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Kirk IK, Weinhold N, Belling K, Skakkebæk NE, Jensen TS, Leffers H, Juul A, Brunak S. Chromosome-wise Protein Interaction Patterns and Their Impact on Functional Implications of Large-Scale Genomic Aberrations. Cell Syst 2017; 4:357-364.e3. [PMID: 28215527 DOI: 10.1016/j.cels.2017.01.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2016] [Revised: 10/23/2016] [Accepted: 01/05/2017] [Indexed: 10/20/2022]
Abstract
Gene copy-number changes influence phenotypes through gene-dosage alteration and subsequent changes of protein complex stoichiometry. Human trisomies where gene copy numbers are increased uniformly over entire chromosomes provide generic cases for studying these relationships. In most trisomies, gene and protein level alterations have fatal consequences. We used genome-wide protein-protein interaction data to identify chromosome-specific patterns of protein interactions. We found that some chromosomes encode proteins that interact infrequently with each other, chromosome 21 in particular. We combined the protein interaction data with transcriptome data from human brain tissue to investigate how this pattern of global interactions may affect cellular function. We identified highly connected proteins that also had coordinated gene expression. These proteins were associated with important neurological functions affecting the characteristic phenotypes for Down syndrome and have previously been validated in mouse knockout experiments. Our approach is general and applicable to other gene-dosage changes, such as arm-level amplifications in cancer.
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Affiliation(s)
- Isa Kristina Kirk
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark; Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Nils Weinhold
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark; Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kirstine Belling
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark; Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Niels Erik Skakkebæk
- Department of Growth and Reproduction, Rigshospitalet and University of Copenhagen, 2100 Copenhagen, Denmark
| | - Thomas Skøt Jensen
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Henrik Leffers
- Department of Growth and Reproduction, Rigshospitalet and University of Copenhagen, 2100 Copenhagen, Denmark
| | - Anders Juul
- Department of Growth and Reproduction, Rigshospitalet and University of Copenhagen, 2100 Copenhagen, Denmark
| | - Søren Brunak
- Department of Systems Biology, Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark; Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
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Marsman RFJ, Wilde AAM, Bezzina CR. Genetic predisposition for sudden cardiac death in myocardial ischaemia: the Arrhythmia Genetics in the NEtherlandS study. Neth Heart J 2011; 19:96-100. [PMID: 21461030 PMCID: PMC3040308 DOI: 10.1007/s12471-010-0070-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Sudden cardiac death from ventricular fibrillation during myocardial infarction is a leading cause of total and cardiovascular mortality. This multifactorial, complex condition clusters in families, suggesting a substantial genetic cause. We carried out a genomewide association study (GWAS) for sudden cardiac death, in the AGNES (Arrhythmia Genetics in the Netherlands) population, consisting of patients with (cases) and without (controls) ventricular fibrillation during a first ST-elevation myocardial infarction. The most significant association was found at chromosome 21q21 (rs2824292; odds ratio = 1.78, 95% CI 1.47–2.13, P = 3.3 × 10−10), 98 kb proximal of the CXADR gene, encoding the Coxsackie and adenovirus receptor. This locus has not previously been implicated in arrhythmia susceptibility. Further research on the mechanism of this locus will ultimately provide novel insight into arrhythmia mechanisms in this condition.
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Affiliation(s)
- R. F. J. Marsman
- Heart Failure Research Center, Department of Experimental Cardiology, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, the Netherlands
| | - A. A. M. Wilde
- Heart Failure Research Center, Department of Experimental Cardiology, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, the Netherlands
- Department of Cardiology, Academic Medical Center, Amsterdam, the Netherlands
| | - C. R. Bezzina
- Heart Failure Research Center, Department of Experimental Cardiology, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, the Netherlands
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Bezzina CR, Pazoki R, Bardai A, Marsman RF, de Jong JSSG, Blom MT, Scicluna BP, Jukema JW, Bindraban NR, Lichtner P, Pfeufer A, Bishopric NH, Roden DM, Meitinger T, Chugh SS, Myerburg RJ, Jouven X, Kääb S, Dekker LRC, Tan HL, Tanck MWT, Wilde AAM. Genome-wide association study identifies a susceptibility locus at 21q21 for ventricular fibrillation in acute myocardial infarction. Nat Genet 2010; 42:688-691. [PMID: 20622880 DOI: 10.1038/ng.623] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Accepted: 06/15/2010] [Indexed: 11/09/2022]
Abstract
Sudden cardiac death from ventricular fibrillation during acute myocardial infarction is a leading cause of total and cardiovascular mortality. To our knowledge, we here report the first genome-wide association study for this trait, conducted in a set of 972 individuals with a first acute myocardial infarction, 515 of whom had ventricular fibrillation and 457 of whom did not, from the Arrhythmia Genetics in The Netherlands (AGNES) study. The most significant association to ventricular fibrillation was found at 21q21 (rs2824292, odds ratio = 1.78, 95% CI 1.47-2.13, P = 3.3 x 10(-10)). The association of rs2824292 with ventricular fibrillation was replicated in an independent case-control set consisting of 146 out-of-hospital cardiac arrest individuals with myocardial infarction complicated by ventricular fibrillation and 391 individuals who survived a myocardial infarction (controls) (odds ratio = 1.49, 95% CI 1.14-1.95, P = 0.004). The closest gene to this SNP is CXADR, which encodes a viral receptor previously implicated in myocarditis and dilated cardiomyopathy and which has recently been identified as a modulator of cardiac conduction. This locus has not previously been implicated in arrhythmia susceptibility.
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Affiliation(s)
- Connie R Bezzina
- Heart Failure Research Center, Department of Experimental Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Raha Pazoki
- Heart Failure Research Center, Department of Experimental Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Abdennasser Bardai
- Heart Failure Research Center, Department of Experimental Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Roos F Marsman
- Heart Failure Research Center, Department of Experimental Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Jonas S S G de Jong
- Heart Failure Research Center, Department of Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Marieke T Blom
- Heart Failure Research Center, Department of Experimental Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Brendon P Scicluna
- Heart Failure Research Center, Department of Experimental Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands.,Durrer Center for Cardiogenetic Research, Amsterdam, The Netherlands
| | - Navin R Bindraban
- Heart Failure Research Center, Department of Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Department of Social Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Peter Lichtner
- Institute of Human Genetics, Klinikum Rechts der Isar Technische Universität München, Munich, Germany
| | - Arne Pfeufer
- Institute of Human Genetics, Klinikum Rechts der Isar Technische Universität München, Munich, Germany.,Institute of Human Genetics, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt, Neuherberg, Germany
| | - Nanette H Bishopric
- Division of Cardiology, Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida, USA.,Department of Pediatrics, University of Miami Miller School of Medicine, Miami, Florida, USA.,Department of Molecular and Cellular Pharmacology, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Dan M Roden
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Thomas Meitinger
- Institute of Human Genetics, Klinikum Rechts der Isar Technische Universität München, Munich, Germany.,Institute of Human Genetics, Helmholtz Zentrum München, Deutsches Forschungszentrum für Gesundheit und Umwelt, Neuherberg, Germany
| | - Sumeet S Chugh
- The Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Robert J Myerburg
- Division of Cardiology, Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Xavier Jouven
- Université Paris Descartes, Assistance Publique-Hopitaux de Paris, Hôpital Européen Georges Pompidou, Paris, France
| | - Stefan Kääb
- Department of Medicine I, University Hospital Grosshadern, Ludwig-Maximilians-Universität, Munich, Germany
| | - Lukas R C Dekker
- Heart Failure Research Center, Department of Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Department of Cardiology, Catharina Hospital, Eindhoven, The Netherlands
| | - Hanno L Tan
- Heart Failure Research Center, Department of Experimental Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Heart Failure Research Center, Department of Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Michael W T Tanck
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Arthur A M Wilde
- Heart Failure Research Center, Department of Experimental Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Heart Failure Research Center, Department of Cardiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
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