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Van Buren E, Radicioni G, Lester S, O’Neal WK, Dang H, Kasela S, Garudadri S, Curtis JL, Han MK, Krishnan JA, Wan ES, Silverman EK, Hastie A, Ortega VE, Lappalainen T, Nawijn MC, van den Berge M, Christenson SA, Li Y, Cho MH, Kesimer M, Kelada SNP. Genetic regulators of sputum mucin concentration and their associations with COPD phenotypes. PLoS Genet 2023; 19:e1010445. [PMID: 37352370 PMCID: PMC10325042 DOI: 10.1371/journal.pgen.1010445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 07/06/2023] [Accepted: 04/26/2023] [Indexed: 06/25/2023] Open
Abstract
Hyper-secretion and/or hyper-concentration of mucus is a defining feature of multiple obstructive lung diseases, including chronic obstructive pulmonary disease (COPD). Mucus itself is composed of a mixture of water, ions, salt and proteins, of which the gel-forming mucins, MUC5AC and MUC5B, are the most abundant. Recent studies have linked the concentrations of these proteins in sputum to COPD phenotypes, including chronic bronchitis (CB) and acute exacerbations (AE). We sought to determine whether common genetic variants influence sputum mucin concentrations and whether these variants are also associated with COPD phenotypes, specifically CB and AE. We performed a GWAS to identify quantitative trait loci for sputum mucin protein concentration (pQTL) in the Sub-Populations and InteRmediate Outcome Measures in COPD Study (SPIROMICS, n = 708 for total mucin, n = 215 for MUC5AC, MUC5B). Subsequently, we tested for associations of mucin pQTL with CB and AE using regression modeling (n = 822-1300). Replication analysis was conducted using data from COPDGene (n = 5740) and by examining results from the UK Biobank. We identified one genome-wide significant pQTL for MUC5AC (rs75401036) and two for MUC5B (rs140324259, rs10001928). The strongest association for MUC5B, with rs140324259 on chromosome 11, explained 14% of variation in sputum MUC5B. Despite being associated with lower MUC5B, the C allele of rs140324259 conferred increased risk of CB (odds ratio (OR) = 1.42; 95% confidence interval (CI): 1.10-1.80) as well as AE ascertained over three years of follow up (OR = 1.41; 95% CI: 1.02-1.94). Associations between rs140324259 and CB or AE did not replicate in COPDGene. However, in the UK Biobank, rs140324259 was associated with phenotypes that define CB, namely chronic mucus production and cough, again with the C allele conferring increased risk. We conclude that sputum MUC5AC and MUC5B concentrations are associated with common genetic variants, and the top locus for MUC5B may influence COPD phenotypes, in particular CB.
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Affiliation(s)
- Eric Van Buren
- Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Giorgia Radicioni
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Sarah Lester
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Wanda K. O’Neal
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Hong Dang
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Silva Kasela
- New York Genome Center, New York, New York, United States of America
- Department of Systems Biology, Columbia University, New York, New York, United States of America
| | - Suresh Garudadri
- Division of Pulmonary, Critical Care, Allergy, & Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Jeffrey L. Curtis
- Pulmonary & Critical Care Medicine Division, University of Michigan, Ann Arbor, Michigan, United States of America
- Medical Service, VA Ann Arbor Healthcare System, Ann Arbor, Michigan, United States of America
| | - MeiLan K. Han
- Pulmonary & Critical Care Medicine Division, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jerry A. Krishnan
- Breathe Chicago Center, University of Illinois, Chicago, Illinois, United States of America
| | - Emily S. Wan
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- VA Boston Healthcare System, Jamaica Plain, Massachusetts, United States of America
| | - Edwin K. Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Annette Hastie
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Victor E. Ortega
- Department of Internal Medicine, Division of Respiratory Medicine, Mayo Clinic, Scottsdale, Arizona, United States of America
| | - Tuuli Lappalainen
- New York Genome Center, New York, New York, United States of America
- Department of Systems Biology, Columbia University, New York, New York, United States of America
| | - Martijn C. Nawijn
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, Groningen, the Netherlands
| | - Maarten van den Berge
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, Groningen, the Netherlands
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Stephanie A. Christenson
- Division of Pulmonary, Critical Care, Allergy, & Sleep Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Yun Li
- Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Michael H. Cho
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Mehmet Kesimer
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Samir N. P. Kelada
- Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina, United States of America
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America
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Packer RJ, Shrine N, Hall R, Melbourne CA, Thompson R, Williams AT, Paynton ML, Guyatt AL, Allen RJ, Lee PH, John C, Campbell A, Hayward C, de Vries M, Vonk JM, Davitte J, Hessel E, Michalovich D, Betts JC, Sayers I, Yeo A, Hall IP, Tobin MD, Wain LV. Genome-wide association study of chronic sputum production implicates loci involved in mucus production and infection. Eur Respir J 2023; 61:2201667. [PMID: 37263751 PMCID: PMC10284065 DOI: 10.1183/13993003.01667-2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/17/2023] [Indexed: 06/03/2023]
Abstract
BACKGROUND Chronic sputum production impacts on quality of life and is a feature of many respiratory diseases. Identification of the genetic variants associated with chronic sputum production in a disease agnostic sample could improve understanding of its causes and identify new molecular targets for treatment. METHODS We conducted a genome-wide association study (GWAS) of chronic sputum production in UK Biobank. Signals meeting genome-wide significance (p<5×10-8) were investigated in additional independent studies, were fine-mapped and putative causal genes identified by gene expression analysis. GWASs of respiratory traits were interrogated to identify whether the signals were driven by existing respiratory disease among the cases and variants were further investigated for wider pleiotropic effects using phenome-wide association studies (PheWASs). RESULTS From a GWAS of 9714 cases and 48 471 controls, we identified six novel genome-wide significant signals for chronic sputum production including signals in the human leukocyte antigen (HLA) locus, chromosome 11 mucin locus (containing MUC2, MUC5AC and MUC5B) and FUT2 locus. The four common variant associations were supported by independent studies with a combined sample size of up to 2203 cases and 17 627 controls. The mucin locus signal had previously been reported for association with moderate-to-severe asthma. The HLA signal was fine-mapped to an amino acid change of threonine to arginine (frequency 36.8%) in HLA-DRB1 (HLA-DRB1*03:147). The signal near FUT2 was associated with expression of several genes including FUT2, for which the direction of effect was tissue dependent. Our PheWAS identified a wide range of associations including blood cell traits, liver biomarkers, infections, gastrointestinal and thyroid-associated diseases, and respiratory disease. CONCLUSIONS Novel signals at the FUT2 and mucin loci suggest that mucin fucosylation may be a driver of chronic sputum production even in the absence of diagnosed respiratory disease and provide genetic support for this pathway as a target for therapeutic intervention.
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Affiliation(s)
- Richard J Packer
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- Leicester NIHR Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Nick Shrine
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Robert Hall
- Centre for Respiratory Research, NIHR Nottingham Biomedical Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Carl A Melbourne
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Rebecca Thompson
- Centre for Respiratory Research, NIHR Nottingham Biomedical Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Alex T Williams
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Megan L Paynton
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Anna L Guyatt
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Richard J Allen
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Paul H Lee
- Department of Population Health Sciences, University of Leicester, Leicester, UK
| | - Catherine John
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- Leicester NIHR Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Maaike de Vries
- University of Groningen, University Medical Center Groningen, Department of Epidemiology and Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - Judith M Vonk
- University of Groningen, University Medical Center Groningen, Department of Epidemiology and Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | | | | | | | | | - Ian Sayers
- Centre for Respiratory Research, NIHR Nottingham Biomedical Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | | | - Ian P Hall
- Centre for Respiratory Research, NIHR Nottingham Biomedical Research Centre, School of Medicine, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Martin D Tobin
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- Leicester NIHR Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Louise V Wain
- Department of Population Health Sciences, University of Leicester, Leicester, UK
- Leicester NIHR Biomedical Research Centre, Glenfield Hospital, Leicester, UK
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Kablar B. Skeletal Muscle's Role in Prenatal Inter-organ Communication: A Phenogenomic Study with Qualitative Citation Analysis. ADVANCES IN ANATOMY, EMBRYOLOGY, AND CELL BIOLOGY 2023; 236:1-19. [PMID: 37955769 DOI: 10.1007/978-3-031-38215-4_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
Gene targeting in mice allows for a complete elimination of skeletal (striated or voluntary) musculature in the body, from the beginning of its development, resulting in our ability to study the consequences of this ablation on other organs. Here I focus on the relationship between the muscle and lung, motor neurons, skeleton, and special senses. Since the inception of my independent laboratory, in 2000, with my team, we published more than 30 papers (and a book chapter), nearly 400 pages of data, on these specific relationships. Here I trace, using Web of Science, nearly 600 citations of this work, to understand its impact. The current report contains a summary of our work and its impact, NCBI's Gene Expression Omnibus accession numbers of all our microarray data, and three clear future directions doable by anyone using our publicly available data. Together, this effort furthers our understanding of inter-organ communication during prenatal development.
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Affiliation(s)
- Boris Kablar
- Department of Medical Neuroscience, Anatomy and Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada.
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Crespo-Lessmann A, Bernal S, del Río E, Rojas E, Martínez-Rivera C, Marina N, Pallarés-Sanmartín A, Pascual S, García-Rivero JL, Padilla-Galo A, Curto E, Cisneros C, Serrano J, Baiget M, Plaza V. Association of the CFTR gene with asthma and airway mucus hypersecretion. PLoS One 2021; 16:e0251881. [PMID: 34086689 PMCID: PMC8177500 DOI: 10.1371/journal.pone.0251881] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 05/05/2021] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Asthma with airway mucus hypersecretion is an inadequately characterized variant of asthma. While several studies have reported that hypersecreting patients may carry genetic variants in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, many of those studies have been questioned for their numerous limitations and contradictory results. OBJECTIVES (1) To determine the presence of genetic variants of the CFTR gene in patients with asthma with and without airway mucus hypersecretion. (2) To identify the clinical, inflammatory and functional characteristics of the asthma phenotype with airway mucus hypersecretion. METHOD Comparative multicentre cross-sectional descriptive study that included 100 patients with asthma (39 hypersecretors and 61 non-hypersecretors). Asthmatic hypersecretion was defined as the presence of cough productive of sputum on most days for at least 3 months in 2 successive years. The patients were tested for fractional exhaled nitric oxide, spirometry, induced sputum cell count, total immunoglobulin E (IgE), peripheral blood eosinophil count, C-reactive protein, blood fibrinogen and blood albumin and underwent a skin prick test. Asthma control and quality of life were assessed by the Asthma Control Test and Mini Asthma Quality of Life questionnaires, respectively. Blood DNA samples were collected from the patients and next-generation sequencing using a MiSeq sequencer and the Illumina platform was used for the CFTR gene analysis. RESULTS Genetic differences were observed in the c.1680-870T>A polymorphism of the CFTR gene, significantly more evident in hypersecretors than in non-hypersecretors: 78.94% vs. 59.32% in the majority allele and 21.05% vs. 40.67% in the minority allele (p = 0.036). Clinically, asthma hypersecretors compared to non-hypersecretors were older (57.4 years vs. 49.4 years; p = 0.004); had greater asthma severity (58.9% vs. 23.7%; p = 0.005); experienced greater airway obstruction (FEV1/FVC% 64.3 vs. 69.5; p = 0.041); had poorer asthma control (60% vs. 29%; p = 0.021); had lower IgE levels (126.4 IU/mL vs. 407.6 IU/mL; p = 0.003); and were less likely to have a positive prick test (37.5% vs. 68.85%; p = 0.011). CONCLUSION The results suggest that patients with asthma and with mucus hypersecretion (1) may have a different phenotype and disease mechanism produced by an intronic polymorphism in the CFTR gene (NM_000492.3:c.1680-870T>A), and (2) may have a poorer clinical outcome characterized by severe disease and poorer asthma control with a non-allergic inflammatory phenotype.
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Affiliation(s)
- Astrid Crespo-Lessmann
- Department of Respiratory Medicine, Hospital de la Santa Creu i Sant Pau, Institute of Sant Pau Biomedical Research (IBB Sant Pau), Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Sara Bernal
- Department of Genetics, Hospital de la Santa Creu i Sant Pau, Institute of Sant Pau Biomedical Research (IBB Sant Pau), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER, U705), Barcelona, Spain
| | - Elisabeth del Río
- Department of Genetics, Hospital de la Santa Creu i Sant Pau, Institute of Sant Pau Biomedical Research (IBB Sant Pau), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER, U705), Barcelona, Spain
| | - Ester Rojas
- Department of Genetics, Hospital de la Santa Creu i Sant Pau, Institute of Sant Pau Biomedical Research (IBB Sant Pau), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER, U705), Barcelona, Spain
| | | | - Nuria Marina
- Department of Respiratory Medicine, H. de Cruces, Barakaldo, Vizcaya, Spain
| | | | - Silvia Pascual
- Department of Respiratory Medicine, H. de Galdakao, Vizcaya, Spain
| | | | - Alicia Padilla-Galo
- Department of Respiratory Medicine, H. Costa del Sol de Marbella, Málaga, Spain
| | - Elena Curto
- Department of Respiratory Medicine, Hospital de la Santa Creu i Sant Pau, Institute of Sant Pau Biomedical Research (IBB Sant Pau), Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Carolina Cisneros
- Department of Respiratory Medicine, H. U. de La Princesa, Madrid, Spain
| | - José Serrano
- Department of Respiratory Medicine, Hospital Comarcal de Inca, Baleares, Spain
| | - Montserrat Baiget
- Department of Genetics, Hospital de la Santa Creu i Sant Pau, Institute of Sant Pau Biomedical Research (IBB Sant Pau), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER, U705), Barcelona, Spain
| | - Vicente Plaza
- Department of Respiratory Medicine, Hospital de la Santa Creu i Sant Pau, Institute of Sant Pau Biomedical Research (IBB Sant Pau), Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Universitat Autònoma de Barcelona, Barcelona, Spain
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Bhatt SP, Bodduluri S, Kizhakke Puliyakote AS, Oelsner EC, Nakhmani A, Lynch DA, Wilson CG, Fortis S, Kim V. Structural airway imaging metrics are differentially associated with persistent chronic bronchitis. Thorax 2021; 76:343-349. [PMID: 33408194 PMCID: PMC8225550 DOI: 10.1136/thoraxjnl-2020-215853] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 11/09/2020] [Accepted: 11/23/2020] [Indexed: 01/06/2023]
Abstract
BACKGROUND Chronic bronchitis (CB) is strongly associated with cigarette smoking, but not all smokers develop CB. We aimed to evaluate whether measures of structural airway disease on CT are differentially associated with CB. METHODS In smokers between ages 45 and 80 years, and with Global Initiative for Obstructive Lung Disease stages 0-4, CB was defined by the classic definition. Airway disease on CT was quantified by (i) wall area percent (WA%) of segmental airways; (ii) Pi10, the square root of the wall area of a hypothetical airway with 10 mm internal perimeter; (iii) total airway count (TAC) and (iv) airway fractal dimension (AFD), a measure of the complex branching pattern and remodelling of airways. CB was also assessed at the 5-year follow-up visit. MEASUREMENTS AND MAIN RESULTS Of 8917 participants, 1734 (19.4%) had CB at baseline. Airway measures were significantly worse in those with CB compared with those without CB: WA% 54.5 (8.8) versus 49.8 (8.3); Pi10 2.58 (0.67) versus 2.28 (0.59) mm; TAC 156.7 (81.6) versus 177.8 (91.1); AFD 1.477 (0.091) versus 1.497 (0.092) (all p<0.001). On follow-up of 5517 participants at 5 years, 399 (7.2%) had persistent CB. With adjustment for between-visits changes in smoking status and lung function, greater WA% and Pi10 were associated with significantly associated with persistent CB, adjusted OR per SD change 1.75, 95% CI 1.56 to 1.97; p<0.001 and 1.66, 95% CI 1.42 to 1.86; p<0.001, respectively. Higher AFD and TAC were associated with significantly lower odds of persistent CB, adjusted OR per SD change 0.76, 95% CI 0.67 to 0.86; p<0.001 and 0.69, 95% CI 0.60 to 0.80; p<0.001, respectively. CONCLUSIONS Higher baseline AFD and TAC are associated with a lower risk of persistent CB, irrespective of changes in smoking status, suggesting preserved airway structure can confer a reserve against CB.
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Affiliation(s)
- Surya P Bhatt
- Pulmonary, Allergy and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
- UAB Lung Imaging Core, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Sandeep Bodduluri
- Pulmonary, Allergy and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
- UAB Lung Imaging Core, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | | | - Arie Nakhmani
- UAB Lung Imaging Core, University of Alabama at Birmingham, Birmingham, AL, USA
- Electrical Engineering, University of Alabama At Birmingham, Birmingham, Alabama, USA
| | - David A Lynch
- Radiology, National Jewish Health, Denver, Colorado, USA
| | - Carla G Wilson
- Division of Biostatistics and Bioinformatics, National Jewish Health, Denver, Colorado, USA
| | - Spyridon Fortis
- Pulmonary, Critical Care and Occupation Medicine, University of Iowa Hospitals and Clinics, Iowa City, Iowa, USA
| | - Victor Kim
- Division of Pulmonary and Critical Care Medicine, Temple University School of Medicine, Philadelphia, Pennsylvania, USA
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ZBTB7B (ThPOK) Is Required for Pathogenesis of Cerebral Malaria and Protection against Pulmonary Tuberculosis. Infect Immun 2020; 88:IAI.00845-19. [PMID: 31792077 DOI: 10.1128/iai.00845-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 11/08/2019] [Indexed: 11/20/2022] Open
Abstract
We used a genome-wide screen in N-ethyl-N-nitrosourea (ENU)-mutagenized mice to identify genes in which recessive loss-of-function mutations protect against pathological neuroinflammation. We identified an R367Q mutation in the ZBTB7B (ThPOK) protein in which homozygosity causes protection against experimental cerebral malaria (ECM) caused by infection with Plasmodium berghei ANKA. Zbtb7bR367Q homozygous mice show a defect in the lymphoid compartment expressed as severe reduction in the number of single-positive CD4 T cells in the thymus and in the periphery, reduced brain infiltration of proinflammatory leukocytes in P. berghei ANKA-infected mice, and reduced production of proinflammatory cytokines by primary T cells ex vivo and in vivo Dampening of proinflammatory immune responses in Zbtb7bR367Q mice is concomitant to increased susceptibility to infection with avirulent (Mycobacterium bovis BCG) and virulent (Mycobacterium tuberculosis H37Rv) mycobacteria. The R367Q mutation maps to the first DNA-binding zinc finger domain of ThPOK and causes loss of base contact by R367 in the major groove of the DNA, which is predicted to impair DNA binding. Global immunoprecipitation of ThPOK-containing chromatin complexes coupled to DNA sequencing (ChIP-seq) identified transcriptional networks and candidate genes likely to play key roles in CD4+ CD8+ T cell development and in the expression of lineage-specific functions of these cells. This study highlights ThPOK as a global regulator of immune function in which alterations may affect normal responses to infectious and inflammatory stimuli.
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Du Y, Zhang H, Xu Y, Ding Y, Chen X, Mei Z, Ding H, Jie Z. Association among genetic polymorphisms of GSTP1, HO-1, and SOD-3 and chronic obstructive pulmonary disease susceptibility. Int J Chron Obstruct Pulmon Dis 2019; 14:2081-2088. [PMID: 31564855 PMCID: PMC6736021 DOI: 10.2147/copd.s213364] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/22/2019] [Indexed: 12/19/2022] Open
Abstract
Background Chronic obstructive pulmonary disease (COPD) is a progressive lung disease characterized by incomplete reversible airflow limitation, which is associated with emphysema and chronic inflammation. Oxidative/antioxidant imbalance is one of the mechanisms of the current pathogenesis of COPD and several recent studies have attempted to uncover genetic causes of COPD and its progression. GST, HO-1, and SOD-3 are important susceptibility genes related to COPD. Methods A total of 300 blood samples were included in two groups: Control group and COPD group. We genotyped 4 single nucleotide polymorphisms (SNPs) from these 3 genes in 150 COPD patients and 150 controls to analyze genetic polymorphisms and interactions with COPD-related quantitative traits using correlation analysis and multivariate logistic regression analysis. Results The results indicated that genotype distributions and allele frequencies of GSTP1, HO-1, and SOD-3 were significantly different between the COPD and the control group, while there is no correlation between the polymorphism of GSTP1, HO-1, SOD3, and the different stages of COPD. Furthermore, multivariate logistic regression analysis indicated that COPD GSTP1-exon5 SNP and HO-1 (GT)n SNP are high-risk factors for COPD and there was interaction between GSTP1 exon5 SNPS and HO-1 (GT)n SNP. More important, the genotypes, AG, GG of GSTP1 exon5 and L/M*S, L/L of HO-1 (GT)n associated with increased 8-iso-prostaglandin F (2 alpha) (8-iso-PGF2) and malondialdehyde (MDA) concentration and decreased catalase (CAT) activity. Conclusion Collectively, this study shows that genetic polymorphisms of GSTP1, HO-1, and SOD-3 are associated with COPD susceptibility.
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Affiliation(s)
- Yong Du
- Department of Pulmonary and Critical Care Medicine, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai 200240, People's Republic of China
| | - Hui Zhang
- Department of Endocrinology, People's Hospital of Rizhao, Rizhao 276800, People's Republic of China
| | - Yan Xu
- Department of Laboratory Medicine, Rizhao Central Hospital, Rizhao 276800, People's Republic of China
| | - Yi Ding
- Department of Pulmonary and Critical Care Medicine, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai 200240, People's Republic of China
| | - Xuru Chen
- Department of Pulmonary and Critical Care Medicine, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai 200240, People's Republic of China
| | - Zhoufang Mei
- Department of Pulmonary and Critical Care Medicine, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai 200240, People's Republic of China
| | - Heyuan Ding
- Department of Endocrinology, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai 200240, People's Republic of China
| | - Zhijun Jie
- Department of Pulmonary and Critical Care Medicine, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai 200240, People's Republic of China
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Picavet HSJ, Blokstra A, Spijkerman AMW, Verschuren WMM. Cohort Profile Update: The Doetinchem Cohort Study 1987-2017: lifestyle, health and chronic diseases in a life course and ageing perspective. Int J Epidemiol 2017; 46:1751-1751g. [PMID: 29040549 PMCID: PMC5837330 DOI: 10.1093/ije/dyx103] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 05/16/2017] [Accepted: 05/22/2017] [Indexed: 12/26/2022] Open
Affiliation(s)
- H S J Picavet
- Centre for Nutrition, Prevention and Health Services, National Institute for Public Health and the Environment, Bilthoven, The Netherlands and
| | - Anneke Blokstra
- Centre for Nutrition, Prevention and Health Services, National Institute for Public Health and the Environment, Bilthoven, The Netherlands and
| | - Annemieke MW Spijkerman
- Centre for Nutrition, Prevention and Health Services, National Institute for Public Health and the Environment, Bilthoven, The Netherlands and
| | - WM Monique Verschuren
- Centre for Nutrition, Prevention and Health Services, National Institute for Public Health and the Environment, Bilthoven, The Netherlands and
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
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Koopmans T, Gosens R. Revisiting asthma therapeutics: focus on WNT signal transduction. Drug Discov Today 2017; 23:49-62. [PMID: 28890197 DOI: 10.1016/j.drudis.2017.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 07/20/2017] [Accepted: 09/01/2017] [Indexed: 12/16/2022]
Abstract
Asthma is a complex disease of the airways that develops as a consequence of both genetic and environmental factors. This interaction has highlighted genes important in early life, particularly those that control lung development, such as the Wingless/Integrase-1 (WNT) signalling pathway. Although aberrant WNT signalling is involved with an array of human conditions, it has received little attention within the context of asthma. Yet it is highly relevant, driving events involved with inflammation, airway remodelling, and airway hyper-responsiveness (AHR). In this review, we revisit asthma therapeutics by examining whether WNT signalling is a valid therapeutic target for asthma.
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Affiliation(s)
- Tim Koopmans
- Department of Molecular Pharmacology, University of Groningen, The Netherlands; Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, The Netherlands
| | - Reinoud Gosens
- Department of Molecular Pharmacology, University of Groningen, The Netherlands; Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, The Netherlands.
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10
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Identification of trans Protein QTL for Secreted Airway Mucins in Mice and a Causal Role for Bpifb1. Genetics 2017; 207:801-812. [PMID: 28851744 DOI: 10.1534/genetics.117.300211] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 08/22/2017] [Indexed: 12/14/2022] Open
Abstract
Mucus hyper-secretion is a hallmark feature of asthma and other muco-obstructive airway diseases. The mucin proteins MUC5AC and MUC5B are the major glycoprotein components of mucus and have critical roles in airway defense. Despite the biomedical importance of these two proteins, the loci that regulate them in the context of natural genetic variation have not been studied. To identify genes that underlie variation in airway mucin levels, we performed genetic analyses in founder strains and incipient lines of the Collaborative Cross (CC) in a house dust mite mouse model of asthma. CC founder strains exhibited significant differences in MUC5AC and MUC5B, providing evidence of heritability. Analysis of gene and protein expression of Muc5ac and Muc5b in incipient CC lines (n = 154) suggested that post-transcriptional events were important regulators of mucin protein content in the airways. Quantitative trait locus (QTL) mapping identified distinct, trans protein QTL for MUC5AC (chromosome 13) and MUC5B (chromosome 2). These two QTL explained 18 and 20% of phenotypic variance, respectively. Examination of the MUC5B QTL allele effects and subsequent phylogenetic analysis allowed us to narrow the MUC5B QTL and identify Bpifb1 as a candidate gene. Bpifb1 mRNA and protein expression were upregulated in parallel to MUC5B after allergen challenge, and Bpifb1 knockout mice exhibited higher MUC5B expression. Thus, BPIFB1 is a novel regulator of MUC5B.
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11
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Weidner J, Jarenbäck L, de Jong K, Vonk JM, van den Berge M, Brandsma CA, Boezen HM, Sin D, Bossé Y, Nickle D, Ankerst J, Bjermer L, Postma DS, Faiz A, Tufvesson E. Sulfatase modifying factor 1 (SUMF1) is associated with Chronic Obstructive Pulmonary Disease. Respir Res 2017; 18:77. [PMID: 28464818 PMCID: PMC5414362 DOI: 10.1186/s12931-017-0562-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 04/21/2017] [Indexed: 12/12/2022] Open
Abstract
Background It has been observed that mice lacking the sulfatase modifying factor (Sumf1) developed an emphysema-like phenotype. However, it is unknown if SUMF1 may play a role in Chronic Obstructive Pulmonary Disease (COPD) in humans. The aim was to investigate if the expression and genetic regulation of SUMF1 differs between smokers with and without COPD. Methods SUMF1 mRNA was investigated in sputum cells and whole blood from controls and COPD patients (all current or former smokers). Expression quantitative trait loci (eQTL) analysis was used to investigate if single nucleotide polymorphisms (SNPs) in SUMF1 were significantly associated with SUMF1 expression. The association of SUMF1 SNPs with COPD was examined in a population based cohort, Lifelines. SUMF1 mRNA from sputum cells, lung tissue, and lung fibroblasts, as well as lung function parameters, were investigated in relation to genotype. Results Certain splice variants of SUMF1 showed a relatively high expression in lung tissue compared to many other tissues. SUMF1 Splice variant 2 and 3 showed lower levels in sputum cells from COPD patients as compared to controls. Twelve SNPs were found significant by eQTL analysis and overlapped with the array used for genotyping of Lifelines. We found alterations in mRNA expression in sputum cells and lung fibroblasts associated with SNP rs11915920 (top hit in eQTL), which validated the results of the lung tissue eQTL analysis. Of the twelve SNPs, two SNPs, rs793391 and rs308739, were found to be associated with COPD in Lifelines. The SNP rs793391 was also confirmed to be associated with lung function changes. Conclusions We show that SUMF1 expression is affected in COPD patients compared to controls, and that SNPs in SUMF1 are associated with an increased risk of COPD. Certain COPD-associated SNPs have effects on either SUMF1 gene expression or on lung function. Collectively, this study shows that SUMF1 is associated with an increased risk of developing COPD. Electronic supplementary material The online version of this article (doi:10.1186/s12931-017-0562-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julie Weidner
- Respiratory Medicine and Allergology, Department of Clinical Sciences Lund, BMC, D12, Lund University, Skåne University Hospital, 221 84, Lund, Sweden
| | - Linnea Jarenbäck
- Respiratory Medicine and Allergology, Department of Clinical Sciences Lund, BMC, D12, Lund University, Skåne University Hospital, 221 84, Lund, Sweden
| | - Kim de Jong
- University Medical Center Groningen, GRIAC (Groningen Research Institute for Asthma and COPD), Department of Epidemiology, University of Groningen, Groningen, The Netherlands
| | - Judith M Vonk
- University Medical Center Groningen, GRIAC (Groningen Research Institute for Asthma and COPD), Department of Epidemiology, University of Groningen, Groningen, The Netherlands
| | - Maarten van den Berge
- University Medical Center Groningen, Department of Pulmonology, GRIAC (Groningen Research Institute for Asthma and COPD), University of Groningen, Groningen, The Netherlands
| | - Corry-Anke Brandsma
- University Medical Center Groningen, Department of Pulmonology, GRIAC (Groningen Research Institute for Asthma and COPD), University of Groningen, Groningen, The Netherlands
| | - H Marike Boezen
- University Medical Center Groningen, GRIAC (Groningen Research Institute for Asthma and COPD), Department of Epidemiology, University of Groningen, Groningen, The Netherlands
| | - Don Sin
- Department of Medicine (Respirology), University of British Columbia, Centre for Heart Lung Innovation, Vancouver, Canada
| | - Yohan Bossé
- Department of Molecular Medicine, Institut universitaire de cardiologie et de pneumologie de Québec, Laval University, Québec, Canada
| | - David Nickle
- Genetics and Pharmacogenomics (GpGx), Merck Research Laboratories, Boston, MA, USA
| | - Jaro Ankerst
- Respiratory Medicine and Allergology, Department of Clinical Sciences Lund, BMC, D12, Lund University, Skåne University Hospital, 221 84, Lund, Sweden
| | - Leif Bjermer
- Respiratory Medicine and Allergology, Department of Clinical Sciences Lund, BMC, D12, Lund University, Skåne University Hospital, 221 84, Lund, Sweden
| | - Dirkje S Postma
- University Medical Center Groningen, Department of Pulmonology, GRIAC (Groningen Research Institute for Asthma and COPD), University of Groningen, Groningen, The Netherlands
| | - Alen Faiz
- University Medical Center Groningen, Department of Pulmonology, GRIAC (Groningen Research Institute for Asthma and COPD), University of Groningen, Groningen, The Netherlands
| | - Ellen Tufvesson
- Respiratory Medicine and Allergology, Department of Clinical Sciences Lund, BMC, D12, Lund University, Skåne University Hospital, 221 84, Lund, Sweden.
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Protective effect of polyacetylene from Dendropanax morbifera Leveille leaves on pulmonary inflammation induced by cigarette smoke and lipopolysaccharide. J Funct Foods 2017. [DOI: 10.1016/j.jff.2017.03.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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13
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Spanjer AIR, Menzen MH, Dijkstra AE, van den Berge M, Boezen HM, Nickle DC, Sin DD, Bossé Y, Brandsma CA, Timens W, Postma DS, Meurs H, Heijink IH, Gosens R. A pro-inflammatory role for the Frizzled-8 receptor in chronic bronchitis. Thorax 2016; 71:312-22. [PMID: 26797711 DOI: 10.1136/thoraxjnl-2015-206958] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 12/21/2015] [Indexed: 11/03/2022]
Abstract
RATIONALE We have previously shown increased expression of the Frizzled-8 receptor of the Wingless/integrase-1 (WNT) signalling pathway in COPD. Here, we investigated if the Frizzled-8 receptor has a functional role in airway inflammation associated with chronic bronchitis. METHODS Acute cigarette-smoke-induced airway inflammation was studied in wild-type and Frizzled-8-deficient mice. Genetic association studies and lung expression quantitative trait loci (eQTL) analyses for Frizzled-8 were performed to evaluate polymorphisms in FZD8 and their relationship to tissue expression in chronic bronchitis. Primary human lung fibroblasts and primary human airway epithelial cells were used for in vitro studies. RESULTS Cigarette-smoke-exposure induced airway inflammation in wild-type mice, which was prevented in Frizzled-8-deficient mice, suggesting a crucial role for Frizzled-8 in airway inflammation. Furthermore, we found a significant genetic association (p=0.009) between single nucleotide polymorphism (SNP) rs663700 in the FZD8 region and chronic mucus hypersecretion, a characteristic of chronic bronchitis, in a large cohort of smoking individuals. We found SNP rs663700 to be a cis-eQTL regulating Frizzled-8 expression in lung tissue. Functional data link mesenchymal Frizzled-8 expression to inflammation as its expression in COPD-derived lung fibroblasts was regulated by pro-inflammatory cytokines in a genotype-dependent manner. Moreover, Frizzled-8 regulates inflammatory cytokine secretion from human lung fibroblasts, which in turn promoted MUC5AC expression by differentiated human airway epithelium. CONCLUSIONS These findings indicate an important pro-inflammatory role for Frizzled-8 and suggest that its expression is related to chronic bronchitis. Furthermore, our findings indicate an unexpected role for fibroblasts in regulating airway inflammation in COPD.
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Affiliation(s)
- Anita I R Spanjer
- Department of Molecular Pharmacology, University of Groningen, Groningen, The Netherlands Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Mark H Menzen
- Department of Molecular Pharmacology, University of Groningen, Groningen, The Netherlands Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Akkelies E Dijkstra
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Maarten van den Berge
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - H Marike Boezen
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - David C Nickle
- Departments of Genetics and Pharmacogenomics, Merck Research Laboratories, Boston, Massachusetts, USA
| | - Don D Sin
- Center for Heart Lung Innovation, The University of British Columbia, Vancouver, British Columbia, Canada Respiratory Division, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec, Québec City, Canada Department of Molecular Medicine, Laval University, Québec City, Canada
| | - Corry-Anke Brandsma
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands Department of Pathology & Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Wim Timens
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands Department of Pathology & Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Dirkje S Postma
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Herman Meurs
- Department of Molecular Pharmacology, University of Groningen, Groningen, The Netherlands Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Irene H Heijink
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands Department of Pathology & Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Reinoud Gosens
- Department of Molecular Pharmacology, University of Groningen, Groningen, The Netherlands Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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14
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The chronic bronchitis phenotype in chronic obstructive pulmonary disease: features and implications. Curr Opin Pulm Med 2016; 21:133-41. [PMID: 25575367 DOI: 10.1097/mcp.0000000000000145] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
PURPOSE OF REVIEW Chronic obstructive pulmonary disease (COPD) is a major public health problem that is projected to rank fifth worldwide in terms of disease burden and third in terms of mortality. Chronic bronchitis is associated with multiple clinical consequences, including hastening lung function decline, increasing risk of exacerbations, reducing health-related quality of life, and possibly raising all-cause mortality. Recent data suggest greater elucidation on the risk factors, radiologic characteristics, and treatment regimens. Our goal was to review the literature on chronic bronchitis that has been published in the past few years. RECENT FINDINGS A growing body of literature that more carefully describes environmental risk factors, epidemiology, and genetics associated with chronic bronchitis. In addition, as computed tomography technology continues to improve, the radiologic phenotype associated with chronic bronchitis is better understood. SUMMARY With these new data, the clinician can recognize the newly described risk factors and the associated phenotype for chronic bronchitis and entertain new treatment options for this high-risk population.
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15
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Obeidat M, Hao K, Bossé Y, Nickle DC, Nie Y, Postma DS, Laviolette M, Sandford AJ, Daley DD, Hogg JC, Elliott WM, Fishbane N, Timens W, Hysi PG, Kaprio J, Wilson JF, Hui J, Rawal R, Schulz H, Stubbe B, Hayward C, Polasek O, Järvelin MR, Zhao JH, Jarvis D, Kähönen M, Franceschini N, North KE, Loth DW, Brusselle GG, Smith AV, Gudnason V, Bartz TM, Wilk JB, O'Connor GT, Cassano PA, Tang W, Wain LV, Soler Artigas M, Gharib SA, Strachan DP, Sin DD, Tobin MD, London SJ, Hall IP, Paré PD. Molecular mechanisms underlying variations in lung function: a systems genetics analysis. THE LANCET. RESPIRATORY MEDICINE 2015; 3:782-95. [PMID: 26404118 PMCID: PMC5021067 DOI: 10.1016/s2213-2600(15)00380-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 08/06/2015] [Accepted: 08/12/2015] [Indexed: 02/02/2023]
Abstract
BACKGROUND Lung function measures reflect the physiological state of the lung, and are essential to the diagnosis of chronic obstructive pulmonary disease (COPD). The SpiroMeta-CHARGE consortium undertook the largest genome-wide association study (GWAS) so far (n=48,201) for forced expiratory volume in 1 s (FEV1) and the ratio of FEV1 to forced vital capacity (FEV1/FVC) in the general population. The lung expression quantitative trait loci (eQTLs) study mapped the genetic architecture of gene expression in lung tissue from 1111 individuals. We used a systems genetics approach to identify single nucleotide polymorphisms (SNPs) associated with lung function that act as eQTLs and change the level of expression of their target genes in lung tissue; termed eSNPs. METHODS The SpiroMeta-CHARGE GWAS results were integrated with lung eQTLs to map eSNPs and the genes and pathways underlying the associations in lung tissue. For comparison, a similar analysis was done in peripheral blood. The lung mRNA expression levels of the eSNP-regulated genes were tested for associations with lung function measures in 727 individuals. Additional analyses identified the pleiotropic effects of eSNPs from the published GWAS catalogue, and mapped enrichment in regulatory regions from the ENCODE project. Finally, the Connectivity Map database was used to identify potential therapeutics in silico that could reverse the COPD lung tissue gene signature. FINDINGS SNPs associated with lung function measures were more likely to be eQTLs and vice versa. The integration mapped the specific genes underlying the GWAS signals in lung tissue. The eSNP-regulated genes were enriched for developmental and inflammatory pathways; by comparison, SNPs associated with lung function that were eQTLs in blood, but not in lung, were only involved in inflammatory pathways. Lung function eSNPs were enriched for regulatory elements and were over-represented among genes showing differential expression during fetal lung development. An mRNA gene expression signature for COPD was identified in lung tissue and compared with the Connectivity Map. This in-silico drug repurposing approach suggested several compounds that reverse the COPD gene expression signature, including a nicotine receptor antagonist. These findings represent novel therapeutic pathways for COPD. INTERPRETATION The system genetics approach identified lung tissue genes driving the variation in lung function and susceptibility to COPD. The identification of these genes and the pathways in which they are enriched is essential to understand the pathophysiology of airway obstruction and to identify novel therapeutic targets and biomarkers for COPD, including drugs that reverse the COPD gene signature in silico. FUNDING The research reported in this article was not specifically funded by any agency. See Acknowledgments for a full list of funders of the lung eQTL study and the Spiro-Meta CHARGE GWAS.
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Affiliation(s)
- Ma'en Obeidat
- University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada
| | - Ke Hao
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yohan Bossé
- Department of Molecular Medicine, Laval University, Québec, QC, Canada; Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec, QC, Canada
| | - David C Nickle
- Merck Research Laboratories, Genetics and Pharmacogenomics, Boston, MA, USA
| | - Yunlong Nie
- University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada
| | - Dirkje S Postma
- University of Groningen, University Medical Center Groningen, Department of Pulmonology, GRIAC Research Institute, University of Groningen, Groningen, Netherlands
| | - Michel Laviolette
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec, QC, Canada
| | - Andrew J Sandford
- University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada; Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Denise D Daley
- University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada; Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - James C Hogg
- University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - W Mark Elliott
- University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Nick Fishbane
- University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada
| | - Wim Timens
- Department of Pathology and Medical Biology, GRIAC Research Institute, University of Groningen, Groningen, Netherlands
| | - Pirro G Hysi
- Department of Twin Research and Genetic Epidemiology, King's College, London, UK
| | - Jaakko Kaprio
- Department of Public Health, and Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland; National Institute for Health and Welfare, Helsinki, Finland
| | - James F Wilson
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK; MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Jennie Hui
- Busselton Population Medical Research Institute, Busselton, WA, Australia; PathWest Laboratory Medicine of Western Australia, Nedlands, WA, Australia; School of Population Health and School of Pahology and Laboratory Medicine, University of Western Australia, Nedlands, WA, Australia
| | - Rajesh Rawal
- Research Unit of Molecular Epidemiology, Helmholtz-Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Institute of Genetic Epidemiology, Helmholtz-Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Holger Schulz
- Institute of Epidemiology I, Helmholtz-Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Comprehensive Pneumology Center Munich (CPC-M), German Center for Lung Research, Munich, Germany
| | - Beate Stubbe
- University Hospital, Department of Internal Medicine B, Greifswald, Germany
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Ozren Polasek
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, UK; Faculty of Medicine, University of Split, Croatia
| | - Marjo-Riitta Järvelin
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College, London, UK; Center for Life Course Epidemiology, Faculty of Medicine, Biocenter Oulu, and Unit of Primary Care, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Jing Hua Zhao
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge UK
| | - Deborah Jarvis
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College, London, UK; Respiratory Epidemiology and Public Health Group, National Heart and Lung Institute, Imperial College, London, UK
| | - Mika Kähönen
- Department of Clinical Physiology, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - Nora Franceschini
- Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Kari E North
- Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA; University of North Carolina Center for Genome Sciences, Chapel Hill, NC, USA
| | - Daan W Loth
- Departments of Epidemiology and Respiratory Medicine, Erasmus MC, Rotterdam, Netherlands
| | - Guy G Brusselle
- Departments of Epidemiology and Respiratory Medicine, Erasmus MC, Rotterdam, Netherlands; Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Albert Vernon Smith
- Icelandic Heart Association, Kopavogur, Iceland; Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland; Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Traci M Bartz
- Cardiovascular Health Research Unit, Departments of Medicine and Biostatistics, University of Washington, Seattle, WA, USA
| | - Jemma B Wilk
- Human Genetics & Computational Biomedicine, Pfizer Worldwide Research and Development, Cambridge, MA, USA
| | - George T O'Connor
- Pulmonary Center, Boston University School of Medicine, Boston, MA, USA; NHLBI Framingham Heart Study, Framingham, MA, USA
| | - Patricia A Cassano
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA; Division of Biostatistics and Epidemiology, Department of Healthcare Policy and Research, Weill Cornell Medical College, NY, USA
| | - Wenbo Tang
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA; Boehringer Ingelheim Pharmaceuticals, Ridgefield, CT, USA
| | - Louise V Wain
- University of Leicester, Genetic Epidemiology Group, Department of Health Sciences, Leicester, UK; National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - María Soler Artigas
- University of Leicester, Genetic Epidemiology Group, Department of Health Sciences, Leicester, UK; National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Sina A Gharib
- Computational Medicine Core, Center for Lung Biology, University of Washington, Seattle, WA, USA; Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
| | - David P Strachan
- Population Health Research Institute, St George's, University of London, London, UK
| | - Don D Sin
- University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada; Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Martin D Tobin
- University of Leicester, Genetic Epidemiology Group, Department of Health Sciences, Leicester, UK; National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Ian P Hall
- University of Nottingham Division of Respiratory Medicine, University Hospital of Nottingham, Nottingham, UK
| | - Peter D Paré
- University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada; Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, BC, Canada.
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Dijkstra AE, Smolonska J, van den Berge M, Wijmenga C, Zanen P, Luinge MA, Platteel M, Lammers JW, Dahlback M, Tosh K, Hiemstra PS, Sterk PJ, Spira A, Vestbo J, Nordestgaard BG, Benn M, Nielsen SF, Dahl M, Verschuren WM, Picavet HSJ, Smit HA, Owsijewitsch M, Kauczor HU, de Koning HJ, Nizankowska-Mogilnicka E, Mejza F, Nastalek P, van Diemen CC, Cho MH, Silverman EK, Crapo JD, Beaty TH, Lomas DA, Bakke P, Gulsvik A, Bossé Y, Obeidat M, Loth DW, Lahousse L, Rivadeneira F, Uitterlinden AG, Hofman A, Stricker BH, Brusselle GG, van Duijn CM, Brouwer U, Koppelman GH, Vonk JM, Nawijn MC, Groen HJM, Timens W, Boezen HM, Postma DS. Correction: Susceptibility to chronic mucus hypersecretion, a genome wide association study. PLoS One 2015; 10:e0129524. [PMID: 26024482 PMCID: PMC4449226 DOI: 10.1371/journal.pone.0129524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Abstract
Chronic obstructive pulmonary disease (COPD) is one of the most common chronic illnesses in the world. The disease encompasses emphysema, chronic bronchitis, and small airway obstruction and can be caused by environmental exposures, primarily cigarette smoking. Since only a small subset of smokers develop COPD, it is believed that host factors interact with the environment to increase the propensity to develop disease. The major pathogenic factors causing disease include infection and inflammation, protease and antiprotease imbalance, and oxidative stress overwhelming antioxidant defenses. In this review, we will discuss the major environmental and host sources for oxidative stress; discuss how oxidative stress regulates chronic bronchitis; review the latest information on genetic predisposition to COPD, specifically focusing on oxidant/antioxidant imbalance; and review future antioxidant therapeutic options for COPD. The complexity of COPD will necessitate a multi-target therapeutic approach. It is likely that antioxidant supplementation and dietary antioxidants will have a place in these future combination therapies.
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Affiliation(s)
- Bernard M Fischer
- Department of Pediatrics, Duke University Medical Center, Durham, NC, USA
| | - Judith A Voynow
- Department of Pediatrics, Children’s Hospital of Richmond at Virginia Commonwealth University, Richmond, VA, USA
| | - Andrew J Ghio
- National Health and Environmental Effects Research Laboratory, US Environmental Protection Agency, Chapel Hill, NC, USA
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Dijkstra AE, Boezen HM, van den Berge M, Vonk JM, Hiemstra PS, Barr RG, Burkart KM, Manichaikul A, Pottinger TD, Silverman EK, Cho MH, Crapo JD, Beaty TH, Bakke P, Gulsvik A, Lomas DA, Bossé Y, Nickle DC, Paré PD, de Koning HJ, Lammers JW, Zanen P, Smolonska J, Wijmenga C, Brandsma CA, Groen HJM, Postma DS. Dissecting the genetics of chronic mucus hypersecretion in smokers with and without COPD. Eur Respir J 2015; 45:60-75. [PMID: 25234806 PMCID: PMC4498483 DOI: 10.1183/09031936.00093314] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Smoking is a notorious risk factor for chronic mucus hypersecretion (CMH). CMH frequently occurs in chronic obstructive pulmonary disease (COPD). The question arises whether the same single-nucleotide polymorphisms (SNPs) are related to CMH in smokers with and without COPD. We performed two genome-wide association studies of CMH under an additive genetic model in male heavy smokers (≥20 pack-years) with COPD (n=849, 39.9% CMH) and without COPD (n=1348, 25.4% CMH), followed by replication and meta-analysis in comparable populations, and assessment of the functional relevance of significantly associated SNPs. Genome-wide association analysis of CMH in COPD and non-COPD subjects yielded no genome-wide significance after replication. In COPD, our top SNP (rs10461985, p=5.43×10(-5)) was located in the GDNF-AS1 gene that is functionally associated with the GDNF gene. Expression of GDNF in bronchial biopsies of COPD patients was significantly associated with CMH (p=0.007). In non-COPD subjects, four SNPs had a p-value <10(-5) in the meta-analysis, including a SNP (rs4863687) in the MAML3 gene, the T-allele showing modest association with CMH (p=7.57×10(-6), OR 1.48) and with significantly increased MAML3 expression in lung tissue (p=2.59×10(-12)). Our data suggest the potential for differential genetic backgrounds of CMH in individuals with and without COPD.
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Affiliation(s)
- Akkelies E Dijkstra
- For lists of the authors' affiliations, and the LifeLines Cohort Study group members and their affiliations, see the Acknowledgements section
| | - H Marike Boezen
- For lists of the authors' affiliations, and the LifeLines Cohort Study group members and their affiliations, see the Acknowledgements section
| | - Maarten van den Berge
- For lists of the authors' affiliations, and the LifeLines Cohort Study group members and their affiliations, see the Acknowledgements section
| | - Judith M Vonk
- For lists of the authors' affiliations, and the LifeLines Cohort Study group members and their affiliations, see the Acknowledgements section
| | - Pieter S Hiemstra
- For lists of the authors' affiliations, and the LifeLines Cohort Study group members and their affiliations, see the Acknowledgements section
| | - R Graham Barr
- For lists of the authors' affiliations, and the LifeLines Cohort Study group members and their affiliations, see the Acknowledgements section
| | - Kirsten M Burkart
- For lists of the authors' affiliations, and the LifeLines Cohort Study group members and their affiliations, see the Acknowledgements section
| | - Ani Manichaikul
- For lists of the authors' affiliations, and the LifeLines Cohort Study group members and their affiliations, see the Acknowledgements section
| | - Tess D Pottinger
- For lists of the authors' affiliations, and the LifeLines Cohort Study group members and their affiliations, see the Acknowledgements section
| | - Edward K Silverman
- For lists of the authors' affiliations, and the LifeLines Cohort Study group members and their affiliations, see the Acknowledgements section
| | - Michael H Cho
- For lists of the authors' affiliations, and the LifeLines Cohort Study group members and their affiliations, see the Acknowledgements section
| | - James D Crapo
- For lists of the authors' affiliations, and the LifeLines Cohort Study group members and their affiliations, see the Acknowledgements section
| | - Terri H Beaty
- For lists of the authors' affiliations, and the LifeLines Cohort Study group members and their affiliations, see the Acknowledgements section
| | - Per Bakke
- For lists of the authors' affiliations, and the LifeLines Cohort Study group members and their affiliations, see the Acknowledgements section
| | - Amund Gulsvik
- For lists of the authors' affiliations, and the LifeLines Cohort Study group members and their affiliations, see the Acknowledgements section
| | - David A Lomas
- For lists of the authors' affiliations, and the LifeLines Cohort Study group members and their affiliations, see the Acknowledgements section
| | - Yohan Bossé
- For lists of the authors' affiliations, and the LifeLines Cohort Study group members and their affiliations, see the Acknowledgements section
| | - David C Nickle
- For lists of the authors' affiliations, and the LifeLines Cohort Study group members and their affiliations, see the Acknowledgements section
| | - Peter D Paré
- For lists of the authors' affiliations, and the LifeLines Cohort Study group members and their affiliations, see the Acknowledgements section
| | - Harry J de Koning
- For lists of the authors' affiliations, and the LifeLines Cohort Study group members and their affiliations, see the Acknowledgements section
| | - Jan-Willem Lammers
- For lists of the authors' affiliations, and the LifeLines Cohort Study group members and their affiliations, see the Acknowledgements section
| | - Pieter Zanen
- For lists of the authors' affiliations, and the LifeLines Cohort Study group members and their affiliations, see the Acknowledgements section
| | - Joanna Smolonska
- For lists of the authors' affiliations, and the LifeLines Cohort Study group members and their affiliations, see the Acknowledgements section
| | - Ciska Wijmenga
- For lists of the authors' affiliations, and the LifeLines Cohort Study group members and their affiliations, see the Acknowledgements section
| | - Corry-Anke Brandsma
- For lists of the authors' affiliations, and the LifeLines Cohort Study group members and their affiliations, see the Acknowledgements section
| | - Harry J M Groen
- For lists of the authors' affiliations, and the LifeLines Cohort Study group members and their affiliations, see the Acknowledgements section
| | - Dirkje S Postma
- For lists of the authors' affiliations, and the LifeLines Cohort Study group members and their affiliations, see the Acknowledgements section
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Genetic susceptibility for chronic bronchitis in chronic obstructive pulmonary disease. Respir Res 2014; 15:113. [PMID: 25241909 PMCID: PMC4190389 DOI: 10.1186/s12931-014-0113-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 09/02/2014] [Indexed: 12/23/2022] Open
Abstract
Background Chronic bronchitis (CB) is one of the classic phenotypes of COPD. The aims of our study were to investigate genetic variants associated with COPD subjects with CB relative to smokers with normal spirometry, and to assess for genetic differences between subjects with CB and without CB within the COPD population. Methods We analyzed data from current and former smokers from three cohorts: the COPDGene Study; GenKOLS (Bergen, Norway); and the Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints (ECLIPSE). CB was defined as having a cough productive of phlegm on most days for at least 3 consecutive months per year for at least 2 consecutive years. CB COPD cases were defined as having both CB and at least moderate COPD based on spirometry. Our primary analysis used smokers with normal spirometry as controls; secondary analysis was performed using COPD subjects without CB as controls. Genotyping was performed on Illumina platforms; results were summarized using fixed-effect meta-analysis. Results For CB COPD relative to smoking controls, we identified a new genome-wide significant locus on chromosome 11p15.5 (rs34391416, OR = 1.93, P = 4.99 × 10-8) as well as significant associations of known COPD SNPs within FAM13A. In addition, a GWAS of CB relative to those without CB within COPD subjects showed suggestive evidence for association on 1q23.3 (rs114931935, OR = 1.88, P = 4.99 × 10-7). Conclusions We found genome-wide significant associations with CB COPD on 4q22.1 (FAM13A) and 11p15.5 (EFCAB4A, CHID1 and AP2A2), and a locus associated with CB within COPD subjects on 1q23.3 (RPL31P11 and ATF6). This study provides further evidence that genetic variants may contribute to phenotypic heterogeneity of COPD. Trial registration ClinicalTrials.gov NCT00608764, NCT00292552 Electronic supplementary material The online version of this article (doi:10.1186/s12931-014-0113-2) contains supplementary material, which is available to authorized users.
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Hobbs BD, Hersh CP. Integrative genomics of chronic obstructive pulmonary disease. Biochem Biophys Res Commun 2014; 452:276-86. [PMID: 25078622 PMCID: PMC4172635 DOI: 10.1016/j.bbrc.2014.07.086] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 07/18/2014] [Indexed: 01/21/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) is a complex disease with both environmental and genetic determinants, the most important of which is cigarette smoking. There is marked heterogeneity in the development of COPD among persons with similar cigarette smoking histories, which is likely partially explained by genetic variation. Genomic approaches such as genomewide association studies and gene expression studies have been used to discover genes and molecular pathways involved in COPD pathogenesis; however, these "first generation" omics studies have limitations. Integrative genomic studies are emerging which can combine genomic datasets to further examine the molecular underpinnings of COPD. Future research in COPD genetics will likely use network-based approaches to integrate multiple genomic data types in order to model the complex molecular interactions involved in COPD pathogenesis. This article reviews the genomic research to date and offers a vision for the future of integrative genomic research in COPD.
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Affiliation(s)
- Brian D Hobbs
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, United States; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, United States; Harvard Medical School, Boston, MA, United States
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, United States; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, United States; Harvard Medical School, Boston, MA, United States.
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