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Seo J, Gaddis NC, Patchen BK, Xu J, Barr RG, O'Connor G, Manichaikul AW, Gharib SA, Dupuis J, North KE, Cassano PA, Hancock DB. Exploiting meta-analysis of genome-wide interaction with serum 25-hydroxyvitamin D to identify novel genetic loci associated with pulmonary function. Am J Clin Nutr 2024; 119:1227-1237. [PMID: 38484975 PMCID: PMC11130669 DOI: 10.1016/j.ajcnut.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 02/12/2024] [Accepted: 03/07/2024] [Indexed: 04/01/2024] Open
Abstract
BACKGROUND Higher 25-hydroxyvitamin D (25(OH)D) concentrations in serum has a positive association with pulmonary function. Investigating genome-wide interactions with 25(OH)D may reveal new biological insights into pulmonary function. OBJECTIVES We aimed to identify novel genetic variants associated with pulmonary function by accounting for 25(OH)D interactions. METHODS We included 211,264 participants from the observational United Kingdom Biobank study with pulmonary function tests (PFTs), genome-wide genotypes, and 25(OH)D concentrations from 4 ancestral backgrounds-European, African, East Asian, and South Asian. Among PFTs, we focused on forced expiratory volume in the first second (FEV1) and forced vital capacity (FVC) because both were previously associated with 25(OH)D. We performed genome-wide association study (GWAS) analyses that accounted for variant×25(OH)D interaction using the joint 2 degree-of-freedom (2df) method, stratified by participants' smoking history and ancestry, and meta-analyzed results. We evaluated interaction effects to determine how variant-PFT associations were modified by 25(OH)D concentrations and conducted pathway enrichment analysis to examine the biological relevance of our findings. RESULTS Our GWAS meta-analyses, accounting for interaction with 25(OH)D, revealed 30 genetic variants significantly associated with FEV1 or FVC (P2df <5.00×10-8) that were not previously reported for PFT-related traits. These novel variant signals were enriched in lung function-relevant pathways, including the p38 MAPK pathway. Among variants with genome-wide-significant 2df results, smoking-stratified meta-analyses identified 5 variants with 25(OH)D interactions that influenced FEV1 in both smoking groups (never smokers P1df interaction<2.65×10-4; ever smokers P1df interaction<1.71×10-5); rs3130553, rs2894186, rs79277477, and rs3130929 associations were only evident in never smokers, and the rs4678408 association was only found in ever smokers. CONCLUSION Genetic variant associations with lung function can be modified by 25(OH)D, and smoking history can further modify variant×25(OH)D interactions. These results expand the known genetic architecture of pulmonary function and add evidence that gene-environment interactions, including with 25(OH)D and smoking, influence lung function.
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Affiliation(s)
- Jungkyun Seo
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, United States
| | - Nathan C Gaddis
- RTI International, Research Triangle Park, NC, United States
| | - Bonnie K Patchen
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, United States
| | - Jiayi Xu
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, United States
| | - R Graham Barr
- Divisions of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Medical Center, New York, NY, United States
| | - George O'Connor
- Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - Ani W Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Sina A Gharib
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, United States; Division of Pulmonary, Critical Care and Sleep Medicine, Computational Medicine Core, Center for Lung Biology, University of Washington, Seattle, WA, United States
| | - Josée Dupuis
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Kari E North
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, United States
| | - Patricia A Cassano
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, United States; Division of Epidemiology, Department of Population Health Sciences, Weill Cornell Medicine, NY, United States
| | - Dana B Hancock
- RTI International, Research Triangle Park, NC, United States.
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Błach J, Siedliński M, Sydor W. Immunology in COPD and the use of combustible cigarettes and heated tobacco products. Eur J Med Res 2023; 28:397. [PMID: 37794516 PMCID: PMC10548761 DOI: 10.1186/s40001-023-01374-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/18/2023] [Indexed: 10/06/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is one of the most common chronic respiratory diseases, characterised by high morbidity and mortality. COPD is characterised by a progressive decline of lung function caused by chronic inflammatory reactions in the lung tissue due to continual exposure to harmful molecules by inhalation. As prevention plays a very important role in COPD, quitting smoking is the most important factor in reducing the decline in lung function. Unfortunately, many people are unable to break their nicotine addiction. This paper summarises current knowledge about combustible cigarettes (CSs) and alternative tobacco products such as heated tobacco products (HTPs) in COPD. The paper focuses on the immunological aspects of COPD and the influence of tobacco products on lung tissue immunology. There are differences in research results between HTPs and CSs in favour of HTPs. More long-term studies are needed to look at the effects of HTPs, especially in COPD. However, there is no doubt that it would be best for patients to give up their nicotine addiction completely.
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Affiliation(s)
- Justyna Błach
- Department of Clinical Immunology, UCH, Cracow, Poland.
| | - Mateusz Siedliński
- Department of Internal Medicine and Rural Medicine, Jagiellonian University Medical College, Cracow, Poland
| | - Wojciech Sydor
- Department of Rheumatology and Immunology, Jagiellonian University Medical College, Cracow, Poland
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Bai X, Schountz T, Buckle AM, Talbert JL, Sandhaus RA, Chan ED. Alpha-1-antitrypsin antagonizes COVID-19: a review of the epidemiology, molecular mechanisms, and clinical evidence. Biochem Soc Trans 2023; 51:1361-1375. [PMID: 37294003 PMCID: PMC10317171 DOI: 10.1042/bst20230078] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 06/10/2023]
Abstract
Alpha-1-antitrypsin (AAT), a serine protease inhibitor (serpin), is increasingly recognized to inhibit SARS-CoV-2 infection and counter many of the pathogenic mechanisms of COVID-19. Herein, we reviewed the epidemiologic evidence, the molecular mechanisms, and the clinical evidence that support this paradigm. As background to our discussion, we first examined the basic mechanism of SARS-CoV-2 infection and contend that despite the availability of vaccines and anti-viral agents, COVID-19 remains problematic due to viral evolution. We next underscored that measures to prevent severe COVID-19 currently exists but teeters on a balance and that current treatment for severe COVID-19 remains grossly suboptimal. We then reviewed the epidemiologic and clinical evidence that AAT deficiency increases risk of COVID-19 infection and of more severe disease, and the experimental evidence that AAT inhibits cell surface transmembrane protease 2 (TMPRSS2) - a host serine protease required for SARS-CoV-2 entry into cells - and that this inhibition may be augmented by heparin. We also elaborated on the panoply of other activities of AAT (and heparin) that could mitigate severity of COVID-19. Finally, we evaluated the available clinical evidence for AAT treatment of COVID-19.
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Affiliation(s)
- Xiyuan Bai
- Department of Medicine, Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, CO, U.S.A
- Department of Academic Affairs, National Jewish Health, Denver, CO, U.S.A
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, U.S.A
| | - Tony Schountz
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, U.S.A
| | - Ashley M. Buckle
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- PTNG Bio, Melbourne, Australia
| | - Janet L. Talbert
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, U.S.A
| | | | - Edward D. Chan
- Department of Medicine, Rocky Mountain Regional Veterans Affairs Medical Center, Aurora, CO, U.S.A
- Department of Academic Affairs, National Jewish Health, Denver, CO, U.S.A
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado School of Medicine, Aurora, CO, U.S.A
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Qiu SL, Sun QX, Zhou JP, Tang HJ, Chen YQ, Chen FS, Feng T, He ZQ, Qin HJ, Duan MC. IL-27 mediates anti-inflammatory effect in cigarette smoke induced emphysema by negatively regulating IFN-γ producing cytotoxic CD8 + T cells in mice. Eur J Immunol 2022; 52:222-236. [PMID: 34559883 DOI: 10.1002/eji.202049076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 07/02/2021] [Accepted: 09/24/2021] [Indexed: 11/09/2022]
Abstract
Chronic airway inflammation mediated by CD8+ T lymphocytes contributes to the pathogenesis of Chronic obstructive pulmonary disease (COPD). Deciphering the fingerprint of the chronic inflammation orchestrated by CD8+ T cells may allow the development of novel approaches to COPD management. Here, the expression of IL-27 and IFN-γ+ CD8+ Tc1 cells were evaluated in patients with COPD and in cigarette smoke-exposed mice. The production of IL-27 by marrow-derived dendritic cells (mDCs) in response to cigarette smoke extract (CSE) was assessed. The role of IL-27 in IFN-γ+ CD8+ Tc1 cells was explored. We demonstrated that elevated IL-27 was accompanied by an exaggerated IFN-γ+ CD8+ Tc1 response in a smoking mouse model of emphysema. We noted that lung dendritic cells were one of the main sources of IL-27 during chronic cigarette smoke exposure. Moreover, CSE directly induced the production of IL-27 by mDCs in vitro. IL-27 negatively regulated the differentiation of IFN-γ+ CD8+ Tc1 cells isolated from cigarette smoke-exposed mice in a STAT1- and STAT3-independent manner. Systemic administration of recombinant IL-27 attenuated IFN-γ+ CD8+ Tc1 response in the late phase of cigarette smoke exposure. Our results uncovered that IL-27 negatively regulates IFN-γ+ CD8+ Tc1 response in the late stage of chronic cigarette smoke exposure, which may provide a new strategy for the anti-inflammatory treatment of smoking-related COPD/emphysema.
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Affiliation(s)
- Shi-Lin Qiu
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Guangxi Medical University, Guangxi, China
| | - Qi-Xiang Sun
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Guangxi Medical University, Guangxi, China
| | - Jian-Peng Zhou
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Guangxi Medical University, Guangxi, China
| | - Hai-Juan Tang
- Department of Respiratory and Critical Care Medicine, the First Affiliated Hospital of Guangxi Medical University, Guangxi, China
| | - Yan-Qiong Chen
- Department of Respiratory and Critical Care Medicine, Wuming Hospital of Guangxi Medical University, Guangxi, China
| | - Fu-Shou Chen
- Department of Respiratory and Critical Care Medicine, Wuming Hospital of Guangxi Medical University, Guangxi, China
| | - Tao Feng
- Department of Respiratory and Critical Care Medicine, Wuming Hospital of Guangxi Medical University, Guangxi, China
| | - Zai-Qing He
- Department of Respiratory and Critical Care Medicine, Wuming Hospital of Guangxi Medical University, Guangxi, China
| | - Hua-Jiao Qin
- Department of Respiratory and Critical Care Medicine, Wuming Hospital of Guangxi Medical University, Guangxi, China
| | - Min-Chao Duan
- Department of Respiratory and Critical Care Medicine, Wuming Hospital of Guangxi Medical University, Guangxi, China
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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: 11] [Impact Index Per Article: 3.7] [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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Lee KS, Kim KH, Oh YM, Han B, Kim WJ. A genome wide association study for lung function in the Korean population using an exome array. Korean J Intern Med 2021; 36:S142-S150. [PMID: 32336055 PMCID: PMC8009153 DOI: 10.3904/kjim.2019.204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 01/09/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND/AIMS Lung function is an objective indicator of diagnosis and prognosis of respiratory diseases. Many common genetic variants have been associated with lung function in multiple ethnic populations. We looked for coding variants associated with forced expiratory volume in 1 second (FEV1) and FEV1/forced vital capacity (FVC) in the Korean general population. METHODS We carried out exome array analysis and lung function measurements of the FEV1 and FEV1/FVC in 7,524 individuals of the Korean population. We evaluated single variants with minor allele frequency greater than 0.5%. We performed look-ups for candidate coding variants associations in the UK Biobank, SpiroMeta, and CHARGE consortia. RESULTS We identified coding variants in the SMIM29 (C6orf1) (p = 1.2 × 10-5) and HMGA1 locus on chromosome 6p21, the GIT2 (p = 6.5 × 10-5) locus on chromosome 12q24, and the ARHGEF40 (p = 9.9 × 10-5) locus on chromosome 14q11 as having a significant association with lung function (FEV1). We also confirmed a previously reported association with lung function and chronic obstructive pulmonary disease in the FAM13A (p = 4.54 × 10-6) locus on chromosome 4q22, in TNXB (p = 1.30 × 10-6) and in AGER (p = 1.09 × 10-8) locus on chromosome 6p21. CONCLUSION Our exome array analysis identified that several protein coding variants were associated with lung function in the Korean population. Common coding variants in SMIM29 (C6orf1), HMGA1, GIT2, FAM13A, TNXB, AGER and low-frequency variant in ARHGEF40 potentially affect lung function, which warrant further study.
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Affiliation(s)
- Kyu-Sun Lee
- Department of Internal Medicine, Kangwon National University School of Medicine, Chuncheon, Korea
| | - Kun Hee Kim
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Yeon-Mok Oh
- Department of Pulmonary and Critical Care Medicine and Clinical Research Center for Chronic Obstructive Airway Disease, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Buhm Han
- Department of Medical Science, Seoul National University College of Medicine, Seoul, Korea
| | - Woo Jin Kim
- Department of Internal Medicine, Kangwon National University School of Medicine, Chuncheon, Korea
- Correspondence to Woo Jin Kim, M.D. Department of Internal Medicine, Kangwon National University School of Medicine, 156 Baengnyeong-ro, Chuncheon 24289, Korea Tel: +82-33-250-7815 Fax: +82-33-255-6567 E-mail:
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7
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Lee YJ, Choi S, Kwon SY, Lee Y, Lee JK, Heo EY, Chung HS, Kim DK. A Genome-Wide Association Study in Early COPD: Identification of One Major Susceptibility Loci. Int J Chron Obstruct Pulmon Dis 2020; 15:2967-2975. [PMID: 33235445 PMCID: PMC7680157 DOI: 10.2147/copd.s269263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 09/23/2020] [Indexed: 12/20/2022] Open
Abstract
Background Identifying the genetic basis of airflow limitation is one of the most interesting issues for understanding chronic obstructive pulmonary disease (COPD) pathophysiology. Several studies have shown that some genetic variants associated with COPD have been identified in genome-wide association study (GWAS), especially in patients with moderate to severe COPD; genetic susceptibility for airflow limitation in the early COPD phase has not been widely studied. Objective We investigated the genetic variants in early COPD. Methods The present study analyzed Gene-environment interaction and phenotype (GENIE) cohort that included participants who received health screening examination. The association between single nucleotide polymorphism (SNP) and susceptibility to early COPD (FEV1 predicted ≥50% and FEV1/FVC <0.7) was tested. Results A total of 130 patients with early COPD and 3478 controls (1700 ever smokers and 1778 never smokers) were recruited. When compared with the total controls, certain SNPs (rs2818103, rs875033, rs9354627, rs34552148) on chromosome 6 were included at the top of our list (p= 5.6 × 10–7 ~9.6 × 10–6) although they did not reach genome-wide significance. When compared with the never smoker controls, two SNPs (rs2857210, rs2621419) of the HLA-DQB2 gene class were persistently associated with susceptibility to early COPD. Conclusion Certain SNPs located on chromosome 6 or the HLA-DQB2 gene were the top-scoring SNPs for the association with susceptibility to early COPD in the Korean GENIE cohort.
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Affiliation(s)
- Ye-Jin Lee
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Internal Medicine, Hallym University Kangdong Sacred Heart Hospital, Seoul, Korea
| | - SeungHo Choi
- Department of Internal Medicine, Healthcare Research Institute, Healthcare System Gangnam Center, Seoul National University Hospital, Seoul 135-984 Korea
| | - Sung-Youn Kwon
- Department of Internal Medicine, Healthcare Research Institute, Healthcare System Gangnam Center, Seoul National University Hospital, Seoul 135-984 Korea
| | - Yunhwan Lee
- Department of Internal Medicine, Healthcare Research Institute, Healthcare System Gangnam Center, Seoul National University Hospital, Seoul 135-984 Korea
| | - Jung Kyu Lee
- Division of Pulmonary and Critical Care Medicine, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
| | - Eun Young Heo
- Division of Pulmonary and Critical Care Medicine, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea
| | - Hee Soon Chung
- Division of Pulmonary and Critical Care Medicine, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea.,Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Deog Kyeom Kim
- Division of Pulmonary and Critical Care Medicine, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, Seoul, Korea.,Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
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8
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Li M, Jiao L, Lyu M, Song J, Bai H, Zhang C, Wu T, Chen X, Ying B. Association of IL27 and STAT3 genetic polymorphism on the susceptibility of tuberculosis in Western Chinese Han population. INFECTION GENETICS AND EVOLUTION 2020; 83:104324. [PMID: 32320824 DOI: 10.1016/j.meegid.2020.104324] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 04/14/2020] [Accepted: 04/15/2020] [Indexed: 02/05/2023]
Abstract
OBJECTIVE Host immune response have a pivotal role in the course of Mycobacterium tuberculosis (Mtb) infection. IL27 plays both pro-inflammatory and anti-inflammatory activities in infectious diseases via STAT1/STAT3 mechanism. To investigate the association of single nucleotide polymorphisms (SNPs) of IL27 and STAT3 on the susceptibility of tuberculosis, we conducted a large size of case-control study in western Chinese Han population. METHODS A total of seven SNPs were genotyped using multiplex ligation detection reaction method in 900 patients with tuberculosis and 1534 healthy controls. RESULTS Variants of three SNPs (rs181206, rs17855750, rs26528) within IL27 gene, the genotype and allele frequencies of rs17855750 were significantly different (p = .013, p = .004, respectively) between the TB patients and healthy controls. Subjects carrying C allele for rs17855750 showed a decreased tuberculosis risk (OR = 0.75, 95% CI = 0.62-0.91, p = .004). Genetic model analysis revealed that dominant modal was associated with lower TB risk (OR = 0.74, 95% CI = 0.60-0.92, p = .042). Haplotype of ACG (representing rs181206, rs17855750 and rs26528) showed a reduced risk to TB (OR = 0.79, 95% CI = 0.65-0.96, p = .017). There were no significant differences between TB cases and healthy controls in the variants of four SNPs (rs1053005, rs2293152, rs744166, rs4796793) within STAT3 gene. CONCLUSIONS The polymorphisms of IL27, rs17855750, but not rs181206 and rs26528, plays a protective role on the susceptibility to TB.
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Affiliation(s)
- Mengjiao Li
- West China Hospital of Sichuan University, Department of Laboratory Medicine, Chengdu, China
| | - Lin Jiao
- West China Hospital of Sichuan University, Department of Laboratory Medicine, Chengdu, China
| | - Mengyuan Lyu
- West China Hospital of Sichuan University, Department of Laboratory Medicine, Chengdu, China
| | - Jiajia Song
- West China Hospital of Sichuan University, Department of Laboratory Medicine, Chengdu, China
| | - Hao Bai
- West China Hospital of Sichuan University, Department of Laboratory Medicine, Chengdu, China
| | - Chunying Zhang
- West China Hospital of Sichuan University, Department of Laboratory Medicine, Chengdu, China
| | - Tao Wu
- West China Hospital of Sichuan University, Department of Laboratory Medicine, Chengdu, China
| | - Xuerong Chen
- West China Hospital of Sichuan University, Department of Laboratory Medicine, Chengdu, China
| | - Binwu Ying
- West China Hospital of Sichuan University, Department of Laboratory Medicine, Chengdu, China.
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9
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Lutz SM, Frederiksen B, Begum F, McDonald MLN, Cho MH, Hobbs BD, Parker MM, DeMeo DL, Hersh CP, Ehringer MA, Young K, Jiang L, Foreman MG, Kinney GL, Make BJ, Lomas DA, Bakke P, Gulsvik A, Crapo JD, Silverman EK, Beaty TH, Hokanson JE. Common and Rare Variants Genetic Association Analysis of Cigarettes per Day Among Ever-Smokers in Chronic Obstructive Pulmonary Disease Cases and Controls. Nicotine Tob Res 2020; 21:714-722. [PMID: 29767774 DOI: 10.1093/ntr/nty095] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 05/09/2018] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Cigarette smoking is a major environmental risk factor for many diseases, including chronic obstructive pulmonary disease (COPD). There are shared genetic influences on cigarette smoking and COPD. Genetic risk factors for cigarette smoking in cohorts enriched for COPD are largely unknown. METHODS We performed genome-wide association analyses for average cigarettes per day (CPD) across the Genetic Epidemiology of COPD (COPDGene) non-Hispanic white (NHW) (n = 6659) and African American (AA) (n = 3260), GenKOLS (the Genetics of Chronic Obstructive Lung Disease) (n = 1671), and ECLIPSE (the Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints) (n = 1942) cohorts. In addition, we performed exome array association analyses across the COPDGene NHW and AA cohorts. We considered analyses across the entire cohort and stratified by COPD case-control status. RESULTS We identified genome-wide significant associations for CPD on chromosome 15q25 across all cohorts (lowest p = 1.78 × 10-15), except in the COPDGene AA cohort alone. Previously reported associations on chromosome 19 had suggestive and directionally consistent associations (RAB4, p = 1.95 × 10-6; CYP2A7, p = 7.50 × 10-5; CYP2B6, p = 4.04 × 10-4). When we stratified by COPD case-control status, single nucleotide polymorphisms on chromosome 15q25 were nominally associated with both NHW COPD cases (β = 0.11, p = 5.58 × 10-4) and controls (β = 0.12, p = 3.86 × 10-5) For the gene-based exome array association analysis of rare variants, there were no exome-wide significant associations. For these previously replicated associations, the most significant results were among COPDGene NHW subjects for CYP2A7 (p = 5.2 × 10-4). CONCLUSIONS In a large genome-wide association study of both common variants and a gene-based association of rare coding variants in ever-smokers, we found genome-wide significant associations on chromosome 15q25 with CPD for common variants, but not for rare coding variants. These results were directionally consistent among COPD cases and controls. IMPLICATIONS We examined both common and rare coding variants associated with CPD in a large population of heavy smokers with and without COPD of NHW and AA descent. We replicated genome-wide significant associations on chromosome 15q25 with CPD for common variants among NHW subjects, but not for rare variants. We demonstrated for the first time that common variants on chromosome 15q25 associated with CPD are similar among COPD cases and controls. Previously reported associations on chromosome 19 showed suggestive and directionally consistent associations among common variants (RAB4, CYP2A7, and CYP2B6) and for rare variants (CYP2A7) among COPDGene NHW subjects. Although the genetic effect sizes for these single nucleotide polymorphisms on chromosome 15q25 are modest, we show that this creates a substantial smoking burden over the lifetime of a smoker.
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Affiliation(s)
- Sharon M Lutz
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Brittni Frederiksen
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Ferdouse Begum
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Merry-Lynn N McDonald
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Brian D Hobbs
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Margaret M Parker
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Marissa A Ehringer
- Institute for Behavioral Genetics, University of Colorado at Boulder, Boulder, CO
| | - Kendra Young
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Lai Jiang
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | | | - Greg L Kinney
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Barry J Make
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, CO
| | - David A Lomas
- UCL Respiratory, University College London, London, UK
| | - Per Bakke
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Amund Gulsvik
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - James D Crapo
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, CO
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - John E Hokanson
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, CO
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10
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Ragland MF, Benway CJ, Lutz SM, Bowler RP, Hecker J, Hokanson JE, Crapo JD, Castaldi PJ, DeMeo DL, Hersh CP, Hobbs BD, Lange C, Beaty TH, Cho MH, Silverman EK. Genetic Advances in Chronic Obstructive Pulmonary Disease. Insights from COPDGene. Am J Respir Crit Care Med 2020; 200:677-690. [PMID: 30908940 DOI: 10.1164/rccm.201808-1455so] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a common and progressive disease that is influenced by both genetic and environmental factors. For many years, knowledge of the genetic basis of COPD was limited to Mendelian syndromes, such as alpha-1 antitrypsin deficiency and cutis laxa, caused by rare genetic variants. Over the past decade, the proliferation of genome-wide association studies, the accessibility of whole-genome sequencing, and the development of novel methods for analyzing genetic variation data have led to a substantial increase in the understanding of genetic variants that play a role in COPD susceptibility and COPD-related phenotypes. COPDGene (Genetic Epidemiology of COPD), a multicenter, longitudinal study of over 10,000 current and former cigarette smokers, has been pivotal to these breakthroughs in understanding the genetic basis of COPD. To date, over 20 genetic loci have been convincingly associated with COPD affection status, with additional loci demonstrating association with COPD-related phenotypes such as emphysema, chronic bronchitis, and hypoxemia. In this review, we discuss the contributions of the COPDGene study to the discovery of these genetic associations as well as the ongoing genetic investigations of COPD subtypes, protein biomarkers, and post-genome-wide association study analysis.
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Affiliation(s)
- Margaret F Ragland
- Division of Pulmonary Sciences and Critical Care Medicine, School of Medicine, and
| | | | | | | | - Julian Hecker
- Harvard T. H. Chan School of Public Health, Boston, Massachusetts; and
| | - John E Hokanson
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Aurora, Colorado
| | | | | | - Dawn L DeMeo
- Channing Division of Network Medicine and.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Craig P Hersh
- Channing Division of Network Medicine and.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Brian D Hobbs
- Channing Division of Network Medicine and.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Christoph Lange
- Harvard T. H. Chan School of Public Health, Boston, Massachusetts; and
| | - Terri H Beaty
- Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland
| | - Michael H Cho
- Channing Division of Network Medicine and.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Edwin K Silverman
- Channing Division of Network Medicine and.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts
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11
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Halu A, Liu S, Baek SH, Hobbs BD, Hunninghake GM, Cho MH, Silverman EK, Sharma A. Exploring the cross-phenotype network region of disease modules reveals concordant and discordant pathways between chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis. Hum Mol Genet 2020; 28:2352-2364. [PMID: 30997486 DOI: 10.1093/hmg/ddz069] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 03/12/2019] [Accepted: 03/23/2019] [Indexed: 12/16/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF) are two pathologically distinct chronic lung diseases that are associated with cigarette smoking. Genetic studies have identified shared loci for COPD and IPF, including several loci with opposite directions of effect. The existence of additional shared genetic loci, as well as potential shared pathobiological mechanisms between the two diseases at the molecular level, remains to be explored. Taking a network-based approach, we built disease modules for COPD and IPF using genome-wide association studies-implicated genes. The two disease modules displayed strong disease signals in an independent gene expression data set of COPD and IPF lung tissue and showed statistically significant overlap and network proximity, sharing 19 genes, including ARHGAP12 and BCHE. To uncover pathways at the intersection of COPD and IPF, we developed a metric, NetPathScore, which prioritizes the pathways of a disease by their network overlap with another disease. Applying NetPathScore to the COPD and IPF disease modules enabled the determination of concordant and discordant pathways between these diseases. Concordant pathways between COPD and IPF included extracellular matrix remodeling, Mitogen-activated protein kinase (MAPK) signaling and ALK pathways, whereas discordant pathways included advanced glycosylation end product receptor signaling and telomere maintenance and extension pathways. Overall, our findings reveal shared molecular interaction regions between COPD and IPF and shed light on the congruent and incongruent biological processes lying at the intersection of these two complex diseases.
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Affiliation(s)
- Arda Halu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Center for Interdisciplinary Cardiovascular Sciences, Cardiovascular Division, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Shikang Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, USA
| | - Seung Han Baek
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Brian D Hobbs
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Critical Care, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Gary M Hunninghake
- Division of Pulmonary and Critical Care, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Critical Care, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Critical Care, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Amitabh Sharma
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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12
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Affiliation(s)
- Andrew J Sandford
- Centre for Heart Lung InnovationUniversity of British Columbia and St. Paul's HospitalVancouver, British Columbia, Canada
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13
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Ortega VE, Li X, O’Neal WK, Lackey L, Ampleford E, Hawkins GA, Grayeski PJ, Laederach A, Barjaktarevic I, Barr RG, Cooper C, Couper D, Han MK, Kanner RE, Kleerup EC, Martinez FJ, Paine R, Peters SP, Pirozzi C, Rennard SI, Woodruff PG, Hoffman EA, Meyers DA, Bleecker ER. The Effects of Rare SERPINA1 Variants on Lung Function and Emphysema in SPIROMICS. Am J Respir Crit Care Med 2020; 201:540-554. [PMID: 31661293 PMCID: PMC7047460 DOI: 10.1164/rccm.201904-0769oc] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 10/24/2019] [Indexed: 01/07/2023] Open
Abstract
Rationale: The role of PI (protease inhibitor) type Z heterozygotes and additional rare variant genotypes in the gene encoding alpha-1 antitrypsin, SERPINA1 (serpin peptidase inhibitor, clade A, member 1), in determining chronic obstructive pulmonary disease risk and severity is controversial.Objectives: To comprehensively evaluate the effects of rare SERPINA1 variants on lung function and emphysema phenotypes in subjects with significant tobacco smoke exposure using deep gene resequencing and alpha-1 antitrypsin concentrations.Methods: DNA samples from 1,693 non-Hispanic white individuals, 385 African Americans, and 90 Hispanics with ≥20 pack-years smoking were resequenced for the identification of rare variants (allele frequency < 0.05) in 16.9 kB of SERPINA1.Measurements and Main Results: White PI Z heterozygotes confirmed by sequencing (MZ; n = 74) had lower post-bronchodilator FEV1 (P = 0.007), FEV1/FVC (P = 0.003), and greater computed tomography-based emphysema (P = 0.02) compared with 1,411 white individuals without PI Z, S, or additional rare variants denoted as VR. PI Z-containing compound heterozygotes (ZS/ZVR; n = 7) had lower FEV1/FVC (P = 0.02) and forced expiratory flow, midexpiratory phase (P = 0.009). Nineteen white heterozygotes for five non-S/Z coding variants associated with lower alpha-1 antitrypsin had greater computed tomography-based emphysema compared with those without rare variants. In African Americans, a 5' untranslated region insertion (rs568223361) was associated with lower alpha-1 antitrypsin and functional small airway disease (P = 0.007).Conclusions: In this integrative deep sequencing study of SERPINA1 with alpha-1 antitrypsin concentrations in a heavy smoker and chronic obstructive pulmonary disease cohort, we confirmed the effects of PI Z heterozygote and compound heterozygote genotypes. We demonstrate the cumulative effects of multiple SERPINA1 variants on alpha-1 antitrypsin deficiency, lung function, and emphysema, thus significantly increasing the frequency of SERPINA1 variation associated with respiratory disease in at-risk smokers.
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Affiliation(s)
- Victor E. Ortega
- Center for Precision Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Xingnan Li
- Department of Medicine, University of Arizona, Tucson, Arizona
| | - Wanda K. O’Neal
- University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Lela Lackey
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Elizabeth Ampleford
- Center for Precision Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Gregory A. Hawkins
- Center for Precision Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Philip J. Grayeski
- University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - Alain Laederach
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Igor Barjaktarevic
- Department of Medicine, David Geffen School of Medicine, Los Angeles, California
| | - R. Graham Barr
- Columbia University Medical Center, New York City, New York
| | - Christopher Cooper
- Department of Medicine, David Geffen School of Medicine, Los Angeles, California
| | - David Couper
- University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina
| | - MeiLan K. Han
- Division of Pulmonary and Critical Care Medicine, Michigan Medicine, University of Michigan, Ann Arbor, Michigan
| | - Richard E. Kanner
- Division of Respiratory, Critical Care, and Occupational Pulmonary Medicine, Department of Medicine, University of Utah Health Sciences Center, Salt Lake City, Utah
| | - Eric C. Kleerup
- Department of Medicine, David Geffen School of Medicine, Los Angeles, California
| | - Fernando J. Martinez
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Weill Cornell Medical College of Cornell University, New York City, New York
| | - Robert Paine
- Division of Respiratory, Critical Care, and Occupational Pulmonary Medicine, Department of Medicine, University of Utah Health Sciences Center, Salt Lake City, Utah
| | - Stephen P. Peters
- Center for Precision Medicine, Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Cheryl Pirozzi
- Division of Respiratory, Critical Care, and Occupational Pulmonary Medicine, Department of Medicine, University of Utah Health Sciences Center, Salt Lake City, Utah
| | - Stephen I. Rennard
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Nebraska, Omaha, Nebraska
- Innovative Medicines and Early Development (IMED) Biotech Unit, AstraZeneca, Cambridge, United Kingdom
| | - Prescott G. Woodruff
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Cardiovascular Research Institute, University of California, San Francisco, California; and
| | - Eric A. Hoffman
- Department of Radiology
- Department of Medicine, and
- Department of Biomedical Engineering, University of Iowa Carver College of Medicine, Iowa City, Iowa
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14
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Paci P, Fiscon G, Conte F, Licursi V, Morrow J, Hersh C, Cho M, Castaldi P, Glass K, Silverman EK, Farina L. Integrated transcriptomic correlation network analysis identifies COPD molecular determinants. Sci Rep 2020; 10:3361. [PMID: 32099002 PMCID: PMC7042269 DOI: 10.1038/s41598-020-60228-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/23/2020] [Indexed: 12/17/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a complex and heterogeneous syndrome. Network-based analysis implemented by SWIM software can be exploited to identify key molecular switches - called "switch genes" - for the disease. Genes contributing to common biological processes or defining given cell types are usually co-regulated and co-expressed, forming expression network modules. Consistently, we found that the COPD correlation network built by SWIM consists of three well-characterized modules: one populated by switch genes, all up-regulated in COPD cases and related to the regulation of immune response, inflammatory response, and hypoxia (like TIMP1, HIF1A, SYK, LY96, BLNK and PRDX4); one populated by well-recognized immune signature genes, all up-regulated in COPD cases; one where the GWAS genes AGER and CAVIN1 are the most representative module genes, both down-regulated in COPD cases. Interestingly, 70% of AGER negative interactors are switch genes including PRDX4, whose activation strongly correlates with the activation of known COPD GWAS interactors SERPINE2, CD79A, and POUF2AF1. These results suggest that SWIM analysis can identify key network modules related to complex diseases like COPD.
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Affiliation(s)
- Paola Paci
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy.
| | - Giulia Fiscon
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Federica Conte
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Valerio Licursi
- Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Jarrett Morrow
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Craig Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Michael Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Peter Castaldi
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kimberly Glass
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Lorenzo Farina
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy
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15
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Friedlander HM, Ford JA, Zaccardelli A, Terrio AV, Cho MH, Sparks JA. Obstructive lung diseases and risk of rheumatoid arthritis. Expert Rev Clin Immunol 2020; 16:37-50. [PMID: 31774329 DOI: 10.1080/1744666x.2019.1698293] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Introduction: Smoking is an established risk factor for both lung diseases and rheumatoid arthritis (RA). Chronic mucosal airway inflammation may result in immune tolerance loss, neoantigen formation, and production of RA-related autoantibodies that increase the subsequent risk of RA. In this review, we aimed to summarize the current evidence supporting the role of obstructive lung diseases and subsequent risk of RA.Areas covered: We identified scientific articles discussing the biologic mechanisms linking mucosal airway inflammation and RA risk. We also identified studies investigating asthma, chronic obstructive pulmonary disease, bronchiectasis, cystic fibrosis, chronic tuberculous and nontuberculous mycobacterial infections, and interstitial lung disease with subsequent risk for RA.Expert opinion: The current evidence supports the hypothesis that mucosal airway inflammation may increase the risk of developing RA. However, most studies investigating this relationship have been retrospective and may not have adequately addressed the role of smoking. Larger prospective studies may provide stronger evidence for obstructive lung disease and RA risk. Determining the role of obstructive lung disease in RA pathogenesis may provide opportunity for RA prevention and screening strategies, while identifying novel biologic mechanisms that could offer targets to improve treatment and outcomes.
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Affiliation(s)
- H Maura Friedlander
- Brigham and Women's Hospital, Division of Rheumatology, Immunology and Allergy, Boston, MA, USA
| | - Julia A Ford
- Brigham and Women's Hospital, Division of Rheumatology, Immunology and Allergy, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Alessandra Zaccardelli
- Brigham and Women's Hospital, Division of Rheumatology, Immunology and Allergy, Boston, MA, USA
| | - Alexsandra V Terrio
- Brigham and Women's Hospital, Division of Rheumatology, Immunology and Allergy, Boston, MA, USA
| | - Michael H Cho
- Harvard Medical School, Boston, MA, USA.,Brigham and Women's Hospital, Division of Pulmonary and Critical Care Medicine, Boston, MA, USA.,Brigham and Women's Hospital, Channing Division of Network Medicine, Boston, MA, USA
| | - Jeffrey A Sparks
- Brigham and Women's Hospital, Division of Rheumatology, Immunology and Allergy, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
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16
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Santoro A, Tomino C, Prinzi G, Lamonaca P, Cardaci V, Fini M, Russo P. Tobacco Smoking: Risk to Develop Addiction, Chronic Obstructive Pulmonary Disease, and Lung Cancer. Recent Pat Anticancer Drug Discov 2019; 14:39-52. [PMID: 30605063 DOI: 10.2174/1574892814666190102122848] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/11/2018] [Accepted: 12/27/2018] [Indexed: 12/24/2022]
Abstract
BACKGROUND The morbidity and mortality associated with tobacco smoking is well established. Nicotine is the addictive component of tobacco. Nicotine, through the non-neuronal α7nicotinic receptor, induces cell proliferation, neo-angiogenesis, epithelial to mesenchymal transition, and inhibits drug-induced apoptosis. OBJECTIVE To understand the genetic, molecular and cellular biology of addiction, chronic obstructive pulmonary disease and lung cancer. METHODS The search for papers to be included in the review was performed during the months of July- September 2018 in the following databases: PubMed (http://www.ncbi.nlm.nih.gov), Scopus (http://www.scopus.com), EMBASE (http://www.elsevier.com/online-tools/embase), and ISI Web of Knowledge (http://apps.webofknowledge.com/). The following searching terms: "nicotine", "nicotinic receptor", and "addiction" or "COPD" or "lung cancer" were used. Patents were retrieved in clinicaltrials.gov (https://clinicaltrials.gov/). All papers written in English were evaluated. The reference list of retrieved articles was also reviewed to identify other eligible studies that were not indexed by the above-mentioned databases. New experimental data on the ability of nicotine to promote transformation of human bronchial epithelial cells, exposed for one hour to Benzo[a]pyrene-7,8-diol-9-10-epoxide, are reported. RESULTS Nicotinic receptors variants and nicotinic receptors upregulation are involved in addiction, chronic obstructive pulmonary disease and/or lung cancer. Nicotine through α7nicotinic receptor upregulation induces complete bronchial epithelial cells transformation. CONCLUSION Genetic studies highlight the involvement of nicotinic receptors variants in addiction, chronic obstructive pulmonary disease and/or lung cancer. A future important step will be to translate these genetic findings to clinical practice. Interventions able to help smoking cessation in nicotine dependence subjects, under patent, are reported.
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Affiliation(s)
- Alessia Santoro
- Clinical and Molecular Epidemiology, IRCSS San Raffaele Pisana, Via di Valcannuta 247, I-00166 Rome, Italy
| | - Carlo Tomino
- Scientific Direction, IRCSS San Raffaele Pisana, Via di Valcannuta 247, I-00166 Rome, Italy
| | - Giulia Prinzi
- Clinical and Molecular Epidemiology, IRCSS San Raffaele Pisana, Via di Valcannuta 247, I-00166 Rome, Italy
| | - Palma Lamonaca
- Clinical and Molecular Epidemiology, IRCSS San Raffaele Pisana, Via di Valcannuta 247, I-00166 Rome, Italy
| | - Vittorio Cardaci
- Pulmonary Rehabilitation, IRCCS San Raffaele Pisana, Via della Pisana, 235, I-00163 Rome, Italy
| | - Massimo Fini
- Scientific Direction, IRCSS San Raffaele Pisana, Via di Valcannuta 247, I-00166 Rome, Italy
| | - Patrizia Russo
- Clinical and Molecular Epidemiology, IRCSS San Raffaele Pisana, Via di Valcannuta 247, I-00166 Rome, Italy
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17
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Exome Sequencing Reveals Immune Genes as Susceptibility Modifiers in Individuals with α 1-Antitrypsin Deficiency. Sci Rep 2019; 9:13088. [PMID: 31511551 PMCID: PMC6739380 DOI: 10.1038/s41598-019-49409-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 08/23/2019] [Indexed: 12/17/2022] Open
Abstract
Alpha-1 antitrypsin deficiency (AATD) is a genetic disorder associated to early onset emphysema, mainly imputable to Pi*ZZ genotype. In spite of the serious potential effects, many AATD individuals do not develop emphysema. To identify genes/variants potentially involved in emphysema development we studied 4 AATD families. Each family had at least one affected sibling with emphysema and one non-affected. Whole Exome Sequencing (WES) was performed on genomic DNA isolated from 9 individuals with AATD (4 affected/5 non-affected). Genetic variants confirmed at least in three families were prioritized using QueryOR and network analysis was used to verify enriched pathways. In affected subjects: 14 genes (57% immune-related) segregated in a recessive model and 21 (29% immune-related) in a dominant model. In non-affected subjects: 21 genes (43% immune-related) segregated in a recessive model and 50 (24% immune-related) in a dominant model. In affected siblings immune genes had an activating function, while where immune-suppressing in non-affected siblings involving antigen processing, MHC-I presentation, TCR and PD-1 signalling. This study describes possible genetic susceptibility factors for emphysema development in AATD, and suggests that gene variants involved in regulation of immune homeostasis and maintenance of self-tolerance contribute to the development or suppression of the disease.
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Russo P, Lococo F, Kisialiou A, Prinzi G, Lamonaca P, Cardaci V, Tomino C, Fini M. Pharmacological Management of Chronic Obstructive Lung Disease (COPD). Focus on Mutations - Part 1. Curr Med Chem 2019; 26:1721-1733. [PMID: 29852859 DOI: 10.2174/0929867325666180601100235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 08/02/2017] [Accepted: 04/02/2018] [Indexed: 12/18/2022]
Abstract
BACKGROUND We report a comprehensive overview of current Chronic Obstructive Lung Disease (COPD) therapies and discuss the development of possible new pharmacological approaches based on "new" knowledge. Specifically, sensitivity/resistance to corticosteroids is evaluated with a special focus on the role of gene mutations in drug response. OBJECTIVE Critically review the opportunities and the challenges occurring in the treatment of COPD. CONCLUSION Findings from "omics" trials should be used to learn more about biological targeted drugs, and to select more specific drugs matching patient's distinctive molecular profile. Specific markers of inflammation such as the percentage of eosinophils are important in determining sensitivity/resistance to corticosteroids. Specific gene variations (Single nucleotide polymorphisms: SNPs) may influence drug sensitivity or resistance. Clinicians working in a real-world need to have a suitable interpretation of molecular results together with a guideline for the treatment and recommendations. Far more translational research is required before new results from omics techniques can be applied in personalized medicine in realworld settings.
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Affiliation(s)
- Patrizia Russo
- Unit of Clinical and Molecular Epidemiology, IRCCS San Raffaele Pisana Via di Valcannuta, 247, I-00166 Rome, Italy
| | - Filippo Lococo
- Unit of Thoracic Surgery, Arcispedale Santa Maria Nuova-IRCCS, Reggio Emilia, Italy
| | - Aliaksei Kisialiou
- Unit of Clinical and Molecular Epidemiology, IRCCS San Raffaele Pisana Via di Valcannuta, 247, I-00166 Rome, Italy
| | - Giulia Prinzi
- Unit of Clinical and Molecular Epidemiology, IRCCS San Raffaele Pisana Via di Valcannuta, 247, I-00166 Rome, Italy
| | - Palma Lamonaca
- Unit of Clinical and Molecular Epidemiology, IRCCS San Raffaele Pisana Via di Valcannuta, 247, I-00166 Rome, Italy
| | - Vittorio Cardaci
- Unit of Pulmonary Rehabilitation, IRCCS San Raffaele Pisana Via di Valcannuta, 247, I-00166 Rome, Italy
| | - Carlo Tomino
- Scientific Direction, IRCCS San Raffaele Pisana Via di Valcannuta, 247, I-00166 Rome, Italy
| | - Massimo Fini
- Scientific Direction, IRCCS San Raffaele Pisana Via di Valcannuta, 247, I-00166 Rome, Italy
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John C, Reeve NF, Free RC, Williams AT, Ntalla I, Farmaki AE, Bethea J, Barton LM, Shrine N, Batini C, Packer R, Terry S, Hargadon B, Wang Q, Melbourne CA, Adams EL, Bee CE, Harrington K, Miola J, Brunskill NJ, Brightling CE, Barwell J, Wallace SE, Hsu R, Shepherd DJ, Hollox EJ, Wain LV, Tobin MD. Cohort Profile: Extended Cohort for E-health, Environment and DNA (EXCEED). Int J Epidemiol 2019; 48:678-679j. [PMID: 31062032 PMCID: PMC6659362 DOI: 10.1093/ije/dyz073] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2019] [Indexed: 12/22/2022] Open
Affiliation(s)
- Catherine John
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Nicola F Reeve
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Robert C Free
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | | | - Ioanna Ntalla
- Department of Health Sciences, University of Leicester, Leicester, UK
- Department of Clinical Pharmacology, William Harvey Research Institute, Barts & The London Medical School, Queen Mary University of London, Charterhouse Square, London, UK
| | - Aliki-Eleni Farmaki
- Department of Health Sciences, University of Leicester, Leicester, UK
- Department of Population Science and Experimental Medicine, Institute of Cardiovascular Science, University College London, London, UK
| | - Jane Bethea
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Linda M Barton
- Department of Haematology, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Nick Shrine
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Chiara Batini
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Richard Packer
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Sarah Terry
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Beverley Hargadon
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Qingning Wang
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Carl A Melbourne
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Emma L Adams
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Catherine E Bee
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Kyla Harrington
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - José Miola
- Leicester Law School, University of Leicester, Leicester, UK
| | - Nigel J Brunskill
- Department of Cardiovascular Sciences University of Leicester, Leicester, UK
| | - Christopher E Brightling
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
- Department of Respiratory Sciences, University of Leicester, Leicester, UK
| | - Julian Barwell
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Susan E Wallace
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Ron Hsu
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - David J Shepherd
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Edward J Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Martin D Tobin
- Department of Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
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20
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Murakami M, Kamimura D, Hirano T. Pleiotropy and Specificity: Insights from the Interleukin 6 Family of Cytokines. Immunity 2019; 50:812-831. [DOI: 10.1016/j.immuni.2019.03.027] [Citation(s) in RCA: 231] [Impact Index Per Article: 46.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/25/2019] [Accepted: 03/26/2019] [Indexed: 02/08/2023]
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21
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Shrine N, Guyatt AL, Erzurumluoglu AM, Jackson VE, Hobbs BD, Melbourne CA, Batini C, Fawcett KA, Song K, Sakornsakolpat P, Li X, Boxall R, Reeve NF, Obeidat M, Zhao JH, Wielscher M, Weiss S, Kentistou KA, Cook JP, Sun BB, Zhou J, Hui J, Karrasch S, Imboden M, Harris SE, Marten J, Enroth S, Kerr SM, Surakka I, Vitart V, Lehtimäki T, Allen RJ, Bakke PS, Beaty TH, Bleecker ER, Bossé Y, Brandsma CA, Chen Z, Crapo JD, Danesh J, DeMeo DL, Dudbridge F, Ewert R, Gieger C, Gulsvik A, Hansell AL, Hao K, Hoffman JD, Hokanson JE, Homuth G, Joshi PK, Joubert P, Langenberg C, Li X, Li L, Lin K, Lind L, Locantore N, Luan J, Mahajan A, Maranville JC, Murray A, Nickle DC, Packer R, Parker MM, Paynton ML, Porteous DJ, Prokopenko D, Qiao D, Rawal R, Runz H, Sayers I, Sin DD, Smith BH, Soler Artigas M, Sparrow D, Tal-Singer R, Timmers PRHJ, Van den Berge M, Whittaker JC, Woodruff PG, Yerges-Armstrong LM, Troyanskaya OG, Raitakari OT, Kähönen M, Polašek O, Gyllensten U, Rudan I, Deary IJ, Probst-Hensch NM, Schulz H, James AL, Wilson JF, Stubbe B, Zeggini E, Jarvelin MR, Wareham N, Silverman EK, Hayward C, Morris AP, Butterworth AS, Scott RA, Walters RG, Meyers DA, Cho MH, Strachan DP, Hall IP, Tobin MD, Wain LV. New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries. Nat Genet 2019; 51:481-493. [PMID: 30804560 PMCID: PMC6397078 DOI: 10.1038/s41588-018-0321-7] [Citation(s) in RCA: 285] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 11/27/2018] [Indexed: 02/02/2023]
Abstract
Reduced lung function predicts mortality and is key to the diagnosis of chronic obstructive pulmonary disease (COPD). In a genome-wide association study in 400,102 individuals of European ancestry, we define 279 lung function signals, 139 of which are new. In combination, these variants strongly predict COPD in independent populations. Furthermore, the combined effect of these variants showed generalizability across smokers and never smokers, and across ancestral groups. We highlight biological pathways, known and potential drug targets for COPD and, in phenome-wide association studies, autoimmune-related and other pleiotropic effects of lung function-associated variants. This new genetic evidence has potential to improve future preventive and therapeutic strategies for COPD.
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Affiliation(s)
- Nick Shrine
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Anna L Guyatt
- Department of Health Sciences, University of Leicester, Leicester, UK
| | | | - Victoria E Jackson
- Department of Health Sciences, University of Leicester, Leicester, UK
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Brian D Hobbs
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Carl A Melbourne
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Chiara Batini
- Department of Health Sciences, University of Leicester, Leicester, UK
| | | | - Kijoung Song
- Target Sciences, GlaxoSmithKline, Collegeville, PA, USA
| | - Phuwanat Sakornsakolpat
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Xingnan Li
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - Ruth Boxall
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- Medical Research Council Population Health Research Unit, University of Oxford, Oxford, UK
| | - Nicola F Reeve
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Ma'en Obeidat
- The University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, British Columbia, Canada
| | - Jing Hua Zhao
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Matthias Wielscher
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
| | - Stefan Weiss
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Katherine A Kentistou
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
- Centre for Cardiovascular Sciences, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - James P Cook
- Department of Biostatistics, University of Liverpool, Liverpool, UK
| | - Benjamin B Sun
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Jian Zhou
- Flatiron Institute, Simons Foundation, New York, NY, USA
| | - Jennie Hui
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- School of Population Health, The University of Western Australia, Crawley, Western Australia, Australia
- PathWest Laboratory Medicine of WA, Sir Charles Gairdner Hospital, Crawley, Western Australia, Australia
- School of Pathology and Laboratory Medicine, The University of Western Australia, Crawley, Western Australia, Australia
| | - Stefan Karrasch
- Institute of Epidemiology, Helmholtz Zentrum Muenchen-German Research Center for Environmental Health, Neuherberg, Germany
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Ludwig-Maximilians-Universität, Munich, Germany
- Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Medea Imboden
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sarah E Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Jonathan Marten
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Stefan Enroth
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala Universitet, Uppsala, Sweden
| | - Shona M Kerr
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Ida Surakka
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- The National Institute for Health and Welfare (THL), Helsinki, Finland
| | - Veronique Vitart
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Richard J Allen
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Per S Bakke
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins University School of Public Health, Baltimore, MD, USA
| | - Eugene R Bleecker
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - Yohan Bossé
- Department of Molecular Medicine, Laval University, Québec, Canada
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec, Canada
| | - Corry-Anke Brandsma
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, GRIAC Research Institute, University of Groningen, Groningen, The Netherlands
| | - Zhengming Chen
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - James D Crapo
- National Jewish Health, Denver, CO, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, National Jewish Health, Denver, CO, USA
| | - John Danesh
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Cambridge Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Cambridge, UK
- Department of Human Genetics, Wellcome Trust Sanger Institute, Cambridge, UK
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Frank Dudbridge
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Ralf Ewert
- Department of Internal Medicine B - Cardiology, Intensive Care, Pulmonary Medicine and Infectious Diseases, University Medicine Greifswald, Greifswald, Germany
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum Muenchen - German Research Center for Environmental Health, Neuherberg, Germany
| | - Amund Gulsvik
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Anna L Hansell
- Centre for Environmental Health & Sustainability, University of Leicester, Leicester, UK
- UK Small Area Health Statistics Unit, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Imperial College Healthcare NHS Trust, St Mary's Hospital, London, UK
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - John E Hokanson
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Philippe Joubert
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec, Canada
- Department of Molecular Biology, Medical Biochemistry, and Pathology, Laval University, Québec, Canada
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Xuan Li
- The University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, British Columbia, Canada
| | - Liming Li
- Department of Epidemiology & Biostatistics, Peking University Health Science Center, Beijing, China
| | - Kuang Lin
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Lars Lind
- Department of Medical Sciences, Cardiovascular Epidemiology, Uppsala University, Uppsala, Sweden
| | | | - Jian'an Luan
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Alison Murray
- The Institute of Medical Sciences, Aberdeen Biomedical Imaging Centre, University of Aberdeen, Aberdeen, UK
| | - David C Nickle
- MRL, Merck & Co., Inc, Kenilworth, NJ, USA
- Gossamer Bio, San Diego, CA, USA
| | - Richard Packer
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Margaret M Parker
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Megan L Paynton
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - David J Porteous
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Dmitry Prokopenko
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dandi Qiao
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Rajesh Rawal
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum Muenchen - German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology and Social Medicine, University of Münster, Münster, Germany
| | - Heiko Runz
- MRL, Merck & Co., Inc, Kenilworth, NJ, USA
| | - Ian Sayers
- Division of Respiratory Medicine and NIHR-Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Don D Sin
- The University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, British Columbia, Canada
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Blair H Smith
- Division of Population Health and Genomics, Ninewells Hospital and Medical School, University of Dundee, Dundee, UK
| | - María Soler Artigas
- Psychiatric Genetics Unit, Group of Psychiatry, Mental Health and Addiction, Vall d'Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain
- Department of Psychiatry, Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Biomedical Network Research Centre on Mental Health (CIBERSAM), Instituto de Salud Carlos III, Barcelona, Spain
| | - David Sparrow
- VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | | | - Paul R H J Timmers
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Maarten Van den Berge
- University of Groningen, University Medical Center Groningen, Department of Pulmonology, GRIAC Research Institute, University of Groningen, Groningen, The Netherlands
| | - John C Whittaker
- Target Sciences - R&D, GSK Medicines Research Centre, Stevenage, UK
| | - Prescott G Woodruff
- UCSF Pulmonary, Critical Care, Allergy and Sleep Medicine, University of California, San Francisco, CA, USA
| | | | - Olga G Troyanskaya
- Department of Computer Science, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Olli T Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, and Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Ozren Polašek
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
- University of Split School of Medicine, Split, Croatia
| | - Ulf Gyllensten
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala Universitet, Uppsala, Sweden
| | - Igor Rudan
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK
- Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Nicole M Probst-Hensch
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Holger Schulz
- Institute of Epidemiology, Helmholtz Zentrum Muenchen-German Research Center for Environmental Health, Neuherberg, Germany
- Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Alan L James
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- Department of Pulmonary Physiology and Sleep Medicine, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- School of Medicine and Pharmacology, The University of Western Australia, Crawley, Western Australia, Australia
| | - James F Wilson
- Centre for Global Health Research, Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Beate Stubbe
- Department of Internal Medicine B - Cardiology, Intensive Care, Pulmonary Medicine and Infectious Diseases, University Medicine Greifswald, Greifswald, Germany
| | - Eleftheria Zeggini
- Wellcome Sanger Institute, Hinxton, UK
- Institute of Translational Genomics, Helmholtz Zentrum Muenchen - German Research Center for Environmental Health, Neuherberg, Germany
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Unit of Primary Health Care, Oulu University Hospital, Oulu, Finland
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Uxbridge, UK
| | - Nick Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Andrew P Morris
- Department of Biostatistics, University of Liverpool, Liverpool, UK
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Adam S Butterworth
- MRC/BHF Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- NIHR Blood and Transplant Research Unit in Donor Health and Genomics, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Robert A Scott
- Target Sciences - R&D, GSK Medicines Research Centre, Stevenage, UK
| | - Robin G Walters
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Deborah A Meyers
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - David P Strachan
- Population Health Research Institute, St George's, University of London, London, UK
| | - Ian P Hall
- Division of Respiratory Medicine and NIHR-Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Martin D Tobin
- Department of Health Sciences, University of Leicester, Leicester, UK.
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK.
| | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, UK.
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK.
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22
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Sakornsakolpat P, Prokopenko D, Lamontagne M, Reeve NF, Guyatt AL, Jackson VE, Shrine N, Qiao D, Bartz TM, Kim DK, Lee MK, Latourelle JC, Li X, Morrow JD, Obeidat M, Wyss AB, Bakke P, Barr RG, Beaty TH, Belinsky SA, Brusselle GG, Crapo JD, de Jong K, DeMeo DL, Fingerlin TE, Gharib SA, Gulsvik A, Hall IP, Hokanson JE, Kim WJ, Lomas DA, London SJ, Meyers DA, O'Connor GT, Rennard SI, Schwartz DA, Sliwinski P, Sparrow D, Strachan DP, Tal-Singer R, Tesfaigzi Y, Vestbo J, Vonk JM, Yim JJ, Zhou X, Bossé Y, Manichaikul A, Lahousse L, Silverman EK, Boezen HM, Wain LV, Tobin MD, Hobbs BD, Cho MH. Genetic landscape of chronic obstructive pulmonary disease identifies heterogeneous cell-type and phenotype associations. Nat Genet 2019; 51:494-505. [PMID: 30804561 PMCID: PMC6546635 DOI: 10.1038/s41588-018-0342-2] [Citation(s) in RCA: 215] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 12/20/2018] [Indexed: 11/09/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is the leading cause of respiratory mortality worldwide. Genetic risk loci provide new insights into disease pathogenesis. We performed a genome-wide association study in 35,735 cases and 222,076 controls from the UK Biobank and additional studies from the International COPD Genetics Consortium. We identified 82 loci associated with P < 5 × 10-8; 47 of these were previously described in association with either COPD or population-based measures of lung function. Of the remaining 35 new loci, 13 were associated with lung function in 79,055 individuals from the SpiroMeta consortium. Using gene expression and regulation data, we identified functional enrichment of COPD risk loci in lung tissue, smooth muscle, and several lung cell types. We found 14 COPD loci shared with either asthma or pulmonary fibrosis. COPD genetic risk loci clustered into groups based on associations with quantitative imaging features and comorbidities. Our analyses provide further support for the genetic susceptibility and heterogeneity of COPD.
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Affiliation(s)
- 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
| | - Dmitry Prokopenko
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Genetics and Aging Research Unit, Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Maxime Lamontagne
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, Quebec, Canada
| | - Nicola F Reeve
- 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
| | - Victoria E Jackson
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK
| | - Nick Shrine
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK
| | - Dandi Qiao
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Traci M Bartz
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Deog Kyeom Kim
- Seoul National University College of Medicine, SMG-SNU Boramae Medical Center, Seoul, South Korea
| | - Mi Kyeong Lee
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Raleigh, NC, USA
| | - Jeanne C Latourelle
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Xingnan Li
- Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - Jarrett D Morrow
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Ma'en Obeidat
- University of British Columbia Center for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Annah B Wyss
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Raleigh, NC, USA
| | - Per Bakke
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - R Graham Barr
- Department of Medicine, College of Physicians and Surgeons and Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Guy G Brusselle
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
- Department of Respiratory Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - James D Crapo
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, National Jewish Health, Denver, CO, USA
| | - Kim de Jong
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands
| | - 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
| | - Tasha E Fingerlin
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
- Department of Biostatistics and Informatics, University of Colorado Denver, Aurora, CO, USA
| | - Sina A Gharib
- Computational Medicine Core, Center for Lung Biology, UW Medicine Sleep Center, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Amund Gulsvik
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Ian P Hall
- Division of Respiratory Medicine, Queen's Medical Centre, University of Nottingham, Nottingham, UK
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham, UK
| | - John E Hokanson
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Woo Jin Kim
- Department of Internal Medicine and Environmental Health Center, School of Medicine, Kangwon National University, Chuncheon, South Korea
| | - David A Lomas
- UCL Respiratory, University College London, London, UK
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Raleigh, NC, USA
| | | | - George T O'Connor
- National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, USA
- Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Stephen I Rennard
- Pulmonary, Critical Care, Sleep and Allergy Division, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, USA
- Clinical Discovery Unit, AstraZeneca, Cambridge, UK
| | - David A Schwartz
- Department of Medicine, School of Medicine, University of Colorado Denver, Aurora, CO, USA
- Department of Immunology, School of Medicine, University of Colorado Denver, Aurora, CO, USA
| | - Pawel Sliwinski
- 2nd Department of Respiratory Medicine, Institute of Tuberculosis and Lung Diseases, Warsaw, Poland
| | - David Sparrow
- VA Boston Healthcare System and Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - David P Strachan
- Population Health Research Institute, St. George's University of London, London, UK
| | | | | | - Jørgen Vestbo
- School of Biological Sciences, University of Manchester, Manchester, UK
| | - Judith M Vonk
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands
| | - Jae-Joon Yim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Xiaobo Zhou
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Yohan Bossé
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, Quebec, Canada
- Department of Molecular Medicine, Laval University, Québec, Québec, Canada
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Lies Lahousse
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Bioanalysis, Ghent University, Ghent, Belgium
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - H Marike Boezen
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands
| | - Louise V 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
| | - 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
| | - 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
| | - 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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Corry DB, Kheradmand F, Luong A, Pandit L. Immunological Mechanisms of Airway Diseases and Pathways to Therapy. Clin Immunol 2019. [DOI: 10.1016/b978-0-7020-6896-6.00041-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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24
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Bhatt SP, Nath HP, Kim YI, Ramachandran R, Watts JR, Terry NLJ, Sonavane S, Deshmane SP, Woodruff PG, Oelsner EC, Bodduluri S, Han MK, Labaki WW, Michael Wells J, Martinez FJ, Barr RG, Dransfield MT. Centrilobular emphysema and coronary artery calcification: mediation analysis in the SPIROMICS cohort. Respir Res 2018; 19:257. [PMID: 30563576 PMCID: PMC6299495 DOI: 10.1186/s12931-018-0946-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 11/20/2018] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) is associated with a two-to-five fold increase in the risk of coronary artery disease independent of shared risk factors. This association is hypothesized to be mediated by systemic inflammation but this link has not been established. METHODS We included 300 participants enrolled in the SPIROMICS cohort, 75 each of lifetime non-smokers, smokers without airflow obstruction, mild-moderate COPD, and severe-very severe COPD. We quantified emphysema and airway disease on computed tomography, characterized visual emphysema subtypes (centrilobular and paraseptal) and airway disease, and used the Weston visual score to quantify coronary artery calcification (CAC). We used the Sobel test to determine whether markers of systemic inflammation mediated a link between spirometric and radiographic features of COPD and CAC. RESULTS FEV1/FVC but not quantitative emphysema or airway wall thickening was associated with CAC (p = 0.036), after adjustment for demographics, diabetes mellitus, hypertension, statin use, and CT scanner type. To explain this discordance, we examined visual subtypes of emphysema and airway disease, and found that centrilobular emphysema but not paraseptal emphysema or bronchial thickening was independently associated with CAC (p = 0.019). MMP3, VCAM1, CXCL5 and CXCL9 mediated 8, 8, 7 and 16% of the association between FEV1/FVC and CAC, respectively. Similar biomarkers partially mediated the association between centrilobular emphysema and CAC. CONCLUSIONS The association between airflow obstruction and coronary calcification is driven primarily by the centrilobular subtype of emphysema, and is linked through bioactive molecules implicated in the pathogenesis of atherosclerosis. TRIAL REGISTRATION ClinicalTrials.gov: Identifier: NCT01969344 .
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Affiliation(s)
- Surya P Bhatt
- Division of Pulmonary, Allergy and Critical Care Medicine and Lung Health Center, University of Alabama at Birmingham, THT 422, 1720, 2nd Avenue South, Birmingham, AL, 35294, USA.
- UAB Lung Imaging Core, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
| | - Hrudaya P Nath
- UAB Lung Imaging Core, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
- Department of Radiology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Young-Il Kim
- Division of Pulmonary, Allergy and Critical Care Medicine and Lung Health Center, University of Alabama at Birmingham, THT 422, 1720, 2nd Avenue South, Birmingham, AL, 35294, USA
- Department of Preventive Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Rekha Ramachandran
- Department of Preventive Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Jubal R Watts
- Department of Radiology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Nina L J Terry
- Department of Radiology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Sushil Sonavane
- Department of Radiology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Swati P Deshmane
- Department of Radiology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - Prescott G Woodruff
- Division of Pulmonary, Critical Care, Allergy and Sleep Medicine, University California San Francisco, San Francisco, CA, 94143, USA
| | - Elizabeth C Oelsner
- Division of Pulmonary, Allergy and Critical Care Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Sandeep Bodduluri
- Division of Pulmonary, Allergy and Critical Care Medicine and Lung Health Center, University of Alabama at Birmingham, THT 422, 1720, 2nd Avenue South, Birmingham, AL, 35294, USA
- UAB Lung Imaging Core, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - MeiLan K Han
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Wassim W Labaki
- Division of Pulmonary and Critical Care Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - J Michael Wells
- Division of Pulmonary, Allergy and Critical Care Medicine and Lung Health Center, University of Alabama at Birmingham, THT 422, 1720, 2nd Avenue South, Birmingham, AL, 35294, USA
- UAB Lung Imaging Core, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
- Birmingham Veterans Affairs Hospital, Birmingham, AL, 35294, USA
| | - Fernando J Martinez
- Division of Pulmonary and Critical Care Medicine, Weill Cornell School of Medicine, New York, NY, 10065, USA
| | - R Graham Barr
- Division of Pulmonary, Allergy and Critical Care Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Mark T Dransfield
- Division of Pulmonary, Allergy and Critical Care Medicine and Lung Health Center, University of Alabama at Birmingham, THT 422, 1720, 2nd Avenue South, Birmingham, AL, 35294, USA
- UAB Lung Imaging Core, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
- Birmingham Veterans Affairs Hospital, Birmingham, AL, 35294, USA
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25
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Hobbs BD, Cho MH. Dissecting respiratory disease heterogeneity through the genetics of diffusing capacity. Eur Respir J 2018; 52:52/3/1801468. [PMID: 30219754 DOI: 10.1183/13993003.01468-2018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 08/15/2018] [Indexed: 11/05/2022]
Affiliation(s)
- Brian D Hobbs
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Michael H Cho
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
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26
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Alpha-1 Antitrypsin PiMZ Genotype Is Associated with Chronic Obstructive Pulmonary Disease in Two Racial Groups. Ann Am Thorac Soc 2018; 14:1280-1287. [PMID: 28380308 DOI: 10.1513/annalsats.201611-838oc] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
RATIONALE Alpha-1 antitrypsin deficiency, caused primarily by homozygosity for the Z allele of the SERPINA1 gene, is a well-established genetic cause of chronic obstructive pulmonary disease (COPD). Whether the heterozygous PiMZ genotype for alpha-1 antitrypsin confers increased risk for COPD has been debated. OBJECTIVES We analyzed 8,271 subjects in the Genetic Epidemiology of COPD (COPDGene) Study, hypothesizing that PiMZ would independently associate with COPD and COPD-related phenotypes. METHODS The COPDGene Study comprises a multiethnic, cross-sectional, observational cohort of non-Hispanic white and African American current and former smokers with at least 10 pack-years of smoking who were enrolled for detailed clinical and genetic studies of COPD and COPD-related traits. We performed multivariate logistic regression analysis for moderate to severe COPD and assessed Pi genotype with other relevant covariates in models stratified by race. We analyzed quantitative characteristics on the basis of volumetric computed tomography with generalized linear models controlling for genotype, scanner type, and similar covariates. RESULTS White PiMZ COPDGene subjects had significantly lower lung function, FEV1 percent predicted (68 ± 28 vs. 75 ± 27; P = 0.0005), and FEV1/FVC ratio (0.59 ± 0.18 vs. 0.63 ± 0.17; P = 0.0008), as well as more radiographic emphysema (P = 0.001), than subjects without alpha-1 antitrypsin Z risk alleles. Similarly, African American PiMZ subjects had lower lung function, FEV1 percent predicted (65 ± 33 vs. 84 ± 25; P = 0.009) and FEV1/FVC (0.61 ± 0.21 vs. 0.71 ± 0.15; P = 0.03). CONCLUSIONS In the COPDGene Study, we demonstrate that PiMZ heterozygous individuals who smoke are at increased risk for COPD and obstructive lung function impairment compared with Z-allele noncarriers, regardless of race. Although severe alpha-1 antitrypsin deficiency is uncommon in African Americans, our study adds further support for initial targeted detection of all subjects with COPD for alpha-1 antitrypsin deficiency, including African Americans. Clinical trial registered with www.clinicaltrials.gov (NCT00608784).
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27
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Morrow JD, Glass K, Cho MH, Hersh CP, Pinto-Plata V, Celli B, Marchetti N, Criner G, Bueno R, Washko G, Choi AMK, Quackenbush J, Silverman EK, DeMeo DL. Human Lung DNA Methylation Quantitative Trait Loci Colocalize with Chronic Obstructive Pulmonary Disease Genome-Wide Association Loci. Am J Respir Crit Care Med 2018; 197:1275-1284. [PMID: 29313708 PMCID: PMC5955059 DOI: 10.1164/rccm.201707-1434oc] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 01/03/2018] [Indexed: 12/23/2022] Open
Abstract
RATIONALE As the third leading cause of death in the United States, the impact of chronic obstructive pulmonary disease (COPD) makes identification of its molecular mechanisms of great importance. Genome-wide association studies (GWASs) have identified multiple genomic regions associated with COPD. However, genetic variation only explains a small fraction of the susceptibility to COPD, and sub-genome-wide significant loci may play a role in pathogenesis. OBJECTIVES Regulatory annotation with epigenetic evidence may give priority for further investigation, particularly for GWAS associations in noncoding regions. We performed integrative genomics analyses using DNA methylation profiling and genome-wide SNP genotyping from lung tissue samples from 90 subjects with COPD and 36 control subjects. METHODS We performed methylation quantitative trait loci (mQTL) analyses, testing for SNPs associated with percent DNA methylation and assessed the colocalization of these results with previous COPD GWAS findings using Bayesian methods in the R package coloc to highlight potential regulatory features of the loci. MEASUREMENTS AND MAIN RESULTS We identified 942,068 unique SNPs and 33,996 unique CpG sites among the significant (5% false discovery rate) cis-mQTL results. The genome-wide significant and subthreshold (P < 10-4) GWAS SNPs were enriched in the significant mQTL SNPs (hypergeometric test P < 0.00001). We observed enrichment for sites located in CpG shores and shelves, but not CpG islands. Using Bayesian colocalization, we identified loci in regions near KCNK3, EEFSEC, PIK3CD, DCDC2C, TCERG1L, FRMD4B, and IL27. CONCLUSIONS Colocalization of mQTL and GWAS loci provides regulatory characterization of significant and subthreshold GWAS findings, supporting a role for genetic control of methylation in COPD pathogenesis.
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Affiliation(s)
| | | | - Michael H. Cho
- Channing Division of Network Medicine
- Division of Pulmonary and Critical Care Medicine, and
| | - Craig P. Hersh
- Channing Division of Network Medicine
- Division of Pulmonary and Critical Care Medicine, and
| | | | | | - Nathaniel Marchetti
- Division of Pulmonary and Critical Care Medicine, Temple University, Philadelphia, Pennsylvania
| | - Gerard Criner
- Division of Pulmonary and Critical Care Medicine, Temple University, Philadelphia, Pennsylvania
| | - Raphael Bueno
- Division of Thoracic Surgery, Brigham and Women’s Hospital, Boston, Massachusetts
| | - George Washko
- Division of Pulmonary and Critical Care Medicine, and
| | - Augustine M. K. Choi
- Department of Medicine, New York Presbyterian/Weill Cornell Medical Center, New York, New York; and
| | - John Quackenbush
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Edwin K. Silverman
- Channing Division of Network Medicine
- Division of Pulmonary and Critical Care Medicine, and
| | - Dawn L. DeMeo
- Channing Division of Network Medicine
- Division of Pulmonary and Critical Care Medicine, and
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Nedeljkovic I, Terzikhan N, Vonk JM, van der Plaat DA, Lahousse L, van Diemen CC, Hobbs BD, Qiao D, Cho MH, Brusselle GG, Postma DS, Boezen HM, van Duijn CM, Amin N. A Genome-Wide Linkage Study for Chronic Obstructive Pulmonary Disease in a Dutch Genetic Isolate Identifies Novel Rare Candidate Variants. Front Genet 2018; 9:133. [PMID: 29725345 PMCID: PMC5916965 DOI: 10.3389/fgene.2018.00133] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 04/03/2018] [Indexed: 01/06/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a complex and heritable disease, associated with multiple genetic variants. Specific familial types of COPD may be explained by rare variants, which have not been widely studied. We aimed to discover rare genetic variants underlying COPD through a genome-wide linkage scan. Affected-only analysis was performed using the 6K Illumina Linkage IV Panel in 142 cases clustered in 27 families from a genetic isolate, the Erasmus Rucphen Family (ERF) study. Potential causal variants were identified by searching for shared rare variants in the exome-sequence data of the affected members of the families contributing most to the linkage peak. The identified rare variants were then tested for association with COPD in a large meta-analysis of several cohorts. Significant evidence for linkage was observed on chromosomes 15q14-15q25 [logarithm of the odds (LOD) score = 5.52], 11p15.4-11q14.1 (LOD = 3.71) and 5q14.3-5q33.2 (LOD = 3.49). In the chromosome 15 peak, that harbors the known COPD locus for nicotinic receptors, and in the chromosome 5 peak we could not identify shared variants. In the chromosome 11 locus, we identified four rare (minor allele frequency (MAF) <0.02), predicted pathogenic, missense variants. These were shared among the affected family members. The identified variants localize to genes including neuroblast differentiation-associated protein (AHNAK), previously associated with blood biomarkers in COPD, phospholipase C Beta 3 (PLCB3), shown to increase airway hyper-responsiveness, solute carrier family 22-A11 (SLC22A11), involved in amino acid metabolism and ion transport, and metallothionein-like protein 5 (MTL5), involved in nicotinate and nicotinamide metabolism. Association of SLC22A11 and MTL5 variants were confirmed in the meta-analysis of 9,888 cases and 27,060 controls. In conclusion, we have identified novel rare variants in plausible genes related to COPD. Further studies utilizing large sample whole-genome sequencing should further confirm the associations at chromosome 11 and investigate the chromosome 15 and 5 linked regions.
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Affiliation(s)
- Ivana Nedeljkovic
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, Netherlands
| | - Natalie Terzikhan
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, Netherlands
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Judith M. Vonk
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Diana A. van der Plaat
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Lies Lahousse
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, Netherlands
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
- Pharmaceutical Care Unit, Department of Bioanalysis, Ghent University, Ghent, Belgium
| | - Cleo C. van Diemen
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - 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
| | - Dandi Qiao
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA, United States
| | - Michael H. Cho
- 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
| | - Guy G. Brusselle
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, Netherlands
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
- Department of Respiratory Medicine, Erasmus Medical Center, Rotterdam, Netherlands
| | - Dirkje S. Postma
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Department of Pulmonary Medicine and Tuberculosis, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - H. M. Boezen
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | | | - Najaf Amin
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, Netherlands
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Sharma S. Integrative Genomics of Emphysema-Associated Genes: Are We Closer to Identifying the Genetic Determinants of Lung Function? Am J Respir Cell Mol Biol 2018; 57:377-378. [PMID: 28960108 DOI: 10.1165/rcmb.2017-0212ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Sunita Sharma
- 1 Division of Pulmonary Sciences and Critical Care Medicine University of Colorado Denver, Colorado
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30
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Morrow JD, Cho MH, Platig J, Zhou X, DeMeo DL, Qiu W, Celli B, Marchetti N, Criner GJ, Bueno R, Washko GR, Glass K, Quackenbush J, Silverman EK, Hersh CP. Ensemble genomic analysis in human lung tissue identifies novel genes for chronic obstructive pulmonary disease. Hum Genomics 2018; 12:1. [PMID: 29335020 PMCID: PMC5769240 DOI: 10.1186/s40246-018-0132-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 01/02/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) significantly associated with chronic obstructive pulmonary disease (COPD). However, many genetic variants show suggestive evidence for association but do not meet the strict threshold for genome-wide significance. Integrative analysis of multiple omics datasets has the potential to identify novel genes involved in disease pathogenesis by leveraging these variants in a functional, regulatory context. RESULTS We performed expression quantitative trait locus (eQTL) analysis using genome-wide SNP genotyping and gene expression profiling of lung tissue samples from 86 COPD cases and 31 controls, testing for SNPs associated with gene expression levels. These results were integrated with a prior COPD GWAS using an ensemble statistical and network methods approach to identify relevant genes and observe them in the context of overall genetic control of gene expression to highlight co-regulated genes and disease pathways. We identified 250,312 unique SNPs and 4997 genes in the cis(local)-eQTL analysis (5% false discovery rate). The top gene from the integrative analysis was MAPT, a gene recently identified in an independent GWAS of lung function. The genes HNRNPAB and PCBP2 with RNA binding activity and the gene ACVR1B were identified in network communities with validated disease relevance. CONCLUSIONS The integration of lung tissue gene expression with genome-wide SNP genotyping and subsequent intersection with prior GWAS and omics studies highlighted candidate genes within COPD loci and in communities harboring known COPD genes. This integration also identified novel disease genes in sub-threshold regions that would otherwise have been missed through GWAS.
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Affiliation(s)
- Jarrett D Morrow
- 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 Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - John Platig
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Xiaobo Zhou
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Weiliang Qiu
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Bartholome Celli
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Nathaniel Marchetti
- Division of Pulmonary and Critical Care Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Gerard J Criner
- Division of Pulmonary and Critical Care Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Raphael Bueno
- Division of Thoracic Surgery, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - George R Washko
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Kimberly Glass
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - John Quackenbush
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - 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 Medicine, Brigham and Women's Hospital, Boston, MA, 02115, 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 Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
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31
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Jackson VE, Latourelle JC, Wain LV, Smith AV, Grove ML, Bartz TM, Obeidat M, Province MA, Gao W, Qaiser B, Porteous DJ, Cassano PA, Ahluwalia TS, Grarup N, Li J, Altmaier E, Marten J, Harris SE, Manichaikul A, Pottinger TD, Li-Gao R, Lind-Thomsen A, Mahajan A, Lahousse L, Imboden M, Teumer A, Prins B, Lyytikäinen LP, Eiriksdottir G, Franceschini N, Sitlani CM, Brody JA, Bossé Y, Timens W, Kraja A, Loukola A, Tang W, Liu Y, Bork-Jensen J, Justesen JM, Linneberg A, Lange LA, Rawal R, Karrasch S, Huffman JE, Smith BH, Davies G, Burkart KM, Mychaleckyj JC, Bonten TN, Enroth S, Lind L, Brusselle GG, Kumar A, Stubbe B, Kähönen M, Wyss AB, Psaty BM, Heckbert SR, Hao K, Rantanen T, Kritchevsky SB, Lohman K, Skaaby T, Pisinger C, Hansen T, Schulz H, Polasek O, Campbell A, Starr JM, Rich SS, Mook-Kanamori DO, Johansson Å, Ingelsson E, Uitterlinden AG, Weiss S, Raitakari OT, Gudnason V, North KE, Gharib SA, Sin DD, Taylor KD, O'Connor GT, Kaprio J, Harris TB, Pederson O, Vestergaard H, Wilson JG, Strauch K, Hayward C, Kerr S, Deary IJ, Barr RG, de Mutsert R, Gyllensten U, Morris AP, Ikram MA, Probst-Hensch N, Gläser S, Zeggini E, Lehtimäki T, Strachan DP, Dupuis J, Morrison AC, Hall IP, Tobin MD, London SJ. Meta-analysis of exome array data identifies six novel genetic loci for lung function. Wellcome Open Res 2018; 3:4. [PMID: 30175238 PMCID: PMC6081985 DOI: 10.12688/wellcomeopenres.12583.3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2018] [Indexed: 01/05/2023] Open
Abstract
Background: Over 90 regions of the genome have been associated with lung function to date, many of which have also been implicated in chronic obstructive pulmonary disease. Methods: We carried out meta-analyses of exome array data and three lung function measures: forced expiratory volume in one second (FEV 1), forced vital capacity (FVC) and the ratio of FEV 1 to FVC (FEV 1/FVC). These analyses by the SpiroMeta and CHARGE consortia included 60,749 individuals of European ancestry from 23 studies, and 7,721 individuals of African Ancestry from 5 studies in the discovery stage, with follow-up in up to 111,556 independent individuals. Results: We identified significant (P<2·8x10 -7) associations with six SNPs: a nonsynonymous variant in RPAP1, which is predicted to be damaging, three intronic SNPs ( SEC24C, CASC17 and UQCC1) and two intergenic SNPs near to LY86 and FGF10. Expression quantitative trait loci analyses found evidence for regulation of gene expression at three signals and implicated several genes, including TYRO3 and PLAU. Conclusions: Further interrogation of these loci could provide greater understanding of the determinants of lung function and pulmonary disease.
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Affiliation(s)
| | | | - Louise V. Wain
- Department of Health Sciences, University of Leicester, Leicester, UK
- National Institute for Health Research, Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Albert V. Smith
- Icelandic Heart Association, 201 Kopavogur, Iceland
- University of Iceland, 101 Reykjavik, Iceland
| | - Megan L. Grove
- 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, TX, 77030, USA
| | - Traci M. Bartz
- Cardiovascular Health Research Unit, Departments of Medicine and Biostatistics, University of Washington, Seattle, WA, 98101, USA
| | - Ma'en Obeidat
- The University of British Columbia Centre for Heart Lung Innovation, St Paul’s Hospital, Vancouver, BC, Canada
| | - Michael A. Province
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Wei Gao
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Beenish Qaiser
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014, Helsinki, Finland
| | - David J. Porteous
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Patricia A. Cassano
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
- Department of Healthcare Policy and Research, Division of Biostatistics and Epidemiology, Weill Cornell Medical College, New York City, NY, USA
| | - Tarunveer S. Ahluwalia
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Gentofte, 2820, Denmark
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jin Li
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Elisabeth Altmaier
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Jonathan Marten
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh , EH4 2XU, UK
| | - Sarah E. Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Tess D. Pottinger
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Preventive Medicine - Division of Health and Biomedical Informatics, Northwestern University - Feinberg School of Medicine, Chicago, IL, USA
| | - Ruifang Li-Gao
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
| | - Allan Lind-Thomsen
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, SE-75108 Uppsala, Sweden
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Lies Lahousse
- Respiratory Medicine, Ghent University Hospital, Ghent, BE9000, Belgium
- Bioanalysis, Ghent University, Ghent, BE9000, Belgium
| | - Medea Imboden
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Bram Prins
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33520, Finland
- Department of Clinical Chemistry, Faculty of Medicine and Life Sciences, University of Tampere, Tampere 33014, Finland
| | | | - Nora Franceschini
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, NC 27514, USA
| | - Colleen M. Sitlani
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec, Department of Molecular Medicine, Laval University, Québec, Canada
| | - Wim Timens
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, NL9713 GZ, Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Aldi Kraja
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Anu Loukola
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014, Helsinki, Finland
| | - Wenbo Tang
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
- Boehringer Ingelheim , Danbury, CT, USA
| | - Yongmei Liu
- Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Jette Bork-Jensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | | | - Allan Linneberg
- Centre for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark
- Department of Clinical Experimental Research, Rigshospitalet, 2600 Glostrup, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Leslie A. Lange
- Department of Medicine, Division of Bioinformatics and Personalized Medicine, University of Colorado Denver, Aurora, CO, USA
| | - Rajesh Rawal
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Stefan Karrasch
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Ludwig-Maximilians-Universität, Munich, Germany
| | - Jennifer E. Huffman
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh , EH4 2XU, UK
| | - Blair H. Smith
- Division of Population Health Sciences, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK
| | - Gail Davies
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Kristin M. Burkart
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Josyf C. Mychaleckyj
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Tobias N. Bonten
- Department of Pulmonology, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
| | - Stefan Enroth
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, SE-75108 Uppsala, Sweden
| | - Lars Lind
- Department of Medical Sciences, Uppsala University Hospital, Uppsala, Sweden
| | - Guy G. Brusselle
- Respiratory Medicine, Ghent University Hospital, Ghent, BE9000, Belgium
- Epidemiology, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
- Respiratory Medicine, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
| | - Ashish Kumar
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Beate Stubbe
- Internal Medicine B, University Medicine Greifswald, Greifswald, 17475, Germany
| | - Understanding Society Scientific Group
- Department of Health Sciences, University of Leicester, Leicester, UK
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- National Institute for Health Research, Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
- Icelandic Heart Association, 201 Kopavogur, Iceland
- University of Iceland, 101 Reykjavik, Iceland
- 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, TX, 77030, USA
- Cardiovascular Health Research Unit, Departments of Medicine and Biostatistics, University of Washington, Seattle, WA, 98101, USA
- The University of British Columbia Centre for Heart Lung Innovation, St Paul’s Hospital, Vancouver, BC, Canada
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014, Helsinki, Finland
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
- Department of Healthcare Policy and Research, Division of Biostatistics and Epidemiology, Weill Cornell Medical College, New York City, NY, USA
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Gentofte, 2820, Denmark
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh , EH4 2XU, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Preventive Medicine - Division of Health and Biomedical Informatics, Northwestern University - Feinberg School of Medicine, Chicago, IL, USA
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, SE-75108 Uppsala, Sweden
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Respiratory Medicine, Ghent University Hospital, Ghent, BE9000, Belgium
- Bioanalysis, Ghent University, Ghent, BE9000, Belgium
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Institute for Community Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33520, Finland
- Department of Clinical Chemistry, Faculty of Medicine and Life Sciences, University of Tampere, Tampere 33014, Finland
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, NC 27514, USA
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
- Institut universitaire de cardiologie et de pneumologie de Québec, Department of Molecular Medicine, Laval University, Québec, Canada
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, NL9713 GZ, Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Boehringer Ingelheim , Danbury, CT, USA
- Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
- Centre for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark
- Department of Clinical Experimental Research, Rigshospitalet, 2600 Glostrup, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Department of Medicine, Division of Bioinformatics and Personalized Medicine, University of Colorado Denver, Aurora, CO, USA
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Ludwig-Maximilians-Universität, Munich, Germany
- Division of Population Health Sciences, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Department of Pulmonology, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
- Department of Medical Sciences, Uppsala University Hospital, Uppsala, Sweden
- Epidemiology, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
- Respiratory Medicine, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Internal Medicine B, University Medicine Greifswald, Greifswald, 17475, Germany
- Department of Clinical Physiology, Tampere University Hospital, Tampere, 33521, Finland
- Department of Clinical Physiology, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, 33014, Finland
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, 27709, USA
- Cardiovascular Health Research Unit, Departments of Epidemiology, Medicine and Health Services, University of Washington, Seattle, WA, 98101, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
- Cardiovascular Health Research Unit, Department of Epidemiology, University of Washington, Seattle, WA, 98101, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-6574, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-6574, USA
- Department of Health Sciences, University of Jyväskylä, Jyväskylä, Fl-40014, Finland
- Sticht Center on Aging, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research, Munich, Germany
- Faculty of Medicine, University of Split, Split, Croatia
- Alzheimer Scotland Research Centre, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Internal Medicine, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, 17475, Germany
- DZHK (German Centre for Cardiovascular Research), partner site: Greifswald, Greifswald, Germany
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, 20521, Finland
- Research Centre of Applied and Preventative Cardiovascular Medicine, University of Turku, Turku, 20014, Finland
- Department of Epidemiology and Carolina Center for Genome Science, University of North Carolina, Chapel Hill, NC, 27514, USA
- Computational Medicine Core, Center for Lung Biology, UW Medicine Sleep Center, Department of Medicine, University of Washington, Seattle, WA, 98109, USA
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
- Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, 02118, USA
- National Heart, Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA, 01702, USA
- Department of Health, University of Helsinki, Helsinki, FI-00014, Finland
- Department of Public Health, National Institute for Health and Welfare, Helsinki, FI-00271, Finland
- National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, 39216, USA
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, 85764, Germany
- Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich, Munich, 81377, Germany
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA
- Department of Biostatistics, University of Liverpool, Liverpool, L69 3GL, UK
- Radiology, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
- Neurology, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
- Department of Internal Medicine - Pulmonary Diseases, Vivantes Klinikum Spandau Berlin, Berlin, 13585, Germany
- Population Health Research Institute, St George's, University of London, London, SW17 0RE, UK
- NIHR Nottingham Biomedical Research Centre and Division of Respiratory Medicine, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere, 33521, Finland
- Department of Clinical Physiology, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, 33014, Finland
| | - Annah B. Wyss
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, 27709, USA
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Departments of Epidemiology, Medicine and Health Services, University of Washington, Seattle, WA, 98101, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Susan R. Heckbert
- Cardiovascular Health Research Unit, Department of Epidemiology, University of Washington, Seattle, WA, 98101, USA
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-6574, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-6574, USA
| | - Taina Rantanen
- Department of Health Sciences, University of Jyväskylä, Jyväskylä, Fl-40014, Finland
| | | | - Kurt Lohman
- Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Tea Skaaby
- Centre for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark
| | - Charlotta Pisinger
- Centre for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Holger Schulz
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research, Munich, Germany
| | - Ozren Polasek
- Faculty of Medicine, University of Split, Split, Croatia
| | - Archie Campbell
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - John M. Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Alzheimer Scotland Research Centre, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Dennis O. Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
| | - Åsa Johansson
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, SE-75108 Uppsala, Sweden
| | - Erik Ingelsson
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - André G. Uitterlinden
- Epidemiology, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
- Internal Medicine, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
| | - Stefan Weiss
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, 17475, Germany
- DZHK (German Centre for Cardiovascular Research), partner site: Greifswald, Greifswald, Germany
| | - Olli T. Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, 20521, Finland
- Research Centre of Applied and Preventative Cardiovascular Medicine, University of Turku, Turku, 20014, Finland
| | - Vilmundur Gudnason
- Icelandic Heart Association, 201 Kopavogur, Iceland
- University of Iceland, 101 Reykjavik, Iceland
| | - Kari E. North
- Department of Epidemiology and Carolina Center for Genome Science, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - Sina A. Gharib
- Computational Medicine Core, Center for Lung Biology, UW Medicine Sleep Center, Department of Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Don D. Sin
- The University of British Columbia Centre for Heart Lung Innovation, St Paul’s Hospital, Vancouver, BC, Canada
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Kent D. Taylor
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - George T. O'Connor
- Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, 02118, USA
- National Heart, Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA, 01702, USA
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014, Helsinki, Finland
- Department of Health, University of Helsinki, Helsinki, FI-00014, Finland
- Department of Public Health, National Institute for Health and Welfare, Helsinki, FI-00271, Finland
| | - Tamara B. Harris
- National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Oluf Pederson
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Henrik Vestergaard
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Gentofte, 2820, Denmark
| | - James G. Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, 85764, Germany
- Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich, Munich, 81377, Germany
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh , EH4 2XU, UK
| | - Shona Kerr
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh , EH4 2XU, UK
| | - Ian J. Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - R. Graham Barr
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA
| | - Renée de Mutsert
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
| | - Ulf Gyllensten
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, SE-75108 Uppsala, Sweden
| | - Andrew P. Morris
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Biostatistics, University of Liverpool, Liverpool, L69 3GL, UK
| | - M. Arfan Ikram
- Epidemiology, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
- Radiology, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
- Neurology, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
| | - Nicole Probst-Hensch
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sven Gläser
- Internal Medicine B, University Medicine Greifswald, Greifswald, 17475, Germany
- Department of Internal Medicine - Pulmonary Diseases, Vivantes Klinikum Spandau Berlin, Berlin, 13585, Germany
| | | | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33520, Finland
- Department of Clinical Chemistry, Faculty of Medicine and Life Sciences, University of Tampere, Tampere 33014, Finland
| | - David P. Strachan
- Population Health Research Institute, St George's, University of London, London, SW17 0RE, UK
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Alanna C. Morrison
- 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, TX, 77030, USA
| | - Ian P. Hall
- NIHR Nottingham Biomedical Research Centre and Division of Respiratory Medicine, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Martin D. Tobin
- Department of Health Sciences, University of Leicester, Leicester, UK
- National Institute for Health Research, Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Stephanie J. London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, 27709, USA
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32
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Jackson VE, Latourelle JC, Wain LV, Smith AV, Grove ML, Bartz TM, Obeidat M, Province MA, Gao W, Qaiser B, Porteous DJ, Cassano PA, Ahluwalia TS, Grarup N, Li J, Altmaier E, Marten J, Harris SE, Manichaikul A, Pottinger TD, Li-Gao R, Lind-Thomsen A, Mahajan A, Lahousse L, Imboden M, Teumer A, Prins B, Lyytikäinen LP, Eiriksdottir G, Franceschini N, Sitlani CM, Brody JA, Bossé Y, Timens W, Kraja A, Loukola A, Tang W, Liu Y, Bork-Jensen J, Justesen JM, Linneberg A, Lange LA, Rawal R, Karrasch S, Huffman JE, Smith BH, Davies G, Burkart KM, Mychaleckyj JC, Bonten TN, Enroth S, Lind L, Brusselle GG, Kumar A, Stubbe B, Kähönen M, Wyss AB, Psaty BM, Heckbert SR, Hao K, Rantanen T, Kritchevsky SB, Lohman K, Skaaby T, Pisinger C, Hansen T, Schulz H, Polasek O, Campbell A, Starr JM, Rich SS, Mook-Kanamori DO, Johansson Å, Ingelsson E, Uitterlinden AG, Weiss S, Raitakari OT, Gudnason V, North KE, Gharib SA, Sin DD, Taylor KD, O'Connor GT, Kaprio J, Harris TB, Pederson O, Vestergaard H, Wilson JG, Strauch K, Hayward C, Kerr S, Deary IJ, Barr RG, de Mutsert R, Gyllensten U, Morris AP, Ikram MA, Probst-Hensch N, Gläser S, Zeggini E, Lehtimäki T, Strachan DP, Dupuis J, Morrison AC, Hall IP, Tobin MD, London SJ. Meta-analysis of exome array data identifies six novel genetic loci for lung function. Wellcome Open Res 2018; 3:4. [PMID: 30175238 PMCID: PMC6081985 DOI: 10.12688/wellcomeopenres.12583.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2018] [Indexed: 07/26/2023] Open
Abstract
Background: Over 90 regions of the genome have been associated with lung function to date, many of which have also been implicated in chronic obstructive pulmonary disease. Methods: We carried out meta-analyses of exome array data and three lung function measures: forced expiratory volume in one second (FEV 1), forced vital capacity (FVC) and the ratio of FEV 1 to FVC (FEV 1/FVC). These analyses by the SpiroMeta and CHARGE consortia included 60,749 individuals of European ancestry from 23 studies, and 7,721 individuals of African Ancestry from 5 studies in the discovery stage, with follow-up in up to 111,556 independent individuals. Results: We identified significant (P<2·8x10 -7) associations with six SNPs: a nonsynonymous variant in RPAP1, which is predicted to be damaging, three intronic SNPs ( SEC24C, CASC17 and UQCC1) and two intergenic SNPs near to LY86 and FGF10. Expression quantitative trait loci analyses found evidence for regulation of gene expression at three signals and implicated several genes, including TYRO3 and PLAU. Conclusions: Further interrogation of these loci could provide greater understanding of the determinants of lung function and pulmonary disease.
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Affiliation(s)
| | | | - Louise V. Wain
- Department of Health Sciences, University of Leicester, Leicester, UK
- National Institute for Health Research, Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Albert V. Smith
- Icelandic Heart Association, 201 Kopavogur, Iceland
- University of Iceland, 101 Reykjavik, Iceland
| | - Megan L. Grove
- 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, TX, 77030, USA
| | - Traci M. Bartz
- Cardiovascular Health Research Unit, Departments of Medicine and Biostatistics, University of Washington, Seattle, WA, 98101, USA
| | - Ma'en Obeidat
- The University of British Columbia Centre for Heart Lung Innovation, St Paul’s Hospital, Vancouver, BC, Canada
| | - Michael A. Province
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Wei Gao
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Beenish Qaiser
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014, Helsinki, Finland
| | - David J. Porteous
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Patricia A. Cassano
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
- Department of Healthcare Policy and Research, Division of Biostatistics and Epidemiology, Weill Cornell Medical College, New York City, NY, USA
| | - Tarunveer S. Ahluwalia
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Gentofte, 2820, Denmark
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jin Li
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Elisabeth Altmaier
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Jonathan Marten
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh , EH4 2XU, UK
| | - Sarah E. Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Tess D. Pottinger
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Preventive Medicine - Division of Health and Biomedical Informatics, Northwestern University - Feinberg School of Medicine, Chicago, IL, USA
| | - Ruifang Li-Gao
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
| | - Allan Lind-Thomsen
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, SE-75108 Uppsala, Sweden
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Lies Lahousse
- Respiratory Medicine, Ghent University Hospital, Ghent, BE9000, Belgium
- Bioanalysis, Ghent University, Ghent, BE9000, Belgium
| | - Medea Imboden
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Bram Prins
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33520, Finland
- Department of Clinical Chemistry, Faculty of Medicine and Life Sciences, University of Tampere, Tampere 33014, Finland
| | | | - Nora Franceschini
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, NC 27514, USA
| | - Colleen M. Sitlani
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec, Department of Molecular Medicine, Laval University, Québec, Canada
| | - Wim Timens
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, NL9713 GZ, Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Aldi Kraja
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Anu Loukola
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014, Helsinki, Finland
| | - Wenbo Tang
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
- Boehringer Ingelheim , Danbury, CT, USA
| | - Yongmei Liu
- Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Jette Bork-Jensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | | | - Allan Linneberg
- Centre for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark
- Department of Clinical Experimental Research, Rigshospitalet, 2600 Glostrup, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Leslie A. Lange
- Department of Medicine, Division of Bioinformatics and Personalized Medicine, University of Colorado Denver, Aurora, CO, USA
| | - Rajesh Rawal
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Stefan Karrasch
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Ludwig-Maximilians-Universität, Munich, Germany
| | - Jennifer E. Huffman
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh , EH4 2XU, UK
| | - Blair H. Smith
- Division of Population Health Sciences, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK
| | - Gail Davies
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Kristin M. Burkart
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Josyf C. Mychaleckyj
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Tobias N. Bonten
- Department of Pulmonology, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
| | - Stefan Enroth
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, SE-75108 Uppsala, Sweden
| | - Lars Lind
- Department of Medical Sciences, Uppsala University Hospital, Uppsala, Sweden
| | - Guy G. Brusselle
- Respiratory Medicine, Ghent University Hospital, Ghent, BE9000, Belgium
- Epidemiology, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
- Respiratory Medicine, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
| | - Ashish Kumar
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Beate Stubbe
- Internal Medicine B, University Medicine Greifswald, Greifswald, 17475, Germany
| | | | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere, 33521, Finland
- Department of Clinical Physiology, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, 33014, Finland
| | - Annah B. Wyss
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, 27709, USA
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Departments of Epidemiology, Medicine and Health Services, University of Washington, Seattle, WA, 98101, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Susan R. Heckbert
- Cardiovascular Health Research Unit, Department of Epidemiology, University of Washington, Seattle, WA, 98101, USA
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-6574, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-6574, USA
| | - Taina Rantanen
- Department of Health Sciences, University of Jyväskylä, Jyväskylä, Fl-40014, Finland
| | | | - Kurt Lohman
- Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Tea Skaaby
- Centre for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark
| | - Charlotta Pisinger
- Centre for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Holger Schulz
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research, Munich, Germany
| | - Ozren Polasek
- Faculty of Medicine, University of Split, Split, Croatia
| | - Archie Campbell
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - John M. Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Alzheimer Scotland Research Centre, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Dennis O. Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
| | - Åsa Johansson
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, SE-75108 Uppsala, Sweden
| | - Erik Ingelsson
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - André G. Uitterlinden
- Epidemiology, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
- Internal Medicine, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
| | - Stefan Weiss
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, 17475, Germany
- DZHK (German Centre for Cardiovascular Research), partner site: Greifswald, Greifswald, Germany
| | - Olli T. Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, 20521, Finland
- Research Centre of Applied and Preventative Cardiovascular Medicine, University of Turku, Turku, 20014, Finland
| | - Vilmundur Gudnason
- Icelandic Heart Association, 201 Kopavogur, Iceland
- University of Iceland, 101 Reykjavik, Iceland
| | - Kari E. North
- Department of Epidemiology and Carolina Center for Genome Science, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - Sina A. Gharib
- Computational Medicine Core, Center for Lung Biology, UW Medicine Sleep Center, Department of Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Don D. Sin
- The University of British Columbia Centre for Heart Lung Innovation, St Paul’s Hospital, Vancouver, BC, Canada
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Kent D. Taylor
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - George T. O'Connor
- Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, 02118, USA
- National Heart, Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA, 01702, USA
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014, Helsinki, Finland
- Department of Health, University of Helsinki, Helsinki, FI-00014, Finland
- Department of Public Health, National Institute for Health and Welfare, Helsinki, FI-00271, Finland
| | - Tamara B. Harris
- National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Oluf Pederson
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Henrik Vestergaard
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Gentofte, 2820, Denmark
| | - James G. Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, 85764, Germany
- Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich, Munich, 81377, Germany
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh , EH4 2XU, UK
| | - Shona Kerr
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh , EH4 2XU, UK
| | - Ian J. Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - R. Graham Barr
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA
| | - Renée de Mutsert
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
| | - Ulf Gyllensten
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, SE-75108 Uppsala, Sweden
| | - Andrew P. Morris
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Biostatistics, University of Liverpool, Liverpool, L69 3GL, UK
| | - M. Arfan Ikram
- Epidemiology, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
- Radiology, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
- Neurology, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
| | - Nicole Probst-Hensch
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sven Gläser
- Internal Medicine B, University Medicine Greifswald, Greifswald, 17475, Germany
- Department of Internal Medicine - Pulmonary Diseases, Vivantes Klinikum Spandau Berlin, Berlin, 13585, Germany
| | | | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33520, Finland
- Department of Clinical Chemistry, Faculty of Medicine and Life Sciences, University of Tampere, Tampere 33014, Finland
| | - David P. Strachan
- Population Health Research Institute, St George's, University of London, London, SW17 0RE, UK
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Alanna C. Morrison
- 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, TX, 77030, USA
| | - Ian P. Hall
- NIHR Nottingham Biomedical Research Centre and Division of Respiratory Medicine, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Martin D. Tobin
- Department of Health Sciences, University of Leicester, Leicester, UK
- National Institute for Health Research, Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Stephanie J. London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, 27709, USA
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33
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Jackson VE, Latourelle JC, Wain LV, Smith AV, Grove ML, Bartz TM, Obeidat M, Province MA, Gao W, Qaiser B, Porteous DJ, Cassano PA, Ahluwalia TS, Grarup N, Li J, Altmaier E, Marten J, Harris SE, Manichaikul A, Pottinger TD, Li-Gao R, Lind-Thomsen A, Mahajan A, Lahousse L, Imboden M, Teumer A, Prins B, Lyytikäinen LP, Eiriksdottir G, Franceschini N, Sitlani CM, Brody JA, Bossé Y, Timens W, Kraja A, Loukola A, Tang W, Liu Y, Bork-Jensen J, Justesen JM, Linneberg A, Lange LA, Rawal R, Karrasch S, Huffman JE, Smith BH, Davies G, Burkart KM, Mychaleckyj JC, Bonten TN, Enroth S, Lind L, Brusselle GG, Kumar A, Stubbe B, Kähönen M, Wyss AB, Psaty BM, Heckbert SR, Hao K, Rantanen T, Kritchevsky SB, Lohman K, Skaaby T, Pisinger C, Hansen T, Schulz H, Polasek O, Campbell A, Starr JM, Rich SS, Mook-Kanamori DO, Johansson Å, Ingelsson E, Uitterlinden AG, Weiss S, Raitakari OT, Gudnason V, North KE, Gharib SA, Sin DD, Taylor KD, O'Connor GT, Kaprio J, Harris TB, Pederson O, Vestergaard H, Wilson JG, Strauch K, Hayward C, Kerr S, Deary IJ, Barr RG, de Mutsert R, Gyllensten U, Morris AP, Ikram MA, Probst-Hensch N, Gläser S, Zeggini E, Lehtimäki T, Strachan DP, Dupuis J, Morrison AC, Hall IP, Tobin MD, London SJ. Meta-analysis of exome array data identifies six novel genetic loci for lung function. Wellcome Open Res 2018; 3:4. [PMID: 30175238 PMCID: PMC6081985 DOI: 10.12688/wellcomeopenres.12583.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2018] [Indexed: 08/09/2023] Open
Abstract
Background: Over 90 regions of the genome have been associated with lung function to date, many of which have also been implicated in chronic obstructive pulmonary disease. Methods: We carried out meta-analyses of exome array data and three lung function measures: forced expiratory volume in one second (FEV 1), forced vital capacity (FVC) and the ratio of FEV 1 to FVC (FEV 1/FVC). These analyses by the SpiroMeta and CHARGE consortia included 60,749 individuals of European ancestry from 23 studies, and 7,721 individuals of African Ancestry from 5 studies in the discovery stage, with follow-up in up to 111,556 independent individuals. Results: We identified significant (P<2·8x10 -7) associations with six SNPs: a nonsynonymous variant in RPAP1, which is predicted to be damaging, three intronic SNPs ( SEC24C, CASC17 and UQCC1) and two intergenic SNPs near to LY86 and FGF10. Expression quantitative trait loci analyses found evidence for regulation of gene expression at three signals and implicated several genes, including TYRO3 and PLAU. Conclusions: Further interrogation of these loci could provide greater understanding of the determinants of lung function and pulmonary disease.
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Affiliation(s)
| | | | - Louise V. Wain
- Department of Health Sciences, University of Leicester, Leicester, UK
- National Institute for Health Research, Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Albert V. Smith
- Icelandic Heart Association, 201 Kopavogur, Iceland
- University of Iceland, 101 Reykjavik, Iceland
| | - Megan L. Grove
- 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, TX, 77030, USA
| | - Traci M. Bartz
- Cardiovascular Health Research Unit, Departments of Medicine and Biostatistics, University of Washington, Seattle, WA, 98101, USA
| | - Ma'en Obeidat
- The University of British Columbia Centre for Heart Lung Innovation, St Paul’s Hospital, Vancouver, BC, Canada
| | - Michael A. Province
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Wei Gao
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Beenish Qaiser
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014, Helsinki, Finland
| | - David J. Porteous
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Patricia A. Cassano
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
- Department of Healthcare Policy and Research, Division of Biostatistics and Epidemiology, Weill Cornell Medical College, New York City, NY, USA
| | - Tarunveer S. Ahluwalia
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Gentofte, 2820, Denmark
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jin Li
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Elisabeth Altmaier
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Jonathan Marten
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh , EH4 2XU, UK
| | - Sarah E. Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Tess D. Pottinger
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Preventive Medicine - Division of Health and Biomedical Informatics, Northwestern University - Feinberg School of Medicine, Chicago, IL, USA
| | - Ruifang Li-Gao
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
| | - Allan Lind-Thomsen
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, SE-75108 Uppsala, Sweden
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Lies Lahousse
- Respiratory Medicine, Ghent University Hospital, Ghent, BE9000, Belgium
- Bioanalysis, Ghent University, Ghent, BE9000, Belgium
| | - Medea Imboden
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Bram Prins
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33520, Finland
- Department of Clinical Chemistry, Faculty of Medicine and Life Sciences, University of Tampere, Tampere 33014, Finland
| | | | - Nora Franceschini
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, NC 27514, USA
| | - Colleen M. Sitlani
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec, Department of Molecular Medicine, Laval University, Québec, Canada
| | - Wim Timens
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, NL9713 GZ, Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Aldi Kraja
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Anu Loukola
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014, Helsinki, Finland
| | - Wenbo Tang
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
- Boehringer Ingelheim , Danbury, CT, USA
| | - Yongmei Liu
- Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Jette Bork-Jensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | | | - Allan Linneberg
- Centre for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark
- Department of Clinical Experimental Research, Rigshospitalet, 2600 Glostrup, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Leslie A. Lange
- Department of Medicine, Division of Bioinformatics and Personalized Medicine, University of Colorado Denver, Aurora, CO, USA
| | - Rajesh Rawal
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Stefan Karrasch
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Ludwig-Maximilians-Universität, Munich, Germany
| | - Jennifer E. Huffman
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh , EH4 2XU, UK
| | - Blair H. Smith
- Division of Population Health Sciences, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK
| | - Gail Davies
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Kristin M. Burkart
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Josyf C. Mychaleckyj
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Tobias N. Bonten
- Department of Pulmonology, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
| | - Stefan Enroth
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, SE-75108 Uppsala, Sweden
| | - Lars Lind
- Department of Medical Sciences, Uppsala University Hospital, Uppsala, Sweden
| | - Guy G. Brusselle
- Respiratory Medicine, Ghent University Hospital, Ghent, BE9000, Belgium
- Epidemiology, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
- Respiratory Medicine, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
| | - Ashish Kumar
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Beate Stubbe
- Internal Medicine B, University Medicine Greifswald, Greifswald, 17475, Germany
| | | | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere, 33521, Finland
- Department of Clinical Physiology, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, 33014, Finland
| | - Annah B. Wyss
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, 27709, USA
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Departments of Epidemiology, Medicine and Health Services, University of Washington, Seattle, WA, 98101, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Susan R. Heckbert
- Cardiovascular Health Research Unit, Department of Epidemiology, University of Washington, Seattle, WA, 98101, USA
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-6574, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-6574, USA
| | - Taina Rantanen
- Department of Health Sciences, University of Jyväskylä, Jyväskylä, Fl-40014, Finland
| | | | - Kurt Lohman
- Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Tea Skaaby
- Centre for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark
| | - Charlotta Pisinger
- Centre for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Holger Schulz
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research, Munich, Germany
| | - Ozren Polasek
- Faculty of Medicine, University of Split, Split, Croatia
| | - Archie Campbell
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - John M. Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Alzheimer Scotland Research Centre, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Dennis O. Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
| | - Åsa Johansson
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, SE-75108 Uppsala, Sweden
| | - Erik Ingelsson
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - André G. Uitterlinden
- Epidemiology, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
- Internal Medicine, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
| | - Stefan Weiss
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, 17475, Germany
- DZHK (German Centre for Cardiovascular Research), partner site: Greifswald, Greifswald, Germany
| | - Olli T. Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, 20521, Finland
- Research Centre of Applied and Preventative Cardiovascular Medicine, University of Turku, Turku, 20014, Finland
| | - Vilmundur Gudnason
- Icelandic Heart Association, 201 Kopavogur, Iceland
- University of Iceland, 101 Reykjavik, Iceland
| | - Kari E. North
- Department of Epidemiology and Carolina Center for Genome Science, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - Sina A. Gharib
- Computational Medicine Core, Center for Lung Biology, UW Medicine Sleep Center, Department of Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Don D. Sin
- The University of British Columbia Centre for Heart Lung Innovation, St Paul’s Hospital, Vancouver, BC, Canada
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Kent D. Taylor
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - George T. O'Connor
- Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, 02118, USA
- National Heart, Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA, 01702, USA
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014, Helsinki, Finland
- Department of Health, University of Helsinki, Helsinki, FI-00014, Finland
- Department of Public Health, National Institute for Health and Welfare, Helsinki, FI-00271, Finland
| | - Tamara B. Harris
- National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Oluf Pederson
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Henrik Vestergaard
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Gentofte, 2820, Denmark
| | - James G. Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, 85764, Germany
- Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich, Munich, 81377, Germany
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh , EH4 2XU, UK
| | - Shona Kerr
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh , EH4 2XU, UK
| | - Ian J. Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - R. Graham Barr
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA
| | - Renée de Mutsert
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
| | - Ulf Gyllensten
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, SE-75108 Uppsala, Sweden
| | - Andrew P. Morris
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Biostatistics, University of Liverpool, Liverpool, L69 3GL, UK
| | - M. Arfan Ikram
- Epidemiology, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
- Radiology, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
- Neurology, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
| | - Nicole Probst-Hensch
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sven Gläser
- Internal Medicine B, University Medicine Greifswald, Greifswald, 17475, Germany
- Department of Internal Medicine - Pulmonary Diseases, Vivantes Klinikum Spandau Berlin, Berlin, 13585, Germany
| | | | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33520, Finland
- Department of Clinical Chemistry, Faculty of Medicine and Life Sciences, University of Tampere, Tampere 33014, Finland
| | - David P. Strachan
- Population Health Research Institute, St George's, University of London, London, SW17 0RE, UK
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Alanna C. Morrison
- 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, TX, 77030, USA
| | - Ian P. Hall
- NIHR Nottingham Biomedical Research Centre and Division of Respiratory Medicine, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Martin D. Tobin
- Department of Health Sciences, University of Leicester, Leicester, UK
- National Institute for Health Research, Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Stephanie J. London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, 27709, USA
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What do polymorphisms tell us about the mechanisms of COPD? Clin Sci (Lond) 2017; 131:2847-2863. [PMID: 29203722 DOI: 10.1042/cs20160718] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 10/22/2017] [Accepted: 11/01/2017] [Indexed: 12/11/2022]
Abstract
COPD (chronic obstructive pulmonary disease) is characterized by irreversible lung airflow obstruction. Cigarette smoke is the major risk factor for COPD development. However, only a minority number of smokers develop COPD, and there are substantial variations in lung function among smokers, suggesting that genetic determinants in COPD susceptibility. During the past decade, genome-wide association studies and exome sequencing have been instrumental to identify the genetic determinants of complex traits, including COPD. Focused studies have revealed mechanisms by which genetic variants contribute to COPD and have led to novel insights in COPD pathogenesis. Through functional investigations of causal variants in COPD, from the proteinase-antiproteinase theory to emerging roles of developmental pathways (such as Hedgehog and Wnt pathways) in COPD, we have greatly expanded our understanding on this complex pulmonary disease. In this review, we critically review functional investigations on roles of genetic polymorphisms in COPD, and discuss future challenges and opportunities in discovering novel mechanisms of functional variants.
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Abstract
Severe alpha-1 antitrypsin (AAT) deficiency is one of the most common serious genetic diseases in adults of European descent. Individuals with AAT deficiency have a greatly increased risk for emphysema and liver disease. Other manifestations include bronchiectasis, necrotizing panniculitis and granulomatosis with polyangiitis. Despite the frequency and potential severity, AAT deficiency remains under-recognized, and there is often a delay in diagnosis. This review will focus on three recent updates that should serve to encourage testing and diagnosis of AAT deficiency: first, the publication of a randomized clinical trial demonstrating the efficacy of intravenous augmentation therapy in slowing the progression of emphysema in AAT deficiency; second, the mounting evidence showing an increased risk of lung disease in heterozygous PI MZ genotype carriers; last, the recent publication of a clinical practice guideline, outlining diagnosis and management. Though it has been recognized for more than fifty years, AAT deficiency exemplifies the modern paradigm of precision medicine, with a diagnostic test that identifies a genetic subtype of a heterogeneous disease, leading to a targeted treatment.
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Affiliation(s)
- Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Ave., Boston, MA, 02115, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
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Radder JE, Zhang Y, Gregory AD, Yu S, Kelly NJ, Leader JK, Kaminski N, Sciurba FC, Shapiro SD. Extreme Trait Whole-Genome Sequencing Identifies PTPRO as a Novel Candidate Gene in Emphysema with Severe Airflow Obstruction. Am J Respir Crit Care Med 2017; 196:159-171. [PMID: 28199135 DOI: 10.1164/rccm.201606-1147oc] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Genetic association studies in chronic obstructive pulmonary disease have primarily tested for association with common variants, the results of which explain only a portion of disease heritability. Because rare variation is also likely to contribute to susceptibility, we used whole-genome sequencing of subjects with clinically extreme phenotypes to identify genomic regions enriched for rare variation contributing to chronic obstructive pulmonary disease susceptibility. OBJECTIVES To identify regions of rare genetic variation contributing to emphysema with severe airflow obstruction. METHODS We identified heavy smokers that were resistant (n = 65) or susceptible (n = 64) to emphysema with severe airflow obstruction in the Pittsburgh Specialized Center of Clinically Oriented Research cohort. We filtered whole-genome sequencing results to include only rare variants and conducted single variant tests, region-based tests across the genome, gene-based tests, and exome-wide tests. MEASUREMENTS AND MAIN RESULTS We identified several suggestive associations with emphysema with severe airflow obstruction, including a suggestive association of all rare variation in a region within the gene ZNF816 (19q13.41; P = 4.5 × 10-6), and a suggestive association of nonsynonymous coding rare variation in the gene PTPRO (P = 4.0 × 10-5). Association of rs61754411, a rare nonsynonymous variant in PTPRO, with emphysema and obstruction was demonstrated in all non-Hispanic white individuals in the Pittsburgh Specialized Center of Clinically Oriented Research cohort. We found that cells containing this variant have decreased signaling in cellular pathways necessary for survival and proliferation. CONCLUSIONS PTPRO is a novel candidate gene in emphysema with severe airflow obstruction, and rs61754411 is a previously unreported rare variant contributing to emphysema susceptibility. Other suggestive candidate genes, such as ZNF816, are of interest for future studies.
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Affiliation(s)
- Josiah E Radder
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and
| | - Yingze Zhang
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and
| | - Alyssa D Gregory
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and
| | - Shibing Yu
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and
| | - Neil J Kelly
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and
| | - Joseph K Leader
- 2 Department of Radiology, University of Pittsburgh, Pittsburgh, Pennsylvania; and
| | - Naftali Kaminski
- 3 Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University, New Haven, Connecticut
| | - Frank C Sciurba
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and
| | - Steven D Shapiro
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and
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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: 6.7] [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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Zhao Z, Jiang C, Zhao D, Li Y, Liang C, Liu W, Wei S, Zhou Y, Zhao Z, Ran P. Two CHRN susceptibility variants for COPD are genetic determinants of emphysema and chest computed tomography manifestations in Chinese patients. Int J Chron Obstruct Pulmon Dis 2017; 12:1447-1455. [PMID: 28553097 PMCID: PMC5439970 DOI: 10.2147/copd.s134010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Quantitative computed tomography (CT) measures of emphysema have been shown to be associated with increased mortality in humans, but genetic variants affecting the quantitative parameters of chest CT that measure degree of emphysema have not yet been examined. In this study, using available chest CT data from a total of 344 emphysema patients, we assessed the correlations between five chronic obstructive pulmonary disease (COPD) susceptibility variants in the cholinergic receptor nicotinic (CHRN) genes and the degree of emphysema and chest CT manifestations. We verified that most of the parameters were significantly correlated with the degree of emphysema. Compared to rs76071148AA and TT genotype carriers, the rs76071148AT genotype carriers exhibited a decreased probability of having severe emphysema (odds ratio [OR] =0.63, 95% confidence interval [CI] =0.40–0.99), whereas the variant rs8040868C allele was negatively correlated with the emphysema index (P=0.002). Interestingly, further stratification analysis grouped by spirometry-diagnosed COPD status revealed that the variant rs8040868C (CT + CC) genotypes exerted a protective effect against severe emphysema with borderline significance (OR =0.41, 95% CI =0.16–1.05) and affected the mean lung density, emphysema index, ratio of airway wall thickness to airway dimensions (AWT/AD), and AWT grade in spirometry-diagnosed non-COPD subjects. The rs76071148 variant was also significantly associated with AWT/AD and AWT grade in those individuals. In summary, we determined that rs8040868 and rs76071148 are promising indicators of the degree of emphysema and chest CT manifestations, especially in spirometry-diagnosed non-COPD subjects.
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Affiliation(s)
- Zhuxiang Zhao
- The State Key Laboratory of Respiratory Diseases, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou.,The Pulmonary Medicine,Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Changbin Jiang
- The State Key Laboratory of Respiratory Diseases, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou
| | - Dongxing Zhao
- The State Key Laboratory of Respiratory Diseases, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou
| | - Yujun Li
- The Pulmonary Medicine,Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Chunxiao Liang
- The State Key Laboratory of Respiratory Diseases, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou
| | - Weifeng Liu
- The Pulmonary Medicine,Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Shuquan Wei
- The Pulmonary Medicine,Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Yumin Zhou
- The State Key Laboratory of Respiratory Diseases, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou
| | - Ziwen Zhao
- The Pulmonary Medicine,Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong, People's Republic of China
| | - Pixin Ran
- The State Key Laboratory of Respiratory Diseases, The First Affiliated Hospital, Guangzhou Medical University, Guangzhou
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39
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Hobbs BD, de Jong K, Lamontagne M, Bossé Y, Shrine N, Artigas MS, Wain LV, Hall IP, Jackson VE, Wyss AB, London SJ, North KE, Franceschini N, Strachan DP, Beaty TH, Hokanson JE, Crapo JD, Castaldi PJ, Chase RP, Bartz TM, Heckbert SR, Psaty BM, Gharib SA, Zanen P, Lammers JW, Oudkerk M, Groen HJ, Locantore N, Tal-Singer R, Rennard SI, Vestbo J, Timens W, Paré PD, Latourelle JC, Dupuis J, O’Connor GT, Wilk JB, Kim WJ, Lee MK, Oh YM, Vonk JM, de Koning HJ, Leng S, Belinsky SA, Tesfaigzi Y, Manichaikul A, Wang XQ, Rich SS, Barr RG, Sparrow D, Litonjua AA, Bakke P, Gulsvik A, Lahousse L, Brusselle GG, Stricker BH, Uitterlinden AG, Ampleford EJ, Bleecker ER, Woodruff PG, Meyers DA, Qiao D, Lomas DA, Yim JJ, Kim DK, Hawrylkiewicz I, Sliwinski P, Hardin M, Fingerlin TE, Schwartz DA, Postma DS, MacNee W, Tobin MD, Silverman EK, Boezen HM, Cho MH. Genetic loci associated with chronic obstructive pulmonary disease overlap with loci for lung function and pulmonary fibrosis. Nat Genet 2017; 49:426-432. [PMID: 28166215 PMCID: PMC5381275 DOI: 10.1038/ng.3752] [Citation(s) in RCA: 256] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 11/23/2016] [Indexed: 12/15/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is a leading cause of mortality worldwide. We performed a genetic association study in 15,256 cases and 47,936 controls, with replication of select top results (P < 5 × 10-6) in 9,498 cases and 9,748 controls. In the combined meta-analysis, we identified 22 loci associated at genome-wide significance, including 13 new associations with COPD. Nine of these 13 loci have been associated with lung function in general population samples, while 4 (EEFSEC, DSP, MTCL1, and SFTPD) are new. We noted two loci shared with pulmonary fibrosis (FAM13A and DSP) but that had opposite risk alleles for COPD. None of our loci overlapped with genome-wide associations for asthma, although one locus has been implicated in joint susceptibility to asthma and obesity. We also identified genetic correlation between COPD and asthma. Our findings highlight new loci associated with COPD, demonstrate the importance of specific loci associated with lung function to COPD, and identify potential regions of genetic overlap between COPD and other respiratory diseases.
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Affiliation(s)
- Brian D. Hobbs
- Channing Division of Network Medicine, Brigham and Women’s
Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and
Women’s Hospital, Boston, MA, USA
| | - Kim de Jong
- University of Groningen, University Medical Center Groningen,
Department of Epidemiology, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen,
Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the
Netherlands
| | - Maxime Lamontagne
- Institut universitaire de cardiologie et de pneumologie de
Québec, Québec, Canada
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de
Québec, Québec, Canada
- Department of Molecular Medicine, Laval University, Québec,
Canada
| | - Nick Shrine
- Genetic Epidemiology Group, Department of Health Sciences,
University of Leicester, Leicester, UK
| | - María Soler Artigas
- Genetic Epidemiology Group, Department of Health Sciences,
University of Leicester, Leicester, UK
| | - Louise V. Wain
- Genetic Epidemiology Group, Department of Health Sciences,
University of Leicester, Leicester, UK
| | - Ian P. Hall
- Division of Respiratory Medicine, Queen’s Medical Centre,
University of Nottingham, Nottingham, UK
| | - Victoria E. Jackson
- Genetic Epidemiology Group, Department of Health Sciences,
University of Leicester, Leicester, UK
| | - Annah B. Wyss
- Epidemiology Branch, National Institute of Environmental Health
Sciences, National Institutes of Health, Department of Health and Human Services,
Research Triangle Park, NC, USA
| | - Stephanie J. London
- Epidemiology Branch, National Institute of Environmental Health
Sciences, National Institutes of Health, Department of Health and Human Services,
Research Triangle Park, NC, USA
| | - Kari E. North
- Department of Epidemiology, University of North Carolina, Chapel
Hill, NC, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel
Hill, NC, USA
| | - David P. Strachan
- Population Health Research Institute, St. George’s,
University of London, London, UK
| | - Terri H. Beaty
- Johns Hopkins University Bloomberg School of Public Health,
Baltimore, MD, USA
| | - John E. Hokanson
- Department of Epidemiology, University of Colorado Anschutz Medical
Campus, Aurora, CO, USA
| | - James D. Crapo
- Department of Medicine, Division of Pulmonary and Critical Care
Medicine, National Jewish Health, Denver, CO, USA
| | - Peter J. Castaldi
- Channing Division of Network Medicine, Brigham and Women’s
Hospital, Boston, MA, USA
- Division of General Internal Medicine, Brigham and Women’s
Hospital, Boston, MA, USA
| | - Robert P. Chase
- Channing Division of Network Medicine, Brigham and Women’s
Hospital, Boston, MA, USA
| | - Traci M. Bartz
- Cardiovascular Health Research Unit, University of Washington,
Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA,
USA
- Department of Biostatistics, University of Washington, Seattle, WA,
USA
| | - Susan R. Heckbert
- Cardiovascular Health Research Unit, University of Washington,
Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA,
USA
- Group Health Research Institute, Group Health Cooperative, Seattle,
WA, USA
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, University of Washington,
Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA,
USA
- Department of Epidemiology, University of Washington, Seattle, WA,
USA
- Group Health Research Institute, Group Health Cooperative, Seattle,
WA, USA
- Department of Health Services, University of Washington, Seattle,
WA, USA
| | - Sina A. Gharib
- Computational Medicine Core, Center for Lung Biology, UW Medicine
Sleep Center, Department of Medicine, University of Washington, Seattle, WA,
USA
| | - Pieter Zanen
- Department of Pulmonology, University Medical Center Utrecht,
University of Utrecht, Utrecht, the Netherlands
| | - Jan W. Lammers
- Department of Pulmonology, University Medical Center Utrecht,
University of Utrecht, Utrecht, the Netherlands
| | - Matthijs Oudkerk
- University of Groningen, University Medical Center Groningen,
Center for Medical Imaging, the Netherlands
| | - H. J. Groen
- University of Groningen, University Medical Center Groningen,
Department of Pulmonology, Groningen, the Netherlands
| | | | | | - Stephen I. Rennard
- Pulmonary, Critical Care, Sleep and Allergy Division, Department of
Internal Medicine, University of Nebraska Medical Center, Omaha, NE, USA
- Clinical Discovery Unit, AstraZeneca, Cambridge, UK
| | - Jørgen Vestbo
- School of Biological Sciences, University of Manchester,
Manchester, UK
| | - Wim Timens
- Department of Pathology and Medical Biology, University of
Groningen, University Medical Center Groningen, GRIAC Research Institute, Groningen,
the Netherlands
| | - Peter D. Paré
- University of British Columbia Center for Heart Lung Innovation and
Institute for Heart and Lung Health, St Paul’s Hospital, Vancouver, British
Columbia, Canada
| | | | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public
Health, Boston, MA, USA
- The National Heart, Lung, and Blood Institute’s Framingham
Heart Study, Framingham, MA, USA
| | - George T. O’Connor
- The National Heart, Lung, and Blood Institute’s Framingham
Heart Study, Framingham, MA, USA
- Pulmonary Center, Department of Medicine, Boston University School
of Medicine, Boston, MA, USA
| | - Jemma B. Wilk
- The National Heart, Lung, and Blood Institute’s Framingham
Heart Study, Framingham, MA, USA
| | - Woo Jin Kim
- Department of Internal Medicine and Environmental Health Center,
School of Medicine, Kangwon National University, Chuncheon, South Korea
| | - Mi Kyeong Lee
- Department of Internal Medicine and Environmental Health Center,
School of Medicine, Kangwon National University, Chuncheon, South Korea
| | - Yeon-Mok Oh
- Department of Pulmonary and Critical Care Medicine, and Clinical
Research Center for Chronic Obstructive Airway Diseases, Asan Medical Center,
University of Ulsan College of Medicine, Seoul, South Korea
| | - Judith M. Vonk
- University of Groningen, University Medical Center Groningen,
Department of Epidemiology, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen,
Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the
Netherlands
| | - Harry J. de Koning
- Department of Public Health, Erasmus Medical Center Rotterdam,
Rotterdam, the Netherlands
| | - Shuguang Leng
- Lovelace Respiratory Research Institute, Albuquerque, NM, USA
| | | | | | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia,
Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia,
Charlottesville, VA, USA
| | - Xin-Qun Wang
- Department of Public Health Sciences, University of Virginia,
Charlottesville, VA, USA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia,
Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia,
Charlottesville, VA, USA
| | - R Graham Barr
- Department of Medicine, College of Physicians and Surgeons and
Department of Epidemiology, Mailman School of Public Health, Columbia University,
New York, NY, USA
| | - David Sparrow
- VA Boston Healthcare System and Department of Medicine, Boston
University School of Medicine, Boston, MA, USA
| | - Augusto A. Litonjua
- Channing Division of Network Medicine, Brigham and Women’s
Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and
Women’s Hospital, Boston, MA, USA
| | - Per Bakke
- Department of Clinical Science, University of Bergen, Bergen,
Norway
| | - Amund Gulsvik
- Department of Clinical Science, University of Bergen, Bergen,
Norway
| | - Lies Lahousse
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the
Netherlands
- Department of Respiratory Medicine, Ghent University Hospital,
Ghent, Belgium
| | - Guy G. Brusselle
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the
Netherlands
- Department of Respiratory Medicine, Ghent University Hospital,
Ghent, Belgium
- Department of Respiratory Medicine, Erasmus Medical Center,
Rotterdam, the Netherlands
| | - Bruno H. Stricker
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the
Netherlands
- Netherlands Health Care Inspectorate, The Hague, the
Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam,
the Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands
Consortium for Healthy Aging (NCHA), Leiden, the Netherlands
| | - André G. Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the
Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam,
the Netherlands
- Netherlands Genomics Initiative (NGI)-sponsored Netherlands
Consortium for Healthy Aging (NCHA), Leiden, the Netherlands
| | - Elizabeth J. Ampleford
- Center for Genomics and Personalized Medicine Research, Wake Forest
University School of Medicine, Winston Salem, NC, USA
| | - Eugene R. Bleecker
- Center for Genomics and Personalized Medicine Research, Wake Forest
University School of Medicine, Winston Salem, NC, USA
| | - Prescott G. Woodruff
- Cardiovascular Research Institute and the Department of Medicine,
Division of Pulmonary, Critical Care, Sleep, and Allergy, University of California
at San Francisco, San Francisco, CA, USA
| | - Deborah A. Meyers
- Center for Genomics and Personalized Medicine Research, Wake Forest
University School of Medicine, Winston Salem, NC, USA
| | - Dandi Qiao
- Channing Division of Network Medicine, Brigham and Women’s
Hospital, Boston, MA, USA
| | | | - Jae-Joon Yim
- Division of Pulmonary and Critical Care Medicine, Department of
Internal Medicine, Seoul National University College of Medicine, Seoul, South
Korea
| | - Deog Kyeom Kim
- Seoul National University College of Medicine, SMG-SNU Boramae
Medical Center, Seoul, South Korea
| | - Iwona Hawrylkiewicz
- 2nd Department of Respiratory Medicine, Institute of Tuberculosis
and Lung Diseases, Warsaw, Poland
| | - Pawel Sliwinski
- 2nd Department of Respiratory Medicine, Institute of Tuberculosis
and Lung Diseases, Warsaw, Poland
| | - Megan Hardin
- Channing Division of Network Medicine, Brigham and Women’s
Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and
Women’s Hospital, Boston, MA, USA
- Clinical Discovery Unit, AstraZeneca, Cambridge, UK
| | - Tasha E. Fingerlin
- Center for Genes, Environment and Health, National Jewish Health,
Denver, CO, USA
- Department of Biostatistics and Informatics, University of Colorado
Denver, Aurora, CO, USA
| | - David A. Schwartz
- Center for Genes, Environment and Health, National Jewish Health,
Denver, CO, USA
- Department of Medicine, School of Medicine, University of Colorado
Denver, Aurora, CO, USA
- Department of Immunology, School of Medicine, University of
Colorado Denver, Aurora, CO, USA
| | - Dirkje S. Postma
- University of Groningen, University Medical Center Groningen,
Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the
Netherlands
- University of Groningen, University Medical Center Groningen,
Department of Pulmonology, Groningen, the Netherlands
| | | | - Martin D. Tobin
- Genetic Epidemiology Group, Department of Health Sciences,
University of Leicester, Leicester, UK
- National Institute for Health Research (NIHR) Leicester Respiratory
Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Edwin K. Silverman
- Channing Division of Network Medicine, Brigham and Women’s
Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and
Women’s Hospital, Boston, MA, USA
| | - H. Marike Boezen
- University of Groningen, University Medical Center Groningen,
Department of Epidemiology, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen,
Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the
Netherlands
| | - Michael H. Cho
- Channing Division of Network Medicine, Brigham and Women’s
Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and
Women’s Hospital, Boston, MA, USA
| | | | | | | | | | | | | | | |
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Matsson H, Söderhäll C, Einarsdottir E, Lamontagne M, Gudmundsson S, Backman H, Lindberg A, Rönmark E, Kere J, Sin D, Postma DS, Bossé Y, Lundbäck B, Klar J. Targeted high-throughput sequencing of candidate genes for chronic obstructive pulmonary disease. BMC Pulm Med 2016; 16:146. [PMID: 27835950 PMCID: PMC5106844 DOI: 10.1186/s12890-016-0309-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 11/06/2016] [Indexed: 12/13/2022] Open
Abstract
Background Reduced lung function in patients with chronic obstructive pulmonary disease (COPD) is likely due to both environmental and genetic factors. We report here a targeted high-throughput DNA sequencing approach to identify new and previously known genetic variants in a set of candidate genes for COPD. Methods Exons in 22 genes implicated in lung development as well as 61 genes and 10 genomic regions previously associated with COPD were sequenced using individual DNA samples from 68 cases with moderate or severe COPD and 66 controls matched for age, gender and smoking. Cases and controls were selected from the Obstructive Lung Disease in Northern Sweden (OLIN) studies. Results In total, 37 genetic variants showed association with COPD (p < 0.05, uncorrected). Several variants previously discovered to be associated with COPD from genetic genome-wide analysis studies were replicated using our sample. Two high-risk variants were followed-up for functional characterization in a large eQTL mapping study of 1,111 human lung specimens. The C allele of a synonymous variant, rs8040868, predicting a p.(S45=) in the gene for cholinergic receptor nicotinic alpha 3 (CHRNA3) was associated with COPD (p = 8.8 x 10−3). This association remained (p = 0.003 and OR = 1.4, 95 % CI 1.1-1.7) when analysing all available cases and controls in OLIN (n = 1,534). The rs8040868 variant is in linkage disequilibrium with rs16969968 previously associated with COPD and altered expression of the CHRNA5 gene. A follow-up analysis for detection of expression quantitative trait loci revealed that rs8040868-C was found to be significantly associated with a decreased expression of the nearby gene cholinergic receptor, nicotinic, alpha 5 (CHRNA5) in lung tissue. Conclusion Our data replicate previous result suggesting CHRNA5 as a candidate gene for COPD and rs8040868 as a risk variant for the development of COPD in the Swedish population. Electronic supplementary material The online version of this article (doi:10.1186/s12890-016-0309-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hans Matsson
- Department of Biosciences and Nutrition, Karolinska Institutet, 7-9, SE-141 83, Huddinge, Sweden. .,Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.
| | - Cilla Söderhäll
- Department of Biosciences and Nutrition, Karolinska Institutet, 7-9, SE-141 83, Huddinge, Sweden.,Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Elisabet Einarsdottir
- Department of Biosciences and Nutrition, Karolinska Institutet, 7-9, SE-141 83, Huddinge, Sweden.,Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Maxime Lamontagne
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec, Canada
| | - Sanna Gudmundsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Helena Backman
- Department of Public Health and Clinical Medicine, Division of Occupational and Environmental Medicine, Umeå University, Umeå, Sweden
| | - Anne Lindberg
- Department of Public Health and Clinical Medicine, Division of Medicine, Umeå University, Umeå, Sweden
| | - Eva Rönmark
- Department of Public Health and Clinical Medicine, Division of Occupational and Environmental Medicine, Umeå University, Umeå, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, 7-9, SE-141 83, Huddinge, Sweden.,Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Don Sin
- The University of British Columbia Center for Heart Lung Innovation, St-Paul's Hospital, Vancouver, Canada
| | - Dirkje S Postma
- Center Groningen, GRIAC research institute, University of Groningen, Groningen, The Netherlands
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec, Canada.,Department of Molecular Medicine, Laval University, Québec, Canada
| | - Bo Lundbäck
- Krefting Research Centre, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Joakim Klar
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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41
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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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42
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Miller S, Henry AP, Hodge E, Kheirallah AK, Billington CK, Rimington TL, Bhaker SK, Obeidat M, Melén E, Merid SK, Swan C, Gowland C, Nelson CP, Stewart CE, Bolton CE, Kilty I, Malarstig A, Parker SG, Moffatt MF, Wardlaw AJ, Hall IP, Sayers I. The Ser82 RAGE Variant Affects Lung Function and Serum RAGE in Smokers and sRAGE Production In Vitro. PLoS One 2016; 11:e0164041. [PMID: 27755550 PMCID: PMC5068780 DOI: 10.1371/journal.pone.0164041] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 09/19/2016] [Indexed: 12/30/2022] Open
Abstract
INTRODUCTION Genome-Wide Association Studies have identified associations between lung function measures and Chronic Obstructive Pulmonary Disease (COPD) and chromosome region 6p21 containing the gene for the Advanced Glycation End Product Receptor (AGER, encoding RAGE). We aimed to (i) characterise RAGE expression in the lung, (ii) identify AGER transcripts, (iii) ascertain if SNP rs2070600 (Gly82Ser C/T) is associated with lung function and serum sRAGE levels and (iv) identify whether the Gly82Ser variant is functionally important in altering sRAGE levels in an airway epithelial cell model. METHODS Immunohistochemistry was used to identify RAGE protein expression in 26 human tissues and qPCR was used to quantify AGER mRNA in lung cells. Gene expression array data was used to identify AGER expression during lung development in 38 fetal lung samples. RNA-Seq was used to identify AGER transcripts in lung cells. sRAGE levels were assessed in cells and patient serum by ELISA. BEAS2B-R1 cells were transfected to overexpress RAGE protein with either the Gly82 or Ser82 variant and sRAGE levels identified. RESULTS Immunohistochemical assessment of 6 adult lung samples identified high RAGE expression in the alveoli of healthy adults and individuals with COPD. AGER/RAGE expression increased across developmental stages in human fetal lung at both the mRNA (38 samples) and protein levels (20 samples). Extensive AGER splicing was identified. The rs2070600T (Ser82) allele is associated with higher FEV1, FEV1/FVC and lower serum sRAGE levels in UK smokers. Using an airway epithelium model overexpressing the Gly82 or Ser82 variants we found that HMGB1 activation of the RAGE-Ser82 receptor results in lower sRAGE production. CONCLUSIONS This study provides new information regarding the expression profile and potential role of RAGE in the human lung and shows a functional role of the Gly82Ser variant. These findings advance our understanding of the potential mechanisms underlying COPD particularly for carriers of this AGER polymorphism.
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Affiliation(s)
- Suzanne Miller
- Division of Respiratory Medicine, University of Nottingham, Nottingham, United Kingdom
- * E-mail:
| | - Amanda P. Henry
- Division of Respiratory Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Emily Hodge
- Division of Respiratory Medicine, University of Nottingham, Nottingham, United Kingdom
| | | | | | - Tracy L. Rimington
- Division of Respiratory Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Sangita K. Bhaker
- Division of Respiratory Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Ma’en Obeidat
- Division of Respiratory Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Simon K. Merid
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Caroline Swan
- Department of Biology, University of York, York, United Kingdom
| | - Catherine Gowland
- Division of Respiratory Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Carl P. Nelson
- Division of Respiratory Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Ceri E. Stewart
- Division of Respiratory Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Charlotte E. Bolton
- Division of Respiratory Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Iain Kilty
- Pfizer Worldwide Research & Development, Cambridge, Massachusetts, United States of America
| | - Anders Malarstig
- Pfizer Worldwide Research & Development, Cambridge, United Kingdom
| | - Stuart G. Parker
- Institute for Ageing and Health, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne, United Kingdom
| | - Miriam F. Moffatt
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Andrew J. Wardlaw
- Institute for Lung Health, Immunity and Inflammation, University of Leicester, Leicester, United Kingdom
| | - Ian P. Hall
- Division of Respiratory Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Ian Sayers
- Division of Respiratory Medicine, University of Nottingham, Nottingham, United Kingdom
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