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Sun BB, Suhre K, Gibson BW. Promises and challenges of populational proteomics in health and disease. Mol Cell Proteomics 2024:100786. [PMID: 38761890 DOI: 10.1016/j.mcpro.2024.100786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 05/20/2024] Open
Abstract
Advances in proteomic assay technologies has significantly increased coverage and throughput, enabling recent increases in the number of large-scale population-based proteomic studies of human plasma and serum. Improvement in multiplexed protein assays have facilitated quantification of thousands of proteins over a large dynamic range, a key requirement for detecting the lowest ranging, and potentially the most disease relevant, blood circulating proteins. In this perspective, we examine how populational proteomic datasets in conjunction with other concurrent omic measures can be leveraged to better understand the genomic and non-genomic correlates of the soluble proteome, constructing biomarker panels for disease prediction, among others. Mass spectrometry workflows are discussed as they are becoming increasingly competitive with the affinity-based array platforms in terms of speed, cost and proteome coverage due to advances in both instrumentation and workflows. Despite much success, there remains considerable challenges such as orthogonal validation and absolute quantification. We also highlight emergent challenges associated with study design, analytical considerations and data integration as population scale studies are run in batches and may involve longitudinal samples collated over many years. Lastly, we take a look at the future of what the nascent next-generation proteomic technologies might provide to the analysis of large sets of blood samples, as well as the difficulties in designing large-scale studies that will likely require participation from multiple and complex funding sources and where data sharing, study designs and financing must be solved.
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Affiliation(s)
- Benjamin B Sun
- Human Genetics, Informatics and Predictive Sciences, Bristol-Myers Squibb, 02141, USA
| | - Karsten Suhre
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, Doha 24144, Qatar; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Bradford W Gibson
- Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA
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Gao SH, Wang GZ, Wang LP, Feng L, Zhou YC, Yu XJ, Liang F, Yang FY, Wang Z, Sun BB, Wang D, Liang LJ, Xie DW, Zhao S, Feng HP, Li X, Li KK, Tang TS, Huang YC, Wang SQ, Zhou GB. Corrigendum to "Mutations and clinical significance of calcium voltage-gated channel subunit alpha 1E (CACNA1E) in non-small cell lung cancer" [Cell Calcium 102 (2022) 102527]. Cell Calcium 2024; 119:102866. [PMID: 38428281 DOI: 10.1016/j.ceca.2024.102866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Affiliation(s)
- S H Gao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences & University of Chinese Academy of Sciences, Beijing, 100101, China; State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - G Z Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - L P Wang
- State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing, 100091, China
| | - L Feng
- Department of Pathology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Y C Zhou
- Department of Thoracic Surgery, the Third Affiliated Hospital of Kunming Medical University (Yunnan Tumor Hospital), Kunming, 650106, China
| | - X J Yu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences & University of Chinese Academy of Sciences, Beijing, 100101, China
| | - F Liang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences & University of Chinese Academy of Sciences, Beijing, 100101, China; State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - F Y Yang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Z Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - B B Sun
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - D Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - L J Liang
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - D W Xie
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - S Zhao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences & University of Chinese Academy of Sciences, Beijing, 100101, China
| | - H P Feng
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences & University of Chinese Academy of Sciences, Beijing, 100101, China
| | - X Li
- Computer Science Department, University of North Georgia, Dahlonega, GA, 30597, United States
| | - K K Li
- Computer Science Department, University of North Georgia, Dahlonega, GA, 30597, United States
| | - T S Tang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences & University of Chinese Academy of Sciences, Beijing, 100101, China
| | - Y C Huang
- Department of Thoracic Surgery, the Third Affiliated Hospital of Kunming Medical University (Yunnan Tumor Hospital), Kunming, 650106, China
| | - S Q Wang
- State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing, 100091, China
| | - G B Zhou
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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3
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Shrine N, Guyatt AL, Erzurumluoglu AM, Jackson VE, Hobbs BD, Melbourne CA, Batini C, Fawcett KA, Song K, Sakornsakolpat P, Li X, Boxall R, Reeve NF, Obeidat M, Zhao JH, Wielscher M, Weiss S, Kentistou KA, Cook JP, Sun BB, Zhou J, Hui J, Karrasch S, Imboden M, Harris SE, Marten J, Enroth S, Kerr SM, Surakka I, Vitart V, Lehtimäki T, Allen RJ, Bakke PS, Beaty TH, Bleecker ER, Bossé Y, Brandsma CA, Chen Z, Crapo JD, Danesh J, DeMeo DL, Dudbridge F, Ewert R, Gieger C, Gulsvik A, Hansell AL, Hao K, Hoffman JD, Hokanson JE, Homuth G, Joshi PK, Joubert P, Langenberg C, Li X, Li L, Lin K, Lind L, Locantore N, Luan J, Mahajan A, Maranville JC, Murray A, Nickle DC, Packer R, Parker MM, Paynton ML, Porteous DJ, Prokopenko D, Qiao D, Rawal R, Runz H, Sayers I, Sin DD, Smith BH, Artigas MS, Sparrow D, Tal-Singer R, Timmers PRHJ, Van den Berge M, Whittaker JC, Woodruff PG, Yerges-Armstrong LM, Troyanskaya OG, Raitakari OT, Kähönen M, Polašek O, Gyllensten U, Rudan I, Deary IJ, Probst-Hensch NM, Schulz H, James AL, Wilson JF, Stubbe B, Zeggini E, Jarvelin MR, Wareham N, Silverman EK, Hayward C, Morris AP, Butterworth AS, Scott RA, Walters RG, Meyers DA, Cho MH, Strachan DP, Hall IP, Tobin MD, Wain LV. Author Correction: New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries. Nat Genet 2024; 56:1032-1033. [PMID: 38641645 DOI: 10.1038/s41588-024-01752-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2024]
Affiliation(s)
- Nick Shrine
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Anna L Guyatt
- Department of Health Sciences, University of Leicester, Leicester, UK
| | | | - Victoria E Jackson
- Department of Health Sciences, University of Leicester, Leicester, UK
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Brian D Hobbs
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Carl A Melbourne
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Chiara Batini
- Department of Health Sciences, University of Leicester, Leicester, UK
| | | | - Kijoung Song
- Target Sciences, GlaxoSmithKline, Collegeville, PA, USA
| | - Phuwanat Sakornsakolpat
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Xingnan Li
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - Ruth Boxall
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Medical Research Council Population Health Research Unit, University of Oxford, Oxford, UK
| | - Nicola F Reeve
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Ma'en Obeidat
- The University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, British Columbia, Canada
| | - Jing Hua Zhao
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Matthias Wielscher
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
| | - Stefan Weiss
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Katherine A Kentistou
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
- Centre for Cardiovascular Sciences, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - James P Cook
- Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Benjamin B Sun
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jian Zhou
- Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Jennie Hui
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- School of Population Health, The University of Western Australia, Crawley, Western Australia, Australia
- PathWest Laboratory Medicine of WA, Sir Charles Gairdner Hospital, Crawley, Western Australia, Australia
- School of Pathology and Laboratory Medicine, The University of Western Australia, Crawley, Western Australia, Australia
| | - Stefan Karrasch
- Institute of Epidemiology, Helmholtz Zentrum Muenchen-German Research Center for Environmental Health, Neuherberg, Germany
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Ludwig-Maximilians-Universität, Munich, Germany
- Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Medea Imboden
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sarah E Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Jonathan Marten
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Stefan Enroth
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala Universitet, Uppsala, Sweden
| | - Shona M Kerr
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Ida Surakka
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- The National Institute for Health and Welfare (THL), Helsinki, Finland
| | - Veronique Vitart
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Richard J Allen
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Per S Bakke
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins University School of Public Health, Baltimore, MD, USA
| | - Eugene R Bleecker
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - Yohan Bossé
- Department of Molecular Medicine, Laval University, Québec, Canada
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec, Canada
| | - Corry-Anke Brandsma
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, GRIAC Research Institute, University of Groningen, Groningen, The Netherlands
| | - Zhengming Chen
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - James D Crapo
- National Jewish Health, Denver, CO, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, CO, USA
| | - John Danesh
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cambridge Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge, UK
- Department of Human Genetics, Wellcome Trust Sanger Institute, Cambridge, UK
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Frank Dudbridge
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Ralf Ewert
- Department of Internal Medicine B - Cardiology, Intensive Care, Pulmonary Medicine and Infectious Diseases, University Medicine Greifswald, Greifswald, Germany
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum Muenchen - German Research Center for Environmental Health, Neuherberg, Germany
| | - Amund Gulsvik
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Anna L Hansell
- Centre for Environmental Health & Sustainability, University of Leicester, Leicester, UK
- UK Small Area Health Statistics Unit, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, St Mary's Hospital, London, UK
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - John E Hokanson
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Philippe Joubert
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec, Canada
- Department of Molecular Biology, Medical Biochemistry, and Pathology, Laval University, Québec, Canada
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Xuan Li
- The University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, British Columbia, Canada
| | - Liming Li
- Department of Epidemiology & Biostatistics, Peking University Health Science Center, Beijing, China
| | - Kuang Lin
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Lars Lind
- Department of Medical Sciences, Cardiovascular Epidemiology, Uppsala University, Uppsala, Sweden
| | | | - Jian'an Luan
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Alison Murray
- The Institute of Medical Sciences, Aberdeen Biomedical Imaging Centre, University of Aberdeen, Aberdeen, UK
| | - David C Nickle
- MRL, Merck & Co., Inc, Kenilworth, NJ, USA
- Gossamer Bio, San Diego, CA, USA
| | - Richard Packer
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Margaret M Parker
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Megan L Paynton
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - David J Porteous
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Dmitry Prokopenko
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dandi Qiao
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Rajesh Rawal
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum Muenchen - German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology and Social Medicine, University of Münster, Münster, Germany
| | - Heiko Runz
- MRL, Merck & Co., Inc, Kenilworth, NJ, USA
| | - Ian Sayers
- Division of Respiratory Medicine and NIHR-Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Don D Sin
- The University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, British Columbia, Canada
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Blair H Smith
- Division of Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - María Soler Artigas
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Barcelona, Spain
| | - David Sparrow
- VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | | | - Paul R H J Timmers
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Maarten Van den Berge
- University of Groningen, University Medical Center Groningen, Department of Pulmonology, GRIAC Research Institute, University of Groningen, Groningen, The Netherlands
| | - John C Whittaker
- Target Sciences - R&D, GSK Medicines Research Centre, Stevenage, UK
| | - Prescott G Woodruff
- UCSF Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA, USA
| | | | - Olga G Troyanskaya
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Olli T Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Ozren Polašek
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
- University of Split School of Medicine, Split, Croatia
| | - Ulf Gyllensten
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala Universitet, Uppsala, Sweden
| | - Igor Rudan
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Nicole M Probst-Hensch
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Holger Schulz
- Institute of Epidemiology, Helmholtz Zentrum Muenchen-German Research Center for Environmental Health, Neuherberg, Germany
- Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Alan L James
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- Department of Pulmonary Physiology and Sleep Medicine, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- School of Medicine and Pharmacology, The University of Western Australia, Crawley, Western Australia, Australia
| | - James F Wilson
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Beate Stubbe
- Department of Internal Medicine B - Cardiology, Intensive Care, Pulmonary Medicine and Infectious Diseases, University Medicine Greifswald, Greifswald, Germany
| | - Eleftheria Zeggini
- Wellcome Sanger Institute, Hinxton, UK
- Institute of Translational Genomics, Helmholtz Zentrum Muenchen - German Research Center for Environmental Health, Neuherberg, Germany
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Unit of Primary Health Care, Oulu University Hospital, Oulu, Finland
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UK
| | - Nick Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Andrew P Morris
- Department of Biostatistics, University of Liverpool, Liverpool, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Adam S Butterworth
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Robert A Scott
- Target Sciences - R&D, GSK Medicines Research Centre, Stevenage, UK
| | - Robin G Walters
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Deborah A Meyers
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - David P Strachan
- Population Health Research Institute, St George's, University of London, London, UK
| | - Ian P Hall
- Division of Respiratory Medicine and NIHR-Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Martin D Tobin
- Department of Health Sciences, University of Leicester, Leicester, UK.
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK.
| | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, UK.
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK.
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Dhindsa RS, Burren OS, Sun BB, Prins BP, Matelska D, Wheeler E, Mitchell J, Oerton E, Hristova VA, Smith KR, Carss K, Wasilewski S, Harper AR, Paul DS, Fabre MA, Runz H, Viollet C, Challis B, Platt A, Vitsios D, Ashley EA, Whelan CD, Pangalos MN, Wang Q, Petrovski S. Rare variant associations with plasma protein levels in the UK Biobank. Nature 2023; 622:339-347. [PMID: 37794183 PMCID: PMC10567546 DOI: 10.1038/s41586-023-06547-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 08/15/2023] [Indexed: 10/06/2023]
Abstract
Integrating human genomics and proteomics can help elucidate disease mechanisms, identify clinical biomarkers and discover drug targets1-4. Because previous proteogenomic studies have focused on common variation via genome-wide association studies, the contribution of rare variants to the plasma proteome remains largely unknown. Here we identify associations between rare protein-coding variants and 2,923 plasma protein abundances measured in 49,736 UK Biobank individuals. Our variant-level exome-wide association study identified 5,433 rare genotype-protein associations, of which 81% were undetected in a previous genome-wide association study of the same cohort5. We then looked at aggregate signals using gene-level collapsing analysis, which revealed 1,962 gene-protein associations. Of the 691 gene-level signals from protein-truncating variants, 99.4% were associated with decreased protein levels. STAB1 and STAB2, encoding scavenger receptors involved in plasma protein clearance, emerged as pleiotropic loci, with 77 and 41 protein associations, respectively. We demonstrate the utility of our publicly accessible resource through several applications. These include detailing an allelic series in NLRC4, identifying potential biomarkers for a fatty liver disease-associated variant in HSD17B13 and bolstering phenome-wide association studies by integrating protein quantitative trait loci with protein-truncating variants in collapsing analyses. Finally, we uncover distinct proteomic consequences of clonal haematopoiesis (CH), including an association between TET2-CH and increased FLT3 levels. Our results highlight a considerable role for rare variation in plasma protein abundance and the value of proteogenomics in therapeutic discovery.
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Affiliation(s)
- Ryan S Dhindsa
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, US.
| | - Oliver S Burren
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Benjamin B Sun
- Translational Sciences, Research & Development, Biogen Inc., Cambridge, MA, US
| | - Bram P Prins
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Dorota Matelska
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Eleanor Wheeler
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Jonathan Mitchell
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Erin Oerton
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Ventzislava A Hristova
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, US
| | - Katherine R Smith
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Keren Carss
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Sebastian Wasilewski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Andrew R Harper
- Clinical Development, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Dirk S Paul
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Margarete A Fabre
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Heiko Runz
- Translational Sciences, Research & Development, Biogen Inc., Cambridge, MA, US
| | - Coralie Viollet
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Benjamin Challis
- Translational Science and Experimental Medicine, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Adam Platt
- Translational Science and Experimental Medicine, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Dimitrios Vitsios
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Euan A Ashley
- Division of Cardiology, Department of Medicine, Stanford University, Palo Alto, CA, USA
| | | | | | - Quanli Wang
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, US
| | - Slavé Petrovski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK.
- Department of Medicine, Austin Health, University of Melbourne, Melbourne, Victoria, Australia.
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5
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Sun BB, Chiou J, Traylor M, Benner C, Hsu YH, Richardson TG, Surendran P, Mahajan A, Robins C, Vasquez-Grinnell SG, Hou L, Kvikstad EM, Burren OS, Davitte J, Ferber KL, Gillies CE, Hedman ÅK, Hu S, Lin T, Mikkilineni R, Pendergrass RK, Pickering C, Prins B, Baird D, Chen CY, Ward LD, Deaton AM, Welsh S, Willis CM, Lehner N, Arnold M, Wörheide MA, Suhre K, Kastenmüller G, Sethi A, Cule M, Raj A, Burkitt-Gray L, Melamud E, Black MH, Fauman EB, Howson JMM, Kang HM, McCarthy MI, Nioi P, Petrovski S, Scott RA, Smith EN, Szalma S, Waterworth DM, Mitnaul LJ, Szustakowski JD, Gibson BW, Miller MR, Whelan CD. Plasma proteomic associations with genetics and health in the UK Biobank. Nature 2023; 622:329-338. [PMID: 37794186 PMCID: PMC10567551 DOI: 10.1038/s41586-023-06592-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/31/2023] [Indexed: 10/06/2023]
Abstract
The Pharma Proteomics Project is a precompetitive biopharmaceutical consortium characterizing the plasma proteomic profiles of 54,219 UK Biobank participants. Here we provide a detailed summary of this initiative, including technical and biological validations, insights into proteomic disease signatures, and prediction modelling for various demographic and health indicators. We present comprehensive protein quantitative trait locus (pQTL) mapping of 2,923 proteins that identifies 14,287 primary genetic associations, of which 81% are previously undescribed, alongside ancestry-specific pQTL mapping in non-European individuals. The study provides an updated characterization of the genetic architecture of the plasma proteome, contextualized with projected pQTL discovery rates as sample sizes and proteomic assay coverages increase over time. We offer extensive insights into trans pQTLs across multiple biological domains, highlight genetic influences on ligand-receptor interactions and pathway perturbations across a diverse collection of cytokines and complement networks, and illustrate long-range epistatic effects of ABO blood group and FUT2 secretor status on proteins with gastrointestinal tissue-enriched expression. We demonstrate the utility of these data for drug discovery by extending the genetic proxied effects of protein targets, such as PCSK9, on additional endpoints, and disentangle specific genes and proteins perturbed at loci associated with COVID-19 susceptibility. This public-private partnership provides the scientific community with an open-access proteomics resource of considerable breadth and depth to help to elucidate the biological mechanisms underlying proteo-genomic discoveries and accelerate the development of biomarkers, predictive models and therapeutics1.
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Affiliation(s)
- Benjamin B Sun
- Translational Sciences, Research & Development, Biogen, Cambridge, MA, USA.
| | - Joshua Chiou
- Internal Medicine Research Unit, Worldwide Research, Development and Medical, Pfizer, Cambridge, MA, USA
| | - Matthew Traylor
- Human Genetics Centre of Excellence, Novo Nordisk Research Centre Oxford, Oxford, UK
| | | | | | - Tom G Richardson
- Human Genetics Centre of Excellence, Novo Nordisk Research Centre Oxford, Oxford, UK
- Genomic Sciences, GlaxoSmithKline, Stevenage, UK
| | | | | | - Chloe Robins
- Genomic Sciences, GlaxoSmithKline, Collegeville, PA, USA
| | | | - Liping Hou
- Population Analytics, Janssen Research & Development, Spring House, PA, USA
| | | | - Oliver S Burren
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | | | - Kyle L Ferber
- Biostatistics, Research and Development, Biogen, Cambridge, MA, USA
| | | | - Åsa K Hedman
- External Science and Innovation Target Sciences, Worldwide Research, Development and Medical, Pfizer, Stockholm, Sweden
| | - Sile Hu
- Human Genetics Centre of Excellence, Novo Nordisk Research Centre Oxford, Oxford, UK
| | - Tinchi Lin
- Analytics and Data Sciences, Biogen, Cambridge, MA, USA
| | - Rajesh Mikkilineni
- Data Science Institute, Takeda Development Center Americas, Cambridge, MA, USA
| | | | | | - Bram Prins
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Denis Baird
- Translational Sciences, Research & Development, Biogen, Cambridge, MA, USA
| | - Chia-Yen Chen
- Translational Sciences, Research & Development, Biogen, Cambridge, MA, USA
| | - Lucas D Ward
- Alnylam Human Genetics, Discovery & Translational Research, Alnylam Pharmaceuticals, Cambridge, MA, USA
| | - Aimee M Deaton
- Alnylam Human Genetics, Discovery & Translational Research, Alnylam Pharmaceuticals, Cambridge, MA, USA
| | | | - Carissa M Willis
- Alnylam Human Genetics, Discovery & Translational Research, Alnylam Pharmaceuticals, Cambridge, MA, USA
| | - Nick Lehner
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Matthias Arnold
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA
| | - Maria A Wörheide
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Karsten Suhre
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Gabi Kastenmüller
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | | | | | - Anil Raj
- Calico Life Sciences, San Francisco, CA, USA
| | | | | | - Mary Helen Black
- Population Analytics, Janssen Research & Development, Spring House, PA, USA
| | - Eric B Fauman
- Internal Medicine Research Unit, Worldwide Research, Development and Medical, Pfizer, Cambridge, MA, USA
| | - Joanna M M Howson
- Human Genetics Centre of Excellence, Novo Nordisk Research Centre Oxford, Oxford, UK
| | | | | | - Paul Nioi
- Alnylam Human Genetics, Discovery & Translational Research, Alnylam Pharmaceuticals, Cambridge, MA, USA
| | - Slavé Petrovski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
- Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
| | | | - Erin N Smith
- Takeda Development Center Americas, San Diego, CA, USA
| | - Sándor Szalma
- Takeda Development Center Americas, San Diego, CA, USA
| | | | | | | | | | - Melissa R Miller
- Internal Medicine Research Unit, Worldwide Research, Development and Medical, Pfizer, Cambridge, MA, USA
| | - Christopher D Whelan
- Translational Sciences, Research & Development, Biogen, Cambridge, MA, USA.
- Neuroscience Data Science, Janssen Research & Development, Cambridge, MA, USA.
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6
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Luo H, Bauer A, Nano J, Petrera A, Rathmann W, Herder C, Hauck SM, Sun BB, Hoyer A, Peters A, Thorand B. Associations of plasma proteomics with type 2 diabetes and related traits: results from the longitudinal KORA S4/F4/FF4 Study. Diabetologia 2023; 66:1655-1668. [PMID: 37308750 DOI: 10.1007/s00125-023-05943-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 04/12/2023] [Indexed: 06/14/2023]
Abstract
AIMS/HYPOTHESIS This study aimed to elucidate the aetiological role of plasma proteins in glucose metabolism and type 2 diabetes development. METHODS We measured 233 proteins at baseline in 1653 participants from the Cooperative Health Research in the Region of Augsburg (KORA) S4 cohort study (median follow-up time: 13.5 years). We used logistic regression in the cross-sectional analysis (n=1300), and Cox regression accounting for interval-censored data in the longitudinal analysis (n=1143). We further applied two-level growth models to investigate associations with repeatedly measured traits (fasting glucose, 2 h glucose, fasting insulin, HOMA-B, HOMA-IR, HbA1c), and two-sample Mendelian randomisation analysis to investigate causal associations. Moreover, we built prediction models using priority-Lasso on top of Framingham-Offspring Risk Score components and evaluated the prediction accuracy through AUC. RESULTS We identified 14, 24 and four proteins associated with prevalent prediabetes (i.e. impaired glucose tolerance and/or impaired fasting glucose), prevalent newly diagnosed type 2 diabetes and incident type 2 diabetes, respectively (28 overlapping proteins). Of these, IL-17D, IL-18 receptor 1, carbonic anhydrase-5A, IL-1 receptor type 2 (IL-1RT2) and matrix extracellular phosphoglycoprotein were novel candidates. IGF binding protein 2 (IGFBP2), lipoprotein lipase (LPL) and paraoxonase 3 (PON3) were inversely associated while fibroblast growth factor 21 was positively associated with incident type 2 diabetes. LPL was longitudinally linked with change in glucose-related traits, while IGFBP2 and PON3 were linked with changes in both insulin- and glucose-related traits. Mendelian randomisation analysis suggested causal effects of LPL on type 2 diabetes and fasting insulin. The simultaneous addition of 12 priority-Lasso-selected biomarkers (IGFBP2, IL-18, IL-17D, complement component C1q receptor, V-set and immunoglobulin domain-containing protein 2, IL-1RT2, LPL, CUB domain-containing protein 1, vascular endothelial growth factor D, PON3, C-C motif chemokine 4 and tartrate-resistant acid phosphatase type 5) significantly improved the predictive performance (ΔAUC 0.0219; 95% CI 0.0052, 0.0624). CONCLUSIONS/INTERPRETATION We identified new candidates involved in the development of derangements in glucose metabolism and type 2 diabetes and confirmed previously reported proteins. Our findings underscore the importance of proteins in the pathogenesis of type 2 diabetes and the identified putative proteins can function as potential pharmacological targets for diabetes treatment and prevention.
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Affiliation(s)
- Hong Luo
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Institute for Medical Information Processing, Biometry and Epidemiology (IBE), Faculty of Medicine, LMU Munich, Pettenkofer School of Public Health, Munich, Germany
| | - Alina Bauer
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Jana Nano
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Institute for Medical Information Processing, Biometry and Epidemiology (IBE), Faculty of Medicine, LMU Munich, Pettenkofer School of Public Health, Munich, Germany
| | - Agnese Petrera
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
| | - Wolfgang Rathmann
- Institute for Biometrics and Epidemiology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine Universität Düsseldorf, Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Düsseldorf, Neuherberg, Germany
| | - Christian Herder
- German Center for Diabetes Research (DZD), Partner Düsseldorf, Neuherberg, Germany
- Institute for Clinical Diabetology, German Diabetes Center, Leibniz Center for Diabetes Research at Heinrich Heine Universität Düsseldorf, Düsseldorf, Germany
- Department of Endocrinology and Diabetology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine Universität Düsseldorf, Düsseldorf, Germany
| | - Stefanie M Hauck
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- German Center for Diabetes Research (DZD), Partner München-Neuherberg, Neuherberg, Germany
| | - Benjamin B Sun
- Translation Sciences, Research & Development, Biogen Inc., Cambridge, MA, USA
| | - Annika Hoyer
- Biostatistics and Medical Biometry, Medical School OWL, Bielefeld University, Bielefeld, Germany
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany
- Institute for Medical Information Processing, Biometry and Epidemiology (IBE), Faculty of Medicine, LMU Munich, Pettenkofer School of Public Health, Munich, Germany
- German Center for Diabetes Research (DZD), Partner München-Neuherberg, Neuherberg, Germany
| | - Barbara Thorand
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health (GmbH), Neuherberg, Germany.
- German Center for Diabetes Research (DZD), Partner München-Neuherberg, Neuherberg, Germany.
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7
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Tao H, Meng F, Zhou Y, Fan J, Liu J, Han Y, Sun BB, Wang G. Transcriptomic and Functional Approaches Unveil the Role of tmRNA in Zinc Acetate Mediated Levofloxacin Sensitivity in Helicobacter pylori. Microbiol Spectr 2022; 10:e0115222. [PMID: 36354329 PMCID: PMC9769675 DOI: 10.1128/spectrum.01152-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 10/17/2022] [Indexed: 11/12/2022] Open
Abstract
Rapid increase in resistance of Helicobacter pylori (H. pylori) has hindered antibiotics-based eradication efforts worldwide and raises the need for additional approaches. Here, we investigate the role of zinc-based compounds in inhibiting H. pylori growth and modulating antibiotic sensitivities, interrogate their downstream transcriptomic changes, and highlight the potential mechanism driving the observed effects. We showed that zinc acetate inhibited H. pylori growth and increased H. pylori sensitivity to levofloxacin. Transcriptomic profiling showed distinct gene expression patterns between zinc acetate treated groups versus controls. In particular, we independently replicated the association between zinc acetate treatment and increased ssrA expression. Knockdown of ssrA restored levofloxacin resistance to levels of the control group. In this study, we first demonstrated the role of zinc acetate in H. pylori growth and antibiotic sensitivities. Additionally, we explored the transcriptomic perturbations of zinc acetate followed by functional knockdown follow-up of differentially expressed ssrA, highlighting the role of tmRNA and trans-translation in H. pylori levofloxacin resistance. Our results provide alternative and complementary strategies for H. pylori treatment and shed light on the underlying mechanisms driving these effects. IMPORTANCE Helicobacter pylori (H. pylori) eradication plays an important role in gastric cancer prevention, but the antimicrobial resistance of H. pylori is fast becoming a growing concern. In this study, we investigated the role of zinc acetate in inhibiting H. pylori growth and modulating antibiotic sensitivities in vitro. Additionally, we explored the transcriptomic perturbations of zinc acetate followed by functional knockdown follow-up of differentially expressed ssrA, highlighting the role of tmRNA and trans-translation in H. pylori levofloxacin resistance. Our results open up a new horizon for the treatment of antibiotic-resistant H. pylori.
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Affiliation(s)
- Hongjin Tao
- Department of Gastroenterology, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, People’s Republic of China
- Medical School of Chinese PLA, Beijing, People’s Republic of China
| | - Fansen Meng
- Department of Gastroenterology, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, People’s Republic of China
| | - Yu Zhou
- Department of Laboratory Medicine, Second Medical Center, Chinese PLA General Hospital, Beijing, People’s Republic of China
| | - Jiao Fan
- Institute of Geriatrics, National Clinical Research Center of Geriatrics Disease, Second Medical Center, Chinese PLA General Hospital, Beijing, People’s Republic of China
| | - Jing Liu
- Institute of Geriatrics, National Clinical Research Center of Geriatrics Disease, Second Medical Center, Chinese PLA General Hospital, Beijing, People’s Republic of China
| | - Yingjie Han
- Department of Oncology, Fifth Medical Center, Chinese PLA General Hospital, Beijing, People’s Republic of China
| | - Benjamin B. Sun
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Gangshi Wang
- Department of Gastroenterology, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, People’s Republic of China
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8
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Sun BB, Loomis SJ, Pizzagalli F, Shatokhina N, Painter JN, Foley CN, Jensen ME, McLaren DG, Chintapalli SS, Zhu AH, Dixon D, Islam T, Ba Gari I, Runz H, Medland SE, Thompson PM, Jahanshad N, Whelan CD. Genetic map of regional sulcal morphology in the human brain from UK biobank data. Nat Commun 2022; 13:6071. [PMID: 36241887 PMCID: PMC9568560 DOI: 10.1038/s41467-022-33829-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 10/05/2022] [Indexed: 12/24/2022] Open
Abstract
Genetic associations with macroscopic brain structure can provide insights into brain function and disease. However, specific associations with measures of local brain folding are largely under-explored. Here, we conducted large-scale genome- and exome-wide associations of regional cortical sulcal measures derived from magnetic resonance imaging scans of 40,169 individuals in UK Biobank. We discovered 388 regional brain folding associations across 77 genetic loci, with genes in associated loci enriched for expression in the cerebral cortex, neuronal development processes, and differential regulation during early brain development. We integrated brain eQTLs to refine genes for various loci, implicated several genes involved in neurodevelopmental disorders, and highlighted global genetic correlations with neuropsychiatric phenotypes. We provide an interactive 3D visualisation of our summary associations, emphasising added resolution of regional analyses. Our results offer new insights into the genetic architecture of brain folding and provide a resource for future studies of sulcal morphology in health and disease.
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Affiliation(s)
- Benjamin B Sun
- Translational Biology, Research & Development, Biogen Inc., Cambridge, MA, US.
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
| | - Stephanie J Loomis
- Translational Biology, Research & Development, Biogen Inc., Cambridge, MA, US
| | - Fabrizio Pizzagalli
- Department of Neuroscience "Rita Levi Montalcini", University of Turin, Turin, Italy
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA, US
| | - Natalia Shatokhina
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA, US
| | - Jodie N Painter
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Christopher N Foley
- MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Optima Partners, Edinburgh, UK
| | - Megan E Jensen
- Clinical Sciences, Research & Development, Biogen Inc., Cambridge, MA, US
| | - Donald G McLaren
- Clinical Sciences, Research & Development, Biogen Inc., Cambridge, MA, US
| | | | - Alyssa H Zhu
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA, US
| | - Daniel Dixon
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA, US
| | - Tasfiya Islam
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA, US
| | - Iyad Ba Gari
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA, US
| | - Heiko Runz
- Translational Biology, Research & Development, Biogen Inc., Cambridge, MA, US
| | - Sarah E Medland
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Paul M Thompson
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA, US.
| | - Neda Jahanshad
- Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, Keck School of Medicine, University of Southern California, Marina del Rey, CA, US.
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9
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Gong M, Han Y, Wang X, Tao H, Meng F, Hou B, Sun BB, Wang G. Effect of Temperature on Metronidazole Resistance in Helicobacter pylori. Front Microbiol 2021; 12:681911. [PMID: 34093508 PMCID: PMC8170400 DOI: 10.3389/fmicb.2021.681911] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 04/23/2021] [Indexed: 01/14/2023] Open
Abstract
Efficacy of Helicobacter pylori (H. pylori) eradication therapy has declined due to rapid rises in antibiotic resistance. We investigated how increased temperature affected H. pylori (NCTC 11637) growth and its sensitivity to metronidazole in vitro. We performed transcriptomic profiling using RNA-sequencing to identify differentially expressed genes (DEGs) associated with increased temperature. Transcriptional pathways involved in temperature-driven metronidazole resistance changes were analyzed through bioinformatic and literature curation approaches. We showed that H. pylori growth was inhibited at 41°C and inhibition was more apparent with prolonged incubation. Resistance to metronidazole was also reduced—minimum inhibitory concentration for metronidazole decreased from > 256 μg/ml at 37°C to 8 μg/ml at 41°C after culturing for 3 days. RNA-sequencing results, which were highly concordant within treatment conditions, revealed more than one third of genes (583/1,552) to be differentially expressed at increased temperatures with similar proportions up and down-regulated. Quantitative real-time PCR validation for 8 out of 10 DEGs tested gave consistent direction in gene expression changes. We found enrichment for redox and oxygen radical pathways, highlighting a mechanistic pathway driving temperature-related metronidazole resistance. Independent literature review of published genes associated with metronidazole resistance revealed 46 gene candidates, 21 of which showed differential expression and 7 out of 9 DEGs associated with “redox” resistance pathways. Sanger sequencing did not detect any changes in genetic sequences for known resistance genes rdxA, frxA nor fdxB. Our findings suggest that temperature increase can inhibit the growth and reduce H. pylori resistance to metronidazole. Redox pathways are possible potential drivers in metronidazole resistance change induced by temperature. Our study provides insight into potential novel approaches in treating antibiotic resistant H. pylori.
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Affiliation(s)
- Meiliang Gong
- Department of Laboratory Medicine, Second Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Yingjie Han
- Department of Gastroenterology, Second Medical Center, Chinese PLA General Hospital, National Clinical Research Center for Geriatric Diseases, Beijing, China.,Department of Oncology, Fifth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Xuning Wang
- Department of Surgery, First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Hongjin Tao
- Department of Gastroenterology, Second Medical Center, Chinese PLA General Hospital, National Clinical Research Center for Geriatric Diseases, Beijing, China
| | - Fansen Meng
- Department of Gastroenterology, Second Medical Center, Chinese PLA General Hospital, National Clinical Research Center for Geriatric Diseases, Beijing, China
| | - Baicun Hou
- Department of Gastroenterology, Second Medical Center, Chinese PLA General Hospital, National Clinical Research Center for Geriatric Diseases, Beijing, China
| | - Benjamin B Sun
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom.,Royal Free Hospital, London, United Kingdom
| | - Gangshi Wang
- Department of Gastroenterology, Second Medical Center, Chinese PLA General Hospital, National Clinical Research Center for Geriatric Diseases, Beijing, China
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10
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Foley CN, Staley JR, Breen PG, Sun BB, Kirk PDW, Burgess S, Howson JMM. A fast and efficient colocalization algorithm for identifying shared genetic risk factors across multiple traits. Nat Commun 2021; 12:764. [PMID: 33536417 PMCID: PMC7858636 DOI: 10.1038/s41467-020-20885-8] [Citation(s) in RCA: 127] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 12/17/2020] [Indexed: 01/30/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified thousands of genomic regions affecting complex diseases. The next challenge is to elucidate the causal genes and mechanisms involved. One approach is to use statistical colocalization to assess shared genetic aetiology across multiple related traits (e.g. molecular traits, metabolic pathways and complex diseases) to identify causal pathways, prioritize causal variants and evaluate pleiotropy. We propose HyPrColoc (Hypothesis Prioritisation for multi-trait Colocalization), an efficient deterministic Bayesian algorithm using GWAS summary statistics that can detect colocalization across vast numbers of traits simultaneously (e.g. 100 traits can be jointly analysed in around 1 s). We perform a genome-wide multi-trait colocalization analysis of coronary heart disease (CHD) and fourteen related traits, identifying 43 regions in which CHD colocalized with ≥1 trait, including 5 previously unknown CHD loci. Across the 43 loci, we further integrate gene and protein expression quantitative trait loci to identify candidate causal genes.
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Affiliation(s)
- Christopher N Foley
- MRC Biostatistics Unit, Cambridge Institute of Public Health, University of Cambridge, Cambridge, CB2 0SR, UK.
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK.
| | - James R Staley
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Philip G Breen
- School of Mathematics, University of Edinburgh, Kings Buildings, Edinburgh, EH9 3JZ, UK
| | - Benjamin B Sun
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Paul D W Kirk
- MRC Biostatistics Unit, Cambridge Institute of Public Health, University of Cambridge, Cambridge, CB2 0SR, UK
| | - Stephen Burgess
- MRC Biostatistics Unit, Cambridge Institute of Public Health, University of Cambridge, Cambridge, CB2 0SR, UK
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Joanna M M Howson
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
- National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge and Cambridge University Hospitals, Cambridge, UK
- Department of Genetics, Novo Nordisk Research Centre Oxford, Oxford, UK
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11
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Qu XL, Yang YL, Liu SX, Shi YP, Lin BC, Sun BB, Zhong X, Yang CZ, Jiang W. [Post-discharge growth of extremely premature infants within corrected age of 24 months]. Zhonghua Er Ke Za Zhi 2021; 58:982-988. [PMID: 33256320 DOI: 10.3760/cma.j.cn112140-20200628-00670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To demonstrate the post-discharge catch-up growth of extremely premature infants (EPI) within 24 months of corrected age. Methods: This study retrospectively collected the anthropomorphic measurements of 311 EPI who visited Shenzhen Maternity and Child Healthcare Hospital from August 2013 to April 2020. These infants were stratified according to gestational age at birth (GA): 23-24+6weeks, 25-26+6weeks, 27-27+6weeks; and birth weight:<750 g, 750-999 g, ≥1 000 g. The anthropomorphic measurements, including weight, length, and head circumference for age, were recorded timely from discharge to 24 months of corrected age. And the growth curve stratified by GA and birth weight were fitted in both chronological age and corrected age, which were then compared with the World Health Organization Child Growth Standards for term infant (2006 version), to investigate the catch-up growth pattern of EPI. And appropriate catch-up was defined as the measurements reached the 25th percentile of WHO growth curve. Results: In these 311 EPI, 184 were males and 127 females, with gestational age of 23-27+6 weeks and birth weight of 480-1 430 g. Regardless of the GA and birth weight, the growth curves fitted in corrected age failed to overlap with that in chronological age by 24 months of corrected age. The growth velocity of weight, length and head circumference in both corrected and chronological age were all positively correlated with GA and birth weight: the 27-27+6weeks group showed a preferable growth pattern than the 25-26+6weeks group, and the curve of the 23-24+6weeks group was most unfavorable; and the same pattern was observed between the subgroups of different birth weight. Furthermore, the GA had more significant impact on the catch-up growth pattern than birth weight did. When assessed with corrected age curve, the weight and length of both male and female EPIs achieved appropriate catch-up by 24 months, as well as the head circumference of girls; whereas, boys' head circumference reached appropriate catch-up at the corrected age of 9 months, but fell behind the 25th percentile after that. However, when assessed with chronological age curve, both boys and girls failed to achieve appropriate catch-up in weight, length and head circumference by age 24 months. And no matter in corrected or chronological age, all physical measurements of girls were lower than those of boys. Conclusions: The rapid catch-up growth of EPI happens within 6 months of corrected age. The lower the birth weight and gestational age, the lower the physical measurements at each corresponding month of age, and the longer it takes to achieve appropriate catch-up. Gestational age has a greater impact on the longitudinal catch-up growth than birth weight does. And girls generally grow slower than boys in either correct or actual age. Before 24 months of corrected age, the growth should be assessed with corrected age rather than chronological age.
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Affiliation(s)
- X L Qu
- Department of Child Psychology and Rehabilitation, Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen 518017, China
| | - Y L Yang
- Department of Child Psychology and Rehabilitation, Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen 518017, China
| | - S X Liu
- Department of Child Psychology and Rehabilitation, Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen 518017, China
| | - Y P Shi
- Department of Neonatology, Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen 518017, China
| | - B C Lin
- Department of Neonatology, Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen 518017, China
| | - B B Sun
- Department of Child Psychology and Rehabilitation, Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen 518017, China
| | - X Zhong
- Department of Child Psychology and Rehabilitation, Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen 518017, China
| | - C Z Yang
- Department of Neonatology, Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen 518017, China
| | - W Jiang
- Department of Child Psychology and Rehabilitation, Shenzhen Maternity and Child Healthcare Hospital, Southern Medical University, Shenzhen 518017, China
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12
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Zheng J, Haberland V, Baird D, Walker V, Haycock PC, Hurle MR, Gutteridge A, Erola P, Liu Y, Luo S, Robinson J, Richardson TG, Staley JR, Elsworth B, Burgess S, Sun BB, Danesh J, Runz H, Maranville JC, Martin HM, Yarmolinsky J, Laurin C, Holmes MV, Liu JZ, Estrada K, Santos R, McCarthy L, Waterworth D, Nelson MR, Smith GD, Butterworth AS, Hemani G, Scott RA, Gaunt TR. Phenome-wide Mendelian randomization mapping the influence of the plasma proteome on complex diseases. Nat Genet 2020; 52:1122-1131. [PMID: 32895551 PMCID: PMC7610464 DOI: 10.1038/s41588-020-0682-6] [Citation(s) in RCA: 131] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/24/2020] [Indexed: 01/23/2023]
Abstract
The human proteome is a major source of therapeutic targets. Recent genetic association analyses of the plasma proteome enable systematic evaluation of the causal consequences of variation in plasma protein levels. Here we estimated the effects of 1,002 proteins on 225 phenotypes using two-sample Mendelian randomization (MR) and colocalization. Of 413 associations supported by evidence from MR, 130 (31.5%) were not supported by results of colocalization analyses, suggesting that genetic confounding due to linkage disequilibrium is widespread in naïve phenome-wide association studies of proteins. Combining MR and colocalization evidence in cis-only analyses, we identified 111 putatively causal effects between 65 proteins and 52 disease-related phenotypes ( https://www.epigraphdb.org/pqtl/ ). Evaluation of data from historic drug development programs showed that target-indication pairs with MR and colocalization support were more likely to be approved, evidencing the value of this approach in identifying and prioritizing potential therapeutic targets.
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Affiliation(s)
- Jie Zheng
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK.
- Proteome MR writing group, .
| | - Valeriia Haberland
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
- Proteome MR writing group
| | - Denis Baird
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
- Proteome MR writing group
| | - Venexia Walker
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
- Proteome MR writing group
| | - Philip C Haycock
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
- Proteome MR writing group
| | - Mark R Hurle
- Human Genetics, GlaxoSmithKline, Collegeville, PA, USA
| | | | - Pau Erola
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
| | - Yi Liu
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
| | - Shan Luo
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
- School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, Hong Kong, China
| | - Jamie Robinson
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
| | - Tom G Richardson
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
| | - James R Staley
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Benjamin Elsworth
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
| | - Stephen Burgess
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Benjamin B Sun
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - John Danesh
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- BHF Centre of Research Excellence, School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Hinxton, UK
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Heiko Runz
- Translational Biology, Biogen, Cambridge, MA, USA
| | - Joseph C Maranville
- Informatics and Predictive Sciences, Celgene Corporation, Cambridge, MA, USA
| | - Hannah M Martin
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - James Yarmolinsky
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
| | - Charles Laurin
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
| | - Michael V Holmes
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
- Medical Research Council Population Health Research Unit, University of Oxford, Oxford, UK
- Clinical Trial Service Unit & Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- National Institute for Health Research, Oxford Biomedical Research Centre, Oxford University Hospital, Oxford, UK
| | - Jimmy Z Liu
- Translational Biology, Biogen, Cambridge, MA, USA
| | | | - Rita Santos
- Functional Genomics, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | | | | | | | - George Davey Smith
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
- Proteome MR writing group
- NIHR Bristol Biomedical Research Centre, Bristol, UK
| | - Adam S Butterworth
- Proteome MR writing group
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- BHF Centre of Research Excellence, School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- NIHR Cambridge Biomedical Research Centre, School of Clinical Medicine, Addenbrooke's Hospital, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Hinxton, UK
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK
- Proteome MR writing group
| | - Robert A Scott
- Proteome MR writing group, .
- Human Genetics, GlaxoSmithKline, Stevenage, UK.
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit (IEU), Bristol Medical School, University of Bristol, Bristol, UK.
- Proteome MR writing group, .
- NIHR Bristol Biomedical Research Centre, Bristol, UK.
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13
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Paige E, Clément M, Lareyre F, Sweeting M, Raffort J, Grenier C, Finigan A, Harrison J, Peters JE, Sun BB, Butterworth AS, Harrison SC, Bown MJ, Lindholt JS, Badger SA, Kullo IJ, Powell J, Norman PE, Scott DJA, Bailey MA, Rose-John S, Danesh J, Freitag DF, Paul DS, Mallat Z. Interleukin-6 Receptor Signaling and Abdominal Aortic Aneurysm Growth Rates. Circ Genom Precis Med 2020; 12:e002413. [PMID: 30657332 PMCID: PMC6383754 DOI: 10.1161/circgen.118.002413] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Supplemental Digital Content is available in the text. Background: The Asp358Ala variant (rs2228145; A>C) in the IL (interleukin)-6 receptor (IL6R) gene has been implicated in the development of abdominal aortic aneurysms (AAAs), but its effect on AAA growth over time is not known. We aimed to investigate the clinical association between the IL6R-Asp358Ala variant and AAA growth and to assess the effect of blocking the IL-6 signaling pathway in mouse models of aortic aneurysm rupture or dissection. Methods: Using data from 2863 participants with AAA from 9 prospective cohorts, age- and sex-adjusted mixed-effects linear regression models were used to estimate the association between the IL6R-Asp358Ala variant and annual change in AAA diameter (mm/y). In a series of complementary randomized trials in mice, the effect of blocking the IL-6 signaling pathways was assessed on plasma biomarkers, systolic blood pressure, aneurysm diameter, and time to aortic rupture and death. Results: After adjusting for age and sex, baseline aneurysm size was 0.55 mm (95% CI, 0.13–0.98 mm) smaller per copy of the minor allele [C] of the Asp358Ala variant. Change in AAA growth was −0.06 mm per year (−0.18 to 0.06) per copy of the minor allele; a result that was not statistically significant. Although all available worldwide data were used, the genetic analyses were not powered for an effect size as small as that observed. In 2 mouse models of AAA, selective blockage of the IL-6 trans-signaling pathway, but not combined blockage of both, the classical and trans-signaling pathways, was associated with improved survival (P<0.05). Conclusions: Our proof-of-principle data are compatible with the concept that IL-6 trans-signaling is relevant to AAA growth, encouraging larger-scale evaluation of this hypothesis.
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Affiliation(s)
- Ellie Paige
- National Centre for Epidemiology and Population Health, Research School of Population Health, The Australian National University, Canberra, Australia (E.P.).,BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care (E.P., M.S., J.E.P., B.B.S., A.S.B., J.D., D.F.F., D.S.P.), University of Cambridge, United Kingdom
| | - Marc Clément
- Division of Cardiovascular Medicine (M.C., F.L., J.R., C.G., A.F., J.H., Z.M.), University of Cambridge, United Kingdom
| | - Fabien Lareyre
- Division of Cardiovascular Medicine (M.C., F.L., J.R., C.G., A.F., J.H., Z.M.), University of Cambridge, United Kingdom.,Université Côte d'Azur, Institut National de la Sante et de la Recherche Medicale, Centre Mediterranéen de Recherche Moleculaire (F.L., J.R.).,University Hospital of Nice, France (F.L., J.R.)
| | - Michael Sweeting
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care (E.P., M.S., J.E.P., B.B.S., A.S.B., J.D., D.F.F., D.S.P.), University of Cambridge, United Kingdom.,Department of Health Sciences (M.S.), University of Leicester
| | - Juliette Raffort
- Division of Cardiovascular Medicine (M.C., F.L., J.R., C.G., A.F., J.H., Z.M.), University of Cambridge, United Kingdom.,Université Côte d'Azur, Institut National de la Sante et de la Recherche Medicale, Centre Mediterranéen de Recherche Moleculaire (F.L., J.R.).,University Hospital of Nice, France (F.L., J.R.)
| | - Céline Grenier
- Division of Cardiovascular Medicine (M.C., F.L., J.R., C.G., A.F., J.H., Z.M.), University of Cambridge, United Kingdom
| | - Alison Finigan
- Division of Cardiovascular Medicine (M.C., F.L., J.R., C.G., A.F., J.H., Z.M.), University of Cambridge, United Kingdom
| | - James Harrison
- Division of Cardiovascular Medicine (M.C., F.L., J.R., C.G., A.F., J.H., Z.M.), University of Cambridge, United Kingdom
| | - James E Peters
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care (E.P., M.S., J.E.P., B.B.S., A.S.B., J.D., D.F.F., D.S.P.), University of Cambridge, United Kingdom.,British Heart Foundation Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge, UK (J.E.P., A.S.B., S.C.H., J.D., D.F.F., D.S.P., Z.M.)
| | - Benjamin B Sun
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care (E.P., M.S., J.E.P., B.B.S., A.S.B., J.D., D.F.F., D.S.P.), University of Cambridge, United Kingdom
| | - Adam S Butterworth
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care (E.P., M.S., J.E.P., B.B.S., A.S.B., J.D., D.F.F., D.S.P.), University of Cambridge, United Kingdom.,British Heart Foundation Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge, UK (J.E.P., A.S.B., S.C.H., J.D., D.F.F., D.S.P., Z.M.).,NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Cambridge, United Kingdom (A.S.B., J.D.)
| | - Seamus C Harrison
- Department of Cardiovascular Sciences, NIHR Leicester Biomedical Research Centre (S.C.H., M.J.B.), University of Leicester.,British Heart Foundation Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge, UK (J.E.P., A.S.B., S.C.H., J.D., D.F.F., D.S.P., Z.M.)
| | - Matthew J Bown
- Department of Cardiovascular Sciences, NIHR Leicester Biomedical Research Centre (S.C.H., M.J.B.), University of Leicester
| | - Jes S Lindholt
- Department of Cardiovascular and Thoracic Surgery, Elitary Research Centre of Individualised Medicine in Arterial Disease, Odense University Hospital, Denmark (J.S.L.)
| | - Stephen A Badger
- Regional Vascular Surgery Unit, Belfast Health and Social Care Trust, United Kingdom (S.A.B.)
| | - Iftikhar J Kullo
- Department of Cardiovascular Medicine, Gonda Vascular Center, Mayo Clinic, Rochester, MN (I.J.K.)
| | - Janet Powell
- Faculty of Medicine, Department of Surgery and Cancer, Imperial College London, United Kingdom (J.P.)
| | - Paul E Norman
- Medical School, University of Western Australia, Perth, Australia (P.E.N.)
| | - D Julian A Scott
- Leeds Vascular Institute, Leeds General Infirmary (D.J.A.S., M.A.B.).,Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, United Kingdom (D.J.A.S., M.A.B.)
| | - Marc A Bailey
- Leeds Vascular Institute, Leeds General Infirmary (D.J.A.S., M.A.B.).,Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, United Kingdom (D.J.A.S., M.A.B.)
| | - Stefan Rose-John
- Department of Biochemistry, Christian-Albrechts-University, Kiel, Germany (S.R.-J.)
| | - John Danesh
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care (E.P., M.S., J.E.P., B.B.S., A.S.B., J.D., D.F.F., D.S.P.), University of Cambridge, United Kingdom.,British Heart Foundation Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge, UK (J.E.P., A.S.B., S.C.H., J.D., D.F.F., D.S.P., Z.M.).,NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Cambridge, United Kingdom (A.S.B., J.D.).,Department of Human Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom (J.D.)
| | - Daniel F Freitag
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care (E.P., M.S., J.E.P., B.B.S., A.S.B., J.D., D.F.F., D.S.P.), University of Cambridge, United Kingdom.,British Heart Foundation Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge, UK (J.E.P., A.S.B., S.C.H., J.D., D.F.F., D.S.P., Z.M.)
| | - Dirk S Paul
- BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care (E.P., M.S., J.E.P., B.B.S., A.S.B., J.D., D.F.F., D.S.P.), University of Cambridge, United Kingdom.,British Heart Foundation Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge, UK (J.E.P., A.S.B., S.C.H., J.D., D.F.F., D.S.P., Z.M.)
| | - Ziad Mallat
- Division of Cardiovascular Medicine (M.C., F.L., J.R., C.G., A.F., J.H., Z.M.), University of Cambridge, United Kingdom.,British Heart Foundation Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge, UK (J.E.P., A.S.B., S.C.H., J.D., D.F.F., D.S.P., Z.M.).,Institut National de la Santé et de la Recherche Médicale, Paris Cardiovascular Research Center, France (Z.M.)
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14
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Teumer A, Li Y, Ghasemi S, Prins BP, Wuttke M, Hermle T, Giri A, Sieber KB, Qiu C, Kirsten H, Tin A, Chu AY, Bansal N, Feitosa MF, Wang L, Chai JF, Cocca M, Fuchsberger C, Gorski M, Hoppmann A, Horn K, Li M, Marten J, Noce D, Nutile T, Sedaghat S, Sveinbjornsson G, Tayo BO, van der Most PJ, Xu Y, Yu Z, Gerstner L, Ärnlöv J, Bakker SJL, Baptista D, Biggs ML, Boerwinkle E, Brenner H, Burkhardt R, Carroll RJ, Chee ML, Chee ML, Chen M, Cheng CY, Cook JP, Coresh J, Corre T, Danesh J, de Borst MH, De Grandi A, de Mutsert R, de Vries APJ, Degenhardt F, Dittrich K, Divers J, Eckardt KU, Ehret G, Endlich K, Felix JF, Franco OH, Franke A, Freedman BI, Freitag-Wolf S, Gansevoort RT, Giedraitis V, Gögele M, Grundner-Culemann F, Gudbjartsson DF, Gudnason V, Hamet P, Harris TB, Hicks AA, Holm H, Foo VHX, Hwang SJ, Ikram MA, Ingelsson E, Jaddoe VWV, Jakobsdottir J, Josyula NS, Jung B, Kähönen M, Khor CC, Kiess W, Koenig W, Körner A, Kovacs P, Kramer H, Krämer BK, Kronenberg F, Lange LA, Langefeld CD, Lee JJM, Lehtimäki T, Lieb W, Lim SC, Lind L, Lindgren CM, Liu J, Loeffler M, Lyytikäinen LP, Mahajan A, Maranville JC, Mascalzoni D, McMullen B, Meisinger C, Meitinger T, Miliku K, Mook-Kanamori DO, Müller-Nurasyid M, Mychaleckyj JC, Nauck M, Nikus K, Ning B, Noordam R, Connell JO, Olafsson I, Palmer ND, Peters A, Podgornaia AI, Ponte B, Poulain T, Pramstaller PP, Rabelink TJ, Raffield LM, Reilly DF, Rettig R, Rheinberger M, Rice KM, Rivadeneira F, Runz H, Ryan KA, Sabanayagam C, Saum KU, Schöttker B, Shaffer CM, Shi Y, Smith AV, Strauch K, Stumvoll M, Sun BB, Szymczak S, Tai ES, Tan NYQ, Taylor KD, Teren A, Tham YC, Thiery J, Thio CHL, Thomsen H, Thorsteinsdottir U, Tönjes A, Tremblay J, Uitterlinden AG, van der Harst P, Verweij N, Vogelezang S, Völker U, Waldenberger M, Wang C, Wilson OD, Wong C, Wong TY, Yang Q, Yasuda M, Akilesh S, Bochud M, Böger CA, Devuyst O, Edwards TL, Ho K, Morris AP, Parsa A, Pendergrass SA, Psaty BM, Rotter JI, Stefansson K, Wilson JG, Susztak K, Snieder H, Heid IM, Scholz M, Butterworth AS, Hung AM, Pattaro C, Köttgen A. Genome-wide association meta-analyses and fine-mapping elucidate pathways influencing albuminuria. Nat Commun 2019; 10:4130. [PMID: 31511532 PMCID: PMC6739370 DOI: 10.1038/s41467-019-11576-0] [Citation(s) in RCA: 118] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 07/23/2019] [Indexed: 02/08/2023] Open
Abstract
Increased levels of the urinary albumin-to-creatinine ratio (UACR) are associated with higher risk of kidney disease progression and cardiovascular events, but underlying mechanisms are incompletely understood. Here, we conduct trans-ethnic (n = 564,257) and European-ancestry specific meta-analyses of genome-wide association studies of UACR, including ancestry- and diabetes-specific analyses, and identify 68 UACR-associated loci. Genetic correlation analyses and risk score associations in an independent electronic medical records database (n = 192,868) reveal connections with proteinuria, hyperlipidemia, gout, and hypertension. Fine-mapping and trans-Omics analyses with gene expression in 47 tissues and plasma protein levels implicate genes potentially operating through differential expression in kidney (including TGFB1, MUC1, PRKCI, and OAF), and allow coupling of UACR associations to altered plasma OAF concentrations. Knockdown of OAF and PRKCI orthologs in Drosophila nephrocytes reduces albumin endocytosis. Silencing fly PRKCI further impairs slit diaphragm formation. These results generate a priority list of genes and pathways for translational research to reduce albuminuria.
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Affiliation(s)
- Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany.
- DZHK (German Center for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany.
| | - Yong Li
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Sahar Ghasemi
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
| | - Bram P Prins
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Matthias Wuttke
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
- Renal Division, Department of Medicine, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Tobias Hermle
- Renal Division, Department of Medicine, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Ayush Giri
- Division of Quantitative Sciences, Department of Obstetrics & Gynecology, Vanderbilt Genetics Institute, Vanderbilt Epidemiology Center, Institute for Medicine and Public Health, Vanderbilt University Medical Center, Nashville, TN, USA
- Biomedical Laboratory Research and Development, Tennessee Valley Healthcare System (626)/Vanderbilt University, Nashville, TN, USA
| | - Karsten B Sieber
- Target Sciences - Genetics, GlaxoSmithKline, Collegeville, PA, USA
| | - Chengxiang Qiu
- Renal Electrolyte and Hypertension Division, Department of Medicine, Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Pennsylvania, PA, USA
| | - Holger Kirsten
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Adrienne Tin
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Epidemiology and Clinical Research, Welch Centre for Prevention, Baltimore, MD, USA
| | - Audrey Y Chu
- Genetics, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Nisha Bansal
- Division of Nephrology, University of Washington, Seattle, WA, USA
- Kidney Research Institute, University of Washington, Seattle, WA, USA
| | - Mary F Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Lihua Wang
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Jin-Fang Chai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Massimiliano Cocca
- Institute for Maternal and Child Health - IRCCS "Burlo Garofolo", Trieste, Italy
| | - Christian Fuchsberger
- Eurac Research, Institute for Biomedicine (affiliated to the University of Lübeck), Bolzano, Italy
| | - Mathias Gorski
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Anselm Hoppmann
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Katrin Horn
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Man Li
- Department of Medicine, Division of Nephrology and Hypertension, University of Utah, Salt Lake City, UT, USA
| | - Jonathan Marten
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Damia Noce
- Eurac Research, Institute for Biomedicine (affiliated to the University of Lübeck), Bolzano, Italy
| | - Teresa Nutile
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso" - CNR, Naples, Italy
| | - Sanaz Sedaghat
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Bamidele O Tayo
- Department of Public Health Sciences, Loyola University Chicago, Maywood, IL, USA
| | - Peter J van der Most
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Yizhe Xu
- Department of Medicine, Division of Nephrology and Hypertension, University of Utah, Salt Lake City, UT, USA
| | - Zhi Yu
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Lea Gerstner
- Renal Division, Department of Medicine, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Johan Ärnlöv
- Department of Neurobiology, Care Sciences and Society, Division of Family Medicine and Primary Care, Karolinska Institutet, Stockholm, Sweden
- School of Health and Social Studies, Dalarna University, Falun, Sweden
| | - Stephan J L Bakker
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Mary L Biggs
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Eric Boerwinkle
- Human Genetics Centre, University of Texas Health Science Centre, Houston, TX, USA
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Centre (DKFZ), Heidelberg, Germany
- Network Aging Research, University of Heidelberg, Heidelberg, Germany
| | - Ralph Burkhardt
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University of Leipzig, Leipzig, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | - Robert J Carroll
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Miao-Li Chee
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Miao-Ling Chee
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Mengmeng Chen
- Renal Division, Department of Medicine, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Ching-Yu Cheng
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - James P Cook
- Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Tanguy Corre
- Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - John Danesh
- Department of Public Health and Primary Care, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Martin H de Borst
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Alessandro De Grandi
- Eurac Research, Institute for Biomedicine (affiliated to the University of Lübeck), Bolzano, Italy
| | - Renée de Mutsert
- Department of Clinical Epidemiology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Aiko P J de Vries
- Section of Nephrology, Department of Internal Medicine, Leiden University Medical Centre, Leiden, The Netherlands
| | - Frauke Degenhardt
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Katalin Dittrich
- Department of Women and Child Health, Hospital for Children and Adolescents, University of Leipzig, Leipzig, Germany
- Centre for Pediatric Research, University of Leipzig, Leipzig, Germany
| | - Jasmin Divers
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Kai-Uwe Eckardt
- Intensive Care Medicine, Charité, Berlin, Germany
- Department of Nephrology and Hypertension, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Georg Ehret
- Cardiology, Geneva University Hospitals, Geneva, Switzerland
| | - Karlhans Endlich
- DZHK (German Center for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
- Department of Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany
| | - Janine F Felix
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Oscar H Franco
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Barry I Freedman
- Internal Medicine - Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Sandra Freitag-Wolf
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Kiel, USA
| | - Ron T Gansevoort
- Department of Internal Medicine, Division of Nephrology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Vilmantas Giedraitis
- Department of Public Health and Caring Sciences, Molecular Geriatrics, Uppsala University, Uppsala, Sweden
| | - Martin Gögele
- Eurac Research, Institute for Biomedicine (affiliated to the University of Lübeck), Bolzano, Italy
| | - Franziska Grundner-Culemann
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | | | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Pavel Hamet
- Montreal University Hospital Research Centre, CHUM, Montreal, QC, Canada
- Medpharmgene, Montreal, QC, Canada
| | - Tamara B Harris
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Andrew A Hicks
- Eurac Research, Institute for Biomedicine (affiliated to the University of Lübeck), Bolzano, Italy
| | - Hilma Holm
- deCODE Genetics, Amgen Inc., Reykjavik, Iceland
| | - Valencia Hui Xian Foo
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Shih-Jen Hwang
- NHLBI's Framingham Heart Study, Framingham, MA, USA
- The Centre for Population Studies, NHLBI, Framingham, MA, USA
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Erik Ingelsson
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, USA
- Molecular Epidemiology and Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- Stanford Diabetes Research Center, Stanford University, Stanford, CA, USA
| | - Vincent W V Jaddoe
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Johanna Jakobsdottir
- Icelandic Heart Association, Holtasmari 1, Kopavogur, IS-201, Iceland
- The Centre of Public Health Sciences, University of Iceland, Sturlugata 8, Reykjavík, IS-101, Iceland
| | - Navya Shilpa Josyula
- Geisinger Research, Biomedical and Translational Informatics Institute, Rockville, MD, USA
| | - Bettina Jung
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere, Finland
- Department of Clinical Physiology, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Chiea-Chuen Khor
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
| | - Wieland Kiess
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Department of Women and Child Health, Hospital for Children and Adolescents, University of Leipzig, Leipzig, Germany
- Centre for Pediatric Research, University of Leipzig, Leipzig, Germany
| | - Wolfgang Koenig
- Deutsches Herzzentrum München, Technische Universität München, Munich, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
- Institute of Epidemiology and Biostatistics, University of Ulm, Ulm, Germany
| | - Antje Körner
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Department of Women and Child Health, Hospital for Children and Adolescents, University of Leipzig, Leipzig, Germany
- Centre for Pediatric Research, University of Leipzig, Leipzig, Germany
| | - Peter Kovacs
- Integrated Research and Treatment Centre Adiposity Diseases, University of Leipzig, Leipzig, Germany
| | - Holly Kramer
- Department of Public Health Sciences, Loyola University Chicago, Maywood, IL, USA
- Division of Nephrology and Hypertension, Loyola University Chicago, Chicago, IL, USA
| | - Bernhard K Krämer
- 5th Department of Medicine (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Florian Kronenberg
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado Denver - Anschutz Medical Campus, Aurora, CO, USA
| | - Carl D Langefeld
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jeannette Jen-Mai Lee
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Wolfgang Lieb
- Institute of Epidemiology and Biobank Popgen, Kiel University, Kiel, Germany
| | - Su-Chi Lim
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Diabetes Centre, Khoo Teck Puat Hospital, Singapore, Singapore
| | - Lars Lind
- Cardiovascular Epidemiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Cecilia M Lindgren
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jianjun Liu
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Markus Loeffler
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere, Finland
- Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford, UK
| | | | - Deborah Mascalzoni
- Eurac Research, Institute for Biomedicine (affiliated to the University of Lübeck), Bolzano, Italy
| | | | - Christa Meisinger
- Independent Research Group Clinical Epidemiology, Helmholtz Zentrum München, German Research Centre for Environmental Health, Neuherberg, Germany
- Chair of Epidemiology Ludwig- Maximilians-Universität München at UNIKA-T Augsburg, Augsburg, Germany
| | - Thomas Meitinger
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Kozeta Miliku
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Centre, Leiden, The Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Centre, Leiden, The Netherlands
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Centre for Environmental Health, Neuherberg, Germany
- Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU, Munich, Germany
- Department of Internal Medicine I (Cardiology), Hospital of the Ludwig-Maximilians-University (LMU) Munich, Munich, Germany
| | - Josyf C Mychaleckyj
- Centre for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Matthias Nauck
- DZHK (German Center for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
- Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Kjell Nikus
- Department of Cardiology, Heart Center, Tampere University Hospital, Tampere, Finland
- Department of Cardiology, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Boting Ning
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Raymond Noordam
- Section of Gerontology and Geriatrics, Department of Internal Medicine, Leiden University Medical Centre, Leiden, The Netherlands
| | | | - Isleifur Olafsson
- Department of Clinical Biochemistry, Landspitali University Hospital, Reykjavik, Iceland
| | | | - Annette Peters
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Centre for Environmental Health, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
| | | | - Belen Ponte
- Service de Néphrologie, Geneva University Hospitals, Geneva, Switzerland
| | - Tanja Poulain
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Peter P Pramstaller
- Eurac Research, Institute for Biomedicine (affiliated to the University of Lübeck), Bolzano, Italy
| | - Ton J Rabelink
- Section of Nephrology, Department of Internal Medicine, Leiden University Medical Centre, Leiden, The Netherlands
- Einthoven Laboratory of Experimental Vascular Research, Leiden University Medical Centre, Leiden, The Netherlands
| | - Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | | | - Rainer Rettig
- Institute of Physiology, University Medicine Greifswald, Karlsburg, Germany
| | - Myriam Rheinberger
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
| | - Kenneth M Rice
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Fernando Rivadeneira
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Heiko Runz
- MRL, Merck & Co., Inc., Kenilworth, NJ, USA
- Biogen Inc., Cambridge, MA, USA
| | - Kathleen A Ryan
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Charumathi Sabanayagam
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Kai-Uwe Saum
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Ben Schöttker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Centre (DKFZ), Heidelberg, Germany
- Network Aging Research, University of Heidelberg, Heidelberg, Germany
| | - Christian M Shaffer
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yuan Shi
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
| | - Albert V Smith
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Centre for Environmental Health, Neuherberg, Germany
- Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU, Munich, Germany
| | - Michael Stumvoll
- Department of Endocrinology and Nephrology, University of Leipzig, Leipzig, Germany
| | - Benjamin B Sun
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Silke Szymczak
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Kiel, USA
| | - E-Shyong Tai
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Nicholas Y Q Tan
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Andrej Teren
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Heart Centre Leipzig, Leipzig, Germany
| | - Yih-Chung Tham
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
| | - Joachim Thiery
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University of Leipzig, Leipzig, Germany
| | - Chris H L Thio
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Hauke Thomsen
- Division of Molecular Genetic Epidemiology, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | | | - Anke Tönjes
- Department of Endocrinology and Nephrology, University of Leipzig, Leipzig, Germany
| | - Johanne Tremblay
- Montreal University Hospital Research Centre, CHUM, Montreal, QC, Canada
- CRCHUM, Montreal, QC, Canada
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Pim van der Harst
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Durrer Centre for Cardiovascular Research, The Netherlands Heart Institute, Utrecht, The Netherlands
| | - Niek Verweij
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Suzanne Vogelezang
- Department of Epidemiology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Uwe Völker
- DZHK (German Center for Cardiovascular Research), Partner Site Greifswald, Greifswald, Germany
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Melanie Waldenberger
- DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Centre for Environmental Health, Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München - German Research Centre for Environmental Health, Neuherberg, Germany
| | - Chaolong Wang
- Genome Institute of Singapore, Agency for Science Technology and Research, Singapore, Singapore
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Otis D Wilson
- Vanderbilt University Medical Centre, Division of Nephrology & Hypertension, Nashville, TN, USA
| | - Charlene Wong
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Tien-Yin Wong
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Ophthalmology & Visual Sciences Academic Clinical Program (Eye ACP), Duke-NUS Medical School, Singapore, Singapore
- Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, Singapore, Singapore
| | - Qiong Yang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Masayuki Yasuda
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore, Singapore
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Shreeram Akilesh
- Kidney Research Institute, University of Washington, Seattle, WA, USA
- Anatomic Pathology, University of Washington Medical Center, Seattle, WA, USA
| | - Murielle Bochud
- Center for Primary Care and Public Health (Unisanté), University of Lausanne, Lausanne, Switzerland
| | - Carsten A Böger
- Department of Nephrology, University Hospital Regensburg, Regensburg, Germany
- Department of Nephrology, Diabetology and Rheumatology, Kliniken Südostbayern, Traunstein, Germany
| | - Olivier Devuyst
- Institute of Physiology, University of Zurich, Zurich, Switzerland
| | - Todd L Edwards
- Division of Epidemiology, Department of Medicine, Vanderbilt Genetics Institute, Vanderbilt University Medical Centre, Nashville, TN, USA
- Department of Veteran's Affairs, Tennessee Valley Healthcare System (626)/Vanderbilt University, Nashville, TN, USA
| | - Kevin Ho
- Kidney Health Research Institute (KHRI), Geisinger, Danville, PA, USA
- Department of Nephrology, Geisinger, Danville, PA, USA
| | - Andrew P Morris
- Department of Biostatistics, University of Liverpool, Liverpool, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Afshin Parsa
- Division of Kidney, Urologic and Hematologic Diseases, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Sarah A Pendergrass
- Geisinger Research, Biomedical and Translational Informatics Institute, Danville, PA, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, Department of Epidemiology, Department of Health Service, University of Washington, Seattle, WA, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
- Department of Pediatrics, Harbor-UCLA Medical Centre, Torrance, CA, USA
- Department of Medicine, Harbor-UCLA Medical Centre, Torrance, CA, USA
| | | | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Centre, Jackson, MS, USA
| | - Katalin Susztak
- Renal Electrolyte and Hypertension Division, Department of Medicine, Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Pennsylvania, PA, USA
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Iris M Heid
- Department of Genetic Epidemiology, University of Regensburg, Regensburg, Germany
| | - Markus Scholz
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany
- LIFE Research Centre for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Adam S Butterworth
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK
| | - Adriana M Hung
- Vanderbilt University Medical Centre, Division of Nephrology & Hypertension, Nashville, TN, USA
- Department of Veteran's Affairs, Tennessee Valley Healthcare System (626)/Vanderbilt University, Nashville, TN, USA
| | - Cristian Pattaro
- Eurac Research, Institute for Biomedicine (affiliated to the University of Lübeck), Bolzano, Italy.
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Department of Biometry, Epidemiology and Medical Bioinformatics, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany.
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
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15
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Shrine N, Guyatt AL, Erzurumluoglu AM, Jackson VE, Hobbs BD, Melbourne CA, Batini C, Fawcett KA, Song K, Sakornsakolpat P, Li X, Boxall R, Reeve NF, Obeidat M, Zhao JH, Wielscher M, Weiss S, Kentistou KA, Cook JP, Sun BB, Zhou J, Hui J, Karrasch S, Imboden M, Harris SE, Marten J, Enroth S, Kerr SM, Surakka I, Vitart V, Lehtimäki T, Allen RJ, Bakke PS, Beaty TH, Bleecker ER, Bossé Y, Brandsma CA, Chen Z, Crapo JD, Danesh J, DeMeo DL, Dudbridge F, Ewert R, Gieger C, Gulsvik A, Hansell AL, Hao K, Hoffman JD, Hokanson JE, Homuth G, Joshi PK, Joubert P, Langenberg C, Li X, Li L, Lin K, Lind L, Locantore N, Luan J, Mahajan A, Maranville JC, Murray A, Nickle DC, Packer R, Parker MM, Paynton ML, Porteous DJ, Prokopenko D, Qiao D, Rawal R, Runz H, Sayers I, Sin DD, Smith BH, Artigas MS, Sparrow D, Tal-Singer R, Timmers PRHJ, Van den Berge M, Whittaker JC, Woodruff PG, Yerges-Armstrong LM, Troyanskaya OG, Raitakari OT, Kähönen M, Polašek O, Gyllensten U, Rudan I, Deary IJ, Probst-Hensch NM, Schulz H, James AL, Wilson JF, Stubbe B, Zeggini E, Jarvelin MR, Wareham N, Silverman EK, Hayward C, Morris AP, Butterworth AS, Scott RA, Walters RG, Meyers DA, Cho MH, Strachan DP, Hall IP, Tobin MD, Wain LV. Author Correction: New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries. Nat Genet 2019; 51:1067. [PMID: 31110354 DOI: 10.1038/s41588-019-0438-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Nick Shrine
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Anna L Guyatt
- Department of Health Sciences, University of Leicester, Leicester, UK
| | | | - Victoria E Jackson
- Department of Health Sciences, University of Leicester, Leicester, UK.,Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Brian D Hobbs
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Carl A Melbourne
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Chiara Batini
- Department of Health Sciences, University of Leicester, Leicester, UK
| | | | - Kijoung Song
- Target Sciences, GlaxoSmithKline, Collegeville, PA, USA
| | - Phuwanat Sakornsakolpat
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Xingnan Li
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - Ruth Boxall
- Nuffield Department of Population Health, University of Oxford, Oxford, UK.,Medical Research Council Population Health Research Unit, University of Oxford, Oxford, UK
| | - Nicola F Reeve
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Ma'en Obeidat
- The University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, British Columbia, Canada
| | - Jing Hua Zhao
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Matthias Wielscher
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health,Imperial College London, London, UK
| | | | - Stefan Weiss
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Katherine A Kentistou
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK.,Centre for Cardiovascular Sciences, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - James P Cook
- Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Benjamin B Sun
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jian Zhou
- Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Jennie Hui
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia.,School of Population Health, The University of Western Australia, Crawley, Western Australia, Australia.,PathWest Laboratory Medicine of WA,Sir Charles Gairdner Hospital, Crawley, Western Australia, Australia.,School of Pathology and Laboratory Medicine, The University of Western Australia, Crawley, Western Australia, Australia
| | - Stefan Karrasch
- Institute of Epidemiology, Helmholtz Zentrum Muenchen-German Research Center for Environmental Health, Neuherberg, Germany.,Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Ludwig-Maximilians-Universität, Munich, Germany.,Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Medea Imboden
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Sarah E Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK.,Centre for Genomic and Experimental Medicine, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Jonathan Marten
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Stefan Enroth
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala Universitet, Uppsala, Sweden
| | - Shona M Kerr
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Ida Surakka
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.,The National Institute for Health and Welfare (THL), Helsinki, Finland
| | - Veronique Vitart
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Richard J Allen
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Per S Bakke
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins University School of Public Health, Baltimore, MD, USA
| | - Eugene R Bleecker
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - Yohan Bossé
- Department of Molecular Medicine, Laval University, Québec, Canada.,Institut Universitaire de Cardiologie et de Pneumologie de Québec,Laval University, Québec, Canada
| | - Corry-Anke Brandsma
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, GRIAC Research Institute,University of Groningen, Groningen, The Netherlands
| | - Zhengming Chen
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - James D Crapo
- National Jewish Health, Denver, CO, USA.,Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, CO, USA
| | - John Danesh
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.,British Heart Foundation Cambridge Centre of Excellence, Division of Cardiovascular Medicine,Addenbrooke's Hospital, Cambridge, UK.,Department of Human Genetics, Wellcome Trust Sanger Institute, Cambridge, UK.,NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Frank Dudbridge
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Ralf Ewert
- Department of Internal Medicine B - Cardiology, Intensive Care, Pulmonary Medicine and Infectious Diseases, University Medicine Greifswald, Greifswald, Germany
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum Muenchen - German Research Center for Environmental Health, Neuherberg, Germany
| | - Amund Gulsvik
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Anna L Hansell
- Centre for Environmental Health & Sustainability, University of Leicester, Leicester, UK.,UK Small Area Health Statistics Unit, MRC-PHE Centre for Environment and Health, School of Public Health,Imperial College London, London, UK.,Imperial College Healthcare NHS Trust,St Mary's Hospital, London, UK
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - John E Hokanson
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Philippe Joubert
- Institut Universitaire de Cardiologie et de Pneumologie de Québec,Laval University, Québec, Canada.,Department of Molecular Biology, Medical Biochemistry, and Pathology,Laval University, Québec, Canada
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Xuan Li
- The University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, British Columbia, Canada
| | - Liming Li
- Department of Epidemiology & Biostatistics, Peking University Health Science Center, Beijing, China
| | - Kuang Lin
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Lars Lind
- Department of Medical Sciences, Cardiovascular Epidemiology,Uppsala University, Uppsala, Sweden
| | | | - Jian'an Luan
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Alison Murray
- The Institute of Medical Sciences, Aberdeen Biomedical Imaging Centre, University of Aberdeen, Aberdeen, UK
| | - David C Nickle
- MRL, Merck & Co., Inc, Kenilworth, NJ, USA.,Gossamer Bio, San Diego, CA, USA
| | - Richard Packer
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Margaret M Parker
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Megan L Paynton
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - David J Porteous
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK.,Centre for Genomic and Experimental Medicine, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Dmitry Prokopenko
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dandi Qiao
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Rajesh Rawal
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum Muenchen - German Research Center for Environmental Health, Neuherberg, Germany.,Institute of Epidemiology and Social Medicine, University of Münster, Münster, Germany
| | - Heiko Runz
- MRL, Merck & Co., Inc, Kenilworth, NJ, USA
| | - Ian Sayers
- Division of Respiratory Medicine and NIHR-Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Don D Sin
- The University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, British Columbia, Canada.,Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Blair H Smith
- Division of Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - María Soler Artigas
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Barcelona, Spain
| | - David Sparrow
- VA Boston Healthcare System, Boston, MA, USA.,Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | | | - Paul R H J Timmers
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Maarten Van den Berge
- University of Groningen, University Medical Center Groningen, Department of Pulmonology, GRIAC Research Institute,University of Groningen, Groningen, The Netherlands
| | - John C Whittaker
- Target Sciences - R&D, GSK Medicines Research Centre, Stevenage, UK
| | - Prescott G Woodruff
- UCSF Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA, USA
| | | | - Olga G Troyanskaya
- Department of Computer Science, Princeton University, Princeton, NJ, USA.,Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Olli T Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland.,Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Life Sciences,University of Tampere, Tampere, Finland
| | - Ozren Polašek
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK.,University of Split School of Medicine, Split, Croatia
| | - Ulf Gyllensten
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala Universitet, Uppsala, Sweden
| | - Igor Rudan
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK.,Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Nicole M Probst-Hensch
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Holger Schulz
- Institute of Epidemiology, Helmholtz Zentrum Muenchen-German Research Center for Environmental Health, Neuherberg, Germany.,Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Alan L James
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia.,Department of Pulmonary Physiology and Sleep Medicine, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia.,School of Medicine and Pharmacology, The University of Western Australia, Crawley, Western Australia, Australia
| | - James F Wilson
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK.,Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Beate Stubbe
- Department of Internal Medicine B - Cardiology, Intensive Care, Pulmonary Medicine and Infectious Diseases, University Medicine Greifswald, Greifswald, Germany
| | - Eleftheria Zeggini
- Wellcome Sanger Institute, Hinxton, UK.,Institute of Translational Genomics, Helmholtz Zentrum Muenchen - German Research Center for Environmental Health, Neuherberg, Germany
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health,Imperial College London, London, UK.,Center for Life Course Health Research, Faculty of Medicine,University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland.,Unit of Primary Health Care, Oulu University Hospital, Oulu, Finland.,Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UK
| | - Nick Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Andrew P Morris
- Department of Biostatistics, University of Liverpool, Liverpool, UK.,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Adam S Butterworth
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.,NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Robert A Scott
- Target Sciences - R&D, GSK Medicines Research Centre, Stevenage, UK
| | - Robin G Walters
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Deborah A Meyers
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - David P Strachan
- Population Health Research Institute, St George's, University of London, London, UK
| | - Ian P Hall
- Division of Respiratory Medicine and NIHR-Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Martin D Tobin
- Department of Health Sciences, University of Leicester, Leicester, UK. .,National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK.
| | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, UK. .,National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK.
| |
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16
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Shrine N, Guyatt AL, Erzurumluoglu AM, Jackson VE, Hobbs BD, Melbourne CA, Batini C, Fawcett KA, Song K, Sakornsakolpat P, Li X, Boxall R, Reeve NF, Obeidat M, Zhao JH, Wielscher M, Weiss S, Kentistou KA, Cook JP, Sun BB, Zhou J, Hui J, Karrasch S, Imboden M, Harris SE, Marten J, Enroth S, Kerr SM, Surakka I, Vitart V, Lehtimäki T, Allen RJ, Bakke PS, Beaty TH, Bleecker ER, Bossé Y, Brandsma CA, Chen Z, Crapo JD, Danesh J, DeMeo DL, Dudbridge F, Ewert R, Gieger C, Gulsvik A, Hansell AL, Hao K, Hoffman JD, Hokanson JE, Homuth G, Joshi PK, Joubert P, Langenberg C, Li X, Li L, Lin K, Lind L, Locantore N, Luan J, Mahajan A, Maranville JC, Murray A, Nickle DC, Packer R, Parker MM, Paynton ML, Porteous DJ, Prokopenko D, Qiao D, Rawal R, Runz H, Sayers I, Sin DD, Smith BH, Soler Artigas M, Sparrow D, Tal-Singer R, Timmers PRHJ, Van den Berge M, Whittaker JC, Woodruff PG, Yerges-Armstrong LM, Troyanskaya OG, Raitakari OT, Kähönen M, Polašek O, Gyllensten U, Rudan I, Deary IJ, Probst-Hensch NM, Schulz H, James AL, Wilson JF, Stubbe B, Zeggini E, Jarvelin MR, Wareham N, Silverman EK, Hayward C, Morris AP, Butterworth AS, Scott RA, Walters RG, Meyers DA, Cho MH, Strachan DP, Hall IP, Tobin MD, Wain LV. New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries. Nat Genet 2019; 51:481-493. [PMID: 30804560 PMCID: PMC6397078 DOI: 10.1038/s41588-018-0321-7] [Citation(s) in RCA: 257] [Impact Index Per Article: 51.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 11/27/2018] [Indexed: 02/02/2023]
Abstract
Reduced lung function predicts mortality and is key to the diagnosis of chronic obstructive pulmonary disease (COPD). In a genome-wide association study in 400,102 individuals of European ancestry, we define 279 lung function signals, 139 of which are new. In combination, these variants strongly predict COPD in independent populations. Furthermore, the combined effect of these variants showed generalizability across smokers and never smokers, and across ancestral groups. We highlight biological pathways, known and potential drug targets for COPD and, in phenome-wide association studies, autoimmune-related and other pleiotropic effects of lung function-associated variants. This new genetic evidence has potential to improve future preventive and therapeutic strategies for COPD.
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Affiliation(s)
- Nick Shrine
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Anna L Guyatt
- Department of Health Sciences, University of Leicester, Leicester, UK
| | | | - Victoria E Jackson
- Department of Health Sciences, University of Leicester, Leicester, UK
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Brian D Hobbs
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Carl A Melbourne
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Chiara Batini
- Department of Health Sciences, University of Leicester, Leicester, UK
| | | | - Kijoung Song
- Target Sciences, GlaxoSmithKline, Collegeville, PA, USA
| | - Phuwanat Sakornsakolpat
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Xingnan Li
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - Ruth Boxall
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Medical Research Council Population Health Research Unit, University of Oxford, Oxford, UK
| | - Nicola F Reeve
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Ma'en Obeidat
- The University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, British Columbia, Canada
| | - Jing Hua Zhao
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Matthias Wielscher
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
| | - Stefan Weiss
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Katherine A Kentistou
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
- Centre for Cardiovascular Sciences, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - James P Cook
- Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Benjamin B Sun
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jian Zhou
- Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Jennie Hui
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- School of Population Health, The University of Western Australia, Crawley, Western Australia, Australia
- PathWest Laboratory Medicine of WA, Sir Charles Gairdner Hospital, Crawley, Western Australia, Australia
- School of Pathology and Laboratory Medicine, The University of Western Australia, Crawley, Western Australia, Australia
| | - Stefan Karrasch
- Institute of Epidemiology, Helmholtz Zentrum Muenchen-German Research Center for Environmental Health, Neuherberg, Germany
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Ludwig-Maximilians-Universität, Munich, Germany
- Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Medea Imboden
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sarah E Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Jonathan Marten
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Stefan Enroth
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala Universitet, Uppsala, Sweden
| | - Shona M Kerr
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Ida Surakka
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- The National Institute for Health and Welfare (THL), Helsinki, Finland
| | - Veronique Vitart
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Richard J Allen
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Per S Bakke
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins University School of Public Health, Baltimore, MD, USA
| | - Eugene R Bleecker
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - Yohan Bossé
- Department of Molecular Medicine, Laval University, Québec, Canada
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec, Canada
| | - Corry-Anke Brandsma
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, GRIAC Research Institute, University of Groningen, Groningen, The Netherlands
| | - Zhengming Chen
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - James D Crapo
- National Jewish Health, Denver, CO, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, CO, USA
| | - John Danesh
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cambridge Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge, UK
- Department of Human Genetics, Wellcome Trust Sanger Institute, Cambridge, UK
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Frank Dudbridge
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Ralf Ewert
- Department of Internal Medicine B - Cardiology, Intensive Care, Pulmonary Medicine and Infectious Diseases, University Medicine Greifswald, Greifswald, Germany
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum Muenchen - German Research Center for Environmental Health, Neuherberg, Germany
| | - Amund Gulsvik
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Anna L Hansell
- Centre for Environmental Health & Sustainability, University of Leicester, Leicester, UK
- UK Small Area Health Statistics Unit, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, St Mary's Hospital, London, UK
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - John E Hokanson
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Philippe Joubert
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec, Canada
- Department of Molecular Biology, Medical Biochemistry, and Pathology, Laval University, Québec, Canada
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Xuan Li
- The University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, British Columbia, Canada
| | - Liming Li
- Department of Epidemiology & Biostatistics, Peking University Health Science Center, Beijing, China
| | - Kuang Lin
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Lars Lind
- Department of Medical Sciences, Cardiovascular Epidemiology, Uppsala University, Uppsala, Sweden
| | | | - Jian'an Luan
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Alison Murray
- The Institute of Medical Sciences, Aberdeen Biomedical Imaging Centre, University of Aberdeen, Aberdeen, UK
| | - David C Nickle
- MRL, Merck & Co., Inc, Kenilworth, NJ, USA
- Gossamer Bio, San Diego, CA, USA
| | - Richard Packer
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Margaret M Parker
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Megan L Paynton
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - David J Porteous
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Dmitry Prokopenko
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dandi Qiao
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Rajesh Rawal
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum Muenchen - German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology and Social Medicine, University of Münster, Münster, Germany
| | - Heiko Runz
- MRL, Merck & Co., Inc, Kenilworth, NJ, USA
| | - Ian Sayers
- Division of Respiratory Medicine and NIHR-Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Don D Sin
- The University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, British Columbia, Canada
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Blair H Smith
- Division of Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - María Soler Artigas
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Barcelona, Spain
| | - David Sparrow
- VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | | | - Paul R H J Timmers
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Maarten Van den Berge
- University of Groningen, University Medical Center Groningen, Department of Pulmonology, GRIAC Research Institute, University of Groningen, Groningen, The Netherlands
| | - John C Whittaker
- Target Sciences - R&D, GSK Medicines Research Centre, Stevenage, UK
| | - Prescott G Woodruff
- UCSF Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA, USA
| | | | - Olga G Troyanskaya
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Olli T Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Ozren Polašek
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
- University of Split School of Medicine, Split, Croatia
| | - Ulf Gyllensten
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala Universitet, Uppsala, Sweden
| | - Igor Rudan
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Nicole M Probst-Hensch
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Holger Schulz
- Institute of Epidemiology, Helmholtz Zentrum Muenchen-German Research Center for Environmental Health, Neuherberg, Germany
- Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Alan L James
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- Department of Pulmonary Physiology and Sleep Medicine, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- School of Medicine and Pharmacology, The University of Western Australia, Crawley, Western Australia, Australia
| | - James F Wilson
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Beate Stubbe
- Department of Internal Medicine B - Cardiology, Intensive Care, Pulmonary Medicine and Infectious Diseases, University Medicine Greifswald, Greifswald, Germany
| | - Eleftheria Zeggini
- Wellcome Sanger Institute, Hinxton, UK
- Institute of Translational Genomics, Helmholtz Zentrum Muenchen - German Research Center for Environmental Health, Neuherberg, Germany
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Unit of Primary Health Care, Oulu University Hospital, Oulu, Finland
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UK
| | - Nick Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Andrew P Morris
- Department of Biostatistics, University of Liverpool, Liverpool, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Adam S Butterworth
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Robert A Scott
- Target Sciences - R&D, GSK Medicines Research Centre, Stevenage, UK
| | - Robin G Walters
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Deborah A Meyers
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - David P Strachan
- Population Health Research Institute, St George's, University of London, London, UK
| | - Ian P Hall
- Division of Respiratory Medicine and NIHR-Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Martin D Tobin
- Department of Health Sciences, University of Leicester, Leicester, UK.
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK.
| | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, UK.
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK.
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17
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Stacey D, Fauman EB, Ziemek D, Sun BB, Harshfield EL, Wood AM, Butterworth AS, Suhre K, Paul DS. ProGeM: a framework for the prioritization of candidate causal genes at molecular quantitative trait loci. Nucleic Acids Res 2019; 47:e3. [PMID: 30239796 PMCID: PMC6326795 DOI: 10.1093/nar/gky837] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 08/31/2018] [Accepted: 09/11/2018] [Indexed: 12/27/2022] Open
Abstract
Quantitative trait locus (QTL) mapping of molecular phenotypes such as metabolites, lipids and proteins through genome-wide association studies represents a powerful means of highlighting molecular mechanisms relevant to human diseases. However, a major challenge of this approach is to identify the causal gene(s) at the observed QTLs. Here, we present a framework for the 'Prioritization of candidate causal Genes at Molecular QTLs' (ProGeM), which incorporates biological domain-specific annotation data alongside genome annotation data from multiple repositories. We assessed the performance of ProGeM using a reference set of 227 previously reported and extensively curated metabolite QTLs. For 98% of these loci, the expert-curated gene was one of the candidate causal genes prioritized by ProGeM. Benchmarking analyses revealed that 69% of the causal candidates were nearest to the sentinel variant at the investigated molecular QTLs, indicating that genomic proximity is the most reliable indicator of 'true positive' causal genes. In contrast, cis-gene expression QTL data led to three false positive candidate causal gene assignments for every one true positive assignment. We provide evidence that these conclusions also apply to other molecular phenotypes, suggesting that ProGeM is a powerful and versatile tool for annotating molecular QTLs. ProGeM is freely available via GitHub.
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Affiliation(s)
- David Stacey
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Eric B Fauman
- Pfizer Worldwide Research & Development, Genome Sciences & Technologies, Cambridge, MA 02142, USA
| | - Daniel Ziemek
- Pfizer Worldwide Research & Development, Inflammation & Immunology, 14167 Berlin, Germany
| | - Benjamin B Sun
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Eric L Harshfield
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Angela M Wood
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Adam S Butterworth
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Karsten Suhre
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, PO 24144, Doha, Qatar
| | - Dirk S Paul
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
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18
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Yao C, Chen G, Song C, Keefe J, Mendelson M, Huan T, Sun BB, Laser A, Maranville JC, Wu H, Ho JE, Courchesne P, Lyass A, Larson MG, Gieger C, Graumann J, Johnson AD, Danesh J, Runz H, Hwang SJ, Liu C, Butterworth AS, Suhre K, Levy D. Author Correction: Genome-wide mapping of plasma protein QTLs identifies putatively causal genes and pathways for cardiovascular disease. Nat Commun 2018; 9:3853. [PMID: 30228274 PMCID: PMC6143533 DOI: 10.1038/s41467-018-06231-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Chen Yao
- Framingham Heart Study, Framingham, 01702, MA, USA.,Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, 20892, MD, USA
| | - George Chen
- Framingham Heart Study, Framingham, 01702, MA, USA.,Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, 20892, MD, USA
| | - Ci Song
- Framingham Heart Study, Framingham, 01702, MA, USA.,Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, 20892, MD, USA.,Department of Medical Sciences, Uppsala University, 75105, Uppsala, Sweden.,Department of Immunology, Genetics and Pathology, Uppsala University, 75105, Uppsala, Sweden
| | - Joshua Keefe
- Framingham Heart Study, Framingham, 01702, MA, USA.,Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, 20892, MD, USA
| | - Michael Mendelson
- Framingham Heart Study, Framingham, 01702, MA, USA.,Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, 20892, MD, USA.,Department of Cardiology, Boston Children's Hospital, Boston, 02115, MA, USA
| | - Tianxiao Huan
- Framingham Heart Study, Framingham, 01702, MA, USA.,Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, 20892, MD, USA
| | - Benjamin B Sun
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Annika Laser
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | | | - Hongsheng Wu
- Computer Science and Networking, Wentworth Institute of Technology, Boston, 02115, MA, USA
| | - Jennifer E Ho
- Cardiovascular Research Center and Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, 02114, MA, USA
| | - Paul Courchesne
- Framingham Heart Study, Framingham, 01702, MA, USA.,Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, 20892, MD, USA
| | - Asya Lyass
- Framingham Heart Study, Framingham, 01702, MA, USA.,Department of Mathematics and Statistics, Boston University, Boston, 02115, MA, USA
| | - Martin G Larson
- Framingham Heart Study, Framingham, 01702, MA, USA.,Department of Biostatistics, Boston University School of Public Health, Boston, 02118, MA, USA
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.,Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany.,German Center for Diabetes Research (DZD), Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Johannes Graumann
- Scientific Service Group Biomolecular Mass Spectrometry, Max Planck Institute for Heart and Lung Research, W.G. Kerckhoff Institute, Ludwigstr. 43, D-61231, Bad Nauheim, Germany
| | - Andrew D Johnson
- Framingham Heart Study, Framingham, 01702, MA, USA.,Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, 20892, MD, USA
| | - John Danesh
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK.,British Heart Foundation Cambridge Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK.,Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1RQ, UK
| | - Heiko Runz
- MRL, Merck & Co., Inc, Kenilworth, 07033, NJ, USA
| | - Shih-Jen Hwang
- Framingham Heart Study, Framingham, 01702, MA, USA.,Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, 20892, MD, USA
| | - Chunyu Liu
- Framingham Heart Study, Framingham, 01702, MA, USA.,Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, 20892, MD, USA
| | - Adam S Butterworth
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK.,NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Karsten Suhre
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, PO 24144, Doha, Qatar
| | - Daniel Levy
- Framingham Heart Study, Framingham, 01702, MA, USA. .,Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, 20892, MD, USA.
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19
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Yao C, Chen G, Song C, Keefe J, Mendelson M, Huan T, Sun BB, Laser A, Maranville JC, Wu H, Ho JE, Courchesne P, Lyass A, Larson MG, Gieger C, Graumann J, Johnson AD, Danesh J, Runz H, Hwang SJ, Liu C, Butterworth AS, Suhre K, Levy D. Genome-wide mapping of plasma protein QTLs identifies putatively causal genes and pathways for cardiovascular disease. Nat Commun 2018; 9:3268. [PMID: 30111768 PMCID: PMC6093935 DOI: 10.1038/s41467-018-05512-x] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 07/09/2018] [Indexed: 01/17/2023] Open
Abstract
Identifying genetic variants associated with circulating protein concentrations (protein quantitative trait loci; pQTLs) and integrating them with variants from genome-wide association studies (GWAS) may illuminate the proteome's causal role in disease and bridge a knowledge gap regarding SNP-disease associations. We provide the results of GWAS of 71 high-value cardiovascular disease proteins in 6861 Framingham Heart Study participants and independent external replication. We report the mapping of over 16,000 pQTL variants and their functional relevance. We provide an integrated plasma protein-QTL database. Thirteen proteins harbor pQTL variants that match coronary disease-risk variants from GWAS or test causal for coronary disease by Mendelian randomization. Eight of these proteins predict new-onset cardiovascular disease events in Framingham participants. We demonstrate that identifying pQTLs, integrating them with GWAS results, employing Mendelian randomization, and prospectively testing protein-trait associations holds potential for elucidating causal genes, proteins, and pathways for cardiovascular disease and may identify targets for its prevention and treatment.
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Affiliation(s)
- Chen Yao
- Framingham Heart Study, Framingham, 01702, MA, USA
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, 20892, MD, USA
| | - George Chen
- Framingham Heart Study, Framingham, 01702, MA, USA
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, 20892, MD, USA
| | - Ci Song
- Framingham Heart Study, Framingham, 01702, MA, USA
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, 20892, MD, USA
- Department of Medical Sciences, Uppsala University, 75105, Uppsala, Sweden
- Department of Immunology, Genetics and Pathology, Uppsala University, 75105, Uppsala, Sweden
| | - Joshua Keefe
- Framingham Heart Study, Framingham, 01702, MA, USA
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, 20892, MD, USA
| | - Michael Mendelson
- Framingham Heart Study, Framingham, 01702, MA, USA
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, 20892, MD, USA
- Department of Cardiology, Boston Children's Hospital, Boston, 02115, MA, USA
| | - Tianxiao Huan
- Framingham Heart Study, Framingham, 01702, MA, USA
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, 20892, MD, USA
| | - Benjamin B Sun
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Annika Laser
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | | | - Hongsheng Wu
- Computer Science and Networking, Wentworth Institute of Technology, Boston, 02115, MA, USA
| | - Jennifer E Ho
- Cardiovascular Research Center and Division of Cardiology, Department of Medicine, Massachusetts General Hospital, Boston, 02114, MA, USA
| | - Paul Courchesne
- Framingham Heart Study, Framingham, 01702, MA, USA
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, 20892, MD, USA
| | - Asya Lyass
- Framingham Heart Study, Framingham, 01702, MA, USA
- Department of Mathematics and Statistics, Boston University, Boston, 02115, MA, USA
| | - Martin G Larson
- Framingham Heart Study, Framingham, 01702, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, 02118, MA, USA
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Johannes Graumann
- Scientific Service Group Biomolecular Mass Spectrometry, Max Planck Institute for Heart and Lung Research, W.G. Kerckhoff Institute, Ludwigstr. 43, D-61231, Bad Nauheim, Germany
| | - Andrew D Johnson
- Framingham Heart Study, Framingham, 01702, MA, USA
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, 20892, MD, USA
| | - John Danesh
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
- British Heart Foundation Cambridge Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1RQ, UK
| | - Heiko Runz
- MRL, Merck & Co., Inc, Kenilworth, 07033, NJ, USA
| | - Shih-Jen Hwang
- Framingham Heart Study, Framingham, 01702, MA, USA
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, 20892, MD, USA
| | - Chunyu Liu
- Framingham Heart Study, Framingham, 01702, MA, USA
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, 20892, MD, USA
| | - Adam S Butterworth
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Karsten Suhre
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, PO 24144, Doha, Qatar
| | - Daniel Levy
- Framingham Heart Study, Framingham, 01702, MA, USA.
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, 20892, MD, USA.
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20
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Sun BB, Maranville JC, Peters JE, Stacey D, Staley JR, Blackshaw J, Burgess S, Jiang T, Paige E, Surendran P, Oliver-Williams C, Kamat MA, Prins BP, Wilcox SK, Zimmerman ES, Chi A, Bansal N, Spain SL, Wood AM, Morrell NW, Bradley JR, Janjic N, Roberts DJ, Ouwehand WH, Todd JA, Soranzo N, Suhre K, Paul DS, Fox CS, Plenge RM, Danesh J, Runz H, Butterworth AS. Genomic atlas of the human plasma proteome. Nature 2018; 558:73-79. [PMID: 29875488 PMCID: PMC6697541 DOI: 10.1038/s41586-018-0175-2] [Citation(s) in RCA: 687] [Impact Index Per Article: 114.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 04/27/2018] [Indexed: 02/02/2023]
Abstract
Although plasma proteins have important roles in biological processes and are the direct targets of many drugs, the genetic factors that control inter-individual variation in plasma protein levels are not well understood. Here we characterize the genetic architecture of the human plasma proteome in healthy blood donors from the INTERVAL study. We identify 1,927 genetic associations with 1,478 proteins, a fourfold increase on existing knowledge, including trans associations for 1,104 proteins. To understand the consequences of perturbations in plasma protein levels, we apply an integrated approach that links genetic variation with biological pathway, disease, and drug databases. We show that protein quantitative trait loci overlap with gene expression quantitative trait loci, as well as with disease-associated loci, and find evidence that protein biomarkers have causal roles in disease using Mendelian randomization analysis. By linking genetic factors to diseases via specific proteins, our analyses highlight potential therapeutic targets, opportunities for matching existing drugs with new disease indications, and potential safety concerns for drugs under development.
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Affiliation(s)
- Benjamin B Sun
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | - James E Peters
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cambridge Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge, UK
| | - David Stacey
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - James R Staley
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - James Blackshaw
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Stephen Burgess
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Tao Jiang
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Ellie Paige
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Praveen Surendran
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Clare Oliver-Williams
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Homerton College, Cambridge, UK
| | - Mihir A Kamat
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Bram P Prins
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | | | - An Chi
- MRL, Merck & Co., Inc., Kenilworth, NJ, USA
| | - Narinder Bansal
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Sarah L Spain
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Angela M Wood
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Nicholas W Morrell
- British Heart Foundation Cambridge Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge, UK
- Division of Respiratory Medicine, Department of Medicine, University of Cambridge, Cambridge, UK
| | - John R Bradley
- NIHR Cambridge Biomedical Research Centre/BioResource, Cambridge University Hospitals, Cambridge, UK
| | | | - David J Roberts
- National Health Service (NHS) Blood and Transplant and Radcliffe Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford, John Radcliffe Hospital, Oxford, UK
- BRC Haematology Theme and Department of Haematology, Churchill Hospital, Oxford, UK
| | - Willem H Ouwehand
- British Heart Foundation Cambridge Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - John A Todd
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Nicole Soranzo
- British Heart Foundation Cambridge Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Karsten Suhre
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Dirk S Paul
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | - Robert M Plenge
- MRL, Merck & Co., Inc., Kenilworth, NJ, USA
- Celgene Inc., Cambridge, MA, USA
| | - John Danesh
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- British Heart Foundation Cambridge Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge, UK.
- Department of Human Genetics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
| | - Heiko Runz
- MRL, Merck & Co., Inc., Kenilworth, NJ, USA
- Biogen Inc., Cambridge, MA, USA
| | - Adam S Butterworth
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
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21
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Sun BB, Ren XC, Fei GH. [Association of sleep-disorders with systemic inflammatory markers and acute exacerbation in chronic obstructive pulmonary disease patients]. Zhonghua Jie He He Hu Xi Za Zhi 2018; 41:345-348. [PMID: 29747277 DOI: 10.3760/cma.j.issn.1001-0939.2018.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To investigate the association of sleep quality with the levels of systemic inflammatory markers in patients with chronic obstructive pulmonary disease(COPD) and the correlations between the frequency of acute exacerbation of COPD (AECOPD) and Pittsburgh sleep quality index (PSQI). Methods: A total of 198 COPD patients admitted in our hospital from October, 2016 to June, 2017 were screened, and 124 patients were eligible for the study. On the first day of hospitalization, the serum samples and clinical data were collected, including white blood cells, lymphocytes, platelet count, CRP and PSQI. Poor sleep quality was defined as PSQI score >5. Results: The percentage of COPD patients with poor sleep quality was about 68%. Poor sleep quality was positively correlated with the frequency of acute exacerbation in COPD patients. The ratio of neutrophil to lymphocyte (NLR), ratio of platelet to lymphocyte (PLR) and levels of CRP were higher in patients with poor sleep quality than those in the control group. NLR, PLR and CRP in peripheral blood of the patients with poor sleep quality were positively correlated with PSQI score. The CRP levels and PSQI score in COPD patients with poor sleep quality group were positively correlated with the frequency of exacerbations in the past year (r=0.437, r=0.430). Conclusion: A high percentage of COPD patients had poor sleep quality, which was positively correlated with the levels of systemic inflammation as well as the frequency of AECOPD.
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Affiliation(s)
- B B Sun
- Respiratory Department, the First Affiliated Hospital of Anhui Medical University, Hefei 230022, China
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22
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Burgess S, Zuber V, Valdes-Marquez E, Sun BB, Hopewell JC. Mendelian randomization with fine-mapped genetic data: Choosing from large numbers of correlated instrumental variables. Genet Epidemiol 2017; 41:714-725. [PMID: 28944551 PMCID: PMC5725678 DOI: 10.1002/gepi.22077] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 08/11/2017] [Accepted: 08/16/2017] [Indexed: 11/08/2022]
Abstract
Mendelian randomization uses genetic variants to make causal inferences about the effect of a risk factor on an outcome. With fine-mapped genetic data, there may be hundreds of genetic variants in a single gene region any of which could be used to assess this causal relationship. However, using too many genetic variants in the analysis can lead to spurious estimates and inflated Type 1 error rates. But if only a few genetic variants are used, then the majority of the data is ignored and estimates are highly sensitive to the particular choice of variants. We propose an approach based on summarized data only (genetic association and correlation estimates) that uses principal components analysis to form instruments. This approach has desirable theoretical properties: it takes the totality of data into account and does not suffer from numerical instabilities. It also has good properties in simulation studies: it is not particularly sensitive to varying the genetic variants included in the analysis or the genetic correlation matrix, and it does not have greatly inflated Type 1 error rates. Overall, the method gives estimates that are less precise than those from variable selection approaches (such as using a conditional analysis or pruning approach to select variants), but are more robust to seemingly arbitrary choices in the variable selection step. Methods are illustrated by an example using genetic associations with testosterone for 320 genetic variants to assess the effect of sex hormone related pathways on coronary artery disease risk, in which variable selection approaches give inconsistent inferences.
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Affiliation(s)
- Stephen Burgess
- MRC Biostatistics Unit, Cambridge, United Kingdom.,Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Verena Zuber
- MRC Biostatistics Unit, Cambridge, United Kingdom.,European Bioinformatics Institute, Hinxton, nr Duxford, United Kingdom
| | - Elsa Valdes-Marquez
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - Benjamin B Sun
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Jemma C Hopewell
- Clinical Trial Service Unit and Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
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Staley JR, Blackshaw J, Kamat MA, Ellis S, Surendran P, Sun BB, Paul DS, Freitag D, Burgess S, Danesh J, Young R, Butterworth AS. PhenoScanner: a database of human genotype-phenotype associations. Bioinformatics 2016; 32:3207-3209. [PMID: 27318201 PMCID: PMC5048068 DOI: 10.1093/bioinformatics/btw373] [Citation(s) in RCA: 790] [Impact Index Per Article: 98.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 06/06/2016] [Indexed: 11/13/2022] Open
Abstract
Summary: PhenoScanner is a curated database of publicly available results from large-scale genetic association studies. This tool aims to facilitate ‘phenome scans’, the cross-referencing of genetic variants with many phenotypes, to help aid understanding of disease pathways and biology. The database currently contains over 350 million association results and over 10 million unique genetic variants, mostly single nucleotide polymorphisms. It is accompanied by a web-based tool that queries the database for associations with user-specified variants, providing results according to the same effect and non-effect alleles for each input variant. The tool provides the option of searching for trait associations with proxies of the input variants, calculated using the European samples from 1000 Genomes and Hapmap. Availability and Implementation: PhenoScanner is available at www.phenoscanner.medschl.cam.ac.uk. Contact:jrs95@medschl.cam.ac.uk Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- James R Staley
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - James Blackshaw
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Mihir A Kamat
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Steve Ellis
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Praveen Surendran
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Benjamin B Sun
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Dirk S Paul
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Daniel Freitag
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Stephen Burgess
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - John Danesh
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK NIHR Blood and Transplant Research Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
| | - Robin Young
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK Robertson Centre for Biostatistics, University of Glasgow, Glasgow G12 8QQ, UK
| | - Adam S Butterworth
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK NIHR Blood and Transplant Research Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK
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Hu J, Zhai SL, Zeng SY, Sun BB, Deng SF, Chen HL, Zheng Y, Wang HX, Li XP, Liu JK, Cheng S, Zhou X, Zhai JQ, Luo ML. Identification of natural recombinants derived from PCV2a and PCV2b. Genet Mol Res 2015; 14:11780-90. [PMID: 26436503 DOI: 10.4238/2015.october.2.12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Porcine circovirus type 2 (PCV2) is considered to be the main pathogen in PC-associated diseases, and significantly affects the global pig-producing industry. PCV2 continuously evolves by point mutations and genome recombinations. In the present study, we aimed to further identify recombinant PCV2 strains. We used polymerase chain reaction to detect PCV2 in the carcasses of pigs with suspected infections from different regions of Guangdong Province in China. DNA was extracted from samples with confirmed infection and full- genome amplification, sequencing, phylogenetic tree construction, gene recombination detection, and sequence alignment were performed in gene recombination analysis. Our results show that recombination occurred between the strains SHC (DQ104421) and ZhuJi2003 (AY579893). The recombination resulted in three recombinants: GD003 (KM503044), GD005 (KM487708), and GD008 (KM487709). Further analyses revealed that these novel recombinants appeared to result from recombination between the PCV2a and PCV2b strains, with crossover regions located in ORF2. This study was a comprehensive analysis that used several different methods, which demonstrated that a cluster of PCV2 strains resulted from the same type of inter-genotypic recombination pattern, with a breakpoint in the structural protein coding region. The results of our study provide both information on the recombination mechanism and disease pathogenesis and useful data for the prevention of PCV2 in the swine industry.
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Affiliation(s)
- J Hu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China
| | - S L Zhai
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China
| | - S Y Zeng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China
| | - B B Sun
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China
| | - S F Deng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China
| | - H L Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China
| | - Y Zheng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China
| | - H X Wang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China
| | - X P Li
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China
| | - J K Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China
| | - S Cheng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China
| | - X Zhou
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China
| | - J Q Zhai
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China
| | - M L Luo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China
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Lever RA, Hussain A, Sun BB, Sage SO, Harper AGS. Conventional protein kinase C isoforms differentially regulate ADP- and thrombin-evoked Ca²⁺ signalling in human platelets. Cell Calcium 2015; 58:577-88. [PMID: 26434503 DOI: 10.1016/j.ceca.2015.09.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 09/22/2015] [Accepted: 09/23/2015] [Indexed: 11/15/2022]
Abstract
Rises in cytosolic Ca(2+) concentration ([Ca(2+)]cyt) are central in platelet activation, yet many aspects of the underlying mechanisms are poorly understood. Most studies examine how experimental manipulations affect agonist-evoked rises in [Ca(2+)]cyt, but these only monitor the net effect of manipulations on the processes controlling [Ca(2+)]cyt (Ca(2+) buffering, sequestration, release, entry and removal), and cannot resolve the source of the Ca(2+) or the transporters or channels affected. To investigate the effects of protein kinase C (PKC) on platelet Ca(2+) signalling, we here monitor Ca(2+) flux around the platelet by measuring net Ca(2+) fluxes to or from the extracellular space and the intracellular Ca(2+) stores, which act as the major sources and sinks for Ca(2+) influx into and efflux from the cytosol, as well as monitoring the cytosolic Na(+) concentration ([Na(+)]cyt), which influences platelet Ca(2+) fluxes via Na(+)/Ca(2+) exchange. The intracellular store Ca(2+) concentration ([Ca(2+)]st) was monitored using Fluo-5N, the extracellular Ca(2+) concentration ([Ca(2+)]ext) was monitored using Fluo-4 whilst [Ca(2+)]cyt and [Na(+)]cyt were monitored using Fura-2 and SFBI, respectively. PKC inhibition using Ro-31-8220 or bisindolylmaleimide I potentiated ADP- and thrombin-evoked rises in [Ca(2+)]cyt in the absence of extracellular Ca(2+). PKC inhibition potentiated ADP-evoked but reduced thrombin-evoked intracellular Ca(2+) release and Ca(2+) removal into the extracellular medium. SERCA inhibition using thapsigargin and 2,5-di(tert-butyl) l,4-benzohydroquinone abolished the effect of PKC inhibitors on ADP-evoked changes in [Ca(2+)]cyt but only reduced the effect on thrombin-evoked responses. Thrombin evokes substantial rises in [Na(+)]cyt which would be expected to reduce Ca(2+) removal via the Na(+)/Ca(2+) exchanger (NCX). Thrombin-evoked rises in [Na(+)]cyt were potentiated by PKC inhibition, an effect which was not due to altered changes in non-selective cation permeability of the plasma membrane as assessed by Mn(2+) quench of Fura-2 fluorescence. PKC inhibition was without effect on thrombin-evoked rises in [Ca(2+)]cyt following SERCA inhibition and either removal of extracellular Na(+) or inhibition of Na(+)/K(+)-ATPase activity by removal of extracellular K(+) or treatment with digoxin. These data suggest that PKC limits ADP-evoked rises in [Ca(2+)]cyt by acceleration of SERCA activity, whilst rises in [Ca(2+)]cyt evoked by the stronger platelet activator thrombin are limited by PKC through acceleration of both SERCA and Na(+)/K(+)-ATPase activity, with the latter limiting the effect of thrombin on rises in [Na(+)]cyt and so forward mode NCX activity. The use of selective PKC inhibitors indicated that conventional and not novel PKC isoforms are responsible for the inhibition of agonist-evoked Ca(2+) signalling.
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Affiliation(s)
- Robert A Lever
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, United Kingdom
| | - Azhar Hussain
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, United Kingdom
| | - Benjamin B Sun
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, United Kingdom
| | - Stewart O Sage
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, United Kingdom
| | - Alan G S Harper
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, United Kingdom; Institute for Science and Technology in Medicine, Keele University, Guy Hilton Research Centre, Thornburrow Drive, Hartshill, Stoke-on-Trent ST4 7QB, United Kingdom.
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Abstract
Rosa chinensis Jacq, a traditional Chinese ornamental flower, is an important landscaping plant in northern China. Since July 2013, leaf blotch symptoms were observed in the Tianjin flower nursery (117°09' E 39°17' N). The garden exhibited 40% disease incidence with observable symptoms on basal leaves that were yellowed from the edge to the inside area on infected leaves, in the shape of a V. Yellow lesions covered one third to one half of the leaf. Yellow halos were observed at the junction of the healthy and diseased tissues. Small tissue pieces from the edges of lesions were disinfected in 70% ethyl alcohol for 30 s and 1% hypochlorite for 1 min, rinsed thrice in sterile water, plated on potato dextrose agar (PDA), and incubated at 25°C in lighted incubator for 4 days. Fungal colonies that developed on PDA were white and cottony with concentric rings. Black and globular acervuli appeared after 10 days at 25°C. Conidia (n = 20), which were fusiform, were 9.20 to 31.31 (avg. 26.5) × 4.83 to 9.11 (avg. 6.9) μm. Conidia of all isolates were five celled. Apical and basal cells were colorless, while the three median cells were dark brown. The single basal appendage of conidia was 2.85 to 16.05 μm in length and the two to three apical appendages were 5.93 to 36.23 μm in length. According to colony and conidia morphology (number of cells, number of appendages), the isolates were initially identified as Pestalotiopsis spp (2). A 525-bp band was produced in a conventional PCR assay. Primers ITS1 (5'TCCGTAGGTGAACCTGCGC3') and ITS4 (5'TCCTCCGCTTATTGATATGC3') were used to amplify and sequence the internal transcribed spacer region of rDNA. A BLAST search of the NCBI databases showed that isolate YJYK-1 had 99% homology with Pestalotiopsis clavispora isolate hz-067 (Accession No. FJ517545.1). Pathogenicity tests of the novel isolate YJYK-1 were conducted by placing agar plugs (5 mm in diameter) from an actively growing colony on PDA on surface-disinfected (70% ethyl alcohol, 30 s) leaves (1). Control leaves were inoculated with sterile PDA plugs. Plants with inoculated leaves (five per treatment) were placed in lighted growth chambers at 25°C for 10 days and watered as needed. Symptoms on inoculated leaves were similar to those previously described in the nursery. Black acervuli were easily found on the necrotic tissues. Control plants did not show any symptoms. Cultures isolated from the lesions were similar to those isolated previously from leaves in the nursery. Koch's postulates were confirmed after re-isolation. Although the diversity of endophytic Pestalotiopsis species and its distribution was investigated and the host plants were also listed in China (3), to our knowledge, this is the first report of P. clavispora causing leaf blotch on rose R. chinensis in China. References: (1) M. I. Ahmed et al. Eur. J. Plant Pathol. 135:619, 2013. (2) J. Y. Lu. Diagnosis of plant diseases. Page 194 in: Pestalotiopsis. J. Y. Lu et al., eds. China Agriculture Press, Beijing, 1995. (3) J. G. Wei et al. Mycosystema 24:481, 2005.
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Affiliation(s)
- Y R Feng
- Tianjin Institute of Plant Protection, Tianjin, 300112, China
| | - B S Liu
- Tianjin Institute of Plant Protection, Tianjin, 300112, China
| | - B B Sun
- Tianjin Institute of Plant Protection, Tianjin, 300112, China
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Feng BZ, Li PQ, Fu L, Sun BB, Zhang XG. Identification of 18 genes encoding necrosis-inducing proteins from the plant pathogen Phytophthora capsici (Pythiaceae: Oomycetes). Genet Mol Res 2011; 10:910-22. [PMID: 21644208 DOI: 10.4238/vol10-2gmr1248] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Phytophthora capsici is an aggressive plant pathogen that affects solanaceous and cucurbitaceous hosts. Necrosis-inducing Phytophthora proteins (NPPs) are a group of secreted toxins found particularly in oomycetes. Several NPPs from Phytophthora species trigger plant cell death and activate host defense gene expression. We isolated 18 P. capsici NPP genes, of which 12 were active during hypha growth from a Phytophthora stain isolated from pepper (Capsicum annuum) plants in China. The 18 predicted proteins had a sequence homology of 46.26%. The 18 Pcnpp sequences had a conserved GHRHDWE motif and fell into two groups. Eleven sequences in group 1 had two conserved cysteine residues, whereas the other seven sequences in group 2 lacked these two cysteine residues. A phylogenetic tree was constructed on the basis of the alignment of the predicted protein sequences of 52 selected NPP genes from oomycetes, fungi and bacteria from Genbank. The tree did not rigorously follow the taxonomic classification of the species; all the NPPs from oomycetes formed their own clusters, while fungal sequences were grouped into two separate clades, indicating that based on NPPs, we can separate oomycetes from fungi and bacteria, and that expansion of the NPP family was a feature of Phytophthora evolution.
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Affiliation(s)
- B Z Feng
- Department of Plant Pathology, Shandong Agricultural University, Shandong, China
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Abstract
We report a ductile beta-type titanium alloy with body-centered cubic (bcc) crystal structure having a low Poisson's ratio of 0.14. The almost identical ultralow bulk and shear moduli of approximately 24 GPa combined with an ultrahigh strength of approximately 0.9 GPa contribute to easy crystal distortion due to much-weakened chemical bonding of atoms in the crystal, leading to significant elastic softening in tension and elastic hardening in compression. The peculiar elastic and plastic deformation behaviors of the alloy are interpreted as a result of approaching the elastic limit of the bcc crystal under applied stress.
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Affiliation(s)
- Y L Hao
- Shenyang National Laboratory for Materials Science, Institute of Metal Research, Chinese Academy of Sciences, 72 Wenhua Road, Shenyang 110016, China.
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Sun BB, Chiu SY. N-type calcium channels and their regulation by GABAB receptors in axons of neonatal rat optic nerve. J Neurosci 1999; 19:5185-94. [PMID: 10377330 PMCID: PMC6782304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023] Open
Abstract
Axons of neonatal rat optic nerves exhibit fast calcium transients in response to brief action potential stimulation. In response to one to four closely spaced action potentials, evoked calcium transients showed a fast-rising phase followed by a decay with a time constant of approximately 2-3 sec. By selective staining of axons or glial cells with calcium dyes, it was shown that the evoked calcium transient originated from axons. The calcium transient was caused by influx because it was eliminated when bath calcium was removed. Pharmacological profile studies with calcium channel subtype-specific peptides suggested that 58% of the evoked calcium influx was accounted for by N-type calcium channels, whereas L- and P/Q-type calcium channels had little, if any, contribution. The identity of the residual calcium influx remains unclear. GABA application caused a dramatic reduction of the amplitude of the action potential and the associated calcium influx. When GABAA receptors were blocked by bicuculline, the inhibitory effect of GABA on the action potential was eliminated, whereas that on the calcium influx was not, indicating involvement of GABAB receptors. Indeed, the calcium influx was inhibited by the GABAB receptor agonist baclofen. This baclofen effect was occluded by a previous block of N-type calcium channels and was unaffected by the broad-spectrum K+ channel blocker 4-AP. We conclude that neonatal rat optic nerve axons express N-type calcium channels, which are subjected to regulation by G-protein-coupled GABAB receptors. We suggest that receptor-mediated inhibition of axonal calcium channels plays a protective role in neonatal anoxic and/or ischemic injury.
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Affiliation(s)
- B B Sun
- Graduate Program in Biophysics, University of Wisconsin School of Medicine, Madison, Wisconsin 53706, USA
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Dong HS, Sun BB, Sun SY. [Clinical application and experimental studies of progesterone in the treatment of ureteral stones]. Zhonghua Wai Ke Za Zhi 1986; 24:77-8, 124. [PMID: 3743270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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