1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Johnson M, Chelysheva I, Öner D, McGinley J, Lin GL, O'Connor D, Robinson H, Drysdale SB, Gammin E, Vernon S, Muller J, Wolfenden H, Westcar S, Anguvaa L, Thwaites RS, Bont L, Wildenbeest J, Martinón-Torres F, Aerssens J, Openshaw PJM, Pollard AJ. A Genome-Wide Association Study of Respiratory Syncytial Virus Infection Severity in Infants. J Infect Dis 2024; 229:S112-S119. [PMID: 38271230 DOI: 10.1093/infdis/jiae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 01/16/2024] [Accepted: 01/20/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Respiratory syncytial virus (RSV) is a significant cause of infant morbidity and mortality worldwide. Most children experience at least one 1 RSV infection by the age of two 2 years, but not all develop severe disease. However, the understanding of genetic risk factors for severe RSV is incomplete. Consequently, we conducted a genome-wide association study of RSV severity. METHODS Disease severity was assessed by the ReSVinet scale, in a cohort of 251 infants aged 1 week to 1 year. Genotyping data were collected from multiple European study sites as part of the RESCEU Consortium. Linear regression models were used to assess the impact of genotype on RSV severity and gene expression as measured by microarray. RESULTS While no SNPs reached the genome-wide statistical significance threshold (P < 5 × 10-8), we identified 816 candidate SNPs with a P-value of <1 × 10-4. Functional annotation of candidate SNPs highlighted genes relevant to neutrophil trafficking and cytoskeletal functions, including LSP1 and RAB27A. Moreover, SNPs within the RAB27A locus significantly altered gene expression (false discovery rate, FDR P < .05). CONCLUSIONS These findings may provide insights into genetic mechanisms driving severe RSV infection, offering biologically relevant information for future investigations.
Collapse
Affiliation(s)
- Mari Johnson
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford
- NIHR Oxford Biomedical Research Centre and Oxford University Hospitals NHS Foundation Trust, United Kingdom
| | - Irina Chelysheva
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford
- NIHR Oxford Biomedical Research Centre and Oxford University Hospitals NHS Foundation Trust, United Kingdom
| | - Deniz Öner
- Biomarkers Infectious Diseases, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Joseph McGinley
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford
- NIHR Oxford Biomedical Research Centre and Oxford University Hospitals NHS Foundation Trust, United Kingdom
| | - Gu-Lung Lin
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford
- NIHR Oxford Biomedical Research Centre and Oxford University Hospitals NHS Foundation Trust, United Kingdom
| | - Daniel O'Connor
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford
- NIHR Oxford Biomedical Research Centre and Oxford University Hospitals NHS Foundation Trust, United Kingdom
| | - Hannah Robinson
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford
- NIHR Oxford Biomedical Research Centre and Oxford University Hospitals NHS Foundation Trust, United Kingdom
| | - Simon B Drysdale
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford
- NIHR Oxford Biomedical Research Centre and Oxford University Hospitals NHS Foundation Trust, United Kingdom
| | - Emma Gammin
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford
- NIHR Oxford Biomedical Research Centre and Oxford University Hospitals NHS Foundation Trust, United Kingdom
| | - Sophie Vernon
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford
- NIHR Oxford Biomedical Research Centre and Oxford University Hospitals NHS Foundation Trust, United Kingdom
| | - Jill Muller
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford
- NIHR Oxford Biomedical Research Centre and Oxford University Hospitals NHS Foundation Trust, United Kingdom
| | | | | | | | - Ryan S Thwaites
- National Heart and Lung Institute, Imperial College London, United Kingdom
| | - Louis Bont
- Department of Paediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Netherlands
| | - Joanne Wildenbeest
- Department of Paediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Netherlands
| | - Federico Martinón-Torres
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela
- Genetics, Vaccines and Infections Research Group, Instituto de Investigación Sanitaria de Santiago, Universidade de Santiago de Compostela
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Jeroen Aerssens
- Biomarkers Infectious Diseases, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Peter J M Openshaw
- National Heart and Lung Institute, Imperial College London, United Kingdom
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford
- NIHR Oxford Biomedical Research Centre and Oxford University Hospitals NHS Foundation Trust, United Kingdom
| |
Collapse
|
3
|
Choi Y, Cha J, Choi S. Evaluation of penalized and machine learning methods for asthma disease prediction in the Korean Genome and Epidemiology Study (KoGES). BMC Bioinformatics 2024; 25:56. [PMID: 38308205 PMCID: PMC10837879 DOI: 10.1186/s12859-024-05677-x] [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: 06/09/2022] [Accepted: 01/26/2024] [Indexed: 02/04/2024] Open
Abstract
BACKGROUND Genome-wide association studies have successfully identified genetic variants associated with human disease. Various statistical approaches based on penalized and machine learning methods have recently been proposed for disease prediction. In this study, we evaluated the performance of several such methods for predicting asthma using the Korean Chip (KORV1.1) from the Korean Genome and Epidemiology Study (KoGES). RESULTS First, single-nucleotide polymorphisms were selected via single-variant tests using logistic regression with the adjustment of several epidemiological factors. Next, we evaluated the following methods for disease prediction: ridge, least absolute shrinkage and selection operator, elastic net, smoothly clipped absolute deviation, support vector machine, random forest, boosting, bagging, naïve Bayes, and k-nearest neighbor. Finally, we compared their predictive performance based on the area under the curve of the receiver operating characteristic curves, precision, recall, F1-score, Cohen's Kappa, balanced accuracy, error rate, Matthews correlation coefficient, and area under the precision-recall curve. Additionally, three oversampling algorithms are used to deal with imbalance problems. CONCLUSIONS Our results show that penalized methods exhibit better predictive performance for asthma than that achieved via machine learning methods. On the other hand, in the oversampling study, randomforest and boosting methods overall showed better prediction performance than penalized methods.
Collapse
Affiliation(s)
- Yongjun Choi
- Department of Applied Artificial Intelligence, College of Computing, Hanyang University, 55 Hanyang-daehak-ro, Sangnok-gu, Ansan, 15588, South Korea
| | - Junho Cha
- Department of Applied Artificial Intelligence, College of Computing, Hanyang University, 55 Hanyang-daehak-ro, Sangnok-gu, Ansan, 15588, South Korea
| | - Sungkyoung Choi
- Department of Applied Artificial Intelligence, College of Computing, Hanyang University, 55 Hanyang-daehak-ro, Sangnok-gu, Ansan, 15588, South Korea.
- Department of Mathematical Data Science, College of Science and Convergence Technology, Hanyang University, 55 Hanyang-daehak-ro, Sangnok-gu, Ansan, 15588, South Korea.
| |
Collapse
|
4
|
Dapas M, Thompson EE, Wentworth-Sheilds W, Clay S, Visness CM, Calatroni A, Sordillo JE, Gold DR, Wood RA, Makhija M, Khurana Hershey GK, Sherenian MG, Gruchalla RS, Gill MA, Liu AH, Kim H, Kattan M, Bacharier LB, Rastogi D, Altman MC, Busse WW, Becker PM, Nicolae D, O’Connor GT, Gern JE, Jackson DJ, Ober C. Multi-omic association study identifies DNA methylation-mediated genotype and smoking exposure effects on lung function in children living in urban settings. PLoS Genet 2023; 19:e1010594. [PMID: 36638096 PMCID: PMC9879483 DOI: 10.1371/journal.pgen.1010594] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 01/26/2023] [Accepted: 12/23/2022] [Indexed: 01/14/2023] Open
Abstract
Impaired lung function in early life is associated with the subsequent development of chronic respiratory disease. Most genetic associations with lung function have been identified in adults of European descent and therefore may not represent those most relevant to pediatric populations and populations of different ancestries. In this study, we performed genome-wide association analyses of lung function in a multiethnic cohort of children (n = 1,035) living in low-income urban neighborhoods. We identified one novel locus at the TDRD9 gene in chromosome 14q32.33 associated with percent predicted forced expiratory volume in one second (FEV1) (p = 2.4x10-9; βz = -0.31, 95% CI = -0.41- -0.21). Mendelian randomization and mediation analyses revealed that this genetic effect on FEV1 was partially mediated by DNA methylation levels at this locus in airway epithelial cells, which were also associated with environmental tobacco smoke exposure (p = 0.015). Promoter-enhancer interactions in airway epithelial cells revealed chromatin interaction loops between FEV1-associated variants in TDRD9 and the promoter region of the PPP1R13B gene, a stimulator of p53-mediated apoptosis. Expression of PPP1R13B in airway epithelial cells was significantly associated the FEV1 risk alleles (p = 1.3x10-5; β = 0.12, 95% CI = 0.06-0.17). These combined results highlight a potential novel mechanism for reduced lung function in urban youth resulting from both genetics and smoking exposure.
Collapse
Affiliation(s)
- Matthew Dapas
- Department of Human Genetics, University of Chicago, Chicago Illinois, United States of America
| | - Emma E. Thompson
- Department of Human Genetics, University of Chicago, Chicago Illinois, United States of America
| | | | - Selene Clay
- Department of Human Genetics, University of Chicago, Chicago Illinois, United States of America
| | | | | | - Joanne E. Sordillo
- Department of Population Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Diane R. Gold
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Robert A. Wood
- Department of Pediatrics, Johns Hopkins University Medical Center, Baltimore, Maryland, United States of America
| | - Melanie Makhija
- Division of Allergy and Immunology, Ann & Robert H. Lurie Children’s Hospital, Chicago, Illinois, United States of America
| | - Gurjit K. Khurana Hershey
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Michael G. Sherenian
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Rebecca S. Gruchalla
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Michelle A. Gill
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Andrew H. Liu
- Department of Allergy and Immunology, Children’s Hospital Colorado, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Haejin Kim
- Department of Medicine, Henry Ford Health System, Detroit, Michigan, United States of America
| | - Meyer Kattan
- Columbia University College of Physicians and Surgeons, New York, New York, United States of America
| | - Leonard B. Bacharier
- Monroe Carell Jr. Children’s Hospital at Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Deepa Rastogi
- Children’s National Health System, Washington, District of Columbia, United States of America
| | - Matthew C. Altman
- Department of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - William W. Busse
- Department of Pediatrics and Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Patrice M. Becker
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Dan Nicolae
- Department of Statistics, University of Chicago, Chicago, Illinois, United States of America
| | - George T. O’Connor
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - James E. Gern
- Department of Pediatrics and Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Daniel J. Jackson
- Department of Pediatrics and Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago Illinois, United States of America
| |
Collapse
|
5
|
Vernet R, Matran R, Zerimech F, Madore AM, Lavoie ME, Gagnon PA, Mohamdi H, Margaritte-Jeannin P, Siroux V, Dizier MH, Demenais F, Laprise C, Nadif R, Bouzigon E. Identification of novel genes influencing eosinophil-specific protein levels in asthma families. J Allergy Clin Immunol 2022; 150:1168-1177. [PMID: 35671886 DOI: 10.1016/j.jaci.2022.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 05/19/2022] [Accepted: 05/25/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Eosinophils play a key role in the asthma allergic response by releasing cytotoxic molecules such as eosinophil cationic protein (ECP) and eosinophil-derived neurotoxin (EDN) that generate epithelium damages. OBJECTIVE To identify genetic variants influencing ECP and EDN levels in asthma-ascertained families. METHODS We performed univariate and bivariate genome-wide association analyses of ECP and EDN levels in 1,018 subjects from EGEA study with follow-up in 153 subjects from SLSJ study and combined the results of these two studies through meta-analysis. We then conducted Bayesian statistical fine-mapping together with quantitative trait locus and functional annotation analyses to identify the most likely functional genetic variants and candidate genes. RESULTS We identified five genome-wide significant loci (P<5x10-8) including seven distinct signals associated with ECP and/or EDN levels. The genes targeted by our fine-mapping and functional search include RNASE2 and RNASE3 (14q11) which encode EDN and ECP respectively and four other genes which regulate ECP/EDN levels. These four genes were the following: JAK1 (1p31) a transcription factor with a key role in the immune response and a potential therapeutic target for eosinophilic asthma, ARHGAP25 (2p13) involved in leukocyte recruitment to inflammatory sites, NDUFA4 (7p21) encoding a component of the mitochondrial respiratory chain and involved in cellular response to stress and CTSL (9q22) involved in immune response, extra-cellular remodeling and allergic inflammation. CONCLUSION This study demonstrates that the analysis of specific phenotypes produced by eosinophils allows identifying genes with a major role in allergic response and inflammation and offering potential therapeutic targets for asthma.
Collapse
Affiliation(s)
- Raphaël Vernet
- Université Paris Cité, INSERM, UMR 1124, Group of Genomic Epidemiology and Multifactorial Diseases, Paris, France
| | - Régis Matran
- Université Lille, CHU Lille, Institut Pasteur de Lille, ULR 4483, F-59000 Lille, France
| | - Farid Zerimech
- Université Lille, CHU Lille, Institut Pasteur de Lille, EA 4483 - IMPECS, F-59000 Lille, France
| | - Anne-Marie Madore
- Basic Sciences department, Université du Québec à Chicoutimi, Saguenay, Québec, Canada, Centre intersectoriel en santé durable, Université du Québec à Chicoutimi, Saguenay, Québec, Canada
| | - Marie-Eve Lavoie
- Basic Sciences department, Université du Québec à Chicoutimi, Saguenay, Québec, Canada, Centre intersectoriel en santé durable, Université du Québec à Chicoutimi, Saguenay, Québec, Canada
| | - Pierre-Alexandre Gagnon
- Basic Sciences department, Université du Québec à Chicoutimi, Saguenay, Québec, Canada, Centre intersectoriel en santé durable, Université du Québec à Chicoutimi, Saguenay, Québec, Canada
| | - Hamida Mohamdi
- Université Paris Cité, INSERM, UMR 1124, Group of Genomic Epidemiology and Multifactorial Diseases, Paris, France
| | - Patricia Margaritte-Jeannin
- Université Paris Cité, INSERM, UMR 1124, Group of Genomic Epidemiology and Multifactorial Diseases, Paris, France
| | - Valérie Siroux
- Inserm, Université Grenoble Alpes, CNRS, IAB, Team of Environmental Epidemiology Applied to the Development and Respiratory Health, Grenoble, France
| | - Marie-Hélène Dizier
- Université Paris Cité, INSERM, UMR 1124, Group of Genomic Epidemiology and Multifactorial Diseases, Paris, France
| | - Florence Demenais
- Université Paris Cité, INSERM, UMR 1124, Group of Genomic Epidemiology and Multifactorial Diseases, Paris, France
| | - Catherine Laprise
- Basic Sciences department, Université du Québec à Chicoutimi, Saguenay, Québec, Canada, Centre intersectoriel en santé durable, Université du Québec à Chicoutimi, Saguenay, Québec, Canada
| | - Rachel Nadif
- Université Paris-Saclay, UVSQ, Univ. Paris-Sud, Inserm, Equipe d'Epidémiologie Respiratoire Intégrative, CESP, 94807, Villejuif, France
| | - Emmanuelle Bouzigon
- Université Paris Cité, INSERM, UMR 1124, Group of Genomic Epidemiology and Multifactorial Diseases, Paris, France.
| |
Collapse
|
6
|
Genome-Wide Association Study of Fluorescent Oxidation Products Accounting for Tobacco Smoking Status in Adults from the French EGEA Study. Antioxidants (Basel) 2022; 11:antiox11050802. [PMID: 35624665 PMCID: PMC9137810 DOI: 10.3390/antiox11050802] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 04/13/2022] [Accepted: 04/18/2022] [Indexed: 12/14/2022] Open
Abstract
Oxidative stress (OS) is the main pathophysiological mechanism involved in several chronic diseases, including asthma. Fluorescent oxidation products (FlOPs), a global biomarker of damage due to OS, is of growing interest in epidemiological studies. We conducted a genome-wide association study (GWAS) of the FlOPs level in 1216 adults from the case-control and family-based EGEA study (mean age 43 years old, 51% women, and 23% current smokers) to identify genetic variants associated with FlOPs. The GWAS was first conducted in the whole sample and then stratified according to smoking status, the main exogenous source of reactive oxygen species. Among the top genetic variants identified by the three GWAS, those located in BMP6 (p = 3 × 10−6), near BMPER (p = 9 × 10−6), in GABRG3 (p = 4 × 10−7), and near ATG5 (p = 2 × 10−9) are the most relevant because of both their link to biological pathways related to OS and their association with several chronic diseases for which the role of OS in their pathophysiology has been pointed out. BMP6 and BMPER are of particular interest due to their involvement in the same biological pathways related to OS and their functional interaction. To conclude, this study, which is the first GWAS of FlOPs, provides new insights into the pathophysiology of chronic OS-related diseases.
Collapse
|
7
|
Probst-Hensch N, Bochud M, Chiolero A, Crivelli L, Dratva J, Flahault A, Frey D, Kuenzli N, Puhan M, Suggs LS, Wirth C. Swiss Cohort & Biobank - The White Paper. Public Health Rev 2022; 43:1605660. [PMID: 36619237 PMCID: PMC9817110 DOI: 10.3389/phrs.2022.1605660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Affiliation(s)
- Nicole Probst-Hensch
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute (Swiss TPH), Allschwil, Switzerland
- University of Basel, Basel, Switzerland
- Swiss School of Public Health (SSPH+), Zürich, Switzerland
- Swiss Society for Public Health, Bern, Switzerland
- *Correspondence: Nicole Probst-Hensch,
| | - Murielle Bochud
- Swiss School of Public Health (SSPH+), Zürich, Switzerland
- Swiss Society for Public Health, Bern, Switzerland
- Department of Epidemiology and Health Systems (DESS), University Center for General Medicine and Public Health (Unisanté), Lausanne, Switzerland
| | - Arnaud Chiolero
- Swiss School of Public Health (SSPH+), Zürich, Switzerland
- Swiss Society for Public Health, Bern, Switzerland
- Population Health Laboratory (#PopHealthLab), University of Fribourg, Fribourg, Switzerland
- Institute of Primary Health Care (BIHAM), University of Bern, Bern, Switzerland
| | - Luca Crivelli
- Swiss School of Public Health (SSPH+), Zürich, Switzerland
- Swiss Society for Public Health, Bern, Switzerland
- Department of Business Economics, Health and Social Care, University of Applied Sciences and Arts of Southern Switzerland, Manno, Switzerland
- Institute of Public Health Università della Svizzera Italiana, Lugano, Switzerland
| | - Julia Dratva
- Swiss School of Public Health (SSPH+), Zürich, Switzerland
- Swiss Society for Public Health, Bern, Switzerland
- Institute of Public Health, Department of Health Sciences, ZHAW Zürich University of Applied Sciences, Winterthur, Switzerland
| | - Antoine Flahault
- Swiss School of Public Health (SSPH+), Zürich, Switzerland
- Swiss Society for Public Health, Bern, Switzerland
- Institute of Global Health, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Daniel Frey
- Swiss Society for Public Health, Bern, Switzerland
| | - Nino Kuenzli
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute (Swiss TPH), Allschwil, Switzerland
- University of Basel, Basel, Switzerland
- Swiss School of Public Health (SSPH+), Zürich, Switzerland
- Swiss Society for Public Health, Bern, Switzerland
| | - Milo Puhan
- Swiss School of Public Health (SSPH+), Zürich, Switzerland
- Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich, Zurich, Switzerland
| | - L. Suzanne Suggs
- Swiss School of Public Health (SSPH+), Zürich, Switzerland
- Swiss Society for Public Health, Bern, Switzerland
- Institute of Public Health Università della Svizzera Italiana, Lugano, Switzerland
| | - Corina Wirth
- Swiss Society for Public Health, Bern, Switzerland
| |
Collapse
|
8
|
Gheerbrant H, Guillien A, Vernet R, Lupinek C, Pison C, Pin I, Demenais F, Nadif R, Bousquet J, Pickl WF, Valenta R, Bouzigon E, Siroux V. Associations between specific IgE sensitization to 26 respiratory allergen molecules and HLA class II alleles in the EGEA cohort. Allergy 2021; 76:2575-2586. [PMID: 33742477 DOI: 10.1111/all.14820] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 01/27/2021] [Accepted: 02/09/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Allergy, the most frequent immune disorder affecting 30% of the world's population, is the consequence of immunoglobin E (IgE) sensitization to allergens. Among the genetic factors suspected to be involved in allergy, the HLA class-II genomic region is a strong candidate. OBJECTIVE To assess the association between HLA class-II alleles and specific IgE (sIgE) sensitization to a large number of respiratory allergen molecules. METHODS The analysis relied on 927 participants of the EGEA cohort, including 497 asthmatics. The study focuses on 26 aeroallergens recognized by sIgE in at least 5% of the study population (determined with the MEDALL chip with sIgE ≥ 0.3 ISU) and 23 imputed HLA class-II alleles. For each sIgE sensitization and HLA class-II allele, we fitted a logistic regression model accounting for familial dependence and adjusted for gender, age, and genetic principal components. p-values were corrected for multiple comparisons (False Discovery Rate). RESULTS Most of the 19 statistically significant associations observed regard pollen allergens (mugwort Art v 1, olive tree Ole e 1, timothy grass Phl p 2, Phl p 5 and plantain Pla l 1), three were mold allergen (Alternaria Alt a 1), and a single one regards house dust mite allergen (Der p 7). No association was observed with pet allergens. The strongest associations were found with mugwort Art v 1 (OR = 5.42 (95%CI, 3.30; 8.88), 4.14 (2.65; 6.47), 3.16 (1.88; 5.31) with DQB1*05:01, DQA1*01:01 and DRB1*01:01, respectively). CONCLUSION Our results support the important role of HLA class-II alleles as immune response genes predisposing their carriers for sensitization to various major pollen allergens.
Collapse
Affiliation(s)
- Hubert Gheerbrant
- Service Hospitalier Universitaire Pneumologie Physiologie Centre Hospitalier Universitaire Grenoble Alpes Grenoble France
- Inserm CNRS IAB Team of Environmental Epidemiology Applied to Reproduction and Respiratory Health University Grenoble Alpes Grenoble France
| | - Alicia Guillien
- Inserm CNRS IAB Team of Environmental Epidemiology Applied to Reproduction and Respiratory Health University Grenoble Alpes Grenoble France
| | - Raphaël Vernet
- UMRS 1124 INSERM Group of Genomic Epidemiology of Multifactorial Diseases Université de Paris Paris France
| | - Christian Lupinek
- Division of Immunopathology Department of Pathophysiology and Allergy Research Center for Pathophysiology, Infectiology and Immunology Medical University of Vienna Vienna Austria
| | - Christophe Pison
- Service Hospitalier Universitaire Pneumologie Physiologie Centre Hospitalier Universitaire Grenoble Alpes Grenoble France
- Inserm 1055 Laboratoire de Bioénergétique Fondamentale et Appliquée Grenoble France
| | - Isabelle Pin
- Inserm CNRS IAB Team of Environmental Epidemiology Applied to Reproduction and Respiratory Health University Grenoble Alpes Grenoble France
- Department of Pediatrics Grenoble‐Alpes University Hospital Grenoble France
| | - Florence Demenais
- UMRS 1124 INSERM Group of Genomic Epidemiology of Multifactorial Diseases Université de Paris Paris France
| | - Rachel Nadif
- Université Paris‐Saclay UVSQ Univ. Paris‐Sud Inserm Équipe d'Épidémiologie respiratoire intégrative CESP Villejuif France
| | - Jean Bousquet
- Arnaud de Villeneuve University Hospital and Inserm Montpellier France
| | - Winfried F. Pickl
- Institute of Immunology Center for Pathophysiology, Infectiology and Immunology Medical University of Vienna Vienna Austria
| | - Rudolf Valenta
- Division of Immunopathology Department of Pathophysiology and Allergy Research Center for Pathophysiology, Infectiology and Immunology Medical University of Vienna Vienna Austria
- NRC Institute of Immunology FMBA of Russia Moscow Russia
- Laboratory for Immunopathology Department of Clinical Immunology and Allergy Sechenov First Moscow State Medical University Moscow Russia
- Karl Landsteiner University of Health Sciences Krems Austria
| | - Emmanuelle Bouzigon
- UMRS 1124 INSERM Group of Genomic Epidemiology of Multifactorial Diseases Université de Paris Paris France
| | - Valérie Siroux
- Inserm CNRS IAB Team of Environmental Epidemiology Applied to Reproduction and Respiratory Health University Grenoble Alpes Grenoble France
| |
Collapse
|
9
|
An artificial neural network approach integrating plasma proteomics and genetic data identifies PLXNA4 as a new susceptibility locus for pulmonary embolism. Sci Rep 2021; 11:14015. [PMID: 34234248 PMCID: PMC8263618 DOI: 10.1038/s41598-021-93390-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 06/21/2021] [Indexed: 02/06/2023] Open
Abstract
Venous thromboembolism is the third common cardiovascular disease and is composed of two entities, deep vein thrombosis (DVT) and its potential fatal form, pulmonary embolism (PE). While PE is observed in ~ 40% of patients with documented DVT, there is limited biomarkers that can help identifying patients at high PE risk. To fill this need, we implemented a two hidden-layers artificial neural networks (ANN) on 376 antibodies and 19 biological traits measured in the plasma of 1388 DVT patients, with or without PE, of the MARTHA study. We used the LIME algorithm to obtain a linear approximate of the resulting ANN prediction model. As MARTHA patients were typed for genotyping DNA arrays, a genome wide association study (GWAS) was conducted on the LIME estimate. Detected single nucleotide polymorphisms (SNPs) were tested for association with PE risk in MARTHA. Main findings were replicated in the EOVT study composed of 143 PE patients and 196 DVT only patients. The derived ANN model for PE achieved an accuracy of 0.89 and 0.79 in our training and testing sets, respectively. A GWAS on the LIME approximate identified a strong statistical association peak (rs1424597: p = 5.3 × 10-7) at the PLXNA4 locus. Homozygote carriers for the rs1424597-A allele were then more frequently observed in PE than in DVT patients from the MARTHA (2% vs. 0.4%, p = 0.005) and the EOVT (3% vs. 0%, p = 0.013) studies. In a sample of 112 COVID-19 patients known to have endotheliopathy leading to acute lung injury and an increased risk of PE, decreased PLXNA4 levels were associated (p = 0.025) with worsened respiratory function. Using an original integrated proteomics and genetics strategy, we identified PLXNA4 as a new susceptibility gene for PE whose exact role now needs to be further elucidated.
Collapse
|
10
|
Probst-Hensch N, Jeong A, Stolz D, Pons M, Soccal PM, Bettschart R, Jarvis D, Holloway JW, Kronenberg F, Imboden M, Schindler C, Lovison GF. Causal Effects of Body Mass Index on Airflow Obstruction and Forced Mid-Expiratory Flow: A Mendelian Randomization Study Taking Interactions and Age-Specific Instruments Into Consideration Toward a Life Course Perspective. Front Public Health 2021; 9:584955. [PMID: 34046380 PMCID: PMC8144328 DOI: 10.3389/fpubh.2021.584955] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 04/01/2021] [Indexed: 11/22/2022] Open
Abstract
Obesity has complex links to respiratory health. Mendelian randomization (MR) enables assessment of causality of body mass index (BMI) effects on airflow obstruction and mid-expiratory flow. In the adult SAPALDIA cohort, recruiting 9,651 population-representative samples aged 18–60 years at baseline (female 51%), BMI and the ratio of forced expiratory volume in 1 second (FEV1) to forced vital capacity (FVC) as well as forced mid-expiratory flow (FEF25–75%) were measured three times over 20 follow-up years. The causal effects of BMI in childhood and adulthood on FEV1/FVC and FEF25–75% were assessed in predictive (BMI averaged over 1st and 2nd, lung function (LF) averaged over 2nd and 3rd follow-up; N = 2,850) and long-term cross-sectional models (BMI and LF averaged over all follow-ups; N = 2,728) by Mendelian Randomization analyses with the use of weighted BMI allele score as an instrument variable and two-stage least squares (2SLS) method. Three different BMI allele scores were applied to specifically capture the part of BMI in adulthood that likely reflects tracking of genetically determined BMI in childhood. The main causal effects were derived from models containing BMI (instrumented by BMI genetic score), age, sex, height, and packyears smoked as covariates. BMI interactions were instrumented by the product of the instrument (BMI genetic score) and the relevant concomitant variable. Causal effects of BMI on FEV1/FVC and FEF25–75% were observed in both the predictive and long-term cross-sectional models. The causal BMI- LF effects were negative and attenuated with increasing age, and stronger if instrumented by gene scores associated with childhood BMI. This non-standard MR approach interrogating causal effects of multiplicative interaction suggests that the genetically rooted part of BMI patterns in childhood may be of particular relevance for the level of small airway function and airflow obstruction later in life. The methodological relevance of the results is first to point to the importance of a life course perspective in studies on the etiological role of BMI in respiratory health, and second to point out novel methodological aspects to be considered in future MR studies on the causal effects of obesity related phenotypes.
Collapse
Affiliation(s)
- Nicole Probst-Hensch
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,Department of Public Health, University of Basel, Basel, Switzerland
| | - Ayoung Jeong
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,Department of Public Health, University of Basel, Basel, Switzerland
| | - Daiana Stolz
- Clinic of Pulmonary Medicine and Respiratory Cell Research, University Hospital Basel, Basel, Switzerland
| | - Marco Pons
- Division of Pulmonary Medicine, Regional Hospital of Lugano, Lugano, Switzerland
| | - Paola M Soccal
- Division of Pulmonary Medicine, Geneva University Hospitals, Geneva, Switzerland
| | | | - Deborah Jarvis
- Medical Research Council-Public Health England, Centre for Environment and Health, Imperial College London, London, United Kingdom.,Population Health and Occupational Disease, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Florian Kronenberg
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Medea Imboden
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,Department of Public Health, University of Basel, Basel, Switzerland
| | - Christian Schindler
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,Department of Public Health, University of Basel, Basel, Switzerland
| | - Gianfranco F Lovison
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,Department of Public Health, University of Basel, Basel, Switzerland.,Department of Economics, Business and Statistics, University of Palermo, Palermo, Italy
| |
Collapse
|
11
|
Trueb B, Zhuang L, Villiger PM. A Novel Mutation in the IL6R Gene Identified in a Family with Asthma Patients. Genet Test Mol Biomarkers 2020; 24:658-664. [PMID: 32907400 DOI: 10.1089/gtmb.2020.0081] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background: Allergic diseases, including asthma, atopic dermatitis, allergic rhinitis, and food allergies, are caused by both environmental and genetic factors. The allergic condition, where genetic factors make up the largest proportion (up to 95%), is asthma. Aim: To identify polymorphisms and mutations in potentially disease-causing genes in a family affected with allergic asthma. Methods: Whole exome sequencing of the index patient was performed via next-generation sequencing. Variants in known allergy-associated susceptibility genes were identified by comparison with the reference genome GRChr37. Results: Seven common polymorphisms and three rare mutations were identified in the allergy-susceptibility genes of the index patient. Only four of these variants co-segregated with a second patient in the same family. These variants occurred in the TENS1, NPSR1, RAD50, and IL6R genes. Discussion: The variants observed in TENS1 and NPSR1 are relatively common (minor allele frequency, MAF ∼0.4), whereas the mutation in RAD50 is rare (MAF 0.0035). The mutation identified in IL6R (S409P) has never been found before. IL6R encodes an important receptor of the inflammatory system. The mutation occurs in the intracellular domain within a tyrosine-based motif, which is required for sorting of the IL6R protein to the basolateral side of polarized cells. It is likely that this rare mutation contributes-together with the other variants-to the predisposition to asthma and other allergic diseases.
Collapse
Affiliation(s)
- Beat Trueb
- Department for BioMedical Research, University of Bern, Bern, Switzerland.,Department of Rheumatology, University Hospital, Bern, Switzerland
| | - Lei Zhuang
- Department for BioMedical Research, University of Bern, Bern, Switzerland.,Department of Rheumatology, University Hospital, Bern, Switzerland
| | - Peter M Villiger
- Department for BioMedical Research, University of Bern, Bern, Switzerland.,Department of Rheumatology, University Hospital, Bern, Switzerland
| |
Collapse
|
12
|
Fonseca H, da Silva TM, Saraiva M, Santolalla ML, Sant’Anna HP, Araujo NM, Lima NP, Rios R, Tarazona-Santos E, Horta BL, Cruz A, Barreto ML, Figueiredo CA. Genomic Regions 10q22.2, 17q21.31, and 2p23.1 Can Contribute to a Lower Lung Function in African Descent Populations. Genes (Basel) 2020; 11:E1047. [PMID: 32899814 PMCID: PMC7565985 DOI: 10.3390/genes11091047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/01/2020] [Accepted: 09/02/2020] [Indexed: 12/02/2022] Open
Abstract
Accumulated evidence supports the contribution of genetic factors in modulating airway function, especially ancestry. We investigated whether genetic polymorphisms can affect lung function in a mixed Brazilian child population using the admixture mapping strategy through RFMix software version 1.5.4 (Stanford University, Stanford, CA, USA), followed by fine mapping, to identify regions whereby local African or European ancestry is associated with lung function measured by the forced expiratory volume in the first second (FEV1)/forced vital capacity (FVC) ratio, an indicator of airway obstruction. The research cohort included 958 individuals aged 4 to 11 years enrolled in the SCAALA (Social Change, Asthma, Allergy in Latin America) Program. We identified that African ancestry at 17q21.31, 10q22.2, and 2p23.1 regions was associated with lower lung function measured by FEV1/FVC p < 1.9 × 10-4. In contrast, European ancestry at 17q21.31 showed an opposite effect. Fine mapping pointed out 5 single nucleotide polymorphisms (SNPs) also associated in our replication cohort (rs10999948, rs373831475, rs8068257, rs6744555, and rs1520322). Our results suggest that genomic regions associated with ancestry may contribute to differences in lung function measurements in African American children in Brazil replicated in a cohort of Brazilian adults. The analysis strategy used in this work is especially important for phenotypes, such as lung function, which has considerable disparities in terms of measurements across different populations.
Collapse
Affiliation(s)
- Héllen Fonseca
- Programa de Pós Graduação em Imunologia (PPGIm), Instituto de Ciências da Saúde, Universidade Federal da Bahia (UFBA), Salvador 40140-100, BA, Brazil; (H.F.); (M.S.); (R.R.)
| | - Thiago M. da Silva
- Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Jequié 45206-190, BA, Brazil;
| | - Mariana Saraiva
- Programa de Pós Graduação em Imunologia (PPGIm), Instituto de Ciências da Saúde, Universidade Federal da Bahia (UFBA), Salvador 40140-100, BA, Brazil; (H.F.); (M.S.); (R.R.)
| | - Meddly L. Santolalla
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (M.L.S.); (H.P.S.); (N.M.A.); (E.T.-S.)
| | - Hanaisa P. Sant’Anna
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (M.L.S.); (H.P.S.); (N.M.A.); (E.T.-S.)
| | - Nathalia M. Araujo
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (M.L.S.); (H.P.S.); (N.M.A.); (E.T.-S.)
| | - Natália P. Lima
- Programa de Pós-Graduação em Epidemiologia, Universidade Federal de Pelotas, Pelotas 96020-220, Rio Grande do Sul, Brazil; (N.P.L.); (B.L.H.)
| | - Raimon Rios
- Programa de Pós Graduação em Imunologia (PPGIm), Instituto de Ciências da Saúde, Universidade Federal da Bahia (UFBA), Salvador 40140-100, BA, Brazil; (H.F.); (M.S.); (R.R.)
| | - Eduardo Tarazona-Santos
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (M.L.S.); (H.P.S.); (N.M.A.); (E.T.-S.)
| | - Bernardo L Horta
- Programa de Pós-Graduação em Epidemiologia, Universidade Federal de Pelotas, Pelotas 96020-220, Rio Grande do Sul, Brazil; (N.P.L.); (B.L.H.)
| | - Alvaro Cruz
- ProAR, Faculdade de Medicina, Universidade Federal da Bahia (UFBA), Salvador 40060-330, BA, Brazil;
| | - Mauricio L. Barreto
- Centro de Integração de dados e Conhecimentos para Saúde (CIDACS), Fiocruz, Salvador 41745-715, BA, Brazil;
| | - Camila A. Figueiredo
- Departamento de Bio-Regulação, Instituto de Ciências da Saúde, Universidade Federal da Bahia (UFBA), Salvador 40110-902, BA, Brazil
| |
Collapse
|
13
|
Feitosa MF, Lunetta KL, Wang L, Wojczynski MK, Kammerer CM, Perls T, Schupf N, Christensen K, Murabito JM, Province MA. Gene discovery for high-density lipoprotein cholesterol level change over time in prospective family studies. Atherosclerosis 2020; 297:102-110. [PMID: 32109663 DOI: 10.1016/j.atherosclerosis.2020.02.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 01/16/2020] [Accepted: 02/12/2020] [Indexed: 01/14/2023]
Abstract
BACKGROUNDS AND AIMS Several genes are known to contribute to the levels and metabolism of HDL-C, however, their protective effects in cardiovascular disease (CVD), healthy aging, and longevity are complex and poorly understood. It is also unclear if these genes predict longitudinal HDL-C change. We aimed to identify loci influencing HDL-C change. METHODS We performed a genome-wide association study (GWAS) with harmonized HDL-C and imputed genotype in three family-based studies recruited for exceptional survival (Long Life Family Study), from community-based (Framingham Heart Study) and enriched for CVD (Family Heart Study). In 7738 individuals with at least 2 visits, we employed a growth curve model to estimate the random linear trajectory parameter of age-sex-adjusted HDL-C for each person. GWAS was performed using a linear regression model on HDL-C change accounting for kinship correlations, population structure, and differences among studies. RESULTS We identified a novel association for HDL-C with GRID1 (p = 5.43 × 10-10), which encodes a glutamate receptor channel subunit involved in synaptic plasticity. Seven suggestive novel loci (p < 1.0 × 10-6; MBOAT2, LINC01876-NR4A2, NTNG2, CYSLTR2, SYNE2, CTXND1-LINC01314, and CYYR1) and a known lipid gene (ABCA10) showed associations with HDL-C change. Two additional sex-specific suggestive loci were identified in women (DCLK2 and KCNJ2). Several of these genetic variants are associated with lipid-related conditions influencing cardiovascular and metabolic health, have predictive regulatory function, and are involved in lipid-related pathways. CONCLUSIONS Modeling longitudinal HDL-C in prospective studies, with differences in healthy aging, longevity and CVD risk, contributed to gene discovery and provided insights into mechanisms of HDL-C regulation.
Collapse
Affiliation(s)
- Mary F Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA.
| | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA; National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA, USA
| | - Lihua Wang
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Mary K Wojczynski
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Candace M Kammerer
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, PA, USA
| | - Thomas Perls
- Department of Medicine, Geriatrics Section, Boston Medical Center, Boston University School of Medicine, MA, USA
| | - Nicole Schupf
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Kaare Christensen
- Unit of Epidemiology, Biostatistics and Biodemography, Department of Public Health, Southern Denmark University, Odense, Denmark
| | - Joanne M Murabito
- National Heart Lung and Blood Institute's and Boston University's Framingham Heart Study, Framingham, MA, USA; Section of General Internal Medicine, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Michael A Province
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| |
Collapse
|
14
|
Campos AI, García-Marín LM, Byrne EM, Martin NG, Cuéllar-Partida G, Rentería ME. Insights into the aetiology of snoring from observational and genetic investigations in the UK Biobank. Nat Commun 2020; 11:817. [PMID: 32060260 PMCID: PMC7021827 DOI: 10.1038/s41467-020-14625-1] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/22/2020] [Indexed: 12/15/2022] Open
Abstract
Although snoring is common in the general population, its aetiology has been largely understudied. Here we report a genetic study on snoring (n ~ 408,000; snorers ~ 152,000) using data from the UK Biobank. We identify 42 genome-wide significant loci, with an SNP-based heritability estimate of ~10% on the liability scale. Genetic correlations with body mass index, alcohol intake, smoking, schizophrenia, anorexia nervosa and neuroticism are observed. Gene-based associations identify 173 genes, including DLEU7, MSRB3 and POC5, highlighting genes expressed in the brain, cerebellum, lungs, blood and oesophagus. We use polygenic scores (PGS) to predict recent snoring and probable obstructive sleep apnoea (OSA) in an independent Australian sample (n ~ 8000). Mendelian randomization analyses suggest a potential causal relationship between high BMI and snoring. Altogether, our results uncover insights into the aetiology of snoring as a complex sleep-related trait and its role in health and disease beyond it being a cardinal symptom of OSA. Snoring is common in the population and tends to be more prevalent in older and/or male individuals. Here, the authors perform GWAS for habitual snoring, identify 41 genomic loci and explore potential causal relationships with anthropometric and cardiometabolic disease traits.
Collapse
Affiliation(s)
- Adrián I Campos
- Genetic Epidemiology Lab, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Luis M García-Marín
- Genetic Epidemiology Lab, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.,Tecnológico de Monterrey, Escuela de Ingeniería y Ciencias, Zapopan, Jalisco, México
| | - Enda M Byrne
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Nicholas G Martin
- Genetic Epidemiology Lab, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Gabriel Cuéllar-Partida
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia. .,University of Queensland Diamantina Institute, Brisbane, QLD, Australia.
| | - Miguel E Rentería
- Genetic Epidemiology Lab, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia. .,Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.
| |
Collapse
|
15
|
Decrue F, Gorlanova O, Usemann J, Frey U. Lung functional development and asthma trajectories. Semin Immunopathol 2020; 42:17-27. [PMID: 31989229 DOI: 10.1007/s00281-020-00784-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 01/15/2020] [Indexed: 01/06/2023]
Abstract
Early life environmental risk factors are associated with chronic respiratory morbidity in child- and adulthood. A possible mechanism for this sustained effect is their influence on early life lung functional growth and development, a susceptible phase of rapid lung growth with increased plasticity. We summarize evidence of hereditary and environmental ante-, peri-, and early postnatal factors on lung functional development, such as air pollution, tobacco exposure, nutrition, intrauterine growth retardation, prematurity, early life infections, microbiome, and allergies and their effect on lung functional trajectories. While some of the factors (e.g., prematurity) directly impair lung growth, the influence of many environmental factors is mediated through inflammatory processes (e.g., recurrent infections or oxidative stress). The timing and nature of these influences and their impact result in degrees of impaired maximal lung functional capacity in early adulthood; and they potentially impact future long-term respiratory morbidity such as chronic asthma or chronic obstructive airway disease (COPD). We discuss possibilities to prevent or modify such early abnormal lung functional growth trajectories and the need for future studies and prevention programs.
Collapse
Affiliation(s)
- Fabienne Decrue
- University Children's Hospital (UKBB), University of Basel, Spitalstrasse 33, 4056, Basel, Switzerland
| | - Olga Gorlanova
- University Children's Hospital (UKBB), University of Basel, Spitalstrasse 33, 4056, Basel, Switzerland
| | - Jakob Usemann
- University Children's Hospital (UKBB), University of Basel, Spitalstrasse 33, 4056, Basel, Switzerland.,Division of Respiratory Medicin, University Children's Hospital Zurich, Zurich, Switzerland
| | - Urs Frey
- University Children's Hospital (UKBB), University of Basel, Spitalstrasse 33, 4056, Basel, Switzerland.
| |
Collapse
|
16
|
Tang HHF, Sly PD, Holt PG, Holt KE, Inouye M. Systems biology and big data in asthma and allergy: recent discoveries and emerging challenges. Eur Respir J 2020; 55:13993003.00844-2019. [PMID: 31619470 DOI: 10.1183/13993003.00844-2019] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 09/12/2019] [Indexed: 12/15/2022]
Abstract
Asthma is a common condition caused by immune and respiratory dysfunction, and it is often linked to allergy. A systems perspective may prove helpful in unravelling the complexity of asthma and allergy. Our aim is to give an overview of systems biology approaches used in allergy and asthma research. Specifically, we describe recent "omic"-level findings, and examine how these findings have been systematically integrated to generate further insight.Current research suggests that allergy is driven by genetic and epigenetic factors, in concert with environmental factors such as microbiome and diet, leading to early-life disturbance in immunological development and disruption of balance within key immuno-inflammatory pathways. Variation in inherited susceptibility and exposures causes heterogeneity in manifestations of asthma and other allergic diseases. Machine learning approaches are being used to explore this heterogeneity, and to probe the pathophysiological patterns or "endotypes" that correlate with subphenotypes of asthma and allergy. Mathematical models are being built based on genomic, transcriptomic and proteomic data to predict or discriminate disease phenotypes, and to describe the biomolecular networks behind asthma.The use of systems biology in allergy and asthma research is rapidly growing, and has so far yielded fruitful results. However, the scale and multidisciplinary nature of this research means that it is accompanied by new challenges. Ultimately, it is hoped that systems medicine, with its integration of omics data into clinical practice, can pave the way to more precise, personalised and effective management of asthma.
Collapse
Affiliation(s)
- Howard H F Tang
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Australia .,Cambridge Baker Systems Genomics Initiative, Dept of Public Health and Primary Care, University of Cambridge, Cambridge, UK.,School of BioSciences, The University of Melbourne, Parkville, Australia
| | - Peter D Sly
- Queensland Children's Medical Research Institute, The University of Queensland, Brisbane, Australia.,Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Patrick G Holt
- Queensland Children's Medical Research Institute, The University of Queensland, Brisbane, Australia.,Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Kathryn E Holt
- Dept of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia.,London School of Hygiene and Tropical Medicine, London, UK
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Australia.,Cambridge Baker Systems Genomics Initiative, Dept of Public Health and Primary Care, University of Cambridge, Cambridge, UK.,School of BioSciences, The University of Melbourne, Parkville, Australia.,The Alan Turing Institute, London, UK
| |
Collapse
|
17
|
Li D, Kang H, Lee S, Won S. Progressive effects of single-nucleotide polymorphisms on 16 phenotypic traits based on longitudinal data. Genes Genomics 2020; 42:393-403. [PMID: 31902109 PMCID: PMC7113194 DOI: 10.1007/s13258-019-00902-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 12/02/2019] [Indexed: 11/26/2022]
Abstract
Background There are many research studies have estimated the heritability of phenotypic traits, but few have considered longitudinal changes in several phenotypic traits together. Objective To evaluate the progressive effect of single nucleotide polymorphisms (SNPs) on prominent health-related phenotypic traits by determining SNP-based heritability (\documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$$h_{snp}^{2}$$\end{document}hsnp2) using longitudinal data. Methods Sixteen phenotypic traits associated with major health indices were observed biennially for 6843 individuals with 10-year follow-up in a Korean community-based cohort. Average SNP heritability and longitudinal changes in the total period were estimated using a two-stage model. Average and periodic differences for each subject were considered responses to estimate SNP heritability. Furthermore, a genome-wide association study (GWAS) was performed for significant SNPs. Results Each SNP heritability for the phenotypic mean of all sixteen traits through 6 periods (baseline and five follow-ups) were significant. Gradually, the forced vital capacity in one second (FEV1) reflected the only significant SNP heritability among longitudinal changes at a false discovery rate (FDR)-adjusted 0.05 significance level (\documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$$h_{snp}^{2} = 0.171$$\end{document}hsnp2=0.171, FDR = 0.0012). On estimating chromosomal heritability, chromosome 2 displayed the highest heritability upon periodic changes in FEV1. SNPs including rs2272402 and rs7209788 displayed a genome-wide significant association with longitudinal changes in FEV1 (P = 1.22 × 10−8 for rs2272402 and P = 3.36 × 10−7 for rs7209788). De novo variants including rs4922117 (near LPL, P = 2.13 × 10−15) of log-transformed high-density lipoprotein (HDL) ratios and rs2335418 (near HMGCR, P = 3.2 \documentclass[12pt]{minimal}
\usepackage{amsmath}
\usepackage{wasysym}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{amsbsy}
\usepackage{mathrsfs}
\usepackage{upgreek}
\setlength{\oddsidemargin}{-69pt}
\begin{document}$$\times$$\end{document}× 10−9) of low-density lipoprotein were detected on GWAS. Conclusion Significant genetic effects on longitudinal changes in FEV1 among the middle-aged general population and chromosome 2 account for most of the genetic variance. Electronic supplementary material The online version of this article (10.1007/s13258-019-00902-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Donghe Li
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Hahn Kang
- Biology Department, Morrissey College of Arts and Sciences, Boston College, Boston, MA, USA
| | - Sanghun Lee
- Department of Medical Consilience, Graduate School, Dankook University, Yongin, Republic of Korea.
| | - Sungho Won
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea.
- Institute of Health and Environment, Seoul National University, Seoul, Republic of Korea.
- Department of Public Health Science, Graduate School of Public Health, Seoul National University, 1 Kwanak-ro Kwanak-gu, Seoul, 151-742, Republic of Korea.
| |
Collapse
|
18
|
Khadzhieva MB, Kuzovlev AN, Salnikova LE. Pneumonia: host susceptibility and shared genetics with pulmonary function and other traits. Clin Exp Immunol 2019; 198:367-380. [PMID: 31487037 DOI: 10.1111/cei.13367] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/29/2019] [Indexed: 12/16/2022] Open
Abstract
Pneumonia is a common and severe infectious lung disease. Host genetics, together with underlying medical and lifestyle conditions, determine pneumonia susceptibility. We performed a secondary analysis of the results of two genome-wide studies for pneumonia in 23andMe participants (40 600 cases/90 039 controls) (Tian et al., 2017) and UK Biobank (BB) participants (12 614 cases/324 585 controls) (via the Global Biobank Engine) and used the GTEx database to correlate the results with expression quantitative trait loci (eQTLs) data in lung and whole blood. In the 23andMe pneumonia single nucleotide polymorphism (SNP) set, 177 genotyped SNPs in the human leukocyte antigen (HLA) region satisfied the genome-wide significance level, P ≤ 5·0E-08. Several target genes (e.g. C4A, VARS2, SFTA2, HLA-C, HLA-DQA2) were unidirectionally regulated by many HLA eSNPs associated with a higher risk of pneumonia. In lung, C4A transcript was up-regulated by 291 pneumonia risk alleles spanning the half the HLA region. Among SNPs correlated with the expression levels of SFTA2 and VARS2, approximately 75% overlapped: all risk alleles were associated with VARS2 up-regulation and SFTA2 down-regulation. To find shared gene loci between pneumonia and pulmonary function (PF), we used data from the Global Biobank Engine and literature on genome-wide association studies (GWAS) of PF in general populations. Numerous gene loci overlapped between pneumonia and PF: 28·8% in the BB data set and 49·2% in the 23andMe data set. Enrichment analysis within the database of Genotypes and Phenotypes (dbGaP) and National Human Genome Research Institute-European Bioinformatics Institute (NHGRI-EBI) Catalog of pneumonia and pneumonia/PF gene sets identified significant overlap between these gene sets and genes related to inflammatory, developmental, neuropsychiatric and cardiovascular and obesity-related traits.
Collapse
Affiliation(s)
- M B Khadzhieva
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia.,N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.,Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - A N Kuzovlev
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia
| | - L E Salnikova
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Moscow, Russia.,N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.,Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
Ierodiakonou D, Coull BA, Zanobetti A, Postma DS, Boezen HM, Vonk JM, McKone EF, Schildcrout JS, Koppelman GH, Croteau-Chonka DC, Lumley T, Koutrakis P, Schwartz J, Gold DR, Weiss ST. Pathway analysis of a genome-wide gene by air pollution interaction study in asthmatic children. JOURNAL OF EXPOSURE SCIENCE & ENVIRONMENTAL EPIDEMIOLOGY 2019; 29:539-547. [PMID: 31028280 PMCID: PMC10730425 DOI: 10.1038/s41370-019-0136-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 11/23/2018] [Accepted: 03/08/2019] [Indexed: 05/05/2023]
Abstract
OBJECTIVES We aimed to investigate the role of genetics in the respiratory response of asthmatic children to air pollution, with a genome-wide level analysis of gene by nitrogen dioxide (NO2) and carbon monoxide (CO) interaction on lung function and to identify biological pathways involved. METHODS We used a two-step method for fast linear mixed model computations for genome-wide association studies, exploring whether variants modify the longitudinal relationship between 4-month average pollution and post-bronchodilator FEV1 in 522 Caucasian and 88 African-American asthmatic children. Top hits were confirmed with classic linear mixed-effect models. We used the improved gene set enrichment analysis for GWAS (i-GSEA4GWAS) to identify plausible pathways. RESULTS Two SNPs near the EPHA3 (rs13090972 and rs958144) and one in TXNDC8 (rs7041938) showed significant interactions with NO2 in Caucasians but we did not replicate this locus in African-Americans. SNP-CO interactions did not reach genome-wide significance. The i-GSEA4GWAS showed a pathway linked to the HO-1/CO system to be associated with CO-related FEV1 changes. For NO2-related FEV1 responses, we identified pathways involved in cellular adhesion, oxidative stress, inflammation, and metabolic responses. CONCLUSION The host lung function response to long-term exposure to pollution is linked to genes involved in cellular adhesion, oxidative stress, inflammatory, and metabolic pathways.
Collapse
Affiliation(s)
- Despo Ierodiakonou
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| | - Brent A Coull
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Antonella Zanobetti
- Environmental Epidemiology and Risk Program, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Dirkje S Postma
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - H Marike Boezen
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Judith M Vonk
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Edward F McKone
- Department of Respiratory Medicine, St. Vincent University Hospital, Dublin, Ireland
| | - Jonathan S Schildcrout
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States
| | - Gerard H Koppelman
- Groningen Research Institute for Asthma and COPD, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Pediatric Pulmonology and Pediatric Allergology-Beatrix Children Hospital, University of Groningen, University Medical Center, Groningen, The Netherlands
| | - Damien C Croteau-Chonka
- Channing Division of Network Medicine, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Thomas Lumley
- Department of Biostatistics, University of Auckland, Auckland, New Zealand
| | - Petros Koutrakis
- Environmental Epidemiology and Risk Program, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Joel Schwartz
- Environmental Epidemiology and Risk Program, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - Diane R Gold
- Environmental Epidemiology and Risk Program, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Channing Division of Network Medicine, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, MA, United States
| |
Collapse
|
21
|
Reconstructing recent population history while mapping rare variants using haplotypes. Sci Rep 2019; 9:5849. [PMID: 30971755 PMCID: PMC6458133 DOI: 10.1038/s41598-019-42385-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 03/28/2019] [Indexed: 12/11/2022] Open
Abstract
Haplotype-based methods are a cost-effective alternative to characterize unobserved rare variants and map disease-associated alleles. Moreover, they can be used to reconstruct recent population history, which shaped distribution of rare variants and thus can be used to guide gene mapping studies. In this study, we analysed Illumina 650 k genotyped dataset on three underrepresented populations from Eastern Europe, where ancestors of Russians came into contact with two indigenous ethnic groups, Bashkirs and Tatars. Using the IBD mapping approach, we identified two rare IBD haplotypes strongly enriched in asthma patients of distinct ethnic background. We reconstructed recent population history using haplotype-based methods to reconcile this contradictory finding. Our ChromoPainter analysis showed that these haplotypes each descend from a single ancestor coming from one of the ethnic groups studied. Next, we used DoRIS approach and showed that source populations for patients exchanged recent (<60 generations) asymmetric gene flow, which supported the ChromoPainter-based scenario that patients share haplotypes through inter-ethnic admixture. Finally, we show that these IBD haplotypes overlap with asthma-associated genomic regions ascertained in European population. This finding is consistent with the fact that the two donor populations for the rare IBD haplotypes: Russians and Tatars have European ancestry.
Collapse
|
22
|
Rana HK, Akhtar MR, Islam MB, Ahmed MB, Liò P, Quinn JMW, Huq F, Moni MA. Genetic effects of welding fumes on the development of respiratory system diseases. Comput Biol Med 2019; 108:142-149. [PMID: 31005006 DOI: 10.1016/j.compbiomed.2019.04.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/03/2019] [Accepted: 04/04/2019] [Indexed: 12/19/2022]
Abstract
BACKGROUND The welding process releases potentially hazardous gases and fumes, mainly composed of metallic oxides, fluorides and silicates. Long term welding fume (WF) inhalation is a recognized health issue that carries a risk of developing chronic health problems, particularly respiratory system diseases (RSDs). Aside from general airway irritation, WF exposure may drive direct cellular responses in the respiratory system which increase risk of RSD, but these are not well understood. METHODS We developed a quantitative framework to identify gene expression effects of WF exposure that may affect RSD development. We analyzed gene expression microarray data from WF-exposed tissues and RSD-affected tissues, including chronic bronchitis (CB), asthma (AS), pulmonary edema (PE), lung cancer (LC) datasets. We built disease-gene (diseasome) association networks and identified dysregulated signaling and ontological pathways, and protein-protein interaction sub-network using neighborhood-based benchmarking and multilayer network topology. RESULTS We observed many genes with altered expression in WF-exposed tissues were also among differentially expressed genes (DEGs) in RSD tissues; for CB, AS, PE and LC there were 34, 27, 50 and 26 genes respectively. DEG analysis, using disease association networks, pathways, ontological analysis and protein-protein interaction sub-network suggest significant links between WF exposure and the development of CB, AS, PE and LC. CONCLUSIONS Our network-based analysis and investigation of the genetic links of WFs and RSDs confirm a number of genes and gene products are plausible participants in RSD development. Our results are a significant resource to identify causal influences on the development of RSDs, particularly in the context of WF exposure.
Collapse
Affiliation(s)
- Humayan Kabir Rana
- Department of Computer Science and Engineering, Green University of Bangladesh, Bangladesh
| | - Mst Rashida Akhtar
- Department of Computer Science and Engineering, Varendra University, Rajshahi, Bangladesh
| | - M Babul Islam
- Department of Applied Physics and Electronic Engineering, University of Rajshahi, Bangladesh
| | - Mohammad Boshir Ahmed
- School of Civil and Environmental Engineering, University of Technology Sydney, NSW, 2007, Australia
| | - Pietro Liò
- Computer Laboratory, The University of Cambridge, 15 JJ Thomson Avenue, Cambridge, UK
| | - Julian M W Quinn
- Bone Biology Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Fazlul Huq
- Discipline of Pathology, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Australia
| | - Mohammad Ali Moni
- Bone Biology Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia; Discipline of Pathology, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Australia.
| |
Collapse
|
23
|
Vaz Fragoso CA, Manini TM, Kairalla JA, Buford TW, Hsu FC, Gill TM, Kritchevsky SB, McDermott MM, Sanders JL, Cummings SR, Tranah GJ. Mitochondrial DNA variants and pulmonary function in older persons. Exp Gerontol 2018; 115:96-103. [PMID: 30508565 DOI: 10.1016/j.exger.2018.11.023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 11/01/2018] [Accepted: 11/28/2018] [Indexed: 12/21/2022]
Abstract
BACKGROUND We provide the first examination of mitochondrial DNA (mtDNA) variants and pulmonary function in older persons. METHODS Cross-sectional associations between mtDNA variants and pulmonary function were evaluated as a combined p-values meta-analysis, using data from two independent cohorts of older persons. The latter included white and black participants, aged ≥70 years, from the Lifestyle Interventions and Independence for Elders study (LIFE) (N = 1247) and the Health, Aging and Body Composition study (Health ABC) (N = 731), respectively. Pulmonary function included the forced expiratory volume in one-second as a Z-score (FEV1z) and the maximal inspiratory pressure (MIP) in cm of water. RESULTS In black participants, significant associations were found between mtDNA variants and MIP: m.7146A > G, COI (p = 3E-5); m.7389 T > C, COI (p = 2E-4); m.15301G > A, CYB (p = 9E-5); m.16265A > G, HV1 (p = 9E-5); meta-analytical p-values <0.0002. Importantly, these mtDNA variants were unique to black participants and were not present in white participants. Moreover, in black participants, aggregate genetic effects on MIP were observed across mutations in oxidative phosphorylation complex IV (p = 0.004), complex V (p = 0.0007), and hypervariable (p = 0.003) regions. The individual and aggregate variant results were significant after adjustment for multiple comparisons. Otherwise, no significant associations were detected for MIP in whites or for FEV1z in whites or blacks. CONCLUSIONS We have shown that mtDNA variants of African origin are cross-sectionally associated with MIP, a measure of respiratory muscle strength. Thus, our results establish the rationale for longitudinal studies to evaluate whether mtDNA variants of African origin identify those at risk of subsequently developing a respiratory muscle impairment (lower MIP values).
Collapse
Affiliation(s)
- Carlos A Vaz Fragoso
- Yale School of Medicine, Department of Medicine, New Haven, CT, United States of America; Veterans Affairs Connecticut Healthcare System, Department of Medicine, West Haven, CT, United States of America.
| | - Todd M Manini
- University of Florida, Department of Aging and Geriatric Research, Gainesville, FL, United States of America
| | - John A Kairalla
- University of Florida, Department of Biostatistics, Gainesville, FL, United States of America
| | - Thomas W Buford
- University of Alabama at Birmingham, Department of Medicine, Birmingham, AL, United States of America
| | - Fang-Chi Hsu
- Wake Forest School of Medicine, Department of Biostatistical Sciences, Winston-Salem, NC, United States of America
| | - Thomas M Gill
- Yale School of Medicine, Department of Medicine, New Haven, CT, United States of America
| | - Stephen B Kritchevsky
- Wake Forest School of Medicine, Sticht Center for Healthy Aging and Alzheimer's Prevention, Winston-Salem, NC, United States of America
| | - Mary M McDermott
- Northwestern University, Feinberg School of Medicine, Chicago, IL, United States of America
| | - Jason L Sanders
- Massachusetts General Hospital, Department of Medicine, Boston, MA, United States of America
| | - Steven R Cummings
- California Pacific Medical Center Research Institute, San Francisco, CA, United States of America
| | - Gregory J Tranah
- California Pacific Medical Center Research Institute, San Francisco, CA, United States of America
| |
Collapse
|
24
|
Wang Z, Sha Q, Fang S, Zhang K, Zhang S. Testing an optimally weighted combination of common and/or rare variants with multiple traits. PLoS One 2018; 13:e0201186. [PMID: 30048520 PMCID: PMC6062080 DOI: 10.1371/journal.pone.0201186] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 07/10/2018] [Indexed: 12/25/2022] Open
Abstract
Recently, joint analysis of multiple traits has become popular because it can increase statistical power to identify genetic variants associated with complex diseases. In addition, there is increasing evidence indicating that pleiotropy is a widespread phenomenon in complex diseases. Currently, most of existing methods test the association between multiple traits and a single genetic variant. However, these methods by analyzing one variant at a time may not be ideal for rare variant association studies because of the allelic heterogeneity as well as the extreme rarity of rare variants. In this article, we developed a statistical method by testing an optimally weighted combination of variants with multiple traits (TOWmuT) to test the association between multiple traits and a weighted combination of variants (rare and/or common) in a genomic region. TOWmuT is robust to the directions of effects of causal variants and is applicable to different types of traits. Using extensive simulation studies, we compared the performance of TOWmuT with the following five existing methods: gene association with multiple traits (GAMuT), multiple sequence kernel association test (MSKAT), adaptive weighting reverse regression (AWRR), single-TOW, and MANOVA. Our results showed that, in all of the simulation scenarios, TOWmuT has correct type I error rates and is consistently more powerful than the other five tests. We also illustrated the usefulness of TOWmuT by analyzing a whole-genome genotyping data from a lung function study.
Collapse
Affiliation(s)
- Zhenchuan Wang
- Department of Mathematical Sciences, Michigan Technological University, Houghton, Michigan, United States of America
| | - Qiuying Sha
- Department of Mathematical Sciences, Michigan Technological University, Houghton, Michigan, United States of America
| | - Shurong Fang
- Department of Mathematics and Computer Science, John Carroll University, University Heights, Ohio, United States of America
| | - Kui Zhang
- Department of Mathematical Sciences, Michigan Technological University, Houghton, Michigan, United States of America
| | - Shuanglin Zhang
- Department of Mathematical Sciences, Michigan Technological University, Houghton, Michigan, United States of America
| |
Collapse
|
25
|
Lima LC, Queiroz GDA, Costa RDS, Alcantara-Neves NM, Marques CR, Costa GNDO, Barreto ML, Figueiredo CAV, Carneiro VL. Genetic variants in RORA are associated with asthma and allergy markers in an admixed population. Cytokine 2018; 113:177-184. [PMID: 30539779 DOI: 10.1016/j.cyto.2018.07.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 06/21/2018] [Accepted: 07/02/2018] [Indexed: 12/14/2022]
Abstract
Asthma and allergy affect hundreds of millions of people from childhood to old age. In most of them, the inflammatory process of respiratory allergies involves the participation of type 2 cytokines, derived from T helper-2 (Th2)-cell, and Group 2 Innate Lymphoid (ILC2) Cells. An efficient memory Th2 cell response is dependent on IL-13 produced by ILC2s, causing allergic lung inflammation and elevated serum levels of immunoglobulin E. ILC2 cells are derived from common lymphoid progenitors and their growing depends on the transcription factor RORA. The aim of this work was to identify genetic variants in RORA associated with asthma phenotypes and allergy markers. Genomic DNA samples of 1246 individuals participating from Social Changes Asthma and Allergy in Latin America Program (SCAALA) have been genotyped using Illumina Human 2.5 Omni Beadchip. Logistics regressions have been performed to analyze the association among RORA variants and asthma, skin prick tests (SPT), specific IgE and type 2 cytokine production. Twelve single nucleotide variants (SNVs) were significantly associated with atopy (P < 0.01), in which four of them, rs10162630, rs17191519, rs17270243, and rs55796775 and their haplotypes were strongly and positively associated (P < 0.001). Furthermore, these variants increased the RORA gene expression in silico analysis. Other SNVs in RORA were associated with allergy markers, atopic and non-atopic asthma. Therefore, it is believed that variants in RORA gene may influence immunologic features of asthma and allergies and could be possible targets for future treatment of allergic diseases.
Collapse
Affiliation(s)
- Louise Correia Lima
- Departamento de Ciências da Vida, Universidade do Estado da Bahia, Salvador, BA, Brazil
| | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Vonk JM, Nieuwenhuis MAE, Dijk FN, Boudier A, Siroux V, Bouzigon E, Probst-Hensch N, Imboden M, Keidel D, Sin D, Bossé Y, Hao K, van den Berge M, Faiz A, Koppelman GH, Postma DS. Novel genes and insights in complete asthma remission: A genome-wide association study on clinical and complete asthma remission. Clin Exp Allergy 2018; 48:1286-1296. [PMID: 29786918 DOI: 10.1111/cea.13181] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 03/25/2018] [Accepted: 03/29/2018] [Indexed: 12/16/2022]
Abstract
BACKGROUND Asthma is a chronic respiratory disease without a cure, although there exists spontaneous remission. Genome-wide association (GWA) studies have pinpointed genes associated with asthma development, but did not investigate asthma remission. OBJECTIVE We performed a GWA study to develop insights in asthma remission. METHODS Clinical remission (ClinR) was defined by the absence of asthma treatment and wheezing in the last year and asthma attacks in the last 3 years and complete remission (ComR) similarly but additionally with normal lung function and absence of bronchial hyperresponsiveness (BHR). A GWA study on both ClinR and ComR was performed in 790 asthmatics with initial doctor diagnosis of asthma and BHR and long-term follow-up. We assessed replication of the 25 top single nucleotide polymorphisms (SNPs) in 2 independent cohorts (total n = 456), followed by expression quantitative loci (eQTL) analyses of the 4 replicated SNPs in lung tissue and epithelium. RESULTS Of the 790 asthmatics, 178 (23%) had ClinR and 55 ComR (7%) after median follow-up of 15.5 (range 3.3-47.8) years. In ClinR, 1 of the 25 SNPs, rs2740102, replicated in a meta-analysis of the replication cohorts, which was an eQTL for POLI in lung tissue. In ComR, 3 SNPs replicated in a meta-analysis of the replication cohorts. The top-hit, rs6581895, almost reached genome-wide significance (P-value 4.68 × 10-7 ) and was an eQTL for FRS2 and CCT in lung tissue. Rs1420101 was a cis-eQTL in lung tissue for IL1RL1 and IL18R1 and a trans-eQTL for IL13. CONCLUSIONS AND CLINICAL RELEVANCE By defining a strict remission phenotype, we identified 3 SNPs to be associated with complete asthma remission, where 2 SNPs have plausible biological relevance in FRS2, CCT, IL1RL1, IL18R1 and IL13.
Collapse
Affiliation(s)
- J 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
| | - M A E Nieuwenhuis
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Department of Pulmonology, Groningen, The Netherlands
| | - F N Dijk
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Groningen, The Netherlands
| | - A Boudier
- INSERM, Team of Environmental Epidemiology applied to Reproduction and Respiratory Health, IAB, Grenoble, France
| | - V Siroux
- INSERM, Team of Environmental Epidemiology applied to Reproduction and Respiratory Health, IAB, Grenoble, France.,Team of Environmental Epidemiology applied to Reproduction and Respiratory Health, IAB, Univ. Grenoble Alpes, Grenoble, France.,CHU de Grenoble, Team of Environmental Epidemiology applied to Reproduction and Respiratory Health, IAB, Grenoble, France
| | - E Bouzigon
- UMR-946, Inserm, Paris, France.,Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Université Paris Diderot, Paris, France
| | - N Probst-Hensch
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - M Imboden
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - D Keidel
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - D Sin
- St Paul's Hospital, The University of British Columbia James Hogg Research Laboratory, Vancouver, BC, Canada.,Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Y Bossé
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Department of Molecular Medicine, Laval University, Québec, QC, Canada
| | - K Hao
- Merck Research Laboratories, Boston, MA, USA
| | - M van den Berge
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Department of Pulmonology, Groningen, The Netherlands
| | - A Faiz
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Department of Pulmonology, Groningen, The Netherlands
| | - G H Koppelman
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Groningen, The Netherlands
| | - D S Postma
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Department of Pulmonology, Groningen, The Netherlands
| |
Collapse
|
27
|
Bush A. A scandal in South Africa: And not just there! Pediatr Pulmonol 2018; 53:698-700. [PMID: 29673131 DOI: 10.1002/ppul.24010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 03/22/2018] [Indexed: 01/01/2023]
Affiliation(s)
- Andrew Bush
- Imperial College, London, UK.,National Heart and Lung Institute, London, UK.,Royal Brompton Harefield NHS Foundation Trust, London, UK
| |
Collapse
|
28
|
Morrow JD, Cho MH, Platig J, Zhou X, DeMeo DL, Qiu W, Celli B, Marchetti N, Criner GJ, Bueno R, Washko GR, Glass K, Quackenbush J, Silverman EK, Hersh CP. Ensemble genomic analysis in human lung tissue identifies novel genes for chronic obstructive pulmonary disease. Hum Genomics 2018; 12:1. [PMID: 29335020 PMCID: PMC5769240 DOI: 10.1186/s40246-018-0132-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 01/02/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) significantly associated with chronic obstructive pulmonary disease (COPD). However, many genetic variants show suggestive evidence for association but do not meet the strict threshold for genome-wide significance. Integrative analysis of multiple omics datasets has the potential to identify novel genes involved in disease pathogenesis by leveraging these variants in a functional, regulatory context. RESULTS We performed expression quantitative trait locus (eQTL) analysis using genome-wide SNP genotyping and gene expression profiling of lung tissue samples from 86 COPD cases and 31 controls, testing for SNPs associated with gene expression levels. These results were integrated with a prior COPD GWAS using an ensemble statistical and network methods approach to identify relevant genes and observe them in the context of overall genetic control of gene expression to highlight co-regulated genes and disease pathways. We identified 250,312 unique SNPs and 4997 genes in the cis(local)-eQTL analysis (5% false discovery rate). The top gene from the integrative analysis was MAPT, a gene recently identified in an independent GWAS of lung function. The genes HNRNPAB and PCBP2 with RNA binding activity and the gene ACVR1B were identified in network communities with validated disease relevance. CONCLUSIONS The integration of lung tissue gene expression with genome-wide SNP genotyping and subsequent intersection with prior GWAS and omics studies highlighted candidate genes within COPD loci and in communities harboring known COPD genes. This integration also identified novel disease genes in sub-threshold regions that would otherwise have been missed through GWAS.
Collapse
Affiliation(s)
- Jarrett D Morrow
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA.
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - John Platig
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Xiaobo Zhou
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Weiliang Qiu
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Bartholome Celli
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Nathaniel Marchetti
- Division of Pulmonary and Critical Care Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Gerard J Criner
- Division of Pulmonary and Critical Care Medicine, Temple University, Philadelphia, PA, 19140, USA
| | - Raphael Bueno
- Division of Thoracic Surgery, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - George R Washko
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Kimberly Glass
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - John Quackenbush
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| |
Collapse
|
29
|
Bohman A, Juodakis J, Oscarsson M, Bacelis J, Bende M, Torinsson Naluai Å. A family-based genome-wide association study of chronic rhinosinusitis with nasal polyps implicates several genes in the disease pathogenesis. PLoS One 2017; 12:e0185244. [PMID: 29253858 PMCID: PMC5734761 DOI: 10.1371/journal.pone.0185244] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 09/09/2017] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The pathogenesis of chronic rhinosinusitis with nasal polyps is largely unknown. Previous studies have given valuable information about genetic variants associated with this disease but much is still unexplained. Our goal was to identify genetic markers and genes associated with susceptibility to chronic rhinosinusitis with nasal polyps using a family-based genome-wide association study. METHODS 427 patients (293 males and 134 females) with CRSwNP and 393 controls (175 males and 218 females) were recruited from several Swedish hospitals. SNP association values were generated using DFAM (implemented in PLINK) and Efficient Mixed Model Association eXpedited (EMMAX). Analyses of pathway enrichment, gene expression levels and expression quantitative trait loci were then performed in turn. RESULTS None of the analysed SNPs reached genome wide significant association of 5.0 x 10-8. Pathway analyses using our top 1000 markers with the most significant association p-values resulted in 138 target genes. A comparison between our target genes and gene expression data from the NCBI Gene Expression Omnibus database showed significant overlap for 36 of these genes. Comparisons with data from expression quantitative trait loci showed the most skewed allelic distributions in cases with chronic rhinosinusitis with nasal polyps compared with controls for the genes HLCS, HLA-DRA, BICD2, VSIR and SLC5A1. CONCLUSION Our study indicates that HLCS, HLA-DRA, BICD2, VSIR and SLC5A1 could be involved in the pathogenesis of chronic rhinosinusitis with nasal polyps. HLA-DRA has been associated with chronic rhinosinusitis with nasal polyps in previous studies and HLCS, BICD2, VSIR and SLC5A1 may be new targets for future research.
Collapse
Affiliation(s)
- Anton Bohman
- Department of Otorhinolaryngology, Uppsala University Hospital, Uppsala, Sweden
| | - Julius Juodakis
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Martin Oscarsson
- Department of Otorhinolaryngology, Skaraborg Hospital, Skövde, Sweden
| | - Jonas Bacelis
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Mats Bende
- Department of Otorhinolaryngology, Skaraborg Hospital, Skövde, Sweden
| | - Åsa Torinsson Naluai
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| |
Collapse
|
30
|
Nyholt DR, Borsook D, Griffiths LR. Migrainomics — identifying brain and genetic markers of migraine. Nat Rev Neurol 2017; 13:725-741. [DOI: 10.1038/nrneurol.2017.151] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
31
|
Cunha MLR, Meijers JCM, Rosendaal FR, Vlieg AVH, Reitsma PH, Middeldorp S. Whole exome sequencing in thrombophilic pedigrees to identify genetic risk factors for venous thromboembolism. PLoS One 2017; 12:e0187699. [PMID: 29117201 PMCID: PMC5695603 DOI: 10.1371/journal.pone.0187699] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 10/24/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Family studies have shown a strong heritability component for venous thromboembolism (VTE), but established genetic risk factors are present in only half of VTE patients. AIM To identify genetic risk factors in two large families with unexplained hereditary VTE. METHODS We performed whole exome sequencing in 10 affected relatives of two unrelated families with an unexplained tendency for VTE. We prioritized variants shared by all affected relatives from both families, and evaluated these in the remaining affected and unaffected individuals. We prioritized variants based on 3 different filter strategies: variants within candidate genes, rare variants across the exome, and SNPs present in patients with familial VTE and with low frequency in the general population. We used whole exome sequencing data available from 96 unrelated VTE cases with a positive family history of VTE from an affected sib study (the GIFT study) to identify additional carriers and compared the risk-allele frequencies with the general population. Variants found in only one individual were also retained for further analysis. Finally, we assessed the association of these variants with VTE in a population-based case-control study (the MEGA study) with 4,291 cases and 4,866 controls. RESULTS Six variants remained as putative disease-risk candidates. These variants are located in 6 genes spread among 3 different loci: 2p21 (PLEKHH2 NM_172069:c.3105T>C, LRPPRC rs372371276, SRBD1 rs34959371), 5q35.2 (UNC5A NM_133369.2:c.1869+23C>A), and 17q25.1 (GPRC5C rs142232982, RAB37 rs556450784). In GIFT, additional carriers were identified only for the variants located in the 2p21 locus. In MEGA, additional carriers for several of these variants were identified in both cases and controls, without a difference in prevalence; no carrier of the UNC5A variant was present. CONCLUSION Despite sequencing of several individuals from two thrombophilic families resulting in 6 candidate variants, we were unable to confirm their relevance as novel thrombophilic defects.
Collapse
Affiliation(s)
- Marisa L. R. Cunha
- Department of Experimental Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
- Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| | - Joost C. M. Meijers
- Department of Experimental Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
- Department of Plasma Proteins, Sanquin, Amsterdam, the Netherlands
| | - Frits R. Rosendaal
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Astrid van Hylckama Vlieg
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Thrombosis and Hemostasis, Leiden University Medical Center, Leiden, the Netherlands
| | - Pieter H. Reitsma
- Department of Thrombosis and Hemostasis, Leiden University Medical Center, Leiden, the Netherlands
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Saskia Middeldorp
- Department of Vascular Medicine, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands
| |
Collapse
|
32
|
Boueiz A, Lutz SM, Cho MH, Hersh CP, Bowler RP, Washko GR, Halper-Stromberg E, Bakke P, Gulsvik A, Laird NM, Beaty TH, Coxson HO, Crapo JD, Silverman EK, Castaldi PJ, DeMeo DL. Genome-Wide Association Study of the Genetic Determinants of Emphysema Distribution. Am J Respir Crit Care Med 2017; 195:757-771. [PMID: 27669027 DOI: 10.1164/rccm.201605-0997oc] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
RATIONALE Emphysema has considerable variability in the severity and distribution of parenchymal destruction throughout the lungs. Upper lobe-predominant emphysema has emerged as an important predictor of response to lung volume reduction surgery. Yet, aside from alpha-1 antitrypsin deficiency, the genetic determinants of emphysema distribution remain largely unknown. OBJECTIVES To identify the genetic influences of emphysema distribution in non-alpha-1 antitrypsin-deficient smokers. METHODS A total of 11,532 subjects with complete genotype and computed tomography densitometry data in the COPDGene (Genetic Epidemiology of Chronic Obstructive Pulmonary Disease [COPD]; non-Hispanic white and African American), ECLIPSE (Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints), and GenKOLS (Genetics of Chronic Obstructive Lung Disease) studies were analyzed. Two computed tomography scan emphysema distribution measures (difference between upper-third and lower-third emphysema; ratio of upper-third to lower-third emphysema) were tested for genetic associations in all study subjects. Separate analyses in each study population were followed by a fixed effect metaanalysis. Single-nucleotide polymorphism-, gene-, and pathway-based approaches were used. In silico functional evaluation was also performed. MEASUREMENTS AND MAIN RESULTS We identified five loci associated with emphysema distribution at genome-wide significance. These loci included two previously reported associations with COPD susceptibility (4q31 near HHIP and 15q25 near CHRNA5) and three new associations near SOWAHB, TRAPPC9, and KIAA1462. Gene set analysis and in silico functional evaluation revealed pathways and cell types that may potentially contribute to the pathogenesis of emphysema distribution. CONCLUSIONS This multicohort genome-wide association study identified new genomic loci associated with differential emphysematous destruction throughout the lungs. These findings may point to new biologic pathways on which to expand diagnostic and therapeutic approaches in chronic obstructive pulmonary disease. Clinical trial registered with www.clinicaltrials.gov (NCT 00608764).
Collapse
Affiliation(s)
- Adel Boueiz
- 1 Channing Division of Network Medicine.,2 Pulmonary and Critical Care Division, Department of Medicine, and
| | - Sharon M Lutz
- 3 Department of Biostatistics, Colorado School of Public Health, University of Colorado, Aurora, Colorado
| | - Michael H Cho
- 1 Channing Division of Network Medicine.,2 Pulmonary and Critical Care Division, Department of Medicine, and
| | - Craig P Hersh
- 1 Channing Division of Network Medicine.,2 Pulmonary and Critical Care Division, Department of Medicine, and
| | - Russell P Bowler
- 4 Division of Pulmonary Medicine, Department of Medicine, National Jewish Health, Denver, Colorado
| | - George R Washko
- 2 Pulmonary and Critical Care Division, Department of Medicine, and
| | - Eitan Halper-Stromberg
- 4 Division of Pulmonary Medicine, Department of Medicine, National Jewish Health, Denver, Colorado
| | - Per Bakke
- 5 Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Amund Gulsvik
- 5 Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Nan M Laird
- 6 Harvard School of Public Health, Boston, Massachusetts
| | - Terri H Beaty
- 7 Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland; and
| | - Harvey O Coxson
- 8 Department of Radiology, University of British Columbia, Vancouver, British Columbia, Canada
| | - James D Crapo
- 4 Division of Pulmonary Medicine, Department of Medicine, National Jewish Health, Denver, Colorado
| | - Edwin K Silverman
- 1 Channing Division of Network Medicine.,2 Pulmonary and Critical Care Division, Department of Medicine, and
| | - Peter J Castaldi
- 1 Channing Division of Network Medicine.,9 Division of General Medicine and Primary Care, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Dawn L DeMeo
- 1 Channing Division of Network Medicine.,2 Pulmonary and Critical Care Division, Department of Medicine, and
| | | |
Collapse
|
33
|
John C, Soler Artigas M, Hui J, Nielsen SF, Rafaels N, Paré PD, Hansel NN, Shrine N, Kilty I, Malarstig A, Jelinsky SA, Vedel-Krogh S, Barnes K, Hall IP, Beilby J, Musk AW, Nordestgaard BG, James A, Wain LV, Tobin MD. Genetic variants affecting cross-sectional lung function in adults show little or no effect on longitudinal lung function decline. Thorax 2017; 72:400-408. [PMID: 28174340 PMCID: PMC5520280 DOI: 10.1136/thoraxjnl-2016-208448] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 11/25/2016] [Indexed: 11/07/2022]
Abstract
BACKGROUND Genome-wide association studies have identified numerous genetic regions that influence cross-sectional lung function. Longitudinal decline in lung function also includes a heritable component but the genetic determinants have yet to be defined. OBJECTIVES We aimed to determine whether regions associated with cross-sectional lung function were also associated with longitudinal decline and to seek novel variants which influence decline. METHODS We analysed genome-wide data from 4167 individuals from the Busselton Health Study cohort, who had undergone spirometry (12 695 observations across eight time points). A mixed model was fitted and weighted risk scores were calculated for the joint effect of 26 known regions on baseline and longitudinal changes in FEV1 and FEV1/FVC. Potential additional regions of interest were identified and followed up in two independent cohorts. RESULTS The 26 regions previously associated with cross-sectional lung function jointly showed a strong effect on baseline lung function (p=4.44×10-16 for FEV1/FVC) but no effect on longitudinal decline (p=0.160 for FEV1/FVC). This was replicated in an independent cohort. 39 additional regions of interest (48 variants) were identified; these associations were not replicated in two further cohorts. CONCLUSIONS Previously identified genetic variants jointly have a strong effect on cross-sectional lung function in adults but little or no effect on the rate of decline of lung function. It is possible that they influence COPD risk through lung development. Although no genetic variants have yet been associated with lung function decline at stringent genome-wide significance, longitudinal change in lung function is heritable suggesting that there is scope for future discoveries.
Collapse
Affiliation(s)
- Catherine John
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK
| | - María Soler Artigas
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK
| | - Jennie Hui
- School of Pathology and Laboratory Medicine, The University of Western Australia, Australia,PathWest, Department of Health, Government of Western Australia, Perth, WA, Australia,Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Western Australia, Australia,School of Population Health, The University of Western Australia, Australia
| | - Sune Fallgaard Nielsen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Denmark
| | - Nicholas Rafaels
- Center for Personalized Medicine and Biomedical Informatics, School of Medicine, University of Colorado, Anschutz Medical Campus
| | - Peter D Paré
- University of British Columbia Centre for Heart Lung Innovation, St Paul's Hospital, Vancouver, British Columbia, Canada
| | - Nadia N Hansel
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Nick Shrine
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK
| | - Iain Kilty
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts, USA
| | | | - Scott A Jelinsky
- Pfizer Worldwide Research and Development, Cambridge, Massachusetts, USA
| | - Signe Vedel-Krogh
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Denmark
| | - Kathleen Barnes
- Center for Personalized Medicine and Biomedical Informatics, School of Medicine, University of Colorado, Anschutz Medical Campus
| | - Ian P Hall
- Division of Respiratory Medicine, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - John Beilby
- School of Pathology and Laboratory Medicine, The University of Western Australia, Australia,PathWest, Department of Health, Government of Western Australia, Perth, WA, Australia,Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Western Australia, Australia
| | - Arthur W Musk
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Western Australia, Australia,School of Population Health, The University of Western Australia, Australia,Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia,School of Medicine and Pharmacology, The University of Western Australia, Australia
| | - Børge G Nordestgaard
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen University Hospital, Denmark
| | - Alan James
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Western Australia, Australia,School of Medicine and Pharmacology, The University of Western Australia, Australia,Department of Pulmonary Physiology and Sleep Medicine/West Australian Sleep Disorders Research Institute, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
| | - Louise V Wain
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK,National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Martin D Tobin
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, UK,National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| |
Collapse
|
34
|
Rava M, Ahmed I, Kogevinas M, Le Moual N, Bouzigon E, Curjuric I, Dizier MH, Dumas O, Gonzalez JR, Imboden M, Mehta AJ, Tubert-Bitter P, Zock JP, Jarvis D, Probst-Hensch NM, Demenais F, Nadif R. Genes Interacting with Occupational Exposures to Low Molecular Weight Agents and Irritants on Adult-Onset Asthma in Three European Studies. ENVIRONMENTAL HEALTH PERSPECTIVES 2017; 125:207-214. [PMID: 27504716 PMCID: PMC5289825 DOI: 10.1289/ehp376] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 04/18/2016] [Accepted: 06/13/2016] [Indexed: 06/06/2023]
Abstract
BACKGROUND The biological mechanisms by which cleaning products and disinfectants-an emerging risk factor-affect respiratory health remain incompletely evaluated. Studying genes by environment interactions (G × E) may help identify new genes related to adult-onset asthma. OBJECTIVES We identified interactions between genetic polymorphisms of a large set of genes involved in the response to oxidative stress and occupational exposures to low molecular weight (LMW) agents or irritants on adult-onset asthma. METHODS Our data came from three large European cohorts: Epidemiological Family-based Study of the Genetics and Environment of Asthma (EGEA), Swiss Cohort Study on Air Pollution and Lung and Heart Disease in Adults (SAPALDIA), and European Community Respiratory Health Survey in Adults (ECRHS). A candidate pathway-based strategy identified 163 genes involved in the response to oxidative stress and potentially related to exposures to LMW agents/irritants. Occupational exposures were evaluated using an asthma job-exposure matrix and job-specific questionnaires for cleaners and healthcare workers. Logistic regression models were used to detect G × E interactions, adjusted for age, sex, and population ancestry, in 2,599 adults (mean age, 47 years; 60% women, 36% exposed, 18% asthmatics). p-Values were corrected for multiple comparisons. RESULTS Ever exposure to LMW agents/irritants was associated with current adult-onset asthma [OR = 1.28 (95% CI: 1.04, 1.58)]. Eight single nucleotide polymorphism (SNP) by exposure interactions at five loci were found at p < 0.005: PLA2G4A (rs932476, chromosome 1), near PLA2R1 (rs2667026, chromosome 2), near RELA (rs931127, rs7949980, chromosome 11), PRKD1 (rs1958980, rs11847351, rs1958987, chromosome 14), and PRKCA (rs6504453, chromosome 17). Results were consistent across the three studies and after accounting for smoking. CONCLUSIONS Using a pathway-based selection process, we identified novel genes potentially involved in adult asthma by interaction with occupational exposure. These genes play a role in the NF-κB pathway, which is involved in inflammation. Citation: Rava M, Ahmed I, Kogevinas M, Le Moual N, Bouzigon E, Curjuric I, Dizier MH, Dumas O, Gonzalez JR, Imboden M, Mehta AJ, Tubert-Bitter P, Zock JP, Jarvis D, Probst-Hensch NM, Demenais F, Nadif R. 2017. Genes interacting with occupational exposures to low molecular weight agents and irritants on adult-onset asthma in three European studies. Environ Health Perspect 125:207-214; http://dx.doi.org/10.1289/EHP376.
Collapse
Affiliation(s)
- Marta Rava
- Inserm, U1168, VIMA: Aging and Chronic Diseases, Epidemiological and Public Health Approaches, Villejuif, France
- Spanish National Cancer Research Centre (CNIO), Genetic and Molecular Epidemiology Group, Human Cancer Genetics Program, Madrid, Spain
| | - Ismail Ahmed
- Inserm UMR 1181 [Biostatistics, Biomathematics, Pharmacoepidemiology and Infectious Diseases (B2PHI)], Villejuif, France
- Institut Pasteur, UMR 1181, B2PHI, Paris, France
- Univ Versailles St.-Quentin-en-Yvelines, UMR 1181, B2PHI, Montigny le Bretonneux, France
| | - Manolis Kogevinas
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
| | - Nicole Le Moual
- Inserm, U1168, VIMA: Aging and Chronic Diseases, Epidemiological and Public Health Approaches, Villejuif, France
- Univ Versailles St.-Quentin-en-Yvelines, UMR-S 1168, Montigny le Bretonneux, France
| | - Emmanuelle Bouzigon
- Inserm, UMR-946, Genetic Variation and Human Diseases Unit, Paris, France
- Univ Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d’Hématologie, Paris, France
| | - Ivan Curjuric
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Switzerland
| | - Marie-Hélène Dizier
- Inserm, UMR-946, Genetic Variation and Human Diseases Unit, Paris, France
- Univ Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d’Hématologie, Paris, France
| | - Orianne Dumas
- Inserm, U1168, VIMA: Aging and Chronic Diseases, Epidemiological and Public Health Approaches, Villejuif, France
- Univ Versailles St.-Quentin-en-Yvelines, UMR-S 1168, Montigny le Bretonneux, France
| | - Juan R. Gonzalez
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
| | - Medea Imboden
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Switzerland
| | - Amar J. Mehta
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Switzerland
- Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Pascale Tubert-Bitter
- Inserm UMR 1181 [Biostatistics, Biomathematics, Pharmacoepidemiology and Infectious Diseases (B2PHI)], Villejuif, France
- Institut Pasteur, UMR 1181, B2PHI, Paris, France
- Univ Versailles St.-Quentin-en-Yvelines, UMR 1181, B2PHI, Montigny le Bretonneux, France
| | - Jan-Paul Zock
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL), Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Deborah Jarvis
- Respiratory Epidemiology and Public Health, Imperial College, London, United Kingdom
- MRC-HPA (Medical Research Council and Health Protection Agency) Centre for Environment and Health, London, United Kingdom
| | - Nicole M. Probst-Hensch
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Switzerland
| | - Florence Demenais
- Inserm, UMR-946, Genetic Variation and Human Diseases Unit, Paris, France
- Univ Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d’Hématologie, Paris, France
| | - Rachel Nadif
- Inserm, U1168, VIMA: Aging and Chronic Diseases, Epidemiological and Public Health Approaches, Villejuif, France
- Univ Versailles St.-Quentin-en-Yvelines, UMR-S 1168, Montigny le Bretonneux, France
| |
Collapse
|
35
|
McGeachie MJ, Yates KP, Zhou X, Guo F, Sternberg AL, Van Natta ML, Wise RA, Szefler SJ, Sharma S, Kho AT, Cho MH, Croteau-Chonka DC, Castaldi PJ, Jain G, Sanyal A, Zhan Y, Lajoie BR, Dekker J, Stamatoyannopoulos J, Covar RA, Zeiger RS, Adkinson NF, Williams PV, Kelly HW, Grasemann H, Vonk JM, Koppelman GH, Postma DS, Raby BA, Houston I, Lu Q, Fuhlbrigge AL, Tantisira KG, Silverman EK, Tonascia J, Strunk RC, Weiss ST. Genetics and Genomics of Longitudinal Lung Function Patterns in Individuals with Asthma. Am J Respir Crit Care Med 2016; 194:1465-1474. [PMID: 27367781 PMCID: PMC5215031 DOI: 10.1164/rccm.201602-0250oc] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 06/30/2016] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Patterns of longitudinal lung function growth and decline in childhood asthma have been shown to be important in determining risk for future respiratory ailments including chronic airway obstruction and chronic obstructive pulmonary disease. OBJECTIVES To determine the genetic underpinnings of lung function patterns in subjects with childhood asthma. METHODS We performed a genome-wide association study of 581 non-Hispanic white individuals with asthma that were previously classified by patterns of lung function growth and decline (normal growth, normal growth with early decline, reduced growth, and reduced growth with early decline). The strongest association was also measured in two additional cohorts: a small asthma cohort and a large chronic obstructive pulmonary disease metaanalysis cohort. Interaction between the genomic region encompassing the most strongly associated single-nucleotide polymorphism and nearby genes was assessed by two chromosome conformation capture assays. MEASUREMENTS AND MAIN RESULTS An intergenic single-nucleotide polymorphism (rs4445257) on chromosome 8 was strongly associated with the normal growth with early decline pattern compared with all other pattern groups (P = 6.7 × 10-9; odds ratio, 2.8; 95% confidence interval, 2.0-4.0); replication analysis suggested this variant had opposite effects in normal growth with early decline and reduced growth with early decline pattern groups. Chromosome conformation capture experiments indicated a chromatin interaction between rs4445257 and the promoter of the distal CSMD3 gene. CONCLUSIONS Early decline in lung function after normal growth is associated with a genetic polymorphism that may also protect against early decline in reduced growth groups. Clinical trial registered with www.clinicaltrials.gov (NCT00000575).
Collapse
Affiliation(s)
- Michael J. McGeachie
- Channing Division of Network Medicine and
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | | | - Xiaobo Zhou
- Channing Division of Network Medicine and
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Feng Guo
- Channing Division of Network Medicine and
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | | | | | - Robert A. Wise
- School of Medicine, Johns Hopkins University, Baltimore, Maryland
| | - Stanley J. Szefler
- National Jewish Health and Research Center, Denver, Colorado
- Children's Hospital Colorado and
| | - Sunita Sharma
- Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, University of Colorado, Denver, Colorado
| | - Alvin T. Kho
- Channing Division of Network Medicine and
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
- Boston Children’s Hospital, Boston, Massachusetts
| | - Michael H. Cho
- Channing Division of Network Medicine and
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Damien C. Croteau-Chonka
- Channing Division of Network Medicine and
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Peter J. Castaldi
- Channing Division of Network Medicine and
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Gaurav Jain
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, and
| | - Amartya Sanyal
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, and
- School of Biological Sciences, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Ye Zhan
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, and
| | - Bryan R. Lajoie
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, and
| | - Job Dekker
- Howard Hughes Medical Institute, Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts
| | | | - Ronina A. Covar
- National Jewish Health and Research Center, Denver, Colorado
- Children's Hospital Colorado and
- University of Colorado, Denver, Colorado
| | - Robert S. Zeiger
- Department of Pediatrics, University of California at San Diego, La Jolla, California
- Kaiser Permanente Southern California Region, San Diego, California
| | | | - Paul V. Williams
- ASTHMA, Inc., Clinical Research Center and Northwest Asthma & Allergy Center, Seattle, Washington
| | - H. William Kelly
- University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | - Hartmut Grasemann
- Division of Respiratory Medicine, Department of Pediatrics, The Hospital for Sick Children and University of Toronto, Toronto, Canada
| | | | - Gerard H. Koppelman
- Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children’s Hospital, and
| | - Dirkje S. Postma
- Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD, Groningen, the Netherlands
| | - Benjamin A. Raby
- Channing Division of Network Medicine and
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Isaac Houston
- Channing Division of Network Medicine and
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Quan Lu
- Program in Molecular and Integrative Physiological Sciences, Departments of Environmental Health and Genetics & Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts; and
| | - Anne L. Fuhlbrigge
- Channing Division of Network Medicine and
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Kelan G. Tantisira
- Channing Division of Network Medicine and
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Edwin K. Silverman
- Channing Division of Network Medicine and
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | | | - Robert C. Strunk
- Division of Allergy, Immunology, and Pulmonary Medicine, Washington University School of Medicine, St. Louis, Missouri
| | - Scott T. Weiss
- Channing Division of Network Medicine and
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| |
Collapse
|
36
|
USP15 regulates type I interferon response and is required for pathogenesis of neuroinflammation. Nat Immunol 2016; 18:54-63. [DOI: 10.1038/ni.3581] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 08/25/2016] [Indexed: 12/21/2022]
|
37
|
Luo W, Obeidat M, Di Narzo AF, Chen R, Sin DD, Paré PD, Hao K. Airway Epithelial Expression Quantitative Trait Loci Reveal Genes Underlying Asthma and Other Airway Diseases. Am J Respir Cell Mol Biol 2016; 54:177-87. [PMID: 26102239 DOI: 10.1165/rcmb.2014-0381oc] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Genome-wide association studies (GWASs) have identified loci that are robustly associated with asthma and related phenotypes; however, the molecular mechanisms underlying these associations need to be explored. The most relevant tissues to study the functional consequences of asthma are the airways. We used publically available data to derive expression quantitative trait loci (eQTLs) for human epithelial cells from small and large airways and applied the eQTLs in the interpretation of GWAS results of asthma and related phenotypes. For the small airways (n = 105), we discovered 660 eQTLs at a 10% false discovery rate (FDR), among which 315 eQTLs were not previously reported in a large-scale eQTL study of whole lung tissue. A large fraction of the identified eQTLs is supported by data from Encyclopedia of DNA Elements (ENCODE) showing that the eQTLs reside in regulatory elements (57.5 and 67.6% of cis- and trans-eQTLs, respectively). Published pulmonary GWAS hits were enriched as airway epithelial eQTLs (9.2-fold). Further, genes regulated by asthma GWAS loci in epithelium are significantly enriched in immune response pathways, such as IL-4 signaling (FDR, 5.2 × 10(-4)). The airway epithelial eQTLs described in this study are complementary to previously reported lung eQTLs and represent a powerful resource to link GWAS-associated variants to their regulatory function and thus elucidate the molecular mechanisms underlying asthma and airway-related conditions.
Collapse
Affiliation(s)
- Wei Luo
- 1 College of Computer Science and Technology, Huaqiao University, Xiamen, China.,2 Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ma'en Obeidat
- 3 The University of British Columbia Center for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada.,4 Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Antonio Fabio Di Narzo
- 2 Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,5 Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York; and
| | - Rong Chen
- 2 Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,5 Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York; and
| | - Don D Sin
- 3 The University of British Columbia Center for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada.,4 Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Peter D Paré
- 3 The University of British Columbia Center for Heart Lung Innovation, St. Paul's Hospital, Vancouver, British Columbia, Canada.,4 Respiratory Division, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ke Hao
- 2 Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,5 Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York; and.,6 Department of Respiratory Medicine, Shanghai Tenth People's Hospital, Tongji University, Shanghai, China
| |
Collapse
|
38
|
Curjuric I, Imboden M, Bridevaux PO, Gerbase MW, Haun M, Keidel D, Kumar A, Pons M, Rochat T, Schikowski T, Schindler C, von Eckardstein A, Kronenberg F, Probst-Hensch NM. Common SIRT1 variants modify the effect of abdominal adipose tissue on aging-related lung function decline. AGE (DORDRECHT, NETHERLANDS) 2016; 38:52. [PMID: 27125385 PMCID: PMC5005914 DOI: 10.1007/s11357-016-9917-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 04/18/2016] [Indexed: 06/05/2023]
Abstract
Lung function is an independent predictor of mortality and serves as an aging marker in never smokers. The protein sirtuin-1 of gene SIRT1 has profound anti-inflammatory effects and regulates metabolic pathways. Its suggested longevity effects on lower organisms remain poorly studied in humans. In 1132 never smokers of the population-based SAPALDIA cohort, we investigated associations between single nucleotide polymorphisms (SNPs; rs730821, rs10997868, rs10823116) of SIRT1 and aging-related lung function decline over 11 years in terms of change in forced expiratory volume in the first second (FEV1), forced vital capacity (FVC), FEV1/FVC ratio, and forced expiratory flow between 25 and 75 % of FVC (FEF25-75) using multiple linear regression models. Interactions between the SIRT1 SNPs and adiposity parameters (body mass index (BMI), its change and weight gain) were tested by including multiplicative interaction terms into the models. SIRT1 polymorphisms exhibited no main effects, but modified the association between obesity measures and FEV1/FVC and FEF25-75 decline (p = 0.009-0.046). Per risk allele, FEV1/FVC decline was accelerated up to -0.5 % (95 % CI -1.0 to 0 %) and -0.7 % (-1.3 to -0.2 %) over interquartile range increases in BMI (2.4 kg/m(2)) or weight (6.5 kg), respectively. For FEF25-75 decline, corresponding estimates were -57 mL/s (-117 to 4 mL/s) and -76 mL/s (-1429 to -9 mL/s). Interactions were not present in participants with genetically lowered C-reactive protein concentrations. Genetic variation in SIRT1 might therefore affect lung function and human longevity by modifying subclinical inflammation arising from abdominal adipose tissue.
Collapse
Grants
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
- Bundesamt für Umwelt
- Bundesamt für Gesundheit
- Bundesamt für Strassen
- Canton’s government of Aargau, Basel-Stadt, Basel-Land, Geneva, Luzern, Ticino, Valais, and Zürich
- Swiss Lung League
- Canton’s Lung League of Basel Stadt/ Basel Landschaft, Geneva, Ticino, Valais, Graubünden and Zurich
- Stiftung ehemals Bündner Heilstätten
- SUVA
- Freiwillige Akademische Gesellschaft
- UBS Wealth Foundation
- Talecris Biotherapeutics GmbH
- Abbott Diagnostics
- European Commission
- Wellcome Trust
Collapse
Affiliation(s)
- Ivan Curjuric
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Socinstrasse 57, P.O. Box, 4002, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
| | - Medea Imboden
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Socinstrasse 57, P.O. Box, 4002, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | | | - Margaret W Gerbase
- Division of Pulmonary Medicine, University Hospitals, Geneva, Switzerland
| | - Margot Haun
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Dirk Keidel
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Socinstrasse 57, P.O. Box, 4002, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Ashish Kumar
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Socinstrasse 57, P.O. Box, 4002, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Marco Pons
- Division of Pulmonary Medicine, Regional Hospital of Lugano, Lugano, Switzerland
| | - Thierry Rochat
- Division of Pulmonary Medicine, University Hospitals, Geneva, Switzerland
| | - Tamara Schikowski
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Socinstrasse 57, P.O. Box, 4002, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Leibniz Research Institute for Environmental Medicine (IUF), Düsseldorf, Germany
| | - Christian Schindler
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Socinstrasse 57, P.O. Box, 4002, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | | | - Florian Kronenberg
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Nicole M Probst-Hensch
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Socinstrasse 57, P.O. Box, 4002, Basel, Switzerland
- University of Basel, Basel, Switzerland
| |
Collapse
|
39
|
Sarnowski C, Laprise C, Malerba G, Moffatt MF, Dizier MH, Morin A, Vincent QB, Rohde K, Esparza-Gordillo J, Margaritte-Jeannin P, Liang L, Lee YA, Bousquet J, Siroux V, Pignatti PF, Cookson WO, Lathrop M, Pastinen T, Demenais F, Bouzigon E. DNA methylation within melatonin receptor 1A (MTNR1A) mediates paternally transmitted genetic variant effect on asthma plus rhinitis. J Allergy Clin Immunol 2016; 138:748-753. [PMID: 27038909 DOI: 10.1016/j.jaci.2015.12.1341] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 11/10/2015] [Accepted: 12/15/2015] [Indexed: 12/23/2022]
Abstract
BACKGROUND Asthma and allergic rhinitis (AR) are common allergic comorbidities with a strong genetic component in which epigenetic mechanisms might be involved. OBJECTIVE We aimed to identify novel risk loci for asthma and AR while accounting for parent-of-origin effect. METHODS We performed a series of genetic analyses, taking into account the parent-of-origin effect in families ascertained through asthma: (1) genome-wide linkage scan of asthma and AR in 615 European families, (2) association analysis with 1233 single nucleotide polymorphisms (SNPs) covering the significant linkage region in 162 French Epidemiological Study on the Genetics and Environment of Asthma families with replication in 154 Canadian Saguenay-Lac-Saint-Jean asthma study families, and (3) association analysis of disease and significant SNPs with DNA methylation (DNAm) at CpG sites in 40 Saguenay-Lac-Saint-Jean asthma study families. RESULTS We detected a significant paternal linkage of the 4q35 region to asthma and allergic rhinitis comorbidity (AAR; P = 7.2 × 10(-5)). Association analysis in this region showed strong evidence for the effect of the paternally inherited G allele of rs10009104 on AAR (P = 1.1 × 10(-5), reaching the multiple-testing corrected threshold). This paternally inherited allele was also significantly associated with DNAm levels at the cg02303933 site (P = 1.7 × 10(-4)). Differential DNAm at this site was found to mediate the identified SNP-AAR association. CONCLUSION By integrating genetic and epigenetic data, we identified that a differentially methylated CpG site within the melatonin receptor 1A (MTNR1A) gene mediates the effect of a paternally transmitted genetic variant on the comorbidity of asthma and AR. This study provides a novel insight into the role of epigenetic mechanisms in patients with allergic respiratory diseases.
Collapse
Affiliation(s)
- Chloé Sarnowski
- INSERM, UMR946, Genetic Variation and Human Diseases Unit, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France
| | | | - Giovanni Malerba
- Section of Biology and Genetics, Department of Mother and Child, and Biology-Genetics, University of Verona, Verona, Italy
| | - Miriam F Moffatt
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Marie-Hélène Dizier
- INSERM, UMR946, Genetic Variation and Human Diseases Unit, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France
| | - Andréanne Morin
- Université du Québec, à Chicoutimi, Québec, Canada; McGill University and Génome Québec Innovation Centre, Montreal, Québec, Canada
| | - Quentin B Vincent
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, UMR1163, Paris, France; Université Paris Descartes, Imagine Institute, Paris, France
| | - Klaus Rohde
- Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany
| | - Jorge Esparza-Gordillo
- Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany; Clinic for Pediatric Allergy, Experimental and Clinical Research Centre, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Patricia Margaritte-Jeannin
- INSERM, UMR946, Genetic Variation and Human Diseases Unit, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France
| | - Liming Liang
- Department of Epidemiology, Harvard School of Public Health, Boston, Mass
| | - Young-Ae Lee
- Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany
| | - Jean Bousquet
- Hôpital Arnaud de Villeneuve, Service des Maladies Respiratoires, Montpellier, France
| | - Valérie Siroux
- Université Grenoble Alpes, IAB, Team of Environmental Epidemiology Applied to Reproduction and Respiratory Health, Grenoble, France; INSERM, IAB, Team of Environmental Epidemiology Applied to Reproduction and Respiratory Health, Grenoble, France; CHU de Grenoble, IAB, Team of Environmental Epidemiology Applied to Reproduction and Respiratory Health, Grenoble, France
| | - Pier Franco Pignatti
- Section of Biology and Genetics, Department of Mother and Child, and Biology-Genetics, University of Verona, Verona, Italy
| | - William O Cookson
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Mark Lathrop
- McGill University and Génome Québec Innovation Centre, Montreal, Québec, Canada
| | - Tomi Pastinen
- McGill University and Génome Québec Innovation Centre, Montreal, Québec, Canada
| | - Florence Demenais
- INSERM, UMR946, Genetic Variation and Human Diseases Unit, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France
| | - Emmanuelle Bouzigon
- INSERM, UMR946, Genetic Variation and Human Diseases Unit, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France.
| |
Collapse
|
40
|
Lung function decline over 25 years of follow-up among black and white adults in the ARIC study cohort. Respir Med 2016; 113:57-64. [PMID: 26905512 DOI: 10.1016/j.rmed.2016.02.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 02/01/2016] [Accepted: 02/07/2016] [Indexed: 11/22/2022]
Abstract
BACKGROUND Interpretation of longitudinal information about lung function decline from middle to older age has been limited by loss to follow-up that may be correlated with baseline lung function or the rate of decline. We conducted these analyses to estimate age-related decline in lung function across groups of race, sex, and smoking status while accounting for dropout from the Atherosclerosis Risk in Communities Study. METHODS We analyzed data from 13,896 black and white participants, aged 45-64 years at the 1987-1989 baseline clinical examination. Using spirometry data collected at baseline and two follow-up visits, we estimated annual population-averaged mean changes in forced expiratory volume in one second (FEV1) and forced vital capacity (FVC) by race, sex, and smoking status using inverse-probability-weighted independence estimating equations conditioning-on-being-alive. RESULTS Estimated rates of FEV1 decline estimated using inverse-probability-weighted independence estimating equations conditioning on being alive were higher among white than black participants at age 45 years (e.g., male never smokers: black: -29.5 ml/year; white: -51.9 ml/year), but higher among black than white participants by age 75 (black: -51.2 ml/year; white: -26). Observed differences by race were more pronounced among men than among women. By smoking status, FEV1 declines were larger among current than former or never smokers at age 45 across all categories of race and sex. By age 60, FEV1 decline was larger among former and never than current smokers. Estimated annual declines generated using unweighted generalized estimating equations were smaller for current smokers at younger ages in all four groups of race and sex compared with results from weighted analyses that accounted for attrition. CONCLUSIONS Using methods accounting for dropout from an approximately 25-year health study, estimated rates of lung function decline varied by age, race, sex, and smoking status, with largest declines observed among current smokers at younger ages.
Collapse
|
41
|
Erosion of Conserved Binding Sites in Personal Genomes Points to Medical Histories. PLoS Comput Biol 2016; 12:e1004711. [PMID: 26845687 PMCID: PMC4742230 DOI: 10.1371/journal.pcbi.1004711] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Accepted: 12/16/2015] [Indexed: 01/02/2023] Open
Abstract
Although many human diseases have a genetic component involving many loci, the majority of studies are statistically underpowered to isolate the many contributing variants, raising the question of the existence of alternate processes to identify disease mutations. To address this question, we collect ancestral transcription factor binding sites disrupted by an individual's variants and then look for their most significant congregation next to a group of functionally related genes. Strikingly, when the method is applied to five different full human genomes, the top enriched function for each is invariably reflective of their very different medical histories. For example, our method implicates "abnormal cardiac output" for a patient with a longstanding family history of heart disease, "decreased circulating sodium level" for an individual with hypertension, and other biologically appealing links for medical histories spanning narcolepsy to axonal neuropathy. Our results suggest that erosion of gene regulation by mutation load significantly contributes to observed heritable phenotypes that manifest in the medical history. The test we developed exposes a hitherto hidden layer of personal variants that promise to shed new light on human disease penetrance, expressivity and the sensitivity with which we can detect them.
Collapse
|
42
|
Pouladi N, Bime C, Garcia JGN, Lussier YA. Complex genetics of pulmonary diseases: lessons from genome-wide association studies and next-generation sequencing. Transl Res 2016; 168:22-39. [PMID: 26006746 PMCID: PMC4658294 DOI: 10.1016/j.trsl.2015.04.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 04/27/2015] [Accepted: 04/29/2015] [Indexed: 12/16/2022]
Abstract
The advent of high-throughput technologies has provided exceptional assistance for lung scientists to discover novel genetic variants underlying the development and progression of complex lung diseases. However, the discovered variants thus far do not explain much of the estimated heritability of complex lung diseases. Here, we review the literature of successfully used genome-wide association studies (GWASs) and identified the polymorphisms that reproducibly underpin the susceptibility to various noncancerous complex lung diseases or affect therapeutic responses. We also discuss the inherent limitations of GWAS approaches and how the use of next-generation sequencing technologies has furthered our understanding about the genetic determinants of these diseases. Next, we describe the contribution of the metagenomics to understand the interactions of the airways microbiome with lung diseases. We then highlight the urgent need for new integrative genomics-phenomics methods to more effectively interrogate and understand multiple downstream "omics" (eg, chromatin modification patterns). Finally, we address the scarcity of genetic studies addressing under-represented populations such as African Americans and Hispanics.
Collapse
Affiliation(s)
- Nima Pouladi
- Department of Medicine, University of Arizona, Tucson, Ariz; Center for Biomedical Informatics and Biostatistics, University of Arizona, Tucson, Ariz; BIO5 Institute, University of Arizona, Tucson, Ariz
| | - Christian Bime
- University of Arizona Health Sciences Center, University of Arizona, Tucson, Ariz; Arizona Respiratory Center, University of Arizona, Tucson, Ariz
| | - Joe G N Garcia
- University of Arizona Health Sciences Center, University of Arizona, Tucson, Ariz; Arizona Respiratory Center, University of Arizona, Tucson, Ariz
| | - Yves A Lussier
- Department of Medicine, University of Arizona, Tucson, Ariz; Center for Biomedical Informatics and Biostatistics, University of Arizona, Tucson, Ariz; BIO5 Institute, University of Arizona, Tucson, Ariz; University of Arizona Health Sciences Center, University of Arizona, Tucson, Ariz; Institute for Genomics and Systems Biology, Argonne National Laboratory and University of Chicago, Chicago, Ill.
| |
Collapse
|
43
|
Koskela J, Katajisto M, Kallio A, Kilpeläinen M, Lindqvist A, Laitinen T. Individual FEV1 Trajectories Can Be Identified from a COPD Cohort. COPD 2016; 13:425-30. [PMID: 26807738 DOI: 10.3109/15412555.2015.1043423] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVE We aim to make use of clinical spirometry data in order to identify individual COPD-patients with divergent trajectories of lung function over time. STUDY DESIGN AND SETTING Hospital-based COPD cohort (N = 607) was followed on average 4.6 years. Each patient had a mean of 8.4 spirometries available. We used a Hierarchical Bayesian Model (HBM) to identify the individuals presenting constant trends in lung function. RESULTS At a probability level of 95%, one third of the patients (180/607) presented rapidly declining FEV1 (mean -78 ml/year, 95% CI -73 to -83 ml) compared to that in the rest of the patients (mean -26 ml/year, 95% CI -23 to -29 ml, p ≤ 2.2 × 10(-16)). Constant improvement of FEV1 was very rare. The rapid decliners more frequently suffered from exacerbations measured by various outcome markers. CONCLUSION Clinical data of unique patients can be utilized to identify diverging trajectories of FEV1 with a high probability. Frequent exacerbations were more prevalent in FEV1-decliners than in the rest of the patients. The result confirmed previously reported association between FEV1 decline and exacerbation rate and further suggested that in clinical practice HBM could improve the identification of high-risk individuals at early stages of the disease.
Collapse
Affiliation(s)
- Jukka Koskela
- a Clinical Research Unit for Pulmonary Diseases and Division of Pulmonology , Helsinki University Central Hospital , Helsinki , Finland
| | - Milla Katajisto
- a Clinical Research Unit for Pulmonary Diseases and Division of Pulmonology , Helsinki University Central Hospital , Helsinki , Finland
| | - Aleksi Kallio
- b CSC- IT Center for Science Ltd., Department of Information and Computer Science, Aalto University , Helsinki Institute for Information Technology (HIIT) , Helsinki , Finland
| | - Maritta Kilpeläinen
- c Division of Medicine, Dept. of Pulmonary Diseases and Clinical Allergology , Turku University Hospital and University of Turku , Turku , Finland
| | - Ari Lindqvist
- a Clinical Research Unit for Pulmonary Diseases and Division of Pulmonology , Helsinki University Central Hospital , Helsinki , Finland
| | - Tarja Laitinen
- a Clinical Research Unit for Pulmonary Diseases and Division of Pulmonology , Helsinki University Central Hospital , Helsinki , Finland.,c Division of Medicine, Dept. of Pulmonary Diseases and Clinical Allergology , Turku University Hospital and University of Turku , Turku , Finland
| |
Collapse
|
44
|
Brehm JM, Man Tse S, Croteau-Chonka DC, Forno E, Litonjua AA, Raby BA, Chen W, Yan Q, Boutaoui N, Acosta-Pérez E, Avila L, Weiss ST, Soto-Quiros M, Cloutier MM, Hu D, Pino-Yanes M, Wenzel SE, Spear ML, Kolls JK, Burchard EG, Canino G, Celedón JC. A Genome-Wide Association Study of Post-bronchodilator Lung Function in Children with Asthma. Am J Respir Crit Care Med 2015; 192:634-7. [PMID: 26325155 DOI: 10.1164/rccm.201501-0047le] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- John M Brehm
- 1 University of Pittsburgh School of Medicine Pittsburgh, Pennsylvania
| | - Sze Man Tse
- 2 Harvard Medical School Boston, Massachusetts
| | | | - Erick Forno
- 1 University of Pittsburgh School of Medicine Pittsburgh, Pennsylvania
| | | | | | - Wei Chen
- 1 University of Pittsburgh School of Medicine Pittsburgh, Pennsylvania
| | - Qi Yan
- 1 University of Pittsburgh School of Medicine Pittsburgh, Pennsylvania
| | - Nadia Boutaoui
- 1 University of Pittsburgh School of Medicine Pittsburgh, Pennsylvania
| | | | | | | | | | | | - Donglei Hu
- 6 University of California at San Francisco San Francisco, California
| | - Maria Pino-Yanes
- 6 University of California at San Francisco San Francisco, California
| | - Sally E Wenzel
- 1 University of Pittsburgh School of Medicine Pittsburgh, Pennsylvania
| | - Melissa L Spear
- 6 University of California at San Francisco San Francisco, California
| | - Jay K Kolls
- 1 University of Pittsburgh School of Medicine Pittsburgh, Pennsylvania
| | | | | | - Juan C Celedón
- 1 University of Pittsburgh School of Medicine Pittsburgh, Pennsylvania
| |
Collapse
|
45
|
de Jong K, Vonk JM, Timens W, Bossé Y, Sin DD, Hao K, Kromhout H, Vermeulen R, Postma DS, Boezen HM. Genome-wide interaction study of gene-by-occupational exposure and effects on FEV1 levels. J Allergy Clin Immunol 2015; 136:1664-1672.e14. [PMID: 25979521 DOI: 10.1016/j.jaci.2015.03.042] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 03/16/2015] [Accepted: 03/31/2015] [Indexed: 11/18/2022]
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) is a complex disease characterized by impaired lung function and airway obstruction resulting from interactions between multiple genes and multiple environmental exposures. Thus far, genome-wide association studies have largely disregarded environmental factors that might trigger the development of lung function impairment and COPD, such as occupational exposures, which are thought to contribute to 15% to 20% of the COPD prevalence. OBJECTIVES We performed a genome-wide interaction study to identify novel susceptibility loci for occupational exposure to biological dust, mineral dust, and gases and fumes in relation to FEV1 levels. METHODS We performed an identification analysis in 12,400 subjects from the LifeLines cohort study and verified our findings in 1436 subjects from a second independent cohort, the Vlagtwedde-Vlaardingen cohort. Additionally, we assessed whether replicated single nucleotide polymorphisms (SNPs) were cis-acting expression (mRNA) quantitative trait loci in lung tissue. RESULTS Of the 7 replicated SNPs that interacted with one of the occupational exposures, several identified loci were plausible candidates that might be involved in biological pathways leading to lung function impairment, such as PCDH9 and GALNT13. Two of the 7 replicated SNPs were cis-acting expression quantitative trait loci associated with gene expression of PDE4D and TMEM176A in lung tissue. CONCLUSION This genome-wide interaction study on occupational exposures in relation to the level of lung function identified several novel genes. Further research should determine whether the identified genes are true susceptibility loci for occupational exposures and whether these SNP-by-exposure interactions consequently contribute to the development of COPD.
Collapse
Affiliation(s)
- Kim de Jong
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Judith M Vonk
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Wim Timens
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec, Department of Molecular Medicine, Laval University, Quebec City, Quebec, Canada
| | - Don D Sin
- Department of Medicine and Center for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Hans Kromhout
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences (IRAS), University of Utrecht, Utrecht, The Netherlands
| | - Roel Vermeulen
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences (IRAS), University of Utrecht, Utrecht, The Netherlands
| | - Dirkje S Postma
- Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Department of Pulmonary Diseases, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - H Marike Boezen
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands; Groningen Research Institute for Asthma and COPD (GRIAC), University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.
| |
Collapse
|
46
|
Genetic variation in uncontrolled childhood asthma despite ICS treatment. THE PHARMACOGENOMICS JOURNAL 2015; 16:158-63. [PMID: 25963336 DOI: 10.1038/tpj.2015.36] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 03/02/2015] [Accepted: 03/26/2015] [Indexed: 11/08/2022]
Abstract
Genetic variation may partly explain asthma treatment response heterogeneity. We aimed to identify common and rare genetic variants associated with asthma that was not well controlled despite inhaled corticosteroid (ICS) treatment. Data of 110 children was collected in the Children Asthma Therapy Optimal trial. Associations of genetic variation with measures of lung function (FEV1%pred), airway hyperresponsiveness (AHR) to methacholine (Mch PD20) and treatment response outcomes were analyzed using the exome chip. The 17q12-21 locus (containing ORMDL3 and GSMDB) previously associated with childhood asthma was investigated separately. Single-nucleotide polymorphisms (SNPs) in the 17q12-21 locus were found nominally associated with the outcomes. The strongest association in this region was found for rs72821893 in KRT25 with FEV1%pred (P=3.75*10(-5)), Mch PD20 (P=0.00095) and Mch PD20-based treatment outcome (P=0.006). No novel single SNPs or burden tests were significantly associated with the outcomes. The 17q12-21 region was associated with FEV1%pred and AHR, and additionally with ICS treatment response.
Collapse
|
47
|
Identification of a nonsynonymous polymorphism in the SVEP1 gene associated with altered clinical outcomes in septic shock. Crit Care Med 2015; 43:101-8. [PMID: 25188548 DOI: 10.1097/ccm.0000000000000604] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVES Mortality from septic shock is highly heritable. The identification of causal genetic factors is insufficient. To discover key contributors, we first identified nonsynonymous single-nucleotide polymorphisms in conserved genomic regions that are predicted to have significant effects on protein function. We then test the hypothesis that these nonsynonymous single-nucleotide polymorphisms across the genome alter clinical outcome of septic shock. DESIGN Genetic-association study plus in vitro experiment using primary cells plus in silico analysis using genomic DNA and protein database. SETTING Twenty-seven ICUs at academic teaching centers in Canada, Australia, and the United States. PATIENTS Patients with septic shock of European ancestry (n = 520). INTERVENTIONS Patients with septic shock were genotyped for 843 nonsynonymous single-nucleotide polymorphisms in conserved regions of the genome and are predicted to have damaging effects from the protein sequence. MEASUREMENTS AND MAIN RESULTS The primary outcome variable was 28-day mortality. Secondary outcome variables were organ dysfunction. Productions of adhesion molecules including interleukin-8, growth-regulated oncogene-α, monocyte chemoattractant protein-1, and monocyte chemoattractant protein-3 were measured in human umbilical vein endothelial cells after SVEP1 gene silencing by RNA interference. Patients with septic shock having the SVEP1 C allele of nonsynonymous single-nucleotide polymorphism, SVEP1 c.2080A>C (p. Gln581His, rs10817033), had a significant increase in the hazard of death over the 28 days (hazard ratio, 1.72; 95% CI, 1.31-2.26; p = 9.7 × 10-5) and increased organ dysfunction and needed more organ support (p < 0.05). Silencing SVEP1 significantly increased interleukin-8, growth-regulated oncogene-α, monocyte chemoattractant protein-1, monocyte chemoattractant protein-3 production in human umbilical vein endothelial cells under lipopolysaccharide stimulation (p < 0.01). CONCLUSIONS C allele of SVEP1 c.2080A>C (p. Gln581His) single-nucleotide polymorphism, a non-synonymous single-nucleotide polymorphism in conserved regions and predicted to have damaging effects on protein structure, was associated with increased 28-day mortality and organ dysfunction of septic shock. SVEP1 appears to regulate molecules of the leukocyte adhesion pathway.
Collapse
|
48
|
Xie J, Wu H, Xu Y, Wu X, Liu X, Shang J, Zhao J, Zhao J, Wang J, Dela Cruz CS, Xiong W, Xu Y. Gene susceptibility identification in a longitudinal study confirms new loci in the development of chronic obstructive pulmonary disease and influences lung function decline. Respir Res 2015; 16:49. [PMID: 25928290 PMCID: PMC4427922 DOI: 10.1186/s12931-015-0209-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 03/27/2015] [Indexed: 12/22/2022] Open
Abstract
Background To identify COPD associated gene susceptibility and lung function in a longitudinal cohort including COPD and subjects who were at risk for developing COPD, and to replicate this in two cross-sectional and longitudinal populations in Chinese Han population. Methods Three cohorts were recruited in this study, including an 18-year follow-up population (306 COPD and 743 control subjects) in one village in 1992 and it changed to 409 COPD and 611 controls in 2010, a 2 year follow-up study in another village (374 COPD and 377 controls) and another 2 year follow-up one in a city (541 COPD and 560 controls) in 2010. Sixteen candidate single nucleotide polymorphisms (SNPs) were selected for genotyping. Among them, 5SNPs in or near HHIP, 1SNP in IREB2 and 1SNP in FAM13A were previously reported to be associated with COPD susceptibility or lung function decline. And another 9SNPs were selected from HapMap website as HHIP tags. In 2010, totaling 1,324 COPD patients and 1,548 healthy controls were finally included in our genetic susceptibility analyses. Results We identified two new regions showing an association with COPD susceptibility in the Human Hedgehog interacting protein (HHIP) rs11100865 and rs7654947, and we confirmed that the family with sequence similarity 13 member A gene (FAM13A) rs7671167 was associated with the development of COPD in Chinese Han population. And the HHIP rs7654947 and FAM13A rs7671167 were associated with lung function decline, and this result was replicated in other two populations. Conclusions These results suggest an important role of the HHIP and FAM13A regions as genetic risk factors for COPD development and lung function decline in Chinese Han population. Future research on these genes should focus on the molecular mechanisms of these genes on developing COPD and creating therapies to alleviate reduced lung function. Electronic supplementary material The online version of this article (doi:10.1186/s12931-015-0209-3) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jungang Xie
- Department of Respiratory and Critical Care Medicine, Tongji hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Hongxu Wu
- Department of Respiratory and Critical Care Medicine, Tongji hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Yuzhu Xu
- Department of Respiratory and Critical Care Medicine, Tongji hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Xiaojie Wu
- Department of Respiratory and Critical Care Medicine, Tongji hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Xue Liu
- Department of Respiratory and Critical Care Medicine, Tongji hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Jin Shang
- Department of Respiratory and Critical Care Medicine, Tongji hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Jianping Zhao
- Department of Respiratory and Critical Care Medicine, Tongji hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Junling Zhao
- Department of Respiratory and Critical Care Medicine, Tongji hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Jianmiao Wang
- Department of Respiratory and Critical Care Medicine, Tongji hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China. .,Section of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, USA.
| | - Charles S Dela Cruz
- Section of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Yale University School of Medicine, New Haven, USA.
| | - Weining Xiong
- Department of Respiratory and Critical Care Medicine, Tongji hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Yongjian Xu
- Department of Respiratory and Critical Care Medicine, Tongji hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| |
Collapse
|
49
|
Bouzigon E, Nadif R, Thompson EE, Concas MP, Kuldanek S, Du G, Brossard M, Lavielle N, Sarnowski C, Vaysse A, Dessen P, van der Valk RJP, Duijts L, Henderson AJ, Jaddoe VWV, de Jongste JC, Dizier MH, Pin I, Matran R, Lathrop M, Pirastu M, Demenais F, Ober C. A common variant in RAB27A gene is associated with fractional exhaled nitric oxide levels in adults. Clin Exp Allergy 2015; 45:797-806. [PMID: 25431337 PMCID: PMC4405185 DOI: 10.1111/cea.12461] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 10/06/2014] [Accepted: 11/19/2014] [Indexed: 12/28/2022]
Abstract
BACKGROUND Exhaled nitric oxide (FeNO) is a biomarker for eosinophilic inflammation in the airways and for responsiveness to corticosteroids in asthmatics. OBJECTIVE We sought to identify in adults the genetic determinants of fractional exhaled nitric oxide (FeNO) levels and to assess whether environmental and disease-related factors influence these associations. METHODS We performed a genome-wide association study of FeNO through meta-analysis of two independent discovery samples of European ancestry: the outbred EGEA study (French Epidemiological study on the Genetics and Environment of Asthma, N = 610 adults) and the Hutterites (N = 601 adults), a founder population living on communal farms. Replication of main findings was assessed in adults from an isolated village in Sardinia (Talana study, N = 450). We then investigated the influence of asthma, atopy and tobacco smoke exposure on these genetic associations, and whether they were also associated with FeNO values in children of the EAGLE (EArly Genetics & Lifecourse Epidemiology, N = 8858) consortium. RESULTS We detected a common variant in RAB27A (rs2444043) associated with FeNO that reached the genome-wide significant level (P = 1.6 × 10(-7) ) in the combined discovery and replication adult data sets. This SNP belongs to member of RAS oncogene family (RAB27A) and was associated with an expression quantitative trait locus for RAB27A in lymphoblastoid cell lines from asthmatics. A second suggestive locus (rs2194437, P = 8.9 × 10(-7) ) located nearby the sodium/calcium exchanger 1 (SLC8A1) was mainly detected in atopic subjects and influenced by inhaled corticosteroid use. These two loci were not associated with childhood FeNO values. CONCLUSIONS AND CLINICAL RELEVANCE This study identified a common variant located in RAB27A gene influencing FeNO levels specifically in adults and with a biological relevance to the regulation of FeNO levels. This study provides new insight into the biological mechanisms underlying FeNO levels in adults.
Collapse
Affiliation(s)
- Emmanuelle Bouzigon
- Inserm, UMR-946, F-75010, Paris, France
- Univ Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d’Hématologie, F-75007, Paris, France
| | - Rachel Nadif
- Inserm, U1018, Centre for research in Epidemiology and Population Health (CESP), Respiratory and Environmental Epidemiology Team, F-94807, Villejuif, France
- Univ Paris-Sud, UMRS 1018, F-94807, Villejuif, France
| | - Emma E. Thompson
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Maria Pina Concas
- Institute of Population Genetics, National Council of Research, Sassari, Italy
| | - Susan Kuldanek
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Gaixin Du
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Myriam Brossard
- Inserm, UMR-946, F-75010, Paris, France
- Univ Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d’Hématologie, F-75007, Paris, France
| | - Nolwenn Lavielle
- Inserm, UMR-946, F-75010, Paris, France
- Univ Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d’Hématologie, F-75007, Paris, France
| | - Chloé Sarnowski
- Inserm, UMR-946, F-75010, Paris, France
- Univ Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d’Hématologie, F-75007, Paris, France
| | - Amaury Vaysse
- Inserm, UMR-946, F-75010, Paris, France
- Univ Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d’Hématologie, F-75007, Paris, France
| | - Philippe Dessen
- Inserm, UMRS 985, Institut Gustave Roussy, F-94805, Villejuif, France
| | - Ralf JP van der Valk
- The Generation R Study Group, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Liesbeth Duijts
- Department of Pediatrics, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- School of Social and Community Medicine, University of Bristol, UK
| | - A John Henderson
- School of Social and Community Medicine, University of Bristol, UK
| | - Vincent WV Jaddoe
- The Generation R Study Group, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Johan C de Jongste
- Department of Pediatrics, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Marie-Hélène Dizier
- Inserm, UMR-946, F-75010, Paris, France
- Univ Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d’Hématologie, F-75007, Paris, France
| | - Isabelle Pin
- INSERM, IAB, Team of Environmental Epidemiology applied to Reproduction and Respiratory Health, F-38000 Grenoble, France
- Univ. Grenoble Alpes, IAB, Team of Environmental Epidemiology applied to Reproduction and Respiratory Health, F-38000 Grenoble, France
- Pédiatrie, CHU de Grenoble, F-38043, Grenoble, France
| | - Régis Matran
- Univ Lille Nord de France, F-59000, Lille, France
- CHU, F-59000, Lille, France
| | - Mark Lathrop
- McGill University and Génome Québec Innovation Centre, Montréal, Canada
| | - Mario Pirastu
- Institute of Population Genetics, National Council of Research, Sassari, Italy
- Ogliastra Genetic Park, Perdasdefogu, Sardinia, Italy
| | - Florence Demenais
- Inserm, UMR-946, F-75010, Paris, France
- Univ Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d’Hématologie, F-75007, Paris, France
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| |
Collapse
|
50
|
[Genetic and environmental factors of asthma and allergy: Results of the EGEA study]. Rev Mal Respir 2015; 32:822-40. [PMID: 25794998 DOI: 10.1016/j.rmr.2014.12.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 12/12/2014] [Indexed: 12/26/2022]
Abstract
INTRODUCTION AND METHODS The EGEA study (epidemiological study on the genetics and environment of asthma, bronchial hyperresponsiveness and atopy), which combines a case-control and a family-based study of asthma case (n=2120 subjects) with three surveys over 20 years, aims to identify environmental and genetic factors associated with asthma and asthma-related phenotypes. We summarize the results of the phenotypic characterization and the investigation of environmental and genetic factors of asthma and asthma-related phenotypes obtained since 2007 in the EGEA study (42 articles). RESULTS Both epidemiological and genetic results confirm the heterogeneity of asthma. These results strengthen the role of the age of disease onset, the allergic status and the level of disease activity in the identification of the different phenotypes of asthma. The deleterious role of active smoking, exposure to air pollution, occupational asthmogenic agents and cleaning products on the prevalence and/or activity of asthma has been confirmed. Accounting for gene-environment interactions allowed the identification of new genetic factors underlying asthma and asthma-related traits and better understanding of their mode of action. CONCLUSION The EGEA study is contributing to the advances in respiratory research at the international level. The new phenotypic, environmental and biological data available in EGEA study will help characterizing the long-term evolution of asthma and the factors associated to this evolution.
Collapse
|