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Thompson MD, Reiner-Link D, Berghella A, Rana BK, Rovati GE, Capra V, Gorvin CM, Hauser AS. G protein-coupled receptor (GPCR) pharmacogenomics. Crit Rev Clin Lab Sci 2024:1-44. [PMID: 39119983 DOI: 10.1080/10408363.2024.2358304] [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: 06/15/2023] [Revised: 09/03/2023] [Accepted: 05/18/2024] [Indexed: 08/10/2024]
Abstract
The field of pharmacogenetics, the investigation of the influence of one or more sequence variants on drug response phenotypes, is a special case of pharmacogenomics, a discipline that takes a genome-wide approach. Massively parallel, next generation sequencing (NGS), has allowed pharmacogenetics to be subsumed by pharmacogenomics with respect to the identification of variants associated with responders and non-responders, optimal drug response, and adverse drug reactions. A plethora of rare and common naturally-occurring GPCR variants must be considered in the context of signals from across the genome. Many fundamentals of pharmacogenetics were established for G protein-coupled receptor (GPCR) genes because they are primary targets for a large number of therapeutic drugs. Functional studies, demonstrating likely-pathogenic and pathogenic GPCR variants, have been integral to establishing models used for in silico analysis. Variants in GPCR genes include both coding and non-coding single nucleotide variants and insertion or deletions (indels) that affect cell surface expression (trafficking, dimerization, and desensitization/downregulation), ligand binding and G protein coupling, and variants that result in alternate splicing encoding isoforms/variable expression. As the breadth of data on the GPCR genome increases, we may expect an increase in the use of drug labels that note variants that significantly impact the clinical use of GPCR-targeting agents. We discuss the implications of GPCR pharmacogenomic data derived from the genomes available from individuals who have been well-phenotyped for receptor structure and function and receptor-ligand interactions, and the potential benefits to patients of optimized drug selection. Examples discussed include the renin-angiotensin system in SARS-CoV-2 (COVID-19) infection, the probable role of chemokine receptors in the cytokine storm, and potential protease activating receptor (PAR) interventions. Resources dedicated to GPCRs, including publicly available computational tools, are also discussed.
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Affiliation(s)
- Miles D Thompson
- Krembil Brain Institute, Toronto Western Hospital, Toronto, Ontario, Canada
| | - David Reiner-Link
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Alessandro Berghella
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Brinda K Rana
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - G Enrico Rovati
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
| | - Valerie Capra
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
| | - Caroline M Gorvin
- Institute of Metabolism and Systems Research (IMSR), University of Birmingham, Birmingham, United Kingdom
| | - Alexander S Hauser
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Li D, Farrell JJ, Mez J, Martin ER, Bush WS, Ruiz A, Boada M, de Rojas I, Mayeux R, Haines JL, Vance MAP, Wang LS, Schellenberg GD, Lunetta KL, Farrer LA. Novel loci for Alzheimer's disease identified by a genome-wide association study in Ashkenazi Jews. Alzheimers Dement 2023; 19:5550-5562. [PMID: 37260021 PMCID: PMC10689571 DOI: 10.1002/alz.13117] [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: 12/28/2022] [Revised: 03/29/2023] [Accepted: 04/11/2023] [Indexed: 06/02/2023]
Abstract
INTRODUCTION Most Alzheimer's disease (AD) loci have been discovered in individuals with European ancestry (EA). METHODS We applied principal component analysis using Gaussian mixture models and an Ashkenazi Jewish (AJ) reference genome-wide association study (GWAS) data set to identify Ashkenazi Jews ascertained in GWAS (n = 42,682), whole genome sequencing (WGS, n = 16,815), and whole exome sequencing (WES, n = 20,504) data sets. The association of AD was tested genome wide (GW) in the GWAS and WGS data sets and exome wide (EW) in all three data sets (EW). Gene-based analyses were performed using aggregated rare variants. RESULTS In addition to apolipoprotein E (APOE), GW analyses (1355 cases and 1661 controls) revealed associations with TREM2 R47H (p = 9.66 × 10-9 ), rs541586606 near RAB3B (p = 5.01 × 10-8 ), and rs760573036 between SPOCK3 and ANXA10 (p = 6.32 × 10-8 ). In EW analyses (1504 cases and 2047 controls), study-wide significant association was observed with rs1003710 near SMAP2 (p = 1.91 × 10-7 ). A significant gene-based association was identified with GIPR (p = 7.34 × 10-7 ). DISCUSSION Our results highlight the efficacy of founder populations for AD genetic studies.
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Affiliation(s)
- Donghe Li
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
| | - John J Farrell
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
| | - Jesse Mez
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
| | - Eden R. Martin
- Dr. John T. Macdonald Foundation, University of Miami, Miami, FL 33136, USA
- Department of Human Genetics, University of Miami, Miami, FL 33136, USA
| | - William S. Bush
- Department of Population & Quantitative Health Science and Cleveland Institute for Computational Biology, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, USA
| | - Agustin Ruiz
- Research Center and Memory Clinic, ACE Alzheimer Center Barcelona, Universitat Internacional de Catalunya, Barcelona, Spain
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Mercè Boada
- Research Center and Memory Clinic, ACE Alzheimer Center Barcelona, Universitat Internacional de Catalunya, Barcelona, Spain
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Itziar de Rojas
- Research Center and Memory Clinic, ACE Alzheimer Center Barcelona, Universitat Internacional de Catalunya, Barcelona, Spain
- CIBERNED, Network Center for Biomedical Research in Neurodegenerative Diseases, National Institute of Health Carlos III, Madrid, Spain
| | - Richard Mayeux
- Taub Institute on Alzheimer's Disease and the Aging Brain, Gertrude H. Sergievsky Center Department of Neurology, Columbia University, 710 West 168th Street, New York, NY 10032, USA
| | - Jonathan L. Haines
- Department of Population & Quantitative Health Science and Cleveland Institute for Computational Biology, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106, USA
| | - Margaret A. Pericak Vance
- Dr. John T. Macdonald Foundation, University of Miami, Miami, FL 33136, USA
- Department of Human Genetics, University of Miami, Miami, FL 33136, USA
- Department of Neurology, University of Miami, Miami, FL 33136, USA
| | - Li-San Wang
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania, 3400 Spruce Street, Philadelphia, PA 19104, USA
| | - Gerard D. Schellenberg
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania, 3400 Spruce Street, Philadelphia, PA 19104, USA
| | - Kathryn L. Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Lindsay A. Farrer
- Department of Medicine (Biomedical Genetics), Boston University Chobanian & Avedisian School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
- Department of Ophthalmology, Boston University Chobanian & Avedisian School of Medicine, 72 East Concord Street, Boston, MA 02118, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
- Department of Epidemiology, Boston University School of Public Health, Boston, MA 02118, USA
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3
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Fan NC, Huang HY, Wang SL, Tseng YL, Chang-Chien J, Tsai HJ, Yao TC. Association of exposure to environmental vanadium and manganese with lung function among young children: A population-based study. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 264:115430. [PMID: 37672937 DOI: 10.1016/j.ecoenv.2023.115430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 07/19/2023] [Accepted: 08/30/2023] [Indexed: 09/08/2023]
Abstract
Exposure to environmental metals has been associated with health outcomes including respiratory health. Little is known about the impact of exposure to environmental metals on lung function among young children in general population. This study aimed to investigate the associations of exposure to metals with lung function among young children in a population-based cohort. A total of 1488 children aged 5-8 years attended a follow-up visit as part of the Longitudinal Investigation of Global Health in Taiwanese Schoolchildren (LIGHTS) cohort. We measured urinary samples of vanadium (median: 1.21 ng/mL; interquartile range (IQR): 0.73-1.98), manganese (median: 0.23 ng/mL; IQR: 0.13-0.47), arsenic (median: 40.51 ng/mL; IQR: 21.66-70.49), nickel (median: 1.09 ng/mL; IQR: 0.31-3.60), and cadmium (median: 0.26 ng/mL; IQR: 0.11-0.43) and performed lung function tests. Urinary vanadium concentrations were inversely associated with FVC (β coefficient for the highest quartile versus the other quartiles: -33.40, p = 0.001), FEV1 (β: -41.31, p < 0.001), FEV1/FVC ratio (β: -1.00, p = 0.009), PEF (β: -92.12, p = 0.004), and FEF25-75 (β: -82.85, p < 0.001), after adjusting for relevant confounders. Urinary manganese concentrations were inversely associated with FVC (β: -26.60, p = 0.007), FEV1 (β: -31.62, p = 0.001), PEF (β: -84.86, p = 0.009), and FEF25-75 (β: -69.21, p = 0.002). Stratification analyses found inverse associations of urinary vanadium and manganese concentrations with lung function parameters predominantly among children exposed to environmental tobacco smoke. We did not find significant associations of urinary arsenic, nickel, and cadmium concentrations with lung function parameters. In conclusion, this study adds new evidence showing inverse associations of vanadium and manganese exposure with lung function among young children in the general population. Children with environmental tobacco smoke exposure are particularly vulnerable to adverse impact of vanadium and manganese exposure on lung function.
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Affiliation(s)
- Nai-Chia Fan
- Division of Nephrology, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan; Graduate Institute of Clinical Medical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - Hsin-Yi Huang
- Division of Allergy, Asthma, and Rheumatology, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Shih-Ling Wang
- Division of Allergy, Asthma, and Rheumatology, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Yu-Lun Tseng
- Division of Allergy, Asthma, and Rheumatology, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Ju Chang-Chien
- Division of Allergy, Asthma, and Rheumatology, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Hui-Ju Tsai
- Institute of Population Health Sciences, National Health Research Institutes, Miaoli, Taiwan.
| | - Tsung-Chieh Yao
- Division of Allergy, Asthma, and Rheumatology, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan; School of Medicine, Chang Gung University College of Medicine, Taoyuan, Taiwan.
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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.
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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
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Gau CC, Lee HJ, Lu HY, Wu CY, Huang HY, Tsai HJ, Yao TC. Association of advanced paternal age with lung function at school age. Respir Res 2022; 23:259. [PMID: 36127724 PMCID: PMC9487029 DOI: 10.1186/s12931-022-02178-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/12/2022] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Epidemiological studies suggest that advanced paternal age impact offspring health, but its impact on respiratory health is unclear. This study aimed to investigate the association of paternal age with lung function and fraction of exhaled nitric oxide (FeNO) in children. METHODS We analyzed data from 1330 single-born children (576 girls, 43.3%; mean age, 6.4 years), who participated in the Longitudinal Investigation of Global Health in Taiwanese Schoolchildren (LIGHTS) cohort and received measurements of lung function and FeNO at 6-year follow-up visits. Covariate-adjusted regression analyses were applied. RESULTS Every 5-year increase in paternal age at birth was associated with 0.51% decrease in FEV1/FVC ratio (95% CI - 0.86 to - 0.15; p = 0.005) and 19.86 mL/s decrease in FEF75 (95% CI: - 34.07 to - 5.65; p = 0.006). Stratified analyses revealed that increasing paternal age at birth was associated with decreasing FEV1/FVC ratio and FEF75 only among children with prenatal exposure to environmental tobacco smoke (ETS) or not being breastfed. Sensitivity analyses using paternal age as a categorical variable found decreasing FEV1/FVC ratio and FEF75 in the groups of paternal age 35-39 and ≥ 40 years. There was no association of paternal age at birth with FeNO. CONCLUSION Our findings provide novel evidence linking advanced paternal age at birth with decreasing lung function in children at school age. Children with prenatal exposure to ETS or not being breastfed are more vulnerable to the adverse effect of advanced paternal age on childhood lung function. Further studies are warranted to confirm this novel adverse effect of advanced paternal age.
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Affiliation(s)
- Chun-Chun Gau
- Division of Allergy, Asthma, and Rheumatology, Department of Pediatrics, Chang Gung Memorial Hospital, 5 Fu-Hsin Street, Kweishan, Taoyuan, Taiwan
- School of Medicine, Chang Gung University College of Medicine, Taoyuan, Taiwan
- Division of Pediatric General Medicine, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Department of Pediatrics, New Taipei Municipal TuCheng Hospital, New Taipei, Taiwan
| | - Hsin-Ju Lee
- Division of Allergy, Asthma, and Rheumatology, Department of Pediatrics, Chang Gung Memorial Hospital, 5 Fu-Hsin Street, Kweishan, Taoyuan, Taiwan
| | - Hung-Yi Lu
- Division of Allergy, Asthma, and Rheumatology, Department of Pediatrics, Chang Gung Memorial Hospital, 5 Fu-Hsin Street, Kweishan, Taoyuan, Taiwan
| | - Chao-Yi Wu
- Division of Allergy, Asthma, and Rheumatology, Department of Pediatrics, Chang Gung Memorial Hospital, 5 Fu-Hsin Street, Kweishan, Taoyuan, Taiwan
- School of Medicine, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Hsin-Yi Huang
- Division of Allergy, Asthma, and Rheumatology, Department of Pediatrics, Chang Gung Memorial Hospital, 5 Fu-Hsin Street, Kweishan, Taoyuan, Taiwan
| | - Hui-Ju Tsai
- Institute of Population Health Sciences, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli County, 35053, Taiwan.
| | - Tsung-Chieh Yao
- Division of Allergy, Asthma, and Rheumatology, Department of Pediatrics, Chang Gung Memorial Hospital, 5 Fu-Hsin Street, Kweishan, Taoyuan, Taiwan.
- School of Medicine, Chang Gung University College of Medicine, Taoyuan, Taiwan.
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Wang T, Wang W, Li W, Duan H, Xu C, Tian X, Zhang D. Genome-wide DNA methylation analysis of pulmonary function in middle and old-aged Chinese monozygotic twins. Respir Res 2021; 22:300. [PMID: 34809630 PMCID: PMC8609861 DOI: 10.1186/s12931-021-01896-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 11/12/2021] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Previous studies have determined the epigenetic association between DNA methylation and pulmonary function among various ethnics, whereas this association is largely unknown in Chinese adults. Thus, we aimed to explore epigenetic relationships between genome-wide DNA methylation levels and pulmonary function among middle-aged Chinese monozygotic twins. METHODS The monozygotic twin sample was drawn from the Qingdao Twin Registry. Pulmonary function was measured by three parameters including forced expiratory volume the first second (FEV1), forced vital capacity (FVC), and FEV1/FVC ratio. Linear mixed effect model was used to regress the methylation level of CpG sites on pulmonary function. After that, we applied Genomic Regions Enrichment of Annotations Tool (GREAT) to predict the genomic regions enrichment, and used comb-p python library to detect differentially methylated regions (DMRs). Gene expression analysis was conducted to validate the results of differentially methylated analyses. RESULTS We identified 112 CpG sites with the level of P < 1 × 10-4 which were annotated to 40 genes. We identified 12 common enriched pathways of three pulmonary function parameters. We detected 39 DMRs located at 23 genes, of which PRDM1 was related to decreased pulmonary function, and MPL, LTB4R2, and EPHB3 were related to increased pulmonary function. The gene expression analyses validated DIP2C, ASB2, SLC6A5, and GAS6 related to decreased pulmonary function. CONCLUSION Our DNA methylation sequencing analysis on identical twins provides new references for the epigenetic regulation on pulmonary function. Several CpG sites, genes, biological pathways and DMRs are considered as possible crucial to pulmonary function.
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Affiliation(s)
- Tong Wang
- Department of Epidemiology and Health Statistics, the College of Public Health of Qingdao University, NO. 308 Ning Xia Street, Qingdao, 266071, Shandong Province, People's Republic of China
| | - Weijing Wang
- Department of Epidemiology and Health Statistics, the College of Public Health of Qingdao University, NO. 308 Ning Xia Street, Qingdao, 266071, Shandong Province, People's Republic of China
| | - Weilong Li
- Population Research Unit, Faculty of Social Sciences, University of Helsinki, Helsinki, Finland
| | - Haiping Duan
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao, Shandong Province, People's Republic of China.,Qingdao Institute of Preventive Medicine, Qingdao, Shandong Province, People's Republic of China
| | - Chunsheng Xu
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao, Shandong Province, People's Republic of China.,Qingdao Institute of Preventive Medicine, Qingdao, Shandong Province, People's Republic of China
| | - Xiaocao Tian
- Qingdao Municipal Center for Disease Control and Prevention, Qingdao, Shandong Province, People's Republic of China.,Qingdao Institute of Preventive Medicine, Qingdao, Shandong Province, People's Republic of China
| | - Dongfeng Zhang
- Department of Epidemiology and Health Statistics, the College of Public Health of Qingdao University, NO. 308 Ning Xia Street, Qingdao, 266071, Shandong Province, People's Republic of China.
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Duan H, Liang L, Liu X, Xie S, Wang C. PARC/CCL18 is Associated with Inflammation, Emphysema Severity and Application of Inhaled Corticosteroids in Hospitalized COPD Patients. Int J Chron Obstruct Pulmon Dis 2021; 16:1287-1297. [PMID: 34007168 PMCID: PMC8121623 DOI: 10.2147/copd.s304488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/19/2021] [Indexed: 11/23/2022] Open
Abstract
Background Pulmonary and activation-regulated chemokine (PARC) also named CC-chemokine ligand 18 (CCL18) is a lung-predominant inflammatory protein that is found in serum. The relationship of PARC/CCL18 with the chronic obstructive pulmonary disease (COPD) is not fully understood. The aim of the present study is to analyze the expression of PARC/CCL18 in COPD. Methods Ninety-eight hospitalized COPD patients and 60 healthy volunteers from January 2019 to December 2019 were recruited in this retrospective study. Gender, age, height, weight, disease duration, smoking status, blood cell classification and count, length of hospital stay (LOS), symptom score, including COPD Assessment Test (CAT) score, modified British Medical Research Council (mMRC) score, lung function and therapy were recorded and serum PARC/CCL18 was analyzed by ELISA. The correlation between symptom score, blood cell classification and count, CRP, lung function parameters and serum levels of PARC/CCL18 and ROC curves of PARC/CCL18 levels and inhaled corticosteroids (ICS) were accessed. Results It was found that serum PARC/CCL18 level in hospitalized COPD population was significantly higher than that in healthy people (p=0.003). COPD patients with emphysema had significantly higher serum level of PARC/CCL18 than those without emphysema (p=0.049). Total lung capacity (TLC) and residual volume (RV)/TLC had positive correlation with serum level of PARC/CCL18 (p=0.001, 0.020, respectively). Furthermore, serum PARC/CCL18 level was predictive for the application ICS (p=0.003) and related to C-reactive protein (p <0.0001) in hospitalized COPD patients. Conclusion PARC/CCL18 is associated with the severity of inflammation and emphysema in COPD. Furthermore, PARC/CCL18 is a predictor of ICS application in the treatment of hospitalized COPD patients.
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Affiliation(s)
- Hongxia Duan
- Department of Respiratory Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Long Liang
- Department of Respiratory Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Xinyang Liu
- Department of Respiratory Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Shuanshuan Xie
- Department of Respiratory Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
| | - Changhui Wang
- Department of Respiratory Medicine, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China
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8
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Perotin JM, Polette M, Deslée G, Dormoy V. CiliOPD: a ciliopathy-associated COPD endotype. Respir Res 2021; 22:74. [PMID: 33639936 PMCID: PMC7912836 DOI: 10.1186/s12931-021-01665-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/11/2021] [Indexed: 12/18/2022] Open
Abstract
The pathophysiology of chronic obstructive pulmonary disease (COPD) relies on airway remodelling and inflammation. Alterations of mucociliary clearance are a major hallmark of COPD caused by structural and functional cilia abnormalities. Using transcriptomic databases of whole lung tissues and isolated small airway epithelial cells (SAEC), we comparatively analysed cilia-associated and ciliopathy-associated gene signatures from a set of 495 genes in 7 datasets including 538 non-COPD and 508 COPD patients. This bio-informatics approach unveils yet undescribed cilia and ciliopathy genes associated with COPD including NEK6 and PROM2 that may contribute to the pathology, and suggests a COPD endotype exhibiting ciliopathy features (CiliOPD).
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Affiliation(s)
- Jeanne-Marie Perotin
- University of Reims Champagne-Ardenne, Inserm, P3Cell UMR-S1250, SFR CAP-SANTE, CHU Maison Blanche, 45 rue Cognacq-Jay, 51092, Reims, France.,Department of Respiratory Diseases, CHU of Reims, Hôpital Maison Blanche, 51092, Reims, France
| | - Myriam Polette
- University of Reims Champagne-Ardenne, Inserm, P3Cell UMR-S1250, SFR CAP-SANTE, CHU Maison Blanche, 45 rue Cognacq-Jay, 51092, Reims, France.,Department of Biopathology, CHU Reims, Hôpital Maison Blanche, 51092, Reims, France
| | - Gaëtan Deslée
- University of Reims Champagne-Ardenne, Inserm, P3Cell UMR-S1250, SFR CAP-SANTE, CHU Maison Blanche, 45 rue Cognacq-Jay, 51092, Reims, France.,Department of Respiratory Diseases, CHU of Reims, Hôpital Maison Blanche, 51092, Reims, France
| | - Valérian Dormoy
- University of Reims Champagne-Ardenne, Inserm, P3Cell UMR-S1250, SFR CAP-SANTE, CHU Maison Blanche, 45 rue Cognacq-Jay, 51092, Reims, France.
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9
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Stein MM, Conery M, Magnaye KM, Clay SM, Billstrand C, Nicolae R, Naughton K, Ober C, Thompson EE. Sex-specific differences in peripheral blood leukocyte transcriptional response to LPS are enriched for HLA region and X chromosome genes. Sci Rep 2021; 11:1107. [PMID: 33441806 PMCID: PMC7806814 DOI: 10.1038/s41598-020-80145-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 12/08/2020] [Indexed: 02/08/2023] Open
Abstract
Sex-specific differences in prevalence are well documented for many common, complex diseases, especially for immune-mediated diseases, yet the precise mechanisms through which factors associated with biological sex exert their effects throughout life are not well understood. We interrogated sex-specific transcriptional responses of peripheral blood leukocytes (PBLs) to innate immune stimulation by lipopolysaccharide (LPS) in 46 male and 66 female members of the Hutterite community, who practice a communal lifestyle. We identified 1217 autosomal and 54 X-linked genes with sex-specific responses to LPS, as well as 71 autosomal and one X-linked sex-specific expression quantitative trait loci (eQTLs). Despite a similar proportion of the 15 HLA genes responding to LPS compared to all expressed autosomal genes, there was a significant over-representation of genes with sex by treatment interactions among HLA genes. We also observed an enrichment of sex-specific differentially expressed genes in response to LPS for X-linked genes compared to autosomal genes, suggesting that HLA and X-linked genes may disproportionately contribute to sex disparities in risk for immune-mediated diseases.
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Affiliation(s)
- Michelle M Stein
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Mitch Conery
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Kevin M Magnaye
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Selene M Clay
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | | | - Raluca Nicolae
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Katherine Naughton
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | - Emma E Thompson
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
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10
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Genetic regulation of gene expression of MIF family members in lung tissue. Sci Rep 2020; 10:16980. [PMID: 33046825 PMCID: PMC7552402 DOI: 10.1038/s41598-020-74121-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 09/08/2020] [Indexed: 12/18/2022] Open
Abstract
Macrophage migration inhibitory factor (MIF) is a cytokine found to be associated with chronic obstructive pulmonary disease (COPD). However, there is no consensus on how MIF levels differ in COPD compared to control conditions and there are no reports on MIF expression in lung tissue. Here we studied gene expression of members of the MIF family MIF, D-Dopachrome Tautomerase (DDT) and DDT-like (DDTL) in a lung tissue dataset with 1087 subjects and identified single nucleotide polymorphisms (SNPs) regulating their gene expression. We found higher MIF and DDT expression in COPD patients compared to non-COPD subjects and found 71 SNPs significantly influencing gene expression of MIF and DDTL. Furthermore, the platform used to measure MIF (microarray or RNAseq) was found to influence the splice variants detected and subsequently the direction of the SNP effects on MIF expression. Among the SNPs found to regulate MIF expression, the major LD block identified was linked to rs5844572, a SNP previously found to be associated with lower diffusion capacity in COPD. This suggests that MIF may be contributing to the pathogenesis of COPD, as SNPs that influence MIF expression are also associated with symptoms of COPD. Our study shows that MIF levels are affected not only by disease but also by genetic diversity (i.e. SNPs). Since none of our significant eSNPs for MIF or DDTL have been described in GWAS for COPD or lung function, MIF expression in COPD patients is more likely a consequence of disease-related factors rather than a cause of the disease.
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11
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Kim HJ, Seo YS, Sung J, Chae J, Yun JM, Kwon H, Cho B, Kim JI, Park JH. A genome-wide by PM 10 interaction study identifies novel loci for lung function near BICD1 and IL1RN-IL1F10 genes in Korean adults. CHEMOSPHERE 2020; 245:125581. [PMID: 31846791 DOI: 10.1016/j.chemosphere.2019.125581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 11/24/2019] [Accepted: 12/07/2019] [Indexed: 06/10/2023]
Abstract
Although several genome-wide interaction studies (GWIS) have been performed in specific European populations to understand the missing link between genetic and environmental factors for lung function, GWIS of Asian samples remain rare. Therefore, we performed a GWIS of exposure to air pollution to identify loci for lung function in Korean adult men. A total of 1826 adult men recruited from two health check-up centers were included in the analysis and the annual mean concentrations of ambient particulate matter with an aerodynamic diameter ≤10 μm (PM10) were used. In case of forced vital capacity (FVC), one SNP (rs12312730) that passed our genome-wide threshold of pint < 1 × 10-5 was detected in the intronic region of the BICD1 gene on chromosome 12. In addition, we found two variants (rs6743376 and rs17042888) located near the IL1RN-IL1F10 gene that were involved in the inflammatory response and associated with decreased FVC via interaction with PM10 exposure. A stratified association analysis according to these SNP genotypes showed that PM10 concentrations in subjects with one or two of the risk alleles, compared with those with the non-risk allele, were significantly correlated with a reduction in FVC. This pattern was replicated in another 892 Korean adult samples. The current study reports the first GWIS discovery in an Asian population: the BICD1 and IL1RN-IL1F10 genes may contribute to the decrease in FVC levels by interacting with PM10 exposure.
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Affiliation(s)
- Hyun-Jin Kim
- National Cancer Control Institute, National Cancer Center, Goyang, South Korea
| | - Yong-Seok Seo
- Disaster Management Research Center, Seoul, South Korea
| | - Joohon Sung
- Institute of Health and Environment, Seoul National University, Seoul, South Korea
| | - Jeesoo Chae
- Bioinformatics Analysis Team, National Cancer Center, Goyang, South Korea
| | - Jae Moon Yun
- Department of Family Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Hyuktae Kwon
- Department of Family Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Belong Cho
- Department of Family Medicine, Seoul National University Hospital, Seoul, South Korea; Department of Family Medicine, Seoul National University College of Medicine, Seoul, South Korea
| | - Jong-Il Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, South Korea; Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, South Korea.
| | - Jin-Ho Park
- Department of Family Medicine, Seoul National University Hospital, Seoul, South Korea; Department of Family Medicine, Seoul National University College of Medicine, Seoul, South Korea.
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12
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Dahlin A, Sordillo JE, McGeachie M, Kelly RS, Tantisira KG, Lutz SM, Lasky-Su J, Wu AC. Genome-wide interaction study reveals age-dependent determinants of responsiveness to inhaled corticosteroids in individuals with asthma. PLoS One 2020; 15:e0229241. [PMID: 32119686 PMCID: PMC7051058 DOI: 10.1371/journal.pone.0229241] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 02/01/2020] [Indexed: 11/19/2022] Open
Abstract
While genome-wide association studies have identified genes involved in differential treatment responses to inhaled corticosteroids (ICS) in asthma, few studies have evaluated the potential effects of age in this context. A significant proportion of asthmatics experience exacerbations (hospitalizations and emergency department visits) during ICS treatment. We evaluated the interaction of genetic variation and age on ICS response (measured by the occurrence of exacerbations) through a genome-wide interaction study (GWIS) of 1,321 adult and child asthmatic patients of European ancestry. We identified 107 genome-wide suggestive (P<10-05) age-by-genotype interactions, two of which also met genome-wide significance (P<5x10-08) (rs34631960 [OR 2.3±1.6-3.3] in thrombospondin type 1 domain-containing protein 4 (THSD4) and rs2328386 [OR 0.5±0.3-0.7] in human immunodeficiency virus type I enhancer binding protein 2 (HIVEP2)) by joint analysis of GWIS results from discovery and replication populations. In addition to THSD4 and HIVEP2, age-by-genotype interactions also prioritized genes previously identified as asthma candidate genes, including DPP10, HDAC9, TBXAS1, FBXL7, and GSDMB/ORMDL3, as pharmacogenomic loci as well. This study is the first to link these genes to a pharmacogenetic trait for asthma.
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Affiliation(s)
- Amber Dahlin
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Joanne E. Sordillo
- Department of Population Medicine, PRecisiOn Medicine Translational Research (PROMoTeR) Center, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts, United States of America
| | - Michael McGeachie
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Rachel S. Kelly
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Kelan G. Tantisira
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Sharon M. Lutz
- Department of Population Medicine, PRecisiOn Medicine Translational Research (PROMoTeR) Center, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts, United States of America
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ann Chen Wu
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Population Medicine, PRecisiOn Medicine Translational Research (PROMoTeR) Center, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts, United States of America
- * E-mail:
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13
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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.
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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
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14
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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.
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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
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15
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Henry AP, Probert K, Stewart CE, Thakker D, Bhaker S, Azimi S, Hall IP, Sayers I. Defining a role for lung function associated gene GSTCD in cell homeostasis. Respir Res 2019; 20:172. [PMID: 31370853 PMCID: PMC6676530 DOI: 10.1186/s12931-019-1146-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 07/25/2019] [Indexed: 12/11/2022] Open
Abstract
Genome wide association (GWA) studies have reproducibly identified signals on chromosome 4q24 associated with lung function and COPD. GSTCD (Glutathione S-transferase C-terminal domain containing) represents a candidate causal gene in this locus, however little is currently known about the function of this protein. We set out to further our understanding of the role of GSTCD in cell functions and homeostasis using multiple molecular and cellular approaches in airway relevant cells. Recombinant expression of human GSTCD in conjunction with a GST activity assay did not identify any enzymatic activity for two GSTCD isoforms questioning the assignment of this protein to this family of enzymes. Protein structure analyses identified a potential methyltransferase domain contained within GSTCD, with these enzymes linked to cell viability and apoptosis. Targeted knockdown (siRNA) of GSTCD in bronchial epithelial cells identified a role for GSTCD in cell viability as proliferation rates were not altered. To provide greater insight we completed transcriptomic analyses on cells with GSTCD expression knocked down and identified several differentially expressed genes including those implicated in airway biology; fibrosis e.g. TGFBR1 and inflammation e.g. IL6R. Pathway based transcriptomic analyses identified an over-representation of genes related to adipogenesis which may suggest additional functions for GSTCD. These findings identify potential additional functions for GSTCD in the context of airway biology beyond the hypothesised GST activity and warrant further investigation.
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Affiliation(s)
- Amanda P Henry
- Division of Respiratory Medicine, National Institute for Health Research, Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK.
| | - Kelly Probert
- Division of Respiratory Medicine, National Institute for Health Research, Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Ceri E Stewart
- Division of Respiratory Medicine, National Institute for Health Research, Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Dhruma Thakker
- Division of Respiratory Medicine, National Institute for Health Research, Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Sangita Bhaker
- Division of Respiratory Medicine, National Institute for Health Research, Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Sheyda Azimi
- Division of Respiratory Medicine, National Institute for Health Research, Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Ian P Hall
- Division of Respiratory Medicine, National Institute for Health Research, Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Ian Sayers
- Division of Respiratory Medicine, National Institute for Health Research, Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
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16
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Dhondalay GK, Rael E, Acharya S, Zhang W, Sampath V, Galli SJ, Tibshirani R, Boyd SD, Maecker H, Nadeau KC, Andorf S. Food allergy and omics. J Allergy Clin Immunol 2019; 141:20-29. [PMID: 29307411 DOI: 10.1016/j.jaci.2017.11.007] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Revised: 11/09/2017] [Accepted: 11/14/2017] [Indexed: 01/06/2023]
Abstract
Food allergy (FA) prevalence has been increasing over the last few decades and is now a global health concern. Current diagnostic methods for FA result in a high number of false-positive results, and the standard of care is either allergen avoidance or use of epinephrine on accidental exposure, although currently with no other approved treatments. The increasing prevalence of FA, lack of robust biomarkers, and inadequate treatments warrants further research into the mechanism underlying food allergies. Recent technological advances have made it possible to move beyond traditional biological techniques to more sophisticated high-throughput approaches. These technologies have created the burgeoning field of omics sciences, which permit a more systematic investigation of biological problems. Omics sciences, such as genomics, epigenomics, transcriptomics, proteomics, metabolomics, microbiomics, and exposomics, have enabled the construction of regulatory networks and biological pathway models. Parallel advances in bioinformatics and computational techniques have enabled the integration, analysis, and interpretation of these exponentially growing data sets and opens the possibility of personalized or precision medicine for FA.
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Affiliation(s)
- Gopal Krishna Dhondalay
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Efren Rael
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Swati Acharya
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Wenming Zhang
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Vanitha Sampath
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Stephen J Galli
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Department of Pathology, Stanford University School of Medicine, Stanford, Calif; Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, Calif
| | - Robert Tibshirani
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Department of Biomedical Data Sciences, Stanford University School of Medicine, Stanford, Calif
| | - Scott D Boyd
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Department of Pathology, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Holden Maecker
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
| | - Kari Christine Nadeau
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif.
| | - Sandra Andorf
- Sean N. Parker Center for Allergy and Asthma Research, Stanford University School of Medicine, Stanford, Calif; Institute for Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, Calif
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17
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Association study in African-admixed populations across the Americas recapitulates asthma risk loci in non-African populations. Nat Commun 2019; 10:880. [PMID: 30787307 PMCID: PMC6382865 DOI: 10.1038/s41467-019-08469-7] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 01/08/2019] [Indexed: 12/15/2022] Open
Abstract
Asthma is a complex disease with striking disparities across racial and ethnic groups. Despite its relatively high burden, representation of individuals of African ancestry in asthma genome-wide association studies (GWAS) has been inadequate, and true associations in these underrepresented minority groups have been inconclusive. We report the results of a genome-wide meta-analysis from the Consortium on Asthma among African Ancestry Populations (CAAPA; 7009 asthma cases, 7645 controls). We find strong evidence for association at four previously reported asthma loci whose discovery was driven largely by non-African populations, including the chromosome 17q12-q21 locus and the chr12q13 region, a novel (and not previously replicated) asthma locus recently identified by the Trans-National Asthma Genetic Consortium (TAGC). An additional seven loci reported by TAGC show marginal evidence for association in CAAPA. We also identify two novel loci (8p23 and 8q24) that may be specific to asthma risk in African ancestry populations.
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18
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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).
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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
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Kulminski AM, Barochia AV, Loika Y, Raghavachari N, Arbeev KG, Wojczynski MK, Thyagarajan B, Vardarajan BN, Christensen K, Yashin AI, Levine SJ. The APOE ε4 allele is associated with a reduction in FEV1/FVC in women: A cross-sectional analysis of the Long Life Family Study. PLoS One 2018; 13:e0206873. [PMID: 30412599 PMCID: PMC6226172 DOI: 10.1371/journal.pone.0206873] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 10/22/2018] [Indexed: 12/14/2022] Open
Abstract
INTRODUCTION Murine studies have shown that apolipoprotein E modulates pulmonary function during development, aging, and allergen-induced airway disease. It is not known whether the polymorphic human APOE gene influences pulmonary function. OBJECTIVES We assessed whether an association exists between the polymorphic human APOE ε2, ε3, and ε4 alleles and pulmonary function among participants in the Long Life Family Study. METHODS Data from 4,468 Caucasian subjects who had genotyping performed for the APOE ε2, ε3, and ε4 alleles were analyzed, with and without stratification by sex. Statistical models were fitted considering the effects of the ε2 allele, defined as ε2/2 or ε2/3 genotypes, and the ε4 allele, defined as ε3/4 or ε4/4 genotypes, which were compared to the ε3/3 genotype. RESULTS The mean FEV1/FVC ratio (the forced expiratory volume in one second divided by the forced vital capacity) was lower among women with the ε4 allele as compared to women with the ε3/3 genotype or the ε2 allele. Carriage of the APOE ε4 allele was associated with FEV1/FVC, which implied lower values. Further analysis showed that the association primarily reflected women without lung disease who were older than 70 years. The association was not mediated by lipid levels, smoking status, body mass index, or cardiovascular disease. CONCLUSIONS This study for the first time identifies that the APOE gene is associated with modified lung physiology in women. This suggests that a link may exist between the APOE ε4 allele, female sex, and a reduction in the FEV1/FVC ratio in older individuals.
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Affiliation(s)
- Alexander M. Kulminski
- Biodemography of Aging Research Unit, Social Sciences Research Institute, Duke University, Durham, NC, United States of America
- * E-mail: (AMK); (SJL)
| | - Amisha V. Barochia
- Laboratory of Asthma and Lung Inflammation, Pulmonary Branch, National Heart, Lung, and Blood Institute, Bethesda, MD, United States of America
| | - Yury Loika
- Biodemography of Aging Research Unit, Social Sciences Research Institute, Duke University, Durham, NC, United States of America
| | - Nalini Raghavachari
- National Institute on Aging, Gateway Building, Suite, Bethesda, MD, United States of America
| | - Konstantin G. Arbeev
- Biodemography of Aging Research Unit, Social Sciences Research Institute, Duke University, Durham, NC, United States of America
| | - Mary K. Wojczynski
- Division of Statistical Genomics, Department of Genetics, School of Medicine, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, United States of America
| | - Badri N. Vardarajan
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, United States of America
| | - Kaare Christensen
- The Danish Aging Research Center, University of Southern Denmark, Odense C, Denmark
- Department of Clinical Genetics and Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense C, Denmark
| | - Anatoliy I. Yashin
- Biodemography of Aging Research Unit, Social Sciences Research Institute, Duke University, Durham, NC, United States of America
| | - Stewart J. Levine
- Laboratory of Asthma and Lung Inflammation, Pulmonary Branch, National Heart, Lung, and Blood Institute, Bethesda, MD, United States of America
- * E-mail: (AMK); (SJL)
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Stein MM, Hrusch CL, Sperling AI, Ober C. Effects of an FcγRIIA polymorphism on leukocyte gene expression and cytokine responses to anti-CD3 and anti-CD28 antibodies. Genes Immun 2018; 20:462-472. [PMID: 29977032 DOI: 10.1038/s41435-018-0038-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 05/21/2018] [Accepted: 05/23/2018] [Indexed: 02/06/2023]
Abstract
The low affinity Fcγ receptor, FcγRIIA, harbors a common missense mutation, rs1801274 (G>A, Arg131His) that modifies binding affinity to human IgG2 and mouse IgG1 antibodies and is associated with increased risk of autoimmune disease. Despite the important role of the Arg131His variant, little is understood about heterozygous genotype effects on global gene expression and cytokine production during an FcγR-dependent response. To address this gap in knowledge, we treated human whole-blood samples from 130 individuals with mouse IgG1 anti-CD3 and anti-CD28 antibodies and characterized the genome-wide gene expression profiles and cytokine production among individuals stratified by rs1801274 genotype. Our analysis revealed that the levels of four cytokines (IFNγ, IL-12, IL-2, TNFα) and global gene expression patterns differed between all three genotype classes. Surprisingly, the heterozygotes showed suboptimal T cell activation compared to cells from individuals homozygous for the higher-affinity FcγRIIA allele (GG; Arg/Arg). The results of this study demonstrate that IgG response varies among all rs1801274 genotype classes and results in profound differences in both cytokine responses and gene expression patterns in blood leukocytes. Because even heterozygotes showed dampened global responses, our data may provide insight into the heterogeneity of outcomes in cytokine release assays and immunotherapy efficacy.
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Affiliation(s)
- Michelle M Stein
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
| | - Cara L Hrusch
- Department of Medicine, Section of Pulmonary and Critical Care Medicine, and the Committee on Immunology, University of Chicago, Chicago, IL, 60637, USA
| | - Anne I Sperling
- Department of Medicine, Section of Pulmonary and Critical Care Medicine, and the Committee on Immunology, University of Chicago, Chicago, IL, 60637, USA
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
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21
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Ni L, Dong C. Roles of Myeloid and Lymphoid Cells in the Pathogenesis of Chronic Obstructive Pulmonary Disease. Front Immunol 2018; 9:1431. [PMID: 29977245 PMCID: PMC6021485 DOI: 10.3389/fimmu.2018.01431] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 06/08/2018] [Indexed: 12/15/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is currently the third largest cause of human mortality in the world after stroke and heart disease. COPD is characterized by sustained inflammation of the airways, leading to destruction of lung tissue and declining pulmonary function. The main risk factor is known to be cigarette smoke currently. However, the strategies for prevention and treatment have not altered significantly for many years. A growing body of evidences indicates that the immune system plays a pivotal role in the pathogenesis of COPD. The repeated and progressive activation of immune cells is at least in part the source of this chronic inflammation. In this review paper, we have conducted an extensive literature search of the studies of immune cells in COPD patients. The objective is to assess the contributions of different immune cell types, the imbalance of pro/anti-inflammatory immune cells, such as M1/M2 macrophages, Tc1/Tc10, and Th17/Treg, and their mediators in the peripheral blood as well as in the lung to the pathogenesis of COPD. Therefore, understanding their roles in COPD development will help us find the potential target to modify this disease. This review focuses predominantly on data derived from human studies but will refer to animal studies where they help understand the disease in humans.
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Affiliation(s)
- Ling Ni
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Chen Dong
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
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Vishweswaraiah S, George L, Purushothaman N, Ganguly K. A candidate gene identification strategy utilizing mouse to human big-data mining: "3R-tenet" in COPD genetic research. Respir Res 2018; 19:92. [PMID: 29871630 PMCID: PMC5989378 DOI: 10.1186/s12931-018-0795-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 04/27/2018] [Indexed: 12/13/2022] Open
Abstract
Background Early life impairments leading to lower lung function by adulthood are considered as risk factors for chronic obstructive pulmonary disease (COPD). Recently, we compared the lung transcriptomic profile between two mouse strains with extreme total lung capacities to identify plausible pulmonary function determining genes using microarray analysis (GSE80078). Advancement of high-throughput techniques like deep sequencing (eg. RNA-seq) and microarray have resulted in an explosion of genomic data in the online public repositories which however remains under-exploited. Strategic curation of publicly available genomic data with a mouse-human translational approach can effectively implement “3R- Tenet” by reducing screening experiments with animals and performing mechanistic studies using physiologically relevant in vitro model systems. Therefore, we sought to analyze the association of functional variations within human orthologs of mouse lung function candidate genes in a publicly available COPD lung RNA-seq data-set. Methods Association of missense single nucleotide polymorphisms, insertions, deletions, and splice junction variants were analyzed for susceptibility to COPD using RNA-seq data of a Korean population (GSE57148). Expression of the associated genes were studied using the Gene Paint (mouse embryo) and Human Protein Atlas (normal adult human lung) databases. The genes were also assessed for replication of the associations and expression in COPD−/mouse cigarette smoke exposed lung tissues using other datasets. Results Significant association (p < 0.05) of variations in 20 genes to higher COPD susceptibility have been detected within the investigated cohort. Association of HJURP, MCRS1 and TLR8 are novel in relation to COPD. The associated ADAM19 and KIT loci have been reported earlier. The remaining 15 genes have also been previously associated to COPD. Differential transcript expression levels of the associated genes in COPD- and/ or mouse emphysematous lung tissues have been detected. Conclusion Our findings suggest strategic mouse-human datamining approaches can identify novel COPD candidate genes using existing datasets in the online repositories. The candidates can be further evaluated for mechanistic role through in vitro studies using appropriate primary cells/cell lines. Functional studies can be limited to transgenic animal models of only well supported candidate genes. This approach will lead to a significant reduction of animal experimentation in respiratory research. Electronic supplementary material The online version of this article (10.1186/s12931-018-0795-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Leema George
- SRM Research Institute, SRM University, Chennai, 603203, India
| | - Natarajan Purushothaman
- Department of Genetic Engineering, School of Bioengineering, Faculty of Engineering and Technology, SRM University, Chennai, 603203, India
| | - Koustav Ganguly
- SRM Research Institute, SRM University, Chennai, 603203, India. .,Work Environment Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Box 287, SE-171 77, Stockholm, Sweden.
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Reppell M, Novembre J. Using pseudoalignment and base quality to accurately quantify microbial community composition. PLoS Comput Biol 2018; 14:e1006096. [PMID: 29659582 PMCID: PMC5945057 DOI: 10.1371/journal.pcbi.1006096] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 05/10/2018] [Accepted: 03/19/2018] [Indexed: 12/31/2022] Open
Abstract
Pooled DNA from multiple unknown organisms arises in a variety of contexts, for example microbial samples from ecological or human health research. Determining the composition of pooled samples can be difficult, especially at the scale of modern sequencing data and reference databases. Here we propose a novel method for taxonomic profiling in pooled DNA that combines the speed and low-memory requirements of k-mer based pseudoalignment with a likelihood framework that uses base quality information to better resolve multiply mapped reads. We apply the method to the problem of classifying 16S rRNA reads using a reference database of known organisms, a common challenge in microbiome research. Using simulations, we show the method is accurate across a variety of read lengths, with different length reference sequences, at different sample depths, and when samples contain reads originating from organisms absent from the reference. We also assess performance in real 16S data, where we reanalyze previous genetic association data to show our method discovers a larger number of quantitative trait associations than other widely used methods. We implement our method in the software Karp, for k-mer based analysis of read pools, to provide a novel combination of speed and accuracy that is uniquely suited for enhancing discoveries in microbial studies.
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Affiliation(s)
- Mark Reppell
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
| | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America
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24
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A decade of research on the 17q12-21 asthma locus: Piecing together the puzzle. J Allergy Clin Immunol 2018; 142:749-764.e3. [PMID: 29307657 PMCID: PMC6172038 DOI: 10.1016/j.jaci.2017.12.974] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/13/2017] [Accepted: 12/16/2017] [Indexed: 12/20/2022]
Abstract
Chromosome 17q12–21 remains the most highly replicated and significant asthma locus. Genotypes in the core region defined by the first genome-wide association study correlate with expression of 2 genes, ORM1-like 3 (ORMDL3) and gasdermin B (GSDMB), making these prime candidate asthma genes, although recent studies have implicated gasdermin A (GSDMA) distal to and post-GPI attachment to proteins 3 (PGAP3) proximal to the core region as independent loci. We review 10 years of studies on the 17q12–21 locus and suggest that genotype-specific risks for asthma at the proximal and distal loci are not specific to early-onset asthma and mediated by PGAP3, ORMDL3, and/or GSDMA expression. We propose that the weak and inconsistent associations of 17q single nucleotide polymorphisms with asthma in African Americans is due to the high frequency of some 17q alleles, the breakdown of linkage disequilibrium on African-derived chromosomes, and possibly different early-life asthma endotypes in these children. Finally, the inconsistent association between asthma and gene expression levels in blood or lung cells from older children and adults suggests that genotype effects may mediate asthma risk or protection during critical developmental windows and/or in response to relevant exposures in early life. Thus studies of young children and ethnically diverse populations are required to fully understand the relationship between genotype and asthma phenotype and the gene regulatory architecture at this locus. (J Allergy Clin Immunol 2018;142:749–64.)
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25
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Hizawa N. Clinical approaches towards asthma and chronic obstructive pulmonary disease based on the heterogeneity of disease pathogenesis. Clin Exp Allergy 2017; 46:678-87. [PMID: 27009427 DOI: 10.1111/cea.12731] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Asthma and chronic obstructive pulmonary disease (COPD) are each heterogeneous disease classifications that include several clinical and pathophysiological phenotypes. This heterogeneity complicates characterization of each disease and, in some cases, hinders the selection of appropriate treatment. Therefore, in recent years, emphasis has been placed on improving our understanding of the various phenotypes of asthma and of COPD and identifying biomarkers for each phenotype. Likewise, the concept of the endotype has been gaining acceptance; an endotype is a disease subtype that is defined by unique or distinctive functional or pathophysiological mechanisms. Endotypes of asthma or COPD may be primarily characterized by increased susceptibility to type 2 inflammation, increased susceptibility to viral infections, bacterial colonization or impaired lung development. The 'Dutch hypothesis' is as follows: gene variants underlying particular endotypes interact with detrimental environmental stimuli (e.g. smoking, viral infection and air pollution) and contribute to the ultimate development of asthma, COPD or both. Novel approaches that involve multidimensional assessment should facilitate identification and management of the components that generate this heterogeneity. Ultimately, patients with chronic inflammatory lung diseases may be treated based on these endotypes as determined by the respective biomarkers that correspond to individual endotypes instead of on disease labels such as asthma, COPD or even asthma-COPD overlap syndrome (ACOS).
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Affiliation(s)
- N Hizawa
- Faculty of Medicine, Department of Pulmonary Medicine, University of Tsukuba, Tsukuba, Japan
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26
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Igartua C, Mozaffari SV, Nicolae DL, Ober C. Rare non-coding variants are associated with plasma lipid traits in a founder population. Sci Rep 2017; 7:16415. [PMID: 29180722 PMCID: PMC5704019 DOI: 10.1038/s41598-017-16550-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 11/14/2017] [Indexed: 12/31/2022] Open
Abstract
Founder populations are ideally suited for studies on the clinical effects of alleles that are rare in general populations but occur at higher frequencies in these isolated populations. Whole genome sequencing in 98 Hutterites, a founder population of European descent, and subsequent imputation revealed 660,238 single nucleotide polymorphisms that are rare (<1%) or absent in European populations, but occur at frequencies >1% in the Hutterites. We examined the effects of these rare in European variants on plasma lipid levels in 828 Hutterites and applied a Bayesian hierarchical framework to prioritize potentially causal variants based on functional annotations. We identified two novel non-coding rare variants associated with LDL cholesterol (rs17242388 in LDLR) and HDL cholesterol (rs189679427 between GOT2 and APOOP5), and replicated previous associations of a splice variant in APOC3 (rs138326449) with triglycerides and HDL-C. All three variants are at well-replicated loci in GWAS but are independent from and have larger effect sizes than the known common variation in these regions. Candidate eQTL analyses in in LCLs in the Hutterites suggest that these rare non-coding variants are likely to mediate their effects on lipid traits by regulating gene expression.
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Affiliation(s)
- Catherine Igartua
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
| | - Sahar V Mozaffari
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.,Committee of Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA
| | - Dan L Nicolae
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.,Department of Statistics, University of Chicago, Chicago, IL, 60637, USA.,Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.,Committee of Genetics, Genomics and Systems Biology, University of Chicago, Chicago, IL, 60637, USA
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Suh Y, Lee C. Genome-wide association study for genetic variants related with maximal voluntary ventilation reveals two novel genomic signals associated with lung function. Medicine (Baltimore) 2017; 96:e8530. [PMID: 29095316 PMCID: PMC5682835 DOI: 10.1097/md.0000000000008530] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Genome-wide association studies (GWAS) for spirometry parameters have been limited to forced vital capacity (FVC), forced expiratory volume in 1 second (FEV1), and their ratio. This study examined to identify genetic variants associated with maximal voluntary ventilation (MVV), an important spirometry parameter presenting inspiratory muscle strength.A total of 8842 Korean subjects participated in the Korean Association REsource Consortium were used to identify nucleotide variants associated with MVV and other spirometry parameters through a GWAS. Genetic associations were determined by employing a mixed model that can control background polygenic effects.The analysis revealed 3 nucleotide variants associated with MVV (P < 5 × 10). One (rs1496255) was also associated with FVC and FEV1. The other 2 variants were identified only for MVV and located in the genes of LOC102724340 (rs41434646) and FHIT (rs9833533). In particular, FHIT represses transcriptional activity of β-catenin, a critical protein for growth of skeletal muscle, and thus might have influenced the level of MVV.The current study revealed 2 novel nucleotide variants as genetic association signals for MVV. The association signals were suggested specific for neuromuscular diseases with a restrictive ventilatory impairment. Further studies are required to understand underlying mechanisms for their influence to restrictive lung diseases.
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28
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George L, Mitra A, Thimraj TA, Irmler M, Vishweswaraiah S, Lunding L, Hühn D, Madurga A, Beckers J, Fehrenbach H, Upadhyay S, Schulz H, Leikauf GD, Ganguly K. Transcriptomic analysis comparing mouse strains with extreme total lung capacities identifies novel candidate genes for pulmonary function. Respir Res 2017; 18:152. [PMID: 28793908 PMCID: PMC5551015 DOI: 10.1186/s12931-017-0629-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 07/25/2017] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Failure to attain peak lung function by early adulthood is a risk factor for chronic lung diseases. Previously, we reported that C3H/HeJ mice have about twice total lung capacity (TLC) compared to JF1/MsJ mice. We identified seven lung function quantitative trait loci (QTL: Lfnq1-Lfnq7) in backcross/intercross mice derived from these inbred strains. We further demonstrated, superoxide dismutase 3, extracellular (Sod3), Kit oncogene (Kit) and secreted phosphoprotein 1 (Spp1) located on these Lfnqs as lung function determinants. Emanating from the concept of early origin of lung disease, we sought to identify novel candidate genes for pulmonary function by investigating lung transcriptome in C3H/HeJ and JF1/MsJ mice at the completion of embryonic development, bulk alveolar formation and maturity. METHODS Design-based stereological analysis was performed to study lung structure in C3H/HeJ and JF1/MsJ mice. Microarray was used for lung transcriptomic analysis [embryonic day 18, postnatal days 28, 70]. Quantitative real time polymerase chain reaction (qRT-PCR), western blot and immunohistochemical analysis were used to confirm selected differences. RESULTS Stereological analysis revealed decreased alveolar number density, elastin to collagen ratio and increased mean alveolar volume in C3H/HeJ mice compared to JF1/MsJ. Gene ontology term "extracellular region" was enriched among the decreased JF1/MsJ transcripts. Candidate genes identified using the expression-QTL strategy include: ATP-binding cassette, sub-family G (WHITE), member 1 (Abcg1), formyl peptide receptor 1 (Fpr1), gamma-aminobutyric acid (GABA) B receptor, 1 (Gabbr1); histocompatibility 2 genes: class II antigen E beta (H2-Eb1), D region locus 1 (H2-D1), and Q region locus 4 (H2-Q4); leucine rich repeat containing 6 (testis) (Lrrc6), radial spoke head 1 homolog (Rsph1), and surfactant associated 2 (Sfta2). Noteworthy genes selected as candidates for their consistent expression include: Wnt inhibitor factor 1 (Wif1), follistatin (Fst), chitinase-like 1 (Chil1), and Chil3. CONCLUSIONS Comparison of late embryonic, adolescent and adult lung transcript profiles between mouse strains with extreme TLCs lead to the identification of candidate genes for pulmonary function that has not been reported earlier. Further mechanistic investigations are warranted to elucidate their mode of action in determining lung function.
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Affiliation(s)
- Leema George
- SRM Research Institute, SRM University, Chennai, 603203 India
| | - Ankita Mitra
- SRM Research Institute, SRM University, Chennai, 603203 India
| | | | - Martin Irmler
- Institute of Experimental Genetics, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, 85764 Neuherberg, Munich Germany
| | | | - Lars Lunding
- Priority Area Asthma & Allergy, Division of Asthma Exacerbation & Regulation, Research Center Borstel, Airway Research Center North (ARCN), 23845 Borstel, Germany
| | - Dorothea Hühn
- Department of Medicine, Pulmonary and Critical Care Medicine, University Medical Centre Giessen and Marburg, Philipps-University Marburg, Marburg, Germany
- Present address: Lahn-Dill-Kliniken, Klinikum Wetzlar, Medizinische Klinik II, Forsthausstraße 1, D-35578 Wetzlar, Germany
| | - Alicia Madurga
- Department of Internal Medicine (Pulmonology), University of Giessen and Marburg Lung Center (UGMLC), 35392, Giessen, Germany
| | - Johannes Beckers
- Institute of Experimental Genetics, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, 85764 Neuherberg, Munich Germany
- German Center for Diabetes Research (DZD), 85764 Neuherberg, Germany
- Experimental Genetics, Technische Universität München, 85354 Freising, Germany
| | - Heinz Fehrenbach
- Priority Area Asthma & Allergy, Division of Experimental Pneumology, Research Center Borstel, Airway Research Center North (ARCN), 23845 Borstel, Germany
| | - Swapna Upadhyay
- Lung and Airway Research, Institute of Environmental Medicine, Karolinska Institutet, Box 287, SE-171 77 Stockholm, Sweden
- Institute of Lung Biology and Disease, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, 85764 Neuherberg, Munich Germany
| | - Holger Schulz
- Institute of Epidemiology I, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, 85764 Neuherberg, Munich Germany
- Comprehensive Pneumology Center Munich (CPC-M), Munich, Germany
| | - George D. Leikauf
- Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15219 USA
| | - Koustav Ganguly
- SRM Research Institute, SRM University, Chennai, 603203 India
- Lung and Airway Research, Institute of Environmental Medicine, Karolinska Institutet, Box 287, SE-171 77 Stockholm, Sweden
- Institute of Lung Biology and Disease, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, 85764 Neuherberg, Munich Germany
- Work Environment Toxicology; Institute of Environmental Medicine, Karolinska Institutet, Box 287, SE-171 77 Stockholm, Sweden
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Lee MK, Hong Y, Kim SY, Kim WJ, London SJ. Epigenome-wide association study of chronic obstructive pulmonary disease and lung function in Koreans. Epigenomics 2017; 9:971-984. [PMID: 28621160 PMCID: PMC5674213 DOI: 10.2217/epi-2017-0002] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 05/03/2017] [Indexed: 11/21/2022] Open
Abstract
AIM To identify differentially methylated probes (DMPs) and regions (DMRs) in relation to chronic obstructive pulmonary disease (COPD) and lung function traits. METHODS We performed an epigenome-wide association study of COPD and spirometric parameters, including forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC) and FEV1/FVC, in blood DNA using the Infinium HumanMethylation450 (n = 100, a Korean COPD cohort). RESULTS We found one significant DMP (cg03559389, DIP2C) and 104 significant DMRs after multiple-testing correction. Of these, 34 DMRs mapped to genes differential expressed with respect to the same trait. Five of the genes were associated with more than two traits: CTU2, USP36, ZNF516, KLK10 and CPT1B. CONCLUSION We identified novel differential methylation loci related to COPD and lung function in blood DNA in Koreans and confirmed previous findings in non-Asians. Epigenetic modification could contribute to the etiology of these phenotypes.
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Affiliation(s)
- Mi Kyeong Lee
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
- Department of Internal Medicine & Environmental Health Center, Kangwon National University Hospital, School of Medicine, Kangwon National University, Chuncheon-si, Gangwon-do 19300, South Korea
| | - Yoonki Hong
- Department of Internal Medicine & Environmental Health Center, Kangwon National University Hospital, School of Medicine, Kangwon National University, Chuncheon-si, Gangwon-do 19300, South Korea
| | - Sun-Young Kim
- Institute of Health & Environment, Seoul National University, Seoul 08826, South Korea
| | - Woo Jin Kim
- Department of Internal Medicine & Environmental Health Center, Kangwon National University Hospital, School of Medicine, Kangwon National University, Chuncheon-si, Gangwon-do 19300, South Korea
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
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Hayden LP, Cho MH, McDonald MLN, Crapo JD, Beaty TH, Silverman EK, Hersh CP. Susceptibility to Childhood Pneumonia: A Genome-Wide Analysis. Am J Respir Cell Mol Biol 2017; 56:20-28. [PMID: 27508494 DOI: 10.1165/rcmb.2016-0101oc] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Previous studies have indicated that in adult smokers, a history of childhood pneumonia is associated with reduced lung function and chronic obstructive pulmonary disease. There have been few previous investigations using genome-wide association studies to investigate genetic predisposition to pneumonia. This study aims to identify the genetic variants associated with the development of pneumonia during childhood and over the course of the lifetime. Study subjects included current and former smokers with and without chronic obstructive pulmonary disease participating in the COPDGene Study. Pneumonia was defined by subject self-report, with childhood pneumonia categorized as having the first episode at <16 years. Genome-wide association studies for childhood pneumonia (843 cases, 9,091 control subjects) and lifetime pneumonia (3,766 cases, 5,659 control subjects) were performed separately in non-Hispanic whites and African Americans. Non-Hispanic white and African American populations were combined in the meta-analysis. Top genetic variants from childhood pneumonia were assessed in network analysis. No single-nucleotide polymorphisms reached genome-wide significance, although we identified potential regions of interest. In the childhood pneumonia analysis, this included variants in NGR1 (P = 6.3 × 10-8), PAK6 (P = 3.3 × 10-7), and near MATN1 (P = 2.8 × 10-7). In the lifetime pneumonia analysis, this included variants in LOC339862 (P = 8.7 × 10-7), RAPGEF2 (P = 8.4 × 10-7), PHACTR1 (P = 6.1 × 10-7), near PRR27 (P = 4.3 × 10-7), and near MCPH1 (P = 2.7 × 10-7). Network analysis of the genes associated with childhood pneumonia included top networks related to development, blood vessel morphogenesis, muscle contraction, WNT signaling, DNA damage, apoptosis, inflammation, and immune response (P ≤ 0.05). We have identified genes potentially associated with the risk of pneumonia. Further research will be required to confirm these associations and to determine biological mechanisms. CLINICAL TRIAL REGISTRATION NCT00608764.
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Affiliation(s)
- Lystra P Hayden
- 1 Division of Respiratory Diseases, Boston Children's Hospital, Boston, Massachusetts.,2 Channing Division of Network Medicine and
| | - Michael H Cho
- 2 Channing Division of Network Medicine and.,3 Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | | | | | - Terri H Beaty
- 5 Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland
| | - Edwin K Silverman
- 2 Channing Division of Network Medicine and.,3 Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Craig P Hersh
- 2 Channing Division of Network Medicine and.,3 Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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31
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Igartua C, Davenport ER, Gilad Y, Nicolae DL, Pinto J, Ober C. Host genetic variation in mucosal immunity pathways influences the upper airway microbiome. MICROBIOME 2017; 5:16. [PMID: 28143570 PMCID: PMC5286564 DOI: 10.1186/s40168-016-0227-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 12/25/2016] [Indexed: 05/08/2023]
Abstract
BACKGROUND The degree to which host genetic variation can modulate microbial communities in humans remains an open question. Here, we performed a genetic mapping study of the microbiome in two accessible upper airway sites, the nasopharynx and the nasal vestibule, during two seasons in 144 adult members of a founder population of European decent. RESULTS We estimated the relative abundances (RAs) of genus level bacteria from 16S rRNA gene sequences and examined associations with 148,653 genetic variants (linkage disequilibrium [LD] r 2 < 0.5) selected from among all common variants discovered in genome sequences in this population. We identified 37 microbiome quantitative trait loci (mbQTLs) that showed evidence of association with the RAs of 22 genera (q < 0.05) and were enriched for genes in mucosal immunity pathways. The most significant association was between the RA of Dermacoccus (phylum Actinobacteria) and a variant 8 kb upstream of TINCR (rs117042385; p = 1.61 × 10-8; q = 0.002), a long non-coding RNA that binds to peptidoglycan recognition protein 3 (PGLYRP3) mRNA, a gene encoding a known antimicrobial protein. A second association was between a missense variant in PGLYRP4 (rs3006458) and the RA of an unclassified genus of family Micrococcaceae (phylum Actinobacteria) (p = 5.10 × 10-7; q = 0.032). CONCLUSIONS Our findings provide evidence of host genetic influences on upper airway microbial composition in humans and implicate mucosal immunity genes in this relationship.
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Affiliation(s)
- Catherine Igartua
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
| | - Emily R Davenport
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Yoav Gilad
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
- Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
| | - Dan L Nicolae
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
- Department of Medicine, University of Chicago, Chicago, IL, 60637, USA
- Department of Statistics, University of Chicago, Chicago, IL, 60637, USA
| | - Jayant Pinto
- Section of Otolaryngology-Head and Neck Surgery, Department of Surgery, University of Chicago, Chicago, IL, 60637, USA
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
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32
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Kim HJ, Min JY, Min KB, Seo YS, Sung J, Yun JM, Kwon H, Cho B, Park JH, Kim JI. CDH13 gene-by-PM 10 interaction effect on lung function decline in Korean men. CHEMOSPHERE 2017; 168:583-589. [PMID: 27839881 DOI: 10.1016/j.chemosphere.2016.11.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 11/03/2016] [Accepted: 11/05/2016] [Indexed: 06/06/2023]
Abstract
Lung function can be influenced by genetic factors, which may explain individual differences in susceptibility to the effects of air pollution. This study investigated whether the effect of particulate matter with an aerodynamic diameter ≤10 μm (PM10) on lung function is modified by Cadherin 13 (CDH13) genetic variants in Korean men. This study included a total of 1827 men who were recruited from two health check-up centers, and the annual average PM10 concentrations were used. A total of 200 single-nucleotide polymorphisms (SNPs) of the CDH13 gene were selected for this study. We found that a SNP in CHD13 intron, rs1862830, had the strongest associations with both forced expiratory volume in 1 s (FEV1) (pint = 1.90 × 10-4) and forced vital capacity (FVC) (pint = 1.88 × 10-3) by interacting with PM10 in a recessive model. A stratified association analysis according to this SNP showed that PM10 in the AG or GG genotype group was not significantly associated with either FEV1 or FVC, whereas in homozygous risk-allele carriers (AA), FEV1 and FVC decreased significantly (by 3.8% and 3.1%, respectively) per 10 μg/m3 of increase in PM10 concentration. This pattern was also reproducible in the independent subgroups that were classified according to recruitment site. The present study replicated the CDH13 gene-by-PM10 interaction effect on lung function at the gene level, revealing that a genetic variant of CDH13 modified the relationship between PM10 and lung function decline in Korean men.
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Affiliation(s)
- Hyun-Jin Kim
- Institute of Health and Environment, Seoul National University, Seoul 08826, South Korea
| | - Jin-Young Min
- Institute of Health and Environment, Seoul National University, Seoul 08826, South Korea
| | - Kyoung-Bok Min
- Department of Preventive Medicine, College of Medicine, Seoul National University, Seoul 03080, South Korea
| | - Yong-Seok Seo
- Institute of Health and Environment, Seoul National University, Seoul 08826, South Korea
| | - Joohon Sung
- Institute of Health and Environment, Seoul National University, Seoul 08826, South Korea
| | - Jae Moon Yun
- Department of Family Medicine, Seoul National University Hospital, Seoul 03080, South Korea
| | - Hyuktae Kwon
- Department of Family Medicine, Seoul National University Hospital, Seoul 03080, South Korea
| | - Belong Cho
- Department of Family Medicine, Seoul National University Hospital, Seoul 03080, South Korea
| | - Jin-Ho Park
- Department of Family Medicine, Seoul National University Hospital, Seoul 03080, South Korea.
| | - Jong-Il Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, South Korea; Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, South Korea.
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Polverino F, Seys LJM, Bracke KR, Owen CA. B cells in chronic obstructive pulmonary disease: moving to center stage. Am J Physiol Lung Cell Mol Physiol 2016; 311:L687-L695. [PMID: 27542809 DOI: 10.1152/ajplung.00304.2016] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 08/15/2016] [Indexed: 12/22/2022] Open
Abstract
Chronic inflammatory responses in the lungs contribute to the development and progression of chronic obstructive pulmonary disease (COPD). Although research studies focused initially on the contributions of the innate immune system to the pathogenesis of COPD, more recent studies have implicated adaptive immune responses in COPD. In particular, studies have demonstrated increases in B cell counts and increases in the number and size of B cell-rich lymphoid follicles in COPD lungs that correlate directly with COPD severity. There are also increases in lung levels of mediators that promote B cell maturation, activation, and survival in COPD patients. B cell products such as autoantibodies directed against lung cells, components of cells, and extracellular matrix proteins are also present in COPD lungs. These autoantibodies may contribute to lung inflammation and injury in COPD patients, in part, by forming immune complexes that activate complement components. Studies of B cell-deficient mice and human COPD patients have linked B cells most strongly to the emphysema phenotype. However, B cells have protective activities during acute exacerbations of COPD by promoting adaptive immune responses that contribute to host defense against pathogens. This review outlines the evidence that links B cells and B cell-rich lymphoid follicles to the pathogenesis of COPD and the mechanisms involved. It also reviews the potential and limitations of B cells as therapeutic targets to slow the progression of human COPD.
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Affiliation(s)
- Francesca Polverino
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts; COPD Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico; University of Parma, Parma, Italy; and
| | - Leen J M Seys
- Laboratory for Translational Research in Obstructive Pulmonary Diseases, Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Ken R Bracke
- Laboratory for Translational Research in Obstructive Pulmonary Diseases, Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Caroline A Owen
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts; COPD Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico;
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Cusanovich DA, Caliskan M, Billstrand C, Michelini K, Chavarria C, De Leon S, Mitrano A, Lewellyn N, Elias JA, Chupp GL, Lang RM, Shah SJ, Decara JM, Gilad Y, Ober C. Integrated analyses of gene expression and genetic association studies in a founder population. Hum Mol Genet 2016; 25:2104-2112. [PMID: 26931462 PMCID: PMC5062579 DOI: 10.1093/hmg/ddw061] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 02/21/2016] [Indexed: 12/17/2022] Open
Abstract
Genome-wide association studies (GWASs) have become a standard tool for dissecting genetic contributions to disease risk. However, these studies typically require extraordinarily large sample sizes to be adequately powered. Strategies that incorporate functional information alongside genetic associations have proved successful in increasing GWAS power. Following this paradigm, we present the results of 20 different genetic association studies for quantitative traits related to complex diseases, conducted in the Hutterites of South Dakota. To boost the power of these association studies, we collected RNA-sequencing data from lymphoblastoid cell lines for 431 Hutterite individuals. We then used Sherlock, a tool that integrates GWAS and expression quantitative trait locus (eQTL) data, to identify weak GWAS signals that are also supported by eQTL data. Using this approach, we found novel associations with quantitative phenotypes related to cardiovascular disease, including carotid intima-media thickness, left atrial volume index, monocyte count and serum YKL-40 levels.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jack A Elias
- Division of Biology and Medicine, Brown University, Providence, RI 02912, USA and
| | - Geoffrey L Chupp
- Pulmonary and Critical Care, Yale School of Medicine, New Haven, CT 06519, USA
| | - Roberto M Lang
- Department of Medicine, Section of Cardiology, University of Chicago, Chicago, IL 60637, USA
| | - Sanjiv J Shah
- Department of Medicine, Section of Cardiology, University of Chicago, Chicago, IL 60637, USA
| | - Jeanne M Decara
- Department of Medicine, Section of Cardiology, University of Chicago, Chicago, IL 60637, USA
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35
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Yamada H, Masuko H, Yatagai Y, Sakamoto T, Kaneko Y, Iijima H, Naito T, Noguchi E, Konno S, Nishimura M, Hirota T, Tamari M, Hizawa N. Role of Lung Function Genes in the Development of Asthma. PLoS One 2016; 11:e0145832. [PMID: 26752288 PMCID: PMC4709100 DOI: 10.1371/journal.pone.0145832] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Accepted: 12/09/2015] [Indexed: 12/02/2022] Open
Abstract
Although our previous GWAS failed to identify SNPs associated with pulmonary function at the level of genomewide significance, it did show that the heritability for FEV1/FVC was 41.6% in a Japanese population, suggesting that the heritability of pulmonary function traits can be explained by the additive effects of multiple common SNPs. In addition, our previous study indicated that pulmonary function genes identified in previous GWASs in non-Japanese populations accounted for 4.3% to 12.0% of the entire estimated heritability of FEV1/FVC in a Japanese population. Therefore, given that many loci with individual weak effects may contribute to asthma risk, in this study, we created a quantitative score of genetic load based on 16 SNPs implicated in lower lung function in both Japanese and non-Japanese populations. This genetic risk score (GRS) for lower FEV1/FVC was consistently associated with the onset of asthma (P = 9.6 × 10(-4)) in 2 independent Japanese populations as well as with the onset of COPD (P = 0.042). Clustering of asthma patients based on GRS levels indicated that an increased GRS may be responsible for the development of a particular phenotype of asthma characterized by early onset, atopy, and severer airflow obstruction.
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Affiliation(s)
- Hideyasu Yamada
- Department of Pulmonology, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hironori Masuko
- Department of Pulmonology, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yohei Yatagai
- Department of Pulmonology, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Tohru Sakamoto
- Department of Pulmonology, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yoshiko Kaneko
- Department of Pulmonology, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | | | | | - Emiko Noguchi
- Department of Medical Genetics, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Satoshi Konno
- Laboratory for Respiratory Diseases, Center for Genomic Medicine, Institute of Physical and Chemical Research, Tsurumi, Kanagawa, Japan
| | - Masaharu Nishimura
- Laboratory for Respiratory Diseases, Center for Genomic Medicine, Institute of Physical and Chemical Research, Tsurumi, Kanagawa, Japan
| | - Tomomitsu Hirota
- First Department of Medicine, School of Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Mayumi Tamari
- First Department of Medicine, School of Medicine, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Nobuyuki Hizawa
- Department of Pulmonology, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
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36
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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
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37
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Genome-Wide Association Studies of the Human Gut Microbiota. PLoS One 2015; 10:e0140301. [PMID: 26528553 PMCID: PMC4631601 DOI: 10.1371/journal.pone.0140301] [Citation(s) in RCA: 176] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 09/05/2015] [Indexed: 12/17/2022] Open
Abstract
The bacterial composition of the human fecal microbiome is influenced by many lifestyle factors, notably diet. It is less clear, however, what role host genetics plays in dictating the composition of bacteria living in the gut. In this study, we examined the association of ~200K host genotypes with the relative abundance of fecal bacterial taxa in a founder population, the Hutterites, during two seasons (n = 91 summer, n = 93 winter, n = 57 individuals collected in both). These individuals live and eat communally, minimizing variation due to environmental exposures, including diet, which could potentially mask small genetic effects. Using a GWAS approach that takes into account the relatedness between subjects, we identified at least 8 bacterial taxa whose abundances were associated with single nucleotide polymorphisms in the host genome in each season (at genome-wide FDR of 20%). For example, we identified an association between a taxon known to affect obesity (genus Akkermansia) and a variant near PLD1, a gene previously associated with body mass index. Moreover, we replicate a previously reported association from a quantitative trait locus (QTL) mapping study of fecal microbiome abundance in mice (genus Lactococcus, rs3747113, P = 3.13 x 10−7). Finally, based on the significance distribution of the associated microbiome QTLs in our study with respect to chromatin accessibility profiles, we identified tissues in which host genetic variation may be acting to influence bacterial abundance in the gut.
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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.
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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
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Livne OE, Han L, Alkorta-Aranburu G, Wentworth-Sheilds W, Abney M, Ober C, Nicolae DL. PRIMAL: Fast and accurate pedigree-based imputation from sequence data in a founder population. PLoS Comput Biol 2015; 11:e1004139. [PMID: 25735005 PMCID: PMC4348507 DOI: 10.1371/journal.pcbi.1004139] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 01/19/2015] [Indexed: 12/31/2022] Open
Abstract
Founder populations and large pedigrees offer many well-known advantages for genetic mapping studies, including cost-efficient study designs. Here, we describe PRIMAL (PedigRee IMputation ALgorithm), a fast and accurate pedigree-based phasing and imputation algorithm for founder populations. PRIMAL incorporates both existing and original ideas, such as a novel indexing strategy of Identity-By-Descent (IBD) segments based on clique graphs. We were able to impute the genomes of 1,317 South Dakota Hutterites, who had genome-wide genotypes for ~300,000 common single nucleotide variants (SNVs), from 98 whole genome sequences. Using a combination of pedigree-based and LD-based imputation, we were able to assign 87% of genotypes with >99% accuracy over the full range of allele frequencies. Using the IBD cliques we were also able to infer the parental origin of 83% of alleles, and genotypes of deceased recent ancestors for whom no genotype information was available. This imputed data set will enable us to better study the relative contribution of rare and common variants on human phenotypes, as well as parental origin effect of disease risk alleles in >1,000 individuals at minimal cost.
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Affiliation(s)
- Oren E. Livne
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Lide Han
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Gorka Alkorta-Aranburu
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - William Wentworth-Sheilds
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Mark Abney
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Carole Ober
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Dan L. Nicolae
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
- Departments of Medicine, and Statistics, The University of Chicago, Chicago, Illinois, United States of America
- * E-mail:
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Tessier A, Bertrand J, Chenel M, Comets E. Comparison of Nonlinear Mixed Effects Models and Noncompartmental Approaches in Detecting Pharmacogenetic Covariates. AAPS JOURNAL 2015; 17:597-608. [PMID: 25693489 DOI: 10.1208/s12248-015-9726-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 01/28/2015] [Indexed: 11/30/2022]
Abstract
Genetic data is now collected in many clinical trials, especially in population pharmacokinetic studies. There is no consensus on methods to test the association between pharmacokinetics and genetic covariates. We performed a simulation study inspired by real clinical trials, using the pharmacokinetics (PK) of a compound under development having a nonlinear bioavailability along with genotypes for 176 single nucleotide polymorphisms (SNPs). Scenarios included 78 subjects extensively sampled (16 observations per subject) to simulate a phase I study, or 384 subjects with the same rich design. Under the alternative hypothesis (H1), six SNPs were drawn randomly to affect the log-clearance under an additive linear model. For each scenario, 200 PK data sets were simulated under the null hypothesis (no gene effect) and H1. We compared 16 combinations of four association tests, a stepwise procedure and three penalised regressions (ridge regression, Lasso, HyperLasso), applied to four pharmacokinetic phenotypes, two observed concentrations, area under the curve estimated by noncompartmental analysis and model-based clearance. The different combinations were compared in terms of true and false positives and probability to detect the genetic effects. In presence of nonlinearity and/or variability in bioavailability, model-based phenotype allowed a higher probability to detect the SNPs than other phenotypes. In a realistic setting with a limited number of subjects, all methods showed a low ability to detect genetic effects. Ridge regression had the best probability to detect SNPs, but also a higher number of false positives. No association test showed a much higher power than the others.
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Affiliation(s)
- Adrien Tessier
- INSERM, IAME, UMR 1137, Faculté de médecine Paris Diderot Paris 7 - site Bichat, 16 rue Henri Huchard, 75018, Paris, France,
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Kim S, Kim H, Cho N, Lee SK, Han BG, Sull JW, Jee SH, Shin C. Identification of FAM13A gene associated with the ratio of FEV1 to FVC in Korean population by genome-wide association studies including gene-environment interactions. J Hum Genet 2015; 60:139-45. [PMID: 25608829 DOI: 10.1038/jhg.2014.118] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 11/28/2014] [Accepted: 12/09/2014] [Indexed: 01/12/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) is a complex, multifactorial disease. Although smoking is a main risk factor for obstructive impairment, not all smokers develop this critical disease. We conducted a genome-wide association study to identify the association between genetic variants and pulmonary function and also examined how these variants relate to lung impairment in accordance with smoking behaviors. Using two community-based cohorts, the Ansan cohort (n=4319) and the Ansung cohort (n=3674), in the Korean Genome Epidemiology Study, we analyzed the association between genetic variants (single-nucleotide polymorphisms and haplotypes) and the ratio of FEV1 to FVC (FEV1/FVC) using multivariate linear regression models. Similar analyses were conducted after stratification by smoking status. Four genome-wide significant signals in the FAM13A gene (the strongest signal at rs2609264, P=1.76 × 10(-7) in a combined set) were associated with FEV1/FVC. For the association with ratio, the effect size in the CTGA haplotype (risk haplotype) was -0.57% (s.e., 0.11; P=2.10 × 10(-7)) as compared with the TCAG haplotype (reference haplotype) in a combined set. There was also a significant interaction of FAM13A haplotypes with heavy smoking on FEV1/FVC (P for interaction=0.028). We confirmed the previously reported association of FAM13A in 4q22.1 with pulmonary function. The FAM13A haplotypes also interacted with heavy smoking to affect the risk of reduced pulmonary function.
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Affiliation(s)
- Soriul Kim
- 1] Institute of Human Genomic Study, Ansan Hospital, Korea University, Ansan, Republic of Korea [2] Department of Public Health, Graduate School, Yonsei University, Seoul, Republic of Korea
| | - Hyun Kim
- Institute of Human Genomic Study, Ansan Hospital, Korea University, Ansan, Republic of Korea
| | - Namhan Cho
- Department of Preventive Medicine, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Seung Ku Lee
- Institute of Human Genomic Study, Ansan Hospital, Korea University, Ansan, Republic of Korea
| | - Bok-Ghee Han
- Center for Genome Science, National Institute of Health, Cheongwon, Republic of Korea
| | - Jae Woong Sull
- Department of Bio-Medical Laboratory Science, College of Health Science, Eulji University, Sungnam, Republic of Korea
| | - Sun Ha Jee
- Department of Epidemiology and Health Promotion, Graduate School of Public Health, Yonsei University, Seoul, Republic of Korea
| | - Chol Shin
- 1] Institute of Human Genomic Study, Ansan Hospital, Korea University, Ansan, Republic of Korea [2] Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Korea University Ansan Hospital, Ansan, Republic of Korea
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Ganguly K, Martin TM, Concel VJ, Upadhyay S, Bein K, Brant KA, George L, Mitra A, Thimraj TA, Fabisiak JP, Vuga LJ, Fattman C, Kaminski N, Schulz H, Leikauf GD. Secreted phosphoprotein 1 is a determinant of lung function development in mice. Am J Respir Cell Mol Biol 2015; 51:637-51. [PMID: 24816281 DOI: 10.1165/rcmb.2013-0471oc] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Secreted phosphoprotein 1 (Spp1) is located within quantitative trait loci associated with lung function that was previously identified by contrasting C3H/HeJ and JF1/Msf mouse strains that have extremely divergent lung function. JF1/Msf mice with diminished lung function had reduced lung SPP1 transcript and protein during the peak stage of alveologenesis (postnatal day [P]14-P28) as compared with C3H/HeJ mice. In addition to a previously identified genetic variant that altered runt-related transcription factor 2 (RUNX2) binding in the Spp1 promoter, we identified another promoter variant in a putative RUNX2 binding site that increased the DNA protein binding. SPP1 induced dose-dependent mouse lung epithelial-15 cell proliferation. Spp1((-/-)) mice have decreased specific total lung capacity/body weight, higher specific compliance, and increased mean airspace chord length (Lm) compared with Spp1((+/+)) mice. Microarray analysis revealed enriched gene ontogeny categories, with numerous genes associated with lung development and/or respiratory disease. Insulin-like growth factor 1, Hedgehog-interacting protein, wingless-related mouse mammary tumor virus integration site 5A, and NOTCH1 transcripts decreased in the lung of P14 Spp1((-/-)) mice as determined by quantitative RT-PCR analysis. SPP1 promotes pneumocyte growth, and mice lacking SPP1 have smaller, more compliant lungs with enlarged airspace (i.e., increased Lm). Microarray analysis suggests a dysregulation of key lung developmental transcripts in gene-targeted Spp1((-/-)) mice, particularly during the peak phase of alveologenesis. In addition to its known roles in lung disease, this study supports SPP1 as a determinant of lung development in mice.
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Affiliation(s)
- Koustav Ganguly
- 1 Department of Environmental and Occupational Health, Graduate School of Public Health
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Aoshiba K, Tsuji T, Itoh M, Yamaguchi K, Nakamura H. An evolutionary medicine approach to understanding factors that contribute to chronic obstructive pulmonary disease. Respiration 2015; 89:243-52. [PMID: 25677028 DOI: 10.1159/000369861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 11/04/2014] [Indexed: 02/05/2023] Open
Abstract
Although many studies have been published on the causes and mechanisms of chronic obstructive pulmonary disease (COPD), the reason for the existence of COPD and the reasons why COPD develops in humans have hardly been studied. Evolutionary medical approaches are required to explain not only the proximate factors, such as the causes and mechanisms of a disease, but the ultimate (evolutionary) factors as well, such as why the disease is present and why the disease develops in humans. According to the concepts of evolutionary medicine, disease susceptibility is acquired as a result of natural selection during the evolutionary process of traits linked to the genes involved in disease susceptibility. In this paper, we discuss the following six reasons why COPD develops in humans based on current evolutionary medical theories: (1) evolutionary constraints; (2) mismatch between environmental changes and evolution; (3) co-evolution with pathogenic microorganisms; (4) life history trade-off; (5) defenses and their costs, and (6) reproductive success at the expense of health. Our perspective pursues evolutionary answers to the fundamental question, 'Why are humans susceptible to this common disease, COPD, despite their long evolutionary history?' We believe that the perspectives offered by evolutionary medicine are essential for researchers to better understand the significance of their work.
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Affiliation(s)
- Kazutetsu Aoshiba
- Department of Respiratory Medicine, Tokyo Medical University Ibaraki Medical Center, Inashiki, Japan
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Yao TC, Tu YL, Chang SW, Tsai HJ, Gu PW, Ning HC, Hua MC, Liao SL, Tsai MH, Chiu CY, Lai SH, Yeh KW, Huang JL. Serum 25-hydroxyvitamin D levels in relation to lung function and exhaled nitric oxide in children. J Pediatr 2014; 165:1098-1103.e1. [PMID: 25282066 DOI: 10.1016/j.jpeds.2014.08.048] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 07/18/2014] [Accepted: 08/22/2014] [Indexed: 01/01/2023]
Abstract
OBJECTIVE To investigate the relationship of vitamin D status with lung function and fraction of exhaled nitric oxide (FeNO) in a population sample of children. STUDY DESIGN A total of 1315 children aged 5-18 years were evaluated using serum 25-hydroxyvitamin D [25(OH)D] levels, spirometry, a single-breath online FeNO measurement, and questionnaires. RESULTS After adjusting for confounders, the mean forced vital capacity was 53.4 mL (SE, 26.5 mL; P = .045), and the mean forced expiratory volume in 1 second was 48.2 mL (SE, 23.6 mL; P = .042) lower for children with insufficient serum 25(OH)D levels (20-29.9 ng/mL) compared with those with sufficient 25(OH)D levels (≥30 ng/mL). The mean difference between children with deficient (<20 ng/mL) and sufficient levels of serum 25(OH)D was 81.9 mL (SE, 26.7 mL; P = .002) for forced vital capacity and 55.2 mL (SE, 23.7 mL; P = .020) for forced expiratory volume in 1 second. There was no significant association between serum 25(OH)D levels and FeNO after adjusting for confounders. CONCLUSIONS Our results demonstrate a significant relationship between insufficient serum vitamin D levels and worse lung function in children in the community with a suggested dose-response effect. Our findings also suggest that vitamin D status is not a significant determinant of FeNO in children in the general population.
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Affiliation(s)
- Tsung-Chieh Yao
- Division of Allergy, Asthma, and Rheumatology, Department of Pediatrics, Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan, Taiwan; Community Medicine Research Center, Chang Gung Memorial Hospital at Keelung, Keelung, Taiwan.
| | - Yu-Ling Tu
- Division of Allergy, Asthma, and Rheumatology, Department of Pediatrics, Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan, Taiwan; Community Medicine Research Center, Chang Gung Memorial Hospital at Keelung, Keelung, Taiwan; Graduate Institute of Clinical Medical Sciences, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Su-Wei Chang
- Clinical Informatics and Medical Statistics Research Center, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Hui-Ju Tsai
- Division of Biostatistics and Bioinformatics, Institutes of Population Health Sciences, National Health Research Institutes, Miaoli, Taiwan; Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL; Department of Genome Medicine, Kaohsiung University, Kaohsiung, Taiwan
| | - Po-Wen Gu
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Hsian-Chen Ning
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Man-Chin Hua
- Community Medicine Research Center, Chang Gung Memorial Hospital at Keelung, Keelung, Taiwan; Department of Pediatrics, Chang Gung Memorial Hospital at Keelung, Keelung, Taiwan
| | - Sui-Ling Liao
- Community Medicine Research Center, Chang Gung Memorial Hospital at Keelung, Keelung, Taiwan; Department of Pediatrics, Chang Gung Memorial Hospital at Keelung, Keelung, Taiwan
| | - Ming-Han Tsai
- Community Medicine Research Center, Chang Gung Memorial Hospital at Keelung, Keelung, Taiwan; Department of Pediatrics, Chang Gung Memorial Hospital at Keelung, Keelung, Taiwan
| | - Chih-Yung Chiu
- Community Medicine Research Center, Chang Gung Memorial Hospital at Keelung, Keelung, Taiwan; Department of Pediatrics, Chang Gung Memorial Hospital at Keelung, Keelung, Taiwan
| | - Shen-Hao Lai
- Community Medicine Research Center, Chang Gung Memorial Hospital at Keelung, Keelung, Taiwan; Division of Pediatric Pulmonology, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Kuo-Wei Yeh
- Division of Allergy, Asthma, and Rheumatology, Department of Pediatrics, Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan, Taiwan; Community Medicine Research Center, Chang Gung Memorial Hospital at Keelung, Keelung, Taiwan
| | - Jing-Long Huang
- Division of Allergy, Asthma, and Rheumatology, Department of Pediatrics, Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan, Taiwan; Community Medicine Research Center, Chang Gung Memorial Hospital at Keelung, Keelung, Taiwan.
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Abstract
Genome-wide association studies (GWAS) have been employed in the field of allergic disease, and significant associations have been published for nearly 100 asthma genes/loci. An outcome of GWAS in allergic disease has been the formation of national and international collaborations leading to consortia meta-analyses, and an appreciation for the specificity of genetic associations to sub-phenotypes of allergic disease. Molecular genetics has undergone a technological revolution, leading to next-generation sequencing strategies that are increasingly employed to hone in on the causal variants associated with allergic diseases. Unmet needs include the inclusion of diverse cohorts and strategies for managing big data.
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Affiliation(s)
- Romina A Ortiz
- Department of Medicine, The Johns Hopkins Asthma and Allergy Center, 5501 Hopkins Bayview Circle, Room 3A.62, Baltimore, MD 21224, USA
| | - Kathleen C Barnes
- Department of Medicine, The Johns Hopkins Asthma and Allergy Center, 5501 Hopkins Bayview Circle, Room 3A.62, Baltimore, MD 21224, USA.
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Campbell CD, Mohajeri K, Malig M, Hormozdiari F, Nelson B, Du G, Patterson KM, Eng C, Torgerson DG, Hu D, Herman C, Chong JX, Ko A, O'Roak BJ, Krumm N, Vives L, Lee C, Roth LA, Rodriguez-Cintron W, Rodriguez-Santana J, Brigino-Buenaventura E, Davis A, Meade K, LeNoir MA, Thyne S, Jackson DJ, Gern JE, Lemanske RF, Shendure J, Abney M, Burchard EG, Ober C, Eichler EE. Whole-genome sequencing of individuals from a founder population identifies candidate genes for asthma. PLoS One 2014; 9:e104396. [PMID: 25116239 PMCID: PMC4130548 DOI: 10.1371/journal.pone.0104396] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 07/12/2014] [Indexed: 12/30/2022] Open
Abstract
Asthma is a complex genetic disease caused by a combination of genetic and environmental risk factors. We sought to test classes of genetic variants largely missed by genome-wide association studies (GWAS), including copy number variants (CNVs) and low-frequency variants, by performing whole-genome sequencing (WGS) on 16 individuals from asthma-enriched and asthma-depleted families. The samples were obtained from an extended 13-generation Hutterite pedigree with reduced genetic heterogeneity due to a small founding gene pool and reduced environmental heterogeneity as a result of a communal lifestyle. We sequenced each individual to an average depth of 13-fold, generated a comprehensive catalog of genetic variants, and tested the most severe mutations for association with asthma. We identified and validated 1960 CNVs, 19 nonsense or splice-site single nucleotide variants (SNVs), and 18 insertions or deletions that were out of frame. As follow-up, we performed targeted sequencing of 16 genes in 837 cases and 540 controls of Puerto Rican ancestry and found that controls carry a significantly higher burden of mutations in IL27RA (2.0% of controls; 0.23% of cases; nominal p = 0.004; Bonferroni p = 0.21). We also genotyped 593 CNVs in 1199 Hutterite individuals. We identified a nominally significant association (p = 0.03; Odds ratio (OR) = 3.13) between a 6 kbp deletion in an intron of NEDD4L and increased risk of asthma. We genotyped this deletion in an additional 4787 non-Hutterite individuals (nominal p = 0.056; OR = 1.69). NEDD4L is expressed in bronchial epithelial cells, and conditional knockout of this gene in the lung in mice leads to severe inflammation and mucus accumulation. Our study represents one of the early instances of applying WGS to complex disease with a large environmental component and demonstrates how WGS can identify risk variants, including CNVs and low-frequency variants, largely untested in GWAS.
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Affiliation(s)
- Catarina D. Campbell
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Kiana Mohajeri
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Maika Malig
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Fereydoun Hormozdiari
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Benjamin Nelson
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Gaixin Du
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Kristen M. Patterson
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Celeste Eng
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Dara G. Torgerson
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Donglei Hu
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Catherine Herman
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Jessica X. Chong
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Arthur Ko
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Brian J. O'Roak
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Niklas Krumm
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Laura Vives
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Choli Lee
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Lindsey A. Roth
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | | | | | - Emerita Brigino-Buenaventura
- Department of Allergy & Immunology, Kaiser Permanente-Vallejo Medical Center, Vallejo, California, United States of America
| | - Adam Davis
- Children's Hospital and Research Center Oakland, Oakland, California, United States of America
| | - Kelley Meade
- Children's Hospital and Research Center Oakland, Oakland, California, United States of America
| | | | - Shannon Thyne
- San Francisco General Hospital, San Francisco, California, and the Department of Pediatrics, University of California San Francisco, San Francisco, California, United States of America
| | - Daniel J. Jackson
- Department of Pediatrics, University of Wisconsin, Madison, Wisconsin, United States of America
| | - James E. Gern
- Department of Pediatrics, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Robert F. Lemanske
- Department of Pediatrics, University of Wisconsin, Madison, Wisconsin, United States of America
- Department of Medicine, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Mark Abney
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Esteban G. Burchard
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
| | - Carole Ober
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Seattle, Washington, United States of America
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Anderson RL, Murray K, Chong JX, Ouwenga R, Antillon M, Chen P, Diaz de Leon L, Swoboda KJ, Lester LA, Das S, Ober C, Waggoner DJ. Disclosure of genetic research results to members of a founder population. J Genet Couns 2014; 23:984-91. [PMID: 24777552 DOI: 10.1007/s10897-014-9721-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 04/01/2014] [Indexed: 11/29/2022]
Abstract
There is currently extensive discussion and debate in the literature on how, when, and to whom genetic research results should be returned (see Genetics in Medicine, April 2012 issue). Here, we describe our experience in disclosing genetic information on Mendelian disorders discovered during the course of our research in the Hutterites. We first assessed attitudes toward the disclosure of carrier results, which revealed that many individuals wanted carrier information and that many intended to use the information in family planning. Based on this information, we developed a pilot study to test and disclose cystic fibrosis (CF) carrier status. Next, a larger scale project was developed in order to disclose genetic research results for 14 diseases to those interested in receiving the information. We developed brochures, offered a live interactive educational program, conducted a consent process, and disclosed results in letters mailed to the consented individuals. Overall, ~80% of individuals who participated in the educational program signed consent forms for the release of their results for 14 diseases. We describe our experience with returning individual genetic research results to participants in a population-based research study.
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Affiliation(s)
- Rebecca L Anderson
- Department of Human Genetics, University of Chicago, 5841 S. Maryland Ave. M/C 0077, Chicago, IL, 60637, USA
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