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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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2
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Hadzic S, Wu CY, Gredic M, Pak O, Loku E, Kraut S, Kojonazarov B, Wilhelm J, Brosien M, Bednorz M, Seimetz M, Günther A, Kosanovic D, Sommer N, Warburton D, Li X, Grimminger F, Ghofrani HA, Schermuly RT, Seeger W, El Agha E, Bellusci S, Weissmann N. Fibroblast growth factor 10 reverses cigarette smoke- and elastase-induced emphysema and pulmonary hypertension in mice. Eur Respir J 2023; 62:2201606. [PMID: 37884305 PMCID: PMC10632559 DOI: 10.1183/13993003.01606-2022] [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: 08/16/2022] [Accepted: 08/28/2023] [Indexed: 10/28/2023]
Abstract
BACKGROUND COPD is an incurable disease and a leading cause of death worldwide. In mice, fibroblast growth factor (FGF)10 is essential for lung morphogenesis, and in humans, polymorphisms in the human FGF10 gene correlate with an increased susceptibility to develop COPD. METHODS We analysed FGF10 signalling in human lung sections and isolated cells from healthy donor, smoker and COPD lungs. The development of emphysema and PH was investigated in Fgf10+/- and Fgfr2b+/- (FGF receptor 2b) mice upon chronic exposure to cigarette smoke. In addition, we overexpressed FGF10 in mice following elastase- or cigarette smoke-induced emphysema and pulmonary hypertension (PH). RESULTS We found impaired FGF10 expression in human lung alveolar walls and in primary interstitial COPD lung fibroblasts. In contrast, FGF10 expression was increased in large pulmonary vessels in COPD lungs. Consequently, we identified impaired FGF10 signalling in alveolar walls as an integral part of the pathomechanism that leads to emphysema and PH development: mice with impaired FGF10 signalling (Fgf10+/- and Fgfr2b+/- ) spontaneously developed lung emphysema, PH and other typical pathomechanistic features that generally arise in response to cigarette smoke exposure. CONCLUSION In a therapeutic approach, FGF10 overexpression successfully restored lung alveolar and vascular structure in mice with established cigarette smoke- and elastase-induced emphysema and PH. FGF10 treatment triggered an initial increase in the number of alveolar type 2 cells that gradually returned to the basal level when the FGF10-mediated repair process progressed. Therefore, the application of recombinant FGF10 or stimulation of the downstream signalling cascade might represent a novel therapeutic strategy in the future.
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Affiliation(s)
- Stefan Hadzic
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany
| | - Cheng-Yu Wu
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany
| | - Marija Gredic
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany
| | - Oleg Pak
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany
| | - Edma Loku
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany
| | - Simone Kraut
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany
| | - Baktybek Kojonazarov
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany
- Institute for Lung Health (ILH), Justus-Liebig-University, Giessen, Germany
| | - Jochen Wilhelm
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany
- Institute for Lung Health (ILH), Justus-Liebig-University, Giessen, Germany
| | - Monika Brosien
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany
| | - Mariola Bednorz
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany
| | - Michael Seimetz
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany
| | - Andreas Günther
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany
| | - Djuro Kosanovic
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany
- Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Natascha Sommer
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany
| | - David Warburton
- Children's Hospital Los Angeles, Los Angeles, CA, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Xiaokun Li
- School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, P.R. China
| | - Friedrich Grimminger
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany
| | - Hossein A Ghofrani
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany
| | - Ralph T Schermuly
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany
| | - Werner Seeger
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany
- Max-Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Elie El Agha
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany
- Institute for Lung Health (ILH), Justus-Liebig-University, Giessen, Germany
| | - Saverio Bellusci
- Oujiang Laboratory (Zheijiang Laboratory for Regenerative Medicine, Vision and Brain Health), School of Pharmaceutical Science, Wenzhou Medical University, Wenzhou, P.R. China
- Laboratory of Extracellular Matrix Remodelling, Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany
- S. Bellusci and N. Weissmann contributed equally to this article as lead authors and supervised the work
| | - Norbert Weissmann
- Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), Justus-Liebig-University, Giessen, Germany
- S. Bellusci and N. Weissmann contributed equally to this article as lead authors and supervised the work
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Kim HK, Kang JO, Lim JE, Ha TW, Jung HU, Lee WJ, Kim DJ, Baek EJ, Adcock IM, Chung KF, Kim TB, Oh B. Genetic differences according to onset age and lung function in asthma: A cluster analysis. Clin Transl Allergy 2023; 13:e12282. [PMID: 37488738 PMCID: PMC10345724 DOI: 10.1002/clt2.12282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 04/19/2023] [Accepted: 06/23/2023] [Indexed: 07/26/2023] Open
Abstract
BACKGROUND The extent of differences between genetic risks associated with various asthma subtypes is still unknown. To better understand the heterogeneity of asthma, we employed an unsupervised method to identify genetic variants specifically associated with asthma subtypes. Our goal was to gain insight into the genetic basis of asthma. METHODS In this study, we utilized the UK Biobank dataset to select asthma patients (All asthma, n = 50,517) and controls (n = 283,410). We excluded 14,431 individuals who had no information on predicted values of forced expiratory volume in one second percent (FEV1%) and onset age, resulting in a final total of 36,086 asthma cases. We conducted k-means clustering based on asthma onset age and predicted FEV1% using these samples (n = 36,086). Cluster-specific genome-wide association studies were then performed, and heritability was estimated via linkage disequilibrium score regression. To further investigate the pathophysiology, we conducted eQTL analysis with GTEx and gene-set enrichment analysis with FUMA. RESULTS Clustering resulted in four distinct clusters: early onset asthmanormalLF (early onset with normal lung function, n = 8172), early onset asthmareducedLF (early onset with reduced lung function, n = 8925), late-onset asthmanormalLF (late-onset with normal lung function, n = 12,481), and late-onset asthmareducedLF (late-onset with reduced lung function, n = 6508). Our GWASs in four clusters and in All asthma sample identified 5 novel loci, 14 novel signals, and 51 cluster-specific signals. Among clusters, early onset asthmanormalLF and late-onset asthmareducedLF were the least correlated (rg = 0.37). Early onset asthmareducedLF showed the highest heritability explained by common variants (h2 = 0.212) and was associated with the largest number of variants (71 single nucleotide polymorphisms). Further, the pathway analysis conducted through eQTL and gene-set enrichment analysis showed that the worsening of symptoms in early onset asthma correlated with lymphocyte activation, pathogen recognition, cytokine receptor activation, and lymphocyte differentiation. CONCLUSIONS Our findings suggest that early onset asthmareducedLF was the most genetically predisposed cluster, and that asthma clusters with reduced lung function were genetically distinct from clusters with normal lung function. Our study revealed the genetic variation between clusters that were segmented based on onset age and lung function, providing an important clue for the genetic mechanism of asthma heterogeneity.
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Affiliation(s)
- Han-Kyul Kim
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul, Korea
| | - Ji-One Kang
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul, Korea
| | - Ji Eun Lim
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul, Korea
| | - Tae-Woong Ha
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul, Korea
| | - Hae Un Jung
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, Korea
| | - Won Jun Lee
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul, Korea
| | - Dong Jun Kim
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, Korea
| | - Eun Ju Baek
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, Korea
- Mendel, Seoul, Korea
| | - Ian M Adcock
- The National Heart and Lung Institute, Imperial College, London, UK
| | - Kian Fan Chung
- The National Heart and Lung Institute, Imperial College, London, UK
| | - Tae-Bum Kim
- Department of Allergy and Clinical Immunology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Bermseok Oh
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul, Korea
- Department of Biomedical Science, Graduate School, Kyung Hee University, Seoul, Korea
- Mendel, Seoul, Korea
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4
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Short Chain Fatty Acid Metabolism in Relation to Gut Microbiota and Genetic Variability. Nutrients 2022; 14:nu14245361. [PMID: 36558520 PMCID: PMC9788597 DOI: 10.3390/nu14245361] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
It is widely accepted that the gut microbiota plays a significant role in modulating inflammatory and immune responses of their host. In recent years, the host-microbiota interface has gained relevance in understanding the development of many non-communicable chronic conditions, including cardiovascular disease, cancer, autoimmunity and neurodegeneration. Importantly, dietary fibre (DF) and associated compounds digested by the microbiota and their resulting metabolites, especially short-chain fatty acids (SCFA), were significantly associated with health beneficial effects, such as via proposed anti-inflammatory mechanisms. However, SCFA metabolic pathways are not fully understood. Major steps include production of SCFA by microbiota, uptake in the colonic epithelium, first-pass effects at the liver, followed by biodistribution and metabolism at the host's cellular level. As dietary patterns do not affect all individuals equally, the host genetic makeup may play a role in the metabolic fate of these metabolites, in addition to other factors that might influence the microbiota, such as age, birth through caesarean, medication intake, alcohol and tobacco consumption, pathogen exposure and physical activity. In this article, we review the metabolic pathways of DF, from intake to the intracellular metabolism of fibre-derived products, and identify possible sources of inter-individual variability related to genetic variation. Such variability may be indicative of the phenotypic flexibility in response to diet, and may be predictive of long-term adaptations to dietary factors, including maladaptation and tissue damage, which may develop into disease in individuals with specific predispositions, thus allowing for a better prediction of potential health effects following personalized intervention with DF.
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Germain A, Perotin JM, Delepine G, Polette M, Deslée G, Dormoy V. Whole-Exome Sequencing of Bronchial Epithelial Cells Reveals a Genetic Print of Airway Remodelling in COPD. Biomedicines 2022; 10:biomedicines10071714. [PMID: 35885019 PMCID: PMC9313052 DOI: 10.3390/biomedicines10071714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 11/16/2022] Open
Abstract
The remodelling of the airways is a hallmark of chronic obstructive pulmonary disease, but it is highly heterogeneous and erratically distributed in the airways. To assess the genetic print of remodelling in chronic obstructive pulmonary disease (COPD), we performed a comparative whole-exome sequencing analysis on microdissected bronchial epithelia. Lung resections from four non-COPD and three COPD subjects (ex-smokers and current smokers) were formalin-fixed paraffin-embedded (FFPE). Non-remodelled and remodelled bronchial epithelia were isolated by laser microdissection. Genomic DNA was captured and sequenced. The comparative quantitative analysis identified a list of 109 genes as having variants in remodelled epithelia and 160 genes as having copy number alterations in remodelled epithelia, mainly in COPD patients. The functional analysis highlighted cilia-associated processes. Therefore, bronchial-remodelled epithelia appeared genetically more altered than non-remodelled epithelia. Characterizing the unique molecular print of airway remodelling in respiratory diseases may help uncover additional factors contributing to epithelial dysfunctions, ultimately providing additional targetable proteins to correct epithelial remodelling and improve lung function.
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Affiliation(s)
- Adeline Germain
- Inserm, P3Cell UMR-S1250, Université de Reims Champagne-Ardenne, SFR CAP-SANTE, 51092 Reims, France; (A.G.); (J.-M.P.); (G.D.); (M.P.); (G.D.)
| | - Jeanne-Marie Perotin
- Inserm, P3Cell UMR-S1250, Université de Reims Champagne-Ardenne, SFR CAP-SANTE, 51092 Reims, France; (A.G.); (J.-M.P.); (G.D.); (M.P.); (G.D.)
- Service de Pneumologie, CHU Reims, Hôpital Maison Blanche, 51092 Reims, France
| | - Gonzague Delepine
- Inserm, P3Cell UMR-S1250, Université de Reims Champagne-Ardenne, SFR CAP-SANTE, 51092 Reims, France; (A.G.); (J.-M.P.); (G.D.); (M.P.); (G.D.)
- Service de Chirurgie Thoracique, CHU Reims, Hôpital Maison Blanche, 51092 Reims, France
| | - Myriam Polette
- Inserm, P3Cell UMR-S1250, Université de Reims Champagne-Ardenne, SFR CAP-SANTE, 51092 Reims, France; (A.G.); (J.-M.P.); (G.D.); (M.P.); (G.D.)
- Laboratoire de Biopathologie, CHU Reims, Hôpital Maison Blanche, 51092 Reims, France
| | - Gaëtan Deslée
- Inserm, P3Cell UMR-S1250, Université de Reims Champagne-Ardenne, SFR CAP-SANTE, 51092 Reims, France; (A.G.); (J.-M.P.); (G.D.); (M.P.); (G.D.)
- Service de Pneumologie, CHU Reims, Hôpital Maison Blanche, 51092 Reims, France
| | - Valérian Dormoy
- Inserm, P3Cell UMR-S1250, Université de Reims Champagne-Ardenne, SFR CAP-SANTE, 51092 Reims, France; (A.G.); (J.-M.P.); (G.D.); (M.P.); (G.D.)
- Correspondence: ; Tel.: +33-(0)3-10-73-62-28
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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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7
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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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8
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Talaminos-Barroso A, Roa-Romero LM, Ortega-Ruiz F, Cejudo-Ramos P, Márquez-Martín E, Reina-Tosina J. Effects of genetics and altitude on lung function. CLINICAL RESPIRATORY JOURNAL 2020; 15:247-256. [PMID: 33112470 DOI: 10.1111/crj.13300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 09/11/2020] [Accepted: 10/23/2020] [Indexed: 12/13/2022]
Abstract
OBJECTIVES The aim of this work is to present a review on the impact of genetics and altitude on lung function from classic and recent studies. DATA SOURCE A systematic search has been carried out in different databases of scientific studies, using keywords related to lung volumes, spirometry, altitude and genetics. RESULTS The results of this work have been structured into three parts. First, the relationship between genes and lung function. Next, a review of the genetic predispositions related to respiratory adaptation of people who inhabit high-altitude regions for millennia. Finally, temporary effects and long-term acclimatisation on respiratory physiology at high altitude are presented. CONCLUSIONS The works focused on the influence of genetics and altitude on lung function are currently of interest in terms of studying the interactions between genetic, epigenetic and environmental factors in the configuration of the pathophysiological adaptation patterns.
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Affiliation(s)
| | | | - Francisco Ortega-Ruiz
- Medical-Surgical Unit of Respiratory Diseases, University Hospital Virgen del Rocio, Seville, Spain.,Spanish Networking Center on Biomedical Research, Area of Respiratory Diseases (CIBERES), Madrid, Spain
| | - Pilar Cejudo-Ramos
- Medical-Surgical Unit of Respiratory Diseases, University Hospital Virgen del Rocio, Seville, Spain.,Spanish Networking Center on Biomedical Research, Area of Respiratory Diseases (CIBERES), Madrid, Spain
| | - Eduardo Márquez-Martín
- Medical-Surgical Unit of Respiratory Diseases, University Hospital Virgen del Rocio, Seville, Spain
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Christiani DC. Pulmonary Function: From Genome-Wide Association Studies to Genome-Wide Interaction Studies. Am J Respir Crit Care Med 2019; 199:557-559. [PMID: 30407846 DOI: 10.1164/rccm.201810-1986ed] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- David C Christiani
- 1 Harvard School of Public Health Boston, Massachusetts and.,2 Massachusetts General Hospital/Harvard Medical School Boston, Massachusetts
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Sakornsakolpat P, Prokopenko D, Lamontagne M, Reeve NF, Guyatt AL, Jackson VE, Shrine N, Qiao D, Bartz TM, Kim DK, Lee MK, Latourelle JC, Li X, Morrow JD, Obeidat M, Wyss AB, Bakke P, Barr RG, Beaty TH, Belinsky SA, Brusselle GG, Crapo JD, de Jong K, DeMeo DL, Fingerlin TE, Gharib SA, Gulsvik A, Hall IP, Hokanson JE, Kim WJ, Lomas DA, London SJ, Meyers DA, O'Connor GT, Rennard SI, Schwartz DA, Sliwinski P, Sparrow D, Strachan DP, Tal-Singer R, Tesfaigzi Y, Vestbo J, Vonk JM, Yim JJ, Zhou X, Bossé Y, Manichaikul A, Lahousse L, Silverman EK, Boezen HM, Wain LV, Tobin MD, Hobbs BD, Cho MH. Genetic landscape of chronic obstructive pulmonary disease identifies heterogeneous cell-type and phenotype associations. Nat Genet 2019; 51:494-505. [PMID: 30804561 PMCID: PMC6546635 DOI: 10.1038/s41588-018-0342-2] [Citation(s) in RCA: 205] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 12/20/2018] [Indexed: 11/09/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is the leading cause of respiratory mortality worldwide. Genetic risk loci provide new insights into disease pathogenesis. We performed a genome-wide association study in 35,735 cases and 222,076 controls from the UK Biobank and additional studies from the International COPD Genetics Consortium. We identified 82 loci associated with P < 5 × 10-8; 47 of these were previously described in association with either COPD or population-based measures of lung function. Of the remaining 35 new loci, 13 were associated with lung function in 79,055 individuals from the SpiroMeta consortium. Using gene expression and regulation data, we identified functional enrichment of COPD risk loci in lung tissue, smooth muscle, and several lung cell types. We found 14 COPD loci shared with either asthma or pulmonary fibrosis. COPD genetic risk loci clustered into groups based on associations with quantitative imaging features and comorbidities. Our analyses provide further support for the genetic susceptibility and heterogeneity of COPD.
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Affiliation(s)
- Phuwanat Sakornsakolpat
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Dmitry Prokopenko
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Genetics and Aging Research Unit, Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Maxime Lamontagne
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, Quebec, Canada
| | - Nicola F Reeve
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK
| | - Anna L Guyatt
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK
| | - Victoria E Jackson
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK
| | - Nick Shrine
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK
| | - Dandi Qiao
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Traci M Bartz
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Deog Kyeom Kim
- Seoul National University College of Medicine, SMG-SNU Boramae Medical Center, Seoul, South Korea
| | - Mi Kyeong Lee
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Raleigh, NC, USA
| | - Jeanne C Latourelle
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Xingnan Li
- Department of Medicine, University of Arizona, Tucson, AZ, USA
| | - Jarrett D Morrow
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Ma'en Obeidat
- University of British Columbia Center for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada
| | - Annah B Wyss
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Raleigh, NC, USA
| | - Per Bakke
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - R Graham Barr
- Department of Medicine, College of Physicians and Surgeons and Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Guy G Brusselle
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
- Department of Respiratory Medicine, Erasmus Medical Center, Rotterdam, the Netherlands
| | - James D Crapo
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, National Jewish Health, Denver, CO, USA
| | - Kim de Jong
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Tasha E Fingerlin
- Center for Genes, Environment and Health, National Jewish Health, Denver, CO, USA
- Department of Biostatistics and Informatics, University of Colorado Denver, Aurora, CO, USA
| | - Sina A Gharib
- Computational Medicine Core, Center for Lung Biology, UW Medicine Sleep Center, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Amund Gulsvik
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Ian P Hall
- Division of Respiratory Medicine, Queen's Medical Centre, University of Nottingham, Nottingham, UK
- National Institute for Health Research Nottingham Biomedical Research Centre, Nottingham, UK
| | - John E Hokanson
- Department of Epidemiology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Woo Jin Kim
- Department of Internal Medicine and Environmental Health Center, School of Medicine, Kangwon National University, Chuncheon, South Korea
| | - David A Lomas
- UCL Respiratory, University College London, London, UK
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Raleigh, NC, USA
| | | | - George T O'Connor
- National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, USA
- Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Stephen I Rennard
- Pulmonary, Critical Care, Sleep and Allergy Division, Department of Internal Medicine, University of Nebraska Medical Center, Omaha, NE, USA
- Clinical Discovery Unit, AstraZeneca, Cambridge, UK
| | - David A Schwartz
- Department of Medicine, School of Medicine, University of Colorado Denver, Aurora, CO, USA
- Department of Immunology, School of Medicine, University of Colorado Denver, Aurora, CO, USA
| | - Pawel Sliwinski
- 2nd Department of Respiratory Medicine, Institute of Tuberculosis and Lung Diseases, Warsaw, Poland
| | - David Sparrow
- VA Boston Healthcare System and Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - David P Strachan
- Population Health Research Institute, St. George's University of London, London, UK
| | | | | | - Jørgen Vestbo
- School of Biological Sciences, University of Manchester, Manchester, UK
| | - Judith M Vonk
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands
| | - Jae-Joon Yim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Xiaobo Zhou
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Yohan Bossé
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec, Quebec, Canada
- Department of Molecular Medicine, Laval University, Québec, Québec, Canada
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Lies Lahousse
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Bioanalysis, Ghent University, Ghent, Belgium
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - H Marike Boezen
- University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, the Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, the Netherlands
| | - Louise V Wain
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK
- National Institute for Health Research Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Martin D Tobin
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK
- National Institute for Health Research Leicester Respiratory Biomedical Research Centre, Glenfield Hospital, Leicester, UK
| | - Brian D Hobbs
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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