151
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Hobbs BD, de Jong K, Lamontagne M, Bossé Y, Shrine N, Artigas MS, Wain LV, Hall IP, Jackson VE, Wyss AB, London SJ, North KE, Franceschini N, Strachan DP, Beaty TH, Hokanson JE, Crapo JD, Castaldi PJ, Chase RP, Bartz TM, Heckbert SR, Psaty BM, Gharib SA, Zanen P, Lammers JW, Oudkerk M, Groen HJ, Locantore N, Tal-Singer R, Rennard SI, Vestbo J, Timens W, Paré PD, Latourelle JC, Dupuis J, O’Connor GT, Wilk JB, Kim WJ, Lee MK, Oh YM, Vonk JM, de Koning HJ, Leng S, Belinsky SA, Tesfaigzi Y, Manichaikul A, Wang XQ, Rich SS, Barr RG, Sparrow D, Litonjua AA, Bakke P, Gulsvik A, Lahousse L, Brusselle GG, Stricker BH, Uitterlinden AG, Ampleford EJ, Bleecker ER, Woodruff PG, Meyers DA, Qiao D, Lomas DA, Yim JJ, Kim DK, Hawrylkiewicz I, Sliwinski P, Hardin M, Fingerlin TE, Schwartz DA, Postma DS, MacNee W, Tobin MD, Silverman EK, Boezen HM, Cho MH. Genetic loci associated with chronic obstructive pulmonary disease overlap with loci for lung function and pulmonary fibrosis. Nat Genet 2017; 49:426-432. [PMID: 28166215 PMCID: PMC5381275 DOI: 10.1038/ng.3752] [Citation(s) in RCA: 256] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 11/23/2016] [Indexed: 12/15/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is a leading cause of mortality worldwide. We performed a genetic association study in 15,256 cases and 47,936 controls, with replication of select top results (P < 5 × 10-6) in 9,498 cases and 9,748 controls. In the combined meta-analysis, we identified 22 loci associated at genome-wide significance, including 13 new associations with COPD. Nine of these 13 loci have been associated with lung function in general population samples, while 4 (EEFSEC, DSP, MTCL1, and SFTPD) are new. We noted two loci shared with pulmonary fibrosis (FAM13A and DSP) but that had opposite risk alleles for COPD. None of our loci overlapped with genome-wide associations for asthma, although one locus has been implicated in joint susceptibility to asthma and obesity. We also identified genetic correlation between COPD and asthma. Our findings highlight new loci associated with COPD, demonstrate the importance of specific loci associated with lung function to COPD, and identify potential regions of genetic overlap between COPD and other respiratory diseases.
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Affiliation(s)
- 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
| | - Kim de Jong
- University of Groningen, University Medical Center Groningen,
Department of Epidemiology, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen,
Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the
Netherlands
| | - Maxime Lamontagne
- Institut universitaire de cardiologie et de pneumologie de
Québec, Québec, Canada
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de
Québec, Québec, Canada
- Department of Molecular Medicine, Laval University, Québec,
Canada
| | - Nick Shrine
- Genetic Epidemiology Group, Department of Health Sciences,
University of Leicester, Leicester, UK
| | - María Soler Artigas
- Genetic Epidemiology Group, Department of Health Sciences,
University of Leicester, Leicester, UK
| | - Louise V. Wain
- Genetic Epidemiology Group, Department of Health Sciences,
University of Leicester, Leicester, UK
| | - Ian P. Hall
- Division of Respiratory Medicine, Queen’s Medical Centre,
University of Nottingham, Nottingham, UK
| | - Victoria E. Jackson
- Genetic Epidemiology Group, Department of Health Sciences,
University of Leicester, Leicester, UK
| | - Annah B. Wyss
- Epidemiology Branch, National Institute of Environmental Health
Sciences, National Institutes of Health, Department of Health and Human Services,
Research Triangle Park, NC, USA
| | - Stephanie J. London
- Epidemiology Branch, National Institute of Environmental Health
Sciences, National Institutes of Health, Department of Health and Human Services,
Research Triangle Park, NC, USA
| | - Kari E. North
- Department of Epidemiology, University of North Carolina, Chapel
Hill, NC, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel
Hill, NC, USA
| | - David P. Strachan
- Population Health Research Institute, St. George’s,
University of London, London, UK
| | - Terri H. Beaty
- Johns Hopkins University Bloomberg School of Public Health,
Baltimore, MD, USA
| | - John E. Hokanson
- Department of Epidemiology, University of Colorado Anschutz Medical
Campus, Aurora, CO, USA
| | - James D. Crapo
- Department of Medicine, Division of Pulmonary and Critical Care
Medicine, National Jewish Health, Denver, CO, USA
| | - Peter J. Castaldi
- Channing Division of Network Medicine, Brigham and Women’s
Hospital, Boston, MA, USA
- Division of General Internal Medicine, Brigham and Women’s
Hospital, Boston, MA, USA
| | - Robert P. Chase
- Channing Division of Network Medicine, Brigham and Women’s
Hospital, Boston, MA, USA
| | - Traci M. Bartz
- Cardiovascular Health Research Unit, University of Washington,
Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA,
USA
- Department of Biostatistics, University of Washington, Seattle, WA,
USA
| | - Susan R. Heckbert
- Cardiovascular Health Research Unit, University of Washington,
Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA,
USA
- Group Health Research Institute, Group Health Cooperative, Seattle,
WA, USA
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, University of Washington,
Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA,
USA
- Department of Epidemiology, University of Washington, Seattle, WA,
USA
- Group Health Research Institute, Group Health Cooperative, Seattle,
WA, USA
- Department of Health Services, University of Washington, Seattle,
WA, USA
| | - Sina A. Gharib
- Computational Medicine Core, Center for Lung Biology, UW Medicine
Sleep Center, Department of Medicine, University of Washington, Seattle, WA,
USA
| | - Pieter Zanen
- Department of Pulmonology, University Medical Center Utrecht,
University of Utrecht, Utrecht, the Netherlands
| | - Jan W. Lammers
- Department of Pulmonology, University Medical Center Utrecht,
University of Utrecht, Utrecht, the Netherlands
| | - Matthijs Oudkerk
- University of Groningen, University Medical Center Groningen,
Center for Medical Imaging, the Netherlands
| | - H. J. Groen
- University of Groningen, University Medical Center Groningen,
Department of Pulmonology, Groningen, the Netherlands
| | | | | | - Stephen I. Rennard
- Pulmonary, Critical Care, Sleep and Allergy Division, Department of
Internal Medicine, University of Nebraska Medical Center, Omaha, NE, USA
- Clinical Discovery Unit, AstraZeneca, Cambridge, UK
| | - Jørgen Vestbo
- School of Biological Sciences, University of Manchester,
Manchester, UK
| | - Wim Timens
- Department of Pathology and Medical Biology, University of
Groningen, University Medical Center Groningen, GRIAC Research Institute, Groningen,
the Netherlands
| | - Peter D. Paré
- University of British Columbia Center for Heart Lung Innovation and
Institute for Heart and Lung Health, St Paul’s Hospital, Vancouver, British
Columbia, Canada
| | | | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public
Health, Boston, MA, USA
- The National Heart, Lung, and Blood Institute’s Framingham
Heart Study, Framingham, MA, USA
| | - George T. O’Connor
- The National Heart, Lung, and Blood Institute’s Framingham
Heart Study, Framingham, MA, USA
- Pulmonary Center, Department of Medicine, Boston University School
of Medicine, Boston, MA, USA
| | - Jemma B. Wilk
- The National Heart, Lung, and Blood Institute’s Framingham
Heart Study, Framingham, MA, USA
| | - Woo Jin Kim
- Department of Internal Medicine and Environmental Health Center,
School of Medicine, Kangwon National University, Chuncheon, South Korea
| | - Mi Kyeong Lee
- Department of Internal Medicine and Environmental Health Center,
School of Medicine, Kangwon National University, Chuncheon, South Korea
| | - Yeon-Mok Oh
- Department of Pulmonary and Critical Care Medicine, and Clinical
Research Center for Chronic Obstructive Airway Diseases, Asan Medical Center,
University of Ulsan College of Medicine, Seoul, South Korea
| | - Judith M. Vonk
- University of Groningen, University Medical Center Groningen,
Department of Epidemiology, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen,
Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the
Netherlands
| | - Harry J. de Koning
- Department of Public Health, Erasmus Medical Center Rotterdam,
Rotterdam, the Netherlands
| | - Shuguang Leng
- Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | | | | | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia,
Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia,
Charlottesville, VA, USA
| | - Xin-Qun Wang
- Department of Public Health Sciences, University of Virginia,
Charlottesville, VA, USA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia,
Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia,
Charlottesville, VA, USA
| | - R Graham Barr
- Department of Medicine, College of Physicians and Surgeons and
Department of Epidemiology, Mailman School of Public Health, Columbia University,
New York, NY, USA
| | - David Sparrow
- VA Boston Healthcare System and Department of Medicine, Boston
University School of Medicine, Boston, MA, USA
| | - Augusto A. Litonjua
- 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
| | - Per Bakke
- Department of Clinical Science, University of Bergen, Bergen,
Norway
| | - Amund Gulsvik
- Department of Clinical Science, University of Bergen, Bergen,
Norway
| | - Lies Lahousse
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the
Netherlands
- Department of Respiratory Medicine, Ghent University Hospital,
Ghent, Belgium
| | - Guy G. Brusselle
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the
Netherlands
- Department of Respiratory Medicine, Ghent University Hospital,
Ghent, Belgium
- Department of Respiratory Medicine, Erasmus Medical Center,
Rotterdam, the Netherlands
| | - Bruno H. Stricker
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the
Netherlands
- Netherlands Health Care Inspectorate, The Hague, the
Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam,
the Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands
Consortium for Healthy Aging (NCHA), Leiden, the Netherlands
| | - André G. Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the
Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam,
the Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands
Consortium for Healthy Aging (NCHA), Leiden, the Netherlands
| | - Elizabeth J. Ampleford
- Center for Genomics and Personalized Medicine Research, Wake Forest
University School of Medicine, Winston Salem, NC, USA
| | - Eugene R. Bleecker
- Center for Genomics and Personalized Medicine Research, Wake Forest
University School of Medicine, Winston Salem, NC, USA
| | - Prescott G. Woodruff
- Cardiovascular Research Institute and the Department of Medicine,
Division of Pulmonary, Critical Care, Sleep, and Allergy, University of California
at San Francisco, San Francisco, CA, USA
| | - Deborah A. Meyers
- Center for Genomics and Personalized Medicine Research, Wake Forest
University School of Medicine, Winston Salem, NC, USA
| | - Dandi Qiao
- Channing Division of Network Medicine, Brigham and Women’s
Hospital, Boston, MA, USA
| | | | - Jae-Joon Yim
- Division of Pulmonary and Critical Care Medicine, Department of
Internal Medicine, Seoul National University College of Medicine, Seoul, South
Korea
| | - Deog Kyeom Kim
- Seoul National University College of Medicine, SMG-SNU Boramae
Medical Center, Seoul, South Korea
| | - Iwona Hawrylkiewicz
- 2nd Department of Respiratory Medicine, Institute of Tuberculosis
and Lung Diseases, Warsaw, Poland
| | - Pawel Sliwinski
- 2nd Department of Respiratory Medicine, Institute of Tuberculosis
and Lung Diseases, Warsaw, Poland
| | - Megan Hardin
- 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
- Clinical Discovery Unit, AstraZeneca, Cambridge, UK
| | - Tasha E. Fingerlin
- Center for Genes, Environment and Health, National Jewish Health,
Denver, CO, USA
- Department of Biostatistics and Informatics, University of Colorado
Denver, Aurora, CO, USA
| | - David A. Schwartz
- Center for Genes, Environment and Health, National Jewish Health,
Denver, CO, USA
- Department of Medicine, School of Medicine, University of Colorado
Denver, Aurora, CO, USA
- Department of Immunology, School of Medicine, University of
Colorado Denver, Aurora, CO, USA
| | - Dirkje S. Postma
- University of Groningen, University Medical Center Groningen,
Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the
Netherlands
- University of Groningen, University Medical Center Groningen,
Department of Pulmonology, Groningen, the Netherlands
| | | | - Martin D. Tobin
- Genetic Epidemiology Group, Department of Health Sciences,
University of Leicester, Leicester, UK
- National Institute for Health Research (NIHR) Leicester Respiratory
Biomedical Research Unit, Glenfield Hospital, Leicester, 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
| | - H. Marike Boezen
- University of Groningen, University Medical Center Groningen,
Department of Epidemiology, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen,
Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the
Netherlands
| | - 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
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152
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House JS, Nichols CE, Li H, Brandenberger C, Virgincar RS, DeGraff LM, Driehuys B, Zeldin DC, London SJ. Vagal innervation is required for pulmonary function phenotype in Htr4-/- mice. Am J Physiol Lung Cell Mol Physiol 2017; 312:L520-L530. [PMID: 28130264 PMCID: PMC5407097 DOI: 10.1152/ajplung.00495.2016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 01/19/2017] [Accepted: 01/25/2017] [Indexed: 11/22/2022] Open
Abstract
Human genome-wide association studies have identified over 50 loci associated with pulmonary function and related phenotypes, yet follow-up studies to determine causal genes or variants are rare. Single nucleotide polymorphisms in serotonin receptor 4 (HTR4) are associated with human pulmonary function in genome-wide association studies and follow-up animal work has demonstrated that Htr4 is causally associated with pulmonary function in mice, although the precise mechanisms were not identified. We sought to elucidate the role of neural innervation and pulmonary architecture in the lung phenotype of Htr4-/- animals. We report here that the Htr4-/- phenotype in mouse is dependent on vagal innervation to the lung. Both ex vivo tracheal ring reactivity and in vivo flexiVent pulmonary functional analyses demonstrate that vagotomy abrogates the Htr4-/- airway hyperresponsiveness phenotype. Hyperpolarized 3He gas magnetic resonance imaging and stereological assessment of wild-type and Htr4-/- mice reveal no observable differences in lung volume, inflation characteristics, or pulmonary microarchitecture. Finally, control of breathing experiments reveal substantive differences in baseline breathing characteristics between mice with/without functional HTR4 in breathing frequency, relaxation time, flow rate, minute volume, time of inspiration and expiration and breathing pauses. These results suggest that HTR4's role in pulmonary function likely relates to neural innervation and control of breathing.
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Affiliation(s)
- John S House
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Cody E Nichols
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Huiling Li
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | | | - Rohan S Virgincar
- Center for In Vivo Microscopy, Duke University Medical Center, Durham, North Carolina.,Biomedical Engineering, Duke University, Durham, North Carolina
| | - Laura M DeGraff
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Bastiaan Driehuys
- Center for In Vivo Microscopy, Duke University Medical Center, Durham, North Carolina.,Biomedical Engineering, Duke University, Durham, North Carolina.,Radiology, Duke University Medical Center, Durham, North Carolina; and
| | - Darryl C Zeldin
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
| | - Stephanie J London
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina; .,Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina
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153
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Qiu F, Li Y, Lu X, Xie C, Nong Q, Wu D, Chen J, Yang L, Zhou Y, Lu J. Rare variant ofMAP2K7is associated with increased risk of COPD in southern and eastern Chinese. Respirology 2017; 22:691-698. [DOI: 10.1111/resp.12976] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 09/11/2016] [Accepted: 09/29/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Fuman Qiu
- Biomedicine Research Center of The Third Affiliated Hospital of GMU, The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity; Guangzhou Medical University; Guangzhou China
| | - Yinyan Li
- Biomedicine Research Center of The Third Affiliated Hospital of GMU, The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity; Guangzhou Medical University; Guangzhou China
| | - Xiaoxiao Lu
- School of Arts and Sciences; Colby-Sawyer College; New London New Hampshire USA
| | - Chenli Xie
- Biomedicine Research Center of The Third Affiliated Hospital of GMU, The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity; Guangzhou Medical University; Guangzhou China
| | - Qingqing Nong
- Department of Environmental Health; Guangxi Medical University; Nanning China
| | - Di Wu
- Biomedicine Research Center of The Third Affiliated Hospital of GMU, The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity; Guangzhou Medical University; Guangzhou China
| | - Jiansong Chen
- Biomedicine Research Center of The Third Affiliated Hospital of GMU, The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity; Guangzhou Medical University; Guangzhou China
| | - Lei Yang
- Biomedicine Research Center of The Third Affiliated Hospital of GMU, The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity; Guangzhou Medical University; Guangzhou China
| | - Yifeng Zhou
- Department of Genetics; Medical College of Soochow University; Suzhou China
| | - Jiachun Lu
- Biomedicine Research Center of The Third Affiliated Hospital of GMU, The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity; Guangzhou Medical University; Guangzhou China
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154
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Artigas MS, Wain LV, Shrine N, McKeever TM, Sayers I, Hall IP, Tobin MD. Targeted Sequencing of Lung Function Loci in Chronic Obstructive Pulmonary Disease Cases and Controls. PLoS One 2017; 12:e0170222. [PMID: 28114305 PMCID: PMC5256917 DOI: 10.1371/journal.pone.0170222] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Accepted: 01/01/2017] [Indexed: 12/15/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is the third leading cause of death worldwide; smoking is the main risk factor for COPD, but genetic factors are also relevant contributors. Genome-wide association studies (GWAS) of the lung function measures used in the diagnosis of COPD have identified a number of loci, however association signals are often broad and collectively these loci only explain a small proportion of the heritability. In order to examine the association with COPD risk of genetic variants down to low allele frequencies, to aid fine-mapping of association signals and to explain more of the missing heritability, we undertook a targeted sequencing study in 300 COPD cases and 300 smoking controls for 26 loci previously reported to be associated with lung function. We used a pooled sequencing approach, with 12 pools of 25 individuals each, enabling high depth (30x) coverage per sample to be achieved. This pooled design maximised sample size and therefore power, but led to challenges during variant-calling since sequencing error rates and minor allele frequencies for rare variants can be very similar. For this reason we employed a rigorous quality control pipeline for variant detection which included the use of 3 independent calling algorithms. In order to avoid false positive associations we also developed tests to detect variants with potential batch effects and removed them before undertaking association testing. We tested for the effects of single variants and the combined effect of rare variants within a locus. We followed up the top signals with data available (only 67% of collapsing methods signals) in 4,249 COPD cases and 11,916 smoking controls from UK Biobank. We provide suggestive evidence for the combined effect of rare variants on COPD risk in TNXB and in sliding windows within MECOM and upstream of HHIP. These findings can lead to an improved understanding of the molecular pathways involved in the development of COPD.
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Affiliation(s)
- María Soler Artigas
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | - Louise V. Wain
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research (NIHR), Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, United Kingdom
| | - Nick Shrine
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | - Tricia M. McKeever
- Division of Respiratory Medicine, Queen’s Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | | | - Ian Sayers
- Division of Respiratory Medicine, Queen’s Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Ian P. Hall
- Division of Respiratory Medicine, Queen’s Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Martin D. Tobin
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research (NIHR), Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, United Kingdom
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155
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Morin A, Laviolette M, Pastinen T, Boulet LP, Laprise C. Combining omics data to identify genes associated with allergic rhinitis. Clin Epigenetics 2017; 9:3. [PMID: 28149331 PMCID: PMC5270349 DOI: 10.1186/s13148-017-0310-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 01/03/2017] [Indexed: 01/26/2023] Open
Abstract
Allergic rhinitis is a common chronic disorder characterized by immunoglobulin E-mediated inflammation. To identify new genes associated with this trait, we performed genome- and epigenome-wide association studies and linked marginally significant CpGs located in genes or its promoter and SNPs located 1 Mb from the CpGs, by identifying cis methylation quantitative trait loci (mQTL). This approach relies on functional cellular aspects rather than stringent statistical correction. We were able to identify one gene with significant cis-mQTL for allergic rhinitis, caudal-type homeobox 1 (CDX1). We also identified 11 genes with marginally significant cis-mQTLs (p < 0.05) including one with both allergic rhinitis with or without asthma (RNF39). Moreover, most SNPs identified were not located closest to the gene they were linked to through cis-mQTLs counting the one linked to CDX1 located in a gene previously associated with asthma and atopic dermatitis. By combining omics data, we were able to identify new genes associated with allergic rhinitis and better assess the genes linked to associated SNPs.
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Affiliation(s)
- Andréanne Morin
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, 740 Dr. Penfield Avenue, Montréal, Québec H3A 1A5 Canada.,Département des sciences fondamentales, Université du Québec à Chicoutimi, 555 boulevard de l'Université, Saguenay, Québec G7H 2B1 Canada
| | - Michel Laviolette
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, 2725 chemin Sainte-Foy, Québec, Québec G1V 4G5 Canada
| | - Tomi Pastinen
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, 740 Dr. Penfield Avenue, Montréal, Québec H3A 1A5 Canada
| | - Louis-Philippe Boulet
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Université Laval, 2725 chemin Sainte-Foy, Québec, Québec G1V 4G5 Canada
| | - Catherine Laprise
- Département des sciences fondamentales, Université du Québec à Chicoutimi, 555 boulevard de l'Université, Saguenay, Québec G7H 2B1 Canada
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156
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Association of nsv823469 copy number loss with decreased risk of chronic obstructive pulmonary disease and pulmonary function in Chinese. Sci Rep 2017; 7:40060. [PMID: 28079130 PMCID: PMC5227687 DOI: 10.1038/srep40060] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 11/30/2016] [Indexed: 01/17/2023] Open
Abstract
It is highly possible that copy number variations (CNVs) in susceptible regions have effects on chronic obstructive pulmonary disease (COPD) development, while long noncoding RNA (lncRNAs) have been shown to cause COPD. We hypothesized that the common CNV, named nsv823469 located on 6p22.1, and covering lncRNAs (major histocompatibility complex, class I, A (HLA-A) and HLA complex group 4B (HCG4B)) has an effect on COPD risk. This association was assessed through a two-stage case-control study, and was further confirmed with COPD and pulmonary function-based family analyses, respectively. The copy number loss (0-copy/1-copy) of nsv823469 significantly decreased risk of COPD compared with normal (2-copy) (OR = 0.77, 95% CI = 0.69–0.85). The loss allele, inducing copy number loss of nsv823469, has a tendency to transmit to offspring or siblings (P = 0.010) and is associated with forced expiratory volume in 1 second (FEV1) (P = 0.030). Furthermore, the copy number loss of nsv823469 in normal pulmonary tissue decreases the expression levels of HCG4B (r = 0.315, P = 0.031) and HLA-A (r = 0.296, P = 0.044). Our data demonstrates that nsv823469 plays a role in COPD and pulmonary function inheritance by potentially altering expression of HCG4B.
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157
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Personalized Medicine. Respir Med 2017. [DOI: 10.1007/978-3-319-43447-6_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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158
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McGeachie MJ, Clemmer GL, Croteau-Chonka DC, Castaldi PJ, Cho MH, Sordillo JE, Lasky-Su JA, Raby BA, Tantisira KG, Weiss ST. Whole genome prediction and heritability of childhood asthma phenotypes. IMMUNITY INFLAMMATION AND DISEASE 2016; 4:487-496. [PMID: 27980782 PMCID: PMC5134727 DOI: 10.1002/iid3.133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 09/01/2016] [Accepted: 09/04/2016] [Indexed: 01/19/2023]
Abstract
Introduction While whole genome prediction (WGP) methods have recently demonstrated successes in the prediction of complex genetic diseases, they have not yet been applied to asthma and related phenotypes. Longitudinal patterns of lung function differ between asthmatics, but these phenotypes have not been assessed for heritability or predictive ability. Herein, we assess the heritability and genetic predictability of asthma‐related phenotypes. Methods We applied several WGP methods to a well‐phenotyped cohort of 832 children with mild‐to‐moderate asthma from CAMP. We assessed narrow‐sense heritability and predictability for airway hyperresponsiveness, serum immunoglobulin E, blood eosinophil count, pre‐ and post‐bronchodilator forced expiratory volume in 1 sec (FEV1), bronchodilator response, steroid responsiveness, and longitudinal patterns of lung function (normal growth, reduced growth, early decline, and their combinations). Prediction accuracy was evaluated using a training/testing set split of the cohort. Results We found that longitudinal lung function phenotypes demonstrated significant narrow‐sense heritability (reduced growth, 95%; normal growth with early decline, 55%). These same phenotypes also showed significant polygenic prediction (areas under the curve [AUCs] 56% to 62%). Including additional demographic covariates in the models increased prediction 4–8%, with reduced growth increasing from 62% to 66% AUC. We found that prediction with a genomic relatedness matrix was improved by filtering available SNPs based on chromatin evidence, and this result extended across cohorts. Conclusions Longitudinal reduced lung function growth displayed extremely high heritability. All phenotypes with significant heritability showed significant polygenic prediction. Using SNP‐prioritization increased prediction across cohorts. WGP methods show promise in predicting asthma‐related heritable traits.
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Affiliation(s)
- Michael J McGeachie
- Channing Division of Network Medicine Brigham and Women's Hospital and Harvard Medical School Boston Massachusetts
| | - George L Clemmer
- Channing Division of Network Medicine Brigham and Women's Hospital and Harvard Medical School Boston Massachusetts
| | - Damien C Croteau-Chonka
- Channing Division of Network Medicine Brigham and Women's Hospital and Harvard Medical School Boston Massachusetts
| | - Peter J Castaldi
- Channing Division of Network Medicine Brigham and Women's Hospital and Harvard Medical School Boston Massachusetts
| | - Michael H Cho
- Channing Division of Network Medicine Brigham and Women's Hospital and Harvard Medical School Boston Massachusetts
| | - Joanne E Sordillo
- Channing Division of Network Medicine Brigham and Women's Hospital and Harvard Medical School Boston Massachusetts
| | - Jessica A Lasky-Su
- Channing Division of Network Medicine Brigham and Women's Hospital and Harvard Medical School Boston Massachusetts
| | - Benjamin A Raby
- Channing Division of Network Medicine Brigham and Women's Hospital and Harvard Medical School Boston Massachusetts
| | - Kelan G Tantisira
- Channing Division of Network Medicine Brigham and Women's Hospital and Harvard Medical School Boston Massachusetts
| | - Scott T Weiss
- Channing Division of Network Medicine Brigham and Women's Hospital and Harvard Medical School Boston Massachusetts
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159
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Matsson H, Söderhäll C, Einarsdottir E, Lamontagne M, Gudmundsson S, Backman H, Lindberg A, Rönmark E, Kere J, Sin D, Postma DS, Bossé Y, Lundbäck B, Klar J. Targeted high-throughput sequencing of candidate genes for chronic obstructive pulmonary disease. BMC Pulm Med 2016; 16:146. [PMID: 27835950 PMCID: PMC5106844 DOI: 10.1186/s12890-016-0309-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 11/06/2016] [Indexed: 12/13/2022] Open
Abstract
Background Reduced lung function in patients with chronic obstructive pulmonary disease (COPD) is likely due to both environmental and genetic factors. We report here a targeted high-throughput DNA sequencing approach to identify new and previously known genetic variants in a set of candidate genes for COPD. Methods Exons in 22 genes implicated in lung development as well as 61 genes and 10 genomic regions previously associated with COPD were sequenced using individual DNA samples from 68 cases with moderate or severe COPD and 66 controls matched for age, gender and smoking. Cases and controls were selected from the Obstructive Lung Disease in Northern Sweden (OLIN) studies. Results In total, 37 genetic variants showed association with COPD (p < 0.05, uncorrected). Several variants previously discovered to be associated with COPD from genetic genome-wide analysis studies were replicated using our sample. Two high-risk variants were followed-up for functional characterization in a large eQTL mapping study of 1,111 human lung specimens. The C allele of a synonymous variant, rs8040868, predicting a p.(S45=) in the gene for cholinergic receptor nicotinic alpha 3 (CHRNA3) was associated with COPD (p = 8.8 x 10−3). This association remained (p = 0.003 and OR = 1.4, 95 % CI 1.1-1.7) when analysing all available cases and controls in OLIN (n = 1,534). The rs8040868 variant is in linkage disequilibrium with rs16969968 previously associated with COPD and altered expression of the CHRNA5 gene. A follow-up analysis for detection of expression quantitative trait loci revealed that rs8040868-C was found to be significantly associated with a decreased expression of the nearby gene cholinergic receptor, nicotinic, alpha 5 (CHRNA5) in lung tissue. Conclusion Our data replicate previous result suggesting CHRNA5 as a candidate gene for COPD and rs8040868 as a risk variant for the development of COPD in the Swedish population. Electronic supplementary material The online version of this article (doi:10.1186/s12890-016-0309-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hans Matsson
- Department of Biosciences and Nutrition, Karolinska Institutet, 7-9, SE-141 83, Huddinge, Sweden. .,Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.
| | - Cilla Söderhäll
- Department of Biosciences and Nutrition, Karolinska Institutet, 7-9, SE-141 83, Huddinge, Sweden.,Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Elisabet Einarsdottir
- Department of Biosciences and Nutrition, Karolinska Institutet, 7-9, SE-141 83, Huddinge, Sweden.,Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Maxime Lamontagne
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec, Canada
| | - Sanna Gudmundsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Helena Backman
- Department of Public Health and Clinical Medicine, Division of Occupational and Environmental Medicine, Umeå University, Umeå, Sweden
| | - Anne Lindberg
- Department of Public Health and Clinical Medicine, Division of Medicine, Umeå University, Umeå, Sweden
| | - Eva Rönmark
- Department of Public Health and Clinical Medicine, Division of Occupational and Environmental Medicine, Umeå University, Umeå, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, 7-9, SE-141 83, Huddinge, Sweden.,Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Don Sin
- The University of British Columbia Center for Heart Lung Innovation, St-Paul's Hospital, Vancouver, Canada
| | - Dirkje S Postma
- Center Groningen, GRIAC research institute, University of Groningen, Groningen, The Netherlands
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec, Canada.,Department of Molecular Medicine, Laval University, Québec, Canada
| | - Bo Lundbäck
- Krefting Research Centre, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Joakim Klar
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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160
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Busch R, Qiu W, Lasky-Su J, Morrow J, Criner G, DeMeo D. Differential DNA methylation marks and gene comethylation of COPD in African-Americans with COPD exacerbations. Respir Res 2016; 17:143. [PMID: 27814717 PMCID: PMC5097392 DOI: 10.1186/s12931-016-0459-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/27/2016] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) is the third-leading cause of death worldwide. Identifying COPD-associated DNA methylation marks in African-Americans may contribute to our understanding of racial disparities in COPD susceptibility. We determined differentially methylated genes and co-methylation network modules associated with COPD in African-Americans recruited during exacerbations of COPD and smoking controls from the Pennsylvania Study of Chronic Obstructive Pulmonary Exacerbations (PA-SCOPE) cohort. METHODS We assessed DNA methylation from whole blood samples in 362 African-American smokers in the PA-SCOPE cohort using the Illumina Infinium HumanMethylation27 BeadChip Array. Final analysis included 19302 CpG probes annotated to the nearest gene transcript after quality control. We tested methylation associations with COPD case-control status using mixed linear models. Weighted gene comethylation networks were constructed using weighted gene coexpression network analysis (WGCNA) and network modules were analyzed for association with COPD. RESULTS There were five differentially methylated CpG probes significantly associated with COPD among African-Americans at an FDR less than 5 %, and seven additional probes that approached significance at an FDR less than 10 %. The top ranked gene association was MAML1, which has been shown to affect NOTCH-dependent angiogenesis in murine lung. Network modeling yielded the "yellow" and "blue" comethylation modules which were significantly associated with COPD (p-value 4 × 10-10 and 4 × 10-9, respectively). The yellow module was enriched for gene sets related to inflammatory pathways known to be relevant to COPD. The blue module contained the top ranked genes in the concurrent differential methylation analysis (FXYD1/LGI4, gene significance p-value 1.2 × 10-26; MAML1, p-value 2.0 × 10-26; CD72, p-value 2.1 × 10-25; and LPO, p-value 7.2 × 10-25), and was significantly associated with lung development processes in Gene Ontology gene-set enrichment analysis. CONCLUSION We identified 12 differentially methylated CpG sites associated with COPD that mapped to biologically plausible genes. Network module comethylation patterns have identified candidate genes that may be contributing to racial differences in COPD susceptibility and severity. COPD-associated comethylation modules contained genes previously associated with lung disease and inflammation and recapitulated known COPD-associated genes. The genes implicated by differential methylation and WGCNA analysis may provide mechanistic targets contributing to COPD susceptibility, exacerbations, and outcomes among African-Americans. TRIAL REGISTRATION Trial Registration: NCT00774176 , Registry: ClinicalTrials.gov, URL: www.clinicaltrials.gov , Date of Enrollment of First Participant: June 2004, Date Registered: 04 January 2008 (retrospectively registered).
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Affiliation(s)
- Robert Busch
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Ave, Room 449, Boston, 02111 MA USA
| | - Weiliang Qiu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Ave, Room 449, Boston, 02111 MA USA
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Ave, Room 449, Boston, 02111 MA USA
| | - Jarrett Morrow
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Ave, Room 449, Boston, 02111 MA USA
| | - Gerard Criner
- Temple Lung Center, Temple University Health System, Philadelphia, PA USA
| | - Dawn DeMeo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Ave, Room 449, Boston, 02111 MA USA
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Genetic Predisposition to COPD: Are There Any Relevant Genes Determining the Susceptibility to Smoking? ACTA ACUST UNITED AC 2016. [DOI: 10.1007/978-981-10-0839-9_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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162
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Sulovari A, Chen YH, Hudziak JJ, Li D. Atlas of human diseases influenced by genetic variants with extreme allele frequency differences. Hum Genet 2016; 136:39-54. [PMID: 27699474 DOI: 10.1007/s00439-016-1734-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 09/27/2016] [Indexed: 12/22/2022]
Abstract
Genetic variants with extreme allele frequency differences (EAFD) may underlie some human health disparities across populations. To identify EAFD loci, we systematically analyzed and characterized 81 million genomic variants from 2504 unrelated individuals of 26 world populations (phase III of the 1000 Genomes Project). Our analyses revealed a total of 434 genes, 15 pathways, and 18 diseases and traits influenced by EAFD variants from five continental populations. They included known EAFD genes, such as LCT (lactose tolerance), SLC24A5 (skin pigmentation), and EDAR (hair morphology). We found many novel EAFD genes, including TBC1D2B (autophagy mediator), TRIM40 (gastrointestinal inflammatory regulator), KRT71, KRT75, KRT83, and KRTAP10-1 (hair and epithelial keratin synthesis), PIK3R3 (insulin receptor interaction), DARS (neurological disorders), and NACA2 (skin inflammatory response). Our results also showed four complex diseases significantly associated with EAFD loci, including asthma (adjusted enrichment P = 4 × 10-8), type I diabetes (P = 6 × 10-9), alcohol consumption (P = 0.0002), and attention deficit/hyperactivity disorder (P = 0.003). This study provides a comprehensive atlas of genes, pathways, and human diseases significantly influenced by EAFD variants.
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Affiliation(s)
- Arvis Sulovari
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, 05405, USA
| | - Yolanda H Chen
- Department of Plant and Soil Science, University of Vermont, Burlington, VT, 05405, USA
| | - James J Hudziak
- Vermont Center for Children, Youth, and Families, Department of Psychiatry, University of Vermont, Burlington, VT, 05405, USA
| | - Dawei Li
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, 05405, USA. .,Department of Computer Science, University of Vermont, Burlington, VT, 05405, USA. .,Neuroscience, Behavior, and Health Initiative, University of Vermont, Burlington, VT, 05405, USA.
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163
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Morrow JD, Cho MH, Hersh CP, Pinto-Plata V, Celli B, Marchetti N, Criner G, Bueno R, Washko G, Glass K, Choi AMK, Quackenbush J, Silverman EK, DeMeo DL. DNA methylation profiling in human lung tissue identifies genes associated with COPD. Epigenetics 2016; 11:730-739. [PMID: 27564456 PMCID: PMC5094634 DOI: 10.1080/15592294.2016.1226451] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 08/05/2016] [Accepted: 08/10/2016] [Indexed: 10/21/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a smoking-related disease characterized by genetic and phenotypic heterogeneity. Although association studies have identified multiple genomic regions with replicated associations to COPD, genetic variation only partially explains the susceptibility to lung disease, and suggests the relevance of epigenetic investigations. We performed genome-wide DNA methylation profiling in homogenized lung tissue samples from 46 control subjects with normal lung function and 114 subjects with COPD, all former smokers. The differentially methylated loci were integrated with previous genome-wide association study results. The top 535 differentially methylated sites, filtered for a minimum mean methylation difference of 5% between cases and controls, were enriched for CpG shelves and shores. Pathway analysis revealed enrichment for transcription factors. The top differentially methylated sites from the intersection with previous GWAS were in CHRM1, GLT1D1, and C10orf11; sorted by GWAS P-value, the top sites included FRMD4A, THSD4, and C10orf11. Epigenetic association studies complement genetic association studies to identify genes potentially involved in COPD pathogenesis. Enrichment for genes implicated in asthma and lung function and for transcription factors suggests the potential pathogenic relevance of genes identified through differential methylation and the intersection with a broader range of GWAS associations.
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Affiliation(s)
- Jarrett D. Morrow
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, 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
| | - Craig P. Hersh
- 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
| | | | - Bartolome Celli
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Nathaniel Marchetti
- Division of Pulmonary and Critical Care Medicine, Temple University, Philadelphia, PA, USA
| | - Gerard Criner
- Division of Pulmonary and Critical Care Medicine, Temple University, Philadelphia, PA, USA
| | - Raphael Bueno
- Division of Thoracic Surgery, Brigham and Women's Hospital, Boston, MA, USA
| | - George Washko
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Kimberly Glass
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Augustine M. K. Choi
- Department of Medicine, New York Presbyterian/Weill Cornell Medical Center, New York, NY, USA
| | - John Quackenbush
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - 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
| | - 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
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164
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van der Plaat DA, de Jong K, Lahousse L, Faiz A, Vonk JM, van Diemen CC, Nedeljkovic I, Amin N, Brusselle GG, Hofman A, Brandsma CA, Bossé Y, Sin DD, Nickle DC, van Duijn CM, Postma DS, Boezen HM. Genome-wide association study on the FEV 1/FVC ratio in never-smokers identifies HHIP and FAM13A. J Allergy Clin Immunol 2016; 139:533-540. [PMID: 27612410 DOI: 10.1016/j.jaci.2016.06.062] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 06/06/2016] [Accepted: 06/10/2016] [Indexed: 01/10/2023]
Abstract
BACKGROUND Although a striking proportion (25% to 45%) of patients with chronic obstructive pulmonary disease are never-smokers, most genetic susceptibility studies have not focused on this group exclusively. OBJECTIVE The aim of this study was to identify common genetic variants associated with FEV1 and its ratio to forced vital capacity (FVC) in never-smokers. METHODS Genome-wide association studies were performed in 5070 never-smokers of the identification cohort LifeLines, and results (P < 10-5) were verified by using a meta-analysis of the Vlagtwedde-Vlaardingen study and the Rotterdam Study I-III (total n = 1966). Furthermore, we aimed to assess the effects of the replicated variants in more detail by performing genetic risk score, expression quantitative trait loci, and variant*ever-smoking interaction analyses. RESULTS We identified associations between the FEV1/FVC ratio and 5 common genetic variants in the identification cohort, and 2 of these associations were replicated. The 2 variants annotated to the genes hedgehog interacting protein (HHIP) and family with sequence similarity 13 member A (FAM13A) were shown to have an additive effect on FEV1/FVC levels in the genetic risk score analysis; were associated with gene expression of HHIP and FAM13A in lung tissue, respectively; and were genome-wide significant in a meta-analysis including both identification and 4 verification cohorts (P < 2.19 × 10-7). Finally, we did not identify significant interactions between the variants and ever smoking. Results of the FEV1 identification analysis were not replicated. CONCLUSION The genes HHIP and FAM13A confer a risk for airway obstruction in general that is not driven exclusively by cigarette smoking, which is the main risk factor for chronic obstructive pulmonary disease.
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Affiliation(s)
- Diana A van der Plaat
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Kim de Jong
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Lies Lahousse
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands; Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Alen Faiz
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Judith M Vonk
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Cleo C van Diemen
- Department of Genetics, University of Groningen, University Medical Center Groningen, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ivana Nedeljkovic
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Najaf Amin
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Guy G Brusselle
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands; Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium; Department of Respiratory Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Corry-Anke Brandsma
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Yohan Bossé
- Department of Molecular, Medicine, Laval University, Institut universitaire de cardiologie et de pneumologie de Québec, Quebec City, Quebec, Canada
| | - Don D Sin
- Department of Medicine, Division of Respiratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada; University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, British Columbia, Canada
| | | | | | - Dirkje S Postma
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - H Marike Boezen
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
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Iniesta R, Stahl D, McGuffin P. Machine learning, statistical learning and the future of biological research in psychiatry. Psychol Med 2016; 46:2455-2465. [PMID: 27406289 PMCID: PMC4988262 DOI: 10.1017/s0033291716001367] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 05/04/2016] [Accepted: 05/12/2016] [Indexed: 11/24/2022]
Abstract
Psychiatric research has entered the age of 'Big Data'. Datasets now routinely involve thousands of heterogeneous variables, including clinical, neuroimaging, genomic, proteomic, transcriptomic and other 'omic' measures. The analysis of these datasets is challenging, especially when the number of measurements exceeds the number of individuals, and may be further complicated by missing data for some subjects and variables that are highly correlated. Statistical learning-based models are a natural extension of classical statistical approaches but provide more effective methods to analyse very large datasets. In addition, the predictive capability of such models promises to be useful in developing decision support systems. That is, methods that can be introduced to clinical settings and guide, for example, diagnosis classification or personalized treatment. In this review, we aim to outline the potential benefits of statistical learning methods in clinical research. We first introduce the concept of Big Data in different environments. We then describe how modern statistical learning models can be used in practice on Big Datasets to extract relevant information. Finally, we discuss the strengths of using statistical learning in psychiatric studies, from both research and practical clinical points of view.
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Affiliation(s)
- R. Iniesta
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, UK
| | - D. Stahl
- Department of Biostatistics, Institute of Psychiatry, Psychology and Neuroscience, King's College London, UK
| | - P. McGuffin
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, UK
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166
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Affiliation(s)
- Fernando D Martinez
- From the Asthma and Airway Disease Research Center, University of Arizona, Tucson
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167
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Shrine N, Tobin MD, Schurmann C, Soler Artigas M, Hui J, Lehtimäki T, Raitakari OT, Pennell CE, Ang QW, Strachan DP, Homuth G, Gläser S, Felix SB, Evans DM, Henderson J, Granell R, Palmer LJ, Huffman J, Hayward C, Scotland G, Malarstig A, Musk B, James AL, Wain LV. Genome-wide association study of copy number variation with lung function identifies a novel signal of association near BANP for forced vital capacity. BMC Genet 2016; 17:116. [PMID: 27514831 PMCID: PMC4981989 DOI: 10.1186/s12863-016-0423-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 07/29/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genome-wide association studies of Single Nucleotide Polymorphisms (SNPs) have identified 55 SNPs associated with lung function. However, little is known about the effect of copy number variants (CNVs) on lung function, although CNVs represent a significant proportion of human genetic polymorphism. To assess the effect of CNVs on lung function quantitative traits, we measured copy number at 2788 previously characterised, common copy number variable regions in 6 independent cohorts (n = 24,237) using intensity data from SNP genotyping experiments. We developed a pipeline for genome-wide association analysis and meta-analysis of CNV genotypes measured across multiple studies using SNP genotype array intensity data from different platform technologies. We then undertook cohort-level genome-wide association studies of CNV with lung function in a subset of 4 cohorts (n < =12,403) with lung function measurements and meta-analysed the results. Follow-up was undertaken for CNVs which were well tagged by SNPs, in up to 146,871 individuals. RESULTS We generated robust copy number calls for 1962 out of 2788 (70 %) known CNV regions genome-wide, with 1103 measured with compatible class frequencies in at least 2 cohorts. We report a novel CNV association (discovery P = 0.0007) with Forced Vital Capacity (FVC) downstream of BANP on chromosome 16 that shows evidence of replication by a tag SNP in two independent studies (replication P = 0.004). In addition, we provide suggestive evidence (discovery P = 0.0002) for a role of complex copy number variation at a previously reported lung function locus, containing the rootletin gene CROCC, that is not tagged by SNPs. CONCLUSIONS We demonstrate how common CNV regions can be reliably and consistently called across cohorts, using an existing calling algorithm and rigorous quality control steps, using SNP genotyping array intensity data. Although many common biallelic CNV regions were well-tagged by common SNPs, we also identified associations with untagged mulitallelic CNV regions thereby illustrating the potential of our approach to identify some of the missing heritability of complex traits.
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Affiliation(s)
- Nick Shrine
- Department of Health Sciences, University of Leicester, University Road, Leicester, LE1 7RH UK
| | - Martin D. Tobin
- Department of Health Sciences, University of Leicester, University Road, Leicester, LE1 7RH UK
- National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, LE3 9QP UK
| | - Claudia Schurmann
- Department of Functional Genomics, University Medicine Greifswald, Interfaculty Institute for Genetics and Functional Genomics, Greifswald, Germany
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, 17475 Greifswald, Germany
| | - María Soler Artigas
- Department of Health Sciences, University of Leicester, University Road, Leicester, LE1 7RH UK
| | - Jennie Hui
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Nedlands, Australia
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, University of Tampere and Tampere University Hospital, Tampere, 33521 Finland
| | - Olli T. Raitakari
- Department of Clinical Physiology, Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku University Hospital, Turku, 20521 Finland
| | - Craig E. Pennell
- School of Women’s and Infants’ Health, The University of Western Australia, Perth, Australia
| | - Qi Wei Ang
- School of Women’s and Infants’ Health, The University of Western Australia, Perth, Australia
| | - David P. Strachan
- Division of Population Health Sciences, St. George’s University of London, London, UK
| | - Georg Homuth
- Department of Functional Genomics, University Medicine Greifswald, Interfaculty Institute for Genetics and Functional Genomics, Greifswald, Germany
| | - Sven Gläser
- Department of Internal Medicine B – Pulmonary Medicine, Weaning and Infectious Diseases and Scientific Division of Pneumology and Pneumological Epidemiology, University Medicine Greifswald, Greifswald, Germany
| | - Stephan B. Felix
- Department of Functional Genomics, University Medicine Greifswald, Interfaculty Institute for Genetics and Functional Genomics, Greifswald, Germany
- Department of Internal Medicine B – Cardiology, University Medicine Greifswald, Greifswald, Germany
| | - David M. Evans
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland Australia
| | - John Henderson
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Raquel Granell
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Lyle J. Palmer
- School of Public Health, University of Adelaide, Adelaide, Australia
| | - Jennifer Huffman
- Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Crewe Road, Edinburgh, EH4 2XU UK
| | - Caroline Hayward
- Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Crewe Road, Edinburgh, EH4 2XU UK
| | - Generation Scotland
- Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Crewe Road, Edinburgh, EH4 2XU UK
| | | | - Bill Musk
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Nedlands, Australia
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, Australia
| | - Alan L. James
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Nedlands, Australia
- Department of Pulmonary Physiology and Sleep Medicine, Sir Charles Gairdner Hospital, Nedlands, Australia
| | - UK BiLEVE
- Department of Health Sciences, University of Leicester, University Road, Leicester, LE1 7RH UK
- National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, LE3 9QP UK
- Department of Functional Genomics, University Medicine Greifswald, Interfaculty Institute for Genetics and Functional Genomics, Greifswald, Germany
- DZHK (German Center for Cardiovascular Research), partner site Greifswald, 17475 Greifswald, Germany
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Nedlands, Australia
- Department of Clinical Chemistry, Fimlab Laboratories, University of Tampere and Tampere University Hospital, Tampere, 33521 Finland
- Department of Clinical Physiology, Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku University Hospital, Turku, 20521 Finland
- School of Women’s and Infants’ Health, The University of Western Australia, Perth, Australia
- Division of Population Health Sciences, St. George’s University of London, London, UK
- Department of Internal Medicine B – Pulmonary Medicine, Weaning and Infectious Diseases and Scientific Division of Pneumology and Pneumological Epidemiology, University Medicine Greifswald, Greifswald, Germany
- Department of Internal Medicine B – Cardiology, University Medicine Greifswald, Greifswald, Germany
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- School of Social and Community Medicine, University of Bristol, Bristol, UK
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Queensland Australia
- School of Public Health, University of Adelaide, Adelaide, Australia
- Institute of Genetics and Molecular Medicine, University of Edinburgh Western General Hospital, Crewe Road, Edinburgh, EH4 2XU UK
- Pfizer Worldwide Research and Development, Sollentuna, Sweden
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, Australia
- Department of Pulmonary Physiology and Sleep Medicine, Sir Charles Gairdner Hospital, Nedlands, Australia
| | - Louise V. Wain
- Department of Health Sciences, University of Leicester, University Road, Leicester, LE1 7RH UK
- National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, LE3 9QP UK
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168
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Lao T, Jiang Z, Yun J, Qiu W, Guo F, Huang C, Mancini JD, Gupta K, Laucho-Contreras ME, Naing ZZC, Zhang L, Perrella MA, Owen CA, Silverman EK, Zhou X. Hhip haploinsufficiency sensitizes mice to age-related emphysema. Proc Natl Acad Sci U S A 2016; 113:E4681-7. [PMID: 27444019 PMCID: PMC4987811 DOI: 10.1073/pnas.1602342113] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Genetic variants in Hedgehog interacting protein (HHIP) have consistently been associated with the susceptibility to develop chronic obstructive pulmonary disease and pulmonary function levels, including the forced expiratory volume in 1 s (FEV1), in general population samples by genome-wide association studies. However, in vivo evidence connecting Hhip to age-related FEV1 decline and emphysema development is lacking. Herein, using Hhip heterozygous mice (Hhip(+/-)), we observed increased lung compliance and spontaneous emphysema in Hhip(+/-) mice starting at 10 mo of age. This increase was preceded by increases in oxidative stress levels in the lungs of Hhip(+/-) vs. Hhip(+/+) mice. To our knowledge, these results provide the first line of evidence that HHIP is involved in maintaining normal lung function and alveolar structures. Interestingly, antioxidant N-acetyl cysteine treatment in mice starting at age of 5 mo improved lung function and prevented emphysema development in Hhip(+/-) mice, suggesting that N-acetyl cysteine treatment limits the progression of age-related emphysema in Hhip(+/-) mice. Therefore, reduced lung function and age-related spontaneous emphysema development in Hhip(+/-) mice may be caused by increased oxidative stress levels in murine lungs as a result of haploinsufficiency of Hhip.
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Affiliation(s)
- Taotao Lao
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Zhiqiang Jiang
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Jeong Yun
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Weiliang Qiu
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Feng Guo
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Chunfang Huang
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - John Dominic Mancini
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Kushagra Gupta
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Maria E Laucho-Contreras
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115; Chronic Obstructive Pulmonary Disease Program, The Lovelace Respiratory Research Institute, Albuquerque, NM 87108
| | - Zun Zar Chi Naing
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Li Zhang
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Mark A Perrella
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115; Pediatric Newborn Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Caroline A Owen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115; Chronic Obstructive Pulmonary Disease Program, The Lovelace Respiratory Research Institute, Albuquerque, NM 87108
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115
| | - Xiaobo Zhou
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115;
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169
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Silverman EK. Risk of Lung Disease in PI MZ Heterozygotes. Current Status and Future Research Directions. Ann Am Thorac Soc 2016; 13 Suppl 4:S341-5. [PMID: 27564671 PMCID: PMC5059493 DOI: 10.1513/annalsats.201507-437kv] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The potential for increased chronic obstructive pulmonary disease (COPD) risk among PI MZ subjects was initially recognized decades ago. However, despite many studies of this topic, it has remained controversial whether such increased risk exists. Several recent studies in large populations strongly support increased risk for COPD among PI MZ subjects. This increased PI MZ risk will need to be understood in the context of other identified COPD genetic determinants and investigations of COPD phenotypic heterogeneity.
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Affiliation(s)
- Edwin K Silverman
- Channing Division of Network Medicine, and Pulmonary and Critical Care Medicine Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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170
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Miller S, Melén E, Merid SK, Hall IP, Sayers I. Genes associated with polymorphic variants predicting lung function are differentially expressed during human lung development. Respir Res 2016; 17:95. [PMID: 27473260 PMCID: PMC4966770 DOI: 10.1186/s12931-016-0410-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 07/20/2016] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Recent meta-analyses of genome-wide association studies have identified single nucleotide polymorphisms (SNPs) within/near 54 genes associated with lung function measures. Current understanding of the contribution of these genes to human lung development is limited. We set out to further define i) the expression profile of these genes during human lung development using a unique set of resources to examine both mRNA and protein expression and ii) the link between key polymorphisms and genes using expression quantitative trait loci (eQTL) approaches. METHODS The mRNA expression profile of lung function associated genes across pseudoglandular and canalicular stages of lung development were determined using expression array data of 38 human fetal lungs. eQTLs were investigated for selected genes using blood cell and lung tissue data. Immunohistochemistry of the top 5 candidates was performed in a panel of 24 fetal lung samples. RESULTS Twenty-nine lung function associated genes were differentially expressed during lung development at the mRNA level. The greatest magnitude of effect was observed for 5 genes; TMEM163, FAM13A and HHIP which had increasing expression and CDC123 and PTCH1 with decreased expression across developmental stages. Focussed eQTL analyses investigating SNPs in these five loci identified several cis-eQTL's. Protein expression of TMEM163 increased and CDC123 decreased with fetal lung age in agreement with mRNA data. Protein expression in FAM13A, HHIP and PTCH1 remained relatively constant throughout lung development. CONCLUSIONS We have identified that > 50 % of lung function associated genes show evidence of differential expression during lung development and we show that in particular TMEM163 and CDC123 are differentially expressed at both the mRNA and protein levels. Our data provides a systematic evaluation of lung function associated genes in this context and offers some insight into the potential role of several of these genes in contributing to human lung development.
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Affiliation(s)
- S Miller
- Division of Respiratory Medicine, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK.
| | - E Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Sachs' Children's Hospital, Stockholm, Sweden
| | - S K Merid
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - I P Hall
- Division of Respiratory Medicine, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK
| | - I Sayers
- Division of Respiratory Medicine, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK
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171
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Yu L, Wang GD, Ruan J, Chen YB, Yang CP, Cao X, Wu H, Liu YH, Du ZL, Wang XP, Yang J, Cheng SC, Zhong L, Wang L, Wang X, Hu JY, Fang L, Bai B, Wang KL, Yuan N, Wu SF, Li BG, Zhang JG, Yang YQ, Zhang CL, Long YC, Li HS, Yang JY, Irwin DM, Ryder OA, Li Y, Wu CI, Zhang YP. Genomic analysis of snub-nosed monkeys (Rhinopithecus) identifies genes and processes related to high-altitude adaptation. Nat Genet 2016; 48:947-52. [DOI: 10.1038/ng.3615] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 06/13/2016] [Indexed: 12/31/2022]
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172
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Hobbs BD, Parker MM, Chen H, Lao T, Hardin M, Qiao D, Hawrylkiewicz I, Sliwinski P, Yim JJ, Kim WJ, Kim DK, Castaldi PJ, Hersh CP, Morrow J, Celli BR, Pinto-Plata VM, Criner GJ, Marchetti N, Bueno R, Agustí A, Make BJ, Crapo JD, Calverley PM, Donner CF, Lomas DA, Wouters EFM, Vestbo J, Paré PD, Levy RD, Rennard SI, Zhou X, Laird NM, Lin X, Beaty TH, Silverman EK, Cho MH. Exome Array Analysis Identifies a Common Variant in IL27 Associated with Chronic Obstructive Pulmonary Disease. Am J Respir Crit Care Med 2016; 194:48-57. [PMID: 26771213 PMCID: PMC4960630 DOI: 10.1164/rccm.201510-2053oc] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 01/15/2016] [Indexed: 12/14/2022] Open
Abstract
RATIONALE Chronic obstructive pulmonary disease (COPD) susceptibility is in part related to genetic variants. Most genetic studies have been focused on genome-wide common variants without a specific focus on coding variants, but common and rare coding variants may also affect COPD susceptibility. OBJECTIVES To identify coding variants associated with COPD. METHODS We tested nonsynonymous, splice, and stop variants derived from the Illumina HumanExome array for association with COPD in five study populations enriched for COPD. We evaluated single variants with a minor allele frequency greater than 0.5% using logistic regression. Results were combined using a fixed effects meta-analysis. We replicated novel single-variant associations in three additional COPD cohorts. MEASUREMENTS AND MAIN RESULTS We included 6,004 control subjects and 6,161 COPD cases across five cohorts for analysis. Our top result was rs16969968 (P = 1.7 × 10(-14)) in CHRNA5, a locus previously associated with COPD susceptibility and nicotine dependence. Additional top results were found in AGER, MMP3, and SERPINA1. A nonsynonymous variant, rs181206, in IL27 (P = 4.7 × 10(-6)) was just below the level of exome-wide significance but attained exome-wide significance (P = 5.7 × 10(-8)) when combined with results from other cohorts. Gene expression datasets revealed an association of rs181206 and the surrounding locus with expression of multiple genes; several were differentially expressed in COPD lung tissue, including TUFM. CONCLUSIONS In an exome array analysis of COPD, we identified nonsynonymous variants at previously described loci and a novel exome-wide significant variant in IL27. This variant is at a locus previously described in genome-wide associations with diabetes, inflammatory bowel disease, and obesity and appears to affect genes potentially related to COPD pathogenesis.
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Affiliation(s)
- Brian D. Hobbs
- Channing Division of Network Medicine
- Division of Pulmonary and Critical Care Medicine
| | | | - Han Chen
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | | | - Megan Hardin
- Channing Division of Network Medicine
- Division of Pulmonary and Critical Care Medicine
| | | | | | - Pawel Sliwinski
- National Tuberculosis and Lung Disease Research Institute, Warsaw, Poland
| | - Jae-Joon Yim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Woo Jin Kim
- Kangwon National University, Chuncheon, South Korea
| | - Deog Kyeom Kim
- Seoul National University Boramae Medical Center, Seoul, South Korea
| | - Peter J. Castaldi
- Channing Division of Network Medicine
- Division of General Medicine and Primary Care, and
| | - Craig P. Hersh
- Channing Division of Network Medicine
- Division of Pulmonary and Critical Care Medicine
| | | | | | - Victor M. Pinto-Plata
- Department of Critical Care Medicine and Pulmonary Disease, Baystate Medical Center, Springfield, Massachusetts
| | | | - Nathaniel Marchetti
- Department of Thoracic Medicine and Surgery, Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Raphael Bueno
- Division of Thoracic Surgery, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Alvar Agustí
- Thorax Institute, Hospital Clinic, IDIBAPS, University of Barcelona, CIBERES, Barcelona, Spain
| | | | | | | | - Claudio F. Donner
- Mondo Medico di I.F.I.M. srl, Multidisciplinary and Rehabilitation Outpatient Clinic, Borgomanero (NO), Italy
| | | | | | - Jorgen Vestbo
- University of Manchester, Manchester, United Kingdom
| | - Peter D. Paré
- University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert D. Levy
- University of British Columbia, Vancouver, British Columbia, Canada
| | - Stephen I. Rennard
- Pulmonary and Critical Care Medicine, University of Nebraska Medical Center, Omaha, Nebraska
- Clinical Discovery Unit, AstraZeneca, Cambridge, United Kingdom; and
| | | | - Nan M. Laird
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Xihong Lin
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Terri H. Beaty
- Department of Epidemiology, Bloomberg School of Public Health, The Johns Hopkins University, Baltimore, Maryland
| | - Edwin K. Silverman
- Channing Division of Network Medicine
- Division of Pulmonary and Critical Care Medicine
| | - Michael H. Cho
- Channing Division of Network Medicine
- Division of Pulmonary and Critical Care Medicine
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173
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Gormley P, Anttila V, Winsvold BS, Palta P, Esko T, Pers TH, Farh KH, Cuenca-Leon E, Muona M, Furlotte NA, Kurth T, Ingason A, McMahon G, Ligthart L, Terwindt GM, Kallela M, Freilinger TM, Ran C, Gordon SG, Stam AH, Steinberg S, Borck G, Koiranen M, Quaye L, Adams HHH, Lehtimäki T, Sarin AP, Wedenoja J, Hinds DA, Buring JE, Schürks M, Ridker PM, Hrafnsdottir MG, Stefansson H, Ring SM, Hottenga JJ, Penninx BWJH, Färkkilä M, Artto V, Kaunisto M, Vepsäläinen S, Malik R, Heath AC, Madden PAF, Martin NG, Montgomery GW, Kurki MI, Kals M, Mägi R, Pärn K, Hämäläinen E, Huang H, Byrnes AE, Franke L, Huang J, Stergiakouli E, Lee PH, Sandor C, Webber C, Cader Z, Muller-Myhsok B, Schreiber S, Meitinger T, Eriksson JG, Salomaa V, Heikkilä K, Loehrer E, Uitterlinden AG, Hofman A, van Duijn CM, Cherkas L, Pedersen LM, Stubhaug A, Nielsen CS, Männikkö M, Mihailov E, Milani L, Göbel H, Esserlind AL, Christensen AF, Hansen TF, Werge T, Kaprio J, Aromaa AJ, Raitakari O, Ikram MA, Spector T, Järvelin MR, Metspalu A, Kubisch C, Strachan DP, Ferrari MD, Belin AC, Dichgans M, Wessman M, van den Maagdenberg AMJM, Zwart JA, Boomsma DI, Smith GD, Stefansson K, Eriksson N, Daly MJ, Neale BM, Olesen J, Chasman DI, Nyholt DR, Palotie A. Meta-analysis of 375,000 individuals identifies 38 susceptibility loci for migraine. Nat Genet 2016; 48:856-66. [PMID: 27322543 DOI: 10.1038/ng.3598] [Citation(s) in RCA: 421] [Impact Index Per Article: 52.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 05/26/2016] [Indexed: 12/16/2022]
Abstract
Migraine is a debilitating neurological disorder affecting around one in seven people worldwide, but its molecular mechanisms remain poorly understood. There is some debate about whether migraine is a disease of vascular dysfunction or a result of neuronal dysfunction with secondary vascular changes. Genome-wide association (GWA) studies have thus far identified 13 independent loci associated with migraine. To identify new susceptibility loci, we carried out a genetic study of migraine on 59,674 affected subjects and 316,078 controls from 22 GWA studies. We identified 44 independent single-nucleotide polymorphisms (SNPs) significantly associated with migraine risk (P < 5 × 10(-8)) that mapped to 38 distinct genomic loci, including 28 loci not previously reported and a locus that to our knowledge is the first to be identified on chromosome X. In subsequent computational analyses, the identified loci showed enrichment for genes expressed in vascular and smooth muscle tissues, consistent with a predominant theory of migraine that highlights vascular etiologies.
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Affiliation(s)
- Padhraig Gormley
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Verneri Anttila
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Bendik S Winsvold
- FORMI, Oslo University Hospital, Oslo, Norway.,Department of Neurology, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Priit Palta
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Tonu Esko
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Estonian Genome Center, University of Tartu, Tartu, Estonia.,Division of Endocrinology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Tune H Pers
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Division of Endocrinology, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Kai-How Farh
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Illumina, San Diego, California, USA
| | - Ester Cuenca-Leon
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Pediatric Neurology, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Mikko Muona
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.,Folkhälsan Institute of Genetics, Helsinki, Finland.,Neuroscience Center, University of Helsinki, Helsinki, Finland.,Molecular Neurology Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | | | - Tobias Kurth
- Institute of Public Health, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | | | - George McMahon
- Medical Research Council (MRC) Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Lannie Ligthart
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
| | - Gisela M Terwindt
- Department of Neurology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Mikko Kallela
- Department of Neurology, Helsinki University Central Hospital, Helsinki, Finland
| | - Tobias M Freilinger
- Department of Neurology and Epileptology, Hertie-Institute for Clinical Brain Research, University of Tuebingen, Tuebingen, Germany.,Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Caroline Ran
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Scott G Gordon
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Anine H Stam
- Department of Neurology, Leiden University Medical Centre, Leiden, the Netherlands
| | | | - Guntram Borck
- Institute of Human Genetics, Ulm University, Ulm, Germany
| | - Markku Koiranen
- Center for Life Course Epidemiology and Systems Medicine, University of Oulu, Oulu, Finland
| | - Lydia Quaye
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Hieab H H Adams
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands.,Department of Radiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, School of Medicine, University of Tampere, Tampere, Finland
| | - Antti-Pekka Sarin
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Juho Wedenoja
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | | | - Julie E Buring
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Markus Schürks
- Department of Neurology, University Duisburg-Essen, Essen, Germany
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | | | | | - Susan M Ring
- Medical Research Council (MRC) Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
| | - Brenda W J H Penninx
- Department of Psychiatry, VU University Medical Centre, Amsterdam, the Netherlands
| | - Markus Färkkilä
- Department of Neurology, Helsinki University Central Hospital, Helsinki, Finland
| | - Ville Artto
- Department of Neurology, Helsinki University Central Hospital, Helsinki, Finland
| | - Mari Kaunisto
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Salli Vepsäläinen
- Department of Neurology, Helsinki University Central Hospital, Helsinki, Finland
| | - Rainer Malik
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Andrew C Heath
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Pamela A F Madden
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Nicholas G Martin
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Grant W Montgomery
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Mitja I Kurki
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.,Department of Neurosurgery, NeuroCenter, Kuopio University Hospital, Kuopio, Finland
| | - Mart Kals
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Kalle Pärn
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Eija Hämäläinen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Hailiang Huang
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Andrea E Byrnes
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
| | - Jie Huang
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Evie Stergiakouli
- Medical Research Council (MRC) Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Phil H Lee
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Cynthia Sandor
- MRC Functional Genomics Unit, Department of Physiology, Anatomy &Genetics, Oxford University, Oxford, UK
| | - Caleb Webber
- MRC Functional Genomics Unit, Department of Physiology, Anatomy &Genetics, Oxford University, Oxford, UK
| | - Zameel Cader
- Nuffield Department of Clinical Neuroscience, University of Oxford, Oxford, UK.,Oxford Headache Centre, John Radcliffe Hospital, Oxford, UK
| | - Bertram Muller-Myhsok
- Max Planck Institute of Psychiatry, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.,Institute of Translational Medicine, University of Liverpool, Liverpool, UK
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian Albrechts University, Kiel, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg, Germany.,Institute of Human Genetics, Technische Universität München, Munich, Germany
| | - Johan G Eriksson
- Department of General Practice and Primary Health Care, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,National Institute for Health and Welfare, Helsinki, Finland
| | - Veikko Salomaa
- National Institute for Health and Welfare, Helsinki, Finland
| | - Kauko Heikkilä
- Institute of Clinical Medicine, University of Helsinki, Helsinki, Finland
| | - Elizabeth Loehrer
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands.,Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Andre G Uitterlinden
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Lynn Cherkas
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | | | - Audun Stubhaug
- Department of Pain Management and Research, Oslo University Hospital, Oslo, Norway.,Medical Faculty, University of Oslo, Oslo, Norway
| | - Christopher S Nielsen
- Department of Pain Management and Research, Oslo University Hospital, Oslo, Norway.,Department of Ageing and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Minna Männikkö
- Center for Life Course Epidemiology and Systems Medicine, University of Oulu, Oulu, Finland
| | | | - Lili Milani
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | | | - Ann-Louise Esserlind
- Danish Headache Center, Department of Neurology, Rigshospitalet, Glostrup Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Anne Francke Christensen
- Danish Headache Center, Department of Neurology, Rigshospitalet, Glostrup Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Folkmann Hansen
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, University of Copenhagen, Roskilde, Denmark
| | - Thomas Werge
- Institute of Biological Psychiatry, MHC Sct. Hans, Mental Health Services Copenhagen, Copenhagen, Denmark.,Institute of Clinical Sciences, Faculty of Medicine and Health Sciences, University of Copenhagen, Copenhagen, Denmark.,iPSYCH-The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Copenhagen, Denmark
| | | | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.,Department of Public Health, University of Helsinki, Helsinki, Finland.,Department of Health, National Institute for Health and Welfare, Helsinki, Finland
| | - Arpo J Aromaa
- National Institute for Health and Welfare, Helsinki, Finland
| | - Olli Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland.,Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands.,Department of Radiology, Erasmus University Medical Center, Rotterdam, the Netherlands.,Department of Neurology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Tim Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Marjo-Riitta Järvelin
- Center for Life Course Epidemiology and Systems Medicine, University of Oulu, Oulu, Finland.,Department of Epidemiology and Biostatistics, MRC Health Protection Agency (HPE) Centre for Environment and Health, School of Public Health, Imperial College London, London, UK.,Biocenter Oulu, University of Oulu, Oulu, Finland.,Unit of Primary Care, Oulu University Hospital, Oulu, Finland
| | | | - Christian Kubisch
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - David P Strachan
- Population Health Research Institute, St George's, University of London, London, UK
| | - Michel D Ferrari
- Department of Neurology, Leiden University Medical Centre, Leiden, the Netherlands
| | - Andrea C Belin
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Martin Dichgans
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig-Maximilians-Universität München, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Maija Wessman
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.,Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Arn M J M van den Maagdenberg
- Department of Neurology, Leiden University Medical Centre, Leiden, the Netherlands.,Department of Human Genetics, Leiden University Medical Centre, Leiden, the Netherlands
| | - John-Anker Zwart
- FORMI, Oslo University Hospital, Oslo, Norway.,Department of Neurology, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
| | - George Davey Smith
- Medical Research Council (MRC) Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Kari Stefansson
- deCODE Genetics, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | | | - Mark J Daly
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Benjamin M Neale
- Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Jes Olesen
- Danish Headache Center, Department of Neurology, Rigshospitalet, Glostrup Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Dale R Nyholt
- Statistical and Genomic Epidemiology Laboratory, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, Queensland, Australia
| | - Aarno Palotie
- Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK.,Analytic and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.,Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA
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174
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Lu Q, Jin C, Sun J, Bowler R, Kechris K, Kaminski N, Zhao H. Post-GWAS Prioritization Through Data Integration Provides Novel Insights on Chronic Obstructive Pulmonary Disease. STATISTICS IN BIOSCIENCES 2016; 2016:1-17. [PMID: 27812370 PMCID: PMC5087812 DOI: 10.1007/s12561-016-9151-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 05/14/2016] [Accepted: 05/24/2016] [Indexed: 01/24/2023]
Abstract
Rich collections of genomic and epigenomic annotations, availabilities of large population cohorts for genome-wide association studies (GWAS), and advancements in data integration techniques provide the unprecedented opportunity to accelerate discoveries in complex disease studies through integrative analyses. In this paper, we apply a variety of approaches to integrate GWAS summary statistics of chronic obstructive pulmonary disease (COPD) with functional annotations to illustrate how data integration could help researchers understand complex human diseases. We show that incorporating functional annotations can better prioritize GWAS signals at both the global and the local levels. Signal prioritization on severe COPD GWAS reveals multiple potential risk loci that are linked with pulmonary functions. Enrichment analysis provides novel insights on the pathogenesis of COPD and hints the existence of genetic contributions to muscle dysfuncion and chronic lung inflammation, two symptoms that are often co-morbid with COPD. Our results suggest that rich signals for COPD genetics are still buried under the Bonferroni-corrected genome-wide significance threshold. Many more biological findings are expected to emerge as more samples are recruited for COPD studies.
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Affiliation(s)
- Qiongshi Lu
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | | | - Jiehuan Sun
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Russell Bowler
- National Jewish Health, Department of Medicine, Denver, CO, USA
| | - Katerina Kechris
- Department of Biostatistics and Informatics, University of Colorado Denver, Denver, CO, USA
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
- Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
- VA Cooperative Studies Program Coordinating Center, West Haven, CT, USA
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175
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Blazer LL, Lima-Fernandes E, Gibson E, Eram MS, Loppnau P, Arrowsmith CH, Schapira M, Vedadi M. PR Domain-containing Protein 7 (PRDM7) Is a Histone 3 Lysine 4 Trimethyltransferase. J Biol Chem 2016; 291:13509-19. [PMID: 27129774 PMCID: PMC4919437 DOI: 10.1074/jbc.m116.721472] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Indexed: 12/22/2022] Open
Abstract
PR domain-containing protein 7 (PRDM7) is a primate-specific histone methyltransferase that is the result of a recent gene duplication of PRDM9. The two proteins are highly homologous, especially in the catalytic PR/SET domain, where they differ by only three amino acid residues. Here we report that PRDM7 is an efficient methyltransferase that selectively catalyzes the trimethylation of H3 lysine 4 (H3K4) both in vitro and in cells. Through selective mutagenesis we have dissected the functional roles of each of the three divergent residues between the PR domains of PRDM7 and PRDM9. These studies indicate that after a single serine to tyrosine mutation at residue 357 (S357Y), PRDM7 regains the substrate specificities and catalytic activities similar to its evolutionary predecessor, including the ability to efficiently methylate H3K36.
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Affiliation(s)
- Levi L Blazer
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | - Evelyne Lima-Fernandes
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | - Elisa Gibson
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | - Mohammad S Eram
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | - Peter Loppnau
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7
| | - Cheryl H Arrowsmith
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, the Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 2M9, and
| | - Matthieu Schapira
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, the Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Masoud Vedadi
- From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, the Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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176
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Liu Y, Xu Y, Guo S, Chen H. T cell factor-4 functions as a co-activator to promote NF-κB-dependent MMP-15 expression in lung carcinoma cells. Sci Rep 2016; 6:24025. [PMID: 27046058 PMCID: PMC4820775 DOI: 10.1038/srep24025] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 03/18/2016] [Indexed: 02/06/2023] Open
Abstract
Both TCF-4 and MMP-15 are closely linked to the development of lung cancer, while the regulatory role of TCF-4 in MMP-15 expression is still obscure. Here we found that expression of TCF-4 and MMP-15 was increased in lung cancer cells or tissues versus the normal ones. With gain-or loss-of -function studies, we demonstrated that TCF-4 positively regulated MMP-15 expression in mRNA and protein levels. With reporter gene assay, we found that TCF-4 regulated MMP-15 expression via a potential NF-κB binding element locating at -2833/-2824 in the mouse MMP-15 promoter. With ChIP and immunoblotting assays, we identified that TCF-4 functioned as a co-activator to potentiate the binding between p65 and MMP-15 promoter. Functionally, TCF-4 silence attenuated the migration activity of LLC cells, while additional overexpression of MMP-15 rescued this effect in cell scratch test and transwell migration assay. In xenograft model, TCF-4 silence-improved tumor lesions in lungs and survival time of LLC-tumor bearing mice were abolished by MMP-15 overexpression. In conclusion, we are the first to identify TCF-4 as a co-activator of NF-κB p65 to promote MMP-15 transcription and potentiate the migration activity of the lung cancer cells. Our findings shed light on the therapeutic strategies of this malignancy.
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Affiliation(s)
- Yuliang Liu
- Department of Respiratory Medicine, First Affiliated Hospital of Chongqing Medical University, 400016, Chongqing, China
| | - Yu Xu
- Department of Respiratory Medicine, Xinqiao Hospital, Third Military Medical University, 400037, Chongqing, China
| | - Shuliang Guo
- Department of Respiratory Medicine, First Affiliated Hospital of Chongqing Medical University, 400016, Chongqing, China
| | - Hong Chen
- Department of Respiratory Medicine, First Affiliated Hospital of Chongqing Medical University, 400016, Chongqing, China
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177
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Yuan YM, Zhang JL, Xu SC, Ye RS, Xu D, Zhang Y, Zhang YJ, Chen YL, Liu YL, Su ZG. Genetic variants of CDH13 determine the susceptibility to chronic obstructive pulmonary disease in a Chinese population. Acta Pharmacol Sin 2016; 37:390-7. [PMID: 26806298 DOI: 10.1038/aps.2015.158] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 09/06/2015] [Indexed: 02/05/2023] Open
Abstract
AIM Adiponectin has been implicated in the development of chronic obstructive pulmonary disease (COPD). The CDH13 gene encodes T-cadherin that is an adiponectin receptor, and genetic variants of CDH13 determine blood adiponectin levels. The aim of this study was to investigate the effects of CDH13 variants on COPD susceptibility in a Chinese population. METHODS Ten single-nucleotide polymorphisms (SNP) in CDH13 were screened using the SNaPshot method in 279 COPD patients and 367 control subjects. Association of genotypes or haplotypes constructed from these loci with COPD was analyzed in different genetic models. RESULTS Among the 10 SNPs tested, rs4783244 and rs12922394 exhibited significant differences in allele or genotype frequencies between COPD patients and control subjects, whereas 8 other SNPs did not. The minor allele T was associated with decreased risk of COPD in the recessive model at rs4783244 (OR=0.42, P=0.023) and in the dominant model at rs12922394 (OR=0.70, P=0.022). The genotype TT at either rs4783244 or rs12922394 was associated with a significantly low level of plasma adiponectin when compared to genotypes GG and CC (P<0.05). Haplotypes GC in block 1 (rs4783244-rs12922394) as well as GTAC and ATGT in block 3 (rs4783266-rs11640522-rs11646849-rs11860282) significantly increased the risk of COPD, whereas haplotypes TT in block 1, TG in block 2 (rs11646011- rs11640875) and ATGC in block 3 were protective against COPD. CONCLUSION CDH13 genetic variants determine Chinese individuals' susceptibility to COPD and thus are efficient genetic biomarkers for early detection of COPD.
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178
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Jackson VE, Ntalla I, Sayers I, Morris R, Whincup P, Casas JP, Amuzu A, Choi M, Dale C, Kumari M, Engmann J, Kalsheker N, Chappell S, Guetta-Baranes T, McKeever TM, Palmer CNA, Tavendale R, Holloway JW, Sayer AA, Dennison EM, Cooper C, Bafadhel M, Barker B, Brightling C, Bolton CE, John ME, Parker SG, Moffat MF, Wardlaw AJ, Connolly MJ, Porteous DJ, Smith BH, Padmanabhan S, Hocking L, Stirrups KE, Deloukas P, Strachan DP, Hall IP, Tobin MD, Wain LV. Exome-wide analysis of rare coding variation identifies novel associations with COPD and airflow limitation in MOCS3, IFIT3 and SERPINA12. Thorax 2016; 71:501-9. [PMID: 26917578 PMCID: PMC4893124 DOI: 10.1136/thoraxjnl-2015-207876] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/29/2016] [Indexed: 01/01/2023]
Abstract
Background Several regions of the genome have shown to be associated with COPD in genome-wide association studies of common variants. Objective To determine rare and potentially functional single nucleotide polymorphisms (SNPs) associated with the risk of COPD and severity of airflow limitation. Methods 3226 current or former smokers of European ancestry with lung function measures indicative of Global Initiative for Chronic Obstructive Lung Disease (GOLD) 2 COPD or worse were genotyped using an exome array. An analysis of risk of COPD was carried out using ever smoking controls (n=4784). Associations with %predicted FEV1 were tested in cases. We followed-up signals of interest (p<10−5) in independent samples from a subset of the UK Biobank population and also undertook a more powerful discovery study by meta-analysing the exome array data and UK Biobank data for variants represented on both arrays. Results Among the associated variants were two in regions previously unreported for COPD; a low frequency non-synonymous SNP in MOCS3 (rs7269297, pdiscovery=3.08×10−6, preplication=0.019) and a rare SNP in IFIT3, which emerged in the meta-analysis (rs140549288, pmeta=8.56×10−6). In the meta-analysis of % predicted FEV1 in cases, the strongest association was shown for a splice variant in a previously unreported region, SERPINA12 (rs140198372, pmeta=5.72×10−6). We also confirmed previously reported associations with COPD risk at MMP12, HHIP, GPR126 and CHRNA5. No associations in novel regions reached a stringent exome-wide significance threshold (p<3.7×10−7). Conclusions This study identified several associations with the risk of COPD and severity of airflow limitation, including novel regions MOCS3, IFIT3 and SERPINA12, which warrant further study.
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Affiliation(s)
| | - Ioanna Ntalla
- Department of Health Sciences, University of Leicester, Leicester, UK William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Ian Sayers
- Division of Respiratory Medicine, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| | - Richard Morris
- School of Social & Community Medicine, University of Bristol, Bristol, UK Department of Primary Care & Population Health, UCL, London, UK
| | - Peter Whincup
- Population Health Research Institute, St George's, University of London, London, UK
| | - Juan-Pablo Casas
- University College London, Farr Institute of Health Informatics, London, UK Cochrane Heart Group, London, UK
| | - Antoinette Amuzu
- Department of Non-communicable Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Minkyoung Choi
- Department of Non-communicable Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Caroline Dale
- Department of Non-communicable Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Meena Kumari
- ISER, University of Essex, Colchester, Essex, UK Department of Epidemiology and Public Health, UCL, London, UK
| | | | - Noor Kalsheker
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Sally Chappell
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | | | - Tricia M McKeever
- Division of Epidemiology and Public Health, Nottingham City Hospital, University of Nottingham, Nottingham, UK
| | - Colin N A Palmer
- Cardiovascular and Diabetes Medicine, School of Medicine, University of Dundee, Dundee, UK
| | - Roger Tavendale
- Cardiovascular and Diabetes Medicine, School of Medicine, University of Dundee, Dundee, UK
| | - John W Holloway
- Human Development & Health, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK NIHR Southampton Respiratory Biomedical Research Unit, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton General Hospital, Southampton, UK
| | - Avan A Sayer
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton General Hospital, Southampton, UK NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton General Hospital, Southampton, UK
| | - Elaine M Dennison
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton General Hospital, Southampton, UK Victoria University, Wellington, New Zealand
| | - Cyrus Cooper
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton General Hospital, Southampton, UK NIHR Southampton Biomedical Research Centre, University of Southampton and University Hospital Southampton NHS Foundation Trust, Southampton General Hospital, Southampton, UK
| | - Mona Bafadhel
- Respiratory Medicine Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Bethan Barker
- Institute for Lung Health, Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK National Institute for Health Research Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Chris Brightling
- Institute for Lung Health, Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK National Institute for Health Research Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Charlotte E Bolton
- Nottingham Respiratory Research Unit, University of Nottingham, City Hospital Campus, Nottingham, UK
| | - Michelle E John
- Nottingham Respiratory Research Unit, University of Nottingham, City Hospital Campus, Nottingham, UK
| | - Stuart G Parker
- Institute for Ageing and Health, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne, UK
| | - Miriam F Moffat
- Department of Molecular Genetics and Genomics, National Heart and Lung Institute, Imperial College London, London, UK
| | - Andrew J Wardlaw
- Institute for Lung Health, Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK National Institute for Health Research Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Martin J Connolly
- Freemasons' Department of Geriatric Medicine, University of Auckland, New Zealand
| | - David J Porteous
- Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Blair H Smith
- Division of Population Health Sciences, University of Dundee, Dundee, UK
| | - Sandosh Padmanabhan
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow, UK
| | - Lynne Hocking
- Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Kathleen E Stirrups
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK Department of Haematology, University of Cambridge, Cambridge, UK
| | - Panos Deloukas
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - David P Strachan
- Population Health Research Institute, St George's, University of London, London, UK
| | - Ian P Hall
- Division of Respiratory Medicine, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| | - Martin D Tobin
- Department of Health Sciences, University of Leicester, Leicester, UK National Institute for Health Research Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, UK
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179
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Xie C, Chen X, Qiu F, Zhang L, Wu D, Chen J, Yang L, Lu J. The role of WWOX polymorphisms on COPD susceptibility and pulmonary function traits in Chinese: a case-control study and family-based analysis. Sci Rep 2016; 6:21716. [PMID: 26902998 PMCID: PMC4763216 DOI: 10.1038/srep21716] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 01/29/2016] [Indexed: 01/21/2023] Open
Abstract
Single nucleotide polymorphisms (SNPs) in the WW domain containing oxidoreductase (WWOX) gene were recently identified to be quantitative trait loci for lung function and thus likely to be susceptible biomarkers for COPD. However, the associations between WWOX SNPs and COPD risk are still unclear. Here, by conducting a two-center case-control study including 1511 COPD cases and 1677 controls and a family-based analysis comprising 95 nuclear pedigrees, we tested the associations between five SNPs that are rs10220974C >T, rs3764340C >G, rs12918952G >A, rs383362G >T, rs12828G >A of WWOX and COPD risk as well as the hereditary inclination of these loci among COPD families. We found that the SNP rs383362G >T was significantly associated with an increased risk of COPD in a T allele-number dependent-manner (OR = 1.30, 95%CI = 1.11 - 1.52). The T allele was more prone to over transmit to sick children and sibs than the G allele (Z = 2.900, P = 0.004). Moreover, the forced expiratory volume in one second/forced vital capacity (FEV1/FVC), FEV1/predicted-FEV1 and annual FEV1 also significantly decreased in the rs383362T carriers compared to the rs383362GG carriers. For other SNPs, no significant association was observed for COPD and pulmonary function. Taken together, our data demonstrated that the SNP rs383362G >T of WWOX plays a role in COPD inheritance.
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Affiliation(s)
- Chenli Xie
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, 195 Dongfengxi Road, Guangzhou 510182, China.,Department of respiratory medicine, The Fifth People's Hospital of Dongguan City, Dongguan 523900, China
| | - Xiaoliang Chen
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, 195 Dongfengxi Road, Guangzhou 510182, China.,Shenzhen Guangming district center for disease control and prevention Shenzhen 518106, China
| | - Fuman Qiu
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, 195 Dongfengxi Road, Guangzhou 510182, China
| | - Lisha Zhang
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, 195 Dongfengxi Road, Guangzhou 510182, China
| | - Di Wu
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, 195 Dongfengxi Road, Guangzhou 510182, China
| | - Jiansong Chen
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, 195 Dongfengxi Road, Guangzhou 510182, China
| | - Lei Yang
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, 195 Dongfengxi Road, Guangzhou 510182, China
| | - Jiachun Lu
- The State Key Lab of Respiratory Disease, The Institute for Chemical Carcinogenesis, Collaborative Innovation Center for Environmental Toxicity, Guangzhou Medical University, 195 Dongfengxi Road, Guangzhou 510182, China
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180
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Rubattu S, Di Castro S, Schulz H, Geurts AM, Cotugno M, Bianchi F, Maatz H, Hummel O, Falak S, Stanzione R, Marchitti S, Scarpino S, Giusti B, Kura A, Gensini GF, Peyvandi F, Mannucci PM, Rasura M, Sciarretta S, Dwinell MR, Hubner N, Volpe M. Ndufc2 Gene Inhibition Is Associated With Mitochondrial Dysfunction and Increased Stroke Susceptibility in an Animal Model of Complex Human Disease. J Am Heart Assoc 2016; 5:e002701. [PMID: 26888427 PMCID: PMC4802485 DOI: 10.1161/jaha.115.002701] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 12/23/2015] [Indexed: 12/30/2022]
Abstract
BACKGROUND The genetic basis of stroke susceptibility remains to be elucidated. STR1 quantitative trait locus (STR1/QTL) was identified on rat chromosome 1 of stroke-prone spontaneously hypertensive rat (SHRSP) upon Japanese-style stroke-permissive diet (JD), and it contributes to 20% of the stroke phenotype variance. METHODS AND RESULTS Nine hundred eighty-six probe sets mapping on STR1 were selected from the Rat RAE230A array and screened through a microarray differential expression analysis in brains of SHRSP and stroke-resistant SHR (SHRSR) fed with either regular diet or JD. The gene encoding Ndufc2 (NADH dehydrogenase [ubiquinone] 1 subunit), mapping 8 Mb apart from STR1/QTL Lod score peak, was found significantly down-regulated under JD in SHRSP compared to SHRSR. Ndufc2 disruption altered complex I assembly and activity, reduced mitochondrial membrane potential and ATP levels, and increased reactive oxygen species production and inflammation both in vitro and in vivo. SHRSR carrying heterozygous Ndufc2 deletion showed renal abnormalities and stroke occurrence under JD, similarly to SHRSP. In humans, T allele variant at NDUFC2/rs11237379 was associated with significant reduction in gene expression and with increased occurrence of early-onset ischemic stroke by recessive mode of transmission (odds ratio [OR], 1.39; CI, 1.07-1.80; P=0.012). Subjects carrying TT/rs11237379 and A allele variant at NDUFC2/rs641836 had further increased risk of stroke (OR=1.56; CI, 1.14-2.13; P=0.006). CONCLUSIONS A significant reduction of Ndufc2 expression causes complex I dysfunction and contributes to stroke susceptibility in SHRSP. Moreover, our current evidence may suggest that Ndufc2 can contribute to an increased occurrence of early-onset ischemic stroke in humans.
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Affiliation(s)
- Speranza Rubattu
- IRCCS Neuromed, Pozzilli (Isernia), Italy Department of Clinical and Molecular Medicine, School of Medicine and Psychology, Sapienza University of Rome, Ospedale S. Andrea, Rome, Italy
| | | | | | - Aron M Geurts
- Department of Physiology and Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI
| | | | | | | | | | | | | | | | - Stefania Scarpino
- Department of Cytology and Histology, School of Medicine and Psychology, University Sapienza of Rome, Ospedale S. Andrea, Rome, Itlay
| | - Betti Giusti
- Department of Experimental and Clinical Medicine, University of Florence, Italy Atherothrombotic Disease Center, AOU Careggi, Florence, Italy
| | - Ada Kura
- Department of Experimental and Clinical Medicine, University of Florence, Italy Atherothrombotic Disease Center, AOU Careggi, Florence, Italy
| | - Gian Franco Gensini
- Department of Experimental and Clinical Medicine, University of Florence, Italy Department of Cardiothoracovascular Medicine, AOU Careggi, Florence, Italy Don Carlo Gnocchi Foundation, Florence, Italy
| | - Flora Peyvandi
- IRCCS Ca' Granda Maggiore Policlinico Hospital Foundation, Milan, Italy
| | | | - Maurizia Rasura
- Stroke Unit, School of Medicine and Psychology, Sapienza University of Rome, Ospedale S. Andrea, Rome, Italy
| | - Sebastiano Sciarretta
- IRCCS Neuromed, Pozzilli (Isernia), Italy Department of Medical-Surgical Sciences and Biotechnologies, Sapienza University of Rome, Latina, Italy
| | - Melinda R Dwinell
- Department of Physiology and Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI
| | | | - Massimo Volpe
- IRCCS Neuromed, Pozzilli (Isernia), Italy Department of Clinical and Molecular Medicine, School of Medicine and Psychology, Sapienza University of Rome, Ospedale S. Andrea, Rome, Italy
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181
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Saferali A, Obeidat M, Bérubé JC, Lamontagne M, Bossé Y, Laviolette M, Hao K, Nickle DC, Timens W, Sin DD, Postma DS, Strug LJ, Gallins PJ, Paré PD, Bingle CD, Sandford AJ. Polymorphisms associated with expression of BPIFA1/BPIFB1 and lung disease severity in cystic fibrosis. Am J Respir Cell Mol Biol 2016; 53:607-14. [PMID: 25574903 DOI: 10.1165/rcmb.2014-0182oc] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
BPI fold containing family A, member 1 (BPIFA1) and BPIFB1 are putative innate immune molecules expressed in the upper airways. Because of their hypothesized roles in airway defense, these molecules may contribute to lung disease severity in cystic fibrosis (CF). We interrogated BPIFA1/BPIFB1 single-nucleotide polymorphisms in data from an association study of CF modifier genes and found an association of the G allele of rs1078761 with increased lung disease severity (P = 2.71 × 10(-4)). We hypothesized that the G allele of rs1078761 is associated with decreased expression of BPIFA1 and/or BPIFB1. Genome-wide lung gene expression and genotyping data from 1,111 individuals with lung disease, including 51 patients with CF, were tested for associations between genotype and BPIFA1 and BPIFB1 gene expression levels. Findings were validated by quantitative PCR in a subset of 77 individuals. Western blotting was used to measure BPIFA1 and BPIFB1 protein levels in 93 lung and 101 saliva samples. The G allele of rs1078761 was significantly associated with decreased mRNA levels of BPIFA1 (P = 4.08 × 10(-15)) and BPIFB1 (P = 0.0314). These findings were confirmed with quantitative PCR and Western blotting. We conclude that the G allele of rs1078761 may be detrimental to lung function in CF owing to decreased levels of BPIFA1 and BPIFB1.
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Affiliation(s)
- Aabida Saferali
- 1 Centre for Heart Lung Innovation, UBC and St. Paul's Hospital, Vancouver, British Columbia
| | - Ma'en Obeidat
- 1 Centre for Heart Lung Innovation, UBC and St. Paul's Hospital, Vancouver, British Columbia
| | | | - Maxime Lamontagne
- 2 Institut Universitaire de Cardiologie et de Pneumologie de Québec and
| | - Yohan Bossé
- 2 Institut Universitaire de Cardiologie et de Pneumologie de Québec and.,3 Department of Molecular Medicine, Laval University, Québec, Quebec
| | - Michel Laviolette
- 2 Institut Universitaire de Cardiologie et de Pneumologie de Québec and
| | - Ke Hao
- 4 Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - David C Nickle
- 5 Merck Research Laboratories, Boston, Massachusetts.,6 Merck, Rahway, New Jersey.,7 Genetics, Rosetta Inpharmatics, Merck, Seattle, Washington
| | - Wim Timens
- Departments of 8 Pathology and Medical Biology and
| | - Don D Sin
- 1 Centre for Heart Lung Innovation, UBC and St. Paul's Hospital, Vancouver, British Columbia
| | - Dirkje S Postma
- 9 Pulmonary Medicine and Tuberculosis, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Lisa J Strug
- 10 Program in Genetics and Genome Biology, The Hospital For Sick Children, and Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Paul J Gallins
- 11 Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; and
| | - Peter D Paré
- 1 Centre for Heart Lung Innovation, UBC and St. Paul's Hospital, Vancouver, British Columbia
| | - Colin D Bingle
- 12 Academic Unit of Respiratory Medicine, Department of Infection and Immunity, University of Sheffield, Sheffield, United Kingdom
| | - Andrew J Sandford
- 1 Centre for Heart Lung Innovation, UBC and St. Paul's Hospital, Vancouver, British Columbia
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182
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Minelli C, Dean CH, Hind M, Alves AC, Amaral AFS, Siroux V, Huikari V, Soler Artigas M, Evans DM, Loth DW, Bossé Y, Postma DS, Sin D, Thompson J, Demenais F, Henderson J, Bouzigon E, Jarvis D, Järvelin MR, Burney P. Association of Forced Vital Capacity with the Developmental Gene NCOR2. PLoS One 2016; 11:e0147388. [PMID: 26836265 PMCID: PMC4737618 DOI: 10.1371/journal.pone.0147388] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 01/04/2016] [Indexed: 12/31/2022] Open
Abstract
Background Forced Vital Capacity (FVC) is an important predictor of all-cause mortality in the absence of chronic respiratory conditions. Epidemiological evidence highlights the role of early life factors on adult FVC, pointing to environmental exposures and genes affecting lung development as risk factors for low FVC later in life. Although highly heritable, a small number of genes have been found associated with FVC, and we aimed at identifying further genetic variants by focusing on lung development genes. Methods Per-allele effects of 24,728 SNPs in 403 genes involved in lung development were tested in 7,749 adults from three studies (NFBC1966, ECRHS, EGEA). The most significant SNP for the top 25 genes was followed-up in 46,103 adults (CHARGE and SpiroMeta consortia) and 5,062 children (ALSPAC). Associations were considered replicated if the replication p-value survived Bonferroni correction (p<0.002; 0.05/25), with a nominal p-value considered as suggestive evidence. For SNPs with evidence of replication, effects on the expression levels of nearby genes in lung tissue were tested in 1,111 lung samples (Lung eQTL consortium), with further functional investigation performed using public epigenomic profiling data (ENCODE). Results NCOR2-rs12708369 showed strong replication in children (p = 0.0002), with replication unavailable in adults due to low imputation quality. This intronic variant is in a strong transcriptional enhancer element in lung fibroblasts, but its eQTL effects could not be tested due to low imputation quality in the eQTL dataset. SERPINE2-rs6754561 replicated at nominal level in both adults (p = 0.036) and children (p = 0.045), while WNT16-rs2707469 replicated at nominal level only in adults (p = 0.026). The eQTL analyses showed association of WNT16-rs2707469 with expression levels of the nearby gene CPED1. We found no statistically significant eQTL effects for SERPINE2-rs6754561. Conclusions We have identified a new gene, NCOR2, in the retinoic acid signalling pathway pointing to a role of vitamin A metabolism in the regulation of FVC. Our findings also support SERPINE2, a COPD gene with weak previous evidence of association with FVC, and suggest WNT16 as a further promising candidate.
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Affiliation(s)
- Cosetta Minelli
- Respiratory Epidemiology, Occupational Medicine and Public Health, National Heart and Lung Institute, Imperial College, London, United Kingdom
- * E-mail:
| | - Charlotte H. Dean
- Leukocyte Biology, National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Mammalian Genetics Unit, MRC Harwell, Oxon, United Kingdom
| | - Matthew Hind
- Respiratory Department, Royal Brompton and Harefield NHS Foundation Trust, London, United Kingdom
| | - Alexessander Couto Alves
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
| | - André F. S. Amaral
- Respiratory Epidemiology, Occupational Medicine and Public Health, National Heart and Lung Institute, Imperial College, London, United Kingdom
- MRC-PHE Centre for Environment & Health, London, United Kingdom
| | - Valerie Siroux
- Univ. Grenoble Alpes, IAB, Team of Environmental Epidemiology applied to Reproduction and Respiratory Health, F-38000, Grenoble, France
- INSERM, IAB, Team of Environmental Epidemiology applied to Reproduction and Respiratory Health, F-38000, Grenoble, France
- CHU de Grenoble, IAB, Team of Environmental Epidemiology applied to Reproduction and Respiratory Health, F-38000, Grenoble, France
| | | | - María Soler Artigas
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | - David M. Evans
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Australia
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - Daan W. Loth
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec, Department of Molecular Medicine, Laval University, Québec, Canada
| | - Dirkje S. Postma
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Don Sin
- The University of British Columbia Center for Heart Lung Innovation, St-Paul’s Hospital, Vancouver, Canada
| | - John Thompson
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | - Florence Demenais
- INSERM, UMRS-946, Genetic Variation of Human Diseases Unit, Paris, France
- Univ. Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d’Hématologie, F-75007, Paris, France
| | - John Henderson
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - SpiroMeta consortium
- SpiroMeta consortium, Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | - CHARGE consortium
- CHARGE consortium, Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - Emmanuelle Bouzigon
- INSERM, UMRS-946, Genetic Variation of Human Diseases Unit, Paris, France
- Univ. Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d’Hématologie, F-75007, Paris, France
| | - Deborah Jarvis
- Respiratory Epidemiology, Occupational Medicine and Public Health, National Heart and Lung Institute, Imperial College, London, United Kingdom
- MRC-PHE Centre for Environment & Health, London, United Kingdom
| | - Marjo-Riitta Järvelin
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
- MRC-PHE Centre for Environment & Health, London, United Kingdom
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Center for Life Course Epidemiology, Faculty of Medicine, P.O. Box 5000, FI-90014 University of Oulu, Oulu, Finland
- Unit of Primary Care, Oulu University Hospital, Kajaanintie 50, P.O. Box 20, FI-90220, Oulu, 90029 OYS, Finland
| | - Peter Burney
- Respiratory Epidemiology, Occupational Medicine and Public Health, National Heart and Lung Institute, Imperial College, London, United Kingdom
- MRC-PHE Centre for Environment & Health, London, United Kingdom
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183
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Pouladi N, Bime C, Garcia JGN, Lussier YA. Complex genetics of pulmonary diseases: lessons from genome-wide association studies and next-generation sequencing. Transl Res 2016; 168:22-39. [PMID: 26006746 PMCID: PMC4658294 DOI: 10.1016/j.trsl.2015.04.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 04/27/2015] [Accepted: 04/29/2015] [Indexed: 12/16/2022]
Abstract
The advent of high-throughput technologies has provided exceptional assistance for lung scientists to discover novel genetic variants underlying the development and progression of complex lung diseases. However, the discovered variants thus far do not explain much of the estimated heritability of complex lung diseases. Here, we review the literature of successfully used genome-wide association studies (GWASs) and identified the polymorphisms that reproducibly underpin the susceptibility to various noncancerous complex lung diseases or affect therapeutic responses. We also discuss the inherent limitations of GWAS approaches and how the use of next-generation sequencing technologies has furthered our understanding about the genetic determinants of these diseases. Next, we describe the contribution of the metagenomics to understand the interactions of the airways microbiome with lung diseases. We then highlight the urgent need for new integrative genomics-phenomics methods to more effectively interrogate and understand multiple downstream "omics" (eg, chromatin modification patterns). Finally, we address the scarcity of genetic studies addressing under-represented populations such as African Americans and Hispanics.
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Affiliation(s)
- Nima Pouladi
- Department of Medicine, University of Arizona, Tucson, Ariz; Center for Biomedical Informatics and Biostatistics, University of Arizona, Tucson, Ariz; BIO5 Institute, University of Arizona, Tucson, Ariz
| | - Christian Bime
- University of Arizona Health Sciences Center, University of Arizona, Tucson, Ariz; Arizona Respiratory Center, University of Arizona, Tucson, Ariz
| | - Joe G N Garcia
- University of Arizona Health Sciences Center, University of Arizona, Tucson, Ariz; Arizona Respiratory Center, University of Arizona, Tucson, Ariz
| | - Yves A Lussier
- Department of Medicine, University of Arizona, Tucson, Ariz; Center for Biomedical Informatics and Biostatistics, University of Arizona, Tucson, Ariz; BIO5 Institute, University of Arizona, Tucson, Ariz; University of Arizona Health Sciences Center, University of Arizona, Tucson, Ariz; Institute for Genomics and Systems Biology, Argonne National Laboratory and University of Chicago, Chicago, Ill.
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184
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Yamada H, Masuko H, Yatagai Y, Sakamoto T, Kaneko Y, Iijima H, Naito T, Noguchi E, Konno S, Nishimura M, Hirota T, Tamari M, Hizawa N. Role of Lung Function Genes in the Development of Asthma. PLoS One 2016; 11:e0145832. [PMID: 26752288 PMCID: PMC4709100 DOI: 10.1371/journal.pone.0145832] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Accepted: 12/09/2015] [Indexed: 12/02/2022] Open
Abstract
Although our previous GWAS failed to identify SNPs associated with pulmonary function at the level of genomewide significance, it did show that the heritability for FEV1/FVC was 41.6% in a Japanese population, suggesting that the heritability of pulmonary function traits can be explained by the additive effects of multiple common SNPs. In addition, our previous study indicated that pulmonary function genes identified in previous GWASs in non-Japanese populations accounted for 4.3% to 12.0% of the entire estimated heritability of FEV1/FVC in a Japanese population. Therefore, given that many loci with individual weak effects may contribute to asthma risk, in this study, we created a quantitative score of genetic load based on 16 SNPs implicated in lower lung function in both Japanese and non-Japanese populations. This genetic risk score (GRS) for lower FEV1/FVC was consistently associated with the onset of asthma (P = 9.6 × 10(-4)) in 2 independent Japanese populations as well as with the onset of COPD (P = 0.042). Clustering of asthma patients based on GRS levels indicated that an increased GRS may be responsible for the development of a particular phenotype of asthma characterized by early onset, atopy, and severer airflow obstruction.
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Affiliation(s)
- Hideyasu Yamada
- Department of Pulmonology, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hironori Masuko
- Department of Pulmonology, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yohei Yatagai
- Department of Pulmonology, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Tohru Sakamoto
- Department of Pulmonology, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yoshiko Kaneko
- Department of Pulmonology, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | | | | | - Emiko Noguchi
- Department of Medical Genetics, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Satoshi Konno
- Laboratory for Respiratory Diseases, Center for Genomic Medicine, Institute of Physical and Chemical Research, Tsurumi, Kanagawa, Japan
| | - Masaharu Nishimura
- Laboratory for Respiratory Diseases, Center for Genomic Medicine, Institute of Physical and Chemical Research, Tsurumi, Kanagawa, Japan
| | - Tomomitsu Hirota
- First Department of Medicine, School of Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Mayumi Tamari
- First Department of Medicine, School of Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Nobuyuki Hizawa
- Department of Pulmonology, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
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185
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Translating Lung Function Genome-Wide Association Study (GWAS) Findings. ADVANCES IN GENETICS 2016; 93:57-145. [DOI: 10.1016/bs.adgen.2015.12.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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186
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Artigas MS, Wain LV, Miller S, Kheirallah AK, Huffman JE, Ntalla I, Shrine N, Obeidat M, Trochet H, McArdle WL, Alves AC, Hui J, Zhao JH, Joshi PK, Teumer A, Albrecht E, Imboden M, Rawal R, Lopez LM, Marten J, Enroth S, Surakka I, Polasek O, Lyytikäinen LP, Granell R, Hysi PG, Flexeder C, Mahajan A, Beilby J, Bossé Y, Brandsma CA, Campbell H, Gieger C, Gläser S, González JR, Grallert H, Hammond CJ, Harris SE, Hartikainen AL, Heliövaara M, Henderson J, Hocking L, Horikoshi M, Hutri-Kähönen N, Ingelsson E, Johansson Å, Kemp JP, Kolcic I, Kumar A, Lind L, Melén E, Musk AW, Navarro P, Nickle DC, Padmanabhan S, Raitakari OT, Ried JS, Ripatti S, Schulz H, Scott RA, Sin DD, Starr JM, Viñuela A, Völzke H, Wild SH, Wright AF, Zemunik T, Jarvis DL, Spector TD, Evans DM, Lehtimäki T, Vitart V, Kähönen M, Gyllensten U, Rudan I, Deary IJ, Karrasch S, Probst-Hensch NM, Heinrich J, Stubbe B, Wilson JF, Wareham NJ, James AL, Morris AP, Jarvelin MR, Hayward C, Sayers I, Strachan DP, Hall IP, Tobin MD. Sixteen new lung function signals identified through 1000 Genomes Project reference panel imputation. Nat Commun 2015; 6:8658. [PMID: 26635082 PMCID: PMC4686825 DOI: 10.1038/ncomms9658] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 09/17/2015] [Indexed: 01/11/2023] Open
Abstract
Lung function measures are used in the diagnosis of chronic obstructive pulmonary disease. In 38,199 European ancestry individuals, we studied genome-wide association of forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC) and FEV1/FVC with 1000 Genomes Project (phase 1)-imputed genotypes and followed up top associations in 54,550 Europeans. We identify 14 novel loci (P<5 × 10(-8)) in or near ENSA, RNU5F-1, KCNS3, AK097794, ASTN2, LHX3, CCDC91, TBX3, TRIP11, RIN3, TEKT5, LTBP4, MN1 and AP1S2, and two novel signals at known loci NPNT and GPR126, providing a basis for new understanding of the genetic determinants of these traits and pulmonary diseases in which they are altered.
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Affiliation(s)
- María Soler Artigas
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester LE1 7RH, UK
| | - Louise V. Wain
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester LE1 7RH, UK
| | - Suzanne Miller
- Division of Respiratory Medicine, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2RD, UK
| | - Abdul Kader Kheirallah
- Division of Respiratory Medicine, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2RD, UK
| | - Jennifer E. Huffman
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH8 9AD, UK
| | - Ioanna Ntalla
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester LE1 7RH, UK
| | - Nick Shrine
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester LE1 7RH, UK
| | - Ma'en Obeidat
- University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, British Columbia, Canada V6Z 1Y6
| | - Holly Trochet
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH8 9AD, UK
- Generation Scotland, A Collaboration between the University Medical Schools and NHS, Aberdeen, Dundee, Edinburgh, Glasgow EH4 2XU, UK
| | - Wendy L. McArdle
- School of Social and Community Medicine, University of Bristol, Bristol BS8 1TH, UK
| | - Alexessander Couto Alves
- Department of Epidemiology and Biostatistics, MRC -PHE Centre for Environment & Health, School of Public Health, Imperial College London, London SW7 2AZ, UK
| | - Jennie Hui
- Busselton Population Medical Research Institute, Busselton, Western Australia 6280, Australia
- PathWest Laboratory Medicine WA, Sir Charles Gairdner Hospital, Western Australia 6009, Australia
- School of Population Health, The University of Western Australia, Western Australia 6009, Australia
- School of Pathology and Laboratory Medicine, The University of Western Australia, Western Australia 6009, Australia
| | - Jing Hua Zhao
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge CB2 0SL, UK
| | - Peter K. Joshi
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AD, Scotland, UK
| | - Alexander Teumer
- University Medicine Greifswald, Community Medicine, SHIP—Clinical Epidemiological Research, Greifswald 17489, Germany
- Department for Genetics and Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald 17489, Germany
| | - Eva Albrecht
- Institute of Genetic Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg D-85764, Germany
| | - Medea Imboden
- Swiss Tropical and Public Health Institute, Basel 4051, Switzerland
- University of Basel, Basel 4001, Switzerland
| | - Rajesh Rawal
- Institute of Genetic Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg D-85764, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg D-85764, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg D-85764, Germany
| | - Lorna M. Lopez
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh EH8 9AD, UK
- Department of Psychology, University of Edinburgh, Edinburgh EH8 9AD, UK
| | - Jonathan Marten
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH8 9AD, UK
| | - Stefan Enroth
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, Uppsala 751 23, Sweden
| | - Ida Surakka
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki FI-00014, Finland
- The National Institute for Health and Welfare (THL), Helsinki FI-00271, Finland
| | - Ozren Polasek
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AD, Scotland, UK
- Department of Public Health, Faculty of Medicine, University of Split, Split 21000, Croatia
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere FI-33101, Finland
- Department of Clinical Chemistry, University of Tampere School of Medicine, Tampere FI-33520, Finland
| | - Raquel Granell
- School of Social and Community Medicine, University of Bristol, Bristol BS8 1TH, UK
| | - Pirro G. Hysi
- KCL Department of Twins Research and Genetic Epidemiology, King's College London, London WC2R 2LS, UK
| | - Claudia Flexeder
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg D-85764, Germany
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - John Beilby
- Busselton Population Medical Research Institute, Busselton, Western Australia 6280, Australia
- PathWest Laboratory Medicine WA, Sir Charles Gairdner Hospital, Western Australia 6009, Australia
- School of Pathology and Laboratory Medicine, The University of Western Australia, Western Australia 6009, Australia
| | - Yohan Bossé
- Department of Molecular Medicine, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec, Canada G1V 0A6
| | - Corry-Anke Brandsma
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen 9700, The Netherlands
| | - Harry Campbell
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AD, Scotland, UK
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg D-85764, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg D-85764, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg D-85764, Germany
| | - Sven Gläser
- Department of Internal Medicine B, Pneumology, Cardiology, Intensive Care, Weaning, Field of Research: Pneumological Epidemiology, University Medicine Greifswald, Greifswald 17489, Germany
| | - Juan R. González
- Centre for Research in Environmental Epidemiology (CREAL), Barcelona E-08003, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid 28029, Spain
- Pompeu Fabra University (UPF), Barcelona 08002, Catalonia, Spain
| | - Harald Grallert
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg D-85764, Germany
| | - Chris J. Hammond
- KCL Department of Twins Research and Genetic Epidemiology, King's College London, London WC2R 2LS, UK
| | - Sarah E. Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh EH8 9AD, UK
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh EH8 9AD, UK
| | - Anna-Liisa Hartikainen
- Department of Obstetrics and Gynecology of Oulu University Hospital ,MRC of Oulu University, Oulu 90220, Finland
| | - Markku Heliövaara
- The National Institute for Health and Welfare (THL), Helsinki FI-00271, Finland
| | - John Henderson
- School of Social and Community Medicine, University of Bristol, Bristol BS8 1TH, UK
| | - Lynne Hocking
- Generation Scotland, A Collaboration between the University Medical Schools and NHS, Aberdeen, Dundee, Edinburgh, Glasgow EH4 2XU, UK
- Division of Applied Health Sciences, University of Aberdeen, Aberdeen, Scotland AB24 3FX, UK
| | - Momoko Horikoshi
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford OX1 2JD, UK
| | - Nina Hutri-Kähönen
- Department of Pediatrics, Tampere University Hospital, Tampere 33521, Finland
- Department of Pediatrics, University of Tampere School of Medicine, Tampere FI-33520, Finland
| | - Erik Ingelsson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala 751 23, Sweden
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Åsa Johansson
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, Uppsala 751 23, Sweden
- Uppsala Clinical Research Centre, Uppsala University, Uppsala 751 23, Sweden
| | - John P. Kemp
- School of Social and Community Medicine, University of Bristol, Bristol BS8 1TH, UK
- Diamantina Institute, Translational Research Institute, University of Queensland, Brisbane, Queensland QLD 4072, Australia
- MRC Integrative Epidemiology Unit, Bristol BS8 1TH, UK
| | - Ivana Kolcic
- Department of Public Health, Faculty of Medicine, University of Split, Split 21000, Croatia
| | - Ashish Kumar
- Swiss Tropical and Public Health Institute, Basel 4051, Switzerland
- University of Basel, Basel 4001, Switzerland
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm SE-171 7, Sweden
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Uppsala 751 23, Sweden
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet and Sachs' Children's Hospital, Stockholm SE-171 7, Sweden
| | - Arthur W. Musk
- Busselton Population Medical Research Institute, Busselton, Western Australia 6280, Australia
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Western Australia 6009, Australia
- School of Medicine and Pharmacology, The University of Western Australia, Western Australia 6009, Australia
| | - Pau Navarro
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH8 9AD, UK
| | - David C. Nickle
- Genetics and Pharmacogenomics, Merck Research Labs, Boston, Massachusetts 02115, USA
| | - Sandosh Padmanabhan
- Generation Scotland, A Collaboration between the University Medical Schools and NHS, Aberdeen, Dundee, Edinburgh, Glasgow EH4 2XU, UK
- Division of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow G12 8TA, Scotland, UK
| | - Olli T. Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku 20520, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku 20014, Finland
| | - Janina S. Ried
- Institute of Genetic Epidemiology, Helmholtz Zentrum München German Research Center for Environmental Health, Neuherberg D-85764, Germany
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki FI-00014, Finland
- Department of Public Health, University of Helsinki, Helsinki FI-00014, Finland
- Department of Human Genomics, Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Holger Schulz
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg D-85764, Germany
- Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research, Munich 85764, Germany
| | - Robert A. Scott
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge CB2 0SL, UK
| | - Don D. Sin
- University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, British Columbia, Canada V6Z 1Y6
- Respiratory Division, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - John M. Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh EH8 9AD, UK
- Alzheimer Scotland Research Centre, University of Edinburgh, Edinburgh EH8 9AD, UK
| | - Ana Viñuela
- KCL Department of Twins Research and Genetic Epidemiology, King's College London, London WC2R 2LS, UK
| | - Henry Völzke
- University Medicine Greifswald, Community Medicine, SHIP—Clinical Epidemiological Research, Greifswald 17489, Germany
| | - Sarah H. Wild
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AD, Scotland, UK
| | - Alan F. Wright
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH8 9AD, UK
| | - Tatijana Zemunik
- Department of Medical Biology, Faculty of Medicine, University of Split, Split 21000, Croatia
| | - Deborah L. Jarvis
- Respiratory Epidemiology and Public Health, Imperial College London, London SW7 2AZ, UK
- MRC Health Protection Agency (HPA) Centre for Environment and Health, Imperial College London, London SW7 2AZ, UK
| | - Tim D. Spector
- KCL Department of Twins Research and Genetic Epidemiology, King's College London, London WC2R 2LS, UK
| | - David M. Evans
- School of Social and Community Medicine, University of Bristol, Bristol BS8 1TH, UK
- Diamantina Institute, Translational Research Institute, University of Queensland, Brisbane, Queensland QLD 4072, Australia
- MRC Integrative Epidemiology Unit, Bristol BS8 1TH, UK
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere FI-33101, Finland
- Department of Clinical Chemistry, University of Tampere School of Medicine, Tampere FI-33520, Finland
| | - Veronique Vitart
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH8 9AD, UK
| | - Mika Kähönen
- Department of Clinical Physiology, University of Tampere and Tampere University Hospital, Tampere 33521, Finland
| | - Ulf Gyllensten
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, Uppsala 751 23, Sweden
| | - Igor Rudan
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AD, Scotland, UK
- Centre for Population Health Sciences, Medical School, University of Edinburgh, Edinburgh EH8 9AD, Scotland, UK
| | - Ian J. Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh EH8 9AD, UK
- Department of Psychology, University of Edinburgh, Edinburgh EH8 9AD, UK
| | - Stefan Karrasch
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg D-85764, Germany
- Institute of General Practice, University Hospital Klinikum rechts der Isar, Technische Universität München, Munich D - 81675, Germany
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Ludwig-Maximilians-Universität, Munich 80539, Germany
| | - Nicole M. Probst-Hensch
- Swiss Tropical and Public Health Institute, Basel 4051, Switzerland
- University of Basel, Basel 4001, Switzerland
| | - Joachim Heinrich
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg D-85764, Germany
- Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research, Munich 85764, Germany
- University Hospital Munich, Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Ludwig-Maximilian University Munich, Munich 80539, Germany
| | - Beate Stubbe
- Department of Internal Medicine B, Pneumology, Cardiology, Intensive Care, Weaning, Field of Research: Pneumological Epidemiology, University Medicine Greifswald, Greifswald 17489, Germany
| | - James F. Wilson
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland EH8 9AD, UK
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AD, Scotland, UK
| | - Nicholas J. Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge CB2 0SL, UK
| | - Alan L. James
- Busselton Population Medical Research Institute, Busselton, Western Australia 6280, Australia
- School of Medicine and Pharmacology, The University of Western Australia, Western Australia 6009, Australia
- Department of Pulmonary Physiology and Sleep Medicine, Sir Charles Gairdner Hospital, Western Australia 6009, Australia
| | - Andrew P. Morris
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
- Department of Biostatistics, University of Liverpool, Liverpool L69 7ZX, UK
- Estonian Genome Centre, University of Tartu, Tartu 50090, Estonia
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, MRC -PHE Centre for Environment & Health, School of Public Health, Imperial College London, London SW7 2AZ, UK
- Center for Life Course Epidemiology, Faculty of Medicine, P.O.Box 5000, FI-90014 University of Oulu, Oulu FI-01051, Finland
- Biocenter Oulu, P.O.Box 5000, Aapistie 5A, FI-90014 University of Oulu, Oulu FI-01051, Finland
- Unit of Primary Care, Oulu University Hospital, Kajaanintie 50, P.O.Box 20, FI-90220 Oulu, 90029 OYS, Finland
| | - Caroline Hayward
- Generation Scotland, A Collaboration between the University Medical Schools and NHS, Aberdeen, Dundee, Edinburgh, Glasgow EH4 2XU, UK
| | - Ian Sayers
- Division of Respiratory Medicine, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2RD, UK
| | - David P. Strachan
- Population Health Research Institute, St George's, University of London, Cranmer Terrace, London WC1B 5DN, UK
| | - Ian P. Hall
- Division of Respiratory Medicine, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2RD, UK
| | - Martin D. Tobin
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester LE1 7RH, UK
- National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester LE3 9QP, UK
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187
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Lutz SM, Cho MH, Young K, Hersh CP, Castaldi PJ, McDonald ML, Regan E, Mattheisen M, DeMeo DL, Parker M, Foreman M, Make BJ, Jensen RL, Casaburi R, Lomas DA, Bhatt SP, Bakke P, Gulsvik A, Crapo JD, Beaty TH, Laird NM, Lange C, Hokanson JE, Silverman EK. A genome-wide association study identifies risk loci for spirometric measures among smokers of European and African ancestry. BMC Genet 2015; 16:138. [PMID: 26634245 PMCID: PMC4668640 DOI: 10.1186/s12863-015-0299-4] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 11/20/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pulmonary function decline is a major contributor to morbidity and mortality among smokers. Post bronchodilator FEV1 and FEV1/FVC ratio are considered the standard assessment of airflow obstruction. We performed a genome-wide association study (GWAS) in 9919 current and former smokers in the COPDGene study (6659 non-Hispanic Whites [NHW] and 3260 African Americans [AA]) to identify associations with spirometric measures (post-bronchodilator FEV1 and FEV1/FVC). We also conducted meta-analysis of FEV1 and FEV1/FVC GWAS in the COPDGene, ECLIPSE, and GenKOLS cohorts (total n = 13,532). RESULTS Among NHW in the COPDGene cohort, both measures of pulmonary function were significantly associated with SNPs at the 15q25 locus [containing CHRNA3/5, AGPHD1, IREB2, CHRNB4] (lowest p-value = 2.17 × 10(-11)), and FEV1/FVC was associated with a genomic region on chromosome 4 [upstream of HHIP] (lowest p-value = 5.94 × 10(-10)); both regions have been previously associated with COPD. For the meta-analysis, in addition to confirming associations to the regions near CHRNA3/5 and HHIP, genome-wide significant associations were identified for FEV1 on chromosome 1 [TGFB2] (p-value = 8.99 × 10(-9)), 9 [DBH] (p-value = 9.69 × 10(-9)) and 19 [CYP2A6/7] (p-value = 3.49 × 10(-8)) and for FEV1/FVC on chromosome 1 [TGFB2] (p-value = 8.99 × 10(-9)), 4 [FAM13A] (p-value = 3.88 × 10(-12)), 11 [MMP3/12] (p-value = 3.29 × 10(-10)) and 14 [RIN3] (p-value = 5.64 × 10(-9)). CONCLUSIONS In a large genome-wide association study of lung function in smokers, we found genome-wide significant associations at several previously described loci with lung function or COPD. We additionally identified a novel genome-wide significant locus with FEV1 on chromosome 9 [DBH] in a meta-analysis of three study populations.
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Affiliation(s)
- Sharon M Lutz
- Department of Biostatistics, University of Colorado Anschutz Medical Campus, 13001 E. 17th Place, B119 Bldg. 500, W3128, Aurora, CO, 80045, USA.
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Kendra Young
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Peter J Castaldi
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Merry-Lynn McDonald
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Elizabeth Regan
- Department of Medicine, National Jewish Health, Denver, CO, USA.
| | - Manuel Mattheisen
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Margaret Parker
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | | | - Barry J Make
- Department of Medicine, National Jewish Health, Denver, CO, USA.
| | - Robert L Jensen
- Division of Pulmonary, Allergy & Critical Care Medicine, LDS Hospital, Salt Lake City, UT, USA.
| | - Richard Casaburi
- Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA.
| | - David A Lomas
- Wolfson Institute for Biomedical Research, University College London, London, UK.
| | - Surya P Bhatt
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Per Bakke
- Department of Clinical Science, University of Bergen, Bergen, Norway.
| | - Amund Gulsvik
- Department of Clinical Science, University of Bergen, Bergen, Norway.
| | - James D Crapo
- Department of Medicine, National Jewish Health, Denver, CO, USA.
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Nan M Laird
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA.
| | - Christoph Lange
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA.
| | - John E Hokanson
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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188
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Barnes PJ, Burney PGJ, Silverman EK, Celli BR, Vestbo J, Wedzicha JA, Wouters EFM. Chronic obstructive pulmonary disease. Nat Rev Dis Primers 2015; 1:15076. [PMID: 27189863 DOI: 10.1038/nrdp.2015.76] [Citation(s) in RCA: 391] [Impact Index Per Article: 43.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is a common disease with high global morbidity and mortality. COPD is characterized by poorly reversible airway obstruction, which is confirmed by spirometry, and includes obstruction of the small airways (chronic obstructive bronchiolitis) and emphysema, which lead to air trapping and shortness of breath in response to physical exertion. The most common risk factor for the development of COPD is cigarette smoking, but other environmental factors, such as exposure to indoor air pollutants - especially in developing countries - might influence COPD risk. Not all smokers develop COPD and the reasons for disease susceptibility in these individuals have not been fully elucidated. Although the mechanisms underlying COPD remain poorly understood, the disease is associated with chronic inflammation that is usually corticosteroid resistant. In addition, COPD involves accelerated ageing of the lungs and an abnormal repair mechanism that might be driven by oxidative stress. Acute exacerbations, which are mainly triggered by viral or bacterial infections, are important as they are linked to a poor prognosis. The mainstay of the management of stable disease is the use of inhaled long-acting bronchodilators, whereas corticosteroids are beneficial primarily in patients who have coexisting features of asthma, such as eosinophilic inflammation and more reversibility of airway obstruction. Apart from smoking cessation, no treatments reduce disease progression. More research is needed to better understand disease mechanisms and to develop new treatments that reduce disease activity and progression.
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Affiliation(s)
- Peter J Barnes
- Airway Disease Section, National Heart and Lung Institute, Imperial College, Dovehouse Street, London SW3 6LY, UK
| | - Peter G J Burney
- Division of Medical Genetics and Population Health, National Heart and Lung Institute, Imperial College, London, UK
| | - Edwin K Silverman
- Channing Division of Network Medicine and Pulmonary and Critical Care Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Bartolome R Celli
- Pulmonary and Critical Care Division, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jørgen Vestbo
- Centre of Respiratory Medicine and Allergy, Manchester Academic Science Centre, University Hospital South Manchester NHS Foundation Trust, Manchester, UK
| | - Jadwiga A Wedzicha
- Airway Disease Section, National Heart and Lung Institute, Imperial College, Dovehouse Street, London SW3 6LY, UK
| | - Emiel F M Wouters
- Department of Respiratory Medicine, Maastricht University Medical Centre, Maastricht, The Netherlands
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189
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Wain LV, Strachan DP, Tobin MD, Hall IP. Use of FEV1 as a measure of lung health in the UK BiLEVE study – Authors' reply. THE LANCET RESPIRATORY MEDICINE 2015; 3:e42-3. [DOI: 10.1016/s2213-2600(15)00460-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 10/23/2015] [Indexed: 10/22/2022]
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190
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Probert K, Miller S, Kheirallah AK, Hall IP. Developmental genetics of the COPD lung. ACTA ACUST UNITED AC 2015. [DOI: 10.1186/s40749-015-0014-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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191
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Brehm JM, Man Tse S, Croteau-Chonka DC, Forno E, Litonjua AA, Raby BA, Chen W, Yan Q, Boutaoui N, Acosta-Pérez E, Avila L, Weiss ST, Soto-Quiros M, Cloutier MM, Hu D, Pino-Yanes M, Wenzel SE, Spear ML, Kolls JK, Burchard EG, Canino G, Celedón JC. A Genome-Wide Association Study of Post-bronchodilator Lung Function in Children with Asthma. Am J Respir Crit Care Med 2015; 192:634-7. [PMID: 26325155 DOI: 10.1164/rccm.201501-0047le] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- John M Brehm
- 1 University of Pittsburgh School of Medicine Pittsburgh, Pennsylvania
| | - Sze Man Tse
- 2 Harvard Medical School Boston, Massachusetts
| | | | - Erick Forno
- 1 University of Pittsburgh School of Medicine Pittsburgh, Pennsylvania
| | | | | | - Wei Chen
- 1 University of Pittsburgh School of Medicine Pittsburgh, Pennsylvania
| | - Qi Yan
- 1 University of Pittsburgh School of Medicine Pittsburgh, Pennsylvania
| | - Nadia Boutaoui
- 1 University of Pittsburgh School of Medicine Pittsburgh, Pennsylvania
| | | | | | | | | | | | - Donglei Hu
- 6 University of California at San Francisco San Francisco, California
| | - Maria Pino-Yanes
- 6 University of California at San Francisco San Francisco, California
| | - Sally E Wenzel
- 1 University of Pittsburgh School of Medicine Pittsburgh, Pennsylvania
| | - Melissa L Spear
- 6 University of California at San Francisco San Francisco, California
| | - Jay K Kolls
- 1 University of Pittsburgh School of Medicine Pittsburgh, Pennsylvania
| | | | | | - Juan C Celedón
- 1 University of Pittsburgh School of Medicine Pittsburgh, Pennsylvania
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192
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Mathieson I, Lazaridis I, Rohland N, Mallick S, Patterson N, Roodenberg SA, Harney E, Stewardson K, Fernandes D, Novak M, Sirak K, Gamba C, Jones ER, Llamas B, Dryomov S, Pickrell J, Arsuaga JL, de Castro JMB, Carbonell E, Gerritsen F, Khokhlov A, Kuznetsov P, Lozano M, Meller H, Mochalov O, Moiseyev V, Guerra MAR, Roodenberg J, Vergès JM, Krause J, Cooper A, Alt KW, Brown D, Anthony D, Lalueza-Fox C, Haak W, Pinhasi R, Reich D. Genome-wide patterns of selection in 230 ancient Eurasians. Nature 2015; 528:499-503. [PMID: 26595274 PMCID: PMC4918750 DOI: 10.1038/nature16152] [Citation(s) in RCA: 730] [Impact Index Per Article: 81.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Accepted: 10/30/2015] [Indexed: 12/18/2022]
Abstract
Ancient DNA makes it possible to directly witness natural selection by analyzing samples from populations before, during and after adaptation events. Here we report the first scan for selection using ancient DNA, capitalizing on the largest genome-wide dataset yet assembled: 230 West Eurasians dating to between 6500 and 1000 BCE, including 163 with newly reported data. The new samples include the first genome-wide data from the Anatolian Neolithic culture whose genetic material we extracted from the DNA-rich petrous bone and who we show were members of the population that was the source of Europe’s first farmers. We also report a complete transect of the steppe region in Samara between 5500 and 1200 BCE that allows us to recognize admixture from at least two external sources into steppe populations during this period. We detect selection at loci associated with diet, pigmentation and immunity, and two independent episodes of selection on height.
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Affiliation(s)
- Iain Mathieson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Iosif Lazaridis
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | | | - Eadaoin Harney
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Daniel Fernandes
- School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland
| | - Mario Novak
- School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland.,Institute for Anthropological Research, Zagreb 10000, Croatia
| | - Kendra Sirak
- School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland.,Department of Anthropology, Emory University, Atlanta, Georgia 30322, USA
| | - Cristina Gamba
- School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland.,Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Eppie R Jones
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences &Environment Institute, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Stanislav Dryomov
- Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.,Department of Paleolithic Archaeology, Institute of Archaeology and Ethnography, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Joseph Pickrell
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Juan Luís Arsuaga
- Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos, 28040 Madrid, Spain.,Departamento de Paleontología, Facultad Ciencias Geológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | | | - Eudald Carbonell
- IPHES. Institut Català de Paleoecologia Humana i Evolució Social, Campus Sescelades-URV, 43007 Tarragona, Spain.,Area de Prehistoria, Universitat Rovira i Virgili (URV), 43002 Tarragona, Spain
| | - Fokke Gerritsen
- Netherlands Institute in Turkey, Istiklal Caddesi, Nur-i Ziya Sokak 5, Beyog˘ lu 34433, Istanbul, Turkey
| | - Aleksandr Khokhlov
- Volga State Academy of Social Sciences and Humanities, Samara 443099, Russia
| | - Pavel Kuznetsov
- Volga State Academy of Social Sciences and Humanities, Samara 443099, Russia
| | - Marina Lozano
- IPHES. Institut Català de Paleoecologia Humana i Evolució Social, Campus Sescelades-URV, 43007 Tarragona, Spain.,Area de Prehistoria, Universitat Rovira i Virgili (URV), 43002 Tarragona, Spain
| | - Harald Meller
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, D-06114 Halle, Germany
| | - Oleg Mochalov
- Volga State Academy of Social Sciences and Humanities, Samara 443099, Russia
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, St Petersburg 199034, Russia
| | - Manuel A Rojo Guerra
- Department of Prehistory and Archaeology, University of Valladolid, 47002 Valladolid, Spain
| | - Jacob Roodenberg
- The Netherlands Institute for the Near East, Leiden RA-2300, the Netherlands
| | - Josep Maria Vergès
- IPHES. Institut Català de Paleoecologia Humana i Evolució Social, Campus Sescelades-URV, 43007 Tarragona, Spain.,Area de Prehistoria, Universitat Rovira i Virgili (URV), 43002 Tarragona, Spain
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, D-07745 Jena, Germany.,Institute for Archaeological Sciences, University of Tübingen, D-72070 Tübingen, Germany
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Biological Sciences &Environment Institute, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Kurt W Alt
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, D-06114 Halle, Germany.,Danube Private University, A-3500 Krems, Austria.,Institute for Prehistory and Archaeological Science, University of Basel, CH-4003 Basel, Switzerland
| | - Dorcas Brown
- Anthropology Department, Hartwick College, Oneonta, New York 13820, USA
| | - David Anthony
- Anthropology Department, Hartwick College, Oneonta, New York 13820, USA
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain
| | - Wolfgang Haak
- Australian Centre for Ancient DNA, School of Biological Sciences &Environment Institute, University of Adelaide, Adelaide, South Australia 5005, Australia.,Max Planck Institute for the Science of Human History, D-07745 Jena, Germany
| | - Ron Pinhasi
- School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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193
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Jha AR, Zhou D, Brown CD, Kreitman M, Haddad GG, White KP. Shared Genetic Signals of Hypoxia Adaptation in Drosophila and in High-Altitude Human Populations. Mol Biol Evol 2015; 33:501-17. [PMID: 26576852 PMCID: PMC4866538 DOI: 10.1093/molbev/msv248] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The ability to withstand low oxygen (hypoxia tolerance) is a polygenic and mechanistically conserved trait that has important implications for both human health and evolution. However, little is known about the diversity of genetic mechanisms involved in hypoxia adaptation in evolving populations. We used experimental evolution and whole-genome sequencing in Drosophila melanogaster to investigate the role of natural variation in adaptation to hypoxia. Using a generalized linear mixed model we identified significant allele frequency differences between three independently evolved hypoxia-tolerant populations and normoxic control populations for approximately 3,800 single nucleotide polymorphisms. Around 50% of these variants are clustered in 66 distinct genomic regions. These regions contain genes that are differentially expressed between hypoxia-tolerant and normoxic populations and several of the differentially expressed genes are associated with metabolic processes. Additional genes associated with respiratory and open tracheal system development also show evidence of directional selection. RNAi-mediated knockdown of several candidate genes’ expression significantly enhanced survival in severe hypoxia. Using genomewide single nucleotide polymorphism data from four high-altitude human populations—Sherpas, Tibetans, Ethiopians, and Andeans, we found that several human orthologs of the genes under selection in flies are also likely under positive selection in all four high-altitude human populations. Thus, our results indicate that selection for hypoxia tolerance can act on standing genetic variation in similar genes and pathways present in organisms diverged by hundreds of millions of years.
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Affiliation(s)
- Aashish R Jha
- Institute for Genomics and Systems Biology, The University of Chicago Department of Human Genetics, The University of Chicago Department of Ecology and Evolution, The University of Chicago
| | - Dan Zhou
- Division of Respiratory Medicine, Department of Pediatrics, University of California at San Diego
| | - Christopher D Brown
- Institute for Genomics and Systems Biology, The University of Chicago Department of Human Genetics, The University of Chicago
| | - Martin Kreitman
- Institute for Genomics and Systems Biology, The University of Chicago Department of Ecology and Evolution, The University of Chicago Committee on Genetics, Genomics and Systems Biology, The University of Chicago
| | - Gabriel G Haddad
- Division of Respiratory Medicine, Department of Pediatrics, University of California at San Diego Department of Neurosciences, University of California at San Diego Rady Children's Hospital, San Diego, CA
| | - Kevin P White
- Institute for Genomics and Systems Biology, The University of Chicago Department of Human Genetics, The University of Chicago Department of Ecology and Evolution, The University of Chicago Committee on Genetics, Genomics and Systems Biology, The University of Chicago
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194
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Luo XJ, Mattheisen M, Li M, Huang L, Rietschel M, Børglum AD, Als TD, van den Oord EJ, Aberg KA, Mors O, Mortensen PB, Luo Z, Degenhardt F, Cichon S, Schulze TG, Nöthen MM, Su B, Zhao Z, Gan L, Yao YG. Systematic Integration of Brain eQTL and GWAS Identifies ZNF323 as a Novel Schizophrenia Risk Gene and Suggests Recent Positive Selection Based on Compensatory Advantage on Pulmonary Function. Schizophr Bull 2015; 41:1294-308. [PMID: 25759474 PMCID: PMC4601704 DOI: 10.1093/schbul/sbv017] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Genome-wide association studies have identified multiple risk variants and loci that show robust association with schizophrenia. Nevertheless, it remains unclear how these variants confer risk to schizophrenia. In addition, the driving force that maintains the schizophrenia risk variants in human gene pool is poorly understood. To investigate whether expression-associated genetic variants contribute to schizophrenia susceptibility, we systematically integrated brain expression quantitative trait loci and genome-wide association data of schizophrenia using Sherlock, a Bayesian statistical framework. Our analyses identified ZNF323 as a schizophrenia risk gene (P = 2.22×10(-6)). Subsequent analyses confirmed the association of the ZNF323 and its expression-associated single nucleotide polymorphism rs1150711 in independent samples (gene-expression: P = 1.40×10(-6); single-marker meta-analysis in the combined discovery and replication sample comprising 44123 individuals: P = 6.85×10(-10)). We found that the ZNF323 was significantly downregulated in hippocampus and frontal cortex of schizophrenia patients (P = .0038 and P = .0233, respectively). Evidence for pleiotropic effects was detected (association of rs1150711 with lung function and gene expression of ZNF323 in lung: P = 6.62×10(-5) and P = 9.00×10(-5), respectively) with the risk allele (T allele) for schizophrenia acting as protective allele for lung function. Subsequent population genetics analyses suggest that the risk allele (T) of rs1150711 might have undergone recent positive selection in human population. Our findings suggest that the ZNF323 is a schizophrenia susceptibility gene whose expression may influence schizophrenia risk. Our study also illustrates a possible mechanism for maintaining schizophrenia risk variants in the human gene pool.
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Affiliation(s)
- Xiong-Jian Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China; These authors contributed equally to this work.
| | - Manuel Mattheisen
- Department of Biomedicine and Centre for Integrative Sequencing (iSEQ), Aarhus University, 8000 Aarhus C, Denmark;,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus and Copenhagen, Denmark;,Department of Genomics, Life & Brain Center, and Institute of Human Genetics, University of Bonn, Bonn, Germany;,These authors contributed equally to this work
| | - Ming Li
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD
| | - Liang Huang
- First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty of Mannheim, University of Heidelberg, Mannheim, Germany
| | - Anders D. Børglum
- Department of Biomedicine and Centre for Integrative Sequencing (iSEQ), Aarhus University, 8000 Aarhus C, Denmark;,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus and Copenhagen, Denmark;,Research Department, Psychiatric Hospital, Aarhus University Hospital, Aarhus, Denmark
| | - Thomas D. Als
- Department of Biomedicine and Centre for Integrative Sequencing (iSEQ), Aarhus University, 8000 Aarhus C, Denmark;,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus and Copenhagen, Denmark
| | - Edwin J. van den Oord
- Center for Biomarker Research and Personalized Medicine, Virginia Commonwealth University
| | - Karolina A. Aberg
- Center for Biomarker Research and Personalized Medicine, Virginia Commonwealth University
| | - Ole Mors
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus and Copenhagen, Denmark;,Centre for Psychiatric Research, Aarhus University Hospital, Risskov, Denmark
| | - Preben Bo Mortensen
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus and Copenhagen, Denmark;,National Centre for Register-based Research, Aarhus University, Aarhus, Denmark
| | - Zhenwu Luo
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC
| | - Franziska Degenhardt
- Department of Genomics, Life & Brain Center, and Institute of Human Genetics, University of Bonn, Bonn, Germany
| | - Sven Cichon
- Division of Medical Genetics, Department of Biomedicine, University Basel, Basel, Switzerland;,Institute of Neuroscience and Medicine (INM-1), Research Center Juelich, Juelich, Germany
| | - Thomas G. Schulze
- Department of Psychiatry and Psychotherapy, University Medical Center Georg-August-Universität, 37075 Goettingen, Germany;,Institute of Psychiatric Phenomics and Genomics (IPPG), Ludwig-Maximilians-University Munich
| | - Markus M. Nöthen
- Department of Genomics, Life & Brain Center, and Institute of Human Genetics, University of Bonn, Bonn, Germany
| | | | | | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zhongming Zhao
- Departments of Biomedical Informatics and Psychiatry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Lin Gan
- Departments of Biomedical Informatics and Psychiatry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province, Kunming Institute of Zoology, Kunming, Yunnan, China;,CAS Center for Excellence in Brain Science, Chinese Academy of Sciences, Shanghai, 200031, China
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Abstract
COPD is a common complex disease characterized by progressive airflow limitation. Several genome-wide association studies (GWASs) have discovered genes that are associated with COPD. Recently, candidate genes for COPD identified by GWASs include CHRNA3/5 (cholinergic nicotine receptor alpha 3/5), IREB2 (iron regulatory binding protein 2), HHIP (hedgehog-interacting protein), FAM13A (family with sequence similarity 13, member A), and AGER (advanced glycosylation end product–specific receptor). Their association with COPD susceptibility has been replicated in multiple populations. Since these candidate genes have not been considered in COPD, their pathological roles are still largely unknown. Herein, we review some evidences that they can be effective drug targets or serve as biomarkers for diagnosis or subtyping. However, more study is required to understand the functional roles of these candidate genes. Future research is needed to characterize the effect of genetic variants, validate gene function in humans and model systems, and elucidate the genes’ transcriptional and posttranscriptional regulatory mechanisms.
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Affiliation(s)
- Woo Jin Kim
- Department of Internal Medicine and Environmental Health Center, Kangwon National University, Chuncheon, South Korea
| | - Sang Do Lee
- Department of Pulmonary and Critical Care Medicine, Clinical Research Center for Chronic Obstructive Airway Diseases, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
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196
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Family-Based Association Study of Pulmonary Function in a Population in Northeast Asia. PLoS One 2015; 10:e0139716. [PMID: 26430897 PMCID: PMC4592257 DOI: 10.1371/journal.pone.0139716] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Accepted: 09/15/2015] [Indexed: 12/22/2022] Open
Abstract
The spirometric measurement of pulmonary function by measuring the forced expiratory volume in one second (FEV1) is a heritable trait that reflects the physiological condition of the lung and airways. Genome-wide linkage and association studies have identified a number of genes and genetic loci associated with pulmonary function. However, limited numbers of studies have been reported for Asian populations. In this study, we aimed to investigate genetic evidence of pulmonary function in a population in northeast Asia. We conducted a family-based association test with 706 GENDISCAN study participants from 72 Mongolian families to determine candidate genetic determinants of pulmonary function. For the replication, we chose seven candidate single nucleotide polymorphisms (SNPs) from the 5 loci, and tested 1062 SNPs for association with FEV1 from 2,729 subjects of the Korea Healthy Twin study. We identified TMEM132C as a potential candidate gene at 12q24.3, which is a previously reported locus of asthma and spirometric indices. We also found two adjacent candidate genes (UNC93A and TTLL2) in the 6q27 region, which has been previously identified as a pulmonary function locus in the Framingham cohort study. Our findings suggest that novel candidate genes (TMEM132C, UNC93A and TTLL2) in two different regions are associated with pulmonary function in a population in northeast Asia.
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197
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Novel insights into the genetics of smoking behaviour, lung function, and chronic obstructive pulmonary disease (UK BiLEVE): a genetic association study in UK Biobank. THE LANCET. RESPIRATORY MEDICINE 2015; 3:769-81. [PMID: 26423011 PMCID: PMC4593935 DOI: 10.1016/s2213-2600(15)00283-0] [Citation(s) in RCA: 270] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 07/07/2015] [Accepted: 07/09/2015] [Indexed: 12/30/2022]
Abstract
BACKGROUND Understanding the genetic basis of airflow obstruction and smoking behaviour is key to determining the pathophysiology of chronic obstructive pulmonary disease (COPD). We used UK Biobank data to study the genetic causes of smoking behaviour and lung health. METHODS We sampled individuals of European ancestry from UK Biobank, from the middle and extremes of the forced expiratory volume in 1 s (FEV1) distribution among heavy smokers (mean 35 pack-years) and never smokers. We developed a custom array for UK Biobank to provide optimum genome-wide coverage of common and low-frequency variants, dense coverage of genomic regions already implicated in lung health and disease, and to assay rare coding variants relevant to the UK population. We investigated whether there were shared genetic causes between different phenotypes defined by extremes of FEV1. We also looked for novel variants associated with extremes of FEV1 and smoking behaviour and assessed regions of the genome that had already shown evidence for a role in lung health and disease. We set genome-wide significance at p<5 × 10(-8). FINDINGS UK Biobank participants were recruited from March 15, 2006, to July 7, 2010. Sample selection for the UK BiLEVE study started on Nov 22, 2012, and was completed on Dec 20, 2012. We selected 50,008 unique samples: 10,002 individuals with low FEV1, 10,000 with average FEV1, and 5002 with high FEV1 from each of the heavy smoker and never smoker groups. We noted a substantial sharing of genetic causes of low FEV1 between heavy smokers and never smokers (p=2.29 × 10(-16)) and between individuals with and without doctor-diagnosed asthma (p=6.06 × 10(-11)). We discovered six novel genome-wide significant signals of association with extremes of FEV1, including signals at four novel loci (KANSL1, TSEN54, TET2, and RBM19/TBX5) and independent signals at two previously reported loci (NPNT and HLA-DQB1/HLA-DQA2). These variants also showed association with COPD, including in individuals with no history of smoking. The number of copies of a 150 kb region containing the 5' end of KANSL1, a gene that is important for epigenetic gene regulation, was associated with extremes of FEV1. We also discovered five new genome-wide significant signals for smoking behaviour, including a variant in NCAM1 (chromosome 11) and a variant on chromosome 2 (between TEX41 and PABPC1P2) that has a trans effect on expression of NCAM1 in brain tissue. INTERPRETATION By sampling from the extremes of the lung function distribution in UK Biobank, we identified novel genetic causes of lung function and smoking behaviour. These results provide new insight into the specific mechanisms underlying airflow obstruction, COPD, and tobacco addiction, and show substantial shared genetic architecture underlying airflow obstruction across individuals, irrespective of smoking behaviour and other airway disease. FUNDING Medical Research Council.
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198
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Obeidat M, Hao K, Bossé Y, Nickle DC, Nie Y, Postma DS, Laviolette M, Sandford AJ, Daley DD, Hogg JC, Elliott WM, Fishbane N, Timens W, Hysi PG, Kaprio J, Wilson JF, Hui J, Rawal R, Schulz H, Stubbe B, Hayward C, Polasek O, Järvelin MR, Zhao JH, Jarvis D, Kähönen M, Franceschini N, North KE, Loth DW, Brusselle GG, Smith AV, Gudnason V, Bartz TM, Wilk JB, O'Connor GT, Cassano PA, Tang W, Wain LV, Soler Artigas M, Gharib SA, Strachan DP, Sin DD, Tobin MD, London SJ, Hall IP, Paré PD. Molecular mechanisms underlying variations in lung function: a systems genetics analysis. THE LANCET. RESPIRATORY MEDICINE 2015; 3:782-95. [PMID: 26404118 PMCID: PMC5021067 DOI: 10.1016/s2213-2600(15)00380-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 08/06/2015] [Accepted: 08/12/2015] [Indexed: 02/02/2023]
Abstract
BACKGROUND Lung function measures reflect the physiological state of the lung, and are essential to the diagnosis of chronic obstructive pulmonary disease (COPD). The SpiroMeta-CHARGE consortium undertook the largest genome-wide association study (GWAS) so far (n=48,201) for forced expiratory volume in 1 s (FEV1) and the ratio of FEV1 to forced vital capacity (FEV1/FVC) in the general population. The lung expression quantitative trait loci (eQTLs) study mapped the genetic architecture of gene expression in lung tissue from 1111 individuals. We used a systems genetics approach to identify single nucleotide polymorphisms (SNPs) associated with lung function that act as eQTLs and change the level of expression of their target genes in lung tissue; termed eSNPs. METHODS The SpiroMeta-CHARGE GWAS results were integrated with lung eQTLs to map eSNPs and the genes and pathways underlying the associations in lung tissue. For comparison, a similar analysis was done in peripheral blood. The lung mRNA expression levels of the eSNP-regulated genes were tested for associations with lung function measures in 727 individuals. Additional analyses identified the pleiotropic effects of eSNPs from the published GWAS catalogue, and mapped enrichment in regulatory regions from the ENCODE project. Finally, the Connectivity Map database was used to identify potential therapeutics in silico that could reverse the COPD lung tissue gene signature. FINDINGS SNPs associated with lung function measures were more likely to be eQTLs and vice versa. The integration mapped the specific genes underlying the GWAS signals in lung tissue. The eSNP-regulated genes were enriched for developmental and inflammatory pathways; by comparison, SNPs associated with lung function that were eQTLs in blood, but not in lung, were only involved in inflammatory pathways. Lung function eSNPs were enriched for regulatory elements and were over-represented among genes showing differential expression during fetal lung development. An mRNA gene expression signature for COPD was identified in lung tissue and compared with the Connectivity Map. This in-silico drug repurposing approach suggested several compounds that reverse the COPD gene expression signature, including a nicotine receptor antagonist. These findings represent novel therapeutic pathways for COPD. INTERPRETATION The system genetics approach identified lung tissue genes driving the variation in lung function and susceptibility to COPD. The identification of these genes and the pathways in which they are enriched is essential to understand the pathophysiology of airway obstruction and to identify novel therapeutic targets and biomarkers for COPD, including drugs that reverse the COPD gene signature in silico. FUNDING The research reported in this article was not specifically funded by any agency. See Acknowledgments for a full list of funders of the lung eQTL study and the Spiro-Meta CHARGE GWAS.
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Affiliation(s)
- Ma'en Obeidat
- University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada
| | - Ke Hao
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yohan Bossé
- Department of Molecular Medicine, Laval University, Québec, QC, Canada; Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec, QC, Canada
| | - David C Nickle
- Merck Research Laboratories, Genetics and Pharmacogenomics, Boston, MA, USA
| | - Yunlong Nie
- University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada
| | - Dirkje S Postma
- University of Groningen, University Medical Center Groningen, Department of Pulmonology, GRIAC Research Institute, University of Groningen, Groningen, Netherlands
| | - Michel Laviolette
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec, QC, Canada
| | - Andrew J Sandford
- University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada; Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Denise D Daley
- University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada; Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - James C Hogg
- University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - W Mark Elliott
- University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Nick Fishbane
- University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada
| | - Wim Timens
- Department of Pathology and Medical Biology, GRIAC Research Institute, University of Groningen, Groningen, Netherlands
| | - Pirro G Hysi
- Department of Twin Research and Genetic Epidemiology, King's College, London, UK
| | - Jaakko Kaprio
- Department of Public Health, and Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland; National Institute for Health and Welfare, Helsinki, Finland
| | - James F Wilson
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Jennie Hui
- Busselton Population Medical Research Institute, Busselton, WA, Australia; PathWest Laboratory Medicine of Western Australia, Nedlands, WA, Australia; School of Population Health and School of Pahology and Laboratory Medicine, University of Western Australia, Nedlands, WA, Australia
| | - Rajesh Rawal
- Research Unit of Molecular Epidemiology, Helmholtz-Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Institute of Genetic Epidemiology, Helmholtz-Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Holger Schulz
- Institute of Epidemiology I, Helmholtz-Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Comprehensive Pneumology Center Munich (CPC-M), German Center for Lung Research, Munich, Germany
| | - Beate Stubbe
- University Hospital, Department of Internal Medicine B, Greifswald, Germany
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Ozren Polasek
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK; Faculty of Medicine, University of Split, Croatia
| | - Marjo-Riitta Järvelin
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College, London, UK; Center for Life Course Epidemiology, Faculty of Medicine, Biocenter Oulu, and Unit of Primary Care, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Jing Hua Zhao
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge UK
| | - Deborah Jarvis
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College, London, UK; Respiratory Epidemiology and Public Health Group, National Heart and Lung Institute, Imperial College, London, UK
| | - Mika Kähönen
- Department of Clinical Physiology, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - Nora Franceschini
- Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Kari E North
- Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA; University of North Carolina Center for Genome Sciences, Chapel Hill, NC, USA
| | - Daan W Loth
- Departments of Epidemiology and Respiratory Medicine, Erasmus MC, Rotterdam, Netherlands
| | - Guy G Brusselle
- Departments of Epidemiology and Respiratory Medicine, Erasmus MC, Rotterdam, Netherlands; Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Albert Vernon Smith
- Icelandic Heart Association, Kopavogur, Iceland; Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland; Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Traci M Bartz
- Cardiovascular Health Research Unit, Departments of Medicine and Biostatistics, University of Washington, Seattle, WA, USA
| | - Jemma B Wilk
- Human Genetics & Computational Biomedicine, Pfizer Worldwide Research and Development, Cambridge, MA, USA
| | - George T O'Connor
- Pulmonary Center, Boston University School of Medicine, Boston, MA, USA; NHLBI Framingham Heart Study, Framingham, MA, USA
| | - Patricia A Cassano
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA; Division of Biostatistics and Epidemiology, Department of Healthcare Policy and Research, Weill Cornell Medical College, NY, USA
| | - Wenbo Tang
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA; Boehringer Ingelheim Pharmaceuticals, Ridgefield, CT, USA
| | - Louise V Wain
- University of Leicester, Genetic Epidemiology Group, Department of Health Sciences, Leicester, UK; National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - María Soler Artigas
- University of Leicester, Genetic Epidemiology Group, Department of Health Sciences, Leicester, UK; National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Sina A Gharib
- Computational Medicine Core, Center for Lung Biology, University of Washington, Seattle, WA, USA; Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
| | - David P Strachan
- Population Health Research Institute, St George's, University of London, London, UK
| | - Don D Sin
- University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada; Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Martin D Tobin
- University of Leicester, Genetic Epidemiology Group, Department of Health Sciences, Leicester, UK; National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Ian P Hall
- University of Nottingham Division of Respiratory Medicine, University Hospital of Nottingham, Nottingham, UK
| | - Peter D Paré
- University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada; Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.
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Ortega VE, Kumar R. The Effect of Ancestry and Genetic Variation on Lung Function Predictions: What Is "Normal" Lung Function in Diverse Human Populations? Curr Allergy Asthma Rep 2015; 15:16. [PMID: 26130473 DOI: 10.1007/s11882-015-0516-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Lung function measures are an invaluable screening test for respiratory health and have been associated with the morbidity and mortality related to different airway disease as well as all-cause mortality. Currently, reference values for spirometric measurements are obtained using equations derived from individual ethnic or racial groups. The rapid expansion of more racially and ethnically diverse populations will challenge current race-based lung function reference equations. Recent international general population studies and ancestry-based genetic studies have found that ancestry and genetic variation are determinants of lung function and have suggested a role for genetic ancestry or gene variants in future lung function reference equations. In this review, we discuss the potential limitations of current lung function reference equations in a global society which is becoming more ethnically, racially, and, thus, genetically diverse. We also focus on how an individual's ancestral background or genetic profile could provide the basis for more accurate, personalized predictions of an individual's baseline lung function.
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Affiliation(s)
- Victor E Ortega
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC, 27157, USA,
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Gharib SA, Loth DW, Soler Artigas M, Birkland TP, Wilk JB, Wain LV, Brody JA, Obeidat M, Hancock DB, Tang W, Rawal R, Boezen HM, Imboden M, Huffman JE, Lahousse L, Alves AC, Manichaikul A, Hui J, Morrison AC, Ramasamy A, Smith AV, Gudnason V, Surakka I, Vitart V, Evans DM, Strachan DP, Deary IJ, Hofman A, Gläser S, Wilson JF, North KE, Zhao JH, Heckbert SR, Jarvis DL, Probst-Hensch N, Schulz H, Barr RG, Jarvelin MR, O'Connor GT, Kähönen M, Cassano PA, Hysi PG, Dupuis J, Hayward C, Psaty BM, Hall IP, Parks WC, Tobin MD, London SJ. Integrative pathway genomics of lung function and airflow obstruction. Hum Mol Genet 2015; 24:6836-48. [PMID: 26395457 DOI: 10.1093/hmg/ddv378] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 09/10/2015] [Indexed: 12/31/2022] Open
Abstract
Chronic respiratory disorders are important contributors to the global burden of disease. Genome-wide association studies (GWASs) of lung function measures have identified several trait-associated loci, but explain only a modest portion of the phenotypic variability. We postulated that integrating pathway-based methods with GWASs of pulmonary function and airflow obstruction would identify a broader repertoire of genes and processes influencing these traits. We performed two independent GWASs of lung function and applied gene set enrichment analysis to one of the studies and validated the results using the second GWAS. We identified 131 significantly enriched gene sets associated with lung function and clustered them into larger biological modules involved in diverse processes including development, immunity, cell signaling, proliferation and arachidonic acid. We found that enrichment of gene sets was not driven by GWAS-significant variants or loci, but instead by those with less stringent association P-values. Next, we applied pathway enrichment analysis to a meta-analyzed GWAS of airflow obstruction. We identified several biologic modules that functionally overlapped with those associated with pulmonary function. However, differences were also noted, including enrichment of extracellular matrix (ECM) processes specifically in the airflow obstruction study. Network analysis of the ECM module implicated a candidate gene, matrix metalloproteinase 10 (MMP10), as a putative disease target. We used a knockout mouse model to functionally validate MMP10's role in influencing lung's susceptibility to cigarette smoke-induced emphysema. By integrating pathway analysis with population-based genomics, we unraveled biologic processes underlying pulmonary function traits and identified a candidate gene for obstructive lung disease.
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Affiliation(s)
- Sina A Gharib
- Computational Medicine Core, Center for Lung Biology, Department of Medicine,
| | - Daan W Loth
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
| | - María Soler Artigas
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK, National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | | | - Jemma B Wilk
- Human Genetics and Computational Biomedicine, Pfizer Global Research and Development, Cambridge, MA, USA
| | - Louise V Wain
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK, National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | | | - Ma'en Obeidat
- University of British Columbia, Centre for Heart Lung Innovation, Vancouver, BC, Canada
| | - Dana B Hancock
- Behavioral and Urban Health Program, Behavioral Health and Criminal Justice Division, Research Triangle Institute (RTI) International, Research Triangle Park, NC, USA
| | - Wenbo Tang
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
| | | | - H Marike Boezen
- Department of Epidemiology, GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Medea Imboden
- Swiss Tropical and Public Health Institute, Basel, Switzerland, University of Basel, Basel, Switzerland
| | | | - Lies Lahousse
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands, Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | | | - Ani Manichaikul
- Center for Public Health Genomics, Division of Biostatistics and Epidemiology, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Jennie Hui
- PathWest Laboratory Medicine WA, Nedlands, Australia, School of Pathology and Laboratory Medicine, School of Population Health, The University of Western Australia, Nedlands, Australia
| | - Alanna C Morrison
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
| | | | - Albert Vernon Smith
- Iceland Heart Association, Kopavogur, Iceland, University of Iceland, Reykjavik, Iceland
| | - Vilmundur Gudnason
- Iceland Heart Association, Kopavogur, Iceland, University of Iceland, Reykjavik, Iceland
| | - Ida Surakka
- Public Health Genomics Unit, Department of Chronic Disease Prevention, National Institute for Health and Welfare (THL), Helsinki, Finland
| | | | - David M Evans
- University of Queensland Diamantina Institute, Translational Research Institute, 37 Kent St Woolloongabba, QLD 4102, Australia, MRC Integrative Epidemiology Unit, Oakfield Road, Oakfield Grove BS82BN, Bristol, UK
| | - David P Strachan
- Population Health Research Institute, St George's, University of London, London, UK
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology
| | - Albert Hofman
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands, Netherlands Genomics Initiative (NGI)-Sponsored Netherlands Consortium for Healthy Aging (NCHA), Rotterdam, The Netherlands
| | - Sven Gläser
- Department of Internal Medicine B, Pneumology, Cardiology, Intensive Care and Infectious Diseases, University Hospital Greifswald, Greifswald, Germany
| | - James F Wilson
- Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh, Scotland, UK
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jing Hua Zhao
- MRC Epidemiology Unit, Institute of Metabolic Science, Addenbrooke's Hospital, Cambridge, UK
| | - Susan R Heckbert
- Cardiovascular Health Research Unit, Department of Epidemiology, Group Health Research Institute, Group Health Cooperative, Seattle, WA, USA
| | - Deborah L Jarvis
- Respiratory Epidemiology and Public Health Group, National Heart and Lung Institute
| | - Nicole Probst-Hensch
- Swiss Tropical and Public Health Institute, Basel, Switzerland, University of Basel, Basel, Switzerland
| | - Holger Schulz
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - R Graham Barr
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, MRC Health Protection Agency (HPA) Centre for Environment and Health, School of Public Health, Imperial College London, London, UK, Institute of Health Sciences, Biocenter Oulu, University of Oulu, Oulu, Finland, Unit of Primary Care, Oulu University Hospital, Oulu, Finland, Department of Children and Young People and Families, National Institute for Health and Welfare, Oulu, Finland
| | - George T O'Connor
- Pulmonary Center, Boston University School of Medicine, Boston, MA, USA, The NHLBI's Framingham Heart Study, Framingham, MA, USA
| | - Mika Kähönen
- Department of Clinical Physiology, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - Patricia A Cassano
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA, Department of Healthcare Policy and Research, Division of Biostatistics and Epidemiology, Weill Cornell Medical College, New York, NY, USA
| | - Pirro G Hysi
- Department of Twins Research and Genetic Epidemiology, King's College, London, UK
| | - Josée Dupuis
- The NHLBI's Framingham Heart Study, Framingham, MA, USA, Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | | | - Bruce M Psaty
- Department of Medicine, Cardiovascular Health Research Unit, Department of Epidemiology, Department of Health Services, University of Washington, Seattle, WA, USA, Group Health Research Institute, Group Health Cooperative, Seattle, WA, USA
| | - Ian P Hall
- Division of Respiratory Medicine, University Hospital of Nottingham, Nottingham, UK
| | - William C Parks
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA and
| | - Martin D Tobin
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK, National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institute of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
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