1
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Collins J, Astle WJ, Megy K, Mumford AD, Vuckovic D. Advances in understanding the pathogenesis of hereditary macrothrombocytopenia. Br J Haematol 2021; 195:25-45. [PMID: 33783834 DOI: 10.1111/bjh.17409] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 02/19/2021] [Indexed: 12/14/2022]
Abstract
Low platelet count, or thrombocytopenia, is a common haematological abnormality, with a wide differential diagnosis, which may represent a clinically significant underlying pathology. Macrothrombocytopenia, the presence of large platelets in combination with thrombocytopenia, can be acquired or hereditary and indicative of a complex disorder. In this review, we discuss the interpretation of platelet count and volume measured by automated haematology analysers and highlight some important technical considerations relevant to the analysis of blood samples with macrothrombocytopenia. We review how large cohorts, such as the UK Biobank and INTERVAL studies, have enabled an accurate description of the distribution and co-variation of platelet parameters in adult populations. We discuss how genome-wide association studies have identified hundreds of genetic associations with platelet count and mean platelet volume, which in aggregate can explain large fractions of phenotypic variance, consistent with a complex genetic architecture and polygenic inheritance. Finally, we describe the large genetic diagnostic and discovery programmes, which, simultaneously to genome-wide association studies, have expanded the repertoire of genes and variants associated with extreme platelet phenotypes. These have advanced our understanding of the pathogenesis of hereditary macrothrombocytopenia and support a future clinical diagnostic strategy that utilises genotype alongside clinical and laboratory phenotype data.
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Affiliation(s)
- Janine Collins
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, Barts Health NHS Trust, London, UK
| | - William J Astle
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge Institute of Public Health, Forvie Site, Robinson Way, Cambridge, UK
| | - Karyn Megy
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- National Health Service Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
- NIHR BioResource, Cambridge University Hospitals NHS Foundation, Cambridge Biomedical Campus, Cambridge, UK
| | - Andrew D Mumford
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Dragana Vuckovic
- Department of Biostatistics and Epidemiology, Faculty of Medicine, Imperial College London, London, UK
- Human Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- National Institute for Health Research Blood and Transplant Research Unit (NIHR BTRU) in Donor Health and Genomics, University of Cambridge, Cambridge, UK
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2
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Choudhuri A, Trompouki E, Abraham BJ, Colli LM, Kock KH, Mallard W, Yang ML, Vinjamur DS, Ghamari A, Sporrij A, Hoi K, Hummel B, Boatman S, Chan V, Tseng S, Nandakumar SK, Yang S, Lichtig A, Superdock M, Grimes SN, Bowman TV, Zhou Y, Takahashi S, Joehanes R, Cantor AB, Bauer DE, Ganesh SK, Rinn J, Albert PS, Bulyk ML, Chanock SJ, Young RA, Zon LI. Common variants in signaling transcription-factor-binding sites drive phenotypic variability in red blood cell traits. Nat Genet 2020; 52:1333-1345. [PMID: 33230299 DOI: 10.1038/s41588-020-00738-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 10/14/2020] [Indexed: 12/13/2022]
Abstract
Genome-wide association studies identify genomic variants associated with human traits and diseases. Most trait-associated variants are located within cell-type-specific enhancers, but the molecular mechanisms governing phenotypic variation are less well understood. Here, we show that many enhancer variants associated with red blood cell (RBC) traits map to enhancers that are co-bound by lineage-specific master transcription factors (MTFs) and signaling transcription factors (STFs) responsive to extracellular signals. The majority of enhancer variants reside on STF and not MTF motifs, perturbing DNA binding by various STFs (BMP/TGF-β-directed SMADs or WNT-induced TCFs) and affecting target gene expression. Analyses of engineered human blood cells and expression quantitative trait loci verify that disrupted STF binding leads to altered gene expression. Our results propose that the majority of the RBC-trait-associated variants that reside on transcription-factor-binding sequences fall in STF target sequences, suggesting that the phenotypic variation of RBC traits could stem from altered responsiveness to extracellular stimuli.
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Affiliation(s)
- Avik Choudhuri
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Eirini Trompouki
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.,Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.,CIBSS Centre for Integrative Biological Signaling Studies, University of Freiburg, Freiburg, Germany
| | - Brian J Abraham
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.,Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Leandro M Colli
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, MD, USA.,Department of Medical Imaging, Hematology, and Medical Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Kian Hong Kock
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA, USA
| | - William Mallard
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,The Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Min-Lee Yang
- Division of Cardiovascular Medicine, Department of Internal Medicine and Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Divya S Vinjamur
- Division of Hematology and Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Alireza Ghamari
- Division of Pediatric Hematology-Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Audrey Sporrij
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Karen Hoi
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Barbara Hummel
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Sonja Boatman
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Victoria Chan
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Sierra Tseng
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Satish K Nandakumar
- Division of Hematology and Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Song Yang
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Asher Lichtig
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Michael Superdock
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Seraj N Grimes
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Summer Institute in Biomedical Informatics, Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Teresa V Bowman
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.,Albert Einstein College of Medicine, Bronx, NY, USA
| | - Yi Zhou
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | | | - Roby Joehanes
- Hebrew Senior Life, Harvard Medical School, Boston, MA, USA.,Framingham Heart Study, National Heart, Blood, and Lung Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alan B Cantor
- Division of Pediatric Hematology-Oncology, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Daniel E Bauer
- Division of Hematology and Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Santhi K Ganesh
- Division of Cardiovascular Medicine, Department of Internal Medicine and Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - John Rinn
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
| | - Paul S Albert
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Program in Biological and Biomedical Sciences, Harvard University, Cambridge, MA, USA.,The Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.,Summer Institute in Biomedical Informatics, Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.,Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research, Cambridge, MA, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Leonard I Zon
- Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA. .,Stem Cell Program and Division of Hematology/Oncology, Children's Hospital Boston, Harvard Stem Cell Institute, Harvard Medical School and Howard Hughes Medical Institute, Boston, MA, USA.
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3
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Villar D, Frost S, Deloukas P, Tinker A. The contribution of non-coding regulatory elements to cardiovascular disease. Open Biol 2020; 10:200088. [PMID: 32603637 PMCID: PMC7574544 DOI: 10.1098/rsob.200088] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 06/08/2020] [Indexed: 12/17/2022] Open
Abstract
Cardiovascular disease collectively accounts for a quarter of deaths worldwide. Genome-wide association studies across a range of cardiovascular traits and pathologies have highlighted the prevalence of common non-coding genetic variants within candidate loci. Here, we review genetic, epigenomic and molecular approaches to investigate the contribution of non-coding regulatory elements in cardiovascular biology. We then discuss recent insights on the emerging role of non-coding variation in predisposition to cardiovascular disease, with a focus on novel mechanistic examples from functional genomics studies. Lastly, we consider the clinical significance of these findings at present, and some of the current challenges facing the field.
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Affiliation(s)
- Diego Villar
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London E1 2AT, UK
| | - Stephanie Frost
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark Street, London E1 2AT, UK
| | - Panos Deloukas
- William Harvey Research Institute, Heart Centre, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Andrew Tinker
- William Harvey Research Institute, Heart Centre, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
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4
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Izzi B, Bonaccio M, de Gaetano G, Cerletti C. Learning by counting blood platelets in population studies: survey and perspective a long way after Bizzozero. J Thromb Haemost 2018; 16:1711-1721. [PMID: 29888860 DOI: 10.1111/jth.14202] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Indexed: 01/13/2023]
Abstract
Platelet count represents a useful tool in clinical practice to discriminate individuals at higher risk of bleeding. Less obvious is the role of platelet count variability within the normal range of distribution in shaping the individual's disease risk profile. Epidemiological studies have shown that platelet count in the adult general population is associated with a number of health outcomes related to hemostasis and thrombosis. However, recent studies are suggesting a possible role of this platelet index also as an independent risk factor. In this review of adult population studies, we will first focus on known genetic and non-genetic determinants of platelet number variability. Next, we will evaluate platelet count as a marker and/or a predictor of disease risk and its interaction with other risk factors. We will then discuss the role of platelet count variability within the normal distribution range as a contribution to disease and mortality risk. The possibility of considering platelet count as a simple, inexpensive indicator of increased risk of disease and death in general populations could open new opportunities to investigate novel platelet pathophysiological roles as well as therapeutic opportunities. Future studies should also consider platelet count, not only platelet function, as a modulator of disease and mortality risk.
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Affiliation(s)
- B Izzi
- Department of Epidemiology and Prevention, IRCCS Istituto Neurologico Mediterraneo Neuromed, Pozzilli (IS), Italy
| | - M Bonaccio
- Department of Epidemiology and Prevention, IRCCS Istituto Neurologico Mediterraneo Neuromed, Pozzilli (IS), Italy
| | - G de Gaetano
- Department of Epidemiology and Prevention, IRCCS Istituto Neurologico Mediterraneo Neuromed, Pozzilli (IS), Italy
| | - C Cerletti
- Department of Epidemiology and Prevention, IRCCS Istituto Neurologico Mediterraneo Neuromed, Pozzilli (IS), Italy
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5
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Antoniani C, Romano O, Miccio A. Concise Review: Epigenetic Regulation of Hematopoiesis: Biological Insights and Therapeutic Applications. Stem Cells Transl Med 2017; 6:2106-2114. [PMID: 29080249 PMCID: PMC5702521 DOI: 10.1002/sctm.17-0192] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 09/28/2017] [Indexed: 12/25/2022] Open
Abstract
Hematopoiesis is the process of blood cell formation starting from hematopoietic stem/progenitor cells (HSPCs). The understanding of regulatory networks involved in hematopoiesis and their impact on gene expression is crucial to decipher the molecular mechanisms that control hematopoietic development in physiological and pathological conditions, and to develop novel therapeutic strategies. An increasing number of epigenetic studies aim at defining, on a genome‐wide scale, the cis‐regulatory sequences (e.g., promoters and enhancers) used by human HSPCs and their lineage‐restricted progeny at different stages of development. In parallel, human genetic studies allowed the discovery of genetic variants mapping to cis‐regulatory elements and associated with hematological phenotypes and diseases. Here, we summarize recent epigenetic and genetic studies in hematopoietic cells that give insights into human hematopoiesis and provide a knowledge basis for the development of novel therapeutic approaches. As an example, we discuss the therapeutic approaches targeting cis‐regulatory regions to reactivate fetal hemoglobin for the treatment of β‐hemoglobinopathies. Epigenetic studies allowed the definition of cis‐regulatory sequences used by human hematopoietic cells. Promoters and enhancers are targeted by transcription factors and are characterized by specific histone modifications. Genetic variants mapping to cis‐regulatory elements are often associated with hematological phenotypes and diseases. In some cases, these variants can alter the binding of transcription factors, thus changing the expression of the target genes. Targeting cis‐regulatory sequences represents a promising therapeutic approach for many hematological diseases. Stem Cells Translational Medicine2017;6:2106–2114
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Affiliation(s)
- Chiara Antoniani
- Laboratory of Chromatin and Gene Regulation During Development, INSERM UMR1163, Imagine Institute, Paris, France.,Paris Descartes, Sorbonne Paris Cité University, Imagine Institute, Paris, France
| | - Oriana Romano
- Laboratory of Chromatin and Gene Regulation During Development, INSERM UMR1163, Imagine Institute, Paris, France.,Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Annarita Miccio
- Laboratory of Chromatin and Gene Regulation During Development, INSERM UMR1163, Imagine Institute, Paris, France.,Paris Descartes, Sorbonne Paris Cité University, Imagine Institute, Paris, France
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6
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Petersen R, Lambourne JJ, Javierre BM, Grassi L, Kreuzhuber R, Ruklisa D, Rosa IM, Tomé AR, Elding H, van Geffen JP, Jiang T, Farrow S, Cairns J, Al-Subaie AM, Ashford S, Attwood A, Batista J, Bouman H, Burden F, Choudry FA, Clarke L, Flicek P, Garner SF, Haimel M, Kempster C, Ladopoulos V, Lenaerts AS, Materek PM, McKinney H, Meacham S, Mead D, Nagy M, Penkett CJ, Rendon A, Seyres D, Sun B, Tuna S, van der Weide ME, Wingett SW, Martens JH, Stegle O, Richardson S, Vallier L, Roberts DJ, Freson K, Wernisch L, Stunnenberg HG, Danesh J, Fraser P, Soranzo N, Butterworth AS, Heemskerk JW, Turro E, Spivakov M, Ouwehand WH, Astle WJ, Downes K, Kostadima M, Frontini M. Platelet function is modified by common sequence variation in megakaryocyte super enhancers. Nat Commun 2017; 8:16058. [PMID: 28703137 PMCID: PMC5511350 DOI: 10.1038/ncomms16058] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 05/19/2017] [Indexed: 12/26/2022] Open
Abstract
Linking non-coding genetic variants associated with the risk of diseases or disease-relevant traits to target genes is a crucial step to realize GWAS potential in the introduction of precision medicine. Here we set out to determine the mechanisms underpinning variant association with platelet quantitative traits using cell type-matched epigenomic data and promoter long-range interactions. We identify potential regulatory functions for 423 of 565 (75%) non-coding variants associated with platelet traits and we demonstrate, through ex vivo and proof of principle genome editing validation, that variants in super enhancers play an important role in controlling archetypical platelet functions. Numerous genetic variants, including those located in the non-coding regions of the genome, are known to be associated with blood cells traits. Here, Frontini and colleagues investigate their potential regulatory functions using epigenomic data and promoter long-range interactions.
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Affiliation(s)
- Romina Petersen
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,National Health Service Blood and Transplant (NHSBT), Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
| | - John J Lambourne
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,National Health Service Blood and Transplant (NHSBT), Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
| | - Biola M Javierre
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Luigi Grassi
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,National Health Service Blood and Transplant (NHSBT), Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,NIHR BioResource-Rare Diseases, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Roman Kreuzhuber
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,National Health Service Blood and Transplant (NHSBT), Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Dace Ruklisa
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,National Health Service Blood and Transplant (NHSBT), Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,Medical Research Council Biostatistics Unit, University of Cambridge, Forvie Site, Cambridge Biomedical Campus, Cambridge CB2 0SR, UK
| | - Isabel M Rosa
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,National Health Service Blood and Transplant (NHSBT), Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
| | - Ana R Tomé
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,National Health Service Blood and Transplant (NHSBT), Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
| | - Heather Elding
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,Strangeways Research Laboratory, The National Institute for Health Research (NIHR) Blood and Transplant Unit in Donor Health and Genomics at the University of Cambridge, University of Cambridge, Cambridge CB1 8RN, UK
| | - Johanna P van Geffen
- Department of Biochemistry, Cardiovascular Research Institute Maastricht, Maastricht University, PO Box 616, 6200 MD Maastricht, The Netherlands
| | - Tao Jiang
- Strangeways Research Laboratory, MRC/British Heart Foundation (BHF) Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Samantha Farrow
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,National Health Service Blood and Transplant (NHSBT), Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
| | - Jonathan Cairns
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Abeer M Al-Subaie
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,National Health Service Blood and Transplant (NHSBT), Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Dammam, P.O. Box 1982, Dammam 31441, Saudi Arabia
| | - Sofie Ashford
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,National Health Service Blood and Transplant (NHSBT), Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,NIHR BioResource-Rare Diseases, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Antony Attwood
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,National Health Service Blood and Transplant (NHSBT), Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,NIHR BioResource-Rare Diseases, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Joana Batista
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,National Health Service Blood and Transplant (NHSBT), Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
| | - Heleen Bouman
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Frances Burden
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,National Health Service Blood and Transplant (NHSBT), Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
| | - Fizzah A Choudry
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,National Health Service Blood and Transplant (NHSBT), Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stephen F Garner
- National Health Service Blood and Transplant (NHSBT), Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
| | - Matthias Haimel
- NIHR BioResource-Rare Diseases, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK.,Department of Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Carly Kempster
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,National Health Service Blood and Transplant (NHSBT), Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
| | - Vasileios Ladopoulos
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
| | - An-Sofie Lenaerts
- NIHR Cambridge Biomedical Research Centre hIPSC Core Facility, Department of Surgery, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0SZ, UK.,Wellcome Trust and MRC Cambridge Stem Cell Institute, Department of Surgery, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0SZ, UK
| | - Paulina M Materek
- NIHR Cambridge Biomedical Research Centre hIPSC Core Facility, Department of Surgery, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0SZ, UK.,Wellcome Trust and MRC Cambridge Stem Cell Institute, Department of Surgery, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0SZ, UK
| | - Harriet McKinney
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,National Health Service Blood and Transplant (NHSBT), Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
| | - Stuart Meacham
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,National Health Service Blood and Transplant (NHSBT), Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,NIHR BioResource-Rare Diseases, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Daniel Mead
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Magdolna Nagy
- Department of Biochemistry, Cardiovascular Research Institute Maastricht, Maastricht University, PO Box 616, 6200 MD Maastricht, The Netherlands
| | - Christopher J Penkett
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,National Health Service Blood and Transplant (NHSBT), Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,NIHR BioResource-Rare Diseases, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Augusto Rendon
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,National Health Service Blood and Transplant (NHSBT), Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,Genomics England Limited, Queen Mary University of London, Dawson Hall, London EC1M 6BQ, UK
| | - Denis Seyres
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,National Health Service Blood and Transplant (NHSBT), Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,NIHR BioResource-Rare Diseases, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Benjamin Sun
- Strangeways Research Laboratory, MRC/British Heart Foundation (BHF) Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Salih Tuna
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,National Health Service Blood and Transplant (NHSBT), Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,NIHR BioResource-Rare Diseases, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Marie-Elise van der Weide
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,National Health Service Blood and Transplant (NHSBT), Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
| | - Steven W Wingett
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Joost H Martens
- Faculty of Science, Department of Molecular Biology, Radboud University, 6525GA Nijmegen, The Netherlands
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Sylvia Richardson
- Medical Research Council Biostatistics Unit, University of Cambridge, Forvie Site, Cambridge Biomedical Campus, Cambridge CB2 0SR, UK
| | - Ludovic Vallier
- Wellcome Trust and MRC Cambridge Stem Cell Institute, Department of Surgery, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0SZ, UK.,The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - David J Roberts
- Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford OX9 3DU, UK.,Department of Haematology, Churchill Hospital, Headington, Oxford OX3 7LE, UK.,NHSBT, John Radcliffe Hospital, Headington, Oxford OX3 9BQ, UK
| | - Kathleen Freson
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, University of Leuven, Leuven 3000, Belgium
| | - Lorenz Wernisch
- Medical Research Council Biostatistics Unit, University of Cambridge, Forvie Site, Cambridge Biomedical Campus, Cambridge CB2 0SR, UK
| | - Hendrik G Stunnenberg
- Faculty of Science, Department of Molecular Biology, Radboud University, 6525GA Nijmegen, The Netherlands
| | - John Danesh
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,Strangeways Research Laboratory, The National Institute for Health Research (NIHR) Blood and Transplant Unit in Donor Health and Genomics at the University of Cambridge, University of Cambridge, Cambridge CB1 8RN, UK.,Strangeways Research Laboratory, MRC/British Heart Foundation (BHF) Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK.,BHF Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Peter Fraser
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK.,Department of Biological Science, Florida State University, Tallahassee, Florida 32303, USA
| | - Nicole Soranzo
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,Strangeways Research Laboratory, The National Institute for Health Research (NIHR) Blood and Transplant Unit in Donor Health and Genomics at the University of Cambridge, University of Cambridge, Cambridge CB1 8RN, UK.,BHF Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Adam S Butterworth
- Strangeways Research Laboratory, The National Institute for Health Research (NIHR) Blood and Transplant Unit in Donor Health and Genomics at the University of Cambridge, University of Cambridge, Cambridge CB1 8RN, UK.,Strangeways Research Laboratory, MRC/British Heart Foundation (BHF) Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK.,BHF Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Johan W Heemskerk
- Department of Biochemistry, Cardiovascular Research Institute Maastricht, Maastricht University, PO Box 616, 6200 MD Maastricht, The Netherlands
| | - Ernest Turro
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,National Health Service Blood and Transplant (NHSBT), Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,NIHR BioResource-Rare Diseases, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK.,Medical Research Council Biostatistics Unit, University of Cambridge, Forvie Site, Cambridge Biomedical Campus, Cambridge CB2 0SR, UK
| | - Mikhail Spivakov
- Nuclear Dynamics Programme, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Willem H Ouwehand
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,National Health Service Blood and Transplant (NHSBT), Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.,Strangeways Research Laboratory, The National Institute for Health Research (NIHR) Blood and Transplant Unit in Donor Health and Genomics at the University of Cambridge, University of Cambridge, Cambridge CB1 8RN, UK.,BHF Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - William J Astle
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,National Health Service Blood and Transplant (NHSBT), Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,Medical Research Council Biostatistics Unit, University of Cambridge, Forvie Site, Cambridge Biomedical Campus, Cambridge CB2 0SR, UK.,Strangeways Research Laboratory, MRC/British Heart Foundation (BHF) Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK.,BHF Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Kate Downes
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,National Health Service Blood and Transplant (NHSBT), Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
| | - Myrto Kostadima
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,National Health Service Blood and Transplant (NHSBT), Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mattia Frontini
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,National Health Service Blood and Transplant (NHSBT), Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,BHF Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
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7
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Tu WJ, Hardy K, Sutton CR, McCuaig R, Li J, Dunn J, Tan A, Brezar V, Morris M, Denyer G, Lee SK, Turner SJ, Seddiki N, Smith C, Khanna R, Rao S. Priming of transcriptional memory responses via the chromatin accessibility landscape in T cells. Sci Rep 2017; 7:44825. [PMID: 28317936 PMCID: PMC5357947 DOI: 10.1038/srep44825] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 02/14/2017] [Indexed: 12/17/2022] Open
Abstract
Memory T cells exhibit transcriptional memory and “remember” their previous pathogenic encounter to increase transcription on re-infection. However, how this transcriptional priming response is regulated is unknown. Here we performed global FAIRE-seq profiling of chromatin accessibility in a human T cell transcriptional memory model. Primary activation induced persistent accessibility changes, and secondary activation induced secondary-specific opening of previously less accessible regions associated with enhanced expression of memory-responsive genes. Increased accessibility occurred largely in distal regulatory regions and was associated with increased histone acetylation and relative H3.3 deposition. The enhanced re-stimulation response was linked to the strength of initial PKC-induced signalling, and PKC-sensitive increases in accessibility upon initial stimulation showed higher accessibility on re-stimulation. While accessibility maintenance was associated with ETS-1, accessibility at re-stimulation-specific regions was linked to NFAT, especially in combination with ETS-1, EGR, GATA, NFκB, and NR4A. Furthermore, NFATC1 was directly regulated by ETS-1 at an enhancer region. In contrast to the factors that increased accessibility, signalling from bHLH and ZEB family members enhanced decreased accessibility upon re-stimulation. Interplay between distal regulatory elements, accessibility, and the combined action of sequence-specific transcription factors allows transcriptional memory-responsive genes to “remember” their initial environmental encounter.
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Affiliation(s)
- Wen Juan Tu
- Faculty of Education, Science, Technology &Mathematics, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Kristine Hardy
- Faculty of Education, Science, Technology &Mathematics, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Christopher R Sutton
- Faculty of Education, Science, Technology &Mathematics, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Robert McCuaig
- Faculty of Education, Science, Technology &Mathematics, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Jasmine Li
- Department of Microbiology, Biomedical Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Department of Microbiology &Immunology, The Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia
| | - Jenny Dunn
- Faculty of Education, Science, Technology &Mathematics, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Abel Tan
- Faculty of Education, Science, Technology &Mathematics, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Vedran Brezar
- INSERM U955 Eq16 Faculte de medicine Henri Mondor and Universite Paris-Est, Creteil/Vaccine Research Institute, Creteil 94010, France
| | - Melanie Morris
- Faculty of Education, Science, Technology &Mathematics, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
| | - Gareth Denyer
- School of Molecular Bioscience, The University of Sydney, Sydney, NSW, Australia
| | - Sau Kuen Lee
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Tumour Immunology Laboratory, Department of Immunology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Stephen J Turner
- Department of Microbiology, Biomedical Discovery Institute, Monash University, Clayton, Victoria 3800, Australia.,Department of Microbiology &Immunology, The Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia
| | - Nabila Seddiki
- INSERM U955 Eq16 Faculte de medicine Henri Mondor and Universite Paris-Est, Creteil/Vaccine Research Institute, Creteil 94010, France
| | - Corey Smith
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Tumour Immunology Laboratory, Department of Immunology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Rajiv Khanna
- QIMR Berghofer Centre for Immunotherapy and Vaccine Development QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,Tumour Immunology Laboratory, Department of Immunology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Sudha Rao
- Faculty of Education, Science, Technology &Mathematics, University of Canberra, Canberra, Australian Capital Territory 2617, Australia
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8
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Jayapal SR, Ang HYK, Wang CQ, Bisteau X, Caldez MJ, Xuan GX, Yu W, Tergaonkar V, Osato M, Lim B, Kaldis P. Cyclin A2 regulates erythrocyte morphology and numbers. Cell Cycle 2016; 15:3070-3081. [PMID: 27657745 DOI: 10.1080/15384101.2016.1234546] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Cyclin A2 is an essential gene for development and in haematopoietic stem cells and therefore its functions in definitive erythropoiesis have not been investigated. We have ablated cyclin A2 in committed erythroid progenitors in vivo using erythropoietin receptor promoter-driven Cre, which revealed its critical role in regulating erythrocyte morphology and numbers. Erythroid-specific cyclin A2 knockout mice are viable but displayed increased mean erythrocyte volume and reduced erythrocyte counts, as well as increased frequency of erythrocytes containing Howell-Jolly bodies. Erythroblasts lacking cyclin A2 displayed defective enucleation, resulting in reduced production of enucleated erythrocytes and increased frequencies of erythrocytes containing nuclear remnants. Deletion of the Cdk inhibitor p27Kip1 but not Cdk2, ameliorated the erythroid defects resulting from deficiency of cyclin A2, confirming the critical role of cyclin A2/Cdk activity in erythroid development. Loss of cyclin A2 in bone marrow cells in semisolid culture prevented the formation of BFU-E but not CFU-E colonies, uncovering its essential role in BFU-E function. Our data unveils the critical functions of cyclin A2 in regulating mammalian erythropoiesis.
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Affiliation(s)
- Senthil Raja Jayapal
- a Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research) , Singapore , Republic of Singapore
| | | | - Chelsia Qiuxia Wang
- a Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research) , Singapore , Republic of Singapore.,c Cancer Science Institute of Singapore, National University of Singapore , Singapore
| | - Xavier Bisteau
- a Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research) , Singapore , Republic of Singapore
| | - Matias J Caldez
- a Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research) , Singapore , Republic of Singapore.,d National University of Singapore (NUS) , Department of Biochemistry , Singapore
| | - Gan Xiao Xuan
- a Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research) , Singapore , Republic of Singapore
| | - Weimiao Yu
- a Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research) , Singapore , Republic of Singapore
| | - Vinay Tergaonkar
- a Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research) , Singapore , Republic of Singapore
| | - Motomi Osato
- c Cancer Science Institute of Singapore, National University of Singapore , Singapore
| | - Bing Lim
- b Genome Institute of Singapore , Singapore
| | - Philipp Kaldis
- a Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research) , Singapore , Republic of Singapore.,d National University of Singapore (NUS) , Department of Biochemistry , Singapore
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9
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Romano O, Peano C, Tagliazucchi GM, Petiti L, Poletti V, Cocchiarella F, Rizzi E, Severgnini M, Cavazza A, Rossi C, Pagliaro P, Ambrosi A, Ferrari G, Bicciato S, De Bellis G, Mavilio F, Miccio A. Transcriptional, epigenetic and retroviral signatures identify regulatory regions involved in hematopoietic lineage commitment. Sci Rep 2016; 6:24724. [PMID: 27095295 PMCID: PMC4837375 DOI: 10.1038/srep24724] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 04/04/2016] [Indexed: 12/21/2022] Open
Abstract
Genome-wide approaches allow investigating the molecular circuitry wiring the genetic and epigenetic programs of human somatic stem cells. Hematopoietic stem/progenitor cells (HSPC) give rise to the different blood cell types; however, the molecular basis of human hematopoietic lineage commitment is poorly characterized. Here, we define the transcriptional and epigenetic profile of human HSPC and early myeloid and erythroid progenitors by a combination of Cap Analysis of Gene Expression (CAGE), ChIP-seq and Moloney leukemia virus (MLV) integration site mapping. Most promoters and transcripts were shared by HSPC and committed progenitors, while enhancers and super-enhancers consistently changed upon differentiation, indicating that lineage commitment is essentially regulated by enhancer elements. A significant fraction of CAGE promoters differentially expressed upon commitment were novel, harbored a chromatin enhancer signature, and may identify promoters and transcribed enhancers driving cell commitment. MLV-targeted genomic regions co-mapped with cell-specific active enhancers and super-enhancers. Expression analyses, together with an enhancer functional assay, indicate that MLV integration can be used to identify bona fide developmentally regulated enhancers. Overall, this study provides an overview of transcriptional and epigenetic changes associated to HSPC lineage commitment, and a novel signature for regulatory elements involved in cell identity.
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Affiliation(s)
- Oriana Romano
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy.,Center for Genomic Research, University of Modena and Reggio Emilia, Modena, Italy.,INSERM UMR 1163, Laboratory of chromatin and gene regulation during development, Paris, France
| | - Clelia Peano
- Institute of Biomedical Technologies, CNR, Milan, Italy
| | | | - Luca Petiti
- Institute of Biomedical Technologies, CNR, Milan, Italy
| | | | | | - Ermanno Rizzi
- Institute of Biomedical Technologies, CNR, Milan, Italy.,Telethon Foundation, Milan, Italy
| | | | - Alessia Cavazza
- Dana Farber Cancer Institute, Harvard Medical School, Boston, US
| | - Claudia Rossi
- San Raffaele-Telethon Institute for Gene Therapy (TIGET), San Raffaele Scientific Institute, Milan, Italy
| | - Pasqualepaolo Pagliaro
- Az. Osp. Policlinico Universitario di Bologna, Policlinico S. Orsola-Malpighi, Unità Operativa di Immunoematologia e Trasfusionale, Bologna, Italy
| | | | - Giuliana Ferrari
- San Raffaele-Telethon Institute for Gene Therapy (TIGET), San Raffaele Scientific Institute, Milan, Italy.,Vita Salute San Raffaele University, Milan, Italy
| | - Silvio Bicciato
- Center for Genomic Research, University of Modena and Reggio Emilia, Modena, Italy
| | | | - Fulvio Mavilio
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy.,Genethon, Evry, France
| | - Annarita Miccio
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy.,INSERM UMR 1163, Laboratory of chromatin and gene regulation during development, Paris, France.,Paris Descartes, Sorbonne Paris Cité University, Imagine Institute, Paris, France
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10
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Becker M, Guadalupe T, Franke B, Hibar DP, Renteria ME, Stein JL, Thompson PM, Francks C, Vernes SC, Fisher SE. Early developmental gene enhancers affect subcortical volumes in the adult human brain. Hum Brain Mapp 2016; 37:1788-800. [PMID: 26890892 DOI: 10.1002/hbm.23136] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Revised: 12/30/2015] [Accepted: 01/26/2016] [Indexed: 11/08/2022] Open
Abstract
Genome-wide association screens aim to identify common genetic variants contributing to the phenotypic variability of complex traits, such as human height or brain morphology. The identified genetic variants are mostly within noncoding genomic regions and the biology of the genotype-phenotype association typically remains unclear. In this article, we propose a complementary targeted strategy to reveal the genetic underpinnings of variability in subcortical brain volumes, by specifically selecting genomic loci that are experimentally validated forebrain enhancers, active in early embryonic development. We hypothesized that genetic variation within these enhancers may affect the development and ultimately the structure of subcortical brain regions in adults. We tested whether variants in forebrain enhancer regions showed an overall enrichment of association with volumetric variation in subcortical structures of >13,000 healthy adults. We observed significant enrichment of genomic loci that affect the volume of the hippocampus within forebrain enhancers (empirical P = 0.0015), a finding which robustly passed the adjusted threshold for testing of multiple brain phenotypes (cutoff of P < 0.0083 at an alpha of 0.05). In analyses of individual single nucleotide polymorphisms (SNPs), we identified an association upstream of the ID2 gene with rs7588305 and variation in hippocampal volume. This SNP-based association survived multiple-testing correction for the number of SNPs analyzed but not for the number of subcortical structures. Targeting known regulatory regions offers a way to understand the underlying biology that connects genotypes to phenotypes, particularly in the context of neuroimaging genetics. This biology-driven approach generates testable hypotheses regarding the functional biology of identified associations. Hum Brain Mapp 37:1788-1800, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Martin Becker
- Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - Tulio Guadalupe
- Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - Barbara Franke
- Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Psychiatry, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Derrek P Hibar
- Imaging Genetics Center, Keck School of Medicine, University of Southern California, Marina Del Rey, California
| | - Miguel E Renteria
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Jason L Stein
- Imaging Genetics Center, Keck School of Medicine, University of Southern California, Marina Del Rey, California.,Department of Neurology, Neurogenetics Program, UCLA School of Medicine, Los Angeles, California
| | - Paul M Thompson
- Imaging Genetics Center, Keck School of Medicine, University of Southern California, Marina Del Rey, California
| | - Clyde Francks
- Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands
| | - Sonja C Vernes
- Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands
| | - Simon E Fisher
- Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands
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11
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Trynka G, Westra HJ, Slowikowski K, Hu X, Xu H, Stranger BE, Klein RJ, Han B, Raychaudhuri S. Disentangling the Effects of Colocalizing Genomic Annotations to Functionally Prioritize Non-coding Variants within Complex-Trait Loci. Am J Hum Genet 2015; 97:139-52. [PMID: 26140449 PMCID: PMC4572568 DOI: 10.1016/j.ajhg.2015.05.016] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 05/26/2015] [Indexed: 01/12/2023] Open
Abstract
Identifying genomic annotations that differentiate causal from trait-associated variants is essential to fine mapping disease loci. Although many studies have identified non-coding functional annotations that overlap disease-associated variants, these annotations often colocalize, complicating the ability to use these annotations for fine mapping causal variation. We developed a statistical approach (Genomic Annotation Shifter [GoShifter]) to assess whether enriched annotations are able to prioritize causal variation. GoShifter defines the null distribution of an annotation overlapping an allele by locally shifting annotations; this approach is less sensitive to biases arising from local genomic structure than commonly used enrichment methods that depend on SNP matching. Local shifting also allows GoShifter to identify independent causal effects from colocalizing annotations. Using GoShifter, we confirmed that variants in expression quantitative trail loci drive gene-expression changes though DNase-I hypersensitive sites (DHSs) near transcription start sites and independently through 3' UTR regulation. We also showed that (1) 15%-36% of trait-associated loci map to DHSs independently of other annotations; (2) loci associated with breast cancer and rheumatoid arthritis harbor potentially causal variants near the summits of histone marks rather than full peak bodies; (3) variants associated with height are highly enriched in embryonic stem cell DHSs; and (4) we can effectively prioritize causal variation at specific loci.
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Affiliation(s)
- Gosia Trynka
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02446, USA; Partners Center for Personalized Genetic Medicine, Boston, MA 02446, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Harm-Jan Westra
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02446, USA; Partners Center for Personalized Genetic Medicine, Boston, MA 02446, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Kamil Slowikowski
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02446, USA; Partners Center for Personalized Genetic Medicine, Boston, MA 02446, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Bioinformatics and Integrative Genomics, Harvard University, Cambridge, MA 02138, USA
| | - Xinli Hu
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02446, USA; Partners Center for Personalized Genetic Medicine, Boston, MA 02446, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard-MIT Division of Health Sciences and Technology, Boston, MA 02115, USA
| | - Han Xu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02215, USA
| | - Barbara E Stranger
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL 60637, USA; Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Robert J Klein
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Buhm Han
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02446, USA; Partners Center for Personalized Genetic Medicine, Boston, MA 02446, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Asan Institute for Life Sciences, Asan Medical Center, Seoul 138-736, Republic of Korea; Department of Medicine, University of Ulsan College of Medicine, Seoul 138-736, Republic of Korea
| | - Soumya Raychaudhuri
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02446, USA; Partners Center for Personalized Genetic Medicine, Boston, MA 02446, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Institute of Inflammation and Repair, University of Manchester, Manchester M13 9PT, UK.
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12
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Ludwig LS, Cho H, Wakabayashi A, Eng JC, Ulirsch JC, Fleming MD, Lodish HF, Sankaran VG. Genome-wide association study follow-up identifies cyclin A2 as a regulator of the transition through cytokinesis during terminal erythropoiesis. Am J Hematol 2015; 90:386-91. [PMID: 25615569 DOI: 10.1002/ajh.23952] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Accepted: 01/13/2015] [Indexed: 01/21/2023]
Abstract
Genome-wide association studies (GWAS) hold tremendous promise to improve our understanding of human biology. Recent GWAS have revealed over 75 loci associated with erythroid traits, including the 4q27 locus that is associated with red blood cell size (mean corpuscular volume). The close linkage disequilibrium block at this locus harbors the CCNA2 gene that encodes cyclin A2. CCNA2 mRNA is highly expressed in human and murine erythroid progenitor cells and regulated by the essential erythroid transcription factor GATA1. To understand the role of cyclin A2 in erythropoiesis, we have reduced expression of this gene using short hairpin RNAs in a primary murine erythroid culture system. We demonstrate that cyclin A2 levels affect erythroid cell size by regulating the passage through cytokinesis during the final cell division of terminal erythropoiesis. Our study provides new insight into cell cycle regulation during terminal erythropoiesis and more generally illustrates the value of functional GWAS follow-up to gain mechanistic insight into hematopoiesis.
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Affiliation(s)
- Leif S. Ludwig
- Division of Hematology/Oncology; Boston Children's Hospital, Harvard Medical School; Boston Massachusetts
- Department of Pediatric Oncology; Dana-Farber Cancer Institute; Harvard Medical School; Boston Massachusetts
- Broad Institute of MIT and Harvard; Cambridge Massachusetts
- Whitehead Institute for Biomedical Research; Cambridge Massachusetts
- Institute for Chemistry and Biochemistry; Freie Universität Berlin; Berlin Germany. Charité-Universitätsmedizin Berlin; Berlin Germany
| | - Hyunjii Cho
- Whitehead Institute for Biomedical Research; Cambridge Massachusetts
- Department of Biology; Massachusetts Institute of Technology; Cambridge Massachusetts
| | - Aoi Wakabayashi
- Division of Hematology/Oncology; Boston Children's Hospital, Harvard Medical School; Boston Massachusetts
- Department of Pediatric Oncology; Dana-Farber Cancer Institute; Harvard Medical School; Boston Massachusetts
- Broad Institute of MIT and Harvard; Cambridge Massachusetts
| | - Jennifer C. Eng
- Whitehead Institute for Biomedical Research; Cambridge Massachusetts
| | - Jacob C. Ulirsch
- Division of Hematology/Oncology; Boston Children's Hospital, Harvard Medical School; Boston Massachusetts
- Department of Pediatric Oncology; Dana-Farber Cancer Institute; Harvard Medical School; Boston Massachusetts
- Broad Institute of MIT and Harvard; Cambridge Massachusetts
| | - Mark D. Fleming
- Department of Pathology; Boston Children's Hospital; Boston Massachusetts
| | - Harvey F. Lodish
- Whitehead Institute for Biomedical Research; Cambridge Massachusetts
- Department of Biology; Massachusetts Institute of Technology; Cambridge Massachusetts
| | - Vijay G. Sankaran
- Division of Hematology/Oncology; Boston Children's Hospital, Harvard Medical School; Boston Massachusetts
- Department of Pediatric Oncology; Dana-Farber Cancer Institute; Harvard Medical School; Boston Massachusetts
- Broad Institute of MIT and Harvard; Cambridge Massachusetts
- Whitehead Institute for Biomedical Research; Cambridge Massachusetts
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13
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Tapper W, Jones AV, Kralovics R, Harutyunyan AS, Zoi K, Leung W, Godfrey AL, Guglielmelli P, Callaway A, Ward D, Aranaz P, White HE, Waghorn K, Lin F, Chase A, Joanna Baxter E, Maclean C, Nangalia J, Chen E, Evans P, Short M, Jack A, Wallis L, Oscier D, Duncombe AS, Schuh A, Mead AJ, Griffiths M, Ewing J, Gale RE, Schnittger S, Haferlach T, Stegelmann F, Döhner K, Grallert H, Strauch K, Tanaka T, Bandinelli S, Giannopoulos A, Pieri L, Mannarelli C, Gisslinger H, Barosi G, Cazzola M, Reiter A, Harrison C, Campbell P, Green AR, Vannucchi A, Cross NC. Genetic variation at MECOM, TERT, JAK2 and HBS1L-MYB predisposes to myeloproliferative neoplasms. Nat Commun 2015; 6:6691. [PMID: 25849990 PMCID: PMC4396373 DOI: 10.1038/ncomms7691] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 02/20/2015] [Indexed: 12/21/2022] Open
Abstract
Clonal proliferation in myeloproliferative neoplasms (MPN) is driven by somatic mutations in JAK2, CALR or MPL, but the contribution of inherited factors is poorly characterized. Using a three-stage genome-wide association study of 3,437 MPN cases and 10,083 controls, we identify two SNPs with genome-wide significance in JAK2(V617F)-negative MPN: rs12339666 (JAK2; meta-analysis P=1.27 × 10(-10)) and rs2201862 (MECOM; meta-analysis P=1.96 × 10(-9)). Two additional SNPs, rs2736100 (TERT) and rs9376092 (HBS1L/MYB), achieve genome-wide significance when including JAK2(V617F)-positive cases. rs9376092 has a stronger effect in JAK2(V617F)-negative cases with CALR and/or MPL mutations (Breslow-Day P=4.5 × 10(-7)), whereas in JAK2(V617F)-positive cases rs9376092 associates with essential thrombocythemia (ET) rather than polycythemia vera (allelic χ(2) P=7.3 × 10(-7)). Reduced MYB expression, previously linked to development of an ET-like disease in model systems, associates with rs9376092 in normal myeloid cells. These findings demonstrate that multiple germline variants predispose to MPN and link constitutional differences in MYB expression to disease phenotype.
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Affiliation(s)
- William Tapper
- Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury SP2 8BJ, UK
| | - Amy V. Jones
- Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury SP2 8BJ, UK
| | - Robert Kralovics
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna 1090, Austria
| | - Ashot S. Harutyunyan
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna 1090, Austria
| | - Katerina Zoi
- Haematology Research Laboratory, Biomedical Research Foundation, Academy of Athens, Athens 11527, Greece
| | - William Leung
- Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury SP2 8BJ, UK
| | - Anna L. Godfrey
- Department of Haematology, Addenbrooke’s Hospital, Cambridge CB2 0XY, UK
- Department of Haematology, University of Cambridge, Cambridge CB2 0XY, UK
| | - Paola Guglielmelli
- Laboratorio Congiunto MMPC, Department of Experimental and Clinical Medicine, University of Florence, Florence 50134, Italy
| | - Alison Callaway
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury SP2 8BJ, UK
| | - Daniel Ward
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury SP2 8BJ, UK
| | - Paula Aranaz
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury SP2 8BJ, UK
| | - Helen E. White
- Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury SP2 8BJ, UK
| | - Katherine Waghorn
- Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury SP2 8BJ, UK
| | - Feng Lin
- Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury SP2 8BJ, UK
| | - Andrew Chase
- Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury SP2 8BJ, UK
| | - E. Joanna Baxter
- Department of Haematology, Addenbrooke’s Hospital, Cambridge CB2 0XY, UK
- Department of Haematology, University of Cambridge, Cambridge CB2 0XY, UK
| | - Cathy Maclean
- Department of Haematology, Addenbrooke’s Hospital, Cambridge CB2 0XY, UK
- Department of Haematology, University of Cambridge, Cambridge CB2 0XY, UK
| | - Jyoti Nangalia
- Department of Haematology, Addenbrooke’s Hospital, Cambridge CB2 0XY, UK
- Department of Haematology, University of Cambridge, Cambridge CB2 0XY, UK
| | - Edwin Chen
- Department of Haematology, Addenbrooke’s Hospital, Cambridge CB2 0XY, UK
- Department of Haematology, University of Cambridge, Cambridge CB2 0XY, UK
| | - Paul Evans
- Haematological Malignancy Diagnostic Service, St James's Institute of Oncology, Bexley Wing, St James's University Hospital, Leeds LS9 7TF, UK
| | - Michael Short
- Haematological Malignancy Diagnostic Service, St James's Institute of Oncology, Bexley Wing, St James's University Hospital, Leeds LS9 7TF, UK
| | - Andrew Jack
- Haematological Malignancy Diagnostic Service, St James's Institute of Oncology, Bexley Wing, St James's University Hospital, Leeds LS9 7TF, UK
| | - Louise Wallis
- Department of Haematology, Royal Bournemouth Hospital, Bournemouth BH7 7DW, UK
| | - David Oscier
- Department of Haematology, Royal Bournemouth Hospital, Bournemouth BH7 7DW, UK
| | - Andrew S. Duncombe
- Department of Haematology, University Hospital Southampton, Southampton SO16 6YD, UK
| | - Anna Schuh
- Oxford Biomedical Research Centre, Molecular Diagnostic Laboratory, Oxford University Hospitals NHS Trust, Oxford OX3 7LE, UK
| | - Adam J. Mead
- Haematopoietic Stem Cell Biology Laboratory, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Michael Griffiths
- School of Cancer Sciences, University of Birmingham,, Birmingham B15 2TT, UK
- West Midlands Regional Genetics Laboratory, Birmingham Women's NHS Foundation Trust, Birmingham B15 2TG, UK
| | - Joanne Ewing
- Birmingham Heartlands Hospital, Birmingham B9 5SS, UK
| | - Rosemary E. Gale
- Department of Haematology, UCL Cancer Institute, London WC1 E6BT, UK
| | | | | | - Frank Stegelmann
- Department of Internal Medicine III, University Hospital of Ulm, Ulm 89081, Germany
| | - Konstanze Döhner
- Department of Internal Medicine III, University Hospital of Ulm, Ulm 89081, Germany
| | - Harald Grallert
- Institute of Epidemiology II, Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany
- German Center for Diabetes Research, Neuherberg 85764, Germany
| | - Konstantin Strauch
- Institute of Epidemiology II, Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, Ludwig-Maximilians-Universität, 80539 Munich, Germany
| | - Toshiko Tanaka
- Longitudinal Study Section, Translational Gerontology Branch, National Institute on Aging, Baltimore, Maryland 21224-6825, USA
| | | | - Andreas Giannopoulos
- Haematology Research Laboratory, Biomedical Research Foundation, Academy of Athens, Athens 11527, Greece
| | - Lisa Pieri
- Laboratorio Congiunto MMPC, Department of Experimental and Clinical Medicine, University of Florence, Florence 50134, Italy
| | - Carmela Mannarelli
- Laboratorio Congiunto MMPC, Department of Experimental and Clinical Medicine, University of Florence, Florence 50134, Italy
| | - Heinz Gisslinger
- Medical University of Vienna, Department of Internal Medicine I, Division of Hematology and Blood Coagulation, Vienna 1090, Austria
| | - Giovanni Barosi
- Center for the Study of Myelofibrosis, IRCCS Policlinico San Matteo Foundation, Pavia 27100, Italy
| | - Mario Cazzola
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Department of Hematology Oncology, Fondazione IRCCS Policlinico San Matteo, Pavia 27100, Italy
| | - Andreas Reiter
- III. Medizinische Klinik, Universitätsmedizin Mannheim, Mannheim 68167, Germany
| | - Claire Harrison
- Department of Haematology, Guy's and St Thomas' NHS Foundation Trust, Guy's Hospital, London SE1 9RT, UK
| | - Peter Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Anthony R. Green
- Department of Haematology, Addenbrooke’s Hospital, Cambridge CB2 0XY, UK
- Department of Haematology, University of Cambridge, Cambridge CB2 0XY, UK
| | - Alessandro Vannucchi
- Laboratorio Congiunto MMPC, Department of Experimental and Clinical Medicine, University of Florence, Florence 50134, Italy
| | - Nicholas C.P. Cross
- Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
- Wessex Regional Genetics Laboratory, Salisbury District Hospital, Salisbury SP2 8BJ, UK
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14
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Reschen ME, Gaulton KJ, Lin D, Soilleux EJ, Morris AJ, Smyth SS, O'Callaghan CA. Lipid-induced epigenomic changes in human macrophages identify a coronary artery disease-associated variant that regulates PPAP2B Expression through Altered C/EBP-beta binding. PLoS Genet 2015; 11:e1005061. [PMID: 25835000 PMCID: PMC4383549 DOI: 10.1371/journal.pgen.1005061] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 02/09/2015] [Indexed: 01/17/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified over 40 loci that affect risk of coronary artery disease (CAD) and the causal mechanisms at the majority of loci are unknown. Recent studies have suggested that many causal GWAS variants influence disease through altered transcriptional regulation in disease-relevant cell types. We explored changes in transcriptional regulation during a key pathophysiological event in CAD, the environmental lipid-induced transformation of macrophages to lipid-laden foam cells. We used a combination of open chromatin mapping with formaldehyde-assisted isolation of regulatory elements (FAIRE-seq) and enhancer and transcription factor mapping using chromatin immuno-precipitation (ChIP-seq) in primary human macrophages before and after exposure to atherogenic oxidized low-density lipoprotein (oxLDL), with resultant foam cell formation. OxLDL-induced foam cell formation was associated with changes in a subset of open chromatin and active enhancer sites that strongly correlated with expression changes of nearby genes. OxLDL-regulated enhancers were enriched for several transcription factors including C/EBP-beta, which has no previously documented role in foam cell formation. OxLDL exposure up-regulated C/EBP-beta expression and increased genomic binding events, most prominently around genes involved in inflammatory response pathways. Variants at CAD-associated loci were significantly and specifically enriched in the subset of chromatin sites altered by oxLDL exposure, including rs72664324 in an oxLDL-induced enhancer at the PPAP2B locus. OxLDL increased C/EBP beta binding to this site and C/EBP beta binding and enhancer activity were stronger with the protective A allele of rs72664324. In addition, expression of the PPAP2B protein product LPP3 was present in foam cells in human atherosclerotic plaques and oxLDL exposure up-regulated LPP3 in macrophages resulting in increased degradation of pro-inflammatory mediators. Our results demonstrate a genetic mechanism contributing to CAD risk at the PPAP2B locus and highlight the value of studying epigenetic changes in disease processes involving pathogenic environmental stimuli. Coronary artery disease is a complex disease where over 40 genomic loci contributing to genetic risk have been identified. However, identifying the precise variants, genomic elements and genes that mediate this risk at each locus has proved challenging. We hypothesized that some genetic risk variants may influence a key step in development of coronary artery disease, which occurs when macrophages encounter environmentally-derived lipid. These cells take up lipid and accumulate in atherosclerotic plaques in the walls of blood vessels where they contribute to the inflammatory atherosclerotic disease process. Therefore, we studied the effects of this lipid exposure on the genomic activity of these cells. Environmental lipid exposure triggered changes in transcriptional regulation and gene expression. Variants at coronary artery disease risk loci were enriched for genomic regions altered by lipid exposure. We studied one such risk variant rs72664324 in detail and found that it altered binding of the C/EBP-beta transcription factor and altered expression of the PPAP2B gene. PPAP2B encodes an enzyme that degrades pro-inflammatory substances. Our study demonstrates a hitherto unknown genetic mechanism underlying atherosclerotic heart disease and demonstrates the value of studying changes in transcriptional regulation in key disease processes involving environmental influences.
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Affiliation(s)
- Michael E. Reschen
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Kyle J. Gaulton
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Da Lin
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Elizabeth J. Soilleux
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford and Department of Cellular Pathology, John Radcliffe Hospital, Oxford, United Kingdom
| | - Andrew J. Morris
- Division of Cardiovascular Medicine, The Gill Heart Institute, University of Kentucky, Lexington, Kentucky, United States of America
- Department of Veterans Affairs Medical Center, Lexington, Kentucky, United States of America
| | - Susan S. Smyth
- Division of Cardiovascular Medicine, The Gill Heart Institute, University of Kentucky, Lexington, Kentucky, United States of America
- Department of Veterans Affairs Medical Center, Lexington, Kentucky, United States of America
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15
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Global Mapping of Open Chromatin Regulatory Elements by Formaldehyde-Assisted Isolation of Regulatory Elements Followed by Sequencing (FAIRE-seq). Methods Mol Biol 2015; 1334:261-72. [PMID: 26404156 DOI: 10.1007/978-1-4939-2877-4_17] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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16
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Hadsell DL, Hadsell LA, Olea W, Rijnkels M, Creighton CJ, Smyth I, Short KM, Cox LL, Cox TC. In-silico QTL mapping of postpubertal mammary ductal development in the mouse uncovers potential human breast cancer risk loci. Mamm Genome 2015; 26:57-79. [PMID: 25552398 DOI: 10.1007/s00335-014-9551-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 12/03/2014] [Indexed: 01/02/2023]
Abstract
Genetic background plays a dominant role in mammary gland development and breast cancer (BrCa). Despite this, the role of genetics is only partially understood. This study used strain-dependent variation in an inbred mouse mapping panel, to identify quantitative trait loci (QTL) underlying structural variation in mammary ductal development, and determined if these QTL correlated with genomic intervals conferring BrCa susceptibility in humans. For about half of the traits, developmental variation among the complete set of strains in this study was greater (P < 0.05) than that of previously studied strains, or strains in current common use for mammary gland biology. Correlations were also detected with previously reported variation in mammary tumor latency and metastasis. In-silico genome-wide association identified 20 mammary development QTL (Mdq). Of these, five were syntenic with previously reported human BrCa loci. The most significant (P = 1 × 10(-11)) association of the study was on MMU6 and contained the genes Plxna4, Plxna4os1, and Chchd3. On MMU5, a QTL was detected (P = 8 × 10(-7)) that was syntenic to a human BrCa locus on h12q24.5 containing the genes Tbx3 and Tbx5. Intersection of linked SNP (r(2) > 0.8) with genomic and epigenomic features, and intersection of candidate genes with gene expression and survival data from human BrCa highlighted several for further study. These results support the conclusion that mammary tumorigenesis and normal ductal development are influenced by common genetic factors and that further studies of genetically diverse mice can improve our understanding of BrCa in humans.
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Affiliation(s)
- Darryl L Hadsell
- Department of Pediatrics, USDA/ARS Children's Nutrition Research Center, Baylor College of Medicine, 1100 Bates St. Suite 10072, Mail Stop: BCM-320, Houston, TX, 77030-2600, USA,
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17
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Englert NA, Luo G, Goldstein JA, Surapureddi S. Epigenetic modification of histone 3 lysine 27: mediator subunit MED25 is required for the dissociation of polycomb repressive complex 2 from the promoter of cytochrome P450 2C9. J Biol Chem 2014; 290:2264-78. [PMID: 25391650 DOI: 10.1074/jbc.m114.579474] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The Mediator complex is vital for the transcriptional regulation of eukaryotic genes. Mediator binds to nuclear receptors at target response elements and recruits chromatin-modifying enzymes and RNA polymerase II. Here, we examine the involvement of Mediator subunit MED25 in the epigenetic regulation of human cytochrome P450 2C9 (CYP2C9). MED25 is recruited to the CYP2C9 promoter through association with liver-enriched HNF4α, and we show that MED25 influences the H3K27 status of the HNF4α binding region. This region was enriched for the activating marker H3K27ac and histone acetyltransferase CREBBP after MED25 overexpression but was trimethylated when MED25 expression was silenced. The epigenetic regulator Polycomb repressive complex (PRC2), which represses expression by methylating H3K27, plays an important role in target gene regulation. Silencing MED25 correlated with increased association of PRC2 not only with the promoter region chromatin but with HNF4α itself. We confirmed the involvement of MED25 for fully functional preinitiation complex recruitment and transcriptional output in vitro. Formaldehyde-assisted isolation of regulatory elements (FAIRE) revealed chromatin conformation changes that were reliant on MED25, indicating that MED25 induced a permissive chromatin state that reflected increases in CYP2C9 mRNA. For the first time, we showed evidence that a functionally relevant human gene is transcriptionally regulated by HNF4α via MED25 and PRC2. CYP2C9 is important for the metabolism of many exogenous chemicals including pharmaceutical drugs as well as endogenous substrates. Thus, MED25 is important for regulating the epigenetic landscape resulting in transcriptional activation of a highly inducible gene, CYP2C9.
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Affiliation(s)
- Neal A Englert
- From the Laboratory of Toxicology and Pharmacology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - George Luo
- From the Laboratory of Toxicology and Pharmacology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Joyce A Goldstein
- From the Laboratory of Toxicology and Pharmacology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Sailesh Surapureddi
- From the Laboratory of Toxicology and Pharmacology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
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18
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Sadee W, Hartmann K, Seweryn M, Pietrzak M, Handelman SK, Rempala GA. Missing heritability of common diseases and treatments outside the protein-coding exome. Hum Genet 2014; 133:1199-215. [PMID: 25107510 PMCID: PMC4169001 DOI: 10.1007/s00439-014-1476-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 07/23/2014] [Indexed: 02/07/2023]
Abstract
Genetic factors strongly influence risk of common human diseases and treatment outcomes but the causative variants remain largely unknown; this gap has been called the 'missing heritability'. We propose several hypotheses that in combination have the potential to narrow the gap. First, given a multi-stage path from wellness to disease, we propose that common variants under positive evolutionary selection represent normal variation and gate the transition between wellness and an 'off-well' state, revealing adaptations to changing environmental conditions. In contrast, genome-wide association studies (GWAS) focus on deleterious variants conveying disease risk, accelerating the path from off-well to illness and finally specific diseases, while common 'normal' variants remain hidden in the noise. Second, epistasis (dynamic gene-gene interactions) likely assumes a central role in adaptations and evolution; yet, GWAS analyses currently are poorly designed to reveal epistasis. As gene regulation is germane to adaptation, we propose that epistasis among common normal regulatory variants, or between common variants and less frequent deleterious variants, can have strong protective or deleterious phenotypic effects. These gene-gene interactions can be highly sensitive to environmental stimuli and could account for large differences in drug response between individuals. Residing largely outside the protein-coding exome, common regulatory variants affect either transcription of coding and non-coding RNAs (regulatory SNPs, or rSNPs) or RNA functions and processing (structural RNA SNPs, or srSNPs). Third, with the vast majority of causative variants yet to be discovered, GWAS rely on surrogate markers, a confounding factor aggravated by the presence of more than one causative variant per gene and by epistasis. We propose that the confluence of these factors may be responsible to large extent for the observed heritability gap.
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Affiliation(s)
- Wolfgang Sadee
- Department of Pharmacology, Center for Pharmacogenomics, College of Medicine, The Ohio State University Wexner Medical Center, 5184A Graves Hall, 333 West 10th Avenue, Columbus, OH, 43210, USA,
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19
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Chen L, Kostadima M, Martens JH, Canu G, Garcia SP, Turro E, Downes K, Macaulay IC, Bielczyk-Maczynska E, Coe S, Farrow S, Poudel P, Burden F, Jansen SB, Astle WJ, Attwood A, Bariana T, de Bono B, Breschi A, Chambers JC, Consortium BRIDGE, Choudry FA, Clarke L, Coupland P, van der Ent M, Erber WN, Jansen JH, Favier R, Fenech ME, Foad N, Freson K, van Geet C, Gomez K, Guigo R, Hampshire D, Kelly AM, Kerstens HH, Kooner JS, Laffan M, Lentaigne C, Labalette C, Martin T, Meacham S, Mumford A, Nürnberg S, Palumbo E, van der Reijden BA, Richardson D, Sammut SJ, Slodkowicz G, Tamuri AU, Vasquez L, Voss K, Watt S, Westbury S, Flicek P, Loos R, Goldman N, Bertone P, Read RJ, Richardson S, Cvejic A, Soranzo N, Ouwehand WH, Stunnenberg HG, Frontini M, Rendon A. Transcriptional diversity during lineage commitment of human blood progenitors. Science 2014; 345:1251033. [PMID: 25258084 PMCID: PMC4254742 DOI: 10.1126/science.1251033] [Citation(s) in RCA: 206] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Blood cells derive from hematopoietic stem cells through stepwise fating events. To characterize gene expression programs driving lineage choice, we sequenced RNA from eight primary human hematopoietic progenitor populations representing the major myeloid commitment stages and the main lymphoid stage. We identified extensive cell type-specific expression changes: 6711 genes and 10,724 transcripts, enriched in non-protein-coding elements at early stages of differentiation. In addition, we found 7881 novel splice junctions and 2301 differentially used alternative splicing events, enriched in genes involved in regulatory processes. We demonstrated experimentally cell-specific isoform usage, identifying nuclear factor I/B (NFIB) as a regulator of megakaryocyte maturation-the platelet precursor. Our data highlight the complexity of fating events in closely related progenitor populations, the understanding of which is essential for the advancement of transplantation and regenerative medicine.
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Affiliation(s)
- Lu Chen
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Myrto Kostadima
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Joost H.A. Martens
- Department of Molecular Biology, Radboud University, Nijmegen, the Netherlands
| | - Giovanni Canu
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Sara P. Garcia
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Ernest Turro
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Kate Downes
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Iain C. Macaulay
- Sanger Institute-EBI Single-Cell Genomics Centre, Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Ewa Bielczyk-Maczynska
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Sophia Coe
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Samantha Farrow
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Pawan Poudel
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Frances Burden
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Sjoert B.G. Jansen
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - William J. Astle
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Medical Research Council Biostatistics Unit, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Antony Attwood
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Tadbir Bariana
- Department of Haematology, University College London Cancer Institute, London, United Kingdom
- The Katharine Dormandy Haemophilia Centre and Thrombosis Unit, Royal Free NHS Trust, London, United Kingdom
| | - Bernard de Bono
- CHIME Institute, University College London, Archway Campus, London, United Kingdom
- Auckland Bioengineering Institute, University of Auckland, New Zealand
| | - Alessandra Breschi
- Centre for Genomic Regulation and University Pompeu Fabra, Barcelona, Spain
| | - John C. Chambers
- Imperial College Healthcare NHS Trust, DuCane Road, London, United Kingdom
- Ealing Hospital NHS Trust, Southall, Middlesex, United Kingdom
| | | | - Fizzah A. Choudry
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Laura Clarke
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Paul Coupland
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Martijn van der Ent
- Department of Molecular Biology, Radboud University, Nijmegen, the Netherlands
| | - Wendy N. Erber
- Pathology and Laboratory Medicine, University of Western Australia, Crawley, Western Australia, Australia
| | - Joop H. Jansen
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rémi Favier
- Assistance Publique-Hopitaux de Paris, Institut National de la Santé et de la Recherche Médicale U1009, Villejuif, France
| | - Matthew E. Fenech
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich, United Kingdom
| | - Nicola Foad
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Kathleen Freson
- Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium
| | - Chris van Geet
- Center for Molecular and Vascular Biology, University of Leuven, Leuven, Belgium
| | - Keith Gomez
- The Katharine Dormandy Haemophilia Centre and Thrombosis Unit, Royal Free NHS Trust, London, United Kingdom
| | - Roderic Guigo
- Centre for Genomic Regulation and University Pompeu Fabra, Barcelona, Spain
| | - Daniel Hampshire
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Anne M. Kelly
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | | | - Jaspal S. Kooner
- Imperial College Healthcare NHS Trust, DuCane Road, London, United Kingdom
- Ealing Hospital NHS Trust, Southall, Middlesex, United Kingdom
| | - Michael Laffan
- Department of Haematology, Hammersmith Campus, Imperial College Academic Health Sciences Centre, Imperial College London, London, United Kingdom
| | - Claire Lentaigne
- Department of Haematology, Hammersmith Campus, Imperial College Academic Health Sciences Centre, Imperial College London, London, United Kingdom
| | - Charlotte Labalette
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Tiphaine Martin
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Twin Research & Genetic Epidemiology, Genetics & Molecular Medicine Division, St Thomas’ Hospital, King’s College, London, United Kingdom
| | - Stuart Meacham
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Andrew Mumford
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, United Kingdom
| | - Sylvia Nürnberg
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Emilio Palumbo
- Centre for Genomic Regulation and University Pompeu Fabra, Barcelona, Spain
| | - Bert A. van der Reijden
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - David Richardson
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Stephen J. Sammut
- Department of Oncology, Addenbrooke’s Cambridge University Hospital NHS Trust, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Cancer Research United Kingdom, Cambridge Institute, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Greg Slodkowicz
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Asif U. Tamuri
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Louella Vasquez
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Katrin Voss
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Stephen Watt
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Sarah Westbury
- School of Clinical Sciences, University of Bristol, United Kingdom
| | - Paul Flicek
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Remco Loos
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Nick Goldman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Paul Bertone
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Genome Biology and Developmental Biology Units, European Molecular Biology Laboratory, Heidelberg, Germany
- Wellcome Trust - Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
| | - Randy J. Read
- Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Sylvia Richardson
- Medical Research Council Biostatistics Unit, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Ana Cvejic
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Nicole Soranzo
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Willem H. Ouwehand
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | | | - Mattia Frontini
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Augusto Rendon
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Medical Research Council Biostatistics Unit, Cambridge Biomedical Campus, Cambridge, United Kingdom
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20
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Fogarty MP, Cannon ME, Vadlamudi S, Gaulton KJ, Mohlke KL. Identification of a regulatory variant that binds FOXA1 and FOXA2 at the CDC123/CAMK1D type 2 diabetes GWAS locus. PLoS Genet 2014; 10:e1004633. [PMID: 25211022 PMCID: PMC4161327 DOI: 10.1371/journal.pgen.1004633] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 07/28/2014] [Indexed: 12/28/2022] Open
Abstract
Many of the type 2 diabetes loci identified through genome-wide association studies localize to non-protein-coding intronic and intergenic regions and likely contain variants that regulate gene transcription. The CDC123/CAMK1D type 2 diabetes association signal on chromosome 10 spans an intergenic region between CDC123 and CAMK1D and also overlaps the CDC123 3′UTR. To gain insight into the molecular mechanisms underlying the association signal, we used open chromatin, histone modifications and transcription factor ChIP-seq data sets from type 2 diabetes-relevant cell types to identify SNPs overlapping predicted regulatory regions. Two regions containing type 2 diabetes-associated variants were tested for enhancer activity using luciferase reporter assays. One SNP, rs11257655, displayed allelic differences in transcriptional enhancer activity in 832/13 and MIN6 insulinoma cells as well as in human HepG2 hepatocellular carcinoma cells. The rs11257655 risk allele T showed greater transcriptional activity than the non-risk allele C in all cell types tested. Using electromobility shift and supershift assays we demonstrated that the rs11257655 risk allele showed allele-specific binding to FOXA1 and FOXA2. We validated FOXA1 and FOXA2 enrichment at the rs11257655 risk allele using allele-specific ChIP in human islets. These results suggest that rs11257655 affects transcriptional activity through altered binding of a protein complex that includes FOXA1 and FOXA2, providing a potential molecular mechanism at this GWAS locus. GWAS have identified more than 1200 loci contributing to risk of disease, including more than 70 loci associated with type 2 diabetes. With a majority of associated variants localized to non-coding regions of the genome, focus has moved to identifying the functional variants explaining the association signals. One mechanism by which variants may act is to affect activity of enhancer elements regulating target gene expression. In this study, we take advantage of recent advances in genome-wide annotation of human regulatory elements to prioritize candidate functional variants at the CDC123/CAMK1D locus. We identify two T2D-associated variants that overlap predicted regulatory enhancer elements. We demonstrate that one variant, rs11257655, shows allele-specific transcriptional enhancer activity in mammalian cell lines relevant to type 2 diabetes. We also show differential protein-DNA binding suggesting that the rs11257655 type 2 diabetes- risk allele increased transcriptional activity through binding a protein complex that includes FOXA1 and FOXA2. This study demonstrates that genome-wide maps of regulatory elements are a useful resource to guide identification of variants differentially affecting transcriptional activity and provides insight into molecular mechanisms underlying a T2D susceptibility locus.
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Affiliation(s)
- Marie P. Fogarty
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Maren E. Cannon
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Swarooparani Vadlamudi
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Kyle J. Gaulton
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Karen L. Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, Chapel Hill, North Carolina, United States of America
- * E-mail:
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21
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Bielczyk-Maczyńska E, Serbanovic-Canic J, Ferreira L, Soranzo N, Stemple DL, Ouwehand WH, Cvejic A. A loss of function screen of identified genome-wide association study Loci reveals new genes controlling hematopoiesis. PLoS Genet 2014; 10:e1004450. [PMID: 25010335 PMCID: PMC4091788 DOI: 10.1371/journal.pgen.1004450] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Accepted: 05/02/2014] [Indexed: 01/01/2023] Open
Abstract
The formation of mature cells by blood stem cells is very well understood at the cellular level and we know many of the key transcription factors that control fate decisions. However, many upstream signalling and downstream effector processes are only partially understood. Genome wide association studies (GWAS) have been particularly useful in providing new directions to dissect these pathways. A GWAS meta-analysis identified 68 genetic loci controlling platelet size and number. Only a quarter of those genes, however, are known regulators of hematopoiesis. To determine function of the remaining genes we performed a medium-throughput genetic screen in zebrafish using antisense morpholino oligonucleotides (MOs) to knock down protein expression, followed by histological analysis of selected genes using a wide panel of different hematopoietic markers. The information generated by the initial knockdown was used to profile phenotypes and to position candidate genes hierarchically in hematopoiesis. Further analysis of brd3a revealed its essential role in differentiation but not maintenance and survival of thrombocytes. Using the from-GWAS-to-function strategy we have not only identified a series of genes that represent novel regulators of thrombopoiesis and hematopoiesis, but this work also represents, to our knowledge, the first example of a functional genetic screening strategy that is a critical step toward obtaining biologically relevant functional data from GWA study for blood cell traits.
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Affiliation(s)
- Ewa Bielczyk-Maczyńska
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge, United Kingdom
| | - Jovana Serbanovic-Canic
- MRC Centre for Developmental and Biomedical Genetics, University of Sheffield, Sheffield, United Kingdom
- Department of Cardiovascular Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Lauren Ferreira
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Nicole Soranzo
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Derek L. Stemple
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Willem H. Ouwehand
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- NHS Blood and Transplant, Cambridge, United Kingdom
| | - Ana Cvejic
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
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22
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Chen CY, Chang IS, Hsiung CA, Wasserman WW. On the identification of potential regulatory variants within genome wide association candidate SNP sets. BMC Med Genomics 2014; 7:34. [PMID: 24920305 PMCID: PMC4066296 DOI: 10.1186/1755-8794-7-34] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 06/02/2014] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Genome wide association studies (GWAS) are a population-scale approach to the identification of segments of the genome in which genetic variations may contribute to disease risk. Current methods focus on the discovery of single nucleotide polymorphisms (SNPs) associated with disease traits. As there are many SNPs within identified risk loci, and the majority of these are situated within non-coding regions, a key challenge is to identify and prioritize variants affecting regulatory sequences that are likely to contribute to the phenotype assessed. METHODS We focused investigation on SNPs within lung and breast cancer GWAS loci that reached genome-wide significance for potential roles in gene regulation with a specific focus on SNPs likely to disrupt transcription factor binding sites. Within risk loci, the regulatory potential of sub-regions was classified using relevant open chromatin and epigenetic high throughput sequencing data sets from the ENCODE project in available cancer and normal cell lines. Furthermore, transcription factor affinity altering variants were predicted by comparison of position weight matrix scores between disease and reference alleles. Lastly, ChIP-seq data of transcription associated factors and topological domains were included as binding evidence and potential gene target inference. RESULTS The sets of SNPs, including both the disease-associated markers and those in high linkage disequilibrium with them, were significantly over-represented in regulatory sequences of cancer and/or normal cells; however, over-representation was generally not restricted to disease-relevant tissue specific regions. The calculated regulatory potential, allelic binding affinity scores and ChIP-seq binding evidence were the three criteria used to prioritize candidates. Fitting all three criteria, we highlighted breast cancer susceptibility SNPs and a borderline lung cancer relevant SNP located in cancer-specific enhancers overlapping multiple distinct transcription associated factor ChIP-seq binding sites. CONCLUSION Incorporating high throughput sequencing epigenetic and transcription factor data sets from both cancer and normal cells into cancer genetic studies reveals potential functional SNPs and informs subsequent characterization efforts.
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Affiliation(s)
- Chih-yu Chen
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia, Canada
| | - I-Shou Chang
- National Institute of Cancer Research, National Health Research Institutes, Zhunan, Taiwan
| | - Chao A Hsiung
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan, Taiwan
| | - Wyeth W Wasserman
- Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
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23
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Heyn H. A symbiotic liaison between the genetic and epigenetic code. Front Genet 2014; 5:113. [PMID: 24822056 PMCID: PMC4013453 DOI: 10.3389/fgene.2014.00113] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Accepted: 04/15/2014] [Indexed: 01/30/2023] Open
Abstract
With rapid advances in sequencing technologies, we are undergoing a paradigm shift from hypothesis- to data-driven research. Genome-wide profiling efforts have given informative insights into biological processes; however, considering the wealth of variation, the major challenge still remains in their meaningful interpretation. In particular sequence variation in non-coding contexts is often challenging to interpret. Here, data integration approaches for the identification of functional genetic variability represent a possible solution. Exemplary, functional linkage analysis integrating genotype and expression data determined regulatory quantitative trait loci and proposed causal relationships. In addition to gene expression, epigenetic regulation and specifically DNA methylation was established as highly valuable surrogate mark for functional variance of the genetic code. Epigenetic modification has served as powerful mediator trait to elucidate mechanisms forming phenotypes in health and disease. Particularly, integrative studies of genetic and DNA methylation data have been able to guide interpretation strategies of risk genotypes, but also proved their value for physiological traits, such as natural human variation and aging. This Review seeks to illustrate the power of data integration in the genomic era exemplified by DNA methylation quantitative trait loci. However, the model is further extendable to virtually all traceable molecular traits.
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Affiliation(s)
- Holger Heyn
- Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute Barcelona, Spain
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24
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Joint analysis of functional genomic data and genome-wide association studies of 18 human traits. Am J Hum Genet 2014; 94:559-73. [PMID: 24702953 DOI: 10.1016/j.ajhg.2014.03.004] [Citation(s) in RCA: 371] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 03/11/2014] [Indexed: 01/23/2023] Open
Abstract
Annotations of gene structures and regulatory elements can inform genome-wide association studies (GWASs). However, choosing the relevant annotations for interpreting an association study of a given trait remains challenging. I describe a statistical model that uses association statistics computed across the genome to identify classes of genomic elements that are enriched with or depleted of loci influencing a trait. The model naturally incorporates multiple types of annotations. I applied the model to GWASs of 18 human traits, including red blood cell traits, platelet traits, glucose levels, lipid levels, height, body mass index, and Crohn disease. For each trait, I used the model to evaluate the relevance of 450 different genomic annotations, including protein-coding genes, enhancers, and DNase-I hypersensitive sites in over 100 tissues and cell lines. The fraction of phenotype-associated SNPs influencing protein sequence ranged from around 2% (for platelet volume) up to around 20% (for low-density lipoprotein cholesterol), repressed chromatin was significantly depleted for SNPs associated with several traits, and cell-type-specific DNase-I hypersensitive sites were enriched with SNPs associated with several traits (for example, the spleen in platelet volume). Finally, reweighting each GWAS by using information from functional genomics increased the number of loci with high-confidence associations by around 5%.
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25
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Abstract
Understanding the functional mechanisms underlying genetic signals associated with complex traits and common diseases, such as cancer, diabetes and Alzheimer's disease, is a formidable challenge. Many genetic signals discovered through genome-wide association studies map to non-protein coding sequences, where their molecular consequences are difficult to evaluate. This article summarizes concepts for the systematic interpretation of non-coding genetic signals using genome annotation data sets in different cellular systems. We outline strategies for the global analysis of multiple association intervals and the in-depth molecular investigation of individual intervals. We highlight experimental techniques to validate candidate (potential causal) regulatory variants, with a focus on novel genome-editing techniques including CRISPR/Cas9. These approaches are also applicable to low-frequency and rare variants, which have become increasingly important in genomic studies of complex traits and diseases. There is a pressing need to translate genetic signals into biological mechanisms, leading to prognostic, diagnostic and therapeutic advances.
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Affiliation(s)
- Dirk S Paul
- UCL Cancer Institute, University College LondonLondon, United Kingdom
| | - Nicole Soranzo
- Wellcome Trust Sanger InstituteHinxton, Cambridge, United Kingdom
- Department of Haematology, University of CambridgeCambridge, United Kingdom
| | - Stephan Beck
- UCL Cancer Institute, University College LondonLondon, United Kingdom
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26
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Chami N, Lettre G. Lessons and Implications from Genome-Wide Association Studies (GWAS) Findings of Blood Cell Phenotypes. Genes (Basel) 2014; 5:51-64. [PMID: 24705286 PMCID: PMC3978511 DOI: 10.3390/genes5010051] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Revised: 01/03/2014] [Accepted: 01/20/2014] [Indexed: 01/10/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified reproducible genetic associations with hundreds of human diseases and traits. The vast majority of these associated single nucleotide polymorphisms (SNPs) are non-coding, highlighting the challenge in moving from genetic findings to mechanistic and functional insights. Nevertheless, large-scale (epi)genomic studies and bioinformatic analyses strongly suggest that GWAS hits are not randomly distributed in the genome but rather pinpoint specific biological pathways important for disease development or phenotypic variation. In this review, we focus on GWAS discoveries for the three main blood cell types: red blood cells, white blood cells and platelets. We summarize the knowledge gained from GWAS of these phenotypes and discuss their possible clinical implications for common (e.g., anemia) and rare (e.g., myeloproliferative neoplasms) human blood-related diseases. Finally, we argue that blood phenotypes are ideal to study the genetics of complex human traits because they are fully amenable to experimental testing.
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Affiliation(s)
- Nathalie Chami
- Montreal Heart Institute, Faculté de Médecine, Université de Montréal, 5000 Bélanger Street, Montréal, QC H1T 1C8, Canada.
| | - Guillaume Lettre
- Montreal Heart Institute, Faculté de Médecine, Université de Montréal, 5000 Bélanger Street, Montréal, QC H1T 1C8, Canada.
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27
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Trynka G, Raychaudhuri S. Using chromatin marks to interpret and localize genetic associations to complex human traits and diseases. Curr Opin Genet Dev 2013; 23:635-41. [PMID: 24287333 DOI: 10.1016/j.gde.2013.10.009] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 09/16/2013] [Accepted: 10/27/2013] [Indexed: 11/26/2022]
Abstract
While studies to associate genomic variants to complex traits have gradually become increasingly productive, the molecular mechanisms that underlie these associations are rarely understood. Because only a small fraction of trait-associated variants can be linked to coding sequences, investigators have speculated that many of the underlying causal alleles influence non-coding gene regulatory sites. Recent studies have successfully identified examples of mechanisms for non-coding alleles at individual loci. Now, genome-wide chromatin assays have resulted in maps of dozens of genomic annotations of the non-coding genome across multiple different tissues, cell types and cell lines. This gives a tremendous opportunity to integrate these annotations with complex trait signals to globally interpret associated variants, and prioritize likely causal alleles. Here, we review the examples of mechanisms by which non-coding, common alleles result in phenotypes. We discuss the efforts to integrate common trait-associated variants with genomic annotations. Finally, we highlight some caveats of these approaches and outline future directions for improvement.
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Affiliation(s)
- Gosia Trynka
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Division of Rheumatology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA; Partners Center for Personalized Genetic Medicine, Boston, MA, USA
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28
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Eldholm V, Haugen A, Zienolddiny S. CTCF mediates the TERT enhancer-promoter interactions in lung cancer cells: identification of a novel enhancer region involved in the regulation of TERT gene. Int J Cancer 2013; 134:2305-13. [PMID: 24174344 DOI: 10.1002/ijc.28570] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 08/19/2013] [Accepted: 10/18/2013] [Indexed: 01/18/2023]
Abstract
Telomerase activation is a hallmark of cancer. Although the regulation of the telomerase reverse transcriptase catalytic subunit (TERT), the rate-limiting factor for telomerase activity, has been studied intensively it remains incompletely understood. In cells devoid of telomerase activity, TERT is embedded in a region of condensed chromatin and the chromatin remodeling protein CCCTC-binding factor (CTCF) has been implicated in the inhibition of TERT expression. The importance of TERT activation for cellular immortalization and carcinogenesis is attested by the fact that the gene is expressed in more than 90% of immortal cell lines and tumors and that gain of TERT is the most frequent amplification event in early stage lung cancer. This study was designed to study the mechanisms of regulation of the TERT gene expression by the CTCF transcription factor in three human lung cancer cell lines, A427, A549 and H838. Depletion of CTCF by siRNA resulted in reduced TERT mRNA levels in two (A427 and A549) of the three cell lines. A novel enhancer element was identified approximately 4.5 kb upstream of the TERT transcription start site. Chromatin immunoprecipitation experiments revealed recruitment of CTCF to this enhancer element. Chromosome conformation capture experiments demonstrated the presence of CTCF-dependent chromatin loops between this enhancer element and the TERT proximal promoter in A427 and A549 cell lines. In summary, the results show that CTCF plays an important role in maintaining TERT expression in a subset of human lung cancer cell lines. This role may be due to CTCF-dependent enhancer-promoter interactions.
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Affiliation(s)
- Vegard Eldholm
- Department of Chemical and Biological Work Environment, National Institute of Occupational Health, Oslo, Norway
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29
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Grundberg E, Meduri E, Sandling J, Hedman Å, Keildson S, Buil A, Busche S, Yuan W, Nisbet J, Sekowska M, Wilk A, Barrett A, Small K, Ge B, Caron M, Shin SY, Lathrop M, Dermitzakis ET, McCarthy MI, Spector TD, Bell JT, Deloukas P. Global analysis of DNA methylation variation in adipose tissue from twins reveals links to disease-associated variants in distal regulatory elements. Am J Hum Genet 2013; 93:876-90. [PMID: 24183450 PMCID: PMC3824131 DOI: 10.1016/j.ajhg.2013.10.004] [Citation(s) in RCA: 288] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Revised: 08/13/2013] [Accepted: 10/04/2013] [Indexed: 12/28/2022] Open
Abstract
Epigenetic modifications such as DNA methylation play a key role in gene regulation and disease susceptibility. However, little is known about the genome-wide frequency, localization, and function of methylation variation and how it is regulated by genetic and environmental factors. We utilized the Multiple Tissue Human Expression Resource (MuTHER) and generated Illumina 450K adipose methylome data from 648 twins. We found that individual CpGs had low variance and that variability was suppressed in promoters. We noted that DNA methylation variation was highly heritable (h(2)median = 0.34) and that shared environmental effects correlated with metabolic phenotype-associated CpGs. Analysis of methylation quantitative-trait loci (metQTL) revealed that 28% of CpGs were associated with nearby SNPs, and when overlapping them with adipose expression quantitative-trait loci (eQTL) from the same individuals, we found that 6% of the loci played a role in regulating both gene expression and DNA methylation. These associations were bidirectional, but there were pronounced negative associations for promoter CpGs. Integration of metQTL with adipose reference epigenomes and disease associations revealed significant enrichment of metQTL overlapping metabolic-trait or disease loci in enhancers (the strongest effects were for high-density lipoprotein cholesterol and body mass index [BMI]). We followed up with the BMI SNP rs713586, a cg01884057 metQTL that overlaps an enhancer upstream of ADCY3, and used bisulphite sequencing to refine this region. Our results showed widespread population invariability yet sequence dependence on adipose DNA methylation but that incorporating maps of regulatory elements aid in linking CpG variation to gene regulation and disease risk in a tissue-dependent manner.
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Affiliation(s)
- Elin Grundberg
- Wellcome Trust Sanger Institute, CB101SA Hinxton, UK
- Department of Twin Research and Genetic Epidemiology, King’s College London, SE17EH London, UK
| | - Eshwar Meduri
- Wellcome Trust Sanger Institute, CB101SA Hinxton, UK
- Department of Twin Research and Genetic Epidemiology, King’s College London, SE17EH London, UK
| | - Johanna K. Sandling
- Wellcome Trust Sanger Institute, CB101SA Hinxton, UK
- Molecular Medicine, Department of Medical Sciences, Uppsala University, 751 85 Uppsala, Sweden
- Science for Life Laboratory, Uppsala University, 751 23 Uppsala, Sweden
| | - Åsa K. Hedman
- Wellcome Trust Centre for Human Genetics, University of Oxford, OX37BN Oxford, UK
| | - Sarah Keildson
- Wellcome Trust Centre for Human Genetics, University of Oxford, OX37BN Oxford, UK
| | - Alfonso Buil
- Department of Genetic Medicine and Development and Institute for Genetics and Genomics in Geneva, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Stephan Busche
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A1A5, Canada
| | - Wei Yuan
- Department of Twin Research and Genetic Epidemiology, King’s College London, SE17EH London, UK
| | - James Nisbet
- Wellcome Trust Sanger Institute, CB101SA Hinxton, UK
| | | | - Alicja Wilk
- Wellcome Trust Sanger Institute, CB101SA Hinxton, UK
| | - Amy Barrett
- Oxford Centre for Diabetes, Endocrinology, & Metabolism, University of Oxford, Churchill Hospital, OX37LJ Oxford, UK
| | - Kerrin S. Small
- Department of Twin Research and Genetic Epidemiology, King’s College London, SE17EH London, UK
| | - Bing Ge
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A1A5, Canada
| | - Maxime Caron
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A1A5, Canada
| | - So-Youn Shin
- Wellcome Trust Sanger Institute, CB101SA Hinxton, UK
| | - Mark Lathrop
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A1A5, Canada
| | - Emmanouil T. Dermitzakis
- Department of Genetic Medicine and Development and Institute for Genetics and Genomics in Geneva, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Mark I. McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, OX37BN Oxford, UK
- Oxford Centre for Diabetes, Endocrinology, & Metabolism, University of Oxford, Churchill Hospital, OX37LJ Oxford, UK
- NIHR Oxford Biomedical Research Centre, Churchill Hospital, OX3 7LE Oxford, UK
| | - Timothy D. Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, SE17EH London, UK
| | - Jordana T. Bell
- Department of Twin Research and Genetic Epidemiology, King’s College London, SE17EH London, UK
| | - Panos Deloukas
- Wellcome Trust Sanger Institute, CB101SA Hinxton, UK
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, EC1M 6BQ London, UK
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Johnsen JM, Nickerson DA, Reiner AP. Massively parallel sequencing: the new frontier of hematologic genomics. Blood 2013; 122:3268-75. [PMID: 24021669 PMCID: PMC3953088 DOI: 10.1182/blood-2013-07-460287] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 08/14/2013] [Indexed: 01/01/2023] Open
Abstract
Genomic technologies are becoming a routine part of human genetic analysis. The exponential growth in DNA sequencing capability has brought an unprecedented understanding of human genetic variation and the identification of thousands of variants that impact human health. In this review, we describe the different types of DNA variation and provide an overview of existing DNA sequencing technologies and their applications. As genomic technologies and knowledge continue to advance, they will become integral in clinical practice. To accomplish the goal of personalized genomic medicine for patients, close collaborations between researchers and clinicians will be essential to develop and curate deep databases of genetic variation and their associated phenotypes.
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Affiliation(s)
- Jill M Johnsen
- Department of Medicine, University of Washington, Seattle, WA
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