1
|
Di Gravio C, Schildcrout JS, Tao R. Efficient designs and analysis of two-phase studies with longitudinal binary data. Biometrics 2024; 80:ujad010. [PMID: 38364804 PMCID: PMC10871867 DOI: 10.1093/biomtc/ujad010] [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: 02/16/2023] [Revised: 08/23/2023] [Accepted: 11/09/2023] [Indexed: 02/18/2024]
Abstract
Researchers interested in understanding the relationship between a readily available longitudinal binary outcome and a novel biomarker exposure can be confronted with ascertainment costs that limit sample size. In such settings, two-phase studies can be cost-effective solutions that allow researchers to target informative individuals for exposure ascertainment and increase estimation precision for time-varying and/or time-fixed exposure coefficients. In this paper, we introduce a novel class of residual-dependent sampling (RDS) designs that select informative individuals using data available on the longitudinal outcome and inexpensive covariates. Together with the RDS designs, we propose a semiparametric analysis approach that efficiently uses all data to estimate the parameters. We describe a numerically stable and computationally efficient EM algorithm to maximize the semiparametric likelihood. We examine the finite sample operating characteristics of the proposed approaches through extensive simulation studies, and compare the efficiency of our designs and analysis approach with existing ones. We illustrate the usefulness of the proposed RDS designs and analysis method in practice by studying the association between a genetic marker and poor lung function among patients enrolled in the Lung Health Study (Connett et al, 1993).
Collapse
Affiliation(s)
- Chiara Di Gravio
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Jonathan S Schildcrout
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, xUnited Kingdom
| | - Ran Tao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, United Kingdom
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, TN 37232, United Kingdom
| |
Collapse
|
2
|
Tian Y, Shepherd BE, Li C, Zeng D, Schildcrout JS. Analyzing clustered continuous response variables with ordinal regression models. Biometrics 2023; 79:3764-3777. [PMID: 37459181 PMCID: PMC10792095 DOI: 10.1111/biom.13904] [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: 07/17/2022] [Accepted: 06/28/2023] [Indexed: 12/21/2023]
Abstract
Continuous response data are regularly transformed to meet regression modeling assumptions. However, approaches taken to identify the appropriate transformation can be ad hoc and can increase model uncertainty. Further, the resulting transformations often vary across studies leading to difficulties with synthesizing and interpreting results. When a continuous response variable is measured repeatedly within individuals or when continuous responses arise from clusters, analyses have the additional challenge caused by within-individual or within-cluster correlations. We extend a widely used ordinal regression model, the cumulative probability model (CPM), to fit clustered, continuous response data using generalized estimating equations for ordinal responses. With the proposed approach, estimates of marginal model parameters, cumulative distribution functions , expectations, and quantiles conditional on covariates can be obtained without pretransformation of the response data. While computational challenges arise with large numbers of distinct values of the continuous response variable, we propose feasible and computationally efficient approaches to fit CPMs under commonly used working correlation structures. We study finite sample operating characteristics of the estimators via simulation and illustrate their implementation with two data examples. One studies predictors of CD4:CD8 ratios in a cohort living with HIV, and the other investigates the association of a single nucleotide polymorphism and lung function decline in a cohort with early chronic obstructive pulmonary disease.
Collapse
Affiliation(s)
- Yuqi Tian
- Department of Biostatistics, Vanderbilt University, Nashville, Tennessee
| | - Bryan E. Shepherd
- Department of Biostatistics, Vanderbilt University, Nashville, Tennessee
| | - Chun Li
- Department of Population and Public Health Sciences, University of Southern California, Los Angeles, California
| | - Donglin Zeng
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | | |
Collapse
|
3
|
Wang AL, Lahousse L, Dahlin A, Edris A, McGeachie M, Lutz SM, Sordillo JE, Brusselle G, Lasky-Su J, Weiss ST, Iribarren C, Lu MX, Tantisira KG, Wu AC. Novel genetic variants associated with inhaled corticosteroid treatment response in older adults with asthma. Thorax 2023; 78:432-441. [PMID: 35501119 PMCID: PMC9810110 DOI: 10.1136/thoraxjnl-2021-217674] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 04/01/2022] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Older adults have the greatest burden of asthma and poorest outcomes. The pharmacogenetics of inhaled corticosteroid (ICS) treatment response is not well studied in older adults. METHODS A genome-wide association study of ICS response was performed in asthmatics of European ancestry in Genetic Epidemiology Research on Adult Health and Aging (GERA) by fitting Cox proportional hazards regression models, followed by validation in the Mass General Brigham (MGB) Biobank and Rotterdam Study. ICS response was measured using two definitions in asthmatics on ICS treatment: (1) absence of oral corticosteroid (OCS) bursts using prescription records and (2) absence of asthma-related exacerbations using diagnosis codes. A fixed-effect meta-analysis was performed for each outcome. The validated single-nucleotide polymorphisms (SNPs) were functionally annotated to standard databases. RESULTS In 5710 subjects in GERA, 676 subjects in MGB Biobank, and 465 subjects in the Rotterdam Study, four novel SNPs on chromosome six near PTCHD4 validated across all cohorts and met genome-wide significance on meta-analysis for the OCS burst outcome. In 4541 subjects in GERA and 505 subjects in MGB Biobank, 152 SNPs with p<5 × 10-5 were validated across these two cohorts for the asthma-related exacerbation outcome. The validated SNPs included methylation and expression quantitative trait loci for CPED1, CRADD and DST for the OCS burst outcome and GM2A, SNW1, CACNA1C, DPH1, and RPS10 for the asthma-related exacerbation outcome. CONCLUSIONS Multiple novel SNPs associated with ICS response were identified in older adult asthmatics. Several SNPs annotated to genes previously associated with asthma and other airway or allergic diseases, including PTCHD4.
Collapse
Affiliation(s)
- Alberta L Wang
- Division of Allergy and Clinical Immunology, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Lies Lahousse
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Amber Dahlin
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Ahmed Edris
- Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Michael McGeachie
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Sharon M Lutz
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, Massachusetts, USA
| | - Joanne E Sordillo
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, Massachusetts, USA
| | - Guy Brusselle
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
- Department of Respiratory Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Carlos Iribarren
- Kaiser Permanente Division of Research, Kaiser Permanente, Oakland, California, USA
| | - Meng X Lu
- Kaiser Permanente Division of Research, Kaiser Permanente, Oakland, California, USA
| | - Kelan G Tantisira
- Division of Pediatric Respiratory Medicine, Rady's Children's Hospital-San Diego, University of California San Diego School of Medicine, San Diego, California, USA
| | - Ann C Wu
- PRecisiOn Medicine Translational Research (PROMoTeR) Center, Department of Population Medicine, Harvard Pilgrim Health Care Institute and Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
4
|
Cho MH, Hobbs BD, Silverman EK. Genetics of chronic obstructive pulmonary disease: understanding the pathobiology and heterogeneity of a complex disorder. THE LANCET. RESPIRATORY MEDICINE 2022; 10:485-496. [PMID: 35427534 PMCID: PMC11197974 DOI: 10.1016/s2213-2600(21)00510-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 10/20/2021] [Accepted: 11/09/2021] [Indexed: 12/20/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is a deadly and highly morbid disease. Susceptibility to and heterogeneity of COPD are incompletely explained by environmental factors such as cigarette smoking. Family-based and population-based studies have shown that a substantial proportion of COPD risk is related to genetic variation. Genetic association studies have identified hundreds of genetic variants that affect risk for COPD, decreased lung function, and other COPD-related traits. These genetic variants are associated with other pulmonary and non-pulmonary traits, demonstrate a genetic basis for at least part of COPD heterogeneity, have a substantial effect on COPD risk in aggregate, implicate early-life events in COPD pathogenesis, and often involve genes not previously suspected to have a role in COPD. Additional progress will require larger genetic studies with more ancestral diversity, improved profiling of rare variants, and better statistical methods. Through integration of genetic data with other omics data and comprehensive COPD phenotypes, as well as functional description of causal mechanisms for genetic risk variants, COPD genetics will continue to inform novel approaches to understanding the pathobiology of COPD and developing new strategies for management and treatment.
Collapse
Affiliation(s)
- Michael H Cho
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA.
| | - Brian D Hobbs
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| |
Collapse
|
5
|
Gravio CD, Tao R, Schildcrout JS. Design and analysis of two-phase studies with multivariate longitudinal data. Biometrics 2022. [PMID: 35014029 DOI: 10.1111/biom.13616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 11/03/2021] [Accepted: 12/10/2021] [Indexed: 11/27/2022]
Abstract
Two-phase studies are crucial when outcome and covariate data are available in a first phase sample (e.g., a cohort study), but costs associated with retrospective ascertainment of a novel exposure limit the size of the second phase sample, in whom the exposure is collected. For longitudinal outcomes, one class of two-phase studies stratifies subjects based on an outcome vector summary (e.g., an average or a slope over time) and oversamples subjects in the extreme value strata while undersampling subjects in the medium value stratum. Based on the choice of the summary, two-phase studies for longitudinal data can increase efficiency of time-varying and/or time-fixed exposure parameter estimates. In this manuscript, we extend efficient, two-phase study designs to multivariate longitudinal continuous outcomes, and we detail two analysis approaches. The first approach is a multiple imputation analysis that combines complete data from subjects selected for phase two with the incomplete data from those not selected. The second approach is a conditional maximum likelihood analysis that is intended for applications where only data from subjects selected for phase two are available. Importantly, we show that both approaches can be applied to secondary analyses of previously conducted two-phase studies. We examine finite sample operating characteristics of the two approaches and use the Lung Health Study (Connett et al., 1993) to examine genetic associations with lung function decline over time. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Chiara Di Gravio
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, 37232, U.S.A
| | - Ran Tao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, 37232, U.S.A.,Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, 37232, U.S.A
| | - Jonathan S Schildcrout
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, 37232, U.S.A
| |
Collapse
|
6
|
Kong N, Chen G, Wang H, Li J, Yin S, Cao X, Wang T, Li X, Li Y, Zhang H, Yu S, Tang J, Sood A, Zheng Y, Leng S. Blood leukocyte count as a systemic inflammatory biomarker associated with a more rapid spirometric decline in a large cohort of iron and steel industry workers. Respir Res 2021; 22:254. [PMID: 34565362 PMCID: PMC8467242 DOI: 10.1186/s12931-021-01849-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 09/17/2021] [Indexed: 12/29/2022] Open
Abstract
Objective Iron and steel industry workers are exposed to high levels of inhalable dust particles that contain various elements, including metals, and cause occupational lung diseases. We aim to assess the relationship between occupational dust exposure, systemic inflammation, and spirometric decline in a cohort of Chinese iron and steel workers. Methods We studied 7513 workers who participated in a Health Surveillance program at Wugang Institute for Occupational Health between 2008 and 2017. Time-weighted exposure intensity (TWEI) of dust was quantified based on self-reported dust exposure history, the experience of occupational hygienists, and historical data of dust exposure for workers with certain job titles. A linear mixed-effects model was used for association analyses. Results The average annual change of lung function was − 50.78 ml/year in forced expiratory volume in 1 s (FEV1) and − 34.36 ml/year in forced vital capacity (FVC) in males, and − 39.06 ml/year in FEV1 and − 26.66 ml/year in FVC in females. Higher TWEI prior to baseline was associated with lower longitudinal measurements of FEV1 and FVC but not with their decline rates. Higher WBC and its differential at baseline were associated with lower longitudinal measurements and a more rapid decline of FEV1 and FVC in a dose-dependent monotonically increasing manner. Moreover, the increase of WBC and its differential post-baseline was also associated with a more rapid decline of FEV1 and FVC. Conclusions Our findings support the important role of systemic inflammation in affecting the temporal change of lung function in iron and steel industry workers. Supplementary Information The online version contains supplementary material available at 10.1186/s12931-021-01849-y.
Collapse
Affiliation(s)
- Nan Kong
- Department of Occupational and Environmental Health, School of Public Health, Qingdao University, Qingdao, 266021, Shandong, China
| | - Guoshun Chen
- Wugang Institute for Occupational Health, Wuyang Iron and Steel Company Limited of Hangang Group in Henan, Wuyang, Henan, China
| | - Haitao Wang
- Department of Occupational and Environmental Health, School of Public Health, Qingdao University, Qingdao, 266021, Shandong, China
| | - Jianyu Li
- Department of Occupational and Environmental Health, School of Public Health, Qingdao University, Qingdao, 266021, Shandong, China
| | - Shuzhen Yin
- Wugang Institute for Occupational Health, Wuyang Iron and Steel Company Limited of Hangang Group in Henan, Wuyang, Henan, China
| | - Xue Cao
- Department of Occupational and Environmental Health, School of Public Health, Qingdao University, Qingdao, 266021, Shandong, China
| | - Tao Wang
- Department of Occupational and Environmental Health, School of Public Health, Qingdao University, Qingdao, 266021, Shandong, China
| | - Xin Li
- Department of Occupational and Environmental Health, School of Public Health, Qingdao University, Qingdao, 266021, Shandong, China
| | - Yanan Li
- Department of Occupational and Environmental Health, School of Public Health, Qingdao University, Qingdao, 266021, Shandong, China
| | - Huanling Zhang
- Wugang Institute for Occupational Health, Wuyang Iron and Steel Company Limited of Hangang Group in Henan, Wuyang, Henan, China
| | - Shanfa Yu
- Henan Medical College, Zhengzhou, Henan, China
| | - Jinglong Tang
- Department of Occupational and Environmental Health, School of Public Health, Qingdao University, Qingdao, 266021, Shandong, China
| | - Akshay Sood
- Department of Internal Medicine, School of Medicine, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Yuxin Zheng
- Department of Occupational and Environmental Health, School of Public Health, Qingdao University, Qingdao, 266021, Shandong, China.
| | - Shuguang Leng
- Department of Occupational and Environmental Health, School of Public Health, Qingdao University, Qingdao, 266021, Shandong, China. .,Department of Internal Medicine, School of Medicine, University of New Mexico, Albuquerque, NM, 87131, USA. .,Cancer Control and Population Sciences, University of New Mexico Comprehensive Cancer Center, Albuquerque, NM, USA.
| |
Collapse
|
7
|
Tong X, Huang T, Zhang M, Chen J, Zhang Z, Li J, Du H, Ling Z, Wu Z, Yang B, Xiao S, Ai H. Four genetic loci affecting swine lung lesions identified by whole-genome sequencing-based association studies. SCIENCE CHINA. LIFE SCIENCES 2021; 64:1571-1574. [PMID: 33521858 DOI: 10.1007/s11427-020-1826-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 09/28/2020] [Indexed: 06/12/2023]
Affiliation(s)
- Xinkai Tong
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Tao Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Mingpeng Zhang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jiaqi Chen
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Zhou Zhang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jingquan Li
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Huipeng Du
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Ziqi Ling
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Zhongzi Wu
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Bin Yang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Shijun Xiao
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Huashui Ai
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China.
| |
Collapse
|
8
|
Tao R, Mercaldo ND, Haneuse S, Maronge JM, Rathouz PJ, Heagerty PJ, Schildcrout JS. Two-wave two-phase outcome-dependent sampling designs, with applications to longitudinal binary data. Stat Med 2021; 40:1863-1876. [PMID: 33442883 DOI: 10.1002/sim.8876] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 12/07/2020] [Accepted: 12/25/2020] [Indexed: 12/26/2022]
Abstract
Two-phase outcome-dependent sampling (ODS) designs are useful when resource constraints prohibit expensive exposure ascertainment on all study subjects. One class of ODS designs for longitudinal binary data stratifies subjects into three strata according to those who experience the event at none, some, or all follow-up times. For time-varying covariate effects, exclusively selecting subjects with response variation can yield highly efficient estimates. However, if interest lies in the association of a time-invariant covariate, or the joint associations of time-varying and time-invariant covariates with the outcome, then the optimal design is unknown. Therefore, we propose a class of two-wave two-phase ODS designs for longitudinal binary data. We split the second-phase sample selection into two waves, between which an interim design evaluation analysis is conducted. The interim design evaluation analysis uses first-wave data to conduct a simulation-based search for the optimal second-wave design that will improve the likelihood of study success. Although we focus on longitudinal binary response data, the proposed design is general and can be applied to other response distributions. We believe that the proposed designs can be useful in settings where (1) the expected second-phase sample size is fixed and one must tailor stratum-specific sampling probabilities to maximize estimation efficiency, or (2) relative sampling probabilities are fixed across sampling strata and one must tailor sample size to achieve a desired precision. We describe the class of designs, examine finite sampling operating characteristics, and apply the designs to an exemplar longitudinal cohort study, the Lung Health Study.
Collapse
Affiliation(s)
- Ran Tao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Nathaniel D Mercaldo
- Departments of Radiology and Neurology, Massachusetts General Hospital and Harvard University, Boston, Massachusetts, USA
| | - Sebastien Haneuse
- Department of Biostatistics, Harvard University, Boston, Massachusetts, USA
| | - Jacob M Maronge
- Department of Statistics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Paul J Rathouz
- Department of Population Health, University of Texas, Austin, Texas, USA
| | - Patrick J Heagerty
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Jonathan S Schildcrout
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| |
Collapse
|
9
|
Hilty M, Wüthrich TM, Godel A, Adelfio R, Aebi S, Burgener SS, Illgen-Wilcke B, Benarafa C. Chronic cigarette smoke exposure and pneumococcal infection induce oropharyngeal microbiota dysbiosis and contribute to long-lasting lung damage in mice. Microb Genom 2020; 6:mgen000485. [PMID: 33295863 PMCID: PMC8116676 DOI: 10.1099/mgen.0.000485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 11/10/2020] [Indexed: 12/17/2022] Open
Abstract
Environmental factors, such as cigarette smoking or lung infections, may influence chronic obstructive pulmonary disease (COPD) progression by modifying the respiratory tract microbiome. However, whether the disease itself induces or maintains dysbiosis remains undefined. In this longitudinal study, we investigated the oropharyngeal microbiota composition and disease progression of mice (in cages of 5-10 mice per cage) before, during and up to 3 months after chronic cigarette smoke exposure or exposure to room air for 6 months. Cigarette smoke exposure induced pulmonary emphysema measurable at the end of exposure for 6 months, as well as 3 months following smoke exposure cessation. Using both classical culture methods and 16S rRNA sequencing, we observed that cigarette smoke exposure altered the relative composition of the oropharyngeal microbiota and reduced its diversity (P <0.001). More than 60 taxa were substantially reduced after 6 months of smoke exposure (P <0.001) However, oropharyngeal microbiota disordering was reversed 3 months after smoke exposure cessation and no significant difference was observed compared to age-matched control mice. The effects of lung infection with Streptococcus pneumoniae on established smoke-induced emphysema and on the oropharyngeal microbiota were also evaluated. Inoculation with S. pneumoniae induced lung damage and altered the microbiota composition for a longer time compared to control groups infected but not previously exposed to smoke (P=0.01). Our data demonstrate effects of cigarette smoke and pneumococcus infection leading to altered microbiota and emphysema development. The reversal of the disordering of the microbiota composition, but not lung damage, following smoke exposure cessation and after clearance of infection suggest that changes in lung structure are not sufficient to sustain a disordered microbiota in mice. Whether changes in the airway microbiota contribute to inducing emphysema requires further investigation.
Collapse
Affiliation(s)
- Markus Hilty
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Tsering M. Wüthrich
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- Institute of Virology and Immunology, 3147 Mittelhäusern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Freiestrasse 1, 3012 Bern, Switzerland
| | - Aurélie Godel
- Institute of Virology and Immunology, 3147 Mittelhäusern, Switzerland
| | - Roberto Adelfio
- Department of Infectious Diseases and Pathobiology (DIP), Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Susanne Aebi
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Sabrina S. Burgener
- Institute of Virology and Immunology, 3147 Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology (DIP), Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | | | - Charaf Benarafa
- Institute of Virology and Immunology, 3147 Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology (DIP), Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| |
Collapse
|
10
|
Paranjapye A, Mutolo MJ, Ebron JS, Leir SH, Harris A. The FOXA1 transcriptional network coordinates key functions of primary human airway epithelial cells. Am J Physiol Lung Cell Mol Physiol 2020; 319:L126-L136. [PMID: 32432922 DOI: 10.1152/ajplung.00023.2020] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The differentiated functions of the human airway epithelium are coordinated by a complex network of transcription factors. These include the pioneer factors Forkhead box A1 and A2 (FOXA1 and FOXA2), which are well studied in several tissues, but their role in airway epithelial cells is poorly characterized. Here, we define the cistrome of FOXA1 and FOXA2 in primary human bronchial epithelial (HBE) cells by chromatin immunoprecipitation with deep-sequencing (ChIP-seq). Next, siRNA-mediated depletion of each factor is used to investigate their transcriptome by RNA-seq. We found that, as predicted from their DNA-binding motifs, genome-wide occupancy of the two factors showed substantial overlap; however, their global impact on gene expression differed. FOXA1 is an abundant transcript in HBE cells, while FOXA2 is expressed at low levels, and both these factors likely exhibit autoregulation and cross-regulation. FOXA1 regulated loci are involved in cell adhesion and the maintenance of epithelial cell identity, particularly through repression of genes associated with epithelial to mesenchymal transition (EMT). FOXA1 also directly targets other transcription factors with a known role in the airway epithelium such as SAM-pointed domain-containing Ets-like factor (SPDEF). The intersection of the cistrome and transcriptome for FOXA1 revealed enrichment of genes involved in epithelial development and tissue morphogenesis. Moreover, depletion of FOXA1 was shown to reduce the transepithelial resistance of HBE cells, confirming the role of this factor in maintaining epithelial barrier integrity.
Collapse
Affiliation(s)
- Alekh Paranjapye
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Michael J Mutolo
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Jey Sabith Ebron
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Shih-Hsing Leir
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, Ohio
| |
Collapse
|
11
|
Schildcrout JS, Haneuse S, Tao R, Zelnick LR, Schisterman EF, Garbett SP, Mercaldo ND, Rathouz PJ, Heagerty PJ. Two-Phase, Generalized Case-Control Designs for the Study of Quantitative Longitudinal Outcomes. Am J Epidemiol 2020; 189:81-90. [PMID: 31165875 DOI: 10.1093/aje/kwz127] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 05/06/2019] [Accepted: 05/14/2019] [Indexed: 01/30/2023] Open
Abstract
We propose a general class of 2-phase epidemiologic study designs for quantitative, longitudinal data that are useful when phase 1 longitudinal outcome and covariate data are available but data on the exposure (e.g., a biomarker) can only be collected on a subset of subjects during phase 2. To conduct a study using a design in the class, one first summarizes the longitudinal outcomes by fitting a simple linear regression of the response on a time-varying covariate for each subject. Sampling strata are defined by splitting the estimated regression intercept or slope distributions into distinct (low, medium, and high) regions. Stratified sampling is then conducted from strata defined by the intercepts, by the slopes, or from a mixture. In general, samples selected with extreme intercept values will yield low variances for associations of time-fixed exposures with the outcome and samples enriched with extreme slope values will yield low variances for associations of time-varying exposures with the outcome (including interactions with time-varying exposures). We describe ascertainment-corrected maximum likelihood and multiple-imputation estimation procedures that permit valid and efficient inferences. We embed all methodological developments within the framework of conducting a substudy that seeks to examine genetic associations with lung function among continuous smokers in the Lung Health Study (United States and Canada, 1986-1994).
Collapse
Affiliation(s)
| | - Sebastien Haneuse
- Department of Biostatistics, T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Ran Tao
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Leila R Zelnick
- Division of Nephrology, Department of Medicine, University of Washington, Seattle, Washington
| | - Enrique F Schisterman
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, Maryland
| | - Shawn P Garbett
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | | | - Paul J Rathouz
- Department of Population Health, Dell Medical School, University of Texas, Austin, Texas
| | - Patrick J Heagerty
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, Washington
| |
Collapse
|
12
|
Flanders WD. Invited Commentary: Two-Phase, Generalized Case-Control Designs for Quantitative Longitudinal Outcomes and Evolution of the Case-Control Study. Am J Epidemiol 2020; 189:91-94. [PMID: 31566676 DOI: 10.1093/aje/kwz200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 08/23/2019] [Accepted: 08/27/2019] [Indexed: 11/12/2022] Open
Abstract
The case-control study design has evolved substantially over the past half century. The design has long been recognized as a way to increase efficiency by studying fewer subjects than would be required for a full cohort study. Historically, it was thought that case-control studies required a rare disease assumption for valid risk ratio estimation, but it was later realized that rare disease was not necessary. Over time, the design and analysis methods were further modified to allow estimation of rate ratios or to allow each person to serve as his/her own control (as we see with case-cohort and case-crossover studies, for example). We now understand that efficiency can be increased through the use of outcome-dependent sampling not only for dichotomous outcomes but also for continuous outcomes in longitudinal studies with repeated outcome measurement during follow-up. In their accompanying paper, Schildcrout et al. (Am J Epidemiol. 2019;000(00):000-000) contribute to our understanding, clearly summarizing many recent advances in study design and analyses that allow more general and efficient use of case-control studies. Their simulations demonstrate that improved efficiency is achieved with these methods when the goal is to estimate associations of exposure with trajectories and patterns of change over time. Here we comment on application of some of these generalized case-control methods to causal inference.
Collapse
Affiliation(s)
- W Dana Flanders
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA 30322.,Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA 30322
| |
Collapse
|
13
|
Li D, Kang H, Lee S, Won S. Progressive effects of single-nucleotide polymorphisms on 16 phenotypic traits based on longitudinal data. Genes Genomics 2020; 42:393-403. [PMID: 31902109 PMCID: PMC7113194 DOI: 10.1007/s13258-019-00902-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 12/02/2019] [Indexed: 11/26/2022]
Abstract
Background There are many research studies have estimated the heritability of phenotypic traits, but few have considered longitudinal changes in several phenotypic traits together. Objective To evaluate the progressive effect of single nucleotide polymorphisms (SNPs) on prominent health-related phenotypic traits by determining SNP-based heritability (\documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$$h_{snp}^{2}$$\end{document}hsnp2) using longitudinal data. Methods Sixteen phenotypic traits associated with major health indices were observed biennially for 6843 individuals with 10-year follow-up in a Korean community-based cohort. Average SNP heritability and longitudinal changes in the total period were estimated using a two-stage model. Average and periodic differences for each subject were considered responses to estimate SNP heritability. Furthermore, a genome-wide association study (GWAS) was performed for significant SNPs. Results Each SNP heritability for the phenotypic mean of all sixteen traits through 6 periods (baseline and five follow-ups) were significant. Gradually, the forced vital capacity in one second (FEV1) reflected the only significant SNP heritability among longitudinal changes at a false discovery rate (FDR)-adjusted 0.05 significance level (\documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$$h_{snp}^{2} = 0.171$$\end{document}hsnp2=0.171, FDR = 0.0012). On estimating chromosomal heritability, chromosome 2 displayed the highest heritability upon periodic changes in FEV1. SNPs including rs2272402 and rs7209788 displayed a genome-wide significant association with longitudinal changes in FEV1 (P = 1.22 × 10−8 for rs2272402 and P = 3.36 × 10−7 for rs7209788). De novo variants including rs4922117 (near LPL, P = 2.13 × 10−15) of log-transformed high-density lipoprotein (HDL) ratios and rs2335418 (near HMGCR, P = 3.2 \documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$$\times$$\end{document}× 10−9) of low-density lipoprotein were detected on GWAS. Conclusion Significant genetic effects on longitudinal changes in FEV1 among the middle-aged general population and chromosome 2 account for most of the genetic variance. Electronic supplementary material The online version of this article (10.1007/s13258-019-00902-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Donghe Li
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Hahn Kang
- Biology Department, Morrissey College of Arts and Sciences, Boston College, Boston, MA, USA
| | - Sanghun Lee
- Department of Medical Consilience, Graduate School, Dankook University, Yongin, Republic of Korea.
| | - Sungho Won
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea.
- Institute of Health and Environment, Seoul National University, Seoul, Republic of Korea.
- Department of Public Health Science, Graduate School of Public Health, Seoul National University, 1 Kwanak-ro Kwanak-gu, Seoul, 151-742, Republic of Korea.
| |
Collapse
|
14
|
Obeidat M, Faiz A, Li X, van den Berge M, Hansel NN, Joubert P, Hao K, Brandsma CA, Rafaels N, Mathias R, Ruczinski I, Beaty TH, Barnes KC, Man SFP, Paré PD, Sin DD. The pharmacogenomics of inhaled corticosteroids and lung function decline in COPD. Eur Respir J 2019; 54:13993003.00521-2019. [PMID: 31537701 DOI: 10.1183/13993003.00521-2019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 08/22/2019] [Indexed: 11/05/2022]
Abstract
Inhaled corticosteroids (ICS) are widely prescribed for patients with chronic obstructive pulmonary disease (COPD), yet have variable outcomes and adverse reactions, which may be genetically determined. The primary aim of the study was to identify the genetic determinants for forced expiratory volume in 1 s (FEV1) changes related to ICS therapy.In the Lung Health Study (LHS)-2, 1116 COPD patients were randomised to the ICS triamcinolone acetonide (n=559) or placebo (n=557) with spirometry performed every 6 months for 3 years. We performed a pharmacogenomic genome-wide association study for the genotype-by-ICS treatment effect on 3 years of FEV1 changes (estimated as slope) in 802 genotyped LHS-2 participants. Replication was performed in 199 COPD patients randomised to the ICS, fluticasone or placebo.A total of five loci showed genotype-by-ICS interaction at p<5×10-6; of these, single nucleotide polymorphism (SNP) rs111720447 on chromosome 7 was replicated (discovery p=4.8×10-6, replication p=5.9×10-5) with the same direction of interaction effect. ENCODE (Encyclopedia of DNA Elements) data revealed that in glucocorticoid-treated (dexamethasone) A549 alveolar cell line, glucocorticoid receptor binding sites were located near SNP rs111720447. In stratified analyses of LHS-2, genotype at SNP rs111720447 was significantly associated with rate of FEV1 decline in patients taking ICS (C allele β 56.36 mL·year-1, 95% CI 29.96-82.76 mL·year-1) and in patients who were assigned to placebo, although the relationship was weaker and in the opposite direction to that in the ICS group (C allele β -27.57 mL·year-1, 95% CI -53.27- -1.87 mL·year-1).The study uncovered genetic factors associated with FEV1 changes related to ICS in COPD patients, which may provide new insight on the potential biology of steroid responsiveness in COPD.
Collapse
Affiliation(s)
- Ma'en Obeidat
- The University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital Vancouver, BC, Canada
| | - Alen Faiz
- University of Groningen, University Medical Center Groningen, Dept of Pulmonology, GRIAC research institute, Groningen, The Netherlands
| | - Xuan Li
- The University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital Vancouver, BC, Canada
| | - Maarten van den Berge
- University of Groningen, University Medical Center Groningen, Dept of Pulmonology, GRIAC research institute, Groningen, The Netherlands
| | - Nadia N Hansel
- Pulmonary and Critical Care Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Philippe Joubert
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec, QC, Canada
| | - Ke Hao
- Dept of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Corry-Anke Brandsma
- University of Groningen, University Medical Center Groningen, Dept of Pulmonology, GRIAC research institute, Groningen, The Netherlands
| | - Nicholas Rafaels
- Division of Biomedical Informatics and Personalized Medicine, Dept of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Rasika Mathias
- Division of Genetic Epidemiology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Ingo Ruczinski
- Dept of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Terri H Beaty
- Dept of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Kathleen C Barnes
- Division of Biomedical Informatics and Personalized Medicine, Dept of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - S F Paul Man
- The University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital Vancouver, BC, Canada
| | - Peter D Paré
- The University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital Vancouver, BC, Canada
| | - Don D Sin
- The University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital Vancouver, BC, Canada
| |
Collapse
|
15
|
Ranjan A, Singh A, Walia GK, Sachdeva MP, Gupta V. Genetic underpinnings of lung function and COPD. J Genet 2019; 98:76. [PMID: 31544798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Spirometry based measurement of lung function is a global initiative for chronic obstructive lung disease (GOLD) standard to diagnose chronic obstructive pulmonary disease (COPD), one of the leading causes of mortality worldwide. The environmental and behavioural risk factors for COPD includes tobacco smoking, air pollutants and biomass fuel exposure, which can induce one or more abnormal lung function patterns. While smoking remains the primary risk factor, only 15-20% smokers develop COPD, indicating that the genetic factors are also likely to play a role. According to the study of Global Burden of Disease 2015, ∼174 million people across the world have COPD. From a comprehensive literature search conducted using the 'PubMed' and 'GWAS Catalogue' databases, and reviewing the literature available, only a limited number of studies were identified which had attempted to investigate the genetics of COPD and lung volumes, implying a huge research gap. With the advent of genomewide association studies several genetic variants linked to lung function and COPD, like HHIP, HTR4, ADAM19 and GSTCD etc., have been found and validated in different population groups, suggesting their potential role in determining lung volume and risk for COPD. This article aims at reviewing the present knowledge of the genetics of lung function and COPD.
Collapse
Affiliation(s)
- Astha Ranjan
- Department of Anthropology, University of Delhi, Delhi 110 007, India.
| | | | | | | | | |
Collapse
|
16
|
Ranjan A, Singh A, Walia GK, Sachdeva MP, Gupta V. Genetic underpinnings of lung function and COPD. J Genet 2019. [DOI: 10.1007/s12041-019-1119-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
17
|
Liu J, Zhao W, Ammous F, Turner ST, Mosley TH, Zhou X, Smith JA. Longitudinal analysis of epigenome-wide DNA methylation reveals novel smoking-related loci in African Americans. Epigenetics 2019; 14:171-184. [PMID: 30764717 PMCID: PMC6557606 DOI: 10.1080/15592294.2019.1581589] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 01/26/2019] [Accepted: 02/03/2019] [Indexed: 10/27/2022] Open
Abstract
Changes in DNA methylation may be a potential mechanism that mediates the effects of smoking on physiological function and subsequent disease risk. Given the dynamic nature of the epigenome, longitudinal studies are indispensable for investigating smoking-induced methylation changes over time. Using blood samples collected approximately five years apart in 380 African Americans (mean age 60.7 years) from the Genetic Epidemiology Network of Arteriopathy (GENOA) study, we measured DNA methylation levels using Illumina HumanMethylation BeadChips. We evaluated the association between Phase 1 smoking status and rate of methylation change, using generalized estimating equation models. Among the 6958 CpG sites examined, smoking status was associated with methylation change for 22 CpGs (false discovery rate q < 0.1), with the majority (91%) becoming less methylated over time. Methylation change was greater in ever smokers than never smokers, and the absolute differences in rates of change ranged from 0.18 to 0.77 per decade in M value, equivalent to a β value change of 0.013 to 0.047 per decade. Significant enrichment was observed for CpG islands, enhancers, and DNAse hypersensitivity sites (p < 0.05). Although biological pathway analyses were not significant, most of the 22 CpGs were within genes known to be associated with cardiovascular disease, cancers, and aging. In conclusion, we identified epigenetic signatures for cigarette smoking that may have been missed in cross-sectional analyses, providing insight into the epigenetic effect of smoking and highlighting the importance of longitudinal analysis in understanding the dynamic human epigenome.
Collapse
Affiliation(s)
- Jiaxuan Liu
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Farah Ammous
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Stephen T. Turner
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN, USA
| | - Thomas H. Mosley
- Memory Impairment and Neurodegenerative Dementia (MIND) Center, University of Mississippi Medical Center, Jackson, MS, USA
| | - Xiang Zhou
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| |
Collapse
|
18
|
Obeidat M, Zhou G, Li X, Hansel NN, Rafaels N, Mathias R, Ruczinski I, Beaty TH, Barnes KC, Paré PD, Sin DD. The genetics of smoking in individuals with chronic obstructive pulmonary disease. Respir Res 2018; 19:59. [PMID: 29631575 PMCID: PMC5892035 DOI: 10.1186/s12931-018-0762-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 03/27/2018] [Indexed: 11/10/2022] Open
Abstract
Background Smoking is the principal modifiable environmental risk factor for chronic obstructive pulmonary disease (COPD) which affects 300 million people and is the 3rd leading cause of death worldwide. Most of the genetic studies of smoking have relied on self-reported smoking status which is vulnerable to reporting and recall bias. Using data from the Lung Health Study (LHS), we sought to identify genetic variants associated with quantitative smoking and cessation in individuals with mild to moderate COPD. Methods The LHS is a longitudinal multicenter study of mild-to-moderate COPD subjects who were all smokers at recruitment. We performed genome-wide association studies (GWASs) for salivary cotinine (n = 4024), exhaled carbon monoxide (eCO) (n = 2854), cigarettes per day (CPD) (n = 2706) and smoking cessation at year 5 follow-up (n = 717 quitters and 2175 smokers). The GWAS analyses were adjusted for age, gender, and genetic principal components. Results For cotinine levels, SNPs near UGT2B10 gene achieved genome-wide significance (i.e. P < 5 × 10− 8) with top SNP rs10023464, P = 1.27 × 10− 11. For eCO levels, one significant SNP was identified which mapped to the CHRNA3 gene (rs12914385, P = 2.38 × 10− 8). A borderline region mapping to KCNMA1 gene was associated with smoking cessation (rs207675, P = 5.95 × 10− 8). Of the identified loci, only the CHRNA3/5 locus showed significant associations with lung function but only in heavy smokers. No regions met genome-wide significance for CPD. Conclusion The study demonstrates that using objective measures of smoking such as eCO and/or salivary cotinine can more precisely capture the genetic contribution to multiple aspects of smoking behaviour. The KCNMA1 gene association with smoking cessation may represent a potential therapeutic target and warrants further studies. Trial registration The Lung Health Study ClinicalTrials.gov Identifier: NCT00000568. Date of registration: October 28, 1999. Electronic supplementary material The online version of this article (10.1186/s12931-018-0762-7) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ma'en Obeidat
- The University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada.
| | - Guohai Zhou
- The University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada
| | - Xuan Li
- The University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, Canada
| | - Nadia N Hansel
- Pulmonary and Critical Care Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Nicholas Rafaels
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO, USA
| | - Rasika Mathias
- Division of Genetic Epidemiology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Terri H Beaty
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Kathleen C Barnes
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO, USA
| | - Peter D Paré
- The 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
| | - Don D Sin
- The 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
| |
Collapse
|
19
|
Obeidat M, Li X, Burgess S, Zhou G, Fishbane N, Hansel NN, Bossé Y, Joubert P, Hao K, Nickle DC, van den Berge M, Timens W, Cho MH, Hobbs BD, de Jong K, Boezen M, Hung RJ, Rafaels N, Mathias R, Ruczinski I, Beaty TH, Barnes KC, Paré PD, Sin DD. Surfactant protein D is a causal risk factor for COPD: results of Mendelian randomisation. Eur Respir J 2017; 50:50/5/1700657. [PMID: 29191953 DOI: 10.1183/13993003.00657-2017] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 08/22/2017] [Indexed: 01/06/2023]
Abstract
Surfactant protein D (SP-D) is produced primarily in the lung and is involved in regulating pulmonary surfactants, lipid homeostasis and innate immunity. Circulating SP-D levels in blood are associated with chronic obstructive pulmonary disease (COPD), although causality remains elusive.In 4061 subjects with COPD, we identified genetic variants associated with serum SP-D levels. We then determined whether these variants affected lung tissue gene expression in 1037 individuals. A Mendelian randomisation framework was then applied, whereby serum SP-D-associated variants were tested for association with COPD risk in 11 157 cases and 36 699 controls and with 11 years decline of lung function in the 4061 individuals.Three regions on chromosomes 6 (human leukocyte antigen region), 10 (SFTPD gene) and 16 (ATP2C2 gene) were associated with serum SP-D levels at genome-wide significance. In Mendelian randomisation analyses, variants associated with increased serum SP-D levels decreased the risk of COPD (estimate -0.19, p=6.46×10-03) and slowed the lung function decline (estimate=0.0038, p=7.68×10-3).Leveraging genetic variation effect on protein, lung gene expression and disease phenotypes provided novel insights into SP-D biology and established a causal link between increased SP-D levels and protection against COPD risk and progression. SP-D represents a very promising biomarker and therapeutic target for COPD.
Collapse
Affiliation(s)
- Ma'en Obeidat
- The University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital Vancouver, Vancouver, BC, Canada
| | - Xuan Li
- The University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital Vancouver, Vancouver, BC, Canada
| | - Stephen Burgess
- Dept of Public Health and Primary Care, University of Cambridge, Cambridge, UK.,MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Guohai Zhou
- The University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital Vancouver, Vancouver, BC, Canada
| | - Nick Fishbane
- The University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital Vancouver, Vancouver, BC, Canada
| | - Nadia N Hansel
- Pulmonary and Critical Care Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Yohan Bossé
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec, QC, Canada.,Dept of Molecular Medicine, Laval University, Québec, QC, Canada
| | - Philippe Joubert
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec, QC, Canada
| | - Ke Hao
- Dept of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Maarten van den Berge
- University of Groningen, University Medical Center Groningen, Dept of Pulmonology, GRIAC Research Institute, Groningen, The Netherlands
| | - Wim Timens
- University of Groningen, University Medical Center Groningen, Dept of Pathology and Medical Biology, GRIAC Research Institute, 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
| | - 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, Dept of Epidemiology, GRIAC Research Institute, Groningen, The Netherlands
| | - Marike Boezen
- University of Groningen, University Medical Center Groningen, Dept of Epidemiology, GRIAC Research Institute, Groningen, The Netherlands
| | - Rayjean J Hung
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
| | - Nicholas Rafaels
- Division of Biomedical Informatics and Personalized Medicine, Dept of Medicine, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO, USA
| | - Rasika Mathias
- Division of Genetic Epidemiology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Ingo Ruczinski
- Dept of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Terri H Beaty
- Dept of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Kathleen C Barnes
- Division of Biomedical Informatics and Personalized Medicine, Dept of Medicine, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO, USA
| | - Peter D Paré
- The University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital Vancouver, Vancouver, BC, Canada
| | - Don D Sin
- The University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital Vancouver, Vancouver, BC, Canada
| | | |
Collapse
|
20
|
John C, Soler Artigas M, Hui J, Nielsen SF, Rafaels N, Paré PD, Hansel NN, Shrine N, Kilty I, Malarstig A, Jelinsky SA, Vedel-Krogh S, Barnes K, Hall IP, Beilby J, Musk AW, Nordestgaard BG, James A, Wain LV, Tobin MD. Genetic variants affecting cross-sectional lung function in adults show little or no effect on longitudinal lung function decline. Thorax 2017; 72:400-408. [PMID: 28174340 PMCID: PMC5520280 DOI: 10.1136/thoraxjnl-2016-208448] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 11/25/2016] [Indexed: 11/07/2022]
Abstract
BACKGROUND Genome-wide association studies have identified numerous genetic regions that influence cross-sectional lung function. Longitudinal decline in lung function also includes a heritable component but the genetic determinants have yet to be defined. OBJECTIVES We aimed to determine whether regions associated with cross-sectional lung function were also associated with longitudinal decline and to seek novel variants which influence decline. METHODS We analysed genome-wide data from 4167 individuals from the Busselton Health Study cohort, who had undergone spirometry (12 695 observations across eight time points). A mixed model was fitted and weighted risk scores were calculated for the joint effect of 26 known regions on baseline and longitudinal changes in FEV1 and FEV1/FVC. Potential additional regions of interest were identified and followed up in two independent cohorts. RESULTS The 26 regions previously associated with cross-sectional lung function jointly showed a strong effect on baseline lung function (p=4.44×10-16 for FEV1/FVC) but no effect on longitudinal decline (p=0.160 for FEV1/FVC). This was replicated in an independent cohort. 39 additional regions of interest (48 variants) were identified; these associations were not replicated in two further cohorts. CONCLUSIONS Previously identified genetic variants jointly have a strong effect on cross-sectional lung function in adults but little or no effect on the rate of decline of lung function. It is possible that they influence COPD risk through lung development. Although no genetic variants have yet been associated with lung function decline at stringent genome-wide significance, longitudinal change in lung function is heritable suggesting that there is scope for future discoveries.
Collapse
Affiliation(s)
- Catherine John
- 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
| | - Jennie Hui
- School of Pathology and Laboratory Medicine, The University of Western Australia, Australia,PathWest, Department of Health, Government of Western Australia, Perth, WA, Australia,Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Western Australia, Australia,School of Population Health, The University of Western Australia, Australia
| | - Sune Fallgaard Nielsen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Denmark
| | - Nicholas Rafaels
- Center for Personalized Medicine and Biomedical Informatics, School of Medicine, University of Colorado, Anschutz Medical Campus
| | - Peter D Paré
- University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, British Columbia, Canada
| | - Nadia N Hansel
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Nick Shrine
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK
| | - Iain Kilty
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts, USA
| | | | - Scott A Jelinsky
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts, USA
| | - Signe Vedel-Krogh
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Denmark
| | - Kathleen Barnes
- Center for Personalized Medicine and Biomedical Informatics, School of Medicine, University of Colorado, Anschutz Medical Campus
| | - Ian P Hall
- Division of Respiratory Medicine, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - John Beilby
- School of Pathology and Laboratory Medicine, The University of Western Australia, Australia,PathWest, Department of Health, Government of Western Australia, Perth, WA, Australia,Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Western Australia, Australia
| | - Arthur W Musk
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Western Australia, Australia,School of Population Health, The University of Western Australia, Australia,Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia,School of Medicine and Pharmacology, The University of Western Australia, Australia
| | - Børge G Nordestgaard
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Denmark
| | - Alan James
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Western Australia, Australia,School of Medicine and Pharmacology, The University of Western Australia, Australia,Department of Pulmonary Physiology and Sleep Medicine/West Australian Sleep Disorders Research Institute, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
| | - Louise V Wain
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK,National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - 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
| |
Collapse
|
21
|
Busch R, Cho MH, Silverman EK. Progress in disease progression genetics: dissecting the genetic origins of lung function decline in COPD. Thorax 2017; 72:389-390. [PMID: 28292852 DOI: 10.1136/thoraxjnl-2016-209666] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Robert Busch
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
22
|
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]
|
23
|
Gao L, Emond MJ, Louie T, Cheadle C, Berger AE, Rafaels N, Vergara C, Kim Y, Taub MA, Ruczinski I, Mathai SC, Rich SS, Nickerson DA, Hummers LK, Bamshad MJ, Hassoun PM, Mathias RA, Barnes KC. Identification of Rare Variants in ATP8B4 as a Risk Factor for Systemic Sclerosis by Whole-Exome Sequencing. Arthritis Rheumatol 2016; 68:191-200. [PMID: 26473621 DOI: 10.1002/art.39449] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 09/24/2015] [Indexed: 01/02/2023]
Abstract
OBJECTIVE To determine the contribution of rare variants as genetic modifiers of the expressivity, penetrance, and severity of systemic sclerosis (SSc). METHODS We performed whole-exome sequencing of 78 European American patients with SSc, including 35 patients without pulmonary arterial hypertension (PAH) and 43 patients with PAH. Association testing of case-control probability for rare variants was performed using the unified sequence kernel association test with optimal kernel weighting and small sample adjustment by comparing all SSc patients with a reference population of 3,179 controls from the Exome Sequencing Project 5,500 exome data set. Replication genotyping was performed in an independent sample of 3,263 patients (415 patients with SSc and 2,848 controls). We conducted expression profiling of messenger RNA from 61 SSc patients (19 without PAH and 42 with PAH) and 41 corresponding controls. RESULTS The ATP8B4 gene was associated with a significant increase in the risk of SSc (P = 2.77 × 10(-7)). Among the 64 ATP8B4 variants tested, a single missense variant, c.1308C>G (F436L, rs55687265), provided the most compelling evidence of association (P = 9.35 × 10(-10), odds ratio [OR] 6.11), which was confirmed in the replication cohort (P = 0.012, OR 1.86) and meta-analysis (P = 1.92 × 10(-7), OR 2.5). Genes involved in E3 ubiquitin-protein ligase complex (ASB10) and cyclic nucleotide gated channelopathies (CNGB3) as well as HLA-DRB5 and HSPB2 (heat-shock protein 27) provided additional evidence of association (P < 10(-5)). Differential ATP8B4 expression was observed among the SSc patients compared to the controls (P = 0.0005). CONCLUSION ATP8B4 may represent a putative genetic risk factor for SSc and pulmonary vascular complications.
Collapse
Affiliation(s)
- Li Gao
- Johns Hopkins University, Baltimore, Maryland
| | | | | | | | | | | | | | - Yoonhee Kim
- National Human Genome Research Institute, NIH, Baltimore, Maryland
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Translating Lung Function Genome-Wide Association Study (GWAS) Findings. ADVANCES IN GENETICS 2016; 93:57-145. [DOI: 10.1016/bs.adgen.2015.12.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
25
|
Abstract
RATIONALE Genome-wide association studies (GWAS) of chronic obstructive pulmonary disease (COPD) have identified disease-susceptibility loci, mostly in subjects of European descent. OBJECTIVES We hypothesized that by studying Hispanic populations we would be able to identify unique loci that contribute to COPD pathogenesis in Hispanics but remain undetected in GWAS of non-Hispanic populations. METHODS We conducted a metaanalysis of two GWAS of COPD in independent cohorts of Hispanics in Costa Rica and the United States (Multi-Ethnic Study of Atherosclerosis [MESA]). We performed a replication study of the top single-nucleotide polymorphisms in an independent Hispanic cohort in New Mexico (the Lovelace Smokers Cohort). We also attempted to replicate prior findings from genome-wide studies in non-Hispanic populations in Hispanic cohorts. MEASUREMENTS AND MAIN RESULTS We found no genome-wide significant association with COPD in our metaanalysis of Costa Rica and MESA. After combining the top results from this metaanalysis with those from our replication study in the Lovelace Smokers Cohort, we identified two single-nucleotide polymorphisms approaching genome-wide significance for an association with COPD. The first (rs858249, combined P value = 6.1 × 10(-8)) is near the genes KLHL7 and NUPL2 on chromosome 7. The second (rs286499, combined P value = 8.4 × 10(-8)) is located in an intron of DLG2. The two most significant single-nucleotide polymorphisms in FAM13A from a previous genome-wide study in non-Hispanics were associated with COPD in Hispanics. CONCLUSIONS We have identified two novel loci (in or near the genes KLHL7/NUPL2 and DLG2) that may play a role in COPD pathogenesis in Hispanic populations.
Collapse
|
26
|
Probert K, Miller S, Kheirallah AK, Hall IP. Developmental genetics of the COPD lung. ACTA ACUST UNITED AC 2015. [DOI: 10.1186/s40749-015-0014-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
27
|
Hansel NN, Paré PD, Rafaels N, Sin DD, Sandford A, Daley D, Vergara C, Huang L, Elliott WM, Pascoe CD, Arsenault BA, Postma DS, Boezen HM, Bossé Y, van den Berge M, Hiemstra PS, Cho MH, Litonjua AA, Sparrow D, Ober C, Wise RA, Connett J, Neptune ER, Beaty TH, Ruczinski I, Mathias RA, Barnes KC. Genome-Wide Association Study Identification of Novel Loci Associated with Airway Responsiveness in Chronic Obstructive Pulmonary Disease. Am J Respir Cell Mol Biol 2015; 53:226-34. [PMID: 25514360 DOI: 10.1165/rcmb.2014-0198oc] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Increased airway responsiveness is linked to lung function decline and mortality in subjects with chronic obstructive pulmonary disease (COPD); however, the genetic contribution to airway responsiveness remains largely unknown. A genome-wide association study (GWAS) was performed using the Illumina (San Diego, CA) Human660W-Quad BeadChip on European Americans with COPD from the Lung Health Study. Linear regression models with correlated meta-analyses, including data from baseline (n = 2,814) and Year 5 (n = 2,657), were used to test for common genetic variants associated with airway responsiveness. Genotypic imputation was performed using reference 1000 Genomes Project data. Expression quantitative trait loci (eQTL) analyses in lung tissues were assessed for the top 10 markers identified, and immunohistochemistry assays assessed protein staining for SGCD and MYH15. Four genes were identified within the top 10 associations with airway responsiveness. Markers on chromosome 9p21.2 flanked by LINGO2 met a predetermined threshold of genome-wide significance (P < 9.57 × 10(-8)). Markers on chromosomes 3q13.1 (flanked by MYH15), 5q33 (SGCD), and 6q21 (PDSS2) yielded suggestive evidence of association (9.57 × 10(-8) < P ≤ 4.6 × 10(-6)). Gene expression studies in lung tissue showed single nucleotide polymorphisms on chromosomes 5 and 3 to act as eQTL for SGCD (P = 2.57 × 10(-9)) and MYH15 (P = 1.62 × 10(-6)), respectively. Immunohistochemistry confirmed localization of SGCD protein to airway smooth muscle and vessels and MYH15 to airway epithelium, vascular endothelium, and inflammatory cells. We identified novel loci associated with airway responsiveness in a GWAS among smokers with COPD. Risk alleles on chromosomes 5 and 3 acted as eQTLs for SGCD and MYH15 messenger RNA, and these proteins were expressed in lung cells relevant to the development of airway responsiveness.
Collapse
Affiliation(s)
- Nadia N Hansel
- 1 Department of Medicine, School of Medicine; and.,Departments of 2 Environmental Health Sciences
| | - Peter D Paré
- 3 Department of Pathology, Centre for Heart Lung Innovation, St. Paul's Hospital, Division of Respirology, University of British Columbia, Vancouver, British Columbia
| | | | - Don D Sin
- 3 Department of Pathology, Centre for Heart Lung Innovation, St. Paul's Hospital, Division of Respirology, University of British Columbia, Vancouver, British Columbia
| | - Andrew Sandford
- 3 Department of Pathology, Centre for Heart Lung Innovation, St. Paul's Hospital, Division of Respirology, University of British Columbia, Vancouver, British Columbia
| | - Denise Daley
- 3 Department of Pathology, Centre for Heart Lung Innovation, St. Paul's Hospital, Division of Respirology, University of British Columbia, Vancouver, British Columbia
| | | | - Lili Huang
- 1 Department of Medicine, School of Medicine; and
| | - W Mark Elliott
- 3 Department of Pathology, Centre for Heart Lung Innovation, St. Paul's Hospital, Division of Respirology, University of British Columbia, Vancouver, British Columbia
| | - Chris D Pascoe
- 3 Department of Pathology, Centre for Heart Lung Innovation, St. Paul's Hospital, Division of Respirology, University of British Columbia, Vancouver, British Columbia
| | - Bryna A Arsenault
- 3 Department of Pathology, Centre for Heart Lung Innovation, St. Paul's Hospital, Division of Respirology, University of British Columbia, Vancouver, British Columbia
| | - Dirkje S Postma
- Departments of 4 Pulmonary Diseases and.,5 Groningen Research Institute for Asthma and COPD Research Institute, University Medical Center Groningen, Groningen; and
| | - H Marike Boezen
- 6 Epidemiology, and.,5 Groningen Research Institute for Asthma and COPD Research Institute, University Medical Center Groningen, Groningen; and
| | - Yohan Bossé
- 7 Department of Molecular Medicine, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec City, Québec, Canada
| | - Maarten van den Berge
- Departments of 4 Pulmonary Diseases and.,5 Groningen Research Institute for Asthma and COPD Research Institute, University Medical Center Groningen, Groningen; and
| | - Pieter S Hiemstra
- 8 Department of Pulmonology, Leiden University Medical Center, Leiden, the Netherlands
| | - Michael H Cho
- 9 Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Augusto A Litonjua
- 9 Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - David Sparrow
- 10 VA Normative Aging Study and Boston University School of Medicine, Boston, Massachusetts
| | - Carole Ober
- 11 Department of Human Genetics, University of Chicago, Chicago, Illinois
| | | | - John Connett
- 12 Division of Biostatistics, School of Public Health, University of Minnesota, St. Paul, Minnesota
| | | | | | - Ingo Ruczinski
- 14 Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | | | - Kathleen C Barnes
- 1 Department of Medicine, School of Medicine; and.,13 Epidemiology, and
| | | |
Collapse
|
28
|
Family-Based Association Study of Pulmonary Function in a Population in Northeast Asia. PLoS One 2015; 10:e0139716. [PMID: 26430897 PMCID: PMC4592257 DOI: 10.1371/journal.pone.0139716] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Accepted: 09/15/2015] [Indexed: 12/22/2022] Open
Abstract
The spirometric measurement of pulmonary function by measuring the forced expiratory volume in one second (FEV1) is a heritable trait that reflects the physiological condition of the lung and airways. Genome-wide linkage and association studies have identified a number of genes and genetic loci associated with pulmonary function. However, limited numbers of studies have been reported for Asian populations. In this study, we aimed to investigate genetic evidence of pulmonary function in a population in northeast Asia. We conducted a family-based association test with 706 GENDISCAN study participants from 72 Mongolian families to determine candidate genetic determinants of pulmonary function. For the replication, we chose seven candidate single nucleotide polymorphisms (SNPs) from the 5 loci, and tested 1062 SNPs for association with FEV1 from 2,729 subjects of the Korea Healthy Twin study. We identified TMEM132C as a potential candidate gene at 12q24.3, which is a previously reported locus of asthma and spirometric indices. We also found two adjacent candidate genes (UNC93A and TTLL2) in the 6q27 region, which has been previously identified as a pulmonary function locus in the Framingham cohort study. Our findings suggest that novel candidate genes (TMEM132C, UNC93A and TTLL2) in two different regions are associated with pulmonary function in a population in northeast Asia.
Collapse
|
29
|
Rooney C, Sethi T. Biomarkers for precision medicine in airways disease. Ann N Y Acad Sci 2015; 1346:18-32. [PMID: 26099690 DOI: 10.1111/nyas.12809] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 05/12/2015] [Accepted: 05/13/2015] [Indexed: 12/22/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is a complex clinical entity. In contrast to previously limited diagnostic definitions, it is now apparent that COPD is a clinically and biologically heterogeneous disease process, overlapping with other airways diseases like chronic asthma. As such, symptomatic response to current standard treatment practices is variable. New clinical guidelines have been altered to reflect this, with the inclusion of symptoms and risk factors in diagnostic and management algorithms. However, as our understanding of COPD pathophysiology deepens, many novel physiological, cellular, proteomic, and genetic markers have been identified. Several have been observed to be independently predictive of distinct clinical disease patterns, which at present are not illustrated by conventional measurements of lung impairment. The potential use of these predictive biomarkers to stratify this diverse patient population could transform the care we offer. We should aim for precision medicine to optimize diagnosis and treatment choices and to monitor and improve clinical outcomes in this disease.
Collapse
Affiliation(s)
| | - Tariq Sethi
- Asthma, Allergy and Lung Biology, King's College London, London, United Kingdom
| |
Collapse
|
30
|
Vestbo J, Lange P. Natural history of COPD: Focusing on change in FEV1. Respirology 2015; 21:34-43. [PMID: 26176980 DOI: 10.1111/resp.12589] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 05/03/2015] [Accepted: 05/06/2015] [Indexed: 11/28/2022]
Abstract
The natural history of chronic obstructive pulmonary disease (COPD) is usually described with a focus on change in forced expiratory volume in 1 s (FEV1 ) over time as this allows for exploration of risk factors for an accelerated decline-and thus of developing COPD. From epidemiological studies we have recognized important risk factors such as smoking, exposure to biomass and occupational exposures, but we have also learnt about features such as chronic bronchitis, airway hyper-responsiveness and asthma that seem to accelerate decline in FEV1 independent of exposures. In addition we are gradually beginning to better link early life events to subsequent risk of disease in adulthood. Although more complicated, our current understanding of COPD has come a long way from being a simple image of smoking leading to poor lungs.
Collapse
Affiliation(s)
- Jørgen Vestbo
- Centre for Respiratory Medicine and Allergy, Manchester Academic Health Science Centre, University Hospital South Manchester, NHS Foundation Trust, Manchester, UK
| | - Peter Lange
- Department of Social Medicine, Institute of Public Health, University of Copenhagen, Copenhagen, Denmark.,Department of Respiratory Medicine, Hvidovre University Hospital, Copenhagen, Denmark
| |
Collapse
|
31
|
Imboden M, Kumar A, Curjuric I, Adam M, Thun GA, Haun M, Tsai MY, Pons M, Bettschart R, Turk A, Rochat T, Künzli N, Schindler C, Kronenberg F, Probst-Hensch NM. Modification of the association between PM10 and lung function decline by cadherin 13 polymorphisms in the SAPALDIA cohort: a genome-wide interaction analysis. ENVIRONMENTAL HEALTH PERSPECTIVES 2015; 123:72-9. [PMID: 25127211 PMCID: PMC4286270 DOI: 10.1289/ehp.1307398] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Accepted: 08/13/2014] [Indexed: 05/03/2023]
Abstract
BACKGROUND Both air pollution and genetic variation have been shown to affect lung function. Their interaction has not been studied on a genome-wide scale to date. OBJECTIVES We aimed to identify, in an agnostic fashion, genes that modify the association between long-term air pollution exposure and annual lung function decline in an adult population-based sample. METHODS A two-stage genome-wide interaction study was performed. The discovery (n = 763) and replication (n = 3,896) samples were derived from the multi-center SAPALDIA cohort (Swiss Cohort Study on Air Pollution and Lung Disease in Adults). Annual rate of decline in the forced mid-expiratory flow (FEF25-75%) was the main end point. Multivariate linear regression analyses were used to identify potential multiplicative interactions between genotypes and 11-year cumulative PM10 exposure. RESULTS We identified a cluster of variants intronic to the CDH13 gene as the only locus with genome-wide significant interactions. The strongest interaction was observed for rs2325934 (p = 8.8 × 10(-10)). Replication of the interaction between this CDH13 variant and cumulative PM10 exposure on annual decline in FEF25-75% was successful (p = 0.008). The interaction was not sensitive to adjustment for smoking or body weight. CONCLUSIONS CDH13 is functionally linked to the adipokine adiponectin, an inflammatory regulator. Future studies need to confirm the interaction and assess how the result relates to previously observed interactions between air pollution and obesity on respiratory function.
Collapse
Affiliation(s)
- Medea Imboden
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Early origins of chronic obstructive lung diseases across the life course. Eur J Epidemiol 2014; 29:871-85. [PMID: 25537319 DOI: 10.1007/s10654-014-9981-5] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 12/06/2014] [Indexed: 12/12/2022]
Abstract
Chronic obstructive lung diseases, like asthma and chronic obstructive pulmonary disease, have high prevalences and are a major public health concern. Chronic obstructive lung diseases have at least part of their origins in early life. Exposure to an adverse environment during critical periods in early life might lead to permanent developmental adaptations which results in impaired lung growth with smaller airways and lower lung volume, altered immunological responses and related inflammation, and subsequently to increased risks of chronic obstructive lung diseases throughout the life course. Various pathways leading from early life factors to respiratory health outcomes in later life have been studied, including fetal and early infant growth patterns, preterm birth, maternal obesity, diet and smoking, children's diet, allergen exposure and respiratory tract infections, and genetic susceptibility. Data on potential adverse factors in the embryonic and preconception period and respiratory health outcomes are scarce. Also, the underlying mechanisms how specific adverse exposures in the fetal and early postnatal period lead to chronic obstructive lung diseases in later life are not yet fully understood. Current studies suggest that interactions between early environmental exposures and genetic factors such as changes in DNA-methylation and RNA expression patterns may explain the early development of chronic obstructive lung diseases. New well-designed epidemiological studies are needed to identify specific critical periods and to elucidate the mechanisms underlying the development of chronic obstructive lung disease throughout the life course.
Collapse
|
33
|
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.
Collapse
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.
| |
Collapse
|
34
|
Kanagaratham C, Marino R, Camateros P, Ren J, Houle D, Sladek R, Vidal SM, Radzioch D. Mapping of a chromosome 12 region associated with airway hyperresponsiveness in a recombinant congenic mouse strain and selection of potential candidate genes by expression and sequence variation analyses. PLoS One 2014; 9:e104234. [PMID: 25111050 PMCID: PMC4128649 DOI: 10.1371/journal.pone.0104234] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 07/08/2014] [Indexed: 01/09/2023] Open
Abstract
In a previous study we determined that BcA86 mice, a strain belonging to a panel of AcB/BcA recombinant congenic strains, have an airway responsiveness phenotype resembling mice from the airway hyperresponsive A/J strain. The majority of the BcA86 genome is however from the hyporesponsive C57BL/6J strain. The aim of this study was to identify candidate regions and genes associated with airway hyperresponsiveness (AHR) by quantitative trait locus (QTL) analysis using the BcA86 strain. Airway responsiveness of 205 F2 mice generated from backcrossing BcA86 strain to C57BL/6J strain was measured and used for QTL analysis to identify genomic regions in linkage with AHR. Consomic mice for the QTL containing chromosomes were phenotyped to study the contribution of each chromosome to lung responsiveness. Candidate genes within the QTL were selected based on expression differences in mRNA from whole lungs, and the presence of coding non-synonymous mutations that were predicted to have a functional effect by amino acid substitution prediction tools. One QTL for AHR was identified on Chromosome 12 with its 95% confidence interval ranging from 54.6 to 82.6 Mbp and a maximum LOD score of 5.11 (p = 3.68×10−3). We confirmed that the genotype of mouse Chromosome 12 is an important determinant of lung responsiveness using a Chromosome 12 substitution strain. Mice with an A/J Chromosome 12 on a C57BL/6J background have an AHR phenotype similar to hyperresponsive strains A/J and BcA86. Within the QTL, genes with deleterious coding variants, such as Foxa1, and genes with expression differences, such as Mettl21d and Snapc1, were selected as possible candidates for the AHR phenotype. Overall, through QTL analysis of a recombinant congenic strain, microarray analysis and coding variant analysis we identified Chromosome 12 and three potential candidate genes to be in linkage with airway responsiveness.
Collapse
Affiliation(s)
- Cynthia Kanagaratham
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- * E-mail:
| | - Rafael Marino
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| | - Pierre Camateros
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| | - John Ren
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Daniel Houle
- Research Institute of the McGill University Health Center, Montreal, Quebec, Canada
| | - Robert Sladek
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Silvia M. Vidal
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Danuta Radzioch
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Faculty of Medicine, Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| |
Collapse
|
35
|
Tang W, Kowgier M, Loth DW, Soler Artigas M, Joubert BR, Hodge E, Gharib SA, Smith AV, Ruczinski I, Gudnason V, Mathias RA, Harris TB, Hansel NN, Launer LJ, Barnes KC, Hansen JG, Albrecht E, Aldrich MC, Allerhand M, Barr RG, Brusselle GG, Couper DJ, Curjuric I, Davies G, Deary IJ, Dupuis J, Fall T, Foy M, Franceschini N, Gao W, Gläser S, Gu X, Hancock DB, Heinrich J, Hofman A, Imboden M, Ingelsson E, James A, Karrasch S, Koch B, Kritchevsky SB, Kumar A, Lahousse L, Li G, Lind L, Lindgren C, Liu Y, Lohman K, Lumley T, McArdle WL, Meibohm B, Morris AP, Morrison AC, Musk B, North KE, Palmer LJ, Probst-Hensch NM, Psaty BM, Rivadeneira F, Rotter JI, Schulz H, Smith LJ, Sood A, Starr JM, Strachan DP, Teumer A, Uitterlinden AG, Völzke H, Voorman A, Wain LV, Wells MT, Wilk JB, Williams OD, Heckbert SR, Stricker BH, London SJ, Fornage M, Tobin MD, O′Connor GT, Hall IP, Cassano PA. Large-scale genome-wide association studies and meta-analyses of longitudinal change in adult lung function. PLoS One 2014; 9:e100776. [PMID: 24983941 PMCID: PMC4077649 DOI: 10.1371/journal.pone.0100776] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 04/17/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have identified numerous loci influencing cross-sectional lung function, but less is known about genes influencing longitudinal change in lung function. METHODS We performed GWAS of the rate of change in forced expiratory volume in the first second (FEV1) in 14 longitudinal, population-based cohort studies comprising 27,249 adults of European ancestry using linear mixed effects model and combined cohort-specific results using fixed effect meta-analysis to identify novel genetic loci associated with longitudinal change in lung function. Gene expression analyses were subsequently performed for identified genetic loci. As a secondary aim, we estimated the mean rate of decline in FEV1 by smoking pattern, irrespective of genotypes, across these 14 studies using meta-analysis. RESULTS The overall meta-analysis produced suggestive evidence for association at the novel IL16/STARD5/TMC3 locus on chromosome 15 (P = 5.71 × 10(-7)). In addition, meta-analysis using the five cohorts with ≥3 FEV1 measurements per participant identified the novel ME3 locus on chromosome 11 (P = 2.18 × 10(-8)) at genome-wide significance. Neither locus was associated with FEV1 decline in two additional cohort studies. We confirmed gene expression of IL16, STARD5, and ME3 in multiple lung tissues. Publicly available microarray data confirmed differential expression of all three genes in lung samples from COPD patients compared with controls. Irrespective of genotypes, the combined estimate for FEV1 decline was 26.9, 29.2 and 35.7 mL/year in never, former, and persistent smokers, respectively. CONCLUSIONS In this large-scale GWAS, we identified two novel genetic loci in association with the rate of change in FEV1 that harbor candidate genes with biologically plausible functional links to lung function.
Collapse
Affiliation(s)
- Wenbo Tang
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, United States of America
| | - Matthew Kowgier
- Ontario Institute for Cancer Research and Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Daan W. Loth
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Netherlands Healthcare Inspectorate, The Hague, the Netherlands
| | - María Soler Artigas
- University of Leicester, Genetic Epidemiology Group, Department of Health Sciences, Leicester, United Kingdom
- National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, United Kingdom
| | - Bonnie R. Joubert
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, U.S. Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - Emily Hodge
- Division of Respiratory Medicine, University Hospital of Nottingham, Nottingham, United Kingdom
| | - Sina A. Gharib
- Computational Medicine Core, Center for Lung Biology, Division of Pulmonary & Critical Care Medicine, Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Albert V. Smith
- Icelandic Heart Association, Kopavogur, Iceland
- University of Iceland, Reykjavik, Iceland
| | - Ingo Ruczinski
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- University of Iceland, Reykjavik, Iceland
| | - Rasika A. Mathias
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Tamara B. Harris
- Laboratory of Epidemiology, Demography, and Biometry, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Nadia N. Hansel
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Lenore J. Launer
- Laboratory of Epidemiology, Demography, and Biometry, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kathleen C. Barnes
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Joyanna G. Hansen
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, United States of America
| | - Eva Albrecht
- Institute of Genetic Epidemiology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Melinda C. Aldrich
- Department of Thoracic Surgery and Division of Epidemiology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Michael Allerhand
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
| | - R. Graham Barr
- Division of General Medicine, Pulmonary, Allergy and Critical Care, Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, New York, United States of America
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - 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
- 22 Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | | | - Ivan Curjuric
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Gail Davies
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Medical Genetics Section, University of Edinburgh Molecular Medicine Centre and MRC Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh, United Kingdom
- Department of Psychology, University of Edinburgh, Edinburgh, United Kingdom
| | - Ian J. Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Department of Psychology, University of Edinburgh, Edinburgh, United Kingdom
| | - Josée Dupuis
- Biostatistics Department, Boston University School of Public Health, Boston, Massachusetts, United States of America
- The National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts, United States of America
| | - Tove Fall
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Millennia Foy
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Nora Franceschini
- Gillings School of Global Public Health, Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Wei Gao
- Biostatistics Department, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Sven Gläser
- Department of Internal Medicine B; Pneumology, Cardiology, Intensive Care Medicine; Field of Research: Pneumology and Pneumological Epidemiology, University Medicine Greifswald, Greifswald, Germany
| | - Xiangjun Gu
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Dana B. Hancock
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, U.S. Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
- Behavioral Health Epidemiology Program, Research Triangle Institute, Research Triangle Park, North Carolina, United States of America
| | - Joachim Heinrich
- Institute of Epidemiology I, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany and Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research, Munich, Germany
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Netherlands Consortium for Healthy Aging, Rotterdam, the Netherlands
| | - Medea Imboden
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Erik Ingelsson
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK and Department of Biostatistics, University of Liverpool, Liverpool, United Kingdom
| | - Alan James
- School of Medicine and Pharmacology, University of Western Australia, Perth, Western Australia, Australia
| | - Stefan Karrasch
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Ludwig-Maximilians-Universität, Munich, Germany
- Institute of General Practice, University Hospital Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Institute of Epidemiology I, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Beate Koch
- Department of Internal Medicine B; Pneumology, Cardiology, Intensive Care Medicine; Field of Research: Pneumology and Pneumological Epidemiology, University Medicine Greifswald, Greifswald, Germany
| | - Stephen B. Kritchevsky
- Sticht Center on Aging, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Ashish Kumar
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK and Department of Biostatistics, University of Liverpool, Liverpool, United Kingdom
| | - Lies Lahousse
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Guo Li
- Cardiovascular Health Research Unit, University of Washington, Seattle, Washington, United States of America
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Cecilia Lindgren
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK and Department of Biostatistics, University of Liverpool, Liverpool, United Kingdom
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Yongmei Liu
- Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Kurt Lohman
- Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Thomas Lumley
- Department of Statistics, University of Auckland, Auckland, New Zealand
| | - Wendy L. McArdle
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Bernd Meibohm
- College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Andrew P. Morris
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK and Department of Biostatistics, University of Liverpool, Liverpool, United Kingdom
| | - Alanna C. Morrison
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Bill Musk
- School of Medicine and Pharmacology, University of Western Australia, Perth, Western Australia, Australia
| | - Kari E. North
- Gillings School of Global Public Health, Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Lyle J. Palmer
- Ontario Institute for Cancer Research and Biostatistics Division, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
- Epidemiology and Obstetrics & Gynaecology, University of Toronto, Toronto, Ontario, Canada
- Samuel Lunenfeld Research Institute, Toronto, Ontario, Canada
| | - Nicole M. Probst-Hensch
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, University of Washington, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Group Health Research Institute, Group Health Cooperative, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Fernando Rivadeneira
- Netherlands Consortium for Healthy Aging, Rotterdam, the Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Jerome I. Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Holger Schulz
- Institute of Epidemiology I, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany and Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research, Munich, Germany
| | - Lewis J. Smith
- Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Akshay Sood
- University of New Mexico, Albuquerque, New Mexico, United States of America
| | - John M. Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, United Kingdom
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, Edinburgh, United Kingdom
| | - David P. Strachan
- Division of Population Health Sciences and Education, St George's, University of London, London, United Kingdom
| | - Alexander Teumer
- Department for Genetics and Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - André G. Uitterlinden
- Netherlands Consortium for Healthy Aging, Rotterdam, the Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Henry Völzke
- Institute for Community Medicine, Study of Health In Pomerania (SHIP)/Clinical Epidemiological Research, University Medicine Greifswald, Greifswald, Germany
| | - Arend Voorman
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Louise V. Wain
- University of Leicester, Genetic Epidemiology Group, Department of Health Sciences, Leicester, United Kingdom
- National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, United Kingdom
| | - Martin T. Wells
- Department of Statistical Science, Cornell University, Ithaca, New York, United States of America
| | - Jemma B. Wilk
- The National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts, United States of America
- Division of Aging, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - O. Dale Williams
- Florida International University, Miami, Florida, United States of America
| | - Susan R. Heckbert
- Cardiovascular Health Research Unit, University of Washington, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Group Health Research Institute, Group Health Cooperative, Seattle, Washington, United States of America
| | - Bruno H. Stricker
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Netherlands Healthcare Inspectorate, The Hague, the Netherlands
| | - Stephanie J. London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, U.S. Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - Myriam Fornage
- Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Martin D. Tobin
- University of Leicester, Genetic Epidemiology Group, Department of Health Sciences, Leicester, United Kingdom
- National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, United Kingdom
| | - George T. O′Connor
- The National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts, United States of America
- Section of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Ian P. Hall
- Division of Respiratory Medicine, University Hospital of Nottingham, Nottingham, United Kingdom
| | - Patricia A. Cassano
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, United States of America
- Department of Health Care Policy and Research, Division of Biostatistics and Epidemiology, Weill Cornell Medical College, New York, New York, United States of America
| |
Collapse
|
36
|
Hardin M, Silverman EK. Chronic Obstructive Pulmonary Disease Genetics: A Review of the Past and a Look Into the Future. CHRONIC OBSTRUCTIVE PULMONARY DISEASES-JOURNAL OF THE COPD FOUNDATION 2014; 1:33-46. [PMID: 28848809 DOI: 10.15326/jcopdf.1.1.2014.0120] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) affects over 10 million Americans.1 This complex disorder demonstrates many different presentations in a wide variety of patients, and results from a combination of environmental exposures and genetic risk factors. Smoking alone does not result in COPD: not all smokers develop COPD and lung function decline among smokers is highly variable. There is growing evidence for genetic risk factors for COPD: early familial aggregation and linkage analysis studies strongly suggested genetic contributions to COPD, and recent genome-wide association studies have identified several genomic regions that are clearly related to COPD susceptibility. However, despite recent advances in COPD genetics, much of the heritability of COPD remains unexplained, and functional studies are only beginning to elucidate a role for the genetic associations that have been identified. Despite this, the future is bright for understanding the genetics of COPD. Improvements in COPD phenotyping, collaborations among COPD study cohorts, and novel integrative approaches to identifying genetic markers all promise to unravel much of this missing heritability and ultimately lead to improvements in our understanding of COPD susceptibility and treatment.
Collapse
Affiliation(s)
- Megan Hardin
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Edwin K Silverman
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| |
Collapse
|
37
|
Thun GA, Imboden M, Künzli N, Rochat T, Keidel D, Haun M, Schindler C, Kronenberg F, Probst-Hensch NM. Follow-up on genome-wide main effects: do polymorphisms modify the air pollution effect on lung function decline in adults? ENVIRONMENT INTERNATIONAL 2014; 64:110-115. [PMID: 24388947 DOI: 10.1016/j.envint.2013.12.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 12/06/2013] [Accepted: 12/13/2013] [Indexed: 06/03/2023]
Abstract
Improved air quality has been found associated with attenuated age-related decline in lung function. But whether genetic polymorphisms strongly associated with lung function play a modifying role in this attenuation process has so far not been investigated. We selected ten single nucleotide polymorphisms derived from the largest genome-wide association studies on lung function and examined whether they modified the association between the change in exposure to particulate matter ≤10μm (ΔPM10) and lung function decline. 4310 participants from the SAPALDIA cohort provided valid spirometry measurements, a detailed pulmonary health questionnaire both at baseline and 11years later as well as blood samples for genetic testing. Spatially and temporally resolved air pollution exposures were assigned on an individual level based on participants' residences. Statistically significant interactions of moderate strength with ΔPM10 were detected for rs2284746. Individuals with the CC genotype had a 21ml slower annual decline of the mid expiratory flow per 10μg/m(3) PM10 reduction over an 10-year period, while the benefits of CG and GG carriers were smaller (14 and 7ml per year, respectively; Pinteraction=0.04). The attenuated annual decline in the percentage of the forced expiratory volume in one second relative to the forced vital capacity (FEV1/FVC) was also increased with the presence of each C-allele (Pinteraction=0.009). We observed further suggestive interactions of similar magnitude in never-smokers, but none of the results would remain statistically significant after correction for multiple testing. We could not find strong evidence that lung function benefits from improved air quality are modified by polymorphisms associated with lung function level in large meta-analyzed genome-wide association studies.
Collapse
Affiliation(s)
- Gian Andri Thun
- Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland.
| | - Medea Imboden
- Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland.
| | - Nino Künzli
- Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland.
| | - Thierry Rochat
- Division of Pulmonary Medicine, University Hospital of Geneva, Geneva, Switzerland.
| | - Dirk Keidel
- Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland.
| | - Margot Haun
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria.
| | - Christian Schindler
- Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland.
| | - Florian Kronenberg
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria.
| | - Nicole M Probst-Hensch
- Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland.
| |
Collapse
|
38
|
Ryan DM, Vincent TL, Salit J, Walters MS, Agosto-Perez F, Shaykhiev R, Strulovici-Barel Y, Downey RJ, Buro-Auriemma LJ, Staudt MR, Hackett NR, Mezey JG, Crystal RG. Smoking dysregulates the human airway basal cell transcriptome at COPD risk locus 19q13.2. PLoS One 2014; 9:e88051. [PMID: 24498427 PMCID: PMC3912203 DOI: 10.1371/journal.pone.0088051] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 01/03/2014] [Indexed: 11/19/2022] Open
Abstract
Genome-wide association studies (GWAS) and candidate gene studies have identified a number of risk loci associated with the smoking-related disease COPD, a disorder that originates in the airway epithelium. Since airway basal cell (BC) stem/progenitor cells exhibit the earliest abnormalities associated with smoking (hyperplasia, squamous metaplasia), we hypothesized that smoker BC have a dysregulated transcriptome, enriched, in part, at known GWAS/candidate gene loci. Massive parallel RNA sequencing was used to compare the transcriptome of BC purified from the airway epithelium of healthy nonsmokers (n = 10) and healthy smokers (n = 7). The chromosomal location of the differentially expressed genes was compared to loci identified by GWAS to confer risk for COPD. Smoker BC have 676 genes differentially expressed compared to nonsmoker BC, dominated by smoking up-regulation. Strikingly, 166 (25%) of these genes are located on chromosome 19, with 13 localized to 19q13.2 (p<10−4 compared to chance), including 4 genes (NFKBIB, LTBP4, EGLN2 and TGFB1) associated with risk for COPD. These observations provide the first direct connection between known genetic risks for smoking-related lung disease and airway BC, the population of lung cells that undergo the earliest changes associated with smoking.
Collapse
Affiliation(s)
- Dorothy M. Ryan
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Thomas L. Vincent
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Jacqueline Salit
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Matthew S. Walters
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Francisco Agosto-Perez
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Renat Shaykhiev
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Yael Strulovici-Barel
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Robert J. Downey
- Thoracic Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Lauren J. Buro-Auriemma
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Michelle R. Staudt
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Neil R. Hackett
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Jason G. Mezey
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America
| | - Ronald G. Crystal
- Department of Genetic Medicine, Weill Cornell Medical College, New York, New York, United States of America
- * E-mail:
| |
Collapse
|
39
|
Goh F, Shaw JG, Savarimuthu Francis SM, Vaughan A, Morrison L, Relan V, Marshall HM, Dent AG, O'Hare PE, Hsiao A, Bowman RV, Fong KM, Yang IA. Personalizing and targeting therapy for COPD: the role of molecular and clinical biomarkers. Expert Rev Respir Med 2013; 7:593-605. [PMID: 24160750 DOI: 10.1586/17476348.2013.842468] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is a heterogeneous disease characterized by persistent airflow limitation. It is the third leading cause of death worldwide, and there are currently no curative strategies for this disease. Many factors contribute to COPD susceptibility, progression and exacerbations. These include cigarette smoking, environmental and occupational pollutants, respiratory infections and comorbidities. As the clinical phenotypes of COPD are so variable, it has been difficult to devise an individualized treatment plan for patients with this complex chronic disease. This review will highlight how potential clinical, inflammatory, genomic and epigenomic biomarkers for COPD could be used to personalize treatment, leading to improved disease management and prevention for our patients.
Collapse
Affiliation(s)
- Felicia Goh
- Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, Australia
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Bossé Y. Research Highlights: Highlights from the latest articles in chronic obstructive pulmonary disease genetics. Per Med 2013; 10:123-125. [DOI: 10.2217/pme.13.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Yohan Bossé
- Laval University, Department of Molecular Medicine, Institut universitaire de cardiologie et de pneumologie de Québec, Pavillon Marguerite-d’Youville, Y4190, 2725 Chemin Sainte-Foy, Québec, Canada
| |
Collapse
|