. These data suggest that SCL regulatory elements are confined to the region between the upstream and downstream flanking genes, a region of 65 kb in human and 8.5 kb in pufferfish. Consistent with this hypothesis, the entire 33-kb pufferfish SCL locus directed appropriate expression to hemopoietic and neural tissue in transgenic zebrafish embryos, as did a 10.4-kb fragment containing the SCL gene and extending to the 5' and 3' flanking genes. These results demonstrate the power of combining the compact genome of the pufferfish with the advantages that zebrafish provide for studies of gene regulation during development. Furthermore, the pufferfish SCL locus provides a powerful tool for the manipulation of hemopoiesis and vasculogenesis in vivo.
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Affiliation(s)
- L M Barton
- Department of Hematology, Cambridge Institute for Medical Research, University of Cambridge, Addenbrookes Hospital, Cambridge CB2 2XY, United Kingdom
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Banham AH, Asante-Owusu RN, Gottgens B, Thompson S, Kingsnorth CS, Mellor E, Casselton LA. An N-Terminal Dimerization Domain Permits Homeodomain Proteins To Choose Compatible Partners and Initiate Sexual Development in the Mushroom Coprinus cinereus. Plant Cell 1995; 7:773-83. [PMID: 12242384 PMCID: PMC160831 DOI: 10.1105/tpc.7.6.773] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The A mating-type locus of the mushroom Coprinus cinereus contains three or more paralogous pairs of genes encoding two families of homeodomain proteins (HD1 and HD2). A successful mating brings together different allelic forms of at least one gene, and this is sufficient to trigger initial steps in sexual development. Previous studies have suggested that development is regulated by heterodimerization between HD1 and HD2 proteins. In this report, we describe 5[prime] gene deletions and 5[prime] end exchanges showing that the N-terminal regions of the proteins are essential for choosing a compatible partner but not for regulating gene transcription. Using an in vitro glutathione S-transferase association assay, we demonstrated heterodimerization between HD1 and HD2 proteins and found that heterodimerization only occurs between compatible protein combinations. The N-terminal regions of the proteins were sufficient to mediate dimerization, and N-terminal swaps resulted in a predicted change in dimerization specificity. By analyzing the N-terminal amino acid sequences of HD1 proteins, we identified two potential coiled-coil motifs whose relative positions vary in paralogous proteins but are both required for in vivo function.
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Affiliation(s)
- A H Banham
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, United Kingdom
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