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Boye C, Nirmalan S, Ranjbaran A, Luca F. Genotype × environment interactions in gene regulation and complex traits. Nat Genet 2024; 56:1057-1068. [PMID: 38858456 DOI: 10.1038/s41588-024-01776-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 04/25/2024] [Indexed: 06/12/2024]
Abstract
Genotype × environment interactions (GxE) have long been recognized as a key mechanism underlying human phenotypic variation. Technological developments over the past 15 years have dramatically expanded our appreciation of the role of GxE in both gene regulation and complex traits. The richness and complexity of these datasets also required parallel efforts to develop robust and sensitive statistical and computational approaches. Although our understanding of the genetic architecture of molecular and complex traits has been maturing, a large proportion of complex trait heritability remains unexplained. Furthermore, there are increasing efforts to characterize the effect of environmental exposure on human health. We therefore review GxE in human gene regulation and complex traits, advocating for a comprehensive approach that jointly considers genetic and environmental factors in human health and disease.
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Affiliation(s)
- Carly Boye
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, US
| | - Shreya Nirmalan
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, US
| | - Ali Ranjbaran
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, US
| | - Francesca Luca
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, US.
- Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, US.
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy.
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Seo J, Gaddis NC, Patchen BK, Xu J, Barr RG, O'Connor G, Manichaikul AW, Gharib SA, Dupuis J, North KE, Cassano PA, Hancock DB. Exploiting meta-analysis of genome-wide interaction with serum 25-hydroxyvitamin D to identify novel genetic loci associated with pulmonary function. Am J Clin Nutr 2024; 119:1227-1237. [PMID: 38484975 PMCID: PMC11130669 DOI: 10.1016/j.ajcnut.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 02/12/2024] [Accepted: 03/07/2024] [Indexed: 04/01/2024] Open
Abstract
BACKGROUND Higher 25-hydroxyvitamin D (25(OH)D) concentrations in serum has a positive association with pulmonary function. Investigating genome-wide interactions with 25(OH)D may reveal new biological insights into pulmonary function. OBJECTIVES We aimed to identify novel genetic variants associated with pulmonary function by accounting for 25(OH)D interactions. METHODS We included 211,264 participants from the observational United Kingdom Biobank study with pulmonary function tests (PFTs), genome-wide genotypes, and 25(OH)D concentrations from 4 ancestral backgrounds-European, African, East Asian, and South Asian. Among PFTs, we focused on forced expiratory volume in the first second (FEV1) and forced vital capacity (FVC) because both were previously associated with 25(OH)D. We performed genome-wide association study (GWAS) analyses that accounted for variant×25(OH)D interaction using the joint 2 degree-of-freedom (2df) method, stratified by participants' smoking history and ancestry, and meta-analyzed results. We evaluated interaction effects to determine how variant-PFT associations were modified by 25(OH)D concentrations and conducted pathway enrichment analysis to examine the biological relevance of our findings. RESULTS Our GWAS meta-analyses, accounting for interaction with 25(OH)D, revealed 30 genetic variants significantly associated with FEV1 or FVC (P2df <5.00×10-8) that were not previously reported for PFT-related traits. These novel variant signals were enriched in lung function-relevant pathways, including the p38 MAPK pathway. Among variants with genome-wide-significant 2df results, smoking-stratified meta-analyses identified 5 variants with 25(OH)D interactions that influenced FEV1 in both smoking groups (never smokers P1df interaction<2.65×10-4; ever smokers P1df interaction<1.71×10-5); rs3130553, rs2894186, rs79277477, and rs3130929 associations were only evident in never smokers, and the rs4678408 association was only found in ever smokers. CONCLUSION Genetic variant associations with lung function can be modified by 25(OH)D, and smoking history can further modify variant×25(OH)D interactions. These results expand the known genetic architecture of pulmonary function and add evidence that gene-environment interactions, including with 25(OH)D and smoking, influence lung function.
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Affiliation(s)
- Jungkyun Seo
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, United States
| | - Nathan C Gaddis
- RTI International, Research Triangle Park, NC, United States
| | - Bonnie K Patchen
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, United States
| | - Jiayi Xu
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, United States
| | - R Graham Barr
- Divisions of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Medical Center, New York, NY, United States
| | - George O'Connor
- Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - Ani W Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Sina A Gharib
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, United States; Division of Pulmonary, Critical Care and Sleep Medicine, Computational Medicine Core, Center for Lung Biology, University of Washington, Seattle, WA, United States
| | - Josée Dupuis
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Kari E North
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, United States
| | - Patricia A Cassano
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, United States; Division of Epidemiology, Department of Population Health Sciences, Weill Cornell Medicine, NY, United States
| | - Dana B Hancock
- RTI International, Research Triangle Park, NC, United States.
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Margaritte-Jeannin P, Vernet R, Budu-Aggrey A, Ege M, Madore AM, Linhard C, Mohamdi H, von Mutius E, Granell R, Demenais F, Laprise C, Bouzigon E, Dizier MH. TNS1 and NRXN1 Genes Interacting With Early-Life Smoking Exposure in Asthma-Plus-Eczema Susceptibility. ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2023; 15:779-794. [PMID: 37957795 PMCID: PMC10643854 DOI: 10.4168/aair.2023.15.6.779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 05/15/2023] [Accepted: 06/13/2023] [Indexed: 11/15/2023]
Abstract
PURPOSE Numerous genes have been associated with allergic diseases (asthma, allergic rhinitis, and eczema), but they explain only part of their heritability. This is partly because most previous studies ignored complex mechanisms such as gene-environment (G-E) interactions and complex phenotypes such as co-morbidity. However, it was recently evidenced that the co-morbidity of asthma-plus-eczema appears as a sub-entity depending on specific genetic factors. Besides, evidence also suggest that gene-by-early life environmental tobacco smoke (ETS) exposure interactions play a role in asthma, but were never investigated for asthma-plus-eczema. To identify genetic variants interacting with ETS exposure that influence asthma-plus-eczema susceptibility. METHODS To conduct a genome-wide interaction study (GWIS) of asthma-plus-eczema according to ETS exposure, we applied a 2-stage strategy with a first selection of single nucleotide polymorphisms (SNPs) from genome-wide association meta-analysis to be tested at a second stage by interaction meta-analysis. All meta-analyses were conducted across 4 studies including a total of 5,516 European-ancestry individuals, of whom 1,164 had both asthma and eczema. RESULTS Two SNPs showed significant interactions with ETS exposure. They were located in 2 genes, NRXN1 (2p16) and TNS1 (2q35), never reported associated and/or interacting with ETS exposure for asthma, eczema or more generally for allergic diseases. TNS1 is a promising candidate gene because of its link to lung and skin diseases with possible interactive effect with tobacco smoke exposure. CONCLUSIONS This first GWIS of asthma-plus-eczema with ETS exposure underlines the importance of studying sub-phenotypes such as co-morbidities as well as G-E interactions to detect new susceptibility genes.
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Affiliation(s)
- Patricia Margaritte-Jeannin
- Université Paris Cité, UMRS 1124, INSERM, Genomic Epidemiology and Multifactorial Diseases Group, Paris, France
| | - Raphaël Vernet
- Université Paris Cité, UMRS 1124, INSERM, Genomic Epidemiology and Multifactorial Diseases Group, Paris, France
| | - Ashley Budu-Aggrey
- Medical Research Council (MRC) Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Markus Ege
- Dr von Hauner Children's Hospital, Ludwig Maximilian University; Institute of Asthma and Allergy prevention, Helmholtz Centre Munich; Comprehensive Pneumology Center Munich (CPC-M), German Center for Lung Research, Munich, Germany
| | - Anne-Marie Madore
- Département des sciences fondamentales, Centre intersectoriel en santé durable (CISD), Université du Québec à Chicoutimi, Saguenay, QC, Canada
| | - Christophe Linhard
- Université Paris Cité, UMRS 1124, INSERM, Genomic Epidemiology and Multifactorial Diseases Group, Paris, France
| | - Hamida Mohamdi
- Université Paris Cité, UMRS 1124, INSERM, Genomic Epidemiology and Multifactorial Diseases Group, Paris, France
| | - Erika von Mutius
- Dr von Hauner Children's Hospital, Ludwig Maximilian University; Institute of Asthma and Allergy prevention, Helmholtz Centre Munich; Comprehensive Pneumology Center Munich (CPC-M), German Center for Lung Research, Munich, Germany
| | - Raquell Granell
- Medical Research Council (MRC) Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Florence Demenais
- Université Paris Cité, UMRS 1124, INSERM, Genomic Epidemiology and Multifactorial Diseases Group, Paris, France
| | - Cathrine Laprise
- Département des sciences fondamentales, Centre intersectoriel en santé durable (CISD), Université du Québec à Chicoutimi, Saguenay, QC, Canada
| | - Emmanuelle Bouzigon
- Université Paris Cité, UMRS 1124, INSERM, Genomic Epidemiology and Multifactorial Diseases Group, Paris, France
| | - Marie-Hélène Dizier
- Université Paris Cité, UMRS 1124, INSERM, Genomic Epidemiology and Multifactorial Diseases Group, Paris, France.
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Nakahara S, Male AG, Turner JA, Calhoun VD, Lim KO, Mueller BA, Bustillo JR, O'Leary DS, Voyvodic J, Belger A, Preda A, Mathalon DH, Ford JM, Guffanti G, Macciardi F, Potkin SG, Van Erp TGM. Auditory oddball hypoactivation in schizophrenia. Psychiatry Res Neuroimaging 2023; 335:111710. [PMID: 37690161 DOI: 10.1016/j.pscychresns.2023.111710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/30/2023] [Accepted: 08/26/2023] [Indexed: 09/12/2023]
Abstract
Individuals with schizophrenia (SZ) show aberrant activations, assessed via functional magnetic resonance imaging (fMRI), during auditory oddball tasks. However, associations with cognitive performance and genetic contributions remain unknown. This study compares individuals with SZ to healthy volunteers (HVs) using two cross-sectional data sets from multi-center brain imaging studies. It examines brain activation to auditory oddball targets, and their associations with cognitive domain performance, schizophrenia polygenic risk scores (PRS), and genetic variation (loci). Both sample 1 (137 SZ vs. 147 HV) and sample 2 (91 SZ vs. 98 HV), showed hypoactivation in SZ in the left-frontal pole, and right frontal orbital, frontal pole, paracingulate, intracalcarine, precuneus, supramarginal and hippocampal cortices, and right thalamus. In SZ, precuneus activity was positively related to cognitive performance. Schizophrenia PRS showed a negative correlation with brain activity in the right-supramarginal cortex. GWA analyses revealed significant single-nucleotide polymorphisms associated with right-supramarginal gyrus activity. RPL36 also predicted right-supramarginal gyrus activity. In addition to replicating hypoactivation for oddball targets in SZ, this study identifies novel relationships between regional activity, cognitive performance, and genetic loci that warrant replication, emphasizing the need for continued data sharing and collaborative efforts.
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Affiliation(s)
- Soichiro Nakahara
- Clinical Translational Neuroscience Laboratory, Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA, 92617, United States; Discovery Accelerator Venture Unit Direct Reprogramming, Astellas Pharma Inc, 21, Miyukigaoka, Tsukuba, Ibaraki 305-8585, Japan
| | - Alie G Male
- Clinical Translational Neuroscience Laboratory, Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA, 92617, United States
| | - Jessica A Turner
- Department of Psychiatry and Behavioral Health, Ohio State University, Columbus, OH, 43210, United States
| | - Vince D Calhoun
- Tri-institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS), Georgia State University, Georgia Institute of Technology, and Emory University 55 Park Pl NE, Atlanta, GA 30303, USA
| | - Kelvin O Lim
- Department of Psychiatry and Behavioral Sciences, University of Minnesota, Minneapolis, MN, 55454, United States
| | - Bryon A Mueller
- Department of Psychiatry and Behavioral Sciences, University of Minnesota, Minneapolis, MN, 55454, United States
| | - Juan R Bustillo
- Departments of Psychiatry & Neurosciences, University of New Mexico, Albuquerque, NM, 87131, United States
| | - Daniel S O'Leary
- Department of Psychiatry, University of Iowa, Iowa City, IA, 52242, United States
| | - James Voyvodic
- Brain Imaging and Analysis Center, Duke University Medical Center, Durham, NC, 27710, United States
| | - Aysenil Belger
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States
| | - Adrian Preda
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA, 92617, United States
| | - Daniel H Mathalon
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, 94143, United States; Veterans Affairs San Francisco Healthcare System, San Francisco, CA, 94121, United States
| | - Judith M Ford
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, 94143, United States; Veterans Affairs San Francisco Healthcare System, San Francisco, CA, 94121, United States; San Francisco Veterans Affairs Medical Center, San Francisco, CA 94121, United States
| | - Guia Guffanti
- Department of Psychiatry at McLean Hospital - Harvard Medical School, Boston, MA, 02478, United States
| | - Fabio Macciardi
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA, 92617, United States
| | - Steven G Potkin
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA, 92617, United States
| | - Theo G M Van Erp
- Clinical Translational Neuroscience Laboratory, Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA, 92617, United States; Center for the Neurobiology of Learning and Memory, University of California Irvine, 309 Qureshey Research Lab, Irvine, CA, 92697, United States.
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Nava-Quiroz KJ, Rojas-Serrano J, Pérez-Rubio G, Buendia-Roldan I, Mejía M, Fernández-López JC, Rodríguez-Henríquez P, Ayala-Alcantar N, Ramos-Martínez E, López-Flores LA, Del Ángel-Pablo AD, Falfán-Valencia R. Molecular Factors in PAD2 ( PADI2) and PAD4 ( PADI4) Are Associated with Interstitial Lung Disease Susceptibility in Rheumatoid Arthritis Patients. Cells 2023; 12:2235. [PMID: 37759458 PMCID: PMC10527441 DOI: 10.3390/cells12182235] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/26/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
Around 50% of rheumatoid arthritis (RA) patients show some extra-articular manifestation, with the lung a usually affected organ; in addition, the presence of anti-citrullinated protein antibodies (ACPA) is a common feature, which is caused by protein citrullination modifications, catalyzed by the peptidyl arginine deiminases (PAD) enzymes. We aimed to identify single nucleotide variants (SNV) in PADI2 and PADI4 genes (PAD2 and PAD4 proteins, respectively) associated with susceptibility to interstitial lung disease (ILD) in RA patients and the PAD2 and PAD4 levels. Material and methods: 867 subjects were included: 118 RA-ILD patients, 133 RA patients, and 616 clinically healthy subjects (CHS). Allelic discrimination was performed in eight SNVs using qPCR, four in PADI2 and four in PADI4. The ELISA technique determined PAD2 and PAD4 levels in serum and bronchoalveolar lavage (BAL) samples, and the population structure was evaluated using 14 informative ancestry markers. Results: The rs1005753-GG (OR = 4.9) in PADI2 and rs11203366-AA (OR = 3.08), rs11203367-GG (OR = 2.4) in PADI4 are associated with genetic susceptibility to RA-ILD as well as the ACTC haplotype (OR = 2.64). In addition, the PAD4 protein is increased in RA-ILD individuals harboring the minor allele homozygous genotype in PADI4 SNVs. Moreover, rs1748033 in PADI4, rs2057094, and rs2076615 in PADI2 are associated with RA susceptibility. In conclusion, in RA patients, single nucleotide variants in PADI4 and PADI2 are associated with ILD susceptibility. The rs1748033 in PADI4 and two different SNVs in PADI2 are associated with RA development but not ILD. PAD4 serum levels are increased in RA-ILD patients.
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Affiliation(s)
- Karol J. Nava-Quiroz
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Tlalpan, Mexico City 14080, Mexico; (K.J.N.-Q.); (G.P.-R.)
- Programa de Maestría y Doctorado en Ciencias Médicas Odontológicas y de la Salud, Universidad Nacional Autónoma de México (UNAM), Mexico City 04100, Mexico
| | - Jorge Rojas-Serrano
- Rheumatology Clinic, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Tlalpan, Mexico City 14080, Mexico
| | - Gloria Pérez-Rubio
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Tlalpan, Mexico City 14080, Mexico; (K.J.N.-Q.); (G.P.-R.)
| | - Ivette Buendia-Roldan
- Translational Research Laboratory on Aging and Pulmonary Fibrosis, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Tlalpan, Mexico City 14080, Mexico
| | - Mayra Mejía
- Diffuse Interstitial Lung Disease Clinic, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Tlalpan, Mexico City 14080, Mexico
| | - Juan Carlos Fernández-López
- Consorcio de Genómica Computacional, Instituto Nacional de Medicina Genómica (INMEGEN), Tlalpan, Mexico City 14610, Mexico
| | - Pedro Rodríguez-Henríquez
- Department of Rheumatology, Hospital General Dr. Manuel Gea González, Tlalpan, Mexico City 14080, Mexico
| | - Noé Ayala-Alcantar
- Banco de Sangre, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Tlalpan, Mexico City 14080, Mexico
| | - Espiridión Ramos-Martínez
- Experimental Medicine Research Unit, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 06720, Mexico
| | - Luis Alberto López-Flores
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Tlalpan, Mexico City 14080, Mexico; (K.J.N.-Q.); (G.P.-R.)
| | - Alma D. Del Ángel-Pablo
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Tlalpan, Mexico City 14080, Mexico; (K.J.N.-Q.); (G.P.-R.)
| | - Ramcés Falfán-Valencia
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Tlalpan, Mexico City 14080, Mexico; (K.J.N.-Q.); (G.P.-R.)
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Cha J, Choi S. Gene-Smoking Interaction Analysis for the Identification of Novel Asthma-Associated Genetic Factors. Int J Mol Sci 2023; 24:12266. [PMID: 37569643 PMCID: PMC10419280 DOI: 10.3390/ijms241512266] [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: 07/01/2023] [Revised: 07/26/2023] [Accepted: 07/30/2023] [Indexed: 08/13/2023] Open
Abstract
Asthma is a complex heterogeneous disease caused by gene-environment interactions. Although numerous genome-wide association studies have been conducted, these interactions have not been systemically investigated. We sought to identify genetic factors associated with the asthma phenotype in 66,857 subjects from the Health Examination Study, Cardiovascular Disease Association Study, and Korea Association Resource Study cohorts. We investigated asthma-associated gene-environment (smoking status) interactions at the level of single nucleotide polymorphisms, genes, and gene sets. We identified two potentially novel (SETDB1 and ZNF8) and five previously reported (DM4C, DOCK8, MMP20, MYL7, and ADCY9) genes associated with increased asthma risk. Numerous gene ontology processes, including regulation of T cell differentiation in the thymus (GO:0033081), were significantly enriched for asthma risk. Functional annotation analysis confirmed the causal relationship between five genes (two potentially novel and three previously reported genes) and asthma through genome-wide functional prediction scores (combined annotation-dependent depletion, deleterious annotation of genetic variants using neural networks, and RegulomeDB). Our findings elucidate the genetic architecture of asthma and improve the understanding of its biological mechanisms. However, further studies are necessary for developing preventive treatments based on environmental factors and understanding the immune system mechanisms that contribute to the etiology of asthma.
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Affiliation(s)
- Junho Cha
- Department of Applied Artificial Intelligence, College of Computing, Hanyang University, 55 Hanyang-daehak-ro, Sangnok-gu, Ansan 15588, Republic of Korea;
| | - Sungkyoung Choi
- Department of Applied Artificial Intelligence, College of Computing, Hanyang University, 55 Hanyang-daehak-ro, Sangnok-gu, Ansan 15588, Republic of Korea;
- Department of Mathematical Data Science, College of Science and Convergence Technology, Hanyang University, 55 Hanyang-daehak-ro, Sangnok-gu, Ansan 15588, Republic of Korea
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Jiang T, Hu W, Zhang S, Ren C, Lin S, Zhou Z, Wu H, Yin J, Tan L. Fibroblast growth factor 10 attenuates chronic obstructive pulmonary disease by protecting against glycocalyx impairment and endothelial apoptosis. Respir Res 2022; 23:269. [PMID: 36183124 PMCID: PMC9526324 DOI: 10.1186/s12931-022-02193-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 09/22/2022] [Indexed: 11/23/2022] Open
Abstract
Background The defects and imbalance in lung repair and structural maintenance contribute to the pathogenesis of chronic obstructive pulmonary diseases (COPD), yet the molecular mechanisms that regulate lung repair process are so far incompletely understood. We hypothesized that cigarette smoking causes glycocalyx impairment and endothelial apoptosis in COPD, which could be repaired by the stimulation of fibroblast growth factor 10 (FGF10)/FGF receptor 1 (FGFR1) signaling. Methods We used immunostaining (immunohistochemical [IHC] and immunofluorescence [IF]) and enzyme-linked immunosorbent assay (ELISA) to detect the levels of glycocalyx components and endothelial apoptosis in animal models and in patients with COPD. We used the murine emphysema model and in vitro studies to determine the protective and reparative role of FGF10/FGFR1. Results Exposure to cigarette smoke caused endothelial glycocalyx impairment and emphysematous changes in murine models and human specimens. Pretreatment of FGF10 attenuated the development of emphysema and the shedding of glycocalyx components induced by CSE in vivo. However, FGF10 did not attenuate the emphysema induced by endothelial-specific killing peptide CGSPGWVRC-GG-D(KLAKLAK)2. Mechanistically, FGF10 alleviated smoke-induced endothelial apoptosis and glycocalyx repair through FGFR1/ERK/SOX9/HS6ST1 signaling in vitro. FGF10 was shown to repair pulmonary glycocalyx injury and endothelial apoptosis, and attenuate smoke-induced COPD through FGFR1 signaling. Conclusions Our results suggest that FGF10 may serve as a potential therapeutic strategy against COPD via endothelial repair and glycocalyx reconstitution. Supplementary Information The online version contains supplementary material available at 10.1186/s12931-022-02193-5. It is the first time to prove the confirm the endothelial glycocalyx impairment in COPD. FGF10 attenuates the development of emphysema and the shedding of glycocalyx induced by CSE in vivo. FGF10 alleviates smoke-induced endothelial apoptosis and glycocalyx repair through FGFR1/ERK/SOX9/HS6ST1 signaling.
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Affiliation(s)
- Tian Jiang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No.180 Fenglin Road, Shanghai, 200032, China.,Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.,Key Laboratory of Lung Inflammation and Injury, Shanghai, 200032, China
| | - Weiping Hu
- Department of Critical Care and Respiratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Shaoyuan Zhang
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No.180 Fenglin Road, Shanghai, 200032, China.,Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.,Key Laboratory of Lung Inflammation and Injury, Shanghai, 200032, China
| | - Changhao Ren
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No.180 Fenglin Road, Shanghai, 200032, China
| | - Siyun Lin
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No.180 Fenglin Road, Shanghai, 200032, China
| | - Zhenyu Zhou
- Department of Vascular Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Hao Wu
- Department of Clinical Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Jun Yin
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No.180 Fenglin Road, Shanghai, 200032, China. .,Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, 200032, China. .,Key Laboratory of Lung Inflammation and Injury, Shanghai, 200032, China.
| | - Lijie Tan
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, No.180 Fenglin Road, Shanghai, 200032, China. .,Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, 200032, China. .,Key Laboratory of Lung Inflammation and Injury, Shanghai, 200032, China.
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8
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Pang H, Lin J, Luo S, Huang G, Li X, Xie Z, Zhou Z. The missing heritability in type 1 diabetes. Diabetes Obes Metab 2022; 24:1901-1911. [PMID: 35603907 PMCID: PMC9545639 DOI: 10.1111/dom.14777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/04/2022] [Accepted: 05/17/2022] [Indexed: 12/15/2022]
Abstract
Type 1 diabetes (T1D) is a complex autoimmune disease characterized by an absolute deficiency of insulin. It affects more than 20 million people worldwide and imposes an enormous financial burden on patients. The underlying pathogenic mechanisms of T1D are still obscure, but it is widely accepted that both genetics and the environment play an important role in its onset and development. Previous studies have identified more than 60 susceptible loci associated with T1D, explaining approximately 80%-85% of the heritability. However, most identified variants confer only small increases in risk, which restricts their potential clinical application. In addition, there is still a so-called 'missing heritability' phenomenon. While the gap between known heritability and true heritability in T1D is small compared with that in other complex traits and disorders, further elucidation of T1D genetics has the potential to bring novel insights into its aetiology and provide new therapeutic targets. Many hypotheses have been proposed to explain the missing heritability, including variants remaining to be found (variants with small effect sizes, rare variants and structural variants) and interactions (gene-gene and gene-environment interactions; e.g. epigenetic effects). In the following review, we introduce the possible sources of missing heritability and discuss the existing related knowledge in the context of T1D.
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Affiliation(s)
- Haipeng Pang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and EndocrinologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Jian Lin
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and EndocrinologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Shuoming Luo
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and EndocrinologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Gan Huang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and EndocrinologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Xia Li
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and EndocrinologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Zhiguo Xie
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and EndocrinologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
| | - Zhiguang Zhou
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, and Department of Metabolism and EndocrinologyThe Second Xiangya Hospital of Central South UniversityChangshaChina
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9
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Li D, Kim W, An J, Kim S, Lee S, Do A, Kim W, Lee S, Yoon D, Lee K, Ha S, Silverman EK, Cho M, Shin C, Won S. Heritability Analyses Uncover Shared Genetic Effects of Lung Function and Change over Time. Genes (Basel) 2022; 13:genes13071261. [PMID: 35886044 PMCID: PMC9316642 DOI: 10.3390/genes13071261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/05/2022] [Accepted: 07/08/2022] [Indexed: 01/27/2023] Open
Abstract
Genetic influence on lung functions has been identified in previous studies; however, the relative longitudinal effects of genetic factors and their interactions with smoking on lung function remain unclear. Here, we identified the longitudinal effects of genetic variants on lung function by determining single nucleotide polymorphism (SNP) heritability and genetic correlations, and by analyzing interactions with smoking. Subject-specific means and annual change rates were calculated for eight spirometric measures obtained from 6622 Korean adults aged 40−69 years every two years for 14 years, and their heritabilities were estimated separately. Statistically significant (p < 0.05) heritability for the subject-specific means of all spirometric measures (8~32%) and change rates of forced expiratory volume in 1 s to forced vital capacity ratio (FEV1/FVC; 16%) and post-bronchodilator FEV1/FVC (17%) were detected. Significant genetic correlations of the change rate with the subject-specific mean were observed for FEV1/FVC (ρg = 0.64) and post-bronchodilator FEV1/FVC (ρg = 0.47). Furthermore, post-bronchodilator FEV1/FVC showed significant heritability of SNP-by-smoking interaction (hGXS2 = 0.4) for the annual change rate. The GWAS also detected genome-wide significant SNPs for FEV1 (rs4793538), FEV1/FVC (rs2704589, rs62201158, and rs9391733), and post-bronchodilator FEV1/FVC (rs2445936). We found statistically significant evidence of heritability role on the change in lung function, and this was shared with the effects on cross-sectional measurements. We also found some evidence of interaction with smoking for the change of lung function.
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Affiliation(s)
- Donghe Li
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea; (D.L.); (A.D.)
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA 02118, USA
| | - Woojin Kim
- Department of Internal Medicine and Environmental Health Center, School of Medicine, Kangwon National University, Chuncheon 24341, Korea;
| | - Jahoon An
- Department of Public Health Science, Graduate School of Public Health, Seoul National University, Seoul 08826, Korea;
| | - Soriul Kim
- Institute for Human Genomic Study, College of Medicine, Korea University, Seoul 136701, Korea; (S.K.); (S.L.)
| | - Seungku Lee
- Institute for Human Genomic Study, College of Medicine, Korea University, Seoul 136701, Korea; (S.K.); (S.L.)
| | - Ahra Do
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea; (D.L.); (A.D.)
| | - Wonji Kim
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA; (W.K.); (E.K.S.); (M.C.)
| | - Sanghun Lee
- Department of Medical Consilience, Graduate School, Dankook University, Yongin 16890, Korea;
| | - Dankyu Yoon
- Division of Allergy and Respiratory Disease Research, Department of Chronic Disease Convergence Research, National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju 28159, Korea;
| | - Kwangbae Lee
- Korea Medical Institute, Seoul 03173, Korea; (K.L.); (S.H.)
| | - Seounguk Ha
- Korea Medical Institute, Seoul 03173, Korea; (K.L.); (S.H.)
| | - Edwin K. Silverman
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA; (W.K.); (E.K.S.); (M.C.)
| | - Michael Cho
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA; (W.K.); (E.K.S.); (M.C.)
| | - Chol Shin
- Institute for Human Genomic Study, College of Medicine, Korea University, Seoul 136701, Korea; (S.K.); (S.L.)
- Division of Pulmonary Sleep and Critical Care Medicine, Department of Internal Medicine, Korea University Ansan Hospital, Ansan 15355, Korea
- Correspondence: (C.S.); (S.W.)
| | - Sungho Won
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea; (D.L.); (A.D.)
- Department of Public Health Science, Graduate School of Public Health, Seoul National University, Seoul 08826, Korea;
- Institute of Health and Environment, Seoul National University, Seoul 08826, Korea
- RexSoft Inc., Seoul 08826, Korea
- Correspondence: (C.S.); (S.W.)
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10
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Fang F, Hazegh K, Mast AE, Triulzi DJ, Spencer BR, Gladwin MT, Busch MP, Kanias T, Page GP. Sex-specific genetic modifiers identified susceptibility of cold stored red blood cells to osmotic hemolysis. BMC Genomics 2022; 23:227. [PMID: 35321643 PMCID: PMC8941732 DOI: 10.1186/s12864-022-08461-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/04/2022] [Indexed: 11/19/2022] Open
Abstract
Background Genetic variants have been found to influence red blood cell (RBC) susceptibility to hemolytic stress and affect transfusion outcomes and the severity of blood diseases. Males have a higher susceptibility to hemolysis than females, but little is known about the genetic mechanism contributing to the difference. Results To investigate the sex differences in RBC susceptibility to hemolysis, we conducted a sex-stratified genome-wide association study and a genome-wide gene-by-sex interaction scan in a multi-ethnic dataset with 12,231 blood donors who have in vitro osmotic hemolysis measurements during routine blood storage. The estimated SNP-based heritability for osmotic hemolysis was found to be significantly higher in males than in females (0.46 vs. 0.41). We identified SNPs associated with sex-specific susceptibility to osmotic hemolysis in five loci (SPTA1, KCNA6, SLC4A1, SUMO1P1, and PAX8) that impact RBC function and hemolysis. Conclusion Our study established a best practice to identify sex-specific genetic modifiers for sexually dimorphic traits in datasets with mixed ancestries, providing evidence of different genetic regulations of RBC susceptibility to hemolysis between sexes. These and other variants may help explain observed sex differences in the severity of hemolytic diseases, such as sickle cell and malaria, as well as the viability of red cell storage and recovery. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08461-4.
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Affiliation(s)
- Fang Fang
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, Durham, NC, USA.
| | | | - Alan E Mast
- Versiti Blood Research Institute, Blood Center of Wisconsin, Milwaukee, WI, USA.,Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Darrell J Triulzi
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Mark T Gladwin
- Pittsburgh Heart, Lung, and Blood Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA, USA.,Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Michael P Busch
- Vitalant Research Institute, San Francisco, CA, USA.,Department of Laboratory Medicine, UCSF, San Francisco, CA, USA
| | - Tamir Kanias
- Vitalant Research Institute, Denver, CO, USA.,Department of Pathology, University of Colorado Denver Anschutz Medical Campus, Aurora, CO, USA
| | - Grier P Page
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, Durham, NC, USA.,Division of Biostatistics and Epidemiology, RTI International, GA, Atlanta, USA
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11
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Melbourne CA, Mesut Erzurumluoglu A, Shrine N, Chen J, Tobin MD, Hansell AL, Wain LV. Genome-wide gene-air pollution interaction analysis of lung function in 300,000 individuals. ENVIRONMENT INTERNATIONAL 2022; 159:107041. [PMID: 34923368 PMCID: PMC8739564 DOI: 10.1016/j.envint.2021.107041] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/25/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Impaired lung function is predictive of mortality and is a key component of chronic obstructive pulmonary disease. Lung function has a strong genetic component but is also affected by environmental factors such as increased exposure to air pollution, but the effect of their interactions is not well understood. OBJECTIVES To identify interactions between genetic variants and air pollution measures which affect COPD risk and lung function. Additionally, to determine whether previously identified lung function genetic association signals showed evidence of interaction with air pollution, considering both individual effects and combined effects using a genetic risk score (GRS). METHODS We conducted a genome-wide gene-air pollution interaction analysis of spirometry measures with three measures of air pollution at home address: particulate matter (PM2.5 & PM10) and nitrogen dioxide (NO2), in approximately 300,000 unrelated European individuals from UK Biobank. We explored air pollution interactions with previously identified lung function signals and determined their combined interaction effect using a GRS. RESULTS We identified seven new genome-wide interaction signals (P<5×10-8), and a further ten suggestive interaction signals (P<5×10-7). Additionally, we found statistical evidence of interaction for FEV1/FVC between PM2.5 and previously identified lung function signal, rs10841302, near AEBP2, suggesting increased susceptibility as copies of the G allele increased (but size of the impact was small - interaction beta: -0.363 percentage points, 95% CI: -0.523, -0.203 per 5 µg/m3). There was no observed interaction between air pollutants and the weighted GRS. DISCUSSION We carried out the largest genome-wide gene-air pollution interaction study of lung function and identified potential effects of clinically relevant size and significance. We observed up to 440 ml lower lung function for certain genotypes when exposed to mean levels of outdoor air pollution, which is approximately equivalent to nine years of average normal loss of lung function in adults.
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Affiliation(s)
- Carl A Melbourne
- Department of Health Sciences, University of Leicester, Leicester, UK
| | | | - Nick Shrine
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Jing Chen
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Martin D Tobin
- Department of Health Sciences, University of Leicester, Leicester, UK; National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Anna L Hansell
- Centre for Environmental Health and Sustainability, University of Leicester, Leicester, UK; National Institute for Health Research Health Protection Research Unit in Environmental Exposures and Health at the University of Leicester, Leicester, UK.
| | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, UK; National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
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12
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Butnariu LI, Țarcă E, Cojocaru E, Rusu C, Moisă ȘM, Leon Constantin MM, Gorduza EV, Trandafir LM. Genetic Modifying Factors of Cystic Fibrosis Phenotype: A Challenge for Modern Medicine. J Clin Med 2021; 10:5821. [PMID: 34945117 PMCID: PMC8707808 DOI: 10.3390/jcm10245821] [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: 11/20/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 12/13/2022] Open
Abstract
Cystic fibrosis (CF) is a monogenic autosomal recessive disease caused by cystic fibrosis transmembrane conductance regulator (CFTR) gene mutations. CF is characterized by a high phenotypic variability present even in patients with the same genotype. This is due to the intervention of modifier genes that interact with both the CFTR gene and environmental factors. The purpose of this review is to highlight the role of non-CFTR genetic factors (modifier genes) that contribute to phenotypic variability in CF. We analyzed literature data starting with candidate gene studies and continuing with extensive studies, such as genome-wide association studies (GWAS) and whole exome sequencing (WES). The results of both types of studies revealed that the number of modifier genes in CF patients is impressive. Their identification offers a new perspective on the pathophysiological mechanisms of the disease, paving the way for the understanding of other genetic disorders. In conclusion, in the future, genetic analysis, such as GWAS and WES, should be performed routinely. A challenge for future research is to integrate their results in the process of developing new classes of drugs, with a goal to improve the prognosis, increase life expectancy, and enhance quality of life among CF patients.
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Affiliation(s)
- Lăcrămioara Ionela Butnariu
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (L.I.B.); (C.R.); (E.V.G.)
| | - Elena Țarcă
- Department of Surgery II—Pediatric Surgery, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iaşi, Romania
| | - Elena Cojocaru
- Department of Morphofunctional Sciences I, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iaşi, Romania
| | - Cristina Rusu
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (L.I.B.); (C.R.); (E.V.G.)
| | - Ștefana Maria Moisă
- Department of Mother and Child, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (Ș.M.M.); (L.M.T.)
| | | | - Eusebiu Vlad Gorduza
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (L.I.B.); (C.R.); (E.V.G.)
| | - Laura Mihaela Trandafir
- Department of Mother and Child, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (Ș.M.M.); (L.M.T.)
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13
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Kim W, Moll M, Qiao D, Hobbs BD, Shrine N, Sakornsakolpat P, Tobin MD, Dudbridge F, Wain LV, Ladd-Acosta C, Chatterjee N, Silverman EK, Cho MH, Beaty TH. Interaction of Cigarette Smoking and Polygenic Risk Score on Reduced Lung Function. JAMA Netw Open 2021; 4:e2139525. [PMID: 34913977 PMCID: PMC8678715 DOI: 10.1001/jamanetworkopen.2021.39525] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
IMPORTANCE The risk of airflow limitation and chronic obstructive pulmonary disease (COPD) is influenced by combinations of cigarette smoking and genetic susceptibility, yet it remains unclear whether gene-by-smoking interactions are associated with quantitative measures of lung function. OBJECTIVE To assess the interaction of cigarette smoking and polygenic risk score in association with reduced lung function. DESIGN, SETTING, AND PARTICIPANTS This UK Biobank cohort study included UK citizens of European ancestry aged 40 to 69 years with genetic and spirometry data passing quality control metrics. Data was analyzed from July 2020 to March 2021. EXPOSURES PRS of combined forced expiratory volume in 1 second (FEV1) and percent of forced vital capacity exhaled in the first second (FEV1/FVC), self-reported pack-years of smoking, ever- vs never-smoking status, and current- vs former- or never-smoking status. MAIN OUTCOMES AND MEASURES FEV1/FVC was the primary outcome. Models were used to test for interactions with models, including the main effects of PRS, different smoking variables, and their cross-product terms. The association between pack-years of smoking and FEV1/FVC were compared for those in the highest vs lowest decile of estimated genetic risk for low lung function. RESULTS We included 319 730 individuals, of whom 24 915 (8%) had moderate-to-severe COPD cases, and 44.4% were men. Participants had a mean (SD) age 56.5 of (8.02) years. The PRS and pack-years were significantly associated with lower FEV1/FVC (PRS: β, -0.03; 95% CI, -0.031 to -0.03; pack-years: β, -0.0064; 95% CI, -0.0064 to -0.0063) and the interaction term (β, -0.0028; 95% CI, -0.0029 to -0.0026). A stepwise increment in estimated effect sizes for these interaction terms was observed per 10 pack-years of smoking exposure. The interaction of PRS with 11 to 20, 31 to 40, and more than 50 pack-years categories were β (interaction) -0.0038 (95% CI, -0.0046 to -0.0031); -0.013 (95% CI, -0.014 to -0.012); and -0.017 (95% CI, -0.019 to -0.016), respectively. There was evidence of significant interaction between PRS with ever- or never- smoking status (β, interaction; -0.0064; 95% CI, -0.0068 to -0.0060) and current or not-current smoking (β, interaction; -0.0091; 95% CI, -0.0097 to -0.0084). For any given level of pack-years of smoking exposure, FEV1/FVC was significantly lower for individuals in the tenth decile (ie, highest risk) than the first decile (ie, lowest risk) of genetic risk. For every 20 pack-years of smoking, those in the tenth decile compared with the first decile of genetic risk showed nearly a 2-fold reduction in FEV1/FVC. CONCLUSIONS AND RELEVANCE COPD is characterized by diminished lung function, and our analyses suggest there is substantial interaction between genome-wide PRS and smoking exposures. While smoking was associated with decreased lung function across all genetic risk categories, the associations were strongest in individuals with higher estimated genetic risk.
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Affiliation(s)
- Woori Kim
- Systems Biology and Computer Science Program, Ann Romney Center for Neurological Diseases, Department of Neurology, Brigham and Women’s Hospital, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Matthew Moll
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Dandi Qiao
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Brian D. Hobbs
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Nick Shrine
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | - Phuwanat Sakornsakolpat
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Martin D. Tobin
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Frank Dudbridge
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | - Louise V. Wain
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom
| | - Christine Ladd-Acosta
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Nilanjan Chatterjee
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, Maryland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
| | - Edwin K. Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Michael H. Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Terri H. Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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14
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Hancock DB. Compelling Interaction of Cigarette Smoking and Polygenetic Risk Emerges for Lung Function and COPD. JAMA Netw Open 2021; 4:e2140347. [PMID: 34913983 DOI: 10.1001/jamanetworkopen.2021.40347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Dana B Hancock
- GenOmics, Bioinformatics, and Translational Research Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, North Carolina
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15
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Yamada M, Motoike IN, Kojima K, Fuse N, Hozawa A, Kuriyama S, Katsuoka F, Tadaka S, Shirota M, Sakurai M, Nakamura T, Hamanaka Y, Suzuki K, Sugawara J, Ogishima S, Uruno A, Kodama EN, Fujino N, Numakura T, Ichikawa T, Mitsune A, Ohe T, Kinoshita K, Ichinose M, Sugiura H, Yamamoto M. Genetic loci for lung function in Japanese adults with adjustment for exhaled nitric oxide levels as airway inflammation indicator. Commun Biol 2021; 4:1288. [PMID: 34782693 PMCID: PMC8593164 DOI: 10.1038/s42003-021-02813-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 10/27/2021] [Indexed: 11/08/2022] Open
Abstract
Lung function reflects the ability of the respiratory system and is utilized for the assessment of respiratory diseases. Because type 2 airway inflammation influences lung function, genome wide association studies (GWAS) for lung function would be improved by adjustment with an indicator of the inflammation. Here, we performed a GWAS for lung function with adjustment for exhaled nitric oxide (FeNO) levels in two independent Japanese populations. Our GWAS with genotype imputations revealed that the RNF5/AGER locus including AGER rs2070600 SNP, which introduces a G82S substitution of AGER, was the most significantly associated with FEV1/FVC. Three other rare missense variants of AGER were further identified. We also found genetic loci with three candidate genes (NOS2, SPSB2 and RIPOR2) associated with FeNO levels. Analyses with the BioBank-Japan GWAS resource revealed genetic links of FeNO and asthma-related traits, and existence of common genetic background for allergic diseases and their biomarkers. Our study identified the genetic locus most strongly associated with airway obstruction in the Japanese population and three genetic loci associated with FeNO, an indicator of type 2 airway inflammation in adults.
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Affiliation(s)
- Mitsuhiro Yamada
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ikuko N Motoike
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kaname Kojima
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Nobuo Fuse
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Atsushi Hozawa
- Department of Preventive Medicine and Epidemiology, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Shinichi Kuriyama
- Department of Preventive Medicine and Epidemiology, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Fumiki Katsuoka
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Shu Tadaka
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Matsuyuki Shirota
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Miyuki Sakurai
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Tomohiro Nakamura
- Department of Health Record Informatics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Yohei Hamanaka
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kichiya Suzuki
- Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Junichi Sugawara
- Department of Community Medical Supports, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Soichi Ogishima
- Department of Health Record Informatics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Akira Uruno
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Eiichi N Kodama
- Department of Community Medical Supports, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Naoya Fujino
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tadahisa Numakura
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tomohiro Ichikawa
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ayumi Mitsune
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takashi Ohe
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kengo Kinoshita
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
- Department of System Bioinformatics, Tohoku University Graduate School of Information Sciences, Sendai, Japan
| | | | - Hisatoshi Sugiura
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan.
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16
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Rare and low-frequency exonic variants and gene-by-smoking interactions in pulmonary function. Sci Rep 2021; 11:19365. [PMID: 34588469 PMCID: PMC8481467 DOI: 10.1038/s41598-021-98120-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 09/02/2021] [Indexed: 02/08/2023] Open
Abstract
Genome-wide association studies have identified numerous common genetic variants associated with spirometric measures of pulmonary function, including forced expiratory volume in one second (FEV1), forced vital capacity, and their ratio. However, variants with lower minor allele frequencies are less explored. We conducted a large-scale gene-smoking interaction meta-analysis on exonic rare and low-frequency variants involving 44,429 individuals of European ancestry in the discovery stage and sought replication in the UK BiLEVE study with 45,133 European ancestry samples and UK Biobank study with 59,478 samples. We leveraged data on cigarette smoking, the major environmental risk factor for reduced lung function, by testing gene-by-smoking interaction effects only and simultaneously testing the genetic main effects and interaction effects. The most statistically significant signal that replicated was a previously reported low-frequency signal in GPR126, distinct from common variant associations in this gene. Although only nominal replication was obtained for a top rare variant signal rs142935352 in one of the two studies, interaction and joint tests for current smoking and PDE3B were significantly associated with FEV1. This study investigates the utility of assessing gene-by-smoking interactions and underscores their effects on potential pulmonary function.
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17
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Abstract
Disease classification, or nosology, was historically driven by careful examination of clinical features of patients. As technologies to measure and understand human phenotypes advanced, so too did classifications of disease, and the advent of genetic data has led to a surge in genetic subtyping in the past decades. Although the fundamental process of refining disease definitions and subtypes is shared across diverse fields, each field is driven by its own goals and technological expertise, leading to inconsistent and conflicting definitions of disease subtypes. Here, we review several classical and recent subtypes and subtyping approaches and provide concrete definitions to delineate subtypes. In particular, we focus on subtypes with distinct causal disease biology, which are of primary interest to scientists, and subtypes with pragmatic medical benefits, which are of primary interest to physicians. We propose genetic heterogeneity as a gold standard for establishing biologically distinct subtypes of complex polygenic disease. We focus especially on methods to find and validate genetic subtypes, emphasizing common pitfalls and how to avoid them.
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Affiliation(s)
- Andy Dahl
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA; .,Department of Neurology, University of California, Los Angeles, California 90024, USA; .,Department of Computational Medicine, University of California, Los Angeles, California 90095, USA
| | - Noah Zaitlen
- Department of Neurology, University of California, Los Angeles, California 90024, USA; .,Department of Computational Medicine, University of California, Los Angeles, California 90095, USA
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18
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Sikdar S, Wyss AB, Lee MK, Hoang TT, Richards M, Beane Freeman LE, Parks C, Thorne PS, Hankinson JL, Umbach DM, Motsinger-Reif A, London SJ. Interaction between Genetic Risk Scores for reduced pulmonary function and smoking, asthma and endotoxin. Thorax 2021; 76:1219-1226. [PMID: 33963087 PMCID: PMC8572320 DOI: 10.1136/thoraxjnl-2020-215624] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 02/17/2021] [Accepted: 03/22/2021] [Indexed: 01/04/2023]
Abstract
Rationale Genome-wide association studies (GWASs) have identified numerous loci associated with lower pulmonary function. Pulmonary function is strongly related to smoking and has also been associated with asthma and dust endotoxin. At the individual SNP level, genome-wide analyses of pulmonary function have not identified appreciable evidence for gene by environment interactions. Genetic Risk Scores (GRSs) may enhance power to identify gene–environment interactions, but studies are few. Methods We analysed 2844 individuals of European ancestry with 1000 Genomes imputed GWAS data from a case–control study of adult asthma nested within a US agricultural cohort. Pulmonary function traits were FEV1, FVC and FEV1/FVC. Using data from a recent large meta-analysis of GWAS, we constructed a weighted GRS for each trait by combining the top (p value<5×10−9) genetic variants, after clumping based on distance (±250 kb) and linkage disequilibrium (r2=0.5). We used linear regression, adjusting for relevant covariates, to estimate associations of each trait with its GRS and to assess interactions. Results Each trait was highly significantly associated with its GRS (all three p values<8.9×10−8). The inverse association of the GRS with FEV1/FVC was stronger for current smokers (pinteraction=0.017) or former smokers (pinteraction=0.064) when compared with never smokers and among asthmatics compared with non-asthmatics (pinteraction=0.053). No significant interactions were observed between any GRS and house dust endotoxin. Conclusions Evaluation of interactions using GRSs supports a greater impact of increased genetic susceptibility on reduced pulmonary function in the presence of smoking or asthma.
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Affiliation(s)
- Sinjini Sikdar
- Department of Mathematics and Statistics, Old Dominion University, Norfolk, Virginia, USA.,Epidemiology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | - Annah B Wyss
- Epidemiology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | - Mi Kyeong Lee
- Epidemiology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | - Thanh T Hoang
- Epidemiology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | | | - Laura E Beane Freeman
- Occupational and Environmental Epidemiology Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Christine Parks
- Epidemiology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | - Peter S Thorne
- Department of Occupational and Environmental Health, University of Iowa, Iowa City, Iowa, USA
| | | | - David M Umbach
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | - Alison Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
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19
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Sepahzad A, Morris-Rosendahl DJ, Davies JC. Cystic Fibrosis Lung Disease Modifiers and Their Relevance in the New Era of Precision Medicine. Genes (Basel) 2021; 12:genes12040562. [PMID: 33924524 PMCID: PMC8069009 DOI: 10.3390/genes12040562] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/08/2021] [Accepted: 04/08/2021] [Indexed: 02/06/2023] Open
Abstract
Our understanding of cystic fibrosis (CF) has grown exponentially since the discovery of the cystic fibrosis transmembrane conductance regulator (CFTR) gene in 1989. With evolving genetic and genomic tools, we have come to better understand the role of CFTR genotypes in the pathophysiology of the disease. This, in turn, has paved the way for the development of modulator therapies targeted at mutations in the CFTR, which are arguably one of the greatest advances in the treatment of CF. These modulator therapies, however, do not target all the mutations in CFTR that are seen in patients with CF and, furthermore, a variation in response is seen in patients with the same genotype who are taking modulator therapies. There is growing evidence to support the role of non-CFTR modifiers, both genetic and environmental, in determining the variation seen in CF morbidity and mortality and also in the response to existing therapies. This review focusses on key findings from studies using candidate gene and genome-wide approaches to identify CF modifier genes of lung disease in cystic fibrosis and considers the interaction between modifiers and the response to modulator therapies. As the use of modulator therapies expands and we gain data around outcomes, it will be of great interest to investigate this interaction further. Going forward, it will also be crucial to better understand the relative influence of genomic versus environmental factors. With this understanding, we can truly begin to deliver personalised care by better profiling the likely disease phenotype for each patient and their response to treatment.
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Affiliation(s)
- Afsoon Sepahzad
- Department of Paediatric Respiratory Medicine, Royal Brompton and Harefield Hospitals, London SW3 6NP, UK;
| | | | - Jane C. Davies
- Department of Paediatric Respiratory Medicine, Royal Brompton and Harefield Hospitals, London SW3 6NP, UK;
- National Heart & Lung Institute, Imperial College London, Emmanuel Kay Building, 1b Manresa Rd, London SW3 6LR, UK
- Correspondence:
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20
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Hsu LA, Chou HH, Teng MS, Wu S, Ko YL. Circulating chemerin levels are determined through circulating platelet counts in nondiabetic Taiwanese people: A bidirectional Mendelian randomization study. Atherosclerosis 2021; 320:61-69. [PMID: 33545615 DOI: 10.1016/j.atherosclerosis.2021.01.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/19/2020] [Accepted: 01/12/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND AND AIMS Platelet count (PLT) is a predictor of metabolic and inflammation-related disorders. Platelets can release prochemerin, which acts as a link between coagulation and inflammation and between innate and adaptive immunity. The causal effect between PLT and circulating chemerin level has not been elucidated. METHODS Nondiabetic participants with samples in the Taiwan Biobank were recruited for a genome-wide association study (GWAS) based on PLT (17,037 participants) and chemerin levels (3887 participants). A bidirectional Mendelian randomization (MR) study was conducted to determine the association between circulating PLT and chemerin levels. RESULTS For a GWAS of PLT, 11 gene loci were found to have genome-wide significance. For a GWAS of chemerin levels, two gene loci, RARRES2 and HLADQA2-HLADQB1, were found to have genome-wide significance. Age, sex, body mass index, leukocyte count, hemoglobin, mean blood pressure, hemoglobin A1C, serum total bilirubin, aspartate aminotransferase, triglyceride, and low-density-lipoprotein cholesterol levels, estimated glomerular filtration rate, and circulating chemerin level were found to be independently associated with PLT through a stepwise regression analysis. A bidirectional MR study revealed weighted genetic risk scores (WGRSs) for PLT were significantly associated with chemerin levels by using a two-stage least-square method in a multivariate analysis (p = 0.0031), and no significant association between chemerin level WGRSs and PLT was noted. Sensitivity analysis further revealed no violation of the exclusion-restriction assumption with PLT-determining genotypes on chemerin levels. CONCLUSIONS Through a bidirectional MR analysis, our data revealed that chemerin levels were determined based on circulating PLT. Circulating chemerin levels can be intermediates between PLT and future metabolic and inflammation-related disorders.
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Affiliation(s)
- Lung-An Hsu
- The First Cardiovascular Division, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taiwan
| | - Hsin-Hua Chou
- Cardiovascular Center and Division of Cardiology, Department of Internal Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taiwan; School of Medicine, Tzu Chi University, Taiwan
| | - Ming-Sheng Teng
- Department of Research, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taiwan
| | - Semon Wu
- Department of Life Science, Chinese Culture University, Taiwan
| | - Yu-Lin Ko
- Cardiovascular Center and Division of Cardiology, Department of Internal Medicine, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taiwan; School of Medicine, Tzu Chi University, Taiwan; Department of Research, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taiwan.
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21
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Dong J, Maj C, Tsavachidis S, Ostrom QT, Gharahkhani P, Anderson LA, Wu AH, Ye W, Bernstein L, Borisov O, Schröder J, Chow WH, Gammon MD, Liu G, Caldas C, Pharoah PD, Risch HA, May A, Gerges C, Anders M, Venerito M, Schmidt T, Izbicki JR, Hölscher AH, Schumacher B, Vashist Y, Neuhaus H, Rösch T, Knapp M, Krawitz P, Böhmer A, Iyer PG, Reid BJ, Lagergren J, Shaheen NJ, Corley DA, Gockel I, Fitzgerald RC, Cook MB, Whiteman DC, Vaughan TL, Schumacher J, Thrift AP. Sex-Specific Genetic Associations for Barrett's Esophagus and Esophageal Adenocarcinoma. Gastroenterology 2020; 159:2065-2076.e1. [PMID: 32918910 PMCID: PMC9057456 DOI: 10.1053/j.gastro.2020.08.052] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 08/04/2020] [Accepted: 08/24/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS Esophageal adenocarcinoma (EA) and its premalignant lesion, Barrett's esophagus (BE), are characterized by a strong and yet unexplained male predominance (with a male-to-female ratio in EA incidence of up to 6:1). Genome-wide association studies (GWAS) have identified more than 20 susceptibility loci for these conditions. However, potential sex differences in genetic associations with BE/EA remain largely unexplored. METHODS Given strong genetic overlap, BE and EA cases were combined into a single case group for analysis. These were compared with population-based controls. We performed sex-specific GWAS of BE/EA in 3 separate studies and then used fixed-effects meta-analysis to provide summary estimates for >9 million variants for male and female individuals. A series of downstream analyses were conducted separately in male and female individuals to identify genes associated with BE/EA and the genetic correlations between BE/EA and other traits. RESULTS We included 6758 male BE/EA cases, 7489 male controls, 1670 female BE/EA cases, and 6174 female controls. After Bonferroni correction, our meta-analysis of sex-specific GWAS identified 1 variant at chromosome 6q11.1 (rs112894788, KHDRBS2-MTRNR2L9, PBONF = .039) that was statistically significantly associated with BE/EA risk in male individuals only, and 1 variant at chromosome 8p23.1 (rs13259457, PRSS55-RP1L1, PBONF = 0.057) associated, at borderline significance, with BE/EA risk in female individuals only. We also observed strong genetic correlations of BE/EA with gastroesophageal reflux disease in male individuals and obesity in female individuals. CONCLUSIONS The identified novel sex-specific variants associated with BE/EA could improve the understanding of the genetic architecture of the disease and the reasons for the male predominance.
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Affiliation(s)
- Jing Dong
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas; Division of Hematology and Oncology, Department of Medicine, Cancer Center, and Genomic Sciences & Precision Medicine Center, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Carlo Maj
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Germany
| | - Spiridon Tsavachidis
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Quinn T Ostrom
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Puya Gharahkhani
- Statistical Genetics, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Lesley A Anderson
- Centre for Public Health, Queen's University Belfast, Belfast, Northern Ireland & Aberdeen Center for Health Data Science, University of Aberdeen, Scotland
| | - Anna H Wu
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Weimin Ye
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Leslie Bernstein
- Department of Population Sciences, Beckman Research Institute and City of Hope Comprehensive Cancer Center, Duarte, California
| | - Oleg Borisov
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Germany
| | - Julia Schröder
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Wong-Ho Chow
- Department of Epidemiology, MD Anderson Cancer Center, Houston, Texas
| | - Marilie D Gammon
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina
| | - Geoffrey Liu
- Pharmacogenomic Epidemiology, Ontario Cancer Institute, Toronto, Ontario, Canada
| | - Carlos Caldas
- Cancer Research UK, Cambridge Institute, Cambridge, UK
| | - Paul D Pharoah
- Department of Oncology, University of Cambridge, Cambridge, UK; Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Harvey A Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, Connecticut
| | - Andrea May
- Department of Medicine II, Sana Klinikum, Offenbach, Germany
| | - Christian Gerges
- Department of Internal Medicine II, Evangelisches Krankenhaus, Düsseldorf, Germany
| | - Mario Anders
- Department of Gastroenterology and Interdisciplinary Endoscopy, Vivantes Wenckebach-Klinikum, Berlin, Germany
| | - Marino Venerito
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University Hospital, Magdeburg, Germany
| | - Thomas Schmidt
- Department of General, Visceral and Transplantation Surgery, University of Heidelberg, Heidelberg, Germany
| | - Jakob R Izbicki
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, University of Hamburg, Hamburg, Germany
| | - Arnulf H Hölscher
- Department of General, Visceral and Cancer Surgery, University of Cologne, Cologne, Germany
| | - Brigitte Schumacher
- Department of Internal Medicine and Gastroenterology, Elisabeth Hospital, Essen, Germany
| | - Yogesh Vashist
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, University of Hamburg, Hamburg, Germany
| | - Horst Neuhaus
- Department of Internal Medicine II, Evangelisches Krankenhaus, Düsseldorf, Germany
| | - Thomas Rösch
- Department of Interdisciplinary Endoscopy, University Hospital Hamburg-Eppendorf, Hamburg, Germany
| | - Michael Knapp
- Institute of Medical Biometry, Informatics and Epidemiology, University of Bonn, Bonn, Germany
| | - Peter Krawitz
- Institute for Genomic Statistics and Bioinformatics, Medical Faculty, University of Bonn, Germany
| | - Anne Böhmer
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Bonn, Germany
| | - Prasad G Iyer
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Brian J Reid
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Jesper Lagergren
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden; School of Cancer and Pharmaceutical Sciences, King's College London, London, UK
| | - Nicholas J Shaheen
- Division of Gastroenterology and Hepatology, University of North Carolina School of Medicine, Chapel Hill, North Carolina
| | - Douglas A Corley
- Division of Research, Kaiser Permanente Northern California, Oakland, California; San Francisco Medical Center, Kaiser Permanente Northern California, San Francisco, California
| | - Ines Gockel
- Department of Visceral, Transplant, Thoracic and Vascular Surgery, University Hospital of Leipzig, Leipzig, Germany
| | - Rebecca C Fitzgerald
- Medical Research Council (MRC) Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK
| | - Michael B Cook
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - David C Whiteman
- Cancer Control, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Thomas L Vaughan
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | - Aaron P Thrift
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas; Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas.
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22
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Portas L, Pereira M, Shaheen SO, Wyss AB, London SJ, Burney PGJ, Hind M, Dean CH, Minelli C. Lung Development Genes and Adult Lung Function. Am J Respir Crit Care Med 2020; 202:853-865. [PMID: 32392078 PMCID: PMC7491406 DOI: 10.1164/rccm.201912-2338oc] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Rationale: Poor lung health in adult life may occur partly through
suboptimal growth and development, as suggested by epidemiological evidence
pointing to early life risk factors. Objectives: To systematically investigate the effects of lung
development genes on adult lung function. Methods: Using UK Biobank data, we tested the association of 391
genes known to influence lung development with FVC and FEV1/FVC. We
split the dataset into two random subsets of 207,616 and 138,411 individuals,
using the larger subset to select the most promising signals and the smaller
subset for replication. Measurements and Main Results: We identified 55 genes, of which 36
(16 for FVC, 19 for FEV1/FVC, and one for both) had not been
identified in the largest, most recent genome-wide study of lung function. Most
of these 36 signals were intronic variants; expression data from blood and lung
tissue showed that the majority affect the expression of the genes they lie
within. Further testing of 34 of these 36 signals in the CHARGE and SpiroMeta
consortia showed that 16 replicated after Bonferroni correction and another 12
replicated at nominal significance level. Of the 55 genes, 53 fell into four
biological categories whose function is to regulate organ size and cell
integrity (growth factors; transcriptional regulators; cell-to-cell adhesion;
extracellular matrix), suggesting that these specific processes are important
for adult lung health. Conclusions: Our study demonstrates the importance of lung
development genes in regulating adult lung function and influencing both
restrictive and obstructive patterns. Further investigation of these
developmental pathways could lead to druggable targets.
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Affiliation(s)
- Laura Portas
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Miguel Pereira
- National Heart and Lung Institute, Imperial College London, London, United Kingdom.,Congenica Ltd., Wellcome Genome Campus, Cambridge, United Kingdom
| | - Seif O Shaheen
- Institute of Population Health Sciences, Queen Mary University of London, London, United Kingdom
| | - Annah B Wyss
- Department of Health and Human Services, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina
| | - Stephanie J London
- Department of Health and Human Services, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina
| | - Peter G J Burney
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Matthew Hind
- National Heart and Lung Institute, Imperial College London, London, United Kingdom.,Department of Respiratory Medicine, Royal Brompton & Harefield NHS Foundation Trust, London, United Kingdom; and
| | - Charlotte H Dean
- National Heart and Lung Institute, Imperial College London, London, United Kingdom.,MRC Harwell Institute, Oxfordshire, United Kingdom
| | - Cosetta Minelli
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
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23
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Kim W, Prokopenko D, Sakornsakolpat P, Hobbs BD, Lutz SM, Hokanson JE, Wain LV, Melbourne CA, Shrine N, Tobin MD, Silverman EK, Cho MH, Beaty TH. Genome-Wide Gene-by-Smoking Interaction Study of Chronic Obstructive Pulmonary Disease. Am J Epidemiol 2020; 190:875-885. [PMID: 33106845 PMCID: PMC8096488 DOI: 10.1093/aje/kwaa227] [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] [Received: 12/01/2019] [Revised: 09/28/2020] [Accepted: 10/13/2020] [Indexed: 01/20/2023] Open
Abstract
Risk of chronic obstructive pulmonary disease (COPD) is determined by both cigarette smoking and genetic susceptibility, but little is known about gene-by-smoking interactions. We performed a genome-wide association analysis of 179,689 controls and 21,077 COPD cases from UK Biobank subjects of European ancestry recruited from 2006 to 2010, considering genetic main effects and gene-by-smoking interaction effects simultaneously (2-degrees-of-freedom (df) test) as well as interaction effects alone (1-df interaction test). We sought to replicate significant results in COPDGene (United States, 2008-2010) and SpiroMeta Consortium (multiple countries, 1947-2015) data. We considered 2 smoking variables: 1) ever/never and 2) current/noncurrent. In the 1-df test, we identified 1 genome-wide significant locus on 15q25.1 (cholinergic receptor nicotinic β4 subunit, or CHRNB4) for ever- and current smoking and identified PI*Z allele (rs28929474) of serpin family A member 1 (SERPINA1) for ever-smoking and 3q26.2 (MDS1 and EVI1 complex locus, or MECOM) for current smoking in an analysis of previously reported COPD loci. In the 2-df test, most of the significant signals were also significant for genetic marginal effects, aside from 16q22.1 (sphingomyelin phosphodiesterase 3, or SMPD3) and 19q13.2 (Egl-9 family hypoxia inducible factor 2, or EGLN2). The significant effects at 15q25.1 and 19q13.2 loci, both previously described in prior genome-wide association studies of COPD or smoking, were replicated in COPDGene and SpiroMeta. We identified interaction effects at previously reported COPD loci; however, we failed to identify novel susceptibility loci.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Terri H Beaty
- Correspondence to Dr. Terri H. Beaty, Department of Epidemiology, Johns Hopkins School of Public Health, 615 N. Wolfe Street, Baltimore, MD 21205 (e-mail: )
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24
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Zhao X, Qiao D, Yang C, Kasela S, Kim W, Ma Y, Shrine N, Batini C, Sofer T, Taliun SAG, Sakornsakolpat P, Balte PP, Prokopenko D, Yu B, Lange LA, Dupuis J, Cade BE, Lee J, Gharib SA, Daya M, Laurie CA, Ruczinski I, Cupples LA, Loehr LR, Bartz TM, Morrison AC, Psaty BM, Vasan RS, Wilson JG, Taylor KD, Durda P, Johnson WC, Cornell E, Guo X, Liu Y, Tracy RP, Ardlie KG, Aguet F, VanDenBerg DJ, Papanicolaou GJ, Rotter JI, Barnes KC, Jain D, Nickerson DA, Muzny DM, Metcalf GA, Doddapaneni H, Dugan-Perez S, Gupta N, Gabriel S, Rich SS, O'Connor GT, Redline S, Reed RM, Laurie CC, Daviglus ML, Preudhomme LK, Burkart KM, Kaplan RC, Wain LV, Tobin MD, London SJ, Lappalainen T, Oelsner EC, Abecasis GR, Silverman EK, Barr RG, Cho MH, Manichaikul A. Whole genome sequence analysis of pulmonary function and COPD in 19,996 multi-ethnic participants. Nat Commun 2020; 11:5182. [PMID: 33057025 PMCID: PMC7598941 DOI: 10.1038/s41467-020-18334-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 08/19/2020] [Indexed: 12/14/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD), diagnosed by reduced lung function, is a leading cause of morbidity and mortality. We performed whole genome sequence (WGS) analysis of lung function and COPD in a multi-ethnic sample of 11,497 participants from population- and family-based studies, and 8499 individuals from COPD-enriched studies in the NHLBI Trans-Omics for Precision Medicine (TOPMed) Program. We identify at genome-wide significance 10 known GWAS loci and 22 distinct, previously unreported loci, including two common variant signals from stratified analysis of African Americans. Four novel common variants within the regions of PIAS1, RGN (two variants) and FTO show evidence of replication in the UK Biobank (European ancestry n ~ 320,000), while colocalization analyses leveraging multi-omic data from GTEx and TOPMed identify potential molecular mechanisms underlying four of the 22 novel loci. Our study demonstrates the value of performing WGS analyses and multi-omic follow-up in cohorts of diverse ancestry.
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Affiliation(s)
- Xutong Zhao
- Center for Statistical Genetics, and Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Dandi Qiao
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Chaojie Yang
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Silva Kasela
- New York Genome Center, New York, NY, 10013, USA
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
| | - Wonji Kim
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Yanlin Ma
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Nick Shrine
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Chiara Batini
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, LE1 7RH, United Kingdom
| | - Tamar Sofer
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Sarah A Gagliano Taliun
- Center for Statistical Genetics, and Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Phuwanat Sakornsakolpat
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Pallavi P Balte
- Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Dmitry Prokopenko
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Bing Yu
- Department of Epidemiology, Human Genetics & Environmental Sciences, UTHealth School of Public Health, Houston, TX, 77030, USA
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado School of Medicine Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Brian E Cade
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Jiwon Lee
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Sina A Gharib
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Michelle Daya
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado School of Medicine Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - Cecelia A Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Ingo Ruczinski
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
- Boston University and the National Heart Lung and Blood Institute's Framingham Heart Study, Framingham, MA, 01702, USA
| | - Laura R Loehr
- Department of Medicine, UNC School of Medicine, Chapel Hill, NC, 27599, USA
| | - Traci M Bartz
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Services, University of Washington, Seattle, WA, 98101, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, 98101, USA
| | - Ramachandran S Vasan
- Boston University and the National Heart Lung and Blood Institute's Framingham Heart Study, Framingham, MA, 01702, USA
- Department of Preventive Medicine and Epidemiology, Boston University School of Medicine and Public Health, Boston, MA, 02118, USA
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, The Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Peter Durda
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - W Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Elaine Cornell
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, The Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Yongmei Liu
- Department of Medicine, Division of Cardiology, Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC, 27701, USA
| | - Russell P Tracy
- Department of Pathology and Laboratory Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT, 05405, USA
| | | | - François Aguet
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - David J VanDenBerg
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - George J Papanicolaou
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, The Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, 90502, 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, 80045, USA
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Donna M Muzny
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Ginger A Metcalf
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Shannon Dugan-Perez
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Namrata Gupta
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Stacey Gabriel
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - George T O'Connor
- Boston University School Of Medicine, Pulmonary Center, Boston, MA, 02118, USA
| | - Susan Redline
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, MA, 02215, USA
| | - Robert M Reed
- Division of Pulmonary and Critical Care Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Cathy C Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Martha L Daviglus
- Institute for Minority Health Research, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | | | - Kristin M Burkart
- Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York, NY, 10461, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Louise V Wain
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, LE1 7RH, United Kingdom
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, LE3 9QP, UK
| | - Martin D Tobin
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, LE1 7RH, United Kingdom
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, LE3 9QP, UK
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Durham, NC, 27709, USA
| | - Tuuli Lappalainen
- New York Genome Center, New York, NY, 10013, USA
- Department of Systems Biology, Columbia University, New York, NY, 10032, USA
| | - Elizabeth C Oelsner
- Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Goncalo R Abecasis
- Center for Statistical Genetics, and Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - R Graham Barr
- Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA.
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25
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Park B, An J, Kim W, Kang HY, Koh SB, Oh B, Jung KJ, Jee SH, Kim WJ, Cho MH, Silverman EK, Park T, Won S. Effect of 6p21 region on lung function is modified by smoking: a genome-wide interaction study. Sci Rep 2020; 10:13075. [PMID: 32753590 PMCID: PMC7403370 DOI: 10.1038/s41598-020-70092-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 07/15/2020] [Indexed: 11/10/2022] Open
Abstract
Smoking is a major risk factor for chronic obstructive pulmonary disease (COPD); however, more than 25% of COPD patients are non-smokers, and gene-by-smoking interactions are expected to affect COPD onset. We aimed to identify the common genetic variants interacting with pack-years of smoking on FEV1/FVC ratios in individuals with normal lung function. A genome-wide interaction study (GWIS) on FEV1/FVC was performed for individuals with FEV1/FVC ratio ≥ 70 in the Korea Associated Resource cohort data, and significant SNPs were validated using data from two other Korean cohorts. The GWIS revealed that rs10947231 and rs8192575 met genome-wide significant levels; For \documentclass[12pt]{minimal}
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\begin{document}$${\text{H}}_{0} :\beta_{SNP} = \beta_{SNP*pack - years} = 0{\text{ vs H}}_{1} : not {\text{H}}_{0} ,$$\end{document}H0:βSNP=βSNP∗pack-years=0vs H1:notH0, the likelihood ratio (LR) test was conducted, and its P values, PLR, for rs10947231 and rs8192575 were 2.23 × 10–12 and 1.18 × 10–8, respectively. Interaction between rs8192575 and smoking is significantly replicated with two additional data (PINT = 0.0454, 0.0131). Expression quantitative trait loci, topologically associated domains, and PrediXcan analyses revealed that rs8192575 is significantly associated with AGER expression. SNPs on the 6p21 region are associated with FEV1/FVC, and the effect of smoking on FEV1/FVC differs among the associated genotypes.
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Affiliation(s)
- Boram Park
- Department of Public Health Sciences, Seoul National University, Seoul, South Korea
| | - Jaehoon An
- Department of Public Health Sciences, Seoul National University, Seoul, South Korea
| | - Wonji Kim
- Interdisciplinary Program of Bioinformatics, Seoul National University, Seoul, South Korea
| | - Hae Yeon Kang
- Department of Internal Medicine, Healthcare Research Institute, Seoul National University Hospital Healthcare System Gangnam Center, Seoul, South Korea
| | - Sang Baek Koh
- Department of Preventive Medicine, Yonsei University Wonju College of Medicine, Wonju, South Korea
| | - Bermseok Oh
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul, South Korea
| | - Keum Ji Jung
- Institute for Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, South Korea
| | - Sun Ha Jee
- Institute for Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, South Korea
| | - Woo Jin Kim
- Department of Internal Medicine and Environmental Health Center, Kangwon National University Hospital, School of Medicine, Kangwon University, Chuncheon, South Korea
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Taesung Park
- Interdisciplinary Program of Bioinformatics, Seoul National University, Seoul, South Korea. .,Department of Statistics, Seoul National University, Seoul, South Korea.
| | - Sungho Won
- Department of Public Health Sciences, Seoul National University, Seoul, South Korea. .,Interdisciplinary Program of Bioinformatics, Seoul National University, Seoul, South Korea. .,Institute of Health and Environment, Seoul National University, Seoul, South Korea.
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26
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Shete S, Liu H, Wang J, Yu R, Sturgis EM, Li G, Dahlstrom KR, Liu Z, Amos CI, Wei Q. A Genome-Wide Association Study Identifies Two Novel Susceptible Regions for Squamous Cell Carcinoma of the Head and Neck. Cancer Res 2020; 80:2451-2460. [PMID: 32276964 PMCID: PMC7299763 DOI: 10.1158/0008-5472.can-19-2360] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 02/06/2020] [Accepted: 04/07/2020] [Indexed: 12/13/2022]
Abstract
To identify genetic variants for risk of squamous cell carcinoma of the head and neck (SCCHN), we conducted a two-phase genome-wide association study consisting of 7,858,089 SNPs in 2,171 cases and 4,493 controls of non-Hispanic white, of which, 434,839 typed and 7,423,250 imputed SNPs were used as the discovery. SNPs with P < 1 × 10-3 were further validated in the OncoArray study of oral and pharynx cancer (5,205 cases and 3,232 controls of European ancestry) from databases of Genotypes and Phenotypes. Meta-analysis of the discovery and replication studies identified one novel locus 6p22.1 (P = 2.96 × 10-9 for the leading rs259919) and two cancer susceptibility loci 6p21.32 (rs3135001, HLA-DQB1) and 6p21.33 (rs1265081, CCHCR1) associated with SCCHN risk. Further stratification by tumor site revealed four known cancer loci (5p15.33, 6p21.32, 6p21.33, and 2p23.1) associated with oral cavity cancer risk and oropharyngeal cancer risk, respectively. In addition, one novel locus 18q22.2 (P = 2.54 × 10-9 for the leading SNP rs142021700) was identified for hypopharynx and larynx cancer risk. For SNPs in those reported or novel loci, we also performed functional annotations by bioinformatics prediction and expression quantitative trait loci analysis. Collectively, our identification of four reported loci (2p23.1, 5p15.33, 6p21.32, and 6p21.33) and two novel loci (6p22.1 and 18q22.2) for SCCHN risk highlight the importance of human leukocyte antigen loci for oropharyngeal cancer risk, suggesting that immunologic mechanisms are implicated in the etiology of this subset of SCCHN. SIGNIFICANCE: Two novel risk loci for SCCHN in non-Hispanic white individuals highlight the importance of immunologic mechanism in the disease etiology.
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Affiliation(s)
- Sanjay Shete
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hongliang Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina
| | - Jian Wang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Robert Yu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Erich M Sturgis
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Guojun Li
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kristina R Dahlstrom
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Zhensheng Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina
| | - Christopher I Amos
- The Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas
| | - Qingyi Wei
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina.
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina
- Department of Population Health Sciences, Duke University Medical School, Durham, North Carolina
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27
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Nakahara S, Stark CE, Turner JA, Calhoun VD, Lim KO, Mueller B, Bustillo JR, O’Leary DS, McEwen S, Voyvodic J, Belger A, Mathalon DH, Ford JM, Macciardi F, Matsumoto M, Potkin SG, van Erp TG. Dentate gyrus volume deficit in schizophrenia. Psychol Med 2020; 50:1267-1277. [PMID: 31155012 PMCID: PMC7068799 DOI: 10.1017/s0033291719001144] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Schizophrenia is associated with robust hippocampal volume deficits but subregion volume deficits, their associations with cognition, and contributing genes remain to be determined. METHODS Hippocampal formation (HF) subregion volumes were obtained using FreeSurfer 6.0 from individuals with schizophrenia (n = 176, mean age ± s.d. = 39.0 ± 11.5, 132 males) and healthy volunteers (n = 173, mean age ± s.d. = 37.6 ± 11.3, 123 males) with similar mean age, gender, handedness, and race distributions. Relationships between the HF subregion volume with the largest between group difference, neuropsychological performance, and single-nucleotide polymorphisms were assessed. RESULTS This study found a significant group by region interaction on hippocampal subregion volumes. Compared to healthy volunteers, individuals with schizophrenia had significantly smaller dentate gyrus (DG) (Cohen's d = -0.57), Cornu Ammonis (CA) 4, molecular layer of the hippocampus, hippocampal tail, and CA 1 volumes, when statistically controlling for intracranial volume; DG (d = -0.43) and CA 4 volumes remained significantly smaller when statistically controlling for mean hippocampal volume. DG volume showed the largest between group difference and significant positive associations with visual memory and speed of processing in the overall sample. Genome-wide association analysis with DG volume as the quantitative phenotype identified rs56055643 (β = 10.8, p < 5 × 10-8, 95% CI 7.0-14.5) on chromosome 3 in high linkage disequilibrium with MOBP. Gene-based analyses identified associations between SLC25A38 and RPSA and DG volume. CONCLUSIONS This study suggests that DG dysfunction is fundamentally involved in schizophrenia pathophysiology, that it may contribute to cognitive abnormalities in schizophrenia, and that underlying biological mechanisms may involve contributions from MOBP, SLC25A38, and RPSA.
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Affiliation(s)
- Soichiro Nakahara
- Clinical Translational Neuroscience Laboratory, Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA, 92617, United States
- Unit 2, Candidate Discovery Science Labs, Drug Discovery Research, Astellas Pharma Inc, 21, Miyukigaoka, Tsukuba, Ibaraki 305-8585, Japan
| | - Craig E.L. Stark
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, 92697, United States
- Center for the Neurobiology of Learning and Memory, University of California Irvine, Irvine, CA, 92697, United States
| | - Jessica A. Turner
- Departments of Psychology and Neuroscience, Georgia State University, Atlanta, GA, 30302, United States
- Mind Research Network, Albuquerque, NM, 87106, United States
| | - Vince D. Calhoun
- Mind Research Network, Albuquerque, NM, 87106, United States
- Department of Electrical and Computer Engineering, University of New Mexico, Albuquerque, NM, 87131, United States
- Departments of Psychiatry & Neuroscience, University of New Mexico, Albuquerque, NM, 87131, United States
| | - Kelvin O. Lim
- Department of Psychiatry, University of Minnesota, Minneapolis, MN, 55454, United States
| | - Bryon Mueller
- Department of Psychiatry, University of Minnesota, Minneapolis, MN, 55454, United States
| | - Juan R. Bustillo
- Departments of Psychiatry & Neuroscience, University of New Mexico, Albuquerque, NM, 87131, United States
| | - Daniel S. O’Leary
- Department of Psychiatry, University of Iowa, Iowa City, IA, 52242, United States
| | - Sarah McEwen
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, 92093, United States
| | - James Voyvodic
- Brain Imaging and Analysis Center, Duke University Medical Center, Durham, NC, 27710, United States
| | - Aysenil Belger
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, United States
| | - Daniel H. Mathalon
- Department of Psychiatry, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, United States
- Veterans Affairs San Francisco Healthcare System, San Francisco, CA, 94121, United States
| | - Judith M. Ford
- Department of Psychiatry, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, United States
- Veterans Affairs San Francisco Healthcare System, San Francisco, CA, 94121, United States
| | - Fabio Macciardi
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA, 92617, United States
| | - Mitsuyuki Matsumoto
- Unit 2, Candidate Discovery Science Labs, Drug Discovery Research, Astellas Pharma Inc, 21, Miyukigaoka, Tsukuba, Ibaraki 305-8585, Japan
| | - Steven G. Potkin
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA, 92617, United States
| | - Theo G.M. van Erp
- Clinical Translational Neuroscience Laboratory, Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA, 92617, United States
- Center for the Neurobiology of Learning and Memory, University of California Irvine, Irvine, CA, 92697, United States
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28
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Williams PT. Spirometric traits show quantile-dependent heritability, which may contribute to their gene-environment interactions with smoking and pollution. PeerJ 2020; 8:e9145. [PMID: 32461834 PMCID: PMC7233273 DOI: 10.7717/peerj.9145] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 04/17/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND "Quantile-dependent expressivity" refers to a genetic effect that is dependent upon whether the phenotype (e.g., spirometric data) is high or low relative to its population distribution. Forced vital capacity (FVC), forced expiratory volume in 1 second (FEV1), and the FEV1/FVC ratio are moderately heritable spirometric traits. The aim of the analyses is to test whether their heritability (h2 ) is constant over all quantiles of their distribution. METHODS Quantile regression was applied to the mean age, sex, height and smoking-adjusted spirometric data over multiple visits in 9,993 offspring-parent pairs and 1,930 sibships from the Framingham Heart Study to obtain robust estimates of offspring-parent (βOP), offspring-midparent (βOM), and full-sib regression slopes (βFS). Nonparametric significance levels were obtained from 1,000 bootstrap samples. βOPs were used as simple indicators of quantile-specific heritability (i.e., h 2 = 2βOP/(1+rspouse), where rspouse was the correlation between spouses). RESULTS βOP ± standard error (SE) decreased by 0.0009 ± 0.0003 (P = 0.003) with every one-percent increment in the population distribution of FEV1/FVC, i.e., βOP ± SE were: 0.182 ± 0.031, 0.152 ± 0.015; 0.136 ± 0.011; 0.121 ± 0.013; and 0.099 ± 0.013 at the 10th, 25th, 50th, 75th, and 90th percentiles of the FEV1/FVC distribution, respectively. These correspond to h2 ± SEs of 0.350 ± 0.060 at the 10th, 0.292 ± 0.029 at the 25th, 0.262 ± 0.020 at the 50th, 0.234 ± 0.025 at the 75th, and 0.191 ± 0.025 at the 90th percentiles of the FEV1/FVC ratio. Maximum mid-expiratory flow (MMEF) h2 ± SEs increased 0.0025 ± 0.0007 (P = 0.0004) with every one-percent increment in its distribution, i.e.: 0.467 ± 0.046, 0.467 ± 0.033, 0.554 ± 0.038, 0.615 ± 0.042, and 0.675 ± 0.060 at the 10th, 25th, 50th, 75th, and 90th percentiles of its distribution. This was due to forced expiratory flow at 75% of FVC (FEF75%), whose quantile-specific h2 increased an average of 0.0042 ± 0.0008 for every one-percent increment in its distribution. It is speculated that previously reported gene-environment interactions may be partially attributable to quantile-specific h2 , i.e., greater heritability in individuals with lower FEV1/FVC due to smoking or airborne particles exposure vs. nonsmoking, unexposed individuals. CONCLUSION Heritabilities of FEV1/FVC, MMEF, and FEF75% from quantile-regression of offspring-parent and sibling spirometric data suggest their quantile-dependent expressivity.
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Affiliation(s)
- Paul T. Williams
- Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States of America
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29
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Wu P, Rybin D, Bielak LF, Feitosa MF, Franceschini N, Li Y, Lu Y, Marten J, Musani SK, Noordam R, Raghavan S, Rose LM, Schwander K, Smith AV, Tajuddin SM, Vojinovic D, Amin N, Arnett DK, Bottinger EP, Demirkan A, Florez JC, Ghanbari M, Harris TB, Launer LJ, Liu J, Liu J, Mook-Kanamori DO, Murray AD, Nalls MA, Peyser PA, Uitterlinden AG, Voortman T, Bouchard C, Chasman D, Correa A, de Mutsert R, Evans MK, Gudnason V, Hayward C, Kao L, Kardia SLR, Kooperberg C, Loos RJF, Province MM, Rankinen T, Redline S, Ridker PM, Rotter JI, Siscovick D, Smith BH, van Duijn C, Zonderman AB, Rao DC, Wilson JG, Dupuis J, Meigs JB, Liu CT, Vassy JL. Smoking-by-genotype interaction in type 2 diabetes risk and fasting glucose. PLoS One 2020; 15:e0230815. [PMID: 32379818 PMCID: PMC7205201 DOI: 10.1371/journal.pone.0230815] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 03/09/2020] [Indexed: 02/07/2023] Open
Abstract
Smoking is a potentially causal behavioral risk factor for type 2 diabetes (T2D), but not all smokers develop T2D. It is unknown whether genetic factors partially explain this variation. We performed genome-environment-wide interaction studies to identify loci exhibiting potential interaction with baseline smoking status (ever vs. never) on incident T2D and fasting glucose (FG). Analyses were performed in participants of European (EA) and African ancestry (AA) separately. Discovery analyses were conducted using genotype data from the 50,000-single-nucleotide polymorphism (SNP) ITMAT-Broad-CARe (IBC) array in 5 cohorts from from the Candidate Gene Association Resource Consortium (n = 23,189). Replication was performed in up to 16 studies from the Cohorts for Heart Aging Research in Genomic Epidemiology Consortium (n = 74,584). In meta-analysis of discovery and replication estimates, 5 SNPs met at least one criterion for potential interaction with smoking on incident T2D at p<1x10-7 (adjusted for multiple hypothesis-testing with the IBC array). Two SNPs had significant joint effects in the overall model and significant main effects only in one smoking stratum: rs140637 (FBN1) in AA individuals had a significant main effect only among smokers, and rs1444261 (closest gene C2orf63) in EA individuals had a significant main effect only among nonsmokers. Three additional SNPs were identified as having potential interaction by exhibiting a significant main effects only in smokers: rs1801232 (CUBN) in AA individuals, rs12243326 (TCF7L2) in EA individuals, and rs4132670 (TCF7L2) in EA individuals. No SNP met significance for potential interaction with smoking on baseline FG. The identification of these loci provides evidence for genetic interactions with smoking exposure that may explain some of the heterogeneity in the association between smoking and T2D.
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Affiliation(s)
- Peitao Wu
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, MA, United States of America
| | - Denis Rybin
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, MA, United States of America
| | - Lawrence F. Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States of America
| | - Mary F. Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Nora Franceschini
- University of North Carolina, Chapel Hill, NC, United States of America
| | - Yize Li
- Division of Biostatistics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Yingchang Lu
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Jonathan Marten
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Solomon K. Musani
- Jackson Heart Study, University of Mississippi Medical Center, MS, United States of America
| | - Raymond Noordam
- Department of Internal Medicine, Section of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Sridharan Raghavan
- Section of Hospital Medicine, Veterans Affairs Eastern Colorado Healthcare System, Denver, CO, United States of America
- Division of General Internal Medicine, University of Colorado School of Medicine, Aurora, CO, United States of America
- Colorado Cardiovascular Outcomes Research Consortium, Aurora, CO, United States of America
| | - Lynda M. Rose
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, United States of America
| | - Karen Schwander
- Division of Biostatistics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Albert V. Smith
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Salman M. Tajuddin
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States of America
| | - Dina Vojinovic
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Najaf Amin
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Donna K. Arnett
- Dean's Office, University of Kentucky College of Public Health, Lexington, Kentucky, United States of America
| | - Erwin P. Bottinger
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Ayse Demirkan
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jose C. Florez
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Massachusetts General Hospital, Boston, MA, United States of America
- Programs in Metabolism and Medical & Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Department of Medicine, Harvard Medical School, Boston, MA, United States of America
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Genetics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Tamara B. Harris
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Intramural Research Program, National Institutes of Health, Bethesda, MD, United States of America
| | - Lenore J. Launer
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Intramural Research Program, National Institutes of Health, Bethesda, MD, United States of America
| | - Jingmin Liu
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Jun Liu
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Dennis O. Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, The Netherlands
| | - Alison D. Murray
- The Institute of Medical Sciences, Aberdeen Biomedical Imaging Centre, University of Aberdeen, Aberdeen, United Kingdom
| | - Mike A. Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, United States of America
- Data Tecnica International LLC, Glen Echo, MD, United States of America
| | - Patricia A. Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States of America
| | - André G. Uitterlinden
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Trudy Voortman
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Claude Bouchard
- Human Genomics Laboratory, Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, LA, United States of America
| | - Daniel Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, United States of America
- Harvard Medical School, Boston, MA, United States of America
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, United States of America
| | - Renée de Mutsert
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Michele K. Evans
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States of America
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- University of Iceland, Reykjavik, Iceland
| | - Caroline Hayward
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Linda Kao
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, United States of America
- Welch Center for Prevention, Epidemiology and Clinical Research, Johns Hopkins University, Baltimore, MD, United States of America
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States of America
| | - Sharon L. R. Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, United States of America
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Ruth J. F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- The Mindich Child Health and Development Institute, Ichan School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Michael M. Province
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO, United States of America
| | - Tuomo Rankinen
- Human Genomics Laboratory, Pennington Biomedical Research Center, Louisiana State University System, Baton Rouge, LA, United States of America
| | - Susan Redline
- Harvard Medical School, Boston, MA, United States of America
- Departments of Medicine, Brigham and Women's Hospital, Boston, MA, United States of America
- Beth Israel Deaconess Medical Center, Boston, MA, United States of America
| | - Paul M. Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, United States of America
- Harvard Medical School, Boston, MA, United States of America
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, United States of America
| | - David Siscovick
- The New York Academy of Medicine, New York, NY, United States of America
| | - Blair H. Smith
- Division of Population Health and Genomics, University of Dundee, Dundee, United Kingdom
| | - Cornelia van Duijn
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Alan B. Zonderman
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, Baltimore, MD, United States of America
| | - D. C. Rao
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, United States of America
| | - James G. Wilson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, United States of America
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, MA, United States of America
- The National Heart, Lung, and Blood Institute’s Framingham Heart Study, Framingham, MA, United States of America
| | - James B. Meigs
- Programs in Metabolism and Medical & Population Genetics, Broad Institute, Cambridge, MA, United States of America
- Division of General Internal Medicine Division, Massachusetts General Hospital, Boston, MA, United States of America
- Department of Medicine, Harvard Medical School, Boston, MA, United States of America
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, MA, United States of America
| | - Jason L. Vassy
- Department of Medicine, Harvard Medical School, Boston, MA, United States of America
- VA Boston Healthcare System, Boston, MA, United States of America
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Freitag-Wolf S, Munz M, Wiehe R, Junge O, Graetz C, Jockel-Schneider Y, Staufenbiel I, Bruckmann C, Lieb W, Franke A, Loos B, Jepsen S, Dommisch H, Schaefer A. Smoking Modifies the Genetic Risk for Early-Onset Periodontitis. J Dent Res 2019; 98:1332-1339. [DOI: 10.1177/0022034519875443] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Periodontitis has low-prevalence, highly severe disease manifestations with an early onset and rapid progression. The diagnosis is based on severe destruction of the alveolar bone in adolescents and young adults. Genetic susceptibility variants and smoking are well-established risk factors, but their interactions in modifying disease susceptibility have not been studied. We aimed to identify genetic risk variants of early-onset periodontitis that unmask their effects on tobacco smoke exposure. To this end, we analyzed 79,780,573 common variants in 741 northwest Europeans diagnosed to have >30% bone loss at >2 teeth before 35 y of age, using imputed genotypes of the OmniExpress BeadChip. Never versus ever smokers were compared in a logistic regression analysis via a case-only approach. To explore the effect of tobacco smoke on the expression of the G×S-associated genes, cultures of primary gingival fibroblasts ( n = 9) were exposed to cigarette smoke extract, and transcripts were quantified by reverse transcription polymerase chain reaction. We identified 16 loci for which our analysis suggested an association with G×S increased disease risk ( P < 5 × 10−5). Nine loci had previously been reported to be associated with spirometric measures of pulmonary function by an earlier G×S genome-wide association study. Genome-wide significant cis expression quantitative trait loci were reported for G×S-associated single-nucleotide polymorphisms at ST8SIA1 and SOST, indicating a causal role of these genes in tobacco-related etiopathology. Notably, SOST is a negative regulator of bone growth, and ST8SIA1 has a role in tissue remodeling. Cigarette smoke extract significantly altered the expression of 2 associated genes: SSH1 ( P = 5 × 10−07), which is required for NF-κB activation and innate immune responses to bacterial invasion, and ST8SIA1 ( P = 0.0048). We conclude that the genetic predisposition to early-onset periodontitis is in part triggered by smoking and that tobacco smoke directly affects the expression of genes involved in bone homeostasis, tissue repair, and immune response.
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Affiliation(s)
- S. Freitag-Wolf
- Institute of Medical Informatics and Statistics, University Hospital Schleswig-Holstein, Kiel University, Germany
| | - M. Munz
- Department of Periodontology and Synoptic Dentistry, Institute for Dental and Craniofacial Sciences, Berlin Institute of Health, Charité–University Medicine Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Institute for Cardiogenetics, University of Lübeck, Lübeck, Germany
| | - R. Wiehe
- Department of Periodontology and Synoptic Dentistry, Institute for Dental and Craniofacial Sciences, Berlin Institute of Health, Charité–University Medicine Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - O. Junge
- Institute of Medical Informatics and Statistics, University Hospital Schleswig-Holstein, Kiel University, Germany
| | - C. Graetz
- Unit of Periodontology, Department of Conservative Dentistry, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Y. Jockel-Schneider
- Clinic of Preventive Dentistry and Periodontology, Department of Periodontology, University Medical Center of the Julius-Maximilians-University, Würzburg, Germany
| | - I. Staufenbiel
- Periodontology and Preventive Dentistry, Department of Conservative Dentistry, Hannover Medical School, Hannover, Germany
| | - C. Bruckmann
- Department of Conservative Dentistry and Periodontology, School of Dentistry, Medical University Vienna, Vienna, Austria
| | - W. Lieb
- Institute of Epidemiology, Christian-Albrechts-University, Kiel, Germany
| | - A. Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - B.G. Loos
- Department of Periodontology and Oral Biochemistry, Academic Centre for Dentistry Amsterdam (ACTA), University of Amsterdam and Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - S. Jepsen
- Operative and Preventive Dentistry, Department of Periodontology, University of Bonn, Bonn, Germany
| | - H. Dommisch
- Department of Periodontology and Synoptic Dentistry, Institute for Dental and Craniofacial Sciences, Berlin Institute of Health, Charité–University Medicine Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - A.S. Schaefer
- Department of Periodontology and Synoptic Dentistry, Institute for Dental and Craniofacial Sciences, Berlin Institute of Health, Charité–University Medicine Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
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Cho HY, Kleeberger SR. Mitochondrial biology in airway pathogenesis and the role of NRF2. Arch Pharm Res 2019; 43:297-320. [PMID: 31486024 DOI: 10.1007/s12272-019-01182-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 08/14/2019] [Indexed: 12/12/2022]
Abstract
A constant improvement in understanding of mitochondrial biology has provided new insights into mitochondrial dysfunction in human disease pathogenesis. Impaired mitochondrial dynamics caused by various stressors are characterized by structural abnormalities and leakage, compromised turnover, and reactive oxygen species overproduction in mitochondria as well as increased mitochondrial DNA mutation frequency, which leads to modified energy production and mitochondria-derived cell signaling. The mitochondrial dysfunction in airway epithelial, smooth muscle, and endothelial cells has been implicated in diseases including chronic obstructive lung diseases and acute lung injury. Increasing evidence indicates that the NRF2-antioxidant response element (ARE) pathway not only enhances redox defense but also facilitates mitochondrial homeostasis and bioenergetics. Identification of functional or potential AREs further supports the role for Nrf2 in mitochondrial dysfunction-associated airway disorders. While clinical reports indicate mixed efficacy, NRF2 agonists acting on respiratory mitochondrial dynamics are potentially beneficial. In lung cancer, growth advantage provided by sustained NRF2 activation is suggested to be through increased cellular antioxidant defense as well as mitochondria reinforcement and metabolic reprogramming to the preferred pathways to meet the increased energy demands of uncontrolled cell proliferation. Further studies are warranted to better understand NRF2 regulation of mitochondrial functions as therapeutic targets in airway disorders.
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Affiliation(s)
- Hye-Youn Cho
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, 111 TW Alexander Dr., Research Triangle Park, NC, 27709, USA.
| | - Steven R Kleeberger
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, 111 TW Alexander Dr., Research Triangle Park, NC, 27709, USA
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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.
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Affiliation(s)
- Astha Ranjan
- Department of Anthropology, University of Delhi, Delhi 110 007, India.
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Henry AP, Probert K, Stewart CE, Thakker D, Bhaker S, Azimi S, Hall IP, Sayers I. Defining a role for lung function associated gene GSTCD in cell homeostasis. Respir Res 2019; 20:172. [PMID: 31370853 PMCID: PMC6676530 DOI: 10.1186/s12931-019-1146-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 07/25/2019] [Indexed: 12/11/2022] Open
Abstract
Genome wide association (GWA) studies have reproducibly identified signals on chromosome 4q24 associated with lung function and COPD. GSTCD (Glutathione S-transferase C-terminal domain containing) represents a candidate causal gene in this locus, however little is currently known about the function of this protein. We set out to further our understanding of the role of GSTCD in cell functions and homeostasis using multiple molecular and cellular approaches in airway relevant cells. Recombinant expression of human GSTCD in conjunction with a GST activity assay did not identify any enzymatic activity for two GSTCD isoforms questioning the assignment of this protein to this family of enzymes. Protein structure analyses identified a potential methyltransferase domain contained within GSTCD, with these enzymes linked to cell viability and apoptosis. Targeted knockdown (siRNA) of GSTCD in bronchial epithelial cells identified a role for GSTCD in cell viability as proliferation rates were not altered. To provide greater insight we completed transcriptomic analyses on cells with GSTCD expression knocked down and identified several differentially expressed genes including those implicated in airway biology; fibrosis e.g. TGFBR1 and inflammation e.g. IL6R. Pathway based transcriptomic analyses identified an over-representation of genes related to adipogenesis which may suggest additional functions for GSTCD. These findings identify potential additional functions for GSTCD in the context of airway biology beyond the hypothesised GST activity and warrant further investigation.
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Affiliation(s)
- Amanda P Henry
- Division of Respiratory Medicine, National Institute for Health Research, Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK.
| | - Kelly Probert
- Division of Respiratory Medicine, National Institute for Health Research, Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Ceri E Stewart
- Division of Respiratory Medicine, National Institute for Health Research, Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Dhruma Thakker
- Division of Respiratory Medicine, National Institute for Health Research, Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Sangita Bhaker
- Division of Respiratory Medicine, National Institute for Health Research, Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Sheyda Azimi
- Division of Respiratory Medicine, National Institute for Health Research, Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Ian P Hall
- Division of Respiratory Medicine, National Institute for Health Research, Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Ian Sayers
- Division of Respiratory Medicine, National Institute for Health Research, Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
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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]
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London SJ, Melén E. Genomic interactions with exposure to inhaled pollutants. J Allergy Clin Immunol 2019; 143:2011-2013.e1. [PMID: 31029775 PMCID: PMC6563341 DOI: 10.1016/j.jaci.2019.04.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 04/17/2019] [Accepted: 04/19/2019] [Indexed: 12/09/2022]
Affiliation(s)
- Stephanie J London
- Epidemiology Branch and Immunity, Inflammation and Disease Laboratory, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC.
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Clinical Science and Education, Karolinska Institutet and Sachs' Children's Hospital, South General Hospital, Stockholm, Sweden
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Ballester-López C, Conlon TM, Ertüz Z, Greiffo FR, Irmler M, Verleden SE, Beckers J, Fernandez IE, Eickelberg O, Yildirim AÖ. The Notch ligand DNER regulates macrophage IFNγ release in chronic obstructive pulmonary disease. EBioMedicine 2019; 43:562-575. [PMID: 31060902 PMCID: PMC6562022 DOI: 10.1016/j.ebiom.2019.03.054] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 02/28/2019] [Accepted: 03/19/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Chronic Obstructive Pulmonary Disease (COPD) is the third leading cause of death worldwide with no curative therapy. A non-canonical Notch ligand, DNER, has been recently identified in GWAS to associate with COPD severity, but its function and contribution to COPD is unknown. METHODS DNER localisation was assessed in lung tissue from healthy and COPD patients, and cigarette smoke (CS) exposed mice. Microarray analysis was performed on WT and DNER deficient M1 and M2 bone marrow-derived macrophages (BMDM), and gene set enrichment undertaken. WT and DNER deficient mice were exposed to CS or filtered air for 3 day and 2 months to assess IFNγ-expressing macrophages and emphysema development. Notch and NFKB active subunits were quantified in WT and DNER deficient LPS-treated and untreated BMDM. FINDINGS Immunofluorescence staining revealed DNER localised to macrophages in lung tissue from COPD patients and mice. Human and murine macrophages showed enhanced DNER expression in response to inflammation. Interestingly, pro-inflammatory DNER deficient BMDMs exhibited impaired NICD1/NFKB dependent IFNγ signalling and reduced nuclear NICD1/NFKB translocation. Furthermore, decreased IFNγ production and Notch1 activation in recruited macrophages from CS exposed DNER deficient mice were observed, protecting against emphysema and lung dysfunction. INTERPRETATION DNER is a novel protein induced in COPD patients and 6 months CS-exposed mice that regulates IFNγ secretion via non-canonical Notch in pro-inflammatory recruited macrophages. These results provide a new pathway involved in COPD immunity that could contribute to the discovery of innovative therapeutic targets. FUNDING This work was supported from the Helmholtz Alliance 'Aging and Metabolic Programming, AMPro'.
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Affiliation(s)
- Carolina Ballester-López
- Comprehensive Pneumology Center (CPC), Institute of Lung Biology and Disease, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Thomas M Conlon
- Comprehensive Pneumology Center (CPC), Institute of Lung Biology and Disease, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Zeynep Ertüz
- Comprehensive Pneumology Center (CPC), Institute of Lung Biology and Disease, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Flavia R Greiffo
- Comprehensive Pneumology Center (CPC), Institute of Lung Biology and Disease, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Martin Irmler
- Institute of Experimental Genetics (IEG), Helmholtz Zentrum München, Munich, Germany
| | | | - Johannes Beckers
- Institute of Experimental Genetics (IEG), Helmholtz Zentrum München, Munich, Germany; Chair of Experimental Genetics, Technische Universität München, Freising, Germany; German Center for Diabetes Research (DZD), Germany
| | - Isis E Fernandez
- Comprehensive Pneumology Center (CPC), Institute of Lung Biology and Disease, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | - Oliver Eickelberg
- Comprehensive Pneumology Center (CPC), Institute of Lung Biology and Disease, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany; Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado, Denver, CO, USA
| | - Ali Önder Yildirim
- Comprehensive Pneumology Center (CPC), Institute of Lung Biology and Disease, Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany.
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Fan M, Lv J, Yu C, Guo Y, Bian Z, Yang S, Yang L, Chen Y, Li F, Zhai Y, Wang P, Chen J, Chen Z, Qi L, Li L. Family History, Tobacco Smoking, and Risk of Ischemic Stroke. J Stroke 2019; 21:175-183. [PMID: 31161762 PMCID: PMC6549063 DOI: 10.5853/jos.2018.03566] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/13/2019] [Accepted: 04/18/2019] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND AND PURPOSE Both genetic factors and smoking are associated with ischemic stroke (IS) risk. However, little is known about the potential interaction of these factors. We aimed to assess whether smoking and a positive family history interact to increase the risk of IS. METHODS The nationwide prospective study recruited 210,000 men and 300,000 women in 2004 to 2008 at ages 30 to 79 years. During 9.7 years of follow-up, we documented 16,923 and 20,656 incident IS cases in men and women without major chronic diseases at baseline, respectively. Multivariable Cox regression models were used to examine associations between family history and IS. Likelihood ratio tests were used to test the smoking-family history interactions on IS. RESULTS About 67.8% (n=135,168) of men ever smoked regularly compared with 2.7% (n=7,775) of women. Among men, a significant interaction between family history and smoking on IS was observed (P for interaction=0.03), with more pronounced association between family history and IS among ever-regular smokers (hazard ratio [HR], 1.21; 95% confidence interval [CI], 1.16 to 1.27) than among never-smokers (HR, 1.11; 95% CI, 1.01 to 1.23). The association between family history and IS among ex-smokers after more than 10 years of cessation (HR, 1.01; 95% CI, 0.85 to 1.20) appeared similar to that among never-smokers. Among women, a similar but not significant interaction between family history and smoking on IS was observed. Ever-regular smokers who had a family history of stroke had the highest risk of IS. CONCLUSIONS Among Chinese men, the association of family history with IS was accentuated by smoking, and such accentuation tended to be lowered by cessation.
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Affiliation(s)
- Mengyu Fan
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Jun Lv
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
- Key Laboratory of Molecular Cardiovascular Sciences (Peking University), Ministry of Education, Beijing, China
- Peking University Institute of Environmental Medicine, Beijing, China
| | - Canqing Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Yu Guo
- Chinese Academy of Medical Sciences, Beijing, China
| | - Zheng Bian
- Chinese Academy of Medical Sciences, Beijing, China
| | - Songchun Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
| | - Ling Yang
- Clinical Trial Service Unit & Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Yiping Chen
- Clinical Trial Service Unit & Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Feifei Li
- NCDs Prevention and Control Department, Qingdao Centers for Disease Control, Qingdao, China
| | - Yaoming Zhai
- NCDs Prevention and Control Department, Qingdao Centers for Disease Control, Qingdao, China
| | - Ping Wang
- NCDs Prevention and Control Department, Liuzhou Centers for Disease Control, Liuzhou, China
| | - Junshi Chen
- China National Center for Food Safety Risk Assessment, Beijing, China
| | - Zhengming Chen
- Clinical Trial Service Unit & Epidemiological Studies Unit (CTSU), Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Lu Qi
- Department of Epidemiology, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
- Department of Nutrition, Harvard School of Public Health, Boston, MA, USA
| | - Liming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, China
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Yang T, Chen H, Tang H, Li D, Wei P. A powerful and data-adaptive test for rare-variant-based gene-environment interaction analysis. Stat Med 2019; 38:1230-1244. [PMID: 30460711 PMCID: PMC6399020 DOI: 10.1002/sim.8037] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 10/17/2018] [Accepted: 10/22/2018] [Indexed: 12/20/2022]
Abstract
As whole-exome/genome sequencing data become increasingly available in genetic epidemiology research consortia, there is emerging interest in testing the interactions between rare genetic variants and environmental exposures that modify the risk of complex diseases. However, testing rare-variant-based gene-by-environment interactions (GxE) is more challenging than testing the genetic main effects due to the difficulty in correctly estimating the latter under the null hypothesis of no GxE effects and the presence of neutral variants. In response, we have developed a family of powerful and data-adaptive GxE tests, called "aGE" tests, in the framework of the adaptive powered score test, originally proposed for testing the genetic main effects. Using extensive simulations, we show that aGE tests can control the type I error rate in the presence of a large number of neutral variants or a nonlinear environmental main effect, and the power is more resilient to the inclusion of neutral variants than that of existing methods. We demonstrate the performance of the proposed aGE tests using Pancreatic Cancer Case-Control Consortium Exome Chip data. An R package "aGE" is available at http://github.com/ytzhong/projects/.
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Affiliation(s)
- Tianzhong Yang
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Department of Biostatistics and Data Science, School of Public Health, The University of Texas Health Science Center at Houston, TX 77030, USA
| | - Han Chen
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health,The University of Texas Health Science Center at Houston, TX77030, USA
- Center for Precision Health, School of Public Health and School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX77030, USA
| | - Hongwei Tang
- Departments of Gastrointestinal Medical Oncology and Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX77030, USA
| | - Donghui Li
- Departments of Gastrointestinal Medical Oncology and Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX77030, USA
| | - Peng Wei
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Xu J, Gaddis NC, Bartz TM, Hou R, Manichaikul AW, Pankratz N, Smith AV, Sun F, Terzikhan N, Markunas CA, Patchen BK, Schu M, Beydoun MA, Brusselle GG, Eiriksdottir G, Zhou X, Wood AC, Graff M, Harris TB, Ikram MA, Jacobs DR, Launer LJ, Lemaitre RN, O’Connor GT, Oelsner EC, Psaty BM, Vasan RS, Rohde RR, Rich SS, Rotter JI, Seshadri S, Smith LJ, Tiemeier H, Tsai MY, Uitterlinden AG, Voruganti VS, Xu H, Zilhão NR, Fornage M, Zillikens MC, London SJ, Barr RG, Dupuis J, Gharib SA, Gudnason V, Lahousse L, North KE, Steffen LM, Cassano PA, Hancock DB. Omega-3 Fatty Acids and Genome-Wide Interaction Analyses Reveal DPP10-Pulmonary Function Association. Am J Respir Crit Care Med 2019; 199:631-642. [PMID: 30199657 PMCID: PMC6396866 DOI: 10.1164/rccm.201802-0304oc] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 09/07/2018] [Indexed: 12/18/2022] Open
Abstract
RATIONALE Omega-3 polyunsaturated fatty acids (n-3 PUFAs) have anti-inflammatory properties that could benefit adults with comprised pulmonary health. OBJECTIVE To investigate n-3 PUFA associations with spirometric measures of pulmonary function tests (PFTs) and determine underlying genetic susceptibility. METHODS Associations of n-3 PUFA biomarkers (α-linolenic acid, eicosapentaenoic acid, docosapentaenoic acid [DPA], and docosahexaenoic acid [DHA]) were evaluated with PFTs (FEV1, FVC, and FEV1/FVC) in meta-analyses across seven cohorts from the Cohorts for Heart and Aging Research in Genomic Epidemiology Consortium (N = 16,134 of European or African ancestry). PFT-associated n-3 PUFAs were carried forward to genome-wide interaction analyses in the four largest cohorts (N = 11,962) and replicated in one cohort (N = 1,687). Cohort-specific results were combined using joint 2 degree-of-freedom (2df) meta-analyses of SNP associations and their interactions with n-3 PUFAs. RESULTS DPA and DHA were positively associated with FEV1 and FVC (P < 0.025), with evidence for effect modification by smoking and by sex. Genome-wide analyses identified a novel association of rs11693320-an intronic DPP10 SNP-with FVC when incorporating an interaction with DHA, and the finding was replicated (P2df = 9.4 × 10-9 across discovery and replication cohorts). The rs11693320-A allele (frequency, ∼80%) was associated with lower FVC (PSNP = 2.1 × 10-9; βSNP = -161.0 ml), and the association was attenuated by higher DHA levels (PSNP×DHA interaction = 2.1 × 10-7; βSNP×DHA interaction = 36.2 ml). CONCLUSIONS We corroborated beneficial effects of n-3 PUFAs on pulmonary function. By modeling genome-wide n-3 PUFA interactions, we identified a novel DPP10 SNP association with FVC that was not detectable in much larger studies ignoring this interaction.
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Affiliation(s)
- Jiayi Xu
- Division of Nutritional Sciences, Cornell University, Ithaca, New York
| | | | - Traci M. Bartz
- Department of Biostatistics
- Cardiovascular Health Research Unit
| | - Ruixue Hou
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, North Carolina
| | - Ani W. Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | | | - Albert V. Smith
- Department of Biostatistics, University of Michigan, Ann Arbor, Michigan
| | - Fangui Sun
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Natalie Terzikhan
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
- Department of Epidemiology
| | - Christina A. Markunas
- Center for Omics Discovery and Epidemiology, Behavioral Health Research Division, and
| | - Bonnie K. Patchen
- Division of Nutritional Sciences, Cornell University, Ithaca, New York
| | - Matthew Schu
- Genomics in Public Health and Medicine Center, Biostatistics and Epidemiology Division, RTI International, Research Triangle Park, North Carolina
| | - May A. Beydoun
- Intramural Research Program, National Institute on Aging, National Institutes of Health, Bethesda, Maryland
| | - Guy G. Brusselle
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
- Department of Epidemiology
- Department of Respiratory Medicine
| | | | - Xia Zhou
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, Minnesota
| | - Alexis C. Wood
- USDA/ARS Children’s Nutrition Research Center, Baylor College of Medicine, Houston, Texas
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Tamara B. Harris
- Intramural Research Program, National Institute on Aging, National Institutes of Health, Bethesda, Maryland
| | | | - David R. Jacobs
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, Minnesota
| | - Lenore J. Launer
- Intramural Research Program, National Institute on Aging, National Institutes of Health, Bethesda, Maryland
| | | | | | | | - Bruce M. Psaty
- Cardiovascular Health Research Unit
- Department of Medicine
- Department of Epidemiology
- Department of Health Services, and
- Kaiser Permanente Washington Health Research Institute, Seattle, Washington
| | - Ramachandran S. Vasan
- Division of Cardiology and Preventive Medicine, Department of Medicine, and
- Boston University’s and NHLBI’s Framingham Heart Study, Framingham, Massachusetts
| | - Rebecca R. Rohde
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Jerome I. Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Department of Pediatrics, Harbor–UCLA Medical Center, Torrance, California
| | - Sudha Seshadri
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts
- Glenn Biggs Institute of Alzheimer's and Neurodegenerative Diseases, University of Texas Health Sciences Center, San Antonio, Texas
| | - Lewis J. Smith
- Division of Pulmonary and Critical Care, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Henning Tiemeier
- Department of Epidemiology
- Department of Psychiatry
- Department of Child and Adolescent Psychiatry, and
| | | | | | - V. Saroja Voruganti
- Department of Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, North Carolina
| | - Hanfei Xu
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | | | - Myriam Fornage
- Institute of Molecular Medicine and
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas
| | - M. Carola Zillikens
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
- Netherlands Genomics Initiative–sponsored Netherlands Consortium for Healthy Aging, Leiden, the Netherlands
| | - Stephanie J. London
- Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina
| | - R. Graham Barr
- Department of Medicine, Columbia University, New York, New York
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Sina A. Gharib
- Department of Medicine
- Center for Lung Biology, University of Washington, Seattle, Washington
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- University of Iceland, Reykjavik, Iceland
| | - Lies Lahousse
- Department of Epidemiology
- Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Kari E. North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Lyn M. Steffen
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, Minnesota
| | - Patricia A. Cassano
- Division of Nutritional Sciences, Cornell University, Ithaca, New York
- Division of Biostatistics and Epidemiology, Department of Healthcare Policy and Research, Weill Cornell Medical College, New York, New York
| | - Dana B. Hancock
- Center for Omics Discovery and Epidemiology, Behavioral Health Research Division, and
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Kim J, Ziyatdinov A, Laville V, Hu FB, Rimm E, Kraft P, Aschard H. Joint Analysis of Multiple Interaction Parameters in Genetic Association Studies. Genetics 2019; 211:483-494. [PMID: 30578273 PMCID: PMC6366922 DOI: 10.1534/genetics.118.301394] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 12/10/2018] [Indexed: 01/24/2023] Open
Abstract
With growing human genetic and epidemiologic data, there has been increased interest for the study of gene-by-environment (G-E) interaction effects. Still, major questions remain on how to test jointly a large number of interactions between multiple SNPs and multiple exposures. In this study, we first compared the relative performance of four fixed-effect joint analysis approaches using simulated data, considering up to 10 exposures and 300 SNPs: (1) omnibus test, (2) multi-exposure and genetic risk score (GRS) test, (3) multi-SNP and environmental risk score (ERS) test, and (4) GRS-ERS test. Our simulations explored both linear and logistic regression while considering three statistics: the Wald test, the Score test, and the likelihood ratio test (LRT). We further applied the approaches to three large sets of human cohort data (n = 37,664), focusing on type 2 diabetes (T2D), obesity, hypertension, and coronary heart disease with smoking, physical activity, diets, and total energy intake. Overall, GRS-based approaches were the most robust, and had the highest power, especially when the G-E interaction effects were correlated with the marginal genetic and environmental effects. We also observed severe miscalibration of joint statistics in logistic models when the number of events per variable was too low when using either the Wald test or LRT test. Finally, our real data application detected nominally significant interaction effects for three outcomes (T2D, obesity, and hypertension), mainly from the GRS-ERS approach. In conclusion, this study provides guidelines for testing multiple interaction parameters in modern human cohorts including extensive genetic and environmental data.
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Affiliation(s)
- Jihye Kim
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115
| | - Andrey Ziyatdinov
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115
| | - Vincent Laville
- Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Institut Pasteur, 75724 Paris, France
| | - Frank B Hu
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115
| | - Eric Rimm
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115
| | - Hugues Aschard
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115
- Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Institut Pasteur, 75724 Paris, France
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41
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Wyss AB, Sofer T, Lee MK, Terzikhan N, Nguyen JN, Lahousse L, Latourelle JC, Smith AV, Bartz TM, Feitosa MF, Gao W, Ahluwalia TS, Tang W, Oldmeadow C, Duan Q, de Jong K, Wojczynski MK, Wang XQ, Noordam R, Hartwig FP, Jackson VE, Wang T, Obeidat M, Hobbs BD, Huan T, Gui H, Parker MM, Hu D, Mogil LS, Kichaev G, Jin J, Graff M, Harris TB, Kalhan R, Heckbert SR, Paternoster L, Burkart KM, Liu Y, Holliday EG, Wilson JG, Vonk JM, Sanders JL, Barr RG, de Mutsert R, Menezes AMB, Adams HHH, van den Berge M, Joehanes R, Levin AM, Liberto J, Launer LJ, Morrison AC, Sitlani CM, Celedón JC, Kritchevsky SB, Scott RJ, Christensen K, Rotter JI, Bonten TN, Wehrmeister FC, Bossé Y, Xiao S, Oh S, Franceschini N, Brody JA, Kaplan RC, Lohman K, McEvoy M, Province MA, Rosendaal FR, Taylor KD, Nickle DC, Williams LK, Burchard EG, Wheeler HE, Sin DD, Gudnason V, North KE, Fornage M, Psaty BM, Myers RH, O'Connor G, Hansen T, Laurie CC, Cassano PA, Sung J, Kim WJ, Attia JR, Lange L, Boezen HM, Thyagarajan B, Rich SS, Mook-Kanamori DO, Horta BL, Uitterlinden AG, Im HK, Cho MH, Brusselle GG, Gharib SA, Dupuis J, Manichaikul A, London SJ. Multiethnic meta-analysis identifies ancestry-specific and cross-ancestry loci for pulmonary function. Nat Commun 2018; 9:2976. [PMID: 30061609 PMCID: PMC6065313 DOI: 10.1038/s41467-018-05369-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 06/21/2018] [Indexed: 02/07/2023] Open
Abstract
Nearly 100 loci have been identified for pulmonary function, almost exclusively in studies of European ancestry populations. We extend previous research by meta-analyzing genome-wide association studies of 1000 Genomes imputed variants in relation to pulmonary function in a multiethnic population of 90,715 individuals of European (N = 60,552), African (N = 8429), Asian (N = 9959), and Hispanic/Latino (N = 11,775) ethnicities. We identify over 50 additional loci at genome-wide significance in ancestry-specific or multiethnic meta-analyses. Using recent fine-mapping methods incorporating functional annotation, gene expression, and differences in linkage disequilibrium between ethnicities, we further shed light on potential causal variants and genes at known and newly identified loci. Several of the novel genes encode proteins with predicted or established drug targets, including KCNK2 and CDK12. Our study highlights the utility of multiethnic and integrative genomics approaches to extend existing knowledge of the genetics of lung function and clinical relevance of implicated loci.
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Affiliation(s)
- Annah B Wyss
- Epidemiology Branch National Institute of Environmental Health Sciences, National Institutes of Health, US Department of Health and Human Services, Research Triangle Park, NC, 27709, USA
| | - Tamar Sofer
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Mi Kyeong Lee
- Epidemiology Branch National Institute of Environmental Health Sciences, National Institutes of Health, US Department of Health and Human Services, Research Triangle Park, NC, 27709, USA
| | - Natalie Terzikhan
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, 9000, Belgium
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3000, CA, The Netherlands
| | - Jennifer N Nguyen
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Lies Lahousse
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3000, CA, The Netherlands
- Department of Bioanalysis, FFW, Ghent University, Ghent, 9000, Belgium
| | - Jeanne C Latourelle
- Department of Neurology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Albert Vernon Smith
- Icelandic Heart Association, Kopavogur, 201, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Traci M Bartz
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Mary F Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Wei Gao
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
| | - Tarunveer S Ahluwalia
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Metabolic Genetics Section, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
- Steno Diabetes Center Copenhagen, Gentofte, 2820, Denmark
| | - Wenbo Tang
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Christopher Oldmeadow
- Hunter Medical Research Institute and Faculty of Health, University of Newcastle, Callaghan, NSW, 2305, Australia
| | - Qing Duan
- Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Kim de Jong
- Department of Epidemiologie, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Mary K Wojczynski
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Xin-Qun Wang
- Division of Biostatistics, Department of Public Health Sciences, University of Virginia, Charlottesville, VA, 22908, USA
| | - Raymond Noordam
- Department of Internal Medicine, Section Gerontology and Geriatrics, Leiden University Medical Center, Leiden, 2300 RC, The Netherlands
| | - Fernando Pires Hartwig
- Postgraduate Program in Epidemiology, Federal University of Pelotas, 96020-220, Pelotas, Brazil
- Medical Research Council Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, BS8 2BN, UK
| | - Victoria E Jackson
- Department of Health Sciences, University of Leicester, Leicester, LE1 7RH, UK
| | - Tianyuan Wang
- Integrative Bioinformatics Support Group National Institute of Environmental Health Sciences, National Institutes of Health, US Department of Health and Human Services, Research Triangle Park, NC, 27709, USA
| | - Ma'en Obeidat
- The University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, V6Z 1Y6, Canada
| | - Brian D Hobbs
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Tianxiao Huan
- The Population Sciences Branch, Division of Intramural Research, National Heart, Lung, and Blood Institute, Bethesda, MD, 20892, USA
| | - Hongsheng Gui
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, MI, 48202, USA
| | - Margaret M Parker
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Donglei Hu
- School of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Lauren S Mogil
- Department of Biology, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Gleb Kichaev
- University of California Los Angeles, Los Angeles, CA, 90095, USA
| | | | - Mariaelisa Graff
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Tamara B Harris
- Department of Health and Human Services, Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ravi Kalhan
- Division of Pulmonary and Critical Care Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Susan R Heckbert
- Department of Epidemiology, Cardiovascular Health Research Unit, University of Washington, Seattle, WA, 98101, USA
| | - Lavinia Paternoster
- Medical Research Council Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, BS8 2BN, UK
| | - Kristin M Burkart
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
| | - Yongmei Liu
- Wake Forest School of Medicine, Winston-Salem, NC, 27101, USA
| | - Elizabeth G Holliday
- Hunter Medical Research Institute and Faculty of Health, University of Newcastle, Callaghan, NSW, 2305, Australia
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - Judith M Vonk
- Department of Epidemiologie, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Jason L Sanders
- Department of Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - R Graham Barr
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY, 10032, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA
| | - Renée de Mutsert
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, 2300 RC, The Netherlands
| | | | - Hieab H H Adams
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3000, CA, The Netherlands
- Department of Radiology, Erasmus University Medical Center, Rotterdam, 3015 GD, The Netherlands
| | - Maarten van den Berge
- Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, 9700 AB, The Netherlands
| | - Roby Joehanes
- Hebrew SeniorLife, Harvard University, Boston, MA, 02131, USA
| | - Albert M Levin
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI, 48202, USA
| | - Jennifer Liberto
- School of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Lenore J Launer
- Department of Health and Human Services, Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Colleen M Sitlani
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
| | - Juan C Celedón
- Division of Pulmonary Medicine, Allergy, and Immunology, Department of Pediatrics, Children's Hospital of Pittsburgh of UPMC, University of Pittsburgh, Pittsburgh, PA, 15224, USA
| | - Stephen B Kritchevsky
- Sticht Center for Healthy Aging and Alzheimer's Prevention, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Rodney J Scott
- Hunter Medical Research Institute and Faculty of Health, University of Newcastle, Callaghan, NSW, 2305, Australia
- Division of Molecular Medicine, Pathology North, NSW Health Pathology, Newcastle, NSW, 2305, Australia
| | - Kaare Christensen
- Department of Epidemiology, Biostatistics and Biodemography, University of Southern Denmark, Odense, 5000, Denmark
| | - Jerome I Rotter
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - Tobias N Bonten
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, 2300 RC, The Netherlands
- Department of Pulmonology, Leiden University Medical Center, Leiden, 2300 RC, The Netherlands
| | | | - Yohan Bossé
- Department of Molecular Medicine, Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec, G1V 4G5, Canada
| | - Shujie Xiao
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, MI, 48202, USA
| | - Sam Oh
- School of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
| | - Robert C Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Kurt Lohman
- Wake Forest School of Medicine, Winston-Salem, NC, 27101, USA
| | - Mark McEvoy
- Hunter Medical Research Institute and Faculty of Health, University of Newcastle, Callaghan, NSW, 2305, Australia
| | - Michael A Province
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Frits R Rosendaal
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, 2300 RC, The Netherlands
| | - Kent D Taylor
- Department of Pediatrics, Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - David C Nickle
- Merck Research Laboratories, GpGx, Merck & Co., Inc., Kenilworth, NJ, 07033, USA
| | - L Keoki Williams
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, MI, 48202, USA
- Department of Internal Medicine, Henry Ford Health System, Detroit, MI, 48202, USA
| | - Esteban G Burchard
- School of Medicine, University of California San Francisco, San Francisco, CA, 94143, USA
- School of Pharmacy, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Heather E Wheeler
- Department of Biology, Loyola University Chicago, Chicago, IL, 60660, USA
| | - Don D Sin
- The University of British Columbia Center for Heart Lung Innovation, St Paul's Hospital, Vancouver, BC, V6Z 1Y6, Canada
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, BC, V5Z 1M9, Canada
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, 201, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, 101, Iceland
| | - Kari E North
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine and Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
- Department of Epidemiology, Cardiovascular Health Research Unit, University of Washington, Seattle, WA, 98101, USA
- Cardiovascular Health Research Unit, Department of Health Services, University of Washington, Seattle, WA, 98101, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, 98101, USA
| | - Richard H Myers
- Department of Neurology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - George O'Connor
- National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, 01702, USA
- Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Metabolic Genetics Section, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Cathy C Laurie
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA
| | - Patricia A Cassano
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, 14853, USA
- Department of Healthcare Policy and Research, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Joohon Sung
- Department of Health Science, School of Public Health, Seoul National University, Seoul, 08826, South Korea
| | - Woo Jin Kim
- Department of Internal Medicine and Environmental Health Center, Kangwon National University, Chuncheon, 24341, South Korea
| | - John R Attia
- Hunter Medical Research Institute and Faculty of Health, University of Newcastle, Callaghan, NSW, 2305, Australia
| | - Leslie Lange
- University of Colorado Denver, Denver, CO, 80204, USA
| | - H Marike Boezen
- Department of Epidemiologie, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, Netherlands
| | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Dennis O Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, 2300 RC, The Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, 2300 RC, The Netherlands
| | - Bernardo Lessa Horta
- Postgraduate Program in Epidemiology, Federal University of Pelotas, 96020-220, Pelotas, Brazil
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, 3015 CN, The Netherlands
| | - Hae Kyung Im
- Section of Genetic Medicine, The University of Chicago, Chicago, IL, 60637, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Guy G Brusselle
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, 9000, Belgium
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, 3000, CA, The Netherlands
- Department of Respiratory Medicine, Erasmus University Medical Center, Rotterdam, 3000 CA, The Netherlands
| | - Sina A Gharib
- Department of Medicine, Computational Medicine Core, Center for Lung Biology, UW Medicine Sleep Center, University of Washington, Seattle, WA, 98109, USA
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, 02118, USA
- National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, 01702, USA
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, 22908, USA
| | - Stephanie J London
- Epidemiology Branch National Institute of Environmental Health Sciences, National Institutes of Health, US Department of Health and Human Services, Research Triangle Park, NC, 27709, USA.
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Burkart KM, Sofer T, London SJ, Manichaikul A, Hartwig FP, Yan Q, Soler Artigas M, Avila L, Chen W, Davis Thomas S, Diaz AA, Hall IP, Horta BL, Kaplan RC, Laurie CC, Menezes AM, Morrison JV, Oelsner EC, Rastogi D, Rich SS, Soto-Quiros M, Stilp AM, Tobin MD, Wain LV, Celedón JC, Barr RG. A Genome-Wide Association Study in Hispanics/Latinos Identifies Novel Signals for Lung Function. The Hispanic Community Health Study/Study of Latinos. Am J Respir Crit Care Med 2018; 198:208-219. [PMID: 29394082 PMCID: PMC6058984 DOI: 10.1164/rccm.201707-1493oc] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 01/30/2018] [Indexed: 12/14/2022] Open
Abstract
RATIONALE Lung function and chronic obstructive pulmonary disease (COPD) are heritable traits. Genome-wide association studies (GWAS) have identified numerous pulmonary function and COPD loci, primarily in cohorts of European ancestry. OBJECTIVES Perform a GWAS of COPD phenotypes in Hispanic/Latino populations to identify loci not previously detected in European populations. METHODS GWAS of lung function and COPD in Hispanic/Latino participants from a population-based cohort. We performed replication studies of novel loci in independent studies. MEASUREMENTS AND MAIN RESULTS Among 11,822 Hispanic/Latino participants, we identified eight novel signals; three replicated in independent populations of European Ancestry. A novel locus for FEV1 in ZSWIM7 (rs4791658; P = 4.99 × 10-9) replicated. A rare variant (minor allele frequency = 0.002) in HAL (rs145174011) was associated with FEV1/FVC (P = 9.59 × 10-9) in a region previously identified for COPD-related phenotypes; it remained significant in conditional analyses but did not replicate. Admixture mapping identified a novel region, with a variant in AGMO (rs41331850), associated with Amerindian ancestry and FEV1, which replicated. A novel locus for FEV1 identified among ever smokers (rs291231; P = 1.92 × 10-8) approached statistical significance for replication in admixed populations of African ancestry, and a novel SNP for COPD in PDZD2 (rs7709630; P = 1.56 × 10-8) regionally replicated. In addition, loci previously identified for lung function in European samples were associated in Hispanic/Latino participants in the Hispanic Community Health Study/Study of Latinos at the genome-wide significance level. CONCLUSIONS We identified novel signals for lung function and COPD in a Hispanic/Latino cohort. Including admixed populations when performing genetic studies may identify variants contributing to genetic etiologies of COPD.
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Affiliation(s)
- Kristin M. Burkart
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Tamar Sofer
- Division of Sleep and Circadian Disorders, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
- Department of Biostatistics, University of Washington School of Public Health, Seattle, Washington
| | - Stephanie J. London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Fernando P. Hartwig
- Postgraduate Program in Epidemiology, Federal University of Pelotas, Pelotas, Brazil
| | - Qi Yan
- Division of Pulmonary Medicine, Allergy, and Immunology, Department of Pediatrics, Children’s Hospital of Pittsburgh of University of Pittsburgh Medical Center, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - María Soler Artigas
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | - Lydiana Avila
- Division of Pediatric Pulmonology, Hospital Nacional de Niños, San José, Costa Rica
| | - Wei Chen
- Division of Pulmonary Medicine, Allergy, and Immunology, Department of Pediatrics, Children’s Hospital of Pittsburgh of University of Pittsburgh Medical Center, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Sonia Davis Thomas
- Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina
| | - Alejandro A. Diaz
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Ian P. Hall
- Division of Respiratory Medicine, Queen’s Medical Centre, University of Nottingham, Nottingham, United Kingdom
| | - Bernardo L. Horta
- Postgraduate Program in Epidemiology, Federal University of Pelotas, Pelotas, Brazil
| | | | - Cathy C. Laurie
- Department of Biostatistics, University of Washington School of Public Health, Seattle, Washington
| | - Ana M. Menezes
- Postgraduate Program in Epidemiology, Federal University of Pelotas, Pelotas, Brazil
| | - Jean V. Morrison
- Department of Human Genetics and Statistics, University of Chicago, Chicago, Illinois
| | - Elizabeth C. Oelsner
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Deepa Rastogi
- Department of Pediatrics, Albert Einstein College of Medicine, New York, New York
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Manuel Soto-Quiros
- Division of Pulmonary Medicine, Allergy, and Immunology, Department of Pediatrics, Children’s Hospital of Pittsburgh of University of Pittsburgh Medical Center, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Adrienne M. Stilp
- Department of Biostatistics, University of Washington School of Public Health, Seattle, Washington
| | - Martin D. Tobin
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom; and
| | - Louise V. Wain
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research, Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, United Kingdom; and
| | - Juan C. Celedón
- Division of Pulmonary Medicine, Allergy, and Immunology, Department of Pediatrics, Children’s Hospital of Pittsburgh of University of Pittsburgh Medical Center, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - R. Graham Barr
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, New York
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
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Genome-wide assessment of gene-by-smoking interactions in COPD. Sci Rep 2018; 8:9319. [PMID: 29915320 PMCID: PMC6006158 DOI: 10.1038/s41598-018-27463-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 05/30/2018] [Indexed: 12/14/2022] Open
Abstract
Cigarette smoke exposure is a major risk factor in chronic obstructive pulmonary disease (COPD) and its interactions with genetic variants could affect lung function. However, few gene-smoking interactions have been reported. In this report, we evaluated the effects of gene-smoking interactions on lung function using Korea Associated Resource (KARE) data with the spirometric variables—forced expiratory volume in 1 s (FEV1). We found that variations in FEV1 were different among smoking status. Thus, we considered a linear mixed model for association analysis under heteroscedasticity according to smoking status. We found a previously identified locus near SOX9 on chromosome 17 to be the most significant based on a joint test of the main and interaction effects of smoking. Smoking interactions were replicated with Gene-Environment of Interaction and phenotype (GENIE), Multi-Ethnic Study of Atherosclerosis-Lung (MESA-Lung), and COPDGene studies. We found that individuals with minor alleles, rs17765644, rs17178251, rs11870732, and rs4793541, tended to have lower FEV1 values, and lung function decreased much faster with age for smokers. There have been very few reports to replicate a common variant gene-smoking interaction, and our results revealed that statistical models for gene-smoking interaction analyses should be carefully selected.
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44
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Levy JI, Quirós-Alcalá L, Fabian MP, Basra K, Hansel NN. Established and Emerging Environmental Contributors to Disparities in Asthma and Chronic Obstructive Pulmonary Disease. CURR EPIDEMIOL REP 2018; 5:114-124. [PMID: 30319934 PMCID: PMC6178976 DOI: 10.1007/s40471-018-0149-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
PURPOSE OF REVIEW Multiple respiratory diseases, including asthma and chronic obstructive pulmonary disease (COPD), display significant socioeconomic and racial/ethnic disparities. The objective of this review is to evaluate the evidence supporting a link between disproportionate environmental exposures and these health disparities. RECENT FINDINGS Studies suggest that various co-occurring factors related to the home environment, neighborhood environment, non-modifiable individual factors, and individual behaviors and attributes can increase or modify the risk of adverse respiratory outcomes among socioeconomically-disadvantaged and racially/ethnically diverse populations. Pollutants in the home environment, including particulate matter, nitrogen dioxide, and pesticides, are elevated among lower socioeconomic status populations and have been implicated in the development or exacerbation of respiratory-related conditions. Neighborhood crime and green space are socioeconomically patterned and linked with asthma outcomes through psychosocial pathways. Non-modifiable individual factors such as genetic predisposition cannot explain environmental health disparities but can increase susceptibility to air pollution and other stressors. Individual behaviors and attributes, including obesity and physical activity, contribute to worse outcomes among those with asthma or COPD. SUMMARY The root causes of these multifactorial exposures are complex, but many likely stem from economic forces and racial/ethnic and economic segregation that influence the home environment, neighborhood environment, and access to healthy foods and consumer products. Critical research needs include investigations that characterize exposure to and health implications of numerous stressors simultaneously, both to guard against potential confounding in epidemiological investigations and to consider the cumulative impact of multiple elevated environmental exposures and sociodemographic stressors on health disparities.
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Affiliation(s)
- Jonathan I. Levy
- Department of Environmental Health, Boston University School of Public Health
| | - Lesliam Quirós-Alcalá
- Maryland Institute for Applied Environmental Health, University of Maryland School of Public Health; Division of Pulmonary & Critical Care Medicine, Johns Hopkins University
| | - M. Patricia Fabian
- Department of Environmental Health, Boston University School of Public Health
| | - Komal Basra
- Department of Environmental Health, Boston University School of Public Health
| | - Nadia N. Hansel
- Division of Pulmonary & Critical Care Medicine, Johns Hopkins University
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45
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Jilling T, Ambalavanan N, Cotten CM, Martin CA, Maheshwari A, Schibler K, Levy J, Page GP. Surgical necrotizing enterocolitis in extremely premature neonates is associated with genetic variations in an intergenic region of chromosome 8. Pediatr Res 2018; 83:943-953. [PMID: 29538362 PMCID: PMC6053310 DOI: 10.1038/pr.2018.33] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 02/08/2018] [Indexed: 12/02/2022]
Abstract
BackgroundTwin studies suggest that genetic factors may account for up to 50% increased risk for necrotizing enterocolitis (NEC), but genome-wide association studies for NEC are lacking.MethodsGenotyping was done on Illumina BeadChip, followed by analysis using PLINK with logistic regression under an additive model.ResultsAmong 751 extremely-low-birth-weight (<1,000 g, >401 g) neonates, 30 had surgical NEC. Two hundred and sixty-one single-nucleotide polymorphisms (SNPs) showed association with NEC at P<0.05, of which 35 were significant at P<10-7. Minor allele(s) in a cluster of SNPs spanning a 43-kb region of chromosome 8 (8q23.3) conferred an odds ratio of 4.72 (95% confidence interval (CI): 2.51-8.88) for elevated risk of NEC. Two smaller clusters on chromosome 14 and chromosome 11 exhibited P values of 10-7-10-8. The chromosome 8 cluster is in an intergenic region between CUB and Sushi multiple domains 3 (-1.43 Mb) and trichorhinophalangeal syndrome I (+542 kb). RNA sequencing in this region identified a potential novel open-reading frame corresponding to a long interspersed element-1 retrotransposable element.ConclusionGenetic variation in an intergenic region of chromosome 8 is associated with increased risk for NEC with a mechanism that is yet to be identified.
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MESH Headings
- Chromosomes, Human, Pair 8
- Cohort Studies
- DNA, Intergenic
- Enterocolitis, Necrotizing/diagnosis
- Enterocolitis, Necrotizing/genetics
- Enterocolitis, Necrotizing/surgery
- Female
- Gene Frequency
- Genetic Predisposition to Disease
- Genetic Variation
- Genome-Wide Association Study
- Genotype
- Humans
- Infant
- Infant, Extremely Low Birth Weight
- Infant, Newborn
- Infant, Newborn, Diseases
- Infant, Premature
- Long Interspersed Nucleotide Elements
- Male
- Oligonucleotide Array Sequence Analysis
- Phenotype
- Polymorphism, Single Nucleotide
- Respiration, Artificial
- Sequence Analysis, RNA
- Signal Transduction
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Affiliation(s)
| | | | | | | | | | - Kurt Schibler
- Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
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46
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Hawkins GA, Mora AL. FAM13A, A Fatty Acid Oxidation Switch in Mitochondria. Friend or Foe in Chronic Obstructive Pulmonary Disease Pathogenesis? Am J Respir Cell Mol Biol 2018; 56:689-691. [PMID: 28569593 DOI: 10.1165/rcmb.2017-0080ed] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Gregory A Hawkins
- 1 Center for Genomics and Personalized Medicine Research Wake Forest School of Medicine Winston-Salem, North Carolina
| | - Ana L Mora
- 2 Division of Pulmonary, Allergy, and Critical Care Medicine Vascular Medicine Institute University of Pittsburgh Pittsburgh, Pennsylvania
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47
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Kim WJ, Park HJ, Choi YJ, Kwon EY, Kim BM, Lee JH, Chang JH, Lee Kang J, Choi JH. Association between Genetic Variations of MERTK and Chronic Obstructive Pulmonary Disease in Koreans. J Korean Med Sci 2018; 33:e56. [PMID: 29359540 PMCID: PMC5785628 DOI: 10.3346/jkms.2018.33.e56] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 12/12/2017] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) is a debilitating lung disease. To date, a large number of clinical studies have been conducted to investigate the association between genetic variations and COPD. However, little is known regarding the genetic susceptibility of Koreans to this disease. MER receptor tyrosine kinase (MERTK) plays important roles in the inhibition of inflammation and in the clearance of apoptotic cells. Here, we investigated the association between genetic variations in MERTK and the development of COPD in Koreans. METHODS We conducted genetic analysis of MERTK using genomic DNA samples from 87 patients with COPD and 88 healthy controls and compared the frequency of each variation or haplotype between the patient and control groups. Subsequently, the effect of each variation was evaluated using in vitro assays. RESULTS Ten variations were identified in this study, four of them for the first time. In addition, we found that the frequency of each variation or haplotype was comparable between the patient and control groups. However, we observed that the frequency for the wild-type haplotype was higher in the control group, compared to that in the group of patients with COPD, in the subgroup analysis of current smokers, although the difference was not statistically significant (P = 0.080). In in vitro assays, we observed that none of the variations affected the activity of the promoter or the expression of MERTK. CONCLUSION Our findings indicate that the susceptibility to COPD is not related to the genetic variations or haplotypes of MERTK in Koreans.
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Affiliation(s)
- Woo Jin Kim
- Department of Internal Medicine and Environmental Health Center, Kangwon National University, Chuncheon, Korea
| | - Hyo Jin Park
- Department of Pharmacology, Tissue Injury Defense Research Center, College of Medicine, Ewha Womans University, Seoul, Korea
| | - Yang Ji Choi
- Department of Pharmacology, Tissue Injury Defense Research Center, College of Medicine, Ewha Womans University, Seoul, Korea
| | - Eun Young Kwon
- Department of Pharmacology, Tissue Injury Defense Research Center, College of Medicine, Ewha Womans University, Seoul, Korea
| | - Bo Min Kim
- Department of Pharmacology, Tissue Injury Defense Research Center, College of Medicine, Ewha Womans University, Seoul, Korea
| | - Jin Hwa Lee
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, College of Medicine, Ewha Womans University, Seoul, Korea
| | - Jung Hyun Chang
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, College of Medicine, Ewha Womans University, Seoul, Korea
| | - Jihee Lee Kang
- Department of Physiology, Tissue Injury Defense Research Center, College of Medicine, Ewha Womans University, Seoul, Korea
| | - Ji Ha Choi
- Department of Pharmacology, Tissue Injury Defense Research Center, College of Medicine, Ewha Womans University, Seoul, Korea.
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48
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Jackson VE, Latourelle JC, Wain LV, Smith AV, Grove ML, Bartz TM, Obeidat M, Province MA, Gao W, Qaiser B, Porteous DJ, Cassano PA, Ahluwalia TS, Grarup N, Li J, Altmaier E, Marten J, Harris SE, Manichaikul A, Pottinger TD, Li-Gao R, Lind-Thomsen A, Mahajan A, Lahousse L, Imboden M, Teumer A, Prins B, Lyytikäinen LP, Eiriksdottir G, Franceschini N, Sitlani CM, Brody JA, Bossé Y, Timens W, Kraja A, Loukola A, Tang W, Liu Y, Bork-Jensen J, Justesen JM, Linneberg A, Lange LA, Rawal R, Karrasch S, Huffman JE, Smith BH, Davies G, Burkart KM, Mychaleckyj JC, Bonten TN, Enroth S, Lind L, Brusselle GG, Kumar A, Stubbe B, Kähönen M, Wyss AB, Psaty BM, Heckbert SR, Hao K, Rantanen T, Kritchevsky SB, Lohman K, Skaaby T, Pisinger C, Hansen T, Schulz H, Polasek O, Campbell A, Starr JM, Rich SS, Mook-Kanamori DO, Johansson Å, Ingelsson E, Uitterlinden AG, Weiss S, Raitakari OT, Gudnason V, North KE, Gharib SA, Sin DD, Taylor KD, O'Connor GT, Kaprio J, Harris TB, Pederson O, Vestergaard H, Wilson JG, Strauch K, Hayward C, Kerr S, Deary IJ, Barr RG, de Mutsert R, Gyllensten U, Morris AP, Ikram MA, Probst-Hensch N, Gläser S, Zeggini E, Lehtimäki T, Strachan DP, Dupuis J, Morrison AC, Hall IP, Tobin MD, London SJ. Meta-analysis of exome array data identifies six novel genetic loci for lung function. Wellcome Open Res 2018; 3:4. [PMID: 30175238 PMCID: PMC6081985 DOI: 10.12688/wellcomeopenres.12583.3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2018] [Indexed: 01/05/2023] Open
Abstract
Background: Over 90 regions of the genome have been associated with lung function to date, many of which have also been implicated in chronic obstructive pulmonary disease. Methods: We carried out meta-analyses of exome array data and three lung function measures: forced expiratory volume in one second (FEV 1), forced vital capacity (FVC) and the ratio of FEV 1 to FVC (FEV 1/FVC). These analyses by the SpiroMeta and CHARGE consortia included 60,749 individuals of European ancestry from 23 studies, and 7,721 individuals of African Ancestry from 5 studies in the discovery stage, with follow-up in up to 111,556 independent individuals. Results: We identified significant (P<2·8x10 -7) associations with six SNPs: a nonsynonymous variant in RPAP1, which is predicted to be damaging, three intronic SNPs ( SEC24C, CASC17 and UQCC1) and two intergenic SNPs near to LY86 and FGF10. Expression quantitative trait loci analyses found evidence for regulation of gene expression at three signals and implicated several genes, including TYRO3 and PLAU. Conclusions: Further interrogation of these loci could provide greater understanding of the determinants of lung function and pulmonary disease.
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Affiliation(s)
| | | | - Louise V. Wain
- Department of Health Sciences, University of Leicester, Leicester, UK
- National Institute for Health Research, Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Albert V. Smith
- Icelandic Heart Association, 201 Kopavogur, Iceland
- University of Iceland, 101 Reykjavik, Iceland
| | - Megan L. Grove
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Traci M. Bartz
- Cardiovascular Health Research Unit, Departments of Medicine and Biostatistics, University of Washington, Seattle, WA, 98101, USA
| | - Ma'en Obeidat
- The University of British Columbia Centre for Heart Lung Innovation, St Paul’s Hospital, Vancouver, BC, Canada
| | - Michael A. Province
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Wei Gao
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Beenish Qaiser
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014, Helsinki, Finland
| | - David J. Porteous
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Patricia A. Cassano
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
- Department of Healthcare Policy and Research, Division of Biostatistics and Epidemiology, Weill Cornell Medical College, New York City, NY, USA
| | - Tarunveer S. Ahluwalia
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Gentofte, 2820, Denmark
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jin Li
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Elisabeth Altmaier
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Jonathan Marten
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh , EH4 2XU, UK
| | - Sarah E. Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Tess D. Pottinger
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Preventive Medicine - Division of Health and Biomedical Informatics, Northwestern University - Feinberg School of Medicine, Chicago, IL, USA
| | - Ruifang Li-Gao
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
| | - Allan Lind-Thomsen
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, SE-75108 Uppsala, Sweden
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Lies Lahousse
- Respiratory Medicine, Ghent University Hospital, Ghent, BE9000, Belgium
- Bioanalysis, Ghent University, Ghent, BE9000, Belgium
| | - Medea Imboden
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Bram Prins
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33520, Finland
- Department of Clinical Chemistry, Faculty of Medicine and Life Sciences, University of Tampere, Tampere 33014, Finland
| | | | - Nora Franceschini
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, NC 27514, USA
| | - Colleen M. Sitlani
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec, Department of Molecular Medicine, Laval University, Québec, Canada
| | - Wim Timens
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, NL9713 GZ, Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Aldi Kraja
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Anu Loukola
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014, Helsinki, Finland
| | - Wenbo Tang
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
- Boehringer Ingelheim , Danbury, CT, USA
| | - Yongmei Liu
- Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Jette Bork-Jensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | | | - Allan Linneberg
- Centre for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark
- Department of Clinical Experimental Research, Rigshospitalet, 2600 Glostrup, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Leslie A. Lange
- Department of Medicine, Division of Bioinformatics and Personalized Medicine, University of Colorado Denver, Aurora, CO, USA
| | - Rajesh Rawal
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Stefan Karrasch
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Ludwig-Maximilians-Universität, Munich, Germany
| | - Jennifer E. Huffman
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh , EH4 2XU, UK
| | - Blair H. Smith
- Division of Population Health Sciences, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK
| | - Gail Davies
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Kristin M. Burkart
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Josyf C. Mychaleckyj
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Tobias N. Bonten
- Department of Pulmonology, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
| | - Stefan Enroth
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, SE-75108 Uppsala, Sweden
| | - Lars Lind
- Department of Medical Sciences, Uppsala University Hospital, Uppsala, Sweden
| | - Guy G. Brusselle
- Respiratory Medicine, Ghent University Hospital, Ghent, BE9000, Belgium
- Epidemiology, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
- Respiratory Medicine, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
| | - Ashish Kumar
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Beate Stubbe
- Internal Medicine B, University Medicine Greifswald, Greifswald, 17475, Germany
| | - Understanding Society Scientific Group
- Department of Health Sciences, University of Leicester, Leicester, UK
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
- National Institute for Health Research, Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
- Icelandic Heart Association, 201 Kopavogur, Iceland
- University of Iceland, 101 Reykjavik, Iceland
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Cardiovascular Health Research Unit, Departments of Medicine and Biostatistics, University of Washington, Seattle, WA, 98101, USA
- The University of British Columbia Centre for Heart Lung Innovation, St Paul’s Hospital, Vancouver, BC, Canada
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014, Helsinki, Finland
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
- Department of Healthcare Policy and Research, Division of Biostatistics and Epidemiology, Weill Cornell Medical College, New York City, NY, USA
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Gentofte, 2820, Denmark
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh , EH4 2XU, UK
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Preventive Medicine - Division of Health and Biomedical Informatics, Northwestern University - Feinberg School of Medicine, Chicago, IL, USA
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, SE-75108 Uppsala, Sweden
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Respiratory Medicine, Ghent University Hospital, Ghent, BE9000, Belgium
- Bioanalysis, Ghent University, Ghent, BE9000, Belgium
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Institute for Community Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33520, Finland
- Department of Clinical Chemistry, Faculty of Medicine and Life Sciences, University of Tampere, Tampere 33014, Finland
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, NC 27514, USA
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
- Institut universitaire de cardiologie et de pneumologie de Québec, Department of Molecular Medicine, Laval University, Québec, Canada
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, NL9713 GZ, Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
- Boehringer Ingelheim , Danbury, CT, USA
- Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
- Centre for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark
- Department of Clinical Experimental Research, Rigshospitalet, 2600 Glostrup, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Department of Medicine, Division of Bioinformatics and Personalized Medicine, University of Colorado Denver, Aurora, CO, USA
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Ludwig-Maximilians-Universität, Munich, Germany
- Division of Population Health Sciences, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Department of Pulmonology, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
- Department of Medical Sciences, Uppsala University Hospital, Uppsala, Sweden
- Epidemiology, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
- Respiratory Medicine, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Internal Medicine B, University Medicine Greifswald, Greifswald, 17475, Germany
- Department of Clinical Physiology, Tampere University Hospital, Tampere, 33521, Finland
- Department of Clinical Physiology, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, 33014, Finland
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, 27709, USA
- Cardiovascular Health Research Unit, Departments of Epidemiology, Medicine and Health Services, University of Washington, Seattle, WA, 98101, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
- Cardiovascular Health Research Unit, Department of Epidemiology, University of Washington, Seattle, WA, 98101, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-6574, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-6574, USA
- Department of Health Sciences, University of Jyväskylä, Jyväskylä, Fl-40014, Finland
- Sticht Center on Aging, Wake Forest School of Medicine, Winston-Salem, NC, USA
- Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research, Munich, Germany
- Faculty of Medicine, University of Split, Split, Croatia
- Alzheimer Scotland Research Centre, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Internal Medicine, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, 17475, Germany
- DZHK (German Centre for Cardiovascular Research), partner site: Greifswald, Greifswald, Germany
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, 20521, Finland
- Research Centre of Applied and Preventative Cardiovascular Medicine, University of Turku, Turku, 20014, Finland
- Department of Epidemiology and Carolina Center for Genome Science, University of North Carolina, Chapel Hill, NC, 27514, USA
- Computational Medicine Core, Center for Lung Biology, UW Medicine Sleep Center, Department of Medicine, University of Washington, Seattle, WA, 98109, USA
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
- Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, 02118, USA
- National Heart, Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA, 01702, USA
- Department of Health, University of Helsinki, Helsinki, FI-00014, Finland
- Department of Public Health, National Institute for Health and Welfare, Helsinki, FI-00271, Finland
- National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, 39216, USA
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, 85764, Germany
- Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich, Munich, 81377, Germany
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA
- Department of Biostatistics, University of Liverpool, Liverpool, L69 3GL, UK
- Radiology, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
- Neurology, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
- Department of Internal Medicine - Pulmonary Diseases, Vivantes Klinikum Spandau Berlin, Berlin, 13585, Germany
- Population Health Research Institute, St George's, University of London, London, SW17 0RE, UK
- NIHR Nottingham Biomedical Research Centre and Division of Respiratory Medicine, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere, 33521, Finland
- Department of Clinical Physiology, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, 33014, Finland
| | - Annah B. Wyss
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, 27709, USA
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Departments of Epidemiology, Medicine and Health Services, University of Washington, Seattle, WA, 98101, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Susan R. Heckbert
- Cardiovascular Health Research Unit, Department of Epidemiology, University of Washington, Seattle, WA, 98101, USA
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-6574, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-6574, USA
| | - Taina Rantanen
- Department of Health Sciences, University of Jyväskylä, Jyväskylä, Fl-40014, Finland
| | | | - Kurt Lohman
- Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Tea Skaaby
- Centre for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark
| | - Charlotta Pisinger
- Centre for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Holger Schulz
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research, Munich, Germany
| | - Ozren Polasek
- Faculty of Medicine, University of Split, Split, Croatia
| | - Archie Campbell
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - John M. Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Alzheimer Scotland Research Centre, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Dennis O. Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
| | - Åsa Johansson
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, SE-75108 Uppsala, Sweden
| | - Erik Ingelsson
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - André G. Uitterlinden
- Epidemiology, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
- Internal Medicine, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
| | - Stefan Weiss
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, 17475, Germany
- DZHK (German Centre for Cardiovascular Research), partner site: Greifswald, Greifswald, Germany
| | - Olli T. Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, 20521, Finland
- Research Centre of Applied and Preventative Cardiovascular Medicine, University of Turku, Turku, 20014, Finland
| | - Vilmundur Gudnason
- Icelandic Heart Association, 201 Kopavogur, Iceland
- University of Iceland, 101 Reykjavik, Iceland
| | - Kari E. North
- Department of Epidemiology and Carolina Center for Genome Science, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - Sina A. Gharib
- Computational Medicine Core, Center for Lung Biology, UW Medicine Sleep Center, Department of Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Don D. Sin
- The University of British Columbia Centre for Heart Lung Innovation, St Paul’s Hospital, Vancouver, BC, Canada
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Kent D. Taylor
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - George T. O'Connor
- Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, 02118, USA
- National Heart, Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA, 01702, USA
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014, Helsinki, Finland
- Department of Health, University of Helsinki, Helsinki, FI-00014, Finland
- Department of Public Health, National Institute for Health and Welfare, Helsinki, FI-00271, Finland
| | - Tamara B. Harris
- National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Oluf Pederson
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Henrik Vestergaard
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Gentofte, 2820, Denmark
| | - James G. Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, 85764, Germany
- Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich, Munich, 81377, Germany
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh , EH4 2XU, UK
| | - Shona Kerr
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh , EH4 2XU, UK
| | - Ian J. Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - R. Graham Barr
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA
| | - Renée de Mutsert
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
| | - Ulf Gyllensten
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, SE-75108 Uppsala, Sweden
| | - Andrew P. Morris
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Biostatistics, University of Liverpool, Liverpool, L69 3GL, UK
| | - M. Arfan Ikram
- Epidemiology, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
- Radiology, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
- Neurology, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
| | - Nicole Probst-Hensch
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sven Gläser
- Internal Medicine B, University Medicine Greifswald, Greifswald, 17475, Germany
- Department of Internal Medicine - Pulmonary Diseases, Vivantes Klinikum Spandau Berlin, Berlin, 13585, Germany
| | | | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33520, Finland
- Department of Clinical Chemistry, Faculty of Medicine and Life Sciences, University of Tampere, Tampere 33014, Finland
| | - David P. Strachan
- Population Health Research Institute, St George's, University of London, London, SW17 0RE, UK
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Alanna C. Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Ian P. Hall
- NIHR Nottingham Biomedical Research Centre and Division of Respiratory Medicine, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Martin D. Tobin
- Department of Health Sciences, University of Leicester, Leicester, UK
- National Institute for Health Research, Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Stephanie J. London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, 27709, USA
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49
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Jackson VE, Latourelle JC, Wain LV, Smith AV, Grove ML, Bartz TM, Obeidat M, Province MA, Gao W, Qaiser B, Porteous DJ, Cassano PA, Ahluwalia TS, Grarup N, Li J, Altmaier E, Marten J, Harris SE, Manichaikul A, Pottinger TD, Li-Gao R, Lind-Thomsen A, Mahajan A, Lahousse L, Imboden M, Teumer A, Prins B, Lyytikäinen LP, Eiriksdottir G, Franceschini N, Sitlani CM, Brody JA, Bossé Y, Timens W, Kraja A, Loukola A, Tang W, Liu Y, Bork-Jensen J, Justesen JM, Linneberg A, Lange LA, Rawal R, Karrasch S, Huffman JE, Smith BH, Davies G, Burkart KM, Mychaleckyj JC, Bonten TN, Enroth S, Lind L, Brusselle GG, Kumar A, Stubbe B, Kähönen M, Wyss AB, Psaty BM, Heckbert SR, Hao K, Rantanen T, Kritchevsky SB, Lohman K, Skaaby T, Pisinger C, Hansen T, Schulz H, Polasek O, Campbell A, Starr JM, Rich SS, Mook-Kanamori DO, Johansson Å, Ingelsson E, Uitterlinden AG, Weiss S, Raitakari OT, Gudnason V, North KE, Gharib SA, Sin DD, Taylor KD, O'Connor GT, Kaprio J, Harris TB, Pederson O, Vestergaard H, Wilson JG, Strauch K, Hayward C, Kerr S, Deary IJ, Barr RG, de Mutsert R, Gyllensten U, Morris AP, Ikram MA, Probst-Hensch N, Gläser S, Zeggini E, Lehtimäki T, Strachan DP, Dupuis J, Morrison AC, Hall IP, Tobin MD, London SJ. Meta-analysis of exome array data identifies six novel genetic loci for lung function. Wellcome Open Res 2018; 3:4. [PMID: 30175238 PMCID: PMC6081985 DOI: 10.12688/wellcomeopenres.12583.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2018] [Indexed: 07/26/2023] Open
Abstract
Background: Over 90 regions of the genome have been associated with lung function to date, many of which have also been implicated in chronic obstructive pulmonary disease. Methods: We carried out meta-analyses of exome array data and three lung function measures: forced expiratory volume in one second (FEV 1), forced vital capacity (FVC) and the ratio of FEV 1 to FVC (FEV 1/FVC). These analyses by the SpiroMeta and CHARGE consortia included 60,749 individuals of European ancestry from 23 studies, and 7,721 individuals of African Ancestry from 5 studies in the discovery stage, with follow-up in up to 111,556 independent individuals. Results: We identified significant (P<2·8x10 -7) associations with six SNPs: a nonsynonymous variant in RPAP1, which is predicted to be damaging, three intronic SNPs ( SEC24C, CASC17 and UQCC1) and two intergenic SNPs near to LY86 and FGF10. Expression quantitative trait loci analyses found evidence for regulation of gene expression at three signals and implicated several genes, including TYRO3 and PLAU. Conclusions: Further interrogation of these loci could provide greater understanding of the determinants of lung function and pulmonary disease.
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Affiliation(s)
| | | | - Louise V. Wain
- Department of Health Sciences, University of Leicester, Leicester, UK
- National Institute for Health Research, Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Albert V. Smith
- Icelandic Heart Association, 201 Kopavogur, Iceland
- University of Iceland, 101 Reykjavik, Iceland
| | - Megan L. Grove
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Traci M. Bartz
- Cardiovascular Health Research Unit, Departments of Medicine and Biostatistics, University of Washington, Seattle, WA, 98101, USA
| | - Ma'en Obeidat
- The University of British Columbia Centre for Heart Lung Innovation, St Paul’s Hospital, Vancouver, BC, Canada
| | - Michael A. Province
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Wei Gao
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Beenish Qaiser
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014, Helsinki, Finland
| | - David J. Porteous
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Patricia A. Cassano
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
- Department of Healthcare Policy and Research, Division of Biostatistics and Epidemiology, Weill Cornell Medical College, New York City, NY, USA
| | - Tarunveer S. Ahluwalia
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Gentofte, 2820, Denmark
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jin Li
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Elisabeth Altmaier
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Jonathan Marten
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh , EH4 2XU, UK
| | - Sarah E. Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Tess D. Pottinger
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Preventive Medicine - Division of Health and Biomedical Informatics, Northwestern University - Feinberg School of Medicine, Chicago, IL, USA
| | - Ruifang Li-Gao
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
| | - Allan Lind-Thomsen
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, SE-75108 Uppsala, Sweden
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Lies Lahousse
- Respiratory Medicine, Ghent University Hospital, Ghent, BE9000, Belgium
- Bioanalysis, Ghent University, Ghent, BE9000, Belgium
| | - Medea Imboden
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Bram Prins
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33520, Finland
- Department of Clinical Chemistry, Faculty of Medicine and Life Sciences, University of Tampere, Tampere 33014, Finland
| | | | - Nora Franceschini
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, NC 27514, USA
| | - Colleen M. Sitlani
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec, Department of Molecular Medicine, Laval University, Québec, Canada
| | - Wim Timens
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, NL9713 GZ, Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Aldi Kraja
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Anu Loukola
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014, Helsinki, Finland
| | - Wenbo Tang
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
- Boehringer Ingelheim , Danbury, CT, USA
| | - Yongmei Liu
- Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Jette Bork-Jensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | | | - Allan Linneberg
- Centre for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark
- Department of Clinical Experimental Research, Rigshospitalet, 2600 Glostrup, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Leslie A. Lange
- Department of Medicine, Division of Bioinformatics and Personalized Medicine, University of Colorado Denver, Aurora, CO, USA
| | - Rajesh Rawal
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Stefan Karrasch
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Ludwig-Maximilians-Universität, Munich, Germany
| | - Jennifer E. Huffman
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh , EH4 2XU, UK
| | - Blair H. Smith
- Division of Population Health Sciences, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK
| | - Gail Davies
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Kristin M. Burkart
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Josyf C. Mychaleckyj
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Tobias N. Bonten
- Department of Pulmonology, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
| | - Stefan Enroth
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, SE-75108 Uppsala, Sweden
| | - Lars Lind
- Department of Medical Sciences, Uppsala University Hospital, Uppsala, Sweden
| | - Guy G. Brusselle
- Respiratory Medicine, Ghent University Hospital, Ghent, BE9000, Belgium
- Epidemiology, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
- Respiratory Medicine, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
| | - Ashish Kumar
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Beate Stubbe
- Internal Medicine B, University Medicine Greifswald, Greifswald, 17475, Germany
| | | | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere, 33521, Finland
- Department of Clinical Physiology, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, 33014, Finland
| | - Annah B. Wyss
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, 27709, USA
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Departments of Epidemiology, Medicine and Health Services, University of Washington, Seattle, WA, 98101, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Susan R. Heckbert
- Cardiovascular Health Research Unit, Department of Epidemiology, University of Washington, Seattle, WA, 98101, USA
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-6574, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-6574, USA
| | - Taina Rantanen
- Department of Health Sciences, University of Jyväskylä, Jyväskylä, Fl-40014, Finland
| | | | - Kurt Lohman
- Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Tea Skaaby
- Centre for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark
| | - Charlotta Pisinger
- Centre for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Holger Schulz
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research, Munich, Germany
| | - Ozren Polasek
- Faculty of Medicine, University of Split, Split, Croatia
| | - Archie Campbell
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - John M. Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Alzheimer Scotland Research Centre, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Dennis O. Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
| | - Åsa Johansson
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, SE-75108 Uppsala, Sweden
| | - Erik Ingelsson
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - André G. Uitterlinden
- Epidemiology, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
- Internal Medicine, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
| | - Stefan Weiss
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, 17475, Germany
- DZHK (German Centre for Cardiovascular Research), partner site: Greifswald, Greifswald, Germany
| | - Olli T. Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, 20521, Finland
- Research Centre of Applied and Preventative Cardiovascular Medicine, University of Turku, Turku, 20014, Finland
| | - Vilmundur Gudnason
- Icelandic Heart Association, 201 Kopavogur, Iceland
- University of Iceland, 101 Reykjavik, Iceland
| | - Kari E. North
- Department of Epidemiology and Carolina Center for Genome Science, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - Sina A. Gharib
- Computational Medicine Core, Center for Lung Biology, UW Medicine Sleep Center, Department of Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Don D. Sin
- The University of British Columbia Centre for Heart Lung Innovation, St Paul’s Hospital, Vancouver, BC, Canada
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Kent D. Taylor
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - George T. O'Connor
- Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, 02118, USA
- National Heart, Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA, 01702, USA
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014, Helsinki, Finland
- Department of Health, University of Helsinki, Helsinki, FI-00014, Finland
- Department of Public Health, National Institute for Health and Welfare, Helsinki, FI-00271, Finland
| | - Tamara B. Harris
- National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Oluf Pederson
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Henrik Vestergaard
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Gentofte, 2820, Denmark
| | - James G. Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, 85764, Germany
- Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich, Munich, 81377, Germany
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh , EH4 2XU, UK
| | - Shona Kerr
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh , EH4 2XU, UK
| | - Ian J. Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - R. Graham Barr
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA
| | - Renée de Mutsert
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
| | - Ulf Gyllensten
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, SE-75108 Uppsala, Sweden
| | - Andrew P. Morris
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Biostatistics, University of Liverpool, Liverpool, L69 3GL, UK
| | - M. Arfan Ikram
- Epidemiology, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
- Radiology, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
- Neurology, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
| | - Nicole Probst-Hensch
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sven Gläser
- Internal Medicine B, University Medicine Greifswald, Greifswald, 17475, Germany
- Department of Internal Medicine - Pulmonary Diseases, Vivantes Klinikum Spandau Berlin, Berlin, 13585, Germany
| | | | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33520, Finland
- Department of Clinical Chemistry, Faculty of Medicine and Life Sciences, University of Tampere, Tampere 33014, Finland
| | - David P. Strachan
- Population Health Research Institute, St George's, University of London, London, SW17 0RE, UK
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Alanna C. Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Ian P. Hall
- NIHR Nottingham Biomedical Research Centre and Division of Respiratory Medicine, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Martin D. Tobin
- Department of Health Sciences, University of Leicester, Leicester, UK
- National Institute for Health Research, Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Stephanie J. London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, 27709, USA
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50
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Jackson VE, Latourelle JC, Wain LV, Smith AV, Grove ML, Bartz TM, Obeidat M, Province MA, Gao W, Qaiser B, Porteous DJ, Cassano PA, Ahluwalia TS, Grarup N, Li J, Altmaier E, Marten J, Harris SE, Manichaikul A, Pottinger TD, Li-Gao R, Lind-Thomsen A, Mahajan A, Lahousse L, Imboden M, Teumer A, Prins B, Lyytikäinen LP, Eiriksdottir G, Franceschini N, Sitlani CM, Brody JA, Bossé Y, Timens W, Kraja A, Loukola A, Tang W, Liu Y, Bork-Jensen J, Justesen JM, Linneberg A, Lange LA, Rawal R, Karrasch S, Huffman JE, Smith BH, Davies G, Burkart KM, Mychaleckyj JC, Bonten TN, Enroth S, Lind L, Brusselle GG, Kumar A, Stubbe B, Kähönen M, Wyss AB, Psaty BM, Heckbert SR, Hao K, Rantanen T, Kritchevsky SB, Lohman K, Skaaby T, Pisinger C, Hansen T, Schulz H, Polasek O, Campbell A, Starr JM, Rich SS, Mook-Kanamori DO, Johansson Å, Ingelsson E, Uitterlinden AG, Weiss S, Raitakari OT, Gudnason V, North KE, Gharib SA, Sin DD, Taylor KD, O'Connor GT, Kaprio J, Harris TB, Pederson O, Vestergaard H, Wilson JG, Strauch K, Hayward C, Kerr S, Deary IJ, Barr RG, de Mutsert R, Gyllensten U, Morris AP, Ikram MA, Probst-Hensch N, Gläser S, Zeggini E, Lehtimäki T, Strachan DP, Dupuis J, Morrison AC, Hall IP, Tobin MD, London SJ. Meta-analysis of exome array data identifies six novel genetic loci for lung function. Wellcome Open Res 2018; 3:4. [PMID: 30175238 PMCID: PMC6081985 DOI: 10.12688/wellcomeopenres.12583.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2018] [Indexed: 08/09/2023] Open
Abstract
Background: Over 90 regions of the genome have been associated with lung function to date, many of which have also been implicated in chronic obstructive pulmonary disease. Methods: We carried out meta-analyses of exome array data and three lung function measures: forced expiratory volume in one second (FEV 1), forced vital capacity (FVC) and the ratio of FEV 1 to FVC (FEV 1/FVC). These analyses by the SpiroMeta and CHARGE consortia included 60,749 individuals of European ancestry from 23 studies, and 7,721 individuals of African Ancestry from 5 studies in the discovery stage, with follow-up in up to 111,556 independent individuals. Results: We identified significant (P<2·8x10 -7) associations with six SNPs: a nonsynonymous variant in RPAP1, which is predicted to be damaging, three intronic SNPs ( SEC24C, CASC17 and UQCC1) and two intergenic SNPs near to LY86 and FGF10. Expression quantitative trait loci analyses found evidence for regulation of gene expression at three signals and implicated several genes, including TYRO3 and PLAU. Conclusions: Further interrogation of these loci could provide greater understanding of the determinants of lung function and pulmonary disease.
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Affiliation(s)
| | | | - Louise V. Wain
- Department of Health Sciences, University of Leicester, Leicester, UK
- National Institute for Health Research, Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Albert V. Smith
- Icelandic Heart Association, 201 Kopavogur, Iceland
- University of Iceland, 101 Reykjavik, Iceland
| | - Megan L. Grove
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Traci M. Bartz
- Cardiovascular Health Research Unit, Departments of Medicine and Biostatistics, University of Washington, Seattle, WA, 98101, USA
| | - Ma'en Obeidat
- The University of British Columbia Centre for Heart Lung Innovation, St Paul’s Hospital, Vancouver, BC, Canada
| | - Michael A. Province
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Wei Gao
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Beenish Qaiser
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014, Helsinki, Finland
| | - David J. Porteous
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Patricia A. Cassano
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
- Department of Healthcare Policy and Research, Division of Biostatistics and Epidemiology, Weill Cornell Medical College, New York City, NY, USA
| | - Tarunveer S. Ahluwalia
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Gentofte, 2820, Denmark
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jin Li
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Elisabeth Altmaier
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Jonathan Marten
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh , EH4 2XU, UK
| | - Sarah E. Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Tess D. Pottinger
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Preventive Medicine - Division of Health and Biomedical Informatics, Northwestern University - Feinberg School of Medicine, Chicago, IL, USA
| | - Ruifang Li-Gao
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
| | - Allan Lind-Thomsen
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, SE-75108 Uppsala, Sweden
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Lies Lahousse
- Respiratory Medicine, Ghent University Hospital, Ghent, BE9000, Belgium
- Bioanalysis, Ghent University, Ghent, BE9000, Belgium
| | - Medea Imboden
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Bram Prins
- Human Genetics, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33520, Finland
- Department of Clinical Chemistry, Faculty of Medicine and Life Sciences, University of Tampere, Tampere 33014, Finland
| | | | - Nora Franceschini
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, NC 27514, USA
| | - Colleen M. Sitlani
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, 98101, USA
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec, Department of Molecular Medicine, Laval University, Québec, Canada
| | - Wim Timens
- Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, NL9713 GZ, Netherlands
- Groningen Research Institute for Asthma and COPD, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Aldi Kraja
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
| | - Anu Loukola
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014, Helsinki, Finland
| | - Wenbo Tang
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, USA
- Boehringer Ingelheim , Danbury, CT, USA
| | - Yongmei Liu
- Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Jette Bork-Jensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | | | - Allan Linneberg
- Centre for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark
- Department of Clinical Experimental Research, Rigshospitalet, 2600 Glostrup, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Leslie A. Lange
- Department of Medicine, Division of Bioinformatics and Personalized Medicine, University of Colorado Denver, Aurora, CO, USA
| | - Rajesh Rawal
- Research Unit of Molecular Epidemiology, Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Stefan Karrasch
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, Ludwig-Maximilians-Universität, Munich, Germany
| | - Jennifer E. Huffman
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh , EH4 2XU, UK
| | - Blair H. Smith
- Division of Population Health Sciences, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK
| | - Gail Davies
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Kristin M. Burkart
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Josyf C. Mychaleckyj
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Tobias N. Bonten
- Department of Pulmonology, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
| | - Stefan Enroth
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, SE-75108 Uppsala, Sweden
| | - Lars Lind
- Department of Medical Sciences, Uppsala University Hospital, Uppsala, Sweden
| | - Guy G. Brusselle
- Respiratory Medicine, Ghent University Hospital, Ghent, BE9000, Belgium
- Epidemiology, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
- Respiratory Medicine, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
| | - Ashish Kumar
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Beate Stubbe
- Internal Medicine B, University Medicine Greifswald, Greifswald, 17475, Germany
| | | | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere, 33521, Finland
- Department of Clinical Physiology, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, 33014, Finland
| | - Annah B. Wyss
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, 27709, USA
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Departments of Epidemiology, Medicine and Health Services, University of Washington, Seattle, WA, 98101, USA
- Kaiser Permanente Washington Health Research Institute, Seattle, WA, USA
| | - Susan R. Heckbert
- Cardiovascular Health Research Unit, Department of Epidemiology, University of Washington, Seattle, WA, 98101, USA
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-6574, USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029-6574, USA
| | - Taina Rantanen
- Department of Health Sciences, University of Jyväskylä, Jyväskylä, Fl-40014, Finland
| | | | - Kurt Lohman
- Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Tea Skaaby
- Centre for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark
| | - Charlotta Pisinger
- Centre for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Holger Schulz
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Comprehensive Pneumology Center Munich (CPC-M), Member of the German Center for Lung Research, Munich, Germany
| | - Ozren Polasek
- Faculty of Medicine, University of Split, Split, Croatia
| | - Archie Campbell
- Centre for Genomic & Experimental Medicine, MRC Institute of Genetics & Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - John M. Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Alzheimer Scotland Research Centre, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Dennis O. Mook-Kanamori
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
| | - Åsa Johansson
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, SE-75108 Uppsala, Sweden
| | - Erik Ingelsson
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - André G. Uitterlinden
- Epidemiology, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
- Internal Medicine, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
| | - Stefan Weiss
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, 17475, Germany
- DZHK (German Centre for Cardiovascular Research), partner site: Greifswald, Greifswald, Germany
| | - Olli T. Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, 20521, Finland
- Research Centre of Applied and Preventative Cardiovascular Medicine, University of Turku, Turku, 20014, Finland
| | - Vilmundur Gudnason
- Icelandic Heart Association, 201 Kopavogur, Iceland
- University of Iceland, 101 Reykjavik, Iceland
| | - Kari E. North
- Department of Epidemiology and Carolina Center for Genome Science, University of North Carolina, Chapel Hill, NC, 27514, USA
| | - Sina A. Gharib
- Computational Medicine Core, Center for Lung Biology, UW Medicine Sleep Center, Department of Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Don D. Sin
- The University of British Columbia Centre for Heart Lung Innovation, St Paul’s Hospital, Vancouver, BC, Canada
- Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Kent D. Taylor
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, 90502, USA
| | - George T. O'Connor
- Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, 02118, USA
- National Heart, Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA, 01702, USA
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014, Helsinki, Finland
- Department of Health, University of Helsinki, Helsinki, FI-00014, Finland
- Department of Public Health, National Institute for Health and Welfare, Helsinki, FI-00271, Finland
| | - Tamara B. Harris
- National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Oluf Pederson
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Henrik Vestergaard
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Gentofte, 2820, Denmark
| | - James G. Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, 39216, USA
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, 85764, Germany
- Chair of Genetic Epidemiology, IBE, Faculty of Medicine, LMU Munich, Munich, 81377, Germany
| | - Caroline Hayward
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh , EH4 2XU, UK
| | - Shona Kerr
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh , EH4 2XU, UK
| | - Ian J. Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
- Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - R. Graham Barr
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY, USA
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA
| | - Renée de Mutsert
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, 2333 ZA, Netherlands
| | - Ulf Gyllensten
- Department of Immunology, Genetics, and Pathology, Biomedical Center, SciLifeLab Uppsala, Uppsala University, SE-75108 Uppsala, Sweden
| | - Andrew P. Morris
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Department of Biostatistics, University of Liverpool, Liverpool, L69 3GL, UK
| | - M. Arfan Ikram
- Epidemiology, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
- Radiology, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
- Neurology, Erasmus Medical Center, Rotterdam, 3000CA, Netherlands
| | - Nicole Probst-Hensch
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sven Gläser
- Internal Medicine B, University Medicine Greifswald, Greifswald, 17475, Germany
- Department of Internal Medicine - Pulmonary Diseases, Vivantes Klinikum Spandau Berlin, Berlin, 13585, Germany
| | | | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33520, Finland
- Department of Clinical Chemistry, Faculty of Medicine and Life Sciences, University of Tampere, Tampere 33014, Finland
| | - David P. Strachan
- Population Health Research Institute, St George's, University of London, London, SW17 0RE, UK
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Alanna C. Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Ian P. Hall
- NIHR Nottingham Biomedical Research Centre and Division of Respiratory Medicine, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Martin D. Tobin
- Department of Health Sciences, University of Leicester, Leicester, UK
- National Institute for Health Research, Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Stephanie J. London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Dept of Health and Human Services, Research Triangle Park, NC, 27709, USA
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