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Grover SP, Mackman N. Anticoagulant SERPINs: Endogenous Regulators of Hemostasis and Thrombosis. Front Cardiovasc Med 2022; 9:878199. [PMID: 35592395 PMCID: PMC9110684 DOI: 10.3389/fcvm.2022.878199] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 03/29/2022] [Indexed: 12/17/2022] Open
Abstract
Appropriate activation of coagulation requires a balance between procoagulant and anticoagulant proteins in blood. Loss in this balance leads to hemorrhage and thrombosis. A number of endogenous anticoagulant proteins, such as antithrombin and heparin cofactor II, are members of the serine protease inhibitor (SERPIN) family. These SERPIN anticoagulants function by forming irreversible inhibitory complexes with target coagulation proteases. Mutations in SERPIN family members, such as antithrombin, can cause hereditary thrombophilias. In addition, low plasma levels of SERPINs have been associated with an increased risk of thrombosis. Here, we review the biological activities of the different anticoagulant SERPINs. We further consider the clinical consequences of SERPIN deficiencies and insights gained from preclinical disease models. Finally, we discuss the potential utility of engineered SERPINs as novel therapies for the treatment of thrombotic pathologies.
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Moll M, Jackson VE, Yu B, Grove ML, London SJ, Gharib SA, Bartz TM, Sitlani CM, Dupuis J, O'Connor GT, Xu H, Cassano PA, Patchen BK, Kim WJ, Park J, Kim KH, Han B, Barr RG, Manichaikul A, Nguyen JN, Rich SS, Lahousse L, Terzikhan N, Brusselle G, Sakornsakolpat P, Liu J, Benway CJ, Hall IP, Tobin MD, Wain LV, Silverman EK, Cho MH, Hobbs BD. A systematic analysis of protein-altering exonic variants in chronic obstructive pulmonary disease. Am J Physiol Lung Cell Mol Physiol 2021; 321:L130-L143. [PMID: 33909500 PMCID: PMC8321852 DOI: 10.1152/ajplung.00009.2021] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 04/15/2021] [Accepted: 04/27/2021] [Indexed: 12/14/2022] Open
Abstract
Genome-wide association studies (GWASs) have identified regions associated with chronic obstructive pulmonary disease (COPD). GWASs of other diseases have shown an approximately 10-fold overrepresentation of nonsynonymous variants, despite limited exonic coverage on genotyping arrays. We hypothesized that a large-scale analysis of coding variants could discover novel genetic associations with COPD, including rare variants with large effect sizes. We performed a meta-analysis of exome arrays from 218,399 controls and 33,851 moderate-to-severe COPD cases. All exome-wide significant associations were present in regions previously identified by GWAS. We did not identify any novel rare coding variants with large effect sizes. Within GWAS regions on chromosomes 5q, 6p, and 15q, four coding variants were conditionally significant (P < 0.00015) when adjusting for lead GWAS single-nucleotide polymorphisms A common gasdermin B (GSDMB) splice variant (rs11078928) previously associated with a decreased risk for asthma was nominally associated with a decreased risk for COPD [minor allele frequency (MAF) = 0.46, P = 1.8e-4]. Two stop variants in coiled-coil α-helical rod protein 1 (CCHCR1), a gene involved in regulating cell proliferation, were associated with COPD (both P < 0.0001). The SERPINA1 Z allele was associated with a random-effects odds ratio of 1.43 for COPD (95% confidence interval = 1.17-1.74), though with marked heterogeneity across studies. Overall, COPD-associated exonic variants were identified in genes involved in DNA methylation, cell-matrix interactions, cell proliferation, and cell death. In conclusion, we performed the largest exome array meta-analysis of COPD to date and identified potential functional coding variants. Future studies are needed to identify rarer variants and further define the role of coding variants in COPD pathogenesis.
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Affiliation(s)
- Matthew Moll
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Victoria E Jackson
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Bing Yu
- School of Public Health, University of Texas Health Science Center, Houston, Texas
| | - Megan L Grove
- School of Public Health, University of Texas Health Science Center, Houston, Texas
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services Research, Research Triangle Park, Durham, North Carolina
| | - Sina A Gharib
- Center for Lung Biology, Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Washington, Seattle, Washington
| | - Traci M Bartz
- Department of Biostatistics, University of Washington, Seattle, Washington
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington
| | - Colleen M Sitlani
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - George T O'Connor
- Division of Pulmonary, Allergy, Sleep, and Critical Care Medicine, Department of Medicine, Pulmonary Center, Boston University School of Medicine, Boston Medical Center, Boston, Massachusetts
| | - Hanfei Xu
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Patricia A Cassano
- Division of Nutritional Sciences, Cornell University, Ithaca, New York
- Division of Epidemiology, Department of Population Health Sciences, Weill Cornell Medicine, New York, New York
| | | | - Woo Jin Kim
- Department of Internal Medicine, Kangwon National University, Chuncheon, South Korea
| | - Jinkyeong Park
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Internal Medicine, Dongguk University Ilsan Hospital, Goyang-Si, Gyeonggi-do, South Korea
| | - Kun Hee Kim
- Department of Convergence Medicine and Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Buhm Han
- Department of Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - R Graham Barr
- Department of Medicine, Columbia University Medical Center, New York, New York
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Jennifer N Nguyen
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Lies Lahousse
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Bioanalysis, Ghent University, Ghent, Belgium
| | - Natalie Terzikhan
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Guy Brusselle
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Phuwanat Sakornsakolpat
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Jiangyuan Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Christopher J Benway
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Ian P Hall
- NIHR Nottingham Biomedical Research Centre, Queen's Medical Centre, Nottingham, United Kingdom
| | - Martin D Tobin
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Edwin K Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
| | - Brian D Hobbs
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
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3
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The Serpin Superfamily and Their Role in the Regulation and Dysfunction of Serine Protease Activity in COPD and Other Chronic Lung Diseases. Int J Mol Sci 2021; 22:ijms22126351. [PMID: 34198546 PMCID: PMC8231800 DOI: 10.3390/ijms22126351] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 06/01/2021] [Accepted: 06/04/2021] [Indexed: 12/21/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a debilitating heterogeneous disease characterised by unregulated proteolytic destruction of lung tissue mediated via a protease-antiprotease imbalance. In COPD, the relationship between the neutrophil serine protease, neutrophil elastase, and its endogenous inhibitor, alpha-1-antitrypsin (AAT) is the best characterised. AAT belongs to a superfamily of serine protease inhibitors known as serpins. Advances in screening technologies have, however, resulted in many members of the serpin superfamily being identified as having differential expression across a multitude of chronic lung diseases compared to healthy individuals. Serpins exhibit a unique suicide-substrate mechanism of inhibition during which they undergo a dramatic conformational change to a more stable form. A limitation is that this also renders them susceptible to disease-causing mutations. Identification of the extent of their physiological/pathological role in the airways would allow further expansion of knowledge regarding the complexity of protease regulation in the lung and may provide wider opportunity for their use as therapeutics to aid the management of COPD and other chronic airways diseases.
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Moll M, Sakornsakolpat P, Shrine N, Hobbs BD, DeMeo DL, John C, Guyatt AL, McGeachie MJ, Gharib SA, Obeidat M, Lahousse L, Wijnant SRA, Brusselle G, Meyers DA, Bleecker ER, Li X, Tal-Singer R, Manichaikul A, Rich SS, Won S, Kim WJ, Do AR, Washko GR, Barr RG, Psaty BM, Bartz TM, Hansel NN, Barnes K, Hokanson JE, Crapo JD, Lynch D, Bakke P, Gulsvik A, Hall IP, Wain L, Weiss ST, Silverman EK, Dudbridge F, Tobin MD, Cho MH. Chronic obstructive pulmonary disease and related phenotypes: polygenic risk scores in population-based and case-control cohorts. THE LANCET. RESPIRATORY MEDICINE 2020; 8:696-708. [PMID: 32649918 PMCID: PMC7429152 DOI: 10.1016/s2213-2600(20)30101-6] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 01/24/2020] [Accepted: 02/17/2020] [Indexed: 01/19/2023]
Abstract
BACKGROUND Genetic factors influence chronic obstructive pulmonary disease (COPD) risk, but the individual variants that have been identified have small effects. We hypothesised that a polygenic risk score using additional variants would predict COPD and associated phenotypes. METHODS We constructed a polygenic risk score using a genome-wide association study of lung function (FEV1 and FEV1/forced vital capacity [FVC]) from the UK Biobank and SpiroMeta. We tested this polygenic risk score in nine cohorts of multiple ethnicities for an association with moderate-to-severe COPD (defined as FEV1/FVC <0·7 and FEV1 <80% of predicted). Associations were tested using logistic regression models, adjusting for age, sex, height, smoking pack-years, and principal components of genetic ancestry. We assessed predictive performance of models by area under the curve. In a subset of studies, we also studied quantitative and qualitative CT imaging phenotypes that reflect parenchymal and airway pathology, and patterns of reduced lung growth. FINDINGS The polygenic risk score was associated with COPD in European (odds ratio [OR] per SD 1·81 [95% CI 1·74-1·88] and non-European (1·42 [1·34-1·51]) populations. Compared with the first decile, the tenth decile of the polygenic risk score was associated with COPD, with an OR of 7·99 (6·56-9·72) in European ancestry and 4·83 (3·45-6·77) in non-European ancestry cohorts. The polygenic risk score was superior to previously described genetic risk scores and, when combined with clinical risk factors (ie, age, sex, and smoking pack-years), showed improved prediction for COPD compared with a model comprising clinical risk factors alone (AUC 0·80 [0·79-0·81] vs 0·76 [0·75-0·76]). The polygenic risk score was associated with CT imaging phenotypes, including wall area percent, quantitative and qualitative measures of emphysema, local histogram emphysema patterns, and destructive emphysema subtypes. The polygenic risk score was associated with a reduced lung growth pattern. INTERPRETATION A risk score comprised of genetic variants can identify a small subset of individuals at markedly increased risk for moderate-to-severe COPD, emphysema subtypes associated with cigarette smoking, and patterns of reduced lung growth. FUNDING US National Institutes of Health, Wellcome Trust.
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Affiliation(s)
- Matthew Moll
- 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
| | - Phuwanat Sakornsakolpat
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA; Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Nick Shrine
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK
| | - 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
| | - 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
| | - Catherine John
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK
| | - Anna L Guyatt
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK
| | - Michael J McGeachie
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Sina A Gharib
- Computational Medicine Core, Center for Lung Biology, Department of Medicine, University of Washington, Seattle, WA, USA; Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Ma'en Obeidat
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA; University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada
| | - Lies Lahousse
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, Netherlands; Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Sara R A Wijnant
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, Netherlands; Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium; Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Guy Brusselle
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, Netherlands; Department of Respiratory Medicine, Erasmus Medical Centre, Rotterdam, Netherlands; Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | | | | | - Xingnan Li
- Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - Ruth Tal-Singer
- GlaxoSmithKline Research and Development, Collegeville, PA, 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
| | - 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
| | - Sungho Won
- Department of Public Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, South Korea; Interdisciplinary Program of Bioinformatics, College of National Sciences, Seoul National University, Seoul, South Korea; Institute of Health and Environment, Seoul National University, Seoul, South Korea
| | - Woo Jin Kim
- Department of Internal Medicine, Kangwon National University, Chuncheon, South Korea
| | - Ah Ra Do
- Interdisciplinary Program of Bioinformatics, College of National Sciences, Seoul National University, Seoul, South Korea
| | - George R Washko
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - R Graham Barr
- Department of Medicine and Department of Epidemiology, Columbia University Medical Center, New York, NY, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA; Kaiser Permanente Washington Health Research Institute, Seattle, WA
| | - Traci M Bartz
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Nadia N Hansel
- School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Kathleen Barnes
- Colorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | | | - James D Crapo
- Division of Pulmonary, Critical Care, and Sleep Medicine, National Jewish Health, Denver, CO, USA
| | - David Lynch
- Department of Radiology, National Jewish Health, Denver, CO, USA
| | - Per Bakke
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Amund Gulsvik
- Division of Respiratory Medicine, Queen's Medical Centre, Nottingham, UK
| | - Ian P Hall
- National Institute for Health Research Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Louise Wain
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK; National Institute for Health Research Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, 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; Harvard Medical School, Boston, MA, USA
| | - Frank Dudbridge
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK
| | - Martin D Tobin
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK; National Institute for Health Research Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK.
| | - 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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5
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Li L, Li SY, Zhong X, Ren J, Tian X, Tuerxun M, Xie C, Li F, Zheng A, Aini P, Yasen M, Wang H, Zou X. SERPINE2 rs16865421 polymorphism is associated with a lower risk of chronic obstructive pulmonary disease in the Uygur population: A case-control study. J Gene Med 2019; 21:e3106. [PMID: 31215134 DOI: 10.1002/jgm.3106] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 05/12/2019] [Accepted: 06/05/2019] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND The present study aimed to investigate the relationship between seven polymorphisms of the serine protease inhibitor-2 (SERPINE2) gene and the risk of chronic obstructive pulmonary disease (COPD) in the Uygur population via a case-control study. METHODS In total, 440 Uygur patients with COPD were included in the patient group and 384 healthy individuals were recruited in the matched control group. Data on demographic variables, smoking status, occupational dust exposure history and living conditions were collected. Polymorphism analysis was performed for seven loci of the SERPINE2 gene by mass spectrometry. RESULTS The genotype distribution of rs16865421 showed a significant difference between the patient and control groups (p < 0.05). Participants carrying the rs16865421-AG heterozygous mutant genotype had a lower risk of COPD compared to those with the rs16865421-A allele (odds ratio = 0.68, 95% confidence interval = 0.47-0.98, p = 0.041). However, no such association was found for rs1438831, rs6734100, rs6748795, rs7583463, rs840088 and rs975278. No significant interaction was observed between the genotypes and risk factors. CONCLUSIONS Polymorphisms of rs16865421-AG carried by the Uygur population may be protective against COPD.
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Affiliation(s)
- Li Li
- Department of Respiratory and Critical Care Medicine, First People's Hospital of Kashgar, Xinjiang, Kashgar, Xinjiang, China
| | - Shi Yue Li
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Guangzhou Medical University, Guangdong, Guangzhou, Guangdong, China
| | - Xuemei Zhong
- Department of Respiratory and Critical Care Medicine, First People's Hospital of Kashgar, Xinjiang, Kashgar, Xinjiang, China
| | - Jie Ren
- Department of Respiratory and Critical Care Medicine, First People's Hospital of Kashgar, Xinjiang, Kashgar, Xinjiang, China
| | - Xuwei Tian
- Department of Respiratory and Critical Care Medicine, First People's Hospital of Kashgar, Xinjiang, Kashgar, Xinjiang, China
| | - Maimaitiaili Tuerxun
- Department of Respiratory and Critical Care Medicine, First People's Hospital of Kashgar, Xinjiang, Kashgar, Xinjiang, China
| | - Chengxin Xie
- Department of Respiratory and Critical Care Medicine, First People's Hospital of Kashgar, Xinjiang, Kashgar, Xinjiang, China
| | - Feifei Li
- Department of Respiratory and Critical Care Medicine, First People's Hospital of Kashgar, Xinjiang, Kashgar, Xinjiang, China
| | - Aifang Zheng
- Department of Respiratory and Critical Care Medicine, First People's Hospital of Kashgar, Xinjiang, Kashgar, Xinjiang, China
| | - Paierda Aini
- Department of Respiratory and Critical Care Medicine, First People's Hospital of Kashgar, Xinjiang, Kashgar, Xinjiang, China
| | - Mukeremu Yasen
- Department of Respiratory and Critical Care Medicine, First People's Hospital of Kashgar, Xinjiang, Kashgar, Xinjiang, China
| | - Huaizhen Wang
- Department of Respiratory and Critical Care Medicine, First People's Hospital of Kashgar, Xinjiang, Kashgar, Xinjiang, China
| | - Xiaoguang Zou
- Department of Respiratory and Critical Care Medicine, First People's Hospital of Kashgar, Xinjiang, Kashgar, Xinjiang, China
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Wadhwa R, Aggarwal T, Malyla V, Kumar N, Gupta G, Chellappan DK, Dureja H, Mehta M, Satija S, Gulati M, Maurya PK, Collet T, Hansbro PM, Dua K. Identification of biomarkers and genetic approaches toward chronic obstructive pulmonary disease. J Cell Physiol 2019; 234:16703-16723. [DOI: 10.1002/jcp.28482] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 02/10/2019] [Accepted: 02/14/2019] [Indexed: 12/26/2022]
Affiliation(s)
- Ridhima Wadhwa
- Faculty of Life Sciences and Biotechnology South Asian University New Delhi India
| | - Taru Aggarwal
- Amity Institute of Biotechnology Amity University Noida Uttar Pradesh India
| | - Vamshikrishna Malyla
- Discipline of Pharmacy, Graduate School of Health University of Technology Sydney New South Wales Australia
- Centre for Inflammation Centenary Institute Sydney New South Wales Australia
| | - Nitesh Kumar
- Amity Institute for Advanced Research & Studies (M&D) Amity University Noida Uttar Pradesh India
| | - Gaurav Gupta
- School of Pharmaceutical Sciences Jaipur National University, Jagatpura Jaipur Rajasthan India
| | - Dinesh Kumar Chellappan
- Department of Life Sciences, School of Pharmacy International Medical University Bukit Jalil Kuala Lumpur Malaysia
| | - Harish Dureja
- Department of Pharmaceutical Sciences Maharishi Dayanand University Rohtak Haryana India
| | - Meenu Mehta
- School of Pharmaceutical Sciences Lovely Professional University Phagwara Punjab India
| | - Saurabh Satija
- School of Pharmaceutical Sciences Lovely Professional University Phagwara Punjab India
| | - Monica Gulati
- School of Pharmaceutical Sciences Lovely Professional University Phagwara Punjab India
| | - Pawan Kumar Maurya
- Department of Biochemistry Central University of Haryana Mahendergarh Haryana India
| | - Trudi Collet
- Innovative Medicines Group, Institute of Health & Biomedical Innovation Queensland University of Technology Brisbane Queensland Australia
| | - Philip Michael Hansbro
- Priority Research Centre for Healthy Lungs University of Newcastle & Hunter Medical Research Institute Newcastle New South Wales Australia
- Centre for Inflammation Centenary Institute Sydney New South Wales Australia
- School of Life Sciences University of Technology Sydney Sydney New South Wales Australia
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health University of Technology Sydney New South Wales Australia
- Priority Research Centre for Healthy Lungs University of Newcastle & Hunter Medical Research Institute Newcastle New South Wales Australia
- Centre for Inflammation Centenary Institute Sydney New South Wales Australia
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7
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Qiao D, Ameli A, Prokopenko D, Chen H, Kho AT, Parker MM, Morrow J, Hobbs BD, Liu Y, Beaty TH, Crapo JD, Barnes KC, Nickerson DA, Bamshad M, Hersh CP, Lomas DA, Agusti A, Make BJ, Calverley PMA, Donner CF, Wouters EF, Vestbo J, Paré PD, Levy RD, Rennard SI, Tal-Singer R, Spitz MR, Sharma A, Ruczinski I, Lange C, Silverman EK, Cho MH. Whole exome sequencing analysis in severe chronic obstructive pulmonary disease. Hum Mol Genet 2018; 27:3801-3812. [PMID: 30060175 PMCID: PMC6196654 DOI: 10.1093/hmg/ddy269] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 07/09/2018] [Accepted: 07/17/2018] [Indexed: 12/13/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD), one of the leading causes of death worldwide, is substantially influenced by genetic factors. Alpha-1 antitrypsin deficiency demonstrates that rare coding variants of large effect can influence COPD susceptibility. To identify additional rare coding variants in patients with severe COPD, we conducted whole exome sequencing analysis in 2543 subjects from two family-based studies (Boston Early-Onset COPD Study and International COPD Genetics Network) and one case-control study (COPDGene). Applying a gene-based segregation test in the family-based data, we identified significant segregation of rare loss of function variants in TBC1D10A and RFPL1 (P-value < 2x10-6), but were unable to find similar variants in the case-control study. In single-variant, gene-based and pathway association analyses, we were unable to find significant findings that replicated or were significant in meta-analysis. However, we found that the top results in the two datasets were in proximity to each other in the protein-protein interaction network (P-value = 0.014), suggesting enrichment of these results for similar biological processes. A network of these association results and their neighbors was significantly enriched in the transforming growth factor beta-receptor binding and cilia-related pathways. Finally, in a more detailed examination of candidate genes, we identified individuals with putative high-risk variants, including patients harboring homozygous mutations in genes associated with cutis laxa and Niemann-Pick Disease Type C. Our results likely reflect heterogeneity of genetic risk for COPD along with limitations of statistical power and functional annotation, and highlight the potential of network analysis to gain insight into genetic association studies.
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Affiliation(s)
- Dandi Qiao
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Asher Ameli
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Physics, Northeastern University, Boston, Massachusetts, United States of America
| | - Dmitry Prokopenko
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Han Chen
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
- Center for Precision Health, School of Public Health and School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Alvin T Kho
- Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Margaret M Parker
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jarrett Morrow
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Brian D Hobbs
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Yanhong Liu
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - James D Crapo
- National Jewish Health, Denver, Colorado, United States of America
| | - Kathleen C Barnes
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Michael Bamshad
- Division of Genetic Medicine, Department of Pediatrics, University of Washington and Seattle Children’s Hospital, Seattle, Washington , United States of America
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | | | - Alvar Agusti
- Respiratory Institute, Hospital Clinic, IDIBAPS, University of Barcelona, CIBERES, Barcelona, Spain
| | - Barry J Make
- National Jewish Health, Denver, Colorado, United States of America
| | | | - Claudio F Donner
- Mondo Medico di I.F.I.M. srl, Multidisciplinary and Rehabilitation Outpatient Clinic, Borgomanero, Novara, Italy
| | - Emiel F Wouters
- Department of Respiratory Medicine, Maastricht University Medical Center, AZ Maastricht, The Netherlands
| | - Jørgen Vestbo
- University of Manchester, Manchester, United Kingdom
| | - Peter D Paré
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, British Columbia V6T, Canada
| | - Robert D Levy
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, British Columbia V6T, Canada
| | - Stephen I Rennard
- University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- AstraZeneca, Cambridge CB2 0RE, United Kingdom
| | - Ruth Tal-Singer
- GSK Research and Development, KingOf Prussia, Pennsylvania, United States of America
| | - Margaret R Spitz
- Dan L. Duncan Comprehensive Cancer Center, Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
| | - Amitabh Sharma
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Christoph Lange
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Channing Division of Network Medicine, Longwood Avenue, Boston, MA, USA
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8
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Abadi A, Alyass A, Robiou du Pont S, Bolker B, Singh P, Mohan V, Diaz R, Engert JC, Yusuf S, Gerstein HC, Anand SS, Meyre D. Penetrance of Polygenic Obesity Susceptibility Loci across the Body Mass Index Distribution. Am J Hum Genet 2017; 101:925-938. [PMID: 29220676 PMCID: PMC5812888 DOI: 10.1016/j.ajhg.2017.10.007] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 10/12/2017] [Indexed: 12/17/2022] Open
Abstract
A growing number of single-nucleotide polymorphisms (SNPs) have been associated with body mass index (BMI) and obesity, but whether the effects of these obesity-susceptibility loci are uniform across the BMI distribution remains unclear. We studied the effects of 37 BMI-associated SNPs in 75,230 adults of European ancestry across BMI percentiles by using conditional quantile regression (CQR) and meta-regression (MR) models. The effects of nine SNPs (24%)-rs1421085 (FTO; p = 8.69 × 10-15), rs6235 (PCSK1; p = 7.11 × 10-6), rs7903146 (TCF7L2; p = 9.60 × 10-6), rs11873305 (MC4R; p = 5.08 × 10-5), rs12617233 (FANCL; p = 5.30 × 10-5), rs11672660 (GIPR; p = 1.64 × 10-4), rs997295 (MAP2K5; p = 3.25 × 10-4), rs6499653 (FTO; p = 6.23 × 10-4), and rs3824755 (NT5C2; p = 7.90 × 10-4)-increased significantly across the sample BMI distribution. We showed that such increases stemmed from unadjusted gene interactions that enhanced the effects of SNPs in persons with a high BMI. When 125 height-associated SNPs were analyzed for comparison, only one (<1%), rs6219 (IGF1, p = 1.80 × 10-4), showed effects that varied significantly across height percentiles. Cumulative gene scores of these SNPs (GS-BMI and GS-height) showed that only GS-BMI had effects that increased significantly across the sample distribution (BMI: p = 7.03 × 10-37; height: p = 0.499). Overall, these findings underscore the importance of gene-gene and gene-environment interactions in shaping the genetic architecture of BMI and advance a method for detecting such interactions by using only the sample outcome distribution.
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Affiliation(s)
- Arkan Abadi
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Akram Alyass
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Sebastien Robiou du Pont
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Ben Bolker
- Department of Mathematics and Statistics, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Pardeep Singh
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Viswanathan Mohan
- Madras Diabetes Research Foundation, Gopalapuram, Chennai 600086, India
| | - Rafael Diaz
- Estudios Clínicos Latino America, Paraguay 160, S2000CVD Rosario, Santa Fe, Argentina
| | | | - Salim Yusuf
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON L8S 4L8, Canada; Population Health Research Institute, McMaster University and Hamilton Health Sciences, Hamilton General Hospital, Hamilton, ON L8S 4L8, Canada; Department of Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Hertzel C Gerstein
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON L8S 4L8, Canada; Population Health Research Institute, McMaster University and Hamilton Health Sciences, Hamilton General Hospital, Hamilton, ON L8S 4L8, Canada; Department of Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Sonia S Anand
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON L8S 4L8, Canada; Population Health Research Institute, McMaster University and Hamilton Health Sciences, Hamilton General Hospital, Hamilton, ON L8S 4L8, Canada; Department of Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - David Meyre
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON L8S 4L8, Canada; Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada.
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9
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Busch R, Hobbs BD, Zhou J, Castaldi PJ, McGeachie MJ, Hardin ME, Hawrylkiewicz I, Sliwinski P, Yim JJ, Kim WJ, Kim DK, Agusti A, Make BJ, Crapo JD, Calverley PM, Donner CF, Lomas DA, Wouters EF, Vestbo J, Tal-Singer R, Bakke P, Gulsvik A, Litonjua AA, Sparrow D, Paré PD, Levy RD, Rennard SI, Beaty TH, Hokanson J, Silverman EK, Cho MH. Genetic Association and Risk Scores in a Chronic Obstructive Pulmonary Disease Meta-analysis of 16,707 Subjects. Am J Respir Cell Mol Biol 2017; 57:35-46. [PMID: 28170284 PMCID: PMC5516277 DOI: 10.1165/rcmb.2016-0331oc] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The heritability of chronic obstructive pulmonary disease (COPD) cannot be fully explained by recognized genetic risk factors identified as achieving genome-wide significance. In addition, the combined contribution of genetic variation to COPD risk has not been fully explored. We sought to determine: (1) whether studies of variants from previous studies of COPD or lung function in a larger sample could identify additional associated variants, particularly for severe COPD; and (2) the impact of genetic risk scores on COPD. We genotyped 3,346 single-nucleotide polymorphisms (SNPs) in 2,588 cases (1,803 severe COPD) and 1,782 control subjects from four cohorts, and performed association testing with COPD, combining these results with existing genotyping data from 6,633 cases (3,497 severe COPD) and 5,704 control subjects. In addition, we developed genetic risk scores from SNPs associated with lung function and COPD and tested their discriminatory power for COPD-related measures. We identified significant associations between SNPs near PPIC (P = 1.28 × 10-8) and PPP4R4/SERPINA1 (P = 1.01 × 10-8) and severe COPD; the latter association may be driven by recognized variants in SERPINA1. Genetic risk scores based on SNPs previously associated with COPD and lung function had a modest ability to discriminate COPD (area under the curve, ∼0.6), and accounted for a mean 0.9-1.9% lower forced expiratory volume in 1 second percent predicted for each additional risk allele. In a large genetic association analysis, we identified associations with severe COPD near PPIC and SERPINA1. A risk score based on combining genetic variants had modest, but significant, effects on risk of COPD and lung function.
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Affiliation(s)
- Robert Busch
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Brian D. Hobbs
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Jin Zhou
- University of Arizona, Tucson, Arizona
| | - Peter J. Castaldi
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Michael J. McGeachie
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Megan E. Hardin
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | | | - 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, Korea
| | - Woo Jin Kim
- Kangwon National University, Chuncheon, Korea
| | - Deog K. Kim
- Seoul National University College of Medicine Boramae Medical Center, Seoul, Korea
| | - Alvar Agusti
- 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, Novara, Italy
| | | | | | - Jørgen Vestbo
- University of Manchester, Manchester, United Kingdom
| | - Ruth Tal-Singer
- GlaxoSmithKline Research and Development, King of Prussia, Pennsylvania
| | - Per Bakke
- University of Bergen, Bergen, Norway
| | | | - Augusto A. Litonjua
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - David Sparrow
- Brigham and Women’s Hospital and the Veterans Administration Medical Center–Jamaica Plain, Jamaica Plain, Massachusetts
| | - Peter D. Paré
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert D. Levy
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Terri H. Beaty
- Department of Epidemiology, Bloomberg School of Public Health, the Johns Hopkins University, Baltimore, Maryland; and
| | - John Hokanson
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Edwin K. Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Michael H. Cho
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
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10
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Yuan C, Chang D, Lu G, Deng X. Genetic polymorphism and chronic obstructive pulmonary disease. Int J Chron Obstruct Pulmon Dis 2017; 12:1385-1393. [PMID: 28546746 PMCID: PMC5436778 DOI: 10.2147/copd.s134161] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a common chronic disease, and its morbidity and mortality are increasing. There are many studies that have tried to explain the pathogenesis of COPD from genetic susceptibility, to identify the susceptibility of COPD factors, which play a role in early prevention, early detection and the early treatment. However, it is well known that COPD is an inflammatory disease characterized by incomplete reversible airflow limitation in which genes interact with the environment. In recent years, many studies have proved gene polymorphisms and COPD correlation. However, there is less research on the relationship between COPD and genome-wide association study (GWAS), epigenetics and apoptosis. In this paper, we summarized the correlation between gene level and COPD from the following four aspects: the GWAS, the gene polymorphism, the epigenetics and the apoptosis, and the relationship between COPD and gene is summarized comprehensively.
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Affiliation(s)
| | - De Chang
- Department of Respiratory Medicine, General Hospital of Chinese People's Armed Police Forces
| | - Guangming Lu
- Institute of Health Management, Chinese PLA General Hospital, Beijing, People's Republic of China
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11
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Farahi N, Paige E, Balla J, Prudence E, Ferreira RC, Southwood M, Appleby SL, Bakke P, Gulsvik A, Litonjua AA, Sparrow D, Silverman EK, Cho MH, Danesh J, Paul DS, Freitag DF, Chilvers ER. Neutrophil-mediated IL-6 receptor trans-signaling and the risk of chronic obstructive pulmonary disease and asthma. Hum Mol Genet 2017; 26:1584-1596. [PMID: 28334838 PMCID: PMC5393150 DOI: 10.1093/hmg/ddx053] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 02/08/2017] [Indexed: 02/02/2023] Open
Abstract
The Asp358Ala variant in the interleukin-6 receptor (IL-6R) gene has been implicated in asthma, autoimmune and cardiovascular disorders, but its role in other respiratory conditions such as chronic obstructive pulmonary disease (COPD) has not been investigated. The aims of this study were to evaluate whether there is an association between Asp358Ala and COPD or asthma risk, and to explore the role of the Asp358Ala variant in sIL-6R shedding from neutrophils and its pro-inflammatory effects in the lung. We undertook logistic regression using data from the UK Biobank and the ECLIPSE COPD cohort. Results were meta-analyzed with summary data from a further three COPD cohorts (7,519 total cases and 35,653 total controls), showing no association between Asp358Ala and COPD (OR = 1.02 [95% CI: 0.96, 1.07]). Data from the UK Biobank showed a positive association between the Asp358Ala variant and atopic asthma (OR = 1.07 [1.01, 1.13]). In a series of in vitro studies using blood samples from 37 participants, we found that shedding of sIL-6R from neutrophils was greater in carriers of the Asp358Ala minor allele than in non-carriers. Human pulmonary artery endothelial cells cultured with serum from homozygous carriers showed an increase in MCP-1 release in carriers of the minor allele, with the difference eliminated upon addition of tocilizumab. In conclusion, there is evidence that neutrophils may be an important source of sIL-6R in the lungs, and the Asp358Ala variant may have pro-inflammatory effects in lung cells. However, we were unable to identify evidence for an association between Asp358Ala and COPD.
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Affiliation(s)
- Neda Farahi
- Division of Respiratory Medicine, Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Ellie Paige
- Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge CB1 8RN, Cambridge, UK
| | - Jozef Balla
- Division of Respiratory Medicine, Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Emily Prudence
- Division of Respiratory Medicine, Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Ricardo C. Ferreira
- JDRF/Wellcome Trust Diabetes and Inflammation Laboratory, Nuffield Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Mark Southwood
- Division of Respiratory Medicine, Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Sarah L. Appleby
- Division of Respiratory Medicine, Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
| | - Per Bakke
- Department of Clinical Science, University of Bergen, Bergen 5021, Norway
| | - Amund Gulsvik
- Department of Clinical Science, University of Bergen, Bergen 5021, Norway
| | - Augusto A. Litonjua
- Brigham and Women’s Hospital and Harvard Medical School, Boston 02115, MA, USA
| | - David Sparrow
- VA Boston Healthcare System and School of Medicine, Boston University, Boston 02132, MA, USA
| | - Edwin K. Silverman
- Brigham and Women’s Hospital and Harvard Medical School, Boston 02115, MA, USA
| | - Michael H. Cho
- Brigham and Women’s Hospital and Harvard Medical School, Boston 02115, MA, USA
| | - John Danesh
- Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge CB1 8RN, Cambridge, UK,British Heart Foundation Centre of Excellence, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK,NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Cambridge, UK,Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Dirk S. Paul
- Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge CB1 8RN, Cambridge, UK
| | - Daniel F. Freitag
- Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge CB1 8RN, Cambridge, UK,To whom correspondence should be addressed at:
| | - Edwin R. Chilvers
- Division of Respiratory Medicine, Department of Medicine, University of Cambridge School of Clinical Medicine, Cambridge CB2 0QQ, UK
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12
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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: 5.0] [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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13
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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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14
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Begum F, Ruczinski I, Hokanson JE, Lutz SM, Parker MM, Cho MH, Hetmanski JB, Scharpf RB, Crapo JD, Silverman EK, Beaty TH. Hemizygous Deletion on Chromosome 3p26.1 Is Associated with Heavy Smoking among African American Subjects in the COPDGene Study. PLoS One 2016; 11:e0164134. [PMID: 27711239 PMCID: PMC5053531 DOI: 10.1371/journal.pone.0164134] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 09/20/2016] [Indexed: 02/04/2023] Open
Abstract
Many well-powered genome-wide association studies have identified genetic determinants of self-reported smoking behaviors and measures of nicotine dependence, but most have not considered the role of structural variants, such as copy number variation (CNVs), influencing these phenotypes. Here, we included 2,889 African American and 6,187 non-Hispanic White subjects from the COPDGene cohort (http://www.copdgene.org) to carefully investigate the role of polymorphic CNVs across the genome on various measures of smoking behavior. We identified a CNV component (a hemizygous deletion) on chromosome 3p26.1 associated with two quantitative phenotypes related to smoking behavior among African Americans. This polymorphic hemizygous deletion is significantly associated with pack-years and cigarettes smoked per day among African American subjects in the COPDGene study. We sought evidence of replication in African Americans from the population based Atherosclerosis Risk in Communities (ARIC) study. While we observed similar CNV counts, the extent of exposure to cigarette smoking among ARIC subjects was quite different and the smaller sample size of heavy smokers in ARIC severely limited statistical power, so we were unable to replicate our findings from the COPDGene cohort. But meta-analyses of COPDGene and ARIC study subjects strengthened our association signal. However, a few linkage studies have reported suggestive linkage to the 3p26.1 region, and a few genome-wide association studies (GWAS) have reported markers in the gene (GRM7) nearest to this 3p26.1 area of polymorphic deletions are associated with measures of nicotine dependence among subjects of European ancestry.
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Affiliation(s)
- Ferdouse Begum
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
- * E-mail:
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - John E. Hokanson
- Department of Epidemiology, Colorado School of Public Health, Aurora, Colorado, United States of America
| | - Sharon M. Lutz
- Department of Biostatisitics and Informatics, Colorado School of Public Health, Aurora, Colorado, United States of America
| | - Margaret M. Parker
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michael H. Cho
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Jacqueline B. Hetmanski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Robert B. Scharpf
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - James D. Crapo
- Department of Medicine, National Jewish Health, Denver, Colorado, United States of America
| | - Edwin K. Silverman
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Terri H. Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
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15
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Hua L, An L, Li L, Zhang Y, Wang C. A bioinformatics strategy for detecting the complexity of Chronic Obstructive Pulmonary Disease in Northern Chinese Han Population. Genes Genet Syst 2016; 87:197-209. [PMID: 22976395 DOI: 10.1266/ggs.87.197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Chronic Obstructive Pulmonary Disease (COPD) is a complex human disease which is driven not only by genetic factors, but also by various environmental variables, such as gender, age and smoking. Therefore, there is a demand for investigating the complexity among various risk factors involved in COPD. In this study, 44 tagging SNPs from EPHX1, GSTP1, SERPINE2 and TGFB1 were selected and genotyped in 310 COPD cases and 203 controls, all of which belong to the Han from North China. We integrated functional prediction algorithms of nonsynonymous SNPs (nsSNPs) into Bayesian network to explore the complex regulatory relationships among disease traits and various risk factors. The results showed that three basic variables (age, sex and smoking) were risk factors of COPD-related trait and phenotype. Besides these environmental risk factors, deleterious nsSNPs were found to perform better than those of significant synonymous SNPs when used as variables to make risk prediction of disease outcome. This study provides further evidences for detecting the complexity of COPD in Northern Chinese Han Population.
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Affiliation(s)
- Lin Hua
- Biomedical Engineering Institute of Capital Medical University, Beijing, China.
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16
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Solleti SK, Srisuma S, Bhattacharya S, Rangel-Moreno J, Bijli KM, Randall TD, Rahman A, Mariani TJ. Serpine2 deficiency results in lung lymphocyte accumulation and bronchus-associated lymphoid tissue formation. FASEB J 2016; 30:2615-26. [PMID: 27059719 DOI: 10.1096/fj.201500159r] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/28/2016] [Indexed: 11/11/2022]
Abstract
Serine proteinase inhibitor, clade E, member 2 (SERPINE2), is a cell- and extracellular matrix-associated inhibitor of thrombin. Although SERPINE2 is a candidate susceptibility gene for chronic obstructive pulmonary disease, the physiologic role of this protease inhibitor in lung development and homeostasis is unknown. We observed spontaneous monocytic-cell infiltration in the lungs of Serpine2-deficient (SE2(-/-)) mice, beginning at or before the time of lung maturity, which resulted in lesions that resembled bronchus-associated lymphoid tissue (BALT). The initiation of lymphocyte accumulation in the lungs of SE2(-/-) mice involved the excessive expression of chemokines, cytokines, and adhesion molecules that are essential for BALT induction, organization, and maintenance. BALT-like lesion formation in the lungs of SE2(-/-) mice was also associated with a significant increase in the activation of thrombin, a recognized target of SE2, and excess stimulation of NF-κB, a major regulator of chemokine expression and inflammation. Finally, systemic delivery of thrombin rapidly stimulated lung chemokine expression in vivo These data uncover a novel mechanism whereby loss of serine protease inhibition leads to lung lymphocyte accumulation.-Solleti, S. K., Srisuma, S., Bhattacharya, S., Rangel-Moreno, J., Bijli, K. M., Randall, T. D., Rahman, A., Mariani, T. J. Serpine2 deficiency results in lung lymphocyte accumulation and bronchus-associated lymphoid tissue formation.
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Affiliation(s)
- Siva Kumar Solleti
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, USA
| | - Sorachai Srisuma
- Department of Physiology, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Soumyaroop Bhattacharya
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, USA
| | - Javier Rangel-Moreno
- Division of Allergy, Immunology, and Rheumatology, University of Rochester Medical Center, Rochester, New York, USA
| | - Kaiser M Bijli
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, USA; Division of Pulmonary, Allergy, and Critical Care Medicine, Emory University/Atlanta Veterans Affairs Medical Center, Atlanta, Georgia, USA
| | - Troy D Randall
- Division of Allergy, Immunology, and Rheumatology, University of Rochester Medical Center, Rochester, New York, USA; Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Arshad Rahman
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, USA
| | - Thomas J Mariani
- Division of Neonatology, Department of Pediatrics, University of Rochester Medical Center, Rochester, New York, USA;
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17
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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: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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18
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Begum F, Ruczinski I, Li S, Silverman EK, Cho MH, Lynch DA, Curran-Everett D, Crapo J, Scharpf RB, Parker MM, Hetmanski JB, Beaty TH. Identifying a Deletion Affecting Total Lung Capacity Among Subjects in the COPDGene Study Cohort. Genet Epidemiol 2015; 40:81-8. [PMID: 26643968 DOI: 10.1002/gepi.21943] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2015] [Revised: 09/21/2015] [Accepted: 10/19/2015] [Indexed: 01/17/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) is a progressive disease with both environmental and genetic risk factors. Genome-wide association studies (GWAS) have identified multiple genomic regions influencing risk of COPD. To thoroughly investigate the genetic etiology of COPD, however, it is also important to explore the role of copy number variants (CNVs) because the presence of structural variants can alter gene expression and can be causal for some diseases. Here, we investigated effects of polymorphic CNVs on quantitative measures of pulmonary function and chest computed tomography (CT) phenotypes among subjects enrolled in COPDGene, a multisite study. COPDGene subjects consist of roughly one-third African American (AA) and two-thirds non-Hispanic white adult smokers (with or without COPD). We estimated CNVs using PennCNV on 9,076 COPDGene subjects using Illumina's Omni-Express genome-wide marker array. We tested for association between polymorphic CNV components (defined as disjoint intervals of copy number regions) for several quantitative phenotypes associated with COPD within each racial group. Among the AAs, we identified a polymorphic CNV on chromosome 5q35.2 located between two genes (FAM153B and SIMK1, but also harboring several pseudo-genes) giving genome-wide significance in tests of association with total lung capacity (TLCCT ) as measured by chest CT scans. This is the first study of genome-wide association tests of polymorphic CNVs and TLCCT . Although the ARIC cohort did not have the phenotype of TLCCT , we found similar counts of CNV deletions and amplifications among AA and European subjects in this second cohort.
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Affiliation(s)
- Ferdouse Begum
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Shengchao Li
- Cancer Genomics Research Laboratory (CGR), Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland, United States of America
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - David A Lynch
- Department of Medicine, National Jewish Health, Denver, Colorado, United States of America
| | - Douglas Curran-Everett
- Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, Colorado, United States of America
| | - James Crapo
- Department of Medicine, National Jewish Health, Denver, Colorado, United States of America
| | - Robert B Scharpf
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Margaret M Parker
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Jacqueline B Hetmanski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
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19
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The Relationship of Educational Attainment with Pulmonary Emphysema and Airway Wall Thickness. Ann Am Thorac Soc 2015; 12:813-20. [DOI: 10.1513/annalsats.201410-485oc] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
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20
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Wan ES, Qiu W, Morrow J, Beaty TH, Hetmanski J, Make BJ, Lomas DA, Silverman EK, DeMeo DL. Genome-wide site-specific differential methylation in the blood of individuals with Klinefelter syndrome. Mol Reprod Dev 2015; 82:377-86. [PMID: 25988574 DOI: 10.1002/mrd.22483] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2015] [Accepted: 03/30/2015] [Indexed: 12/25/2022]
Abstract
Klinefelter syndrome (KS) (47 XXY) is a common sex-chromosome aneuploidy with an estimated prevalence of one in every 660 male births. Investigations into the associations between DNA methylation and the highly variable clinical manifestations of KS have largely focused on the supernumerary X chromosome; systematic investigations of the epigenome have been limited. We obtained genome-wide DNA methylation data from peripheral blood using the Illumina HumanMethylation450K platform in 5 KS (47 XXY) versus 102 male (46 XY) and 113 female (46 XX) control subjects participating in the COPDGene Study. Empirical Bayes-mediated models were used to test for differential methylation by KS status. CpG sites with a false-discovery rate < 0.05 in the discovery cohort which were available on the first-generation HumanMethylation 27 K platform were further examined in an independent replication cohort of 2 KS subjects, 590 male, and 495 female controls drawn from the International COPD Genetics Network (ICGN). Differential methylation at sites throughout the genome were identified, including 86 CpG sites that were differentially methylated in KS subjects relative to both male and female controls. CpG sites annotated to the HEN1 methyltransferase homolog 1 (HENMT1), calcyclin-binding protein (CACYBP), and GTPase-activating protein (SH3 domain)-binding protein 1 (G3BP1) genes were among the "KS-specific" loci that were replicated in ICGN. We conclude that site-specific differential methylation exists throughout the genome in KS. The functional impact and clinical relevance of these differentially methylated loci should be explored in future studies.
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Affiliation(s)
- Emily S Wan
- Channing Division of Network Medicine, Brigham & Women's Hospital, Boston, Massachusetts.,Division of Pulmonary and Critical Care, Brigham & Women's Hospital, Boston, Massachusetts
| | - Weiliang Qiu
- Channing Division of Network Medicine, Brigham & Women's Hospital, Boston, Massachusetts
| | - Jarrett Morrow
- Channing Division of Network Medicine, Brigham & Women's Hospital, Boston, Massachusetts
| | - Terri H Beaty
- Department of Biostatistics and Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Jacqueline Hetmanski
- Department of Biostatistics and Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Barry J Make
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, Colorado
| | - David A Lomas
- Wolfson Institute for Biomedical Research, University College London, London, United Kingdom
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham & Women's Hospital, Boston, Massachusetts.,Division of Pulmonary and Critical Care, Brigham & Women's Hospital, Boston, Massachusetts
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham & Women's Hospital, Boston, Massachusetts.,Division of Pulmonary and Critical Care, Brigham & Women's Hospital, Boston, Massachusetts
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21
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Increased expression of protease nexin-1 in fibroblasts during idiopathic pulmonary fibrosis regulates thrombin activity and fibronectin expression. J Transl Med 2014; 94:1237-46. [PMID: 25199049 DOI: 10.1038/labinvest.2014.111] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 07/03/2014] [Accepted: 07/29/2014] [Indexed: 11/08/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic diffuse lung disease characterized by an accumulation of excess fibrous material in the lung. Protease nexin-1 (PN-1) is a tissue serpin produced by many cell types, including lung fibroblasts. PN-1 is capable of regulating proteases of both coagulation and fibrinolysis systems, by inhibiting, respectively, thrombin and plasminergic enzymes. PN-1 is thus a good candidate for regulating tissue remodeling occurring during IPF. We demonstrated a significant increase of PN-1 expression in lung tissue extracts, lung fibroblasts and bronchoalveolar lavage fluids of patients with IPF. The increase of PN-1 expression was reproduced after stimulation of control lung fibroblasts by transforming growth factor-β, a major pro-fibrotic cytokine involved in IPF. Another serpin, plasminogen activator inhibitor-1 (PAI-1) is also overexpressed in fibrotic fibroblasts. Unlike PAI-1, cell-bound PN-1 as well as secreted PN-1 from IPF and stimulated fibroblasts were shown to inhibit efficiently thrombin activity, indicating that both serpins should exhibit complementary roles in IPF pathogenesis, via their different preferential antiprotease activities. Moreover, we observed that overexpression of PN-1 induced by transfection of control fibroblasts led to increased fibronectin expression, whereas PN-1 silencing induced in fibrotic fibroblasts led to decreased fibronectin expression. Overexpression of PN-1 lacking either its antiprotease activity or its binding capacity to glycosaminoglycans had no effect on fibronectin expression. These novel findings suggest that modulation of PN-1 expression in lung fibroblasts may also have a role in the development of IPF by directly influencing the expression of extracellular matrix proteins. Our data provide new insights into the role of PN-1 in the poorly understood pathological processes involved in IPF and could therefore give rise to new therapeutic approaches.
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22
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Genetic susceptibility for chronic bronchitis in chronic obstructive pulmonary disease. Respir Res 2014; 15:113. [PMID: 25241909 PMCID: PMC4190389 DOI: 10.1186/s12931-014-0113-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 09/02/2014] [Indexed: 12/23/2022] Open
Abstract
Background Chronic bronchitis (CB) is one of the classic phenotypes of COPD. The aims of our study were to investigate genetic variants associated with COPD subjects with CB relative to smokers with normal spirometry, and to assess for genetic differences between subjects with CB and without CB within the COPD population. Methods We analyzed data from current and former smokers from three cohorts: the COPDGene Study; GenKOLS (Bergen, Norway); and the Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints (ECLIPSE). CB was defined as having a cough productive of phlegm on most days for at least 3 consecutive months per year for at least 2 consecutive years. CB COPD cases were defined as having both CB and at least moderate COPD based on spirometry. Our primary analysis used smokers with normal spirometry as controls; secondary analysis was performed using COPD subjects without CB as controls. Genotyping was performed on Illumina platforms; results were summarized using fixed-effect meta-analysis. Results For CB COPD relative to smoking controls, we identified a new genome-wide significant locus on chromosome 11p15.5 (rs34391416, OR = 1.93, P = 4.99 × 10-8) as well as significant associations of known COPD SNPs within FAM13A. In addition, a GWAS of CB relative to those without CB within COPD subjects showed suggestive evidence for association on 1q23.3 (rs114931935, OR = 1.88, P = 4.99 × 10-7). Conclusions We found genome-wide significant associations with CB COPD on 4q22.1 (FAM13A) and 11p15.5 (EFCAB4A, CHID1 and AP2A2), and a locus associated with CB within COPD subjects on 1q23.3 (RPL31P11 and ATF6). This study provides further evidence that genetic variants may contribute to phenotypic heterogeneity of COPD. Trial registration ClinicalTrials.gov NCT00608764, NCT00292552 Electronic supplementary material The online version of this article (doi:10.1186/s12931-014-0113-2) contains supplementary material, which is available to authorized users.
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23
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Hobbs BD, Hersh CP. Integrative genomics of chronic obstructive pulmonary disease. Biochem Biophys Res Commun 2014; 452:276-86. [PMID: 25078622 PMCID: PMC4172635 DOI: 10.1016/j.bbrc.2014.07.086] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 07/18/2014] [Indexed: 01/21/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) is a complex disease with both environmental and genetic determinants, the most important of which is cigarette smoking. There is marked heterogeneity in the development of COPD among persons with similar cigarette smoking histories, which is likely partially explained by genetic variation. Genomic approaches such as genomewide association studies and gene expression studies have been used to discover genes and molecular pathways involved in COPD pathogenesis; however, these "first generation" omics studies have limitations. Integrative genomic studies are emerging which can combine genomic datasets to further examine the molecular underpinnings of COPD. Future research in COPD genetics will likely use network-based approaches to integrate multiple genomic data types in order to model the complex molecular interactions involved in COPD pathogenesis. This article reviews the genomic research to date and offers a vision for the future of integrative genomic research in COPD.
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Affiliation(s)
- Brian D Hobbs
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, United States; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, United States; Harvard Medical School, Boston, MA, United States
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, United States; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, United States; Harvard Medical School, Boston, MA, United States.
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24
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McDonald MLN, Mattheisen M, Cho MH, Liu YY, Harshfield B, Hersh CP, Bakke P, Gulsvik A, Lange C, Beaty TH, Silverman EK. Beyond GWAS in COPD: probing the landscape between gene-set associations, genome-wide associations and protein-protein interaction networks. Hum Hered 2014; 78:131-9. [PMID: 25171373 PMCID: PMC4415367 DOI: 10.1159/000365589] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 07/01/2014] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES To use a systems biology approach to integrate genotype and protein-protein interaction (PPI) data to identify disease network modules associated with chronic obstructive pulmonary disease (COPD) and to perform traditional pathway analysis. METHODS We utilized a standard gene-set association approach (FORGE) using gene-based association analysis and gene-set definitions from the molecular signatures database (MSigDB). As a discovery step, we analyzed GWAS results from 2 well-characterized COPD cohorts: COPDGene and GenKOLS. We used a third well-characterized COPD case-control cohort for replication: ECLIPSE. Next, we used dmGWAS, a method that integrates GWAS results with PPI, to identify COPD disease modules. RESULTS No gene-sets reached experiment-wide significance in either discovery population. We identified a consensus network of 10 genes identified in modules by integrating GWAS results with PPI that replicated in COPDGene, GenKOLS, and ECLIPSE. Members of 4 gene-sets were enriched among these 10 genes: (i) lung adenocarcinoma tumor-sequencing genes, (ii) IL-7 pathway genes, (iii) kidney cell response to arsenic, and (iv) CD4 T-cell responses. Further, several genes have also been associated with pathophysiology relevant to COPD including KCNK3, NEDD4L, and RIN3. In particular, KCNK3 has been associated with pulmonary arterial hypertension, a common complication in advanced COPD. CONCLUSION We report a set of new genes that may influence the etiology of COPD that would not have been identified using traditional GWAS and pathway analyses alone.
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Affiliation(s)
- Merry-Lynn Noelle McDonald
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Manuel Mattheisen
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedicine and Centre for integrative Sequencing (iSEQ), Aarhus University, Aarhus, Denmark
| | - Michael H. Cho
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Benjamin Harshfield
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Craig P. Hersh
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, 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
| | | | - Terri H. Beaty
- Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - Edwin K. Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
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25
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Lee JH, McDonald MLN, Cho MH, Wan ES, Castaldi PJ, Hunninghake GM, Marchetti N, Lynch DA, Crapo JD, Lomas DA, Coxson HO, Bakke PS, Silverman EK, Hersh CP, the COPDGene and ECLIPSE Investigators. DNAH5 is associated with total lung capacity in chronic obstructive pulmonary disease. Respir Res 2014; 15:97. [PMID: 25134640 PMCID: PMC4169636 DOI: 10.1186/s12931-014-0097-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 08/07/2014] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) is characterized by expiratory flow limitation, causing air trapping and lung hyperinflation. Hyperinflation leads to reduced exercise tolerance and poor quality of life in COPD patients. Total lung capacity (TLC) is an indicator of hyperinflation particularly in subjects with moderate-to-severe airflow obstruction. The aim of our study was to identify genetic variants associated with TLC in COPD. METHODS We performed genome-wide association studies (GWASs) in white subjects from three cohorts: the COPDGene Study; the Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints (ECLIPSE); and GenKOLS (Bergen, Norway). All subjects were current or ex-smokers with at least moderate airflow obstruction, defined by a ratio of forced expiratory volume in 1 second to forced vital capacity (FEV1/FVC) <0.7 and FEV1 < 80% predicted on post-bronchodilator spirometry. TLC was calculated by using volumetric computed tomography scans at full inspiration (TLCCT). Genotyping in each cohort was completed, with statistical imputation of additional markers. To find genetic variants associated with TLCCT, linear regression models were used, with adjustment for age, sex, pack-years of smoking, height, and principal components for genetic ancestry. Results were summarized using fixed-effect meta-analysis. RESULTS Analysis of a total of 4,543 COPD subjects identified one genome-wide significant locus on chromosome 5p15.2 (rs114929486, β = 0.42L, P = 4.66 × 10-8). CONCLUSIONS In COPD, TLCCT was associated with a SNP in dynein, axonemal, heavy chain 5 (DNAH5), a gene in which genetic variants can cause primary ciliary dyskinesia. DNAH5 could have an effect on hyperinflation in COPD.
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Affiliation(s)
- Jin Hwa Lee
- />Channing Division of Network Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA
- />Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, School of Medicine, Ewha Womans University, Seoul, South Korea
| | - Merry-Lynn N McDonald
- />Channing Division of Network Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA
| | - Michael H Cho
- />Channing Division of Network Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA
- />Division of Pulmonary and Critical Care, Brigham and Women’s Hospital, Boston, MA USA
| | - Emily S Wan
- />Channing Division of Network Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA
- />Division of Pulmonary and Critical Care, Brigham and Women’s Hospital, Boston, MA USA
| | - Peter J Castaldi
- />Channing Division of Network Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA
| | - Gary M Hunninghake
- />Division of Pulmonary and Critical Care, Brigham and Women’s Hospital, Boston, MA USA
| | - Nathaniel Marchetti
- />Division of Pulmonary and Critical Care Medicine, Department of Medicine, Temple University School of Medicine, Philadelphia, PA USA
| | | | | | - David A Lomas
- />Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Harvey O Coxson
- />Department of Radiology, University of British Columbia, Vancouver, Canada
| | - Per S Bakke
- />Department of Clinical Science, University of Bergen, Bergen, Norway
- />Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Edwin K Silverman
- />Channing Division of Network Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA
- />Division of Pulmonary and Critical Care, Brigham and Women’s Hospital, Boston, MA USA
| | - Craig P Hersh
- />Channing Division of Network Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA
- />Division of Pulmonary and Critical Care, Brigham and Women’s Hospital, Boston, MA USA
| | - the COPDGene and ECLIPSE Investigators
- />Channing Division of Network Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115 USA
- />Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, School of Medicine, Ewha Womans University, Seoul, South Korea
- />Division of Pulmonary and Critical Care, Brigham and Women’s Hospital, Boston, MA USA
- />Division of Pulmonary and Critical Care Medicine, Department of Medicine, Temple University School of Medicine, Philadelphia, PA USA
- />National Jewish Health, Denver, CO USA
- />Wolfson Institute for Biomedical Research, University College London, London, UK
- />Department of Radiology, University of British Columbia, Vancouver, Canada
- />Department of Clinical Science, University of Bergen, Bergen, Norway
- />Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
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26
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Cho MH, McDonald MLN, Zhou X, Mattheisen M, Castaldi PJ, Hersh CP, Demeo DL, Sylvia JS, Ziniti J, Laird NM, Lange C, Litonjua AA, Sparrow D, Casaburi R, Barr RG, Regan EA, Make BJ, Hokanson JE, Lutz S, Dudenkov TM, Farzadegan H, Hetmanski JB, Tal-Singer R, Lomas DA, Bakke P, Gulsvik A, Crapo JD, Silverman EK, Beaty TH. Risk loci for chronic obstructive pulmonary disease: a genome-wide association study and meta-analysis. THE LANCET. RESPIRATORY MEDICINE 2014; 2:214-25. [PMID: 24621683 PMCID: PMC4176924 DOI: 10.1016/s2213-2600(14)70002-5] [Citation(s) in RCA: 257] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
BACKGROUND The genetic risk factors for susceptibility to chronic obstructive pulmonary disease (COPD) are still largely unknown. Additional genetic variants are likely to be identified by genome-wide association studies in larger cohorts or specific subgroups. We sought to identify risk loci for moderate to severe and severe COPD with data from several cohort studies. METHODS We combined genome-wide association analysis data from participants in the COPDGene study (non-Hispanic white and African-American ethnic origin) and the ECLIPSE, NETT/NAS, and Norway GenKOLS studies (self-described white ethnic origin). We did analyses comparing control individuals with individuals with moderate to severe COPD and with a subset of individuals with severe COPD. Single nucleotide polymorphisms yielding a p value of less than 5 × 10(-7) in the meta-analysis at loci not previously described were genotyped in individuals from the family-based ICGN study. We combined results in a joint meta-analysis (threshold for significance p<5 × 10(-8)). FINDINGS Analysis of 6633 individuals with moderate to severe COPD and 5704 control individuals confirmed association at three known loci: CHRNA3 (p=6·38 × 10(-14)), FAM13A (p=1·12 × 10(-14)), and HHIP (p=1·57 × 10(-12)). We also showed significant evidence of association at a novel locus near RIN3 (p=5·25 × 10(-9)). In the overall meta-analysis (ie, including data from 2859 ICGN participants), the association with RIN3 remained significant (p=5·4 × 10(-9)). 3497 individuals were included in our analysis of severe COPD. The effect estimates for the loci near HHIP and CHRNA3 were significantly stronger in severe disease than in moderate to severe disease (p<0·01). We also identified associations at two additional loci: MMP12 (overall joint meta-analysis p=2·6 × 10(-9)) and TGFB2 (overall joint meta-analysis p=8·3 × 10(-9)). INTERPRETATION We have confirmed associations with COPD at three known loci and identified three new genome-wide significant associations. Genetic variants other than in α-1 antitrypsin increase the risk of COPD. FUNDING US National Heart, Lung, and Blood Institute; the Alpha-1 Foundation; the COPD Foundation through contributions from AstraZeneca, Boehringer Ingelheim, Novartis, and Sepracor; GlaxoSmithKline; Centers for Medicare and Medicaid Services; Agency for Healthcare Research and Quality; and US Department of Veterans Affairs.
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Affiliation(s)
- 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.
| | - Merry-Lynn N McDonald
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Xiaobo Zhou
- 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
| | - Manuel Mattheisen
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA; Harvard School of Public Health, Boston, MA, USA
| | - Peter J Castaldi
- Channing Division of Network 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
| | - 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
| | - Jody S Sylvia
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - John Ziniti
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Nan M Laird
- Harvard School of Public Health, 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
| | - David Sparrow
- School of Public Health and School of Medicine, Boston University, Boston, MA, USA; Veterans Administration Boston Healthcare System, Boston, MA, USA
| | - Richard Casaburi
- Los Angeles Biomedical Research Institute at Harbor UCLA Medical Center, Torrance, CA, USA
| | - R Graham Barr
- Department of Medicine, College of Physicians and Surgeons, Mailman School of Public Health, Columbia University, New York, NY, USA; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Elizabeth A Regan
- National Jewish Health, Denver, CO, USA; Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Aurora, CO, USA
| | | | - John E Hokanson
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Aurora, CO, USA
| | - Sharon Lutz
- Department of Bioinformatics and Statistics, Colorado School of Public Health, University of Colorado Denver, Aurora, CO, USA
| | - Tanda Murray Dudenkov
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Homayoon Farzadegan
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Jacqueline B Hetmanski
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Ruth Tal-Singer
- GlaxoSmithKline Research and Development, King Of Prussia, PA, USA
| | | | - Per Bakke
- Department of Clinical Science, University of Bergen, Bergen, Norway; Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Amund Gulsvik
- Department of Clinical Science, University of Bergen, Bergen, Norway; Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | | | - 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
| | - Terri H Beaty
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
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Arja C, Ravuri RR, Pulamaghatta VN, Surapaneni KM, Raya P, Adimoolam C, Kanala KR. Genetic determinants of chronic obstructive pulmonary disease in South Indian male smokers. PLoS One 2014; 9:e89957. [PMID: 24587150 PMCID: PMC3933698 DOI: 10.1371/journal.pone.0089957] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 01/25/2014] [Indexed: 11/18/2022] Open
Abstract
The development of chronic obstructive pulmonary disease, upon exposure to tobacco smoke, is the cumulative effect of defects in several genes. With the aim of understanding the genetic structure that is characteristic of our patient population, we selected forty two single nucleotide polymorphisms of twenty genes based on previous studies and genotyped a total of 382 samples, which included 236 patients and 146 controls using Sequenom MassARRAY system. Allele frequencies of rs2276109 (MMP12) and rs1800925 (IL13) differed significantly between patients and controls (p = 0.013 and 0.044 respectively). Genotype analysis showed association of rs2276109 (MMP12) under additive and dominant models (p = 0.017, p = 0.012 respectively), rs1800925 (IL13) under additive model (p = 0.047) and under recessive model, rs1695 (GSTP1; p = 0.034), rs729631, rs975278, rs7583463 (SERPINE2; p = 0.024, 0.024 and 0.012 respectively), rs2568494, rs10851906 (IREB2; p = 0.026 and 0.041 respectively) and rs7671167 (FAM13A; p = 0.029). The minor alleles of rs1695 (G), rs7671167 (T), rs729631 (G), rs975278 (A) and rs7583463 (A) showed significant negative association whereas those of rs2276109 (G), rs2568494 (A), rs10851906 (G) and rs1800469 (T; TGF-β) showed significant positive association with lung function under different genetic models. Haplotypes carrying A allele of rs2276109, G allele of rs1695 showed negative correlation with lung function. Haplotypes carrying major alleles of rs7671167 (C) of FAM13A and rs729631 (C), rs975278 (G), rs7583463 (C) of SERPINE2 had protective effect on lung function. Haplotypes of IREB2 carrying major alleles of rs2568494 (G), rs2656069 (A), rs10851906 (A), rs965604 (C) and minor alleles of rs1964678 (T), rs12593229 (T) showed negative correlation with lung function. In conclusion, our study replicated the results of most of the previous studies. However, the positive correlation between the minor alleles of rs2568494 (A) and rs10851906 (G) of IREB2 and lung function needs further investigation.
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Affiliation(s)
- Cholendra Arja
- Department Of Anthropology, Division Of Human Genetics, Sri Venkateswara University, Tirupati, Andhra Pradesh, India
| | | | | | - Krishna Mohan Surapaneni
- Department Of Biochemistry, Saveetha Medical College & Hospital, Faculty Of Medicine, Saveetha University, Chennai, Tamil Nadu, India
| | - Premanand Raya
- Premananda Allergy And Chest Hospital, Tirupati, Andhra Pradesh, India
| | | | - Kodanda Reddy Kanala
- Department Of Anthropology, Division Of Human Genetics, Sri Venkateswara University, Tirupati, Andhra Pradesh, India
- * E-mail:
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Abstract
Why only 20% of smokers develop clinically relevant chronic obstructive pulmonary disease (COPD) was a puzzle for many years. Now, epidemiologic studies point clearly toward a large heritable component. The combination of genome-wide association studies and candidate gene analysis is helping to identify those genetic variants responsible for an individual's susceptibility to developing COPD. In this review, the current data implicating specific loci and genes in the pathogenesis of COPD are examined.
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Affiliation(s)
- Stefan J Marciniak
- Division of Respiratory Medicine, Department of Medicine, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK; Cambridge Institute for Medical Research (CIMR), University of Cambridge, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, UK.
| | - David A Lomas
- University College London, 1st Floor, Maple House, 149 Tottenham Court Road, London W1T 7NF, UK
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29
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Faner R, Tal-Singer R, Riley JH, Celli B, Vestbo J, MacNee W, Bakke P, Calverley PMA, Coxson H, Crim C, Edwards LD, Locantore N, Lomas DA, Miller BE, Rennard SI, Wouters EFM, Yates JC, Silverman EK, Agusti A. Lessons from ECLIPSE: a review of COPD biomarkers. Thorax 2013; 69:666-72. [PMID: 24310110 DOI: 10.1136/thoraxjnl-2013-204778] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The Evaluation of COPD Longitudinally to Identify Predictive Surrogate End-points (ECLIPSE) study was a large 3-year observational controlled multicentre international study aimed at defining clinically relevant subtypes of chronic obstructive pulmonary disease (COPD) and identifying novel biomarkers and genetic factors. So far, the ECLIPSE study has produced more than 50 original publications and 75 communications to international meetings, many of which have significantly influenced our understanding of COPD. However, because there is not one paper reporting the biomarker results of the ECLIPSE study that may serve as a reference for practising clinicians, researchers and healthcare providers from academia, industry and government agencies interested in COPD, we decided to write a review summarising the main biomarker findings in ECLIPSE.
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Affiliation(s)
- Rosa Faner
- Fundació Investigació Sanitària Illes Balears (FISIB), Ciber Enfermedades Respiratorias (CIBERES), Barcelona, Catalunya, Spain
| | - Ruth Tal-Singer
- GlaxoSmithKline Research and Development, King of Prussia, Pennsylvania, USA
| | - John H Riley
- GlaxoSmithKline Research and Development, Stevenage, UK
| | - Bartolomé Celli
- Channing Division of Network Medicine and Pulmonary and Critical Care Division, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Jørgen Vestbo
- Department of Respiratory Medicine, Odense University Hospital, and Clinical Institute, University of Southern Denmark, Odense, Denmark Respiratory and Allergy Research Group, Manchester Academic Health Sciences Centre, University Hospital South Manchester NHS Foundation Trust, Manchester, UK
| | - William MacNee
- University of Edinburgh, MRC Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh, UK
| | - Per Bakke
- Department of Thoracic Medicine, Institute of Clinical Science, University of Bergen, Haukeland University Hospital, Bergen, Norway
| | - Peter M A Calverley
- Division of Infection and Immunity Clinical Sciences Centre, University Hospital Aintree, Liverpool, UK
| | - Harvey Coxson
- Department of Radiology, Vancouver General Hospital, University of British Columbia, Vancouver, British Columbia, Canada
| | - Courtney Crim
- GlaxoSmithKline Research and Development, Research Triangle Park, North Carolina, USA
| | - Lisa D Edwards
- GlaxoSmithKline Research and Development, Research Triangle Park, North Carolina, USA
| | - Nick Locantore
- GlaxoSmithKline Research and Development, Research Triangle Park, North Carolina, USA
| | - David A Lomas
- Division of Medicine, University College London, London, UK
| | - Bruce E Miller
- GlaxoSmithKline Research and Development, King of Prussia, Pennsylvania, USA
| | - Stephen I Rennard
- Department of Pulmonary and Critical Care Medicine, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Emiel F M Wouters
- Department of Respiratory Medicine, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Julie C Yates
- GlaxoSmithKline Research and Development, Research Triangle Park, North Carolina, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine and Pulmonary and Critical Care Division, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Alvar Agusti
- Fundació Investigació Sanitària Illes Balears (FISIB), Ciber Enfermedades Respiratorias (CIBERES), Barcelona, Catalunya, Spain Thorax Institute, Hospital Clinic, IDIBAPS, Univ. Barcelona, Barcelona, Spain
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Kerkhof M, Boezen HM, Granell R, Wijga AH, Brunekreef B, Smit HA, de Jongste JC, Thijs C, Mommers M, Penders J, Henderson J, Koppelman GH, Postma DS. Transient early wheeze and lung function in early childhood associated with chronic obstructive pulmonary disease genes. J Allergy Clin Immunol 2013; 133:68-76.e1-4. [PMID: 23886569 DOI: 10.1016/j.jaci.2013.06.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 05/01/2013] [Accepted: 06/05/2013] [Indexed: 10/26/2022]
Abstract
BACKGROUND It has been hypothesized that a disturbed early lung development underlies the susceptibility to chronic obstructive pulmonary disease (COPD). Little is known about whether subjects genetically predisposed to COPD show their first symptoms or reduced lung function in childhood. OBJECTIVE We investigated whether replicated genes for COPD associate with transient early wheeze (TEW) and lung function levels in 6- to 8-year-old children and whether cigarette smoke exposure in utero and after birth (environmental tobacco smoke [ETS]) modifies these effects. METHODS The association of COPD-related genotypes of 20 single nucleotide polymorphisms in 15 genes with TEW, FEV1, forced vital capacity (FVC), and FEV1/FVC ratio was studied in the Prevention and Incidence of Asthma and Mite Allergy (PIAMA) birth cohort (n = 1996) and replicated in the Child, parents and health: lifestyle and genetic constitution (KOALA) and Avon Longitudinal Study of Parents and Children (ALSPAC) cohorts. RESULTS AGER showed replicated association with FEV1/FVC ratio. TNS1 associated with more TEW in PIAMA and lower FEV1 in ALSPAC. TNS1 interacted with ETS in PIAMA, showing lower FEV1 in exposed children. HHIP rs1828591 interacted with cigarette smoke exposure in utero in PIAMA and with ETS in ALSPAC, with lower lung function in nonexposed children. SERPINE2, FAM13A, and MMP12 associated with higher FEV1 and FVC, and SERPINE2, HHIP, and TGFB1 interacted with cigarette smoke exposure in utero in PIAMA only, showing adverse effects of exposure on FEV1 being limited to children with genotypes conferring the lowest risk of COPD. CONCLUSION Our findings indicate relevant involvement of at least 3 COPD genes in lung development and lung growth by demonstrating associations pointing toward reduced airway caliber in early childhood. Furthermore, our results suggest that COPD genes are involved in the infant's lung response to smoke exposure in utero and in early life.
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Affiliation(s)
- Marjan Kerkhof
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; GRIAC Institute, 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; GRIAC Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Raquel Granell
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Alet H Wijga
- Centre for Prevention and Health Services Research, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Bert Brunekreef
- Institute for Risk Assessment Science, Utrecht University, Utrecht, The Netherlands; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Henriëtte A Smit
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Johan C de Jongste
- Department of Pediatrics, Division of Respiratory Medicine, Erasmus University Medical Center/Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Carel Thijs
- Department of Epidemiology, Maastricht University School for Public Health and Primary Care CAPHRI, Maastricht, The Netherlands
| | - Monique Mommers
- Department of Epidemiology, Maastricht University School for Public Health and Primary Care CAPHRI, Maastricht, The Netherlands
| | - John Penders
- Department of Epidemiology, Maastricht University School for Public Health and Primary Care CAPHRI, Maastricht, The Netherlands
| | - John Henderson
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Gerard H Koppelman
- Department of Paediatric Pulmonology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Dirkje S Postma
- Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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Kukkonen MK, Tiili E, Vehmas T, Oksa P, Piirilä P, Hirvonen A. Association of genes of protease-antiprotease balance pathway to lung function and emphysema subtypes. BMC Pulm Med 2013; 13:36. [PMID: 23734748 PMCID: PMC3680142 DOI: 10.1186/1471-2466-13-36] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 05/29/2013] [Indexed: 12/11/2022] Open
Abstract
Background The imbalance between proteases and antiproteases has been proposed to participate to the pathogenesis of chronic obstructive pulmonary disease (COPD) and emphysema. Gene level variation in different metalloproteinases, metalloproteinase inhibitors, and cytokines affecting them may contribute to this imbalance and destruction of the lung parenchyma. We investigated whether polymorphisms in selected protease-antiprotease balance pathway genes predispose to different emphysema subtypes (centrilobular, paraseptal, panlobular, and bullae) and airflow limitation among Finnish construction workers. Methods Eleven single nucleotide polymorphisms (SNPs) from seven genes (GC: rs7041 and rs4588; MMP1: rs1799750; MMP9: rs3918242; MMP12: rs652438; TIMP2: rs2277698; TNF: rs1799724 and rs1800629; TGFB1: rs1800469, rs1800470, and rs2241718) were analyzed from 951 clinically and radiologically characterized construction workers. The genotype and haplotype data was compared to different emphysematous signs confirmed with high resolution computed tomography (HRCT), forced vital capacity (FVC), forced expiratory volume in one second (FEV1), and maximal expiratory flow at 50% of FVC (MEF50) by using linear and logistic regression analyses, adjusted for potential confounders. Results The TIMP2 rs2277698 SNP was associated with overall (p = 0.022) and paraseptal (p = 0.010) emphysema, as well as with FEV1/FVC ratio (p = 0.035) and MEF50 (p = 0.008). The TGFB1 rs2241718 and MMP9 rs3918242 SNPs were associated with centrilobular emphysema (p = 0.022 and p = 0.008), and the TNF rs1800629 SNP with paraseptal emphysema (p = 0.017). In stratified analysis, individuals with at least one TIMP2 rs2277698 or TNF rs1800629 variant allele were found to be at around two-fold risk for pathological paraseptal changes (OR 1.94, 95% CI 1.14-3.30; OR 2.10, 95% CI 1.24-3.56). On the contrary, the risk for pathological centrilobular changes was halved for individuals with at least one MMP9 rs3918242 (OR 0.51, 95% CI 0.30-0.86) or TGFB1 rs2241718 (OR 0.53, 95% CI 0.30-0.90) variant allele, or TGFB1 rs1800469-rs1800470 AT-haplotype (OR 0.55, 95% CI 0.33-0.93). MEF50, in turn, was significantly reduced among individuals with at least one TIMP2 rs2277698 variant allele (p = 0.011). Conclusion Our findings strengthen the hypothesis of the importance of protease-antiprotease balance in pathogenesis of emphysema and shed light on the aetiology of different emphysema subtypes by associating MMP9 and TGFB1 to centrilobular emphysema, and TIMP2 and TNF to paraseptal emphysema and/or airflow obstruction.
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Affiliation(s)
- Mari K Kukkonen
- Finnish Institute of Occupational Health, Topeliuksenkatu 41 a A, FI-00250, Helsinki, Finland.
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32
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Siedlinski M, Tingley D, Lipman PJ, Cho MH, Litonjua AA, Sparrow D, Bakke P, Gulsvik A, Lomas DA, Anderson W, Kong X, Rennard SI, Beaty TH, Hokanson JE, Crapo JD, Lange C, Silverman EK, the COPDGene and ECLIPSE Investigators. Dissecting direct and indirect genetic effects on chronic obstructive pulmonary disease (COPD) susceptibility. Hum Genet 2013; 132:431-41. [PMID: 23299987 PMCID: PMC3600068 DOI: 10.1007/s00439-012-1262-3] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Accepted: 12/24/2012] [Indexed: 10/27/2022]
Abstract
Cigarette smoking is the major environmental risk factor for chronic obstructive pulmonary disease (COPD). Genome-wide association studies have provided compelling associations for three loci with COPD. In this study, we aimed to estimate direct, i.e., independent from smoking, and indirect effects of those loci on COPD development using mediation analysis. We included a total of 3,424 COPD cases and 1,872 unaffected controls with data on two smoking-related phenotypes: lifetime average smoking intensity and cumulative exposure to tobacco smoke (pack years). Our analysis revealed that effects of two linked variants (rs1051730 and rs8034191) in the AGPHD1/CHRNA3 cluster on COPD development are significantly, yet not entirely, mediated by the smoking-related phenotypes. Approximately 30% of the total effect of variants in the AGPHD1/CHRNA3 cluster on COPD development was mediated by pack years. Simultaneous analysis of modestly (r (2) = 0.21) linked markers in CHRNA3 and IREB2 revealed that an even larger (~42%) proportion of the total effect of the CHRNA3 locus on COPD was mediated by pack years after adjustment for an IREB2 single nucleotide polymorphism. This study confirms the existence of direct effects of the AGPHD1/CHRNA3, IREB2, FAM13A and HHIP loci on COPD development. While the association of the AGPHD1/CHRNA3 locus with COPD is significantly mediated by smoking-related phenotypes, IREB2 appears to affect COPD independently of smoking.
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Affiliation(s)
- Mateusz Siedlinski
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA 02115, USA
| | - Dustin Tingley
- Department of Government, Harvard University, Cambridge, MA, USA
| | - Peter J. Lipman
- Department of Biostatistics, Harvard School of Public Health, Boston, USA
| | - Michael H. Cho
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA 02115, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Augusto A. Litonjua
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA 02115, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - David Sparrow
- Veterans Affairs Boston Healthcare System and Boston University Schools of Public Health and Medicine, Boston, MA, USA
| | - Per Bakke
- Department of Thoracic Medicine, Haukeland University Hospital and Institute of Medicine, University of Bergen, Bergen, Norway
| | - Amund Gulsvik
- Department of Thoracic Medicine, Haukeland University Hospital and Institute of Medicine, University of Bergen, Bergen, Norway
| | - David A. Lomas
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Wayne Anderson
- GlaxoSmithKline Research and Development, Research Triangle Park, NC, USA
| | - Xiangyang Kong
- GlaxoSmithKline Research and Development, King of Prussia, PA, USA
| | - Stephen I. Rennard
- Department of Pulmonary and Critical Care Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Terri H. Beaty
- Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - John E. Hokanson
- Colorado School of Public Health, University of Colorado Denver, Aurora, CO, USA
| | - James D. Crapo
- Department of Medicine, National Jewish Health, Denver, CO, USA
| | - Christoph Lange
- Department of Biostatistics, Harvard School of Public Health, Boston, USA
| | - Edwin K. Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, 181 Longwood Avenue, Boston, MA 02115, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
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Abstract
A greater understanding of the regulatory processes contributing to lung development could be helpful to identify strategies to ameliorate morbidity and mortality in premature infants and to identify individuals at risk for congenital and/or chronic lung diseases. Over the past decade, genomics technologies have enabled the production of rich gene expression databases providing information for all genes across developmental time or in diseased tissue. These data sets facilitate systems biology approaches for identifying underlying biological modules and programs contributing to the complex processes of normal development and those that may be associated with disease states. The next decade will undoubtedly see rapid and significant advances in redefining both lung development and disease at the systems level.
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Affiliation(s)
- Soumyaroop Bhattacharya
- Division of Neonatology and Program in Pediatric Molecular and Personalized Medicine, University of Rochester Medical Center, Rochester, New York, USA
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Wan ES, Qiu W, Baccarelli A, Carey VJ, Bacherman H, Rennard SI, Agustí A, Anderson WH, Lomas DA, DeMeo DL. Systemic steroid exposure is associated with differential methylation in chronic obstructive pulmonary disease. Am J Respir Crit Care Med 2012; 186:1248-55. [PMID: 23065012 PMCID: PMC3622442 DOI: 10.1164/rccm.201207-1280oc] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 09/27/2012] [Indexed: 02/06/2023] Open
Abstract
RATIONALE Systemic glucocorticoids are used therapeutically to treat a variety of medical conditions. Epigenetic processes such as DNA methylation may reflect exposure to glucocorticoids and may be involved in mediating the responses and side effects associated with these medications. OBJECTIVES To test the hypothesis that differences in DNA methylation are associated with current systemic steroid use. METHODS We obtained DNA methylation data at 27,578 CpG sites in 14,475 genes throughout the genome in two large, independent cohorts: the International COPD Genetics Network (n(discovery) = 1,085) and the Boston Early Onset COPD study (n(replication) = 369). Sites were tested for association with current systemic steroid use using generalized linear mixed models. MEASUREMENTS AND MAIN RESULTS A total of 511 sites demonstrated significant differential methylation by systemic corticosteroid use in all three of our primary models. Pyrosequencing validation confirmed robust differential methylation at CpG sites annotated to genes such as SLC22A18, LRP3, HIPK3, SCNN1A, FXYD1, IRF7, AZU1, SIT1, GPR97, ABHD16B, and RABGEF1. Functional annotation clustering demonstrated significant enrichment in intrinsic membrane components, hemostasis and coagulation, cellular ion homeostasis, leukocyte and lymphocyte activation and chemotaxis, protein transport, and responses to nutrients. CONCLUSIONS Our analyses suggest that systemic steroid use is associated with site-specific differential methylation throughout the genome. Differentially methylated CpG sites were found in biologically plausible and previously unsuspected pathways; these genes and pathways may be relevant in the development of novel targeted therapies.
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Affiliation(s)
- Emily S Wan
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, USA.
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35
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Wain LV, Soler Artigas M, Tobin MD. What can genetics tell us about the cause of fixed airflow obstruction? Clin Exp Allergy 2012; 42:1176-82. [PMID: 22805464 DOI: 10.1111/j.1365-2222.2012.03967.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is a major cause of chronic morbidity and mortality worldwide with smoking being the most important risk factor of the disease. However, lung function and COPD are known to also have a genetic component and a deeper knowledge of the genetic architecture of the disease could lead to further understanding of predisposition to COPD and also to development of new therapeutic interventions. Genetic linkage studies and candidate gene association studies have not provided evidence to convincingly identify the genes underlying lung function or COPD. However, recent large genome-wide association studies (GWAS) including tens of thousands of individuals have identified 26 variants at different loci in the human genome that show robust association with quantitative lung function measures in the general population. A growing number of these variants are being shown to be associated with COPD. Following the identification of these new lung function loci, the challenge now lies in refining the signals to identify the causative variants underlying the association signals and relating these signals to the molecular pathways that underlie lung function.
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Affiliation(s)
- L V Wain
- Department of Health Sciences, University of Leicester, Leicester, UK
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36
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Kim DK, Cho MH, Hersh CP, Lomas DA, Miller BE, Kong X, Bakke P, Gulsvik A, Agustí A, Wouters E, Celli B, Coxson H, Vestbo J, MacNee W, Yates JC, Rennard S, Litonjua A, Qiu W, Beaty TH, Crapo JD, Riley JH, Tal-Singer R, Silverman EK. Genome-wide association analysis of blood biomarkers in chronic obstructive pulmonary disease. Am J Respir Crit Care Med 2012; 186:1238-47. [PMID: 23144326 DOI: 10.1164/rccm.201206-1013oc] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
RATIONALE A genome-wide association study (GWAS) for circulating chronic obstructive pulmonary disease (COPD) biomarkers could identify genetic determinants of biomarker levels and COPD susceptibility. OBJECTIVES To identify genetic variants of circulating protein biomarkers and novel genetic determinants of COPD. METHODS GWAS was performed for two pneumoproteins, Clara cell secretory protein (CC16) and surfactant protein D (SP-D), and five systemic inflammatory markers (C-reactive protein, fibrinogen, IL-6, IL-8, and tumor necrosis factor-α) in 1,951 subjects with COPD. For genome-wide significant single nucleotide polymorphisms (SNPs) (P < 1 × 10(-8)), association with COPD susceptibility was tested in 2,939 cases with COPD and 1,380 smoking control subjects. The association of candidate SNPs with mRNA expression in induced sputum was also elucidated. MEASUREMENTS AND MAIN RESULTS Genome-wide significant susceptibility loci affecting biomarker levels were found only for the two pneumoproteins. Two discrete loci affecting CC16, one region near the CC16 coding gene (SCGB1A1) on chromosome 11 and another locus approximately 25 Mb away from SCGB1A1, were identified, whereas multiple SNPs on chromosomes 6 and 16, in addition to SNPs near SFTPD, had genome-wide significant associations with SP-D levels. Several SNPs affecting circulating CC16 levels were significantly associated with sputum mRNA expression of SCGB1A1 (P = 0.009-0.03). Several SNPs highly associated with CC16 or SP-D levels were nominally associated with COPD in a collaborative GWAS (P = 0.001-0.049), although these COPD associations were not replicated in two additional cohorts. CONCLUSIONS Distant genetic loci and biomarker-coding genes affect circulating levels of COPD-related pneumoproteins. A subset of these protein quantitative trait loci may influence their gene expression in the lung and/or COPD susceptibility. Clinical trial registered with www.clinicaltrials.gov (NCT 00292552).
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Affiliation(s)
- Deog Kyeom Kim
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
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Abstract
A genetic contribution to develop chronic obstructive pulmonary disease (COPD) is well established. However, the specific genes responsible for enhanced risk or host differences in susceptibility to smoke exposure remain poorly understood. The goal of this review is to provide a comprehensive literature overview on the genetics of COPD, highlight the most promising findings during the last few years, and ultimately provide an updated COPD gene list. Candidate gene studies on COPD and related phenotypes indexed in PubMed before January 5, 2012 are tabulated. An exhaustive list of publications for any given gene was looked for. This well-documented COPD candidate-gene list is expected to serve many purposes for future replication studies and meta-analyses as well as for reanalyzing collected genomic data in the field. In addition, this review summarizes recent genetic loci identified by genome-wide association studies on COPD, lung function, and related complications. Assembling resources, integrative genomic approaches, and large sample sizes of well-phenotyped subjects is part of the path forward to elucidate the genetic basis of this debilitating disease.
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Affiliation(s)
- Yohan Bossé
- Centre de recherche Institut universitaire de cardiologie et de pneumologie de Québec, Quebec, Canada.
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Guo Y, Gong Y, Shi G, Yang K, Pan C, Li M, Li Q, Cheng Q, Dai R, Fan L, Wan H. Single-nucleotide polymorphisms in the TSPYL-4 and NT5DC1 genes are associated with susceptibility to chronic obstructive pulmonary disease. Mol Med Rep 2012; 6:631-8. [PMID: 22736055 DOI: 10.3892/mmr.2012.964] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2012] [Accepted: 06/18/2012] [Indexed: 11/06/2022] Open
Abstract
The risk of developing chronic obstructive pulmonary disease (COPD) is partially determined by genetic and environmental factors. Many published candidate gene studies show conflicting results due to ethnic differences and sample sizes. The number of these studies carried out in Chinese populations is small. To investigate candidate genes and haplotypes for susceptibility to COPD in a southern Han Chinese population, we performed genotyping of DNA samples in 200 COPD patients and 250 control subjects by analyzing 54 single-nucleotide polymorphisms (SNPs) in 23 genes associated with the development of COPD and/or pulmonary function identified by genome-wide association studies (GWAS). We also performed linkage disequilibrium (LD) and haplotype analysis according to the results of genotyping. The frequencies of the SNP [rs3749893 of testis‑specific protein Y-encoded-like 4 (TSPYL-4) gene] G allele and SNP [rs1052443 of 5'-nucleotidase domain containing 1 (NT5DC1) gene] A allele were significantly higher in the cases studied compared to the control subjects (P=0.032, P<0.05, OR=0.692, 95% CI 0.495‑0.970; P=0.0205, P<0.05, OR=0.670, 95% CI 0.477-0.941, respectively). Results showed that two blocks of SNPs (rs1052443 and rs3749893; rs11155242 and rs6937121) had sufficient precision to allow construction of a haplotype block. We constructed the TSPYL-4 and NT5DC1 haplotypes of the cases and controls, but no significant difference between the two groups was found. rs3749893 A allele of TSPYL-4 and rs1052443 C allele of NT5DC1 were associated with a protective effect against the deterioration of pulmonary function. In conclusion, TSPYL-4 and NT5DC1 gene polymorphisms are associated with susceptibility to COPD and pulmonary function.
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Affiliation(s)
- Yi Guo
- Department of Respiratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University (SJTU), School of Medicine, Shanghai 200025, PR China
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Wan ES, Qiu W, Baccarelli A, Carey VJ, Bacherman H, Rennard SI, Agusti A, Anderson W, Lomas DA, Demeo DL. Cigarette smoking behaviors and time since quitting are associated with differential DNA methylation across the human genome. Hum Mol Genet 2012; 21:3073-82. [PMID: 22492999 DOI: 10.1093/hmg/dds135] [Citation(s) in RCA: 242] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The impact of cigarette smoking can persist for extended periods following smoking cessation and may involve epigenetic reprogramming. Changes in DNA methylation associated with smoking may help to identify molecular pathways that contribute to the latency between exposure and disease onset. Cross-sectional cohort data from subjects in the International COPD Genetics Network (n = 1085) and the Boston Early-Onset COPD study (n = 369) were analyzed as the discovery and replication cohorts, respectively. Genome-wide methylation data on 27 578 CpG sites in 14 475 genes were obtained on DNA from peripheral blood leukocytes using the Illumina HumanMethylation27K Beadchip in both cohorts. We identified 15 sites significantly associated with current smoking, 2 sites associated with cumulative smoke exposure, and, within the subset of former smokers, 3 sites associated with time since quitting cigarettes. Two loci, factor II receptor-like 3 (F2RL3) and G-protein-coupled receptor 15 (GPR15), were significantly associated in all three analyses and were validated by pyrosequencing. These findings (i) identify a novel locus (GPR15) associated with cigarette smoking and (ii) suggest the existence of dynamic, site-specific methylation changes in response to smoking which may contribute to the extended risks associated with cigarette smoking that persist after cessation.
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Affiliation(s)
- Emily S Wan
- Channing Laboratory and the Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, MA 02115, USA.
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40
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Cho MH, Castaldi PJ, Wan ES, Siedlinski M, Hersh CP, Demeo DL, Himes BE, Sylvia JS, Klanderman BJ, Ziniti JP, Lange C, Litonjua AA, Sparrow D, Regan EA, Make BJ, Hokanson JE, Murray T, Hetmanski JB, Pillai SG, Kong X, Anderson WH, Tal-Singer R, Lomas DA, Coxson HO, Edwards LD, MacNee W, Vestbo J, Yates JC, Agusti A, Calverley PMA, Celli B, Crim C, Rennard S, Wouters E, Bakke P, Gulsvik A, Crapo JD, Beaty TH, Silverman EK. A genome-wide association study of COPD identifies a susceptibility locus on chromosome 19q13. Hum Mol Genet 2012; 21:947-57. [PMID: 22080838 PMCID: PMC3298111 DOI: 10.1093/hmg/ddr524] [Citation(s) in RCA: 185] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Revised: 10/26/2011] [Accepted: 11/07/2011] [Indexed: 12/18/2022] Open
Abstract
The genetic risk factors for chronic obstructive pulmonary disease (COPD) are still largely unknown. To date, genome-wide association studies (GWASs) of limited size have identified several novel risk loci for COPD at CHRNA3/CHRNA5/IREB2, HHIP and FAM13A; additional loci may be identified through larger studies. We performed a GWAS using a total of 3499 cases and 1922 control subjects from four cohorts: the Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints (ECLIPSE); the Normative Aging Study (NAS) and National Emphysema Treatment Trial (NETT); Bergen, Norway (GenKOLS); and the COPDGene study. Genotyping was performed on Illumina platforms with additional markers imputed using 1000 Genomes data; results were summarized using fixed-effect meta-analysis. We identified a new genome-wide significant locus on chromosome 19q13 (rs7937, OR = 0.74, P = 2.9 × 10(-9)). Genotyping this single nucleotide polymorphism (SNP) and another nearby SNP in linkage disequilibrium (rs2604894) in 2859 subjects from the family-based International COPD Genetics Network study (ICGN) demonstrated supportive evidence for association for COPD (P = 0.28 and 0.11 for rs7937 and rs2604894), pre-bronchodilator FEV(1) (P = 0.08 and 0.04) and severe (GOLD 3&4) COPD (P = 0.09 and 0.017). This region includes RAB4B, EGLN2, MIA and CYP2A6, and has previously been identified in association with cigarette smoking behavior.
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Affiliation(s)
- Michael H Cho
- Channing Laboratory, Brigham & Women’s Hospital, Boston, MA 02115, USA.
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Rutten EPA, Bakke PS, Pillai SG, Wagers S, Grydeland TB, Gulsvik A, Wouters EFM. The association between body composition and self-reported co-morbidity in subjects with chronic obstructive pulmonary disease. ACTA ACUST UNITED AC 2012. [DOI: 10.4236/ojim.2012.22019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Kukkonen MK, Tiili E, Hämäläinen S, Vehmas T, Oksa P, Piirilä P, Hirvonen A. SERPINE2 haplotype as a risk factor for panlobular type of emphysema. BMC MEDICAL GENETICS 2011; 12:157. [PMID: 22145704 PMCID: PMC3269992 DOI: 10.1186/1471-2350-12-157] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Accepted: 12/07/2011] [Indexed: 12/02/2022]
Abstract
Background SERPINE2 (serpin peptidase inhibitor, clade E, member 2) has previously been identified as a positional candidate gene for chronic obstructive pulmonary disease (COPD) and has subsequently been associated to COPD and emphysema in several populations. We aimed to further examine the role of SERPINE2 polymorphisms in the development of pulmonary emphysema and different emphysema subtypes. Methods Four single nucleotide polymorphisms (SNPs) in SERPINE2 were analyzed from 951 clinically and radiologically examined Finnish construction workers. The genotype and haplotype data was compared to different emphysematous signs confirmed with high-resolution computed tomography (HRCT), forced vital capacity (FVC), forced expiratory volume in one second (FEV1), diffusing capacity (DLCO), and specific diffusing capacity (DLCO/VA). Results Three of the studied SERPINE2 SNPs (rs729631, rs975278, and rs6748795) were found to be in tight linkage disequilibrium. Therefore, only one of these SNPs (rs729631) was included in the subsequent analyses, in addition to the rs840088 SNP which was in moderate linkage with the other three studied SNPs. The rs729631 SNP showed a significant association with panlobular emphysema (p = 0.003). In further analysis, the variant allele of the rs729631 SNP was found to pose over two-fold risk (OR 2.22, 95% CI 1.05-4.72) for overall panlobular changes and over four-fold risk (OR 4.37, 95% CI 1.61-11.86) for pathological panlobular changes. A haplotype consisting of variant alleles of both rs729631 and rs840088 SNPs was found to pose an almost four-fold risk for overall panlobular (OR 3.72, 95% CI 1.56-8.90) and subnormal (OR 3.98, 95% CI 1.55-10.20) emphysema. Conclusions Our results support the previously found association between SERPINE2 polymorphisms and pulmonary emphysema. As a novel finding, our study suggests that the SERPINE2 gene may in particular be involved in the development of panlobular changes, i.e., the same type of changes that are involved in alpha-1-antitrypsin (AAT) -deficiency.
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Castaldi PJ, Cho MH, Litonjua AA, Bakke P, Gulsvik A, Lomas DA, Anderson W, Beaty TH, Hokanson JE, Crapo JD, Laird N, Silverman EK, COPDGene and Eclipse Investigators. The association of genome-wide significant spirometric loci with chronic obstructive pulmonary disease susceptibility. Am J Respir Cell Mol Biol 2011; 45:1147-53. [PMID: 21659657 PMCID: PMC3262664 DOI: 10.1165/rcmb.2011-0055oc] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Collaborators] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Accepted: 06/04/2011] [Indexed: 01/23/2023] Open
Abstract
Two recent metaanalyses of genome-wide association studies conducted by the CHARGE and SpiroMeta consortia identified novel loci yielding evidence of association at or near genome-wide significance (GWS) with FEV(1) and FEV(1)/FVC. We hypothesized that a subset of these markers would also be associated with chronic obstructive pulmonary disease (COPD) susceptibility. Thirty-two single-nucleotide polymorphisms (SNPs) in or near 17 genes in 11 previously identified GWS spirometric genomic regions were tested for association with COPD status in four COPD case-control study samples (NETT/NAS, the Norway case-control study, ECLIPSE, and the first 1,000 subjects in COPDGene; total sample size, 3,456 cases and 1,906 controls). In addition to testing the 32 spirometric GWS SNPs, we tested a dense panel of imputed HapMap2 SNP markers from the 17 genes located near the 32 GWS SNPs and in a set of 21 well studied COPD candidate genes. Of the previously identified GWS spirometric genomic regions, three loci harbored SNPs associated with COPD susceptibility at a 5% false discovery rate: the 4q24 locus including FLJ20184/INTS12/GSTCD/NPNT, the 6p21 locus including AGER and PPT2, and the 5q33 locus including ADAM19. In conclusion, markers previously associated at or near GWS with spirometric measures were tested for association with COPD status in data from four COPD case-control studies, and three loci showed evidence of association with COPD susceptibility at a 5% false discovery rate.
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Affiliation(s)
- Peter J Castaldi
- Institute for Clinical Research and Health Policy Studies, Tufts Medical Center, Boston, Massachusetts, USA.
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Collaborators
Jeffrey Curtis, Ella Kazerooni, Nicola Hanania, Philip Alapat, Venkata Bandi, Kalpalatha Guntupalli, Elizabeth Guy, Antara Mallampalli, Charles Trinh, Mustafa Atik, Dawn DeMeo, Craig Hersh, George Washko, Francine Jacobson, R Graham Barr, Byron Thomashow, John Austin, Neil MacIntyre, Lacey Washington, H Page McAdams, Richard Rosiello, Timothy Bresnahan, Charlene McEvoy, Joseph Tashjian, Robert Wise, Nadia Hansel, Robert Brown, Gregory Diette, Richard Casaburi, Janos Porszasz, Hans Fischer, Matt Budoff, Amir Sharafkhaneh, Charles Trinh, Hirani Kamal, Roham Darvishi, Dennis Niewoehner, Tadashi Allen, Quentin Anderson, Kathryn Rice, Marilyn Foreman, Gloria Westney, Eugene Berkowitz, Russell Bowler, Adam Friedlander, David Lynch, Joyce Schroeder, John Newell, Gerard Criner, Victor Kim, Nathaniel Marchetti, Aditi Satti, A James Mamary, Robert Steiner, Chandra Dass, William Bailey, Mark Dransfield, Hrudaya Nath, Joe Ramsdell, Paul Friedman, Geoffrey McLennan, Edwin J R van Beek, Brad Thompson, Dwight Look, Fernando Martinez, MeiLan Han, Ella Kazerooni, Christine Wendt, Tadashi Allen, Frank Sciurba, Joel Weissfeld, Carl Fuhrman, Jessica Bon, Antonio Anzueto, Sandra Adams, Carlos Orozco, Mario Ruiz,
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44
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Abstract
PURPOSE Polymorphisms of several candidate genes have been studied and associated with the development of chronic obstructive pulmonary disease (COPD). One such candidate is the SERPINE2 (Serpin peptidase inhibitor, clade E member 2) gene. MATERIALS AND METHODS To assess whether the SERPINE2 gene is associated with COPD in a Chinese Han population. Samples were collected from a Chinese Han population and analyzed for the association of single nucleotide polymor phisms (SNPs) or haplotypes of SERPINE2 gene with COPD in a case-control study. Three SNPs including rs840088 G/A in intron 1, rs1438831 A/G in 5' upstream sequence and rs3795879 G/A in intron 3 were detected using the polymerase chain reaction (PCR)-based restriction fragment length polymorphism technique in 409 COPD subjects and 411 controls. Genotyping of the SREPINE2 polymorphisms at positions rs840088, rs1438831and rs3795879 was performed. RESULTS We found that none of the rs840088G/A, rs1438831G/A and rs3795879 G/A polymorphisms were associated with the disease. The p-values were 0.630, 0.208 and 0.398 respectively. CONCLUSION Our data suggested that there was no significant association between SERPINE2 polymorphism and COPD susceptibility in the Chinese Han population.
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Affiliation(s)
- Aihua Wang
- Department of Respiratory, Qilu Hospital of Shandong University, Shandong, China
| | - Yingqiu Yin
- Department of Pulmonary Medicine, Yuebei People's Hospital, Shaoguan, China
| | - Ping Chen
- Department of Pharmacy, Shandong Provincial Hospital, Shandong, China
| | - Qiji Liu
- Department of medical genetics, School of Medicine, Shandong University, Shandong, China
| | - Qinfeng Yu
- Department of Respiratory, Qilu Hospital of Shandong University, Shandong, China
| | - Wei Xiao
- Department of Respiratory, Qilu Hospital of Shandong University, Shandong, China
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Siedlinski M, Cho MH, Bakke P, Gulsvik A, Lomas DA, Anderson W, Kong X, Rennard SI, Beaty TH, Hokanson JE, Crapo JD, Silverman EK, the COPDGene and ECLIPSE Investigators. Genome-wide association study of smoking behaviours in patients with COPD. Thorax 2011; 66:894-902. [PMID: 21685187 PMCID: PMC3302576 DOI: 10.1136/thoraxjnl-2011-200154] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Collaborators] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Background Cigarette smoking is a major risk factor for chronic obstructive pulmonary disease (COPD) and COPD severity. Previous genome-wide association studies (GWAS) have identified numerous single nucleotide polymorphisms (SNPs) associated with the number of cigarettes smoked per day (CPD) and a dopamine beta-hydroxylase (DBH) locus associated with smoking cessation in multiple populations. Objective To identify SNPs associated with lifetime average and current CPD, age at smoking initiation, and smoking cessation in patients with COPD. Methods GWAS were conducted in four independent cohorts encompassing 3441 ever-smoking patients with COPD (Global Initiative for Obstructive Lung Disease stage II or higher). Untyped SNPs were imputed using the HapMap (phase II) panel. Results from all cohorts were meta-analysed. Results Several SNPs near the HLA region on chromosome 6p21 and in an intergenic region on chromosome 2q21 showed associations with age at smoking initiation, both with the lowest p=2×10(-7). No SNPs were associated with lifetime average CPD, current CPD or smoking cessation with p<10(-6). Nominally significant associations with candidate SNPs within cholinergic receptors, nicotinic, alpha 3/5 (CHRNA3/CHRNA5; eg, p=0.00011 for SNP rs1051730) and cytochrome P450, family 2, subfamily A, polypeptide 6 (CYP2A6; eg, p=2.78×10(-5) for a non-synonymous SNP rs1801272) regions were observed for lifetime average CPD, however only CYP2A6 showed evidence of significant association with current CPD. A candidate SNP (rs3025343) in DBH was significantly (p=0.015) associated with smoking cessation. Conclusion The authors identified two candidate regions associated with age at smoking initiation in patients with COPD. Associations of CHRNA3/CHRNA5 and CYP2A6 loci with CPD and DBH with smoking cessation are also likely of importance in the smoking behaviours of patients with COPD.
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Affiliation(s)
- Mateusz Siedlinski
- Channing Laboratory, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Michael H. Cho
- Channing Laboratory, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Per Bakke
- Department of Thoracic Medicine, Haukeland University Hospital and Institute of Medicine, University of Bergen, Bergen, Norway
| | - Amund Gulsvik
- Department of Thoracic Medicine, Haukeland University Hospital and Institute of Medicine, University of Bergen, Bergen, Norway
| | - David A. Lomas
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Wayne Anderson
- GlaxoSmithKline Research and Development, Research Triangle Park, NC, USA
| | - Xiangyang Kong
- GlaxoSmithKline Research and Development, King Of Prussia, PA, US
| | - Stephen I. Rennard
- Department of Pulmonary and Critical Care Medicine, University of Nebraska Medical Center - Omaha, NE, USA
| | - Terri H. Beaty
- Johns Hopkins School of Public Health, Baltimore, MD, USA
| | - John E. Hokanson
- Colorado School of Public Health, University of Colorado Denver, Aurora, CO, USA
| | - James D. Crapo
- Department of Medicine, National Jewish Health, Denver, CO, USA
| | - Edwin K. Silverman
- Channing Laboratory, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
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Collaborators
Harvey Coxson, Lisa Edwards, Katharine Knobil, David Lomas, William MacNee, Edwin Silverman, Ruth Tal-Singer, Jørgen Vestbo, Julie Yates, Alvar Agusti, Peter Calverley, Bartolome Celli, Bruce Miller, William MacNee, Stephen Rennard, Ruth Tal-Singer, Emiel Wouters, Julie Yates, Yavor Ivanov, Kosta Kostov, Jean Bourbeau, Mark Fitzgerald, Paul Hernandez, Kieran Killian, Robert Levy, Francois Maltais, Denis O'Donnell, Jan Krepelka, Jørgen Vestbo, Emiel Wouters, Dean Quinn, Per Bakke, Mitja Kosnik, Alvar Agusti, Jaume Sauleda, Yuri Feschenko, Vladamir Gavrisyuk, Lyudmila Yashina, Nadezhda Monogarova, Peter Calverley, David Lomas, William MacNee, David Singh, Jadwiga Wedzicha, Antonio Anzueto, San Antonio, Sidney Braman, Richard Casaburi, Bart Celli, Glenn Giessel, Mark Gotfried, Gary Greenwald, Nicola Hanania, Don Mahler, Barry Make, Stephen Rennard, Carolyn Rochester, Paul Scanlon, Dan Schuller, Frank Sciurba, Amir Sharafkhaneh, Thomas Siler, Edwin Silverman, Adam Wanner, Robert Wise, Richard ZuWallack, Joshua Benditt, Gerard Criner, Malcolm DeCamp, Philip Diaz, Mark Ginsburg, Larry Kaiser, Marcia Katz, Mark Krasna, Neil MacIntyre, Barry Make, Rob McKenna, Fernando Martinez, Zab Mosenifar, John Reilly, Andrew Ries, Paul Scanlon, Frank Sciurba, James Utz, Jeffrey Curtis, Ella Kazerooni, Nicola Hanania, Philip Alapat, Venkata Bandi, Kalpalatha Guntupalli, Elizabeth Guy, Antara Mallampalli, Charles Trinh, Mustafa Atik, Dawn DeMeo, Craig Hersh, George Washko, Francine Jacobson, R Graham Barr, Byron Thomashow, John Austin, Neil MacIntyre, Lacey Washington, H Page McAdams, Richard Rosiello, Timothy Bresnahan, Charlene McEvoy, Joseph Tashjian, Robert Wise, Nadia Hansel, Robert Brown, Gregory Diette, Richard Casaburi, Janos Porszasz, Hans Fischer, Matt Budoff, Michael E DeBakey, Amir Sharafkhaneh, Charles Trinh, Hirani Kamal, Roham Darvishi, Dennis Niewoehner, Tadashi Allen, Quentin Anderson, Kathryn Rice, Marilyn Foreman, Gloria Westney, Eugene Berkowitz, Russell Bowler, Adam Friedlander, David Lynch, Joyce Schroeder, John Newell, Gerard Criner, Victor Kim, Nathaniel Marchetti, Aditi Satti, A James Mamary, Robert Steiner, Chandra Dass, William Bailey, Mark Dransfield, Hrudaya Nath, Joe Ramsdell, Paul Friedman, Geoffrey McLennan, Edwin JR van Beek, Brad Thompson, Dwight Look, Fernando Martinez, MeiLan Han, Ella Kazerooni, Christine Wendt, Frank Sciurba, Joel Weissfeld, Carl Fuhrman, Jessica Bon, San Antonio, Antonio Anzueto, Sandra Adams, Carlos Orozco, Mario Ruiz, James Crapo, Edwin Silverman, Barry Make, Elizabeth Regan, Sarah Moyle, Terri Beaty, Barbara Klanderman, Nan Laird, Christoph Lange, Michael Cho, Stephanie Santorico, John Hokanson, Dawn DeMeo, Nadia Hansel, Craig Hersh, Jacqueline Hetmanski, David Lynch, Joyce Schroeder, John Newell, John Reilly, Harvey Coxson, Philip Judy, Eric Hoffman, George Washko, Raul San Jose Estepar, James Ross, Rebecca Leek, Jordan Zach, Alex Kluiber, Jered Sieren, Heather Baumhauer, Verity McArthur, Dzimitry Kazlouski, Andrew Allen, Tanya Mann, Anastasia Rodionova, Robert Jensen, Homayoon Farzadegan, Stacey Meyerer, Shivam Chandan, Samantha Bragan, James Murphy, Douglas Everett, Carla Wilson, Ruthie Knowles, Amber Powell, Joe Piccoli, Maura Robinson, Margaret Forbes, Martina Wamboldt, John Hokanson, Marci Sontag, Jennifer Black-Shinn, Gregory Kinney,
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Genetics of sputum gene expression in chronic obstructive pulmonary disease. PLoS One 2011; 6:e24395. [PMID: 21949713 PMCID: PMC3174957 DOI: 10.1371/journal.pone.0024395] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 08/09/2011] [Indexed: 12/31/2022] Open
Abstract
Previous expression quantitative trait loci (eQTL) studies have performed genetic association studies for gene expression, but most of these studies examined lymphoblastoid cell lines from non-diseased individuals. We examined the genetics of gene expression in a relevant disease tissue from chronic obstructive pulmonary disease (COPD) patients to identify functional effects of known susceptibility genes and to find novel disease genes. By combining gene expression profiling on induced sputum samples from 131 COPD cases from the ECLIPSE Study with genomewide single nucleotide polymorphism (SNP) data, we found 4315 significant cis-eQTL SNP-probe set associations (3309 unique SNPs). The 3309 SNPs were tested for association with COPD in a genomewide association study (GWAS) dataset, which included 2940 COPD cases and 1380 controls. Adjusting for 3309 tests (p<1.5e-5), the two SNPs which were significantly associated with COPD were located in two separate genes in a known COPD locus on chromosome 15: CHRNA5 and IREB2. Detailed analysis of chromosome 15 demonstrated additional eQTLs for IREB2 mapping to that gene. eQTL SNPs for CHRNA5 mapped to multiple linkage disequilibrium (LD) bins. The eQTLs for IREB2 and CHRNA5 were not in LD. Seventy-four additional eQTL SNPs were associated with COPD at p<0.01. These were genotyped in two COPD populations, finding replicated associations with a SNP in PSORS1C1, in the HLA-C region on chromosome 6. Integrative analysis of GWAS and gene expression data from relevant tissue from diseased subjects has located potential functional variants in two known COPD genes and has identified a novel COPD susceptibility locus.
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Fischer BM, Pavlisko E, Voynow JA. Pathogenic triad in COPD: oxidative stress, protease-antiprotease imbalance, and inflammation. Int J Chron Obstruct Pulmon Dis 2011; 6:413-21. [PMID: 21857781 PMCID: PMC3157944 DOI: 10.2147/copd.s10770] [Citation(s) in RCA: 196] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Indexed: 01/07/2023] Open
Abstract
Patients with chronic obstructive pulmonary disease (COPD) exhibit dominant features of chronic bronchitis, emphysema, and/or asthma, with a common phenotype of airflow obstruction. COPD pulmonary physiology reflects the sum of pathological changes in COPD, which can occur in large central airways, small peripheral airways, and the lung parenchyma. Quantitative or high-resolution computed tomography is used as a surrogate measure for assessment of disease progression. Different biological or molecular markers have been reported that reflect the mechanistic or pathogenic triad of inflammation, proteases, and oxidants and correspond to the different aspects of COPD histopathology. Similar to the pathogenic triad markers, genetic variations or polymorphisms have also been linked to COPD-associated inflammation, protease–antiprotease imbalance, and oxidative stress. Furthermore, in recent years, there have been reports identifying aging-associated mechanistic markers as downstream consequences of the pathogenic triad in the lungs from COPD patients. For this review, the authors have limited their discussion to a review of mechanistic markers and genetic variations and their association with COPD histopathology and disease status.
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Affiliation(s)
- Bernard M Fischer
- Department of Pediatrics, Duke University Medical Center, Durham, NC 27710, USA.
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Wan ES, Cho MH, Boutaoui N, Klanderman BJ, Sylvia JS, Ziniti JP, Won S, Lange C, Pillai SG, Anderson WH, Kong X, Lomas DA, Bakke PS, Gulsvik A, Regan EA, Murphy JR, Make BJ, Crapo JD, Wouters EF, Celli BR, Silverman EK, DeMeo DL, on behalf of the Evaluation of Chronic Obstructive Pulmonary Disease Longitudinally to Identify Predictive Surrogate End-Points (ECLIPSE), Norway-Bergen cohort, National Emphysema Treatment Trial, and COPD Gene investigators. Genome-wide association analysis of body mass in chronic obstructive pulmonary disease. Am J Respir Cell Mol Biol 2011; 45:304-10. [PMID: 21037115 PMCID: PMC3266061 DOI: 10.1165/rcmb.2010-0294oc] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Accepted: 09/30/2010] [Indexed: 11/24/2022] Open
Abstract
Cachexia, whether assessed by body mass index (BMI) or fat-free mass index (FFMI), affects a significant proportion of patients with chronic obstructive pulmonary disease (COPD), and is an independent risk factor for increased mortality, increased emphysema, and more severe airflow obstruction. The variable development of cachexia among patients with COPD suggests a role for genetic susceptibility. The objective of the present study was to determine genetic susceptibility loci involved in the development of low BMI and FFMI in subjects with COPD. A genome-wide association study (GWAS) of BMI was conducted in three independent cohorts of European descent with Global Initiative for Chronic Obstructive Lung Disease stage II or higher COPD: Evaluation of COPD Longitudinally to Identify Predictive Surrogate End-Points (ECLIPSE; n = 1,734); Norway-Bergen cohort (n = 851); and a subset of subjects from the National Emphysema Treatment Trial (NETT; n = 365). A genome-wide association of FFMI was conducted in two of the cohorts (ECLIPSE and Norway). In the combined analyses, a significant association was found between rs8050136, located in the first intron of the fat mass and obesity-associated (FTO) gene, and BMI (P = 4.97 × 10(-7)) and FFMI (P = 1.19 × 10(-7)). We replicated the association in a fourth, independent cohort consisting of 502 subjects with COPD from COPDGene (P = 6 × 10(-3)). Within the largest contributing cohort of our analysis, lung function, as assessed by forced expiratory volume at 1 second, varied significantly by FTO genotype. Our analysis suggests a potential role for the FTO locus in the determination of anthropomorphic measures associated with COPD.
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Affiliation(s)
- Emily S. Wan
- Channing Laboratory, Boston, Massachusetts; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts; Department of Statistics, Chung-Ang University, Seoul, Korea; Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts; GlaxoSmithKline Research and Development, Research Triangle Park, North Carolina; GlaxoSmithKline Research and Development, King of Prussia, Pennsylvania; Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom; Department of Thoracic Medicine, Haukeland University Hospital and Institute of Medicine, University of Bergen, Bergen, Norway; National Jewish Health, Denver, Colorado; and Maastricht University Medical Center, Maastricht, The Netherlands
| | - Michael H. Cho
- Channing Laboratory, Boston, Massachusetts; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts; Department of Statistics, Chung-Ang University, Seoul, Korea; Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts; GlaxoSmithKline Research and Development, Research Triangle Park, North Carolina; GlaxoSmithKline Research and Development, King of Prussia, Pennsylvania; Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom; Department of Thoracic Medicine, Haukeland University Hospital and Institute of Medicine, University of Bergen, Bergen, Norway; National Jewish Health, Denver, Colorado; and Maastricht University Medical Center, Maastricht, The Netherlands
| | - Nadia Boutaoui
- Channing Laboratory, Boston, Massachusetts; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts; Department of Statistics, Chung-Ang University, Seoul, Korea; Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts; GlaxoSmithKline Research and Development, Research Triangle Park, North Carolina; GlaxoSmithKline Research and Development, King of Prussia, Pennsylvania; Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom; Department of Thoracic Medicine, Haukeland University Hospital and Institute of Medicine, University of Bergen, Bergen, Norway; National Jewish Health, Denver, Colorado; and Maastricht University Medical Center, Maastricht, The Netherlands
| | - Barbara J. Klanderman
- Channing Laboratory, Boston, Massachusetts; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts; Department of Statistics, Chung-Ang University, Seoul, Korea; Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts; GlaxoSmithKline Research and Development, Research Triangle Park, North Carolina; GlaxoSmithKline Research and Development, King of Prussia, Pennsylvania; Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom; Department of Thoracic Medicine, Haukeland University Hospital and Institute of Medicine, University of Bergen, Bergen, Norway; National Jewish Health, Denver, Colorado; and Maastricht University Medical Center, Maastricht, The Netherlands
| | - Jody S. Sylvia
- Channing Laboratory, Boston, Massachusetts; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts; Department of Statistics, Chung-Ang University, Seoul, Korea; Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts; GlaxoSmithKline Research and Development, Research Triangle Park, North Carolina; GlaxoSmithKline Research and Development, King of Prussia, Pennsylvania; Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom; Department of Thoracic Medicine, Haukeland University Hospital and Institute of Medicine, University of Bergen, Bergen, Norway; National Jewish Health, Denver, Colorado; and Maastricht University Medical Center, Maastricht, The Netherlands
| | - John P. Ziniti
- Channing Laboratory, Boston, Massachusetts; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts; Department of Statistics, Chung-Ang University, Seoul, Korea; Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts; GlaxoSmithKline Research and Development, Research Triangle Park, North Carolina; GlaxoSmithKline Research and Development, King of Prussia, Pennsylvania; Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom; Department of Thoracic Medicine, Haukeland University Hospital and Institute of Medicine, University of Bergen, Bergen, Norway; National Jewish Health, Denver, Colorado; and Maastricht University Medical Center, Maastricht, The Netherlands
| | - Sungho Won
- Channing Laboratory, Boston, Massachusetts; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts; Department of Statistics, Chung-Ang University, Seoul, Korea; Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts; GlaxoSmithKline Research and Development, Research Triangle Park, North Carolina; GlaxoSmithKline Research and Development, King of Prussia, Pennsylvania; Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom; Department of Thoracic Medicine, Haukeland University Hospital and Institute of Medicine, University of Bergen, Bergen, Norway; National Jewish Health, Denver, Colorado; and Maastricht University Medical Center, Maastricht, The Netherlands
| | - Christoph Lange
- Channing Laboratory, Boston, Massachusetts; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts; Department of Statistics, Chung-Ang University, Seoul, Korea; Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts; GlaxoSmithKline Research and Development, Research Triangle Park, North Carolina; GlaxoSmithKline Research and Development, King of Prussia, Pennsylvania; Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom; Department of Thoracic Medicine, Haukeland University Hospital and Institute of Medicine, University of Bergen, Bergen, Norway; National Jewish Health, Denver, Colorado; and Maastricht University Medical Center, Maastricht, The Netherlands
| | - Sreekumar G. Pillai
- Channing Laboratory, Boston, Massachusetts; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts; Department of Statistics, Chung-Ang University, Seoul, Korea; Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts; GlaxoSmithKline Research and Development, Research Triangle Park, North Carolina; GlaxoSmithKline Research and Development, King of Prussia, Pennsylvania; Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom; Department of Thoracic Medicine, Haukeland University Hospital and Institute of Medicine, University of Bergen, Bergen, Norway; National Jewish Health, Denver, Colorado; and Maastricht University Medical Center, Maastricht, The Netherlands
| | - Wayne H. Anderson
- Channing Laboratory, Boston, Massachusetts; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts; Department of Statistics, Chung-Ang University, Seoul, Korea; Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts; GlaxoSmithKline Research and Development, Research Triangle Park, North Carolina; GlaxoSmithKline Research and Development, King of Prussia, Pennsylvania; Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom; Department of Thoracic Medicine, Haukeland University Hospital and Institute of Medicine, University of Bergen, Bergen, Norway; National Jewish Health, Denver, Colorado; and Maastricht University Medical Center, Maastricht, The Netherlands
| | - Xiangyang Kong
- Channing Laboratory, Boston, Massachusetts; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts; Department of Statistics, Chung-Ang University, Seoul, Korea; Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts; GlaxoSmithKline Research and Development, Research Triangle Park, North Carolina; GlaxoSmithKline Research and Development, King of Prussia, Pennsylvania; Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom; Department of Thoracic Medicine, Haukeland University Hospital and Institute of Medicine, University of Bergen, Bergen, Norway; National Jewish Health, Denver, Colorado; and Maastricht University Medical Center, Maastricht, The Netherlands
| | - David A. Lomas
- Channing Laboratory, Boston, Massachusetts; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts; Department of Statistics, Chung-Ang University, Seoul, Korea; Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts; GlaxoSmithKline Research and Development, Research Triangle Park, North Carolina; GlaxoSmithKline Research and Development, King of Prussia, Pennsylvania; Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom; Department of Thoracic Medicine, Haukeland University Hospital and Institute of Medicine, University of Bergen, Bergen, Norway; National Jewish Health, Denver, Colorado; and Maastricht University Medical Center, Maastricht, The Netherlands
| | - Per S. Bakke
- Channing Laboratory, Boston, Massachusetts; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts; Department of Statistics, Chung-Ang University, Seoul, Korea; Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts; GlaxoSmithKline Research and Development, Research Triangle Park, North Carolina; GlaxoSmithKline Research and Development, King of Prussia, Pennsylvania; Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom; Department of Thoracic Medicine, Haukeland University Hospital and Institute of Medicine, University of Bergen, Bergen, Norway; National Jewish Health, Denver, Colorado; and Maastricht University Medical Center, Maastricht, The Netherlands
| | - Amund Gulsvik
- Channing Laboratory, Boston, Massachusetts; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts; Department of Statistics, Chung-Ang University, Seoul, Korea; Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts; GlaxoSmithKline Research and Development, Research Triangle Park, North Carolina; GlaxoSmithKline Research and Development, King of Prussia, Pennsylvania; Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom; Department of Thoracic Medicine, Haukeland University Hospital and Institute of Medicine, University of Bergen, Bergen, Norway; National Jewish Health, Denver, Colorado; and Maastricht University Medical Center, Maastricht, The Netherlands
| | - Elizabeth A. Regan
- Channing Laboratory, Boston, Massachusetts; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts; Department of Statistics, Chung-Ang University, Seoul, Korea; Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts; GlaxoSmithKline Research and Development, Research Triangle Park, North Carolina; GlaxoSmithKline Research and Development, King of Prussia, Pennsylvania; Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom; Department of Thoracic Medicine, Haukeland University Hospital and Institute of Medicine, University of Bergen, Bergen, Norway; National Jewish Health, Denver, Colorado; and Maastricht University Medical Center, Maastricht, The Netherlands
| | - James R. Murphy
- Channing Laboratory, Boston, Massachusetts; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts; Department of Statistics, Chung-Ang University, Seoul, Korea; Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts; GlaxoSmithKline Research and Development, Research Triangle Park, North Carolina; GlaxoSmithKline Research and Development, King of Prussia, Pennsylvania; Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom; Department of Thoracic Medicine, Haukeland University Hospital and Institute of Medicine, University of Bergen, Bergen, Norway; National Jewish Health, Denver, Colorado; and Maastricht University Medical Center, Maastricht, The Netherlands
| | - Barry J. Make
- Channing Laboratory, Boston, Massachusetts; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts; Department of Statistics, Chung-Ang University, Seoul, Korea; Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts; GlaxoSmithKline Research and Development, Research Triangle Park, North Carolina; GlaxoSmithKline Research and Development, King of Prussia, Pennsylvania; Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom; Department of Thoracic Medicine, Haukeland University Hospital and Institute of Medicine, University of Bergen, Bergen, Norway; National Jewish Health, Denver, Colorado; and Maastricht University Medical Center, Maastricht, The Netherlands
| | - James D. Crapo
- Channing Laboratory, Boston, Massachusetts; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts; Department of Statistics, Chung-Ang University, Seoul, Korea; Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts; GlaxoSmithKline Research and Development, Research Triangle Park, North Carolina; GlaxoSmithKline Research and Development, King of Prussia, Pennsylvania; Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom; Department of Thoracic Medicine, Haukeland University Hospital and Institute of Medicine, University of Bergen, Bergen, Norway; National Jewish Health, Denver, Colorado; and Maastricht University Medical Center, Maastricht, The Netherlands
| | - Emiel F. Wouters
- Channing Laboratory, Boston, Massachusetts; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts; Department of Statistics, Chung-Ang University, Seoul, Korea; Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts; GlaxoSmithKline Research and Development, Research Triangle Park, North Carolina; GlaxoSmithKline Research and Development, King of Prussia, Pennsylvania; Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom; Department of Thoracic Medicine, Haukeland University Hospital and Institute of Medicine, University of Bergen, Bergen, Norway; National Jewish Health, Denver, Colorado; and Maastricht University Medical Center, Maastricht, The Netherlands
| | - Bartolome R. Celli
- Channing Laboratory, Boston, Massachusetts; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts; Department of Statistics, Chung-Ang University, Seoul, Korea; Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts; GlaxoSmithKline Research and Development, Research Triangle Park, North Carolina; GlaxoSmithKline Research and Development, King of Prussia, Pennsylvania; Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom; Department of Thoracic Medicine, Haukeland University Hospital and Institute of Medicine, University of Bergen, Bergen, Norway; National Jewish Health, Denver, Colorado; and Maastricht University Medical Center, Maastricht, The Netherlands
| | - Edwin K. Silverman
- Channing Laboratory, Boston, Massachusetts; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts; Department of Statistics, Chung-Ang University, Seoul, Korea; Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts; GlaxoSmithKline Research and Development, Research Triangle Park, North Carolina; GlaxoSmithKline Research and Development, King of Prussia, Pennsylvania; Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom; Department of Thoracic Medicine, Haukeland University Hospital and Institute of Medicine, University of Bergen, Bergen, Norway; National Jewish Health, Denver, Colorado; and Maastricht University Medical Center, Maastricht, The Netherlands
| | - Dawn L. DeMeo
- Channing Laboratory, Boston, Massachusetts; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts; Department of Statistics, Chung-Ang University, Seoul, Korea; Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts; GlaxoSmithKline Research and Development, Research Triangle Park, North Carolina; GlaxoSmithKline Research and Development, King of Prussia, Pennsylvania; Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom; Department of Thoracic Medicine, Haukeland University Hospital and Institute of Medicine, University of Bergen, Bergen, Norway; National Jewish Health, Denver, Colorado; and Maastricht University Medical Center, Maastricht, The Netherlands
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49
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Lipman PJ, Cho MH, Bakke P, Gulsvik A, Kong X, Lomas DA, Anderson W, Silverman EK, Lange C. On the follow-up of genome-wide association studies: an overall test for the most promising SNPs. Genet Epidemiol 2011; 35:303-9. [PMID: 21374717 PMCID: PMC4096304 DOI: 10.1002/gepi.20578] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Revised: 01/13/2011] [Accepted: 01/31/2011] [Indexed: 11/09/2022]
Abstract
Even in large-scale genome-wide association studies (GWASs), only a fraction of the true associations are detected at the genome-wide significance level. When few or no associations reach the significance threshold, one strategy is to follow up on the most promising candidates, i.e. the single nucleotide polymorphisms (SNPs) with the smallest association-test P-values, by genotyping them in additional studies. In this communication, we propose an overall test for GWASs that analyzes the SNPs with the most promising P-values simultaneously and therefore allows an early assessment of whether the follow-up of the selected SNPs is likely promising. We theoretically derive the properties of the proposed overall test under the null hypothesis and assess its power based on simulation studies. An application to a GWAS for chronic obstructive pulmonary disease suggests that there are true association signals among the top SNPs and that an additional follow-up study is promising.
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Affiliation(s)
- Peter J Lipman
- Department of Biostatistics, Harvard School of Public Health, Boston, MA 02115, USA.
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Abstract
Although, to our knowledge, there has been no exhaustive or credible review of the evidence of the disease burden of COPD in China, COPD has become an increasing public health concern to the Chinese medical community. The purpose of this article is to review the evidence and evaluate and clarify the disease burden of COPD in China with the aim of improving effective management. We reviewed previous studies of COPD in China, which included data on prevalence, mortality, disease burden, risk factors, diagnosis, and management by searching related Web sites, including PubMed, ProQuest, and Thomson Reuters' Web of Knowledge, as well as major Chinese databases and government Web sites. Reported COPD prevalence varied between 5% and 13% in different provinces/cities across China. In 2008, COPD ranked fourth as a leading cause of death in urban areas and third in rural areas. In addition, COPD accounted for 1.6% of all hospital admissions in China in that year. The high prevalence of smoking and biomass fuel use acted as major contributors to the high occurrence of COPD in China. Management of COPD in China should focus on adjusting the distribution of medical resources and on addressing public health policies to facilitate earlier diagnosis in rural areas, aim to reduce smoking prevalence, improve patients' self-management, and keep physicians' knowledge up to date and consistent with current guidelines. COPD is one of the most challenging medical issues facing China because of its influence on both personal and public health and its impact on the economy. Optimal management strategies should be adopted and strengthened immediately.
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Affiliation(s)
- Xiaocong Fang
- Department of Pulmonary Medicine, Research Institute of Respiratory Disease, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiangdong Wang
- Department of Pulmonary Medicine, Research Institute of Respiratory Disease, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chunxue Bai
- Department of Pulmonary Medicine, Research Institute of Respiratory Disease, Zhongshan Hospital, Fudan University, Shanghai, China.
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