251
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Wain LV, Sayers I, Soler Artigas M, Portelli MA, Zeggini E, Obeidat M, Sin DD, Bossé Y, Nickle D, Brandsma CA, Malarstig A, Vangjeli C, Jelinsky SA, John S, Kilty I, McKeever T, Shrine NRG, Cook JP, Patel S, Spector TD, Hollox EJ, Hall IP, Tobin MD. Whole exome re-sequencing implicates CCDC38 and cilia structure and function in resistance to smoking related airflow obstruction. PLoS Genet 2014; 10:e1004314. [PMID: 24786987 PMCID: PMC4006731 DOI: 10.1371/journal.pgen.1004314] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 03/06/2014] [Indexed: 11/19/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a leading cause of global morbidity and mortality and, whilst smoking remains the single most important risk factor, COPD risk is heritable. Of 26 independent genomic regions showing association with lung function in genome-wide association studies, eleven have been reported to show association with airflow obstruction. Although the main risk factor for COPD is smoking, some individuals are observed to have a high forced expired volume in 1 second (FEV1) despite many years of heavy smoking. We hypothesised that these "resistant smokers" may harbour variants which protect against lung function decline caused by smoking and provide insight into the genetic determinants of lung health. We undertook whole exome re-sequencing of 100 heavy smokers who had healthy lung function given their age, sex, height and smoking history and applied three complementary approaches to explore the genetic architecture of smoking resistance. Firstly, we identified novel functional variants in the "resistant smokers" and looked for enrichment of these novel variants within biological pathways. Secondly, we undertook association testing of all exonic variants individually with two independent control sets. Thirdly, we undertook gene-based association testing of all exonic variants. Our strongest signal of association with smoking resistance for a non-synonymous SNP was for rs10859974 (P = 2.34 × 10(-4)) in CCDC38, a gene which has previously been reported to show association with FEV1/FVC, and we demonstrate moderate expression of CCDC38 in bronchial epithelial cells. We identified an enrichment of novel putatively functional variants in genes related to cilia structure and function in resistant smokers. Ciliary function abnormalities are known to be associated with both smoking and reduced mucociliary clearance in patients with COPD. We suggest that genetic influences on the development or function of cilia in the bronchial epithelium may affect growth of cilia or the extent of damage caused by tobacco smoke.
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Affiliation(s)
- Louise V. Wain
- University of Leicester, Department of Health Sciences, Leicester, United Kingdom
- * E-mail:
| | - Ian Sayers
- Division of Respiratory Medicine, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom
| | - María Soler Artigas
- University of Leicester, Department of Health Sciences, Leicester, United Kingdom
| | - Michael A. Portelli
- Division of Respiratory Medicine, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom
| | | | - Ma'en Obeidat
- University of British Columbia Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, Canada
| | - Don D. Sin
- University of British Columbia Centre for Heart Lung Innovation, St. Paul's Hospital, Vancouver, Canada
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec, Department of Molecular Medicine, Laval University, Québec, Canada
| | - David Nickle
- Merck Research Laboratories, Boston, Massachusetts, United States of America
- Merck, Rahway, New Jersey, United States of America
| | - Corry-Anke Brandsma
- University of Groningen, University Medical Center Groningen, Department of Pathology and Medical Biology, GRIAC Research Institute, Groningen, The Netherlands
| | | | | | - Scott A. Jelinsky
- Pfizer Worldwide R&D, Cambridge, Massachusetts, United States of America
| | - Sally John
- Pfizer Worldwide R&D, Cambridge, Massachusetts, United States of America
| | - Iain Kilty
- Pfizer Worldwide R&D, Cambridge, Massachusetts, United States of America
| | - Tricia McKeever
- School of Community Health Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Nick R. G. Shrine
- University of Leicester, Department of Health Sciences, Leicester, United Kingdom
| | - James P. Cook
- University of Leicester, Department of Health Sciences, Leicester, United Kingdom
| | - Shrina Patel
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Tim D. Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Edward J. Hollox
- University of Leicester, Department of Genetics, Leicester, United Kingdom
| | - Ian P. Hall
- Division of Respiratory Medicine, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom
| | - Martin D. Tobin
- University of Leicester, Department of Health Sciences, Leicester, United Kingdom
- National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, United Kingdom
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252
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Vucic EA, Chari R, Thu KL, Wilson IM, Cotton AM, Kennett JY, Zhang M, Lonergan KM, Steiling K, Brown CJ, McWilliams A, Ohtani K, Lenburg ME, Sin DD, Spira A, MacAulay CE, Lam S, Lam WL. DNA methylation is globally disrupted and associated with expression changes in chronic obstructive pulmonary disease small airways. Am J Respir Cell Mol Biol 2014; 50:912-22. [PMID: 24298892 PMCID: PMC4068945 DOI: 10.1165/rcmb.2013-0304oc] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 12/03/2013] [Indexed: 01/06/2023] Open
Abstract
DNA methylation is an epigenetic modification that is highly disrupted in response to cigarette smoke and involved in a wide spectrum of malignant and nonmalignant diseases, but surprisingly not previously assessed in small airways of patients with chronic obstructive pulmonary disease (COPD). Small airways are the primary sites of airflow obstruction in COPD. We sought to determine whether DNA methylation patterns are disrupted in small airway epithelia of patients with COPD, and evaluate whether changes in gene expression are associated with these disruptions. Genome-wide methylation and gene expression analysis were performed on small airway epithelial DNA and RNA obtained from the same patient during bronchoscopy, using Illumina's Infinium HM27 and Affymetrix's Genechip Human Gene 1.0 ST arrays. To control for known effects of cigarette smoking on DNA methylation, methylation and gene expression profiles were compared between former smokers with and without COPD matched for age, pack-years, and years of smoking cessation. Our results indicate that aberrant DNA methylation is (1) a genome-wide phenomenon in small airways of patients with COPD, and (2) associated with altered expression of genes and pathways important to COPD, such as the NF-E2-related factor 2 oxidative response pathway. DNA methylation is likely an important mechanism contributing to modulation of genes important to COPD pathology. Because these methylation events may underlie disease-specific gene expression changes, their characterization is a critical first step toward the development of epigenetic markers and an opportunity for developing novel epigenetic therapeutic interventions for COPD.
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Affiliation(s)
- Emily A. Vucic
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Raj Chari
- Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Kelsie L. Thu
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Ian M. Wilson
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Allison M. Cotton
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jennifer Y. Kennett
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - May Zhang
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Kim M. Lonergan
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Katrina Steiling
- Division of Computational Biomedicine, Department of Medicine, Boston University Medical Center, Boston, Massachusetts; and
| | - Carolyn J. Brown
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Annette McWilliams
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Keishi Ohtani
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Marc E. Lenburg
- Division of Computational Biomedicine, Department of Medicine, Boston University Medical Center, Boston, Massachusetts; and
| | - Don D. Sin
- University of British Columbia James Hogg Research Centre and the Institute of Heart and Lung Health, St. Paul’s Hospital, Vancouver, British Columbia, Canada
| | - Avrum Spira
- Division of Computational Biomedicine, Department of Medicine, Boston University Medical Center, Boston, Massachusetts; and
| | - Calum E. MacAulay
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Stephen Lam
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Wan L. Lam
- Department of Integrative Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
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253
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Longer telomere length in COPD patients with α1-antitrypsin deficiency independent of lung function. PLoS One 2014; 9:e95600. [PMID: 24763308 PMCID: PMC3998943 DOI: 10.1371/journal.pone.0095600] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 03/28/2014] [Indexed: 01/22/2023] Open
Abstract
Oxidative stress is involved in the pathogenesis of airway obstruction in α1-antitrypsin deficient patients. This may result in a shortening of telomere length, resulting in cellular senescence. To test whether telomere length differs in α1-antitrypsin deficient patients compared with controls, we measured telomere length in DNA from peripheral blood cells of 217 α1-antitrypsin deficient patients and 217 control COPD patients. We also tested for differences in telomere length between DNA from blood and DNA from lung tissue in a subset of 51 controls. We found that telomere length in the blood was significantly longer in α1-antitrypsin deficient COPD patients compared with control COPD patients (p = 1×10−29). Telomere length was not related to lung function in α1-antitrypsin deficient patients (p = 0.3122) or in COPD controls (p = 0.1430). Although mean telomere length was significantly shorter in the blood when compared with the lungs (p = 0.0078), telomere length was correlated between the two tissue types (p = 0.0122). Our results indicate that telomere length is better preserved in α1-antitrypsin deficient COPD patients than in non-deficient patients. In addition, measurement of telomere length in the blood may be a suitable surrogate for measurement in the lung.
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254
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Susceptibility to chronic mucus hypersecretion, a genome wide association study. PLoS One 2014; 9:e91621. [PMID: 24714607 PMCID: PMC3979657 DOI: 10.1371/journal.pone.0091621] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 11/21/2013] [Indexed: 01/04/2023] Open
Abstract
Background Chronic mucus hypersecretion (CMH) is associated with an increased frequency of respiratory infections, excess lung function decline, and increased hospitalisation and mortality rates in the general population. It is associated with smoking, but it is unknown why only a minority of smokers develops CMH. A plausible explanation for this phenomenon is a predisposing genetic constitution. Therefore, we performed a genome wide association (GWA) study of CMH in Caucasian populations. Methods GWA analysis was performed in the NELSON-study using the Illumina 610 array, followed by replication and meta-analysis in 11 additional cohorts. In total 2,704 subjects with, and 7,624 subjects without CMH were included, all current or former heavy smokers (≥20 pack-years). Additional studies were performed to test the functional relevance of the most significant single nucleotide polymorphism (SNP). Results A strong association with CMH, consistent across all cohorts, was observed with rs6577641 (p = 4.25×10−6, OR = 1.17), located in intron 9 of the special AT-rich sequence-binding protein 1 locus (SATB1) on chromosome 3. The risk allele (G) was associated with higher mRNA expression of SATB1 (4.3×10−9) in lung tissue. Presence of CMH was associated with increased SATB1 mRNA expression in bronchial biopsies from COPD patients. SATB1 expression was induced during differentiation of primary human bronchial epithelial cells in culture. Conclusions Our findings, that SNP rs6577641 is associated with CMH in multiple cohorts and is a cis-eQTL for SATB1, together with our additional observation that SATB1 expression increases during epithelial differentiation provide suggestive evidence that SATB1 is a gene that affects CMH.
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255
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Burkart KM, Manichaikul A, Wilk JB, Ahmed FS, Burke GL, Enright P, Hansel NN, Haynes D, Heckbert SR, Hoffman EA, Kaufman JD, Kurai J, Loehr L, London SJ, Meng Y, O’Connor GT, Oelsner E, Petrini M, Pottinger TD, Powell CA, Redline S, Rotter JI, Smith LJ, Artigas MS, Tobin MD, Tsai MY, Watson K, White W, Young TR, Rich SS, Barr RG. APOM and high-density lipoprotein cholesterol are associated with lung function and per cent emphysema. Eur Respir J 2014; 43:1003-17. [PMID: 23900982 PMCID: PMC4041087 DOI: 10.1183/09031936.00147612] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is linked to cardiovascular disease; however, there are few studies on the associations of cardiovascular genes with COPD. We assessed the association of lung function with 2100 genes selected for cardiovascular diseases among 20 077 European-Americans and 6900 African-Americans. We performed replication of significant loci in the other racial group and an independent consortium of Europeans, tested the associations of significant loci with per cent emphysema and examined gene expression in an independent sample. We then tested the association of a related lipid biomarker with forced expiratory volume in 1 s (FEV1)/forced vital capacity (FVC) ratio and per cent emphysema. We identified one new polymorphism for FEV1/FVC (rs805301) in European-Americans (p=1.3×10(-6)) and a second (rs707974) in the combined European-American and African-American analysis (p=1.38×10(-7)). Both single-nucleotide polymorphisms (SNPs) flank the gene for apolipoprotein M (APOM), a component of high-density lipoprotein (HDL) cholesterol. Both were replicated in an independent cohort. SNPs in a second gene related to apolipoprotein M and HDL, PCSK9, were associated with FEV1/FVC ratio among African-Americans. rs707974 was associated with per cent emphysema among European-Americans and African-Americans and APOM expression was related to FEV1/FVC ratio and per cent emphysema. Higher HDL levels were associated with lower FEV1/FVC ratio and greater per cent emphysema. These findings suggest a novel role for the apolipoprotein M/HDL pathway in the pathogenesis of COPD and emphysema.
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Affiliation(s)
- Kristin M Burkart
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA
| | - Jemma B Wilk
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Firas S Ahmed
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY
- Department of Radiology, College of Physicians and Surgeons, Columbia University, New York, NY
| | - Gregory L Burke
- Department of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC
| | - Paul Enright
- Department of Medicine, University of Arizona, Tucson, AZ
| | - Nadia N Hansel
- Department of Medicine, Johns Hopkins University, Baltimore, MD
| | - Demondes Haynes
- Department of Medicine, University of Mississippi, Jackson, MS
| | - Susan R Heckbert
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA
| | - Eric A Hoffman
- Department of Radiology, University of Iowa, Iowa City, IA
| | - Joel D Kaufman
- Departments of Environmental & Occupational Health Sciences, Medicine, and Epidemiology, University of Washington Seattle, WA
| | - Jun Kurai
- Department of Medicine, Mount Sinai Hospital, New York, NY
| | - Laura Loehr
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health and Human Services, Research Triangle Park, NC
| | - Yang Meng
- The Broad Institute of MIT and Harvard, Cambridge MA
| | - George T O’Connor
- Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA and NHLBI Framingham Heart Study, Framingham, MA
| | - Elizabeth Oelsner
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY
| | - Marcy Petrini
- Department of Medicine, University of Mississippi, Jackson, MS
| | - Tess D Pottinger
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY
| | | | - Susan Redline
- Department of Medicine, Brigham and Women’s Hospital, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA
| | - Jerome I Rotter
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Lewis J Smith
- Department of Medicine, Northwestern University, Chicago, IL
| | - María Soler Artigas
- Department of Health Sciences, Genetic Epidemiology Group, University of Leicester, Leicester, UK
| | - Martin D Tobin
- Department of Health Sciences, Genetic Epidemiology Group, University of Leicester, Leicester, UK
- National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, UK
| | - Michael Y Tsai
- Department of Laboratory Medical Pathology, University of Minnesota, Minneapolis, MN
| | - Karol Watson
- Department of Medicine, University of California, Los Angeles, Los Angeles
| | - Wendy White
- Jackson Heart Study, Tougaloo College, Tougaloo, MS
| | - Taylor R Young
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health and Human Services, Research Triangle Park, NC
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA
| | - R Graham Barr
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, NY
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY
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256
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Admixture fine-mapping in African Americans implicates XAF1 as a possible sarcoidosis risk gene. PLoS One 2014; 9:e92646. [PMID: 24663488 PMCID: PMC3963923 DOI: 10.1371/journal.pone.0092646] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 02/25/2014] [Indexed: 12/23/2022] Open
Abstract
Sarcoidosis is a complex, multi-organ granulomatous disease with a likely genetic component. West African ancestry confers a higher risk for sarcoidosis than European ancestry. Admixture mapping provides the most direct method to locate genes that underlie such ethnic variation in disease risk. We sought to identify genetic risk variants within four previously-identified ancestry-associated regions—6p24.3–p12.1, 17p13.3–13.1, 2p13.3–q12.1, and 6q23.3–q25.2—in a sample of 2,727 African Americans. We used logistic regression fit by generalized estimating equations and the MIX score statistic to determine which variants within ancestry-associated regions were associated with risk and responsible for the admixture signal. Fine mapping was performed by imputation, based on a previous genome-wide association study; significant variants were validated by direct genotyping. Within the 6p24.3–p12.1 locus, the most significant ancestry-adjusted SNP was rs74318745 (p = 9.4*10−11), an intronic SNP within the HLA-DRA gene that did not solely explain the admixture signal, indicating the presence of more than a single risk variant within this well-established sarcoidosis risk region. The locus on chromosome 17p13.3–13.1 revealed a novel sarcoidosis risk SNP, rs6502976 (p = 9.5*10−6), within intron 5 of the gene X-linked Inhibitor of Apoptosis Associated Factor 1 (XAF1) that accounted for the majority of the admixture linkage signal. Immunohistochemical expression studies demonstrated lack of expression of XAF1 and a corresponding high level of expression of its downstream target, X-linked Inhibitor of Apoptosis (XIAP) in sarcoidosis granulomas. In conclusion, ancestry and association fine mapping revealed a novel sarcoidosis susceptibility gene, XAF1, which has not been identified by previous genome-wide association studies. Based on the known biology of the XIAP/XAF1 apoptosis pathway and the differential expression patterns of XAF1 and XIAP in sarcoidosis granulomas, we suggest that this pathway may play a role in the maintenance of sarcoidosis granulomas.
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257
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Halley YA, Dowd SE, Decker JE, Seabury PM, Bhattarai E, Johnson CD, Rollins D, Tizard IR, Brightsmith DJ, Peterson MJ, Taylor JF, Seabury CM. A draft de novo genome assembly for the northern bobwhite (Colinus virginianus) reveals evidence for a rapid decline in effective population size beginning in the Late Pleistocene. PLoS One 2014; 9:e90240. [PMID: 24621616 PMCID: PMC3951200 DOI: 10.1371/journal.pone.0090240] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Accepted: 01/27/2014] [Indexed: 11/20/2022] Open
Abstract
Wild populations of northern bobwhites (Colinus virginianus; hereafter bobwhite) have declined across nearly all of their U.S. range, and despite their importance as an experimental wildlife model for ecotoxicology studies, no bobwhite draft genome assembly currently exists. Herein, we present a bobwhite draft de novo genome assembly with annotation, comparative analyses including genome-wide analyses of divergence with the chicken (Gallus gallus) and zebra finch (Taeniopygia guttata) genomes, and coalescent modeling to reconstruct the demographic history of the bobwhite for comparison to other birds currently in decline (i.e., scarlet macaw; Ara macao). More than 90% of the assembled bobwhite genome was captured within <40,000 final scaffolds (N50 = 45.4 Kb) despite evidence for approximately 3.22 heterozygous polymorphisms per Kb, and three annotation analyses produced evidence for >14,000 unique genes and proteins. Bobwhite analyses of divergence with the chicken and zebra finch genomes revealed many extremely conserved gene sequences, and evidence for lineage-specific divergence of noncoding regions. Coalescent models for reconstructing the demographic history of the bobwhite and the scarlet macaw provided evidence for population bottlenecks which were temporally coincident with human colonization of the New World, the late Pleistocene collapse of the megafauna, and the last glacial maximum. Demographic trends predicted for the bobwhite and the scarlet macaw also were concordant with how opposing natural selection strategies (i.e., skewness in the r-/K-selection continuum) would be expected to shape genome diversity and the effective population sizes in these species, which is directly relevant to future conservation efforts.
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Affiliation(s)
- Yvette A. Halley
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Scot E. Dowd
- Molecular Research LP, Shallowater, Texas, United States of America
| | - Jared E. Decker
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Paul M. Seabury
- ElanTech Inc., Greenbelt, Maryland, United States of America
| | - Eric Bhattarai
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Charles D. Johnson
- Genomics and Bioinformatics Core, Texas A&M AgriLife Research, College Station, Texas, United States of America
| | - Dale Rollins
- Rolling Plains Quail Research Ranch, Rotan, Texas, United States of America
| | - Ian R. Tizard
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Donald J. Brightsmith
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
| | - Markus J. Peterson
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Jeremy F. Taylor
- Division of Animal Sciences, University of Missouri, Columbia, Missouri, United States of America
| | - Christopher M. Seabury
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
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258
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Cho MH, McDonald MLN, Zhou X, Mattheisen M, Castaldi PJ, Hersh CP, Demeo DL, Sylvia JS, Ziniti J, Laird NM, Lange C, Litonjua AA, Sparrow D, Casaburi R, Barr RG, Regan EA, Make BJ, Hokanson JE, Lutz S, Dudenkov TM, Farzadegan H, Hetmanski JB, Tal-Singer R, Lomas DA, Bakke P, Gulsvik A, Crapo JD, Silverman EK, Beaty TH. Risk loci for chronic obstructive pulmonary disease: a genome-wide association study and meta-analysis. THE LANCET. RESPIRATORY MEDICINE 2014; 2:214-25. [PMID: 24621683 PMCID: PMC4176924 DOI: 10.1016/s2213-2600(14)70002-5] [Citation(s) in RCA: 236] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
BACKGROUND The genetic risk factors for susceptibility to chronic obstructive pulmonary disease (COPD) are still largely unknown. Additional genetic variants are likely to be identified by genome-wide association studies in larger cohorts or specific subgroups. We sought to identify risk loci for moderate to severe and severe COPD with data from several cohort studies. METHODS We combined genome-wide association analysis data from participants in the COPDGene study (non-Hispanic white and African-American ethnic origin) and the ECLIPSE, NETT/NAS, and Norway GenKOLS studies (self-described white ethnic origin). We did analyses comparing control individuals with individuals with moderate to severe COPD and with a subset of individuals with severe COPD. Single nucleotide polymorphisms yielding a p value of less than 5 × 10(-7) in the meta-analysis at loci not previously described were genotyped in individuals from the family-based ICGN study. We combined results in a joint meta-analysis (threshold for significance p<5 × 10(-8)). FINDINGS Analysis of 6633 individuals with moderate to severe COPD and 5704 control individuals confirmed association at three known loci: CHRNA3 (p=6·38 × 10(-14)), FAM13A (p=1·12 × 10(-14)), and HHIP (p=1·57 × 10(-12)). We also showed significant evidence of association at a novel locus near RIN3 (p=5·25 × 10(-9)). In the overall meta-analysis (ie, including data from 2859 ICGN participants), the association with RIN3 remained significant (p=5·4 × 10(-9)). 3497 individuals were included in our analysis of severe COPD. The effect estimates for the loci near HHIP and CHRNA3 were significantly stronger in severe disease than in moderate to severe disease (p<0·01). We also identified associations at two additional loci: MMP12 (overall joint meta-analysis p=2·6 × 10(-9)) and TGFB2 (overall joint meta-analysis p=8·3 × 10(-9)). INTERPRETATION We have confirmed associations with COPD at three known loci and identified three new genome-wide significant associations. Genetic variants other than in α-1 antitrypsin increase the risk of COPD. FUNDING US National Heart, Lung, and Blood Institute; the Alpha-1 Foundation; the COPD Foundation through contributions from AstraZeneca, Boehringer Ingelheim, Novartis, and Sepracor; GlaxoSmithKline; Centers for Medicare and Medicaid Services; Agency for Healthcare Research and Quality; and US Department of Veterans Affairs.
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Affiliation(s)
- Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA.
| | - Merry-Lynn N McDonald
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Xiaobo Zhou
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Manuel Mattheisen
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA; Harvard School of Public Health, Boston, MA, USA
| | - Peter J Castaldi
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dawn L Demeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jody S Sylvia
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - John Ziniti
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Nan M Laird
- Harvard School of Public Health, Boston, MA, USA
| | | | - Augusto A Litonjua
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - David Sparrow
- School of Public Health and School of Medicine, Boston University, Boston, MA, USA; Veterans Administration Boston Healthcare System, Boston, MA, USA
| | - Richard Casaburi
- Los Angeles Biomedical Research Institute at Harbor UCLA Medical Center, Torrance, CA, USA
| | - R Graham Barr
- Department of Medicine, College of Physicians and Surgeons, Mailman School of Public Health, Columbia University, New York, NY, USA; Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Elizabeth A Regan
- National Jewish Health, Denver, CO, USA; Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Aurora, CO, USA
| | | | - John E Hokanson
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Aurora, CO, USA
| | - Sharon Lutz
- Department of Bioinformatics and Statistics, Colorado School of Public Health, University of Colorado Denver, Aurora, CO, USA
| | - Tanda Murray Dudenkov
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Homayoon Farzadegan
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Jacqueline B Hetmanski
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Ruth Tal-Singer
- GlaxoSmithKline Research and Development, King Of Prussia, PA, USA
| | | | - Per Bakke
- Department of Clinical Science, University of Bergen, Bergen, Norway; Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | - Amund Gulsvik
- Department of Clinical Science, University of Bergen, Bergen, Norway; Department of Thoracic Medicine, Haukeland University Hospital, Bergen, Norway
| | | | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Terri H Beaty
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
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Thun GA, Imboden M, Künzli N, Rochat T, Keidel D, Haun M, Schindler C, Kronenberg F, Probst-Hensch NM. Follow-up on genome-wide main effects: do polymorphisms modify the air pollution effect on lung function decline in adults? ENVIRONMENT INTERNATIONAL 2014; 64:110-115. [PMID: 24388947 DOI: 10.1016/j.envint.2013.12.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 12/06/2013] [Accepted: 12/13/2013] [Indexed: 06/03/2023]
Abstract
Improved air quality has been found associated with attenuated age-related decline in lung function. But whether genetic polymorphisms strongly associated with lung function play a modifying role in this attenuation process has so far not been investigated. We selected ten single nucleotide polymorphisms derived from the largest genome-wide association studies on lung function and examined whether they modified the association between the change in exposure to particulate matter ≤10μm (ΔPM10) and lung function decline. 4310 participants from the SAPALDIA cohort provided valid spirometry measurements, a detailed pulmonary health questionnaire both at baseline and 11years later as well as blood samples for genetic testing. Spatially and temporally resolved air pollution exposures were assigned on an individual level based on participants' residences. Statistically significant interactions of moderate strength with ΔPM10 were detected for rs2284746. Individuals with the CC genotype had a 21ml slower annual decline of the mid expiratory flow per 10μg/m(3) PM10 reduction over an 10-year period, while the benefits of CG and GG carriers were smaller (14 and 7ml per year, respectively; Pinteraction=0.04). The attenuated annual decline in the percentage of the forced expiratory volume in one second relative to the forced vital capacity (FEV1/FVC) was also increased with the presence of each C-allele (Pinteraction=0.009). We observed further suggestive interactions of similar magnitude in never-smokers, but none of the results would remain statistically significant after correction for multiple testing. We could not find strong evidence that lung function benefits from improved air quality are modified by polymorphisms associated with lung function level in large meta-analyzed genome-wide association studies.
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Affiliation(s)
- Gian Andri Thun
- Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland.
| | - Medea Imboden
- Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland.
| | - Nino Künzli
- Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland.
| | - Thierry Rochat
- Division of Pulmonary Medicine, University Hospital of Geneva, Geneva, Switzerland.
| | - Dirk Keidel
- Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland.
| | - Margot Haun
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria.
| | - Christian Schindler
- Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland.
| | - Florian Kronenberg
- Division of Genetic Epidemiology, Department of Medical Genetics, Molecular and Clinical Pharmacology, Innsbruck Medical University, Innsbruck, Austria.
| | - Nicole M Probst-Hensch
- Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland.
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260
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Manichaikul A, Hoffman EA, Smolonska J, Gao W, Cho MH, Baumhauer H, Budoff M, Austin JHM, Washko GR, Carr JJ, Kaufman JD, Pottinger T, Powell CA, Wijmenga C, Zanen P, Groen HJM, Postma DS, Wanner A, Rouhani FN, Brantly ML, Powell R, Smith BM, Rabinowitz D, Raffel LJ, Hinckley Stukovsky KD, Crapo JD, Beaty TH, Hokanson JE, Silverman EK, Dupuis J, O’Connor GT, Boezen HM, Rich SS, Barr RG. Genome-wide study of percent emphysema on computed tomography in the general population. The Multi-Ethnic Study of Atherosclerosis Lung/SNP Health Association Resource Study. Am J Respir Crit Care Med 2014; 189:408-18. [PMID: 24383474 PMCID: PMC3977717 DOI: 10.1164/rccm.201306-1061oc] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 12/18/2013] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Pulmonary emphysema overlaps partially with spirometrically defined chronic obstructive pulmonary disease and is heritable, with moderately high familial clustering. OBJECTIVES To complete a genome-wide association study (GWAS) for the percentage of emphysema-like lung on computed tomography in the Multi-Ethnic Study of Atherosclerosis (MESA) Lung/SNP Health Association Resource (SHARe) Study, a large, population-based cohort in the United States. METHODS We determined percent emphysema and upper-lower lobe ratio in emphysema defined by lung regions less than -950 HU on cardiac scans. Genetic analyses were reported combined across four race/ethnic groups: non-Hispanic white (n = 2,587), African American (n = 2,510), Hispanic (n = 2,113), and Chinese (n = 704) and stratified by race and ethnicity. MEASUREMENTS AND MAIN RESULTS Among 7,914 participants, we identified regions at genome-wide significance for percent emphysema in or near SNRPF (rs7957346; P = 2.2 × 10(-8)) and PPT2 (rs10947233; P = 3.2 × 10(-8)), both of which replicated in an additional 6,023 individuals of European ancestry. Both single-nucleotide polymorphisms were previously implicated as genes influencing lung function, and analyses including lung function revealed independent associations for percent emphysema. Among Hispanics, we identified a genetic locus for upper-lower lobe ratio near the α-mannosidase-related gene MAN2B1 (rs10411619; P = 1.1 × 10(-9); minor allele frequency [MAF], 4.4%). Among Chinese, we identified single-nucleotide polymorphisms associated with upper-lower lobe ratio near DHX15 (rs7698250; P = 1.8 × 10(-10); MAF, 2.7%) and MGAT5B (rs7221059; P = 2.7 × 10(-8); MAF, 2.6%), which acts on α-linked mannose. Among African Americans, a locus near a third α-mannosidase-related gene, MAN1C1 (rs12130495; P = 9.9 × 10(-6); MAF, 13.3%) was associated with percent emphysema. CONCLUSIONS Our results suggest that some genes previously identified as influencing lung function are independently associated with emphysema rather than lung function, and that genes related to α-mannosidase may influence risk of emphysema.
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Affiliation(s)
- Ani Manichaikul
- Center for Public Health Genomics, and
- Department of Public Health Sciences, Division of Biostatistics and Epidemiology, University of Virginia, Charlottesville, Virginia
| | - Eric A. Hoffman
- Department of Radiology, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | | | - Wei Gao
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Michael H. Cho
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, and
| | - Heather Baumhauer
- Department of Radiology, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - Matthew Budoff
- Division of Cardiology, Los Angeles Biomedical Research Institute, Torrance, California
| | - John H. M. Austin
- Department of Radiology, Columbia University Medical Center, New York, New York
| | - George R. Washko
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham & Women's Hospital, Boston, Massachusetts
| | - J. Jeffrey Carr
- Department of Radiology, Wake Forest University, Winston-Salem, North Carolina
| | - Joel D. Kaufman
- Department of Environmental & Occupational Health Sciences, Medicine, and Epidemiology, and
| | - Tess Pottinger
- Department of Medicine, College of Physicians and Surgeons
| | | | | | - Pieter Zanen
- Department of Pulmonology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Dirkje S. Postma
- Department of Pulmonology, and
- GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Adam Wanner
- Division of Pulmonary and Critical Care Medicine, University of Miami Miller School of Medicine, Miami, Florida
| | - Farshid N. Rouhani
- Division of Pulmonary Critical Care and Sleep Medicine, College of Medicine, University of Florida, Gainesville, Florida
| | - Mark L. Brantly
- Division of Pulmonary Critical Care and Sleep Medicine, College of Medicine, University of Florida, Gainesville, Florida
| | - Rhea Powell
- Department of Medicine, College of Physicians and Surgeons
| | | | | | - Leslie J. Raffel
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | | | - James D. Crapo
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, National Jewish Health, Denver, Colorado
| | - Terri H. Beaty
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - John E. Hokanson
- Department of Epidemiology, Colorado School of Public Health, University of Colorado Denver, Denver, Colorado
| | - Edwin K. Silverman
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, and
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
- The National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts; and
| | - George T. O’Connor
- The National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts; and
- Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts
| | - H. Marike Boezen
- Department of Epidemiology
- GRIAC Research Institute, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - R. Graham Barr
- Department of Medicine, College of Physicians and Surgeons
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
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261
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Hansel NN, Mathias RA. On the Threshold from Genome-Wide Association Studies to Whole-Genome Sequencing. Looking for Signal in All the Right Places. Am J Respir Crit Care Med 2014; 189:381-3. [DOI: 10.1164/rccm.201401-0048ed] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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262
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Affiliation(s)
- Ozren Polasek
- Ozren Polasek, Centre for Global Health, Medical School, University of Split, Split, Croatia,
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263
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Zaravinos A, Kanellou P, Lambrou GI, Spandidos DA. Gene set enrichment analysis of the NF-κB/Snail/YY1/RKIP circuitry in multiple myeloma. Tumour Biol 2014; 35:4987-5005. [PMID: 24481661 DOI: 10.1007/s13277-014-1659-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 01/14/2014] [Indexed: 12/27/2022] Open
Abstract
The presence of a dysregulated NF-κB/Snail/YY1/RKIP loop was recently established in metastatic prostate cancer cells and non-Hodgkin's lymphoma; however, its involvement in multiple myeloma (MM) has yet to be investigated. Aim of the study was to investigate the role of the NF-κB/Snail/YY1/RKIP circuitry in MM and how each gene is correlated with the remaining genes of the loop. Using gene set enrichment analysis and gene neighbours analysis in data received from four datasets included in the Multiple Myeloma Genomics Portal of the Multiple Myeloma Research Consortium, we identified various enriched gene sets associated with each member of the NF-κB/Snail/YY1/RKIP circuitry. In each dataset, the 20 most co-expressed genes with the circuitry genes were isolated subjected to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment. Among many, we highlighted on FNDC3B, TPD52, BBX, MBNL1 and MFAP2. Many co-expressed genes participated in the regulation of metabolic processes and nucleic acid binding, or were transcription factor binding genes and genes with metallopeptidase activity. The transcription factors FOXO4, GATA binding factor, Sp1 and AP4 most likely affect the expression of the NF-κB/Snail/YY1/RKIP circuitry genes. Computational analysis of various GEO datasets revealed elevated YY1 and RKIP levels in MM vs. the normal plasma cells, as well as elevated RKIP levels in MM vs. normal B lymphocytes. The present study highlights the relationships of the NF-κB/Snail/YY1/RKIP circuitry genes with specific cancer-related gene sets in multiple myeloma.
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Affiliation(s)
- Apostolos Zaravinos
- Laboratory of Virology, Medical School, University of Crete, 71110, Heraklion, Greece,
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264
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Abstract
Ion channels are essential for basic cellular function and for processes including sensory perception and intercellular communication in multicellular organisms. Voltage-gated potassium (Kv) channels facilitate dynamic cellular repolarization during an action potential, opening in response to membrane depolarization to facilitate K+ efflux. In both excitable and nonexcitable cells other, constitutively active, K+ channels provide a relatively constant repolarizing force to control membrane potential, ion homeostasis, and secretory processes. Of the forty known human Kv channel pore-forming α subunits that coassemble in various combinations to form the fundamental tetrameric channel pore and voltage sensor module, KCNQ1 is unique. KCNQ1 stands alone in having the capacity to form either channels that are voltage-dependent and require membrane depolarization for activation, or constitutively active channels. In mammals, KCNQ1 regulates processes including gastric acid secretion, thyroid hormone biosynthesis, salt and glucose homeostasis, and cell volume and in some species is required for rhythmic beating of the heart. In this review, the author discusses the unique functional properties, regulation, cell biology, diverse physiological roles, and involvement in human disease states of this chameleonic K+ channel.
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265
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Crump SM, Abbott GW. Arrhythmogenic KCNE gene variants: current knowledge and future challenges. Front Genet 2014; 5:3. [PMID: 24478792 PMCID: PMC3900874 DOI: 10.3389/fgene.2014.00003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 01/04/2014] [Indexed: 11/13/2022] Open
Abstract
There are twenty-five known inherited cardiac arrhythmia susceptibility genes, all of which encode either ion channel pore-forming subunits or proteins that regulate aspects of ion channel biology such as function, trafficking, and localization. The human KCNE gene family comprises five potassium channel regulatory subunits, sequence variants in each of which are associated with cardiac arrhythmias. KCNE gene products exhibit promiscuous partnering and in some cases ubiquitous expression, hampering efforts to unequivocally correlate each gene to specific native potassium currents. Likewise, deducing the molecular etiology of cardiac arrhythmias in individuals harboring rare KCNE gene variants, or more common KCNE polymorphisms, can be challenging. In this review we provide an update on putative arrhythmia-causing KCNE gene variants, and discuss current thinking and future challenges in the study of molecular mechanisms of KCNE-associated cardiac rhythm disturbances.
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Affiliation(s)
- Shawn M Crump
- Bioelectricity Laboratory, Department of Pharmacology, Department of Physiology and Biophysics, School of Medicine, University of California Irvine, CA, USA
| | - Geoffrey W Abbott
- Bioelectricity Laboratory, Department of Pharmacology, Department of Physiology and Biophysics, School of Medicine, University of California Irvine, CA, USA
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266
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Vallath S, Hynds RE, Succony L, Janes SM, Giangreco A. Targeting EGFR signalling in chronic lung disease: therapeutic challenges and opportunities. Eur Respir J 2014; 44:513-22. [PMID: 24435005 DOI: 10.1183/09031936.00146413] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Chronic respiratory diseases, including pulmonary fibrosis, chronic obstructive pulmonary disease (COPD) and lung cancer, are the second leading cause of death among Europeans. Despite this, there have been only a few therapeutic advances in these conditions over the past 20 years. In this review we provide evidence that targeting the epidermal growth factor receptor (EGFR) signalling pathway may represent a novel therapeutic panacea for treating chronic lung disease. Using evidence from human patient samples, transgenic animal models, and cell and molecular biology studies we highlight the roles of this signalling pathway in lung development, homeostasis, repair, and disease ontogeny. We identify mechanisms underlying lung EGFR pathway regulation and suggest how targeting these mechanisms using new and existing therapies has the potential to improve future lung cancer, COPD and pulmonary fibrosis patient outcomes.
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Affiliation(s)
- Sabari Vallath
- Lungs for Living Research Centre, Division of Medicine, University College London, UK
| | - Robert E Hynds
- Lungs for Living Research Centre, Division of Medicine, University College London, UK
| | - Laura Succony
- Lungs for Living Research Centre, Division of Medicine, University College London, UK
| | - Sam M Janes
- Lungs for Living Research Centre, Division of Medicine, University College London, UK
| | - Adam Giangreco
- Lungs for Living Research Centre, Division of Medicine, University College London, UK
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267
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Kim WJ, Lee MK, Shin C, Cho NH, Lee SD, Oh YM, Sung J. Genome-wide association studies identify locus on 6p21 influencing lung function in the Korean population. Respirology 2014; 19:360-8. [PMID: 24387323 DOI: 10.1111/resp.12230] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 09/12/2013] [Accepted: 10/15/2013] [Indexed: 11/27/2022]
Abstract
BACKGROUND AND OBJECTIVE Loss of lung function is an important chronic obstructive pulmonary disease phenotype and decreased forced expiratory volume in 1 s (FEV₁) is an independent risk factor of morbidity and mortality. Genome-wide association studies (GWAS) identifying genetic variants underlying lung function have been performed mostly in Caucasian populations. In this study, we aimed to identify genetic variants influencing lung function in a Korean population. METHODS GWAS on lung function (FEV₁ and FEV₁/forced vital capacity (FVC) ratio) were performed in two cohort studies. A population-based cohort, the Korean Association Resource phase 3 (KARE3) (6223 subjects), served as a discovery set. The replication analysis was performed in a family-based cohort, the Healthy Twin Study (HTS; 2730 subjects). Dense single-nucleotide polymorphism array data from each study were imputed and used for genetic analysis. RESULTS At the discovery phase, variants in 6p21 and 17q24 showed the strongest association with FEV₁/FVC ratio and FEV₁. Several variants in FAM13A on 4q22 locus exhibited positive association with FEV₁/FVC ratio. In the replication set, PPT2 in the 6p21 region showed significant association with lung function in the HTS, although the 4q22 locus and the 17q24 locus were not replicated. CONCLUSIONS We identified that PPT2 on chromosome 6p21 is associated with loss of lung function in the Korean population.
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Affiliation(s)
- Woo Jin Kim
- Department of Internal Medicine, Environmental Health Center, Kangwon National University Hospital, School of Medicine, Kangwon National University, Chuncheon, Korea
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268
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Wain LV, Odenthal-Hesse L, Abujaber R, Sayers I, Beardsmore C, Gaillard EA, Chappell S, Dogaru CM, McKeever T, Guetta-Baranes T, Kalsheker N, Kuehni CE, Hall IP, Tobin MD, Hollox EJ. Copy number variation of the beta-defensin genes in europeans: no supporting evidence for association with lung function, chronic obstructive pulmonary disease or asthma. PLoS One 2014; 9:e84192. [PMID: 24404154 PMCID: PMC3880289 DOI: 10.1371/journal.pone.0084192] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 11/13/2013] [Indexed: 12/23/2022] Open
Abstract
Lung function measures are heritable, predict mortality and are relevant in diagnosis of chronic obstructive pulmonary disease (COPD). COPD and asthma are diseases of the airways with major public health impacts and each have a heritable component. Genome-wide association studies of SNPs have revealed novel genetic associations with both diseases but only account for a small proportion of the heritability. Complex copy number variation may account for some of the missing heritability. A well-characterised genomic region of complex copy number variation contains beta-defensin genes (DEFB103, DEFB104 and DEFB4), which have a role in the innate immune response. Previous studies have implicated these and related genes as being associated with asthma or COPD. We hypothesised that copy number variation of these genes may play a role in lung function in the general population and in COPD and asthma risk. We undertook copy number typing of this locus in 1149 adult and 689 children using a paralogue ratio test and investigated association with COPD, asthma and lung function. Replication of findings was assessed in a larger independent sample of COPD cases and smoking controls. We found evidence for an association of beta-defensin copy number with COPD in the adult cohort (OR = 1.4, 95%CI:1.02-1.92, P = 0.039) but this finding, and findings from a previous study, were not replicated in a larger follow-up sample(OR = 0.89, 95%CI:0.72-1.07, P = 0.217). No robust evidence of association with asthma in children was observed. We found no evidence for association between beta-defensin copy number and lung function in the general populations. Our findings suggest that previous reports of association of beta-defensin copy number with COPD should be viewed with caution. Suboptimal measurement of copy number can lead to spurious associations. Further beta-defensin copy number measurement in larger sample sizes of COPD cases and children with asthma are needed.
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Affiliation(s)
- Louise V. Wain
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | | | - Razan Abujaber
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Ian Sayers
- Division of Respiratory Medicine, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Caroline Beardsmore
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, United Kingdom
- Institute for Lung Health, National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, United Kingdom
| | - Erol A. Gaillard
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, United Kingdom
- Institute for Lung Health, National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, United Kingdom
| | - Sally Chappell
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Cristian M. Dogaru
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Tricia McKeever
- School of Community Health Sciences, University of Nottingham, Nottingham, United Kingdom
| | | | - Noor Kalsheker
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Claudia E. Kuehni
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Ian P. Hall
- Division of Respiratory Medicine, School of Medicine, University of Nottingham, Nottingham, United Kingdom
| | - Martin D. Tobin
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- Department of Genetics, University of Leicester, Leicester, United Kingdom
- Institute for Lung Health, National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, United Kingdom
| | - Edward J. Hollox
- Department of Genetics, University of Leicester, Leicester, United Kingdom
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269
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Zhou JJ, Cho MH, Castaldi PJ, Hersh CP, Silverman EK, Laird NM. Heritability of chronic obstructive pulmonary disease and related phenotypes in smokers. Am J Respir Crit Care Med 2013; 188:941-7. [PMID: 23972146 DOI: 10.1164/rccm.201302-0263oc] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Previous studies of chronic obstructive pulmonary disease (COPD) have suggested that genetic factors play an important role in the development of disease. However, single-nucleotide polymorphisms that are associated with COPD in genome-wide association studies have been shown to account for only a small percentage of the genetic variance in phenotypes of COPD, such as spirometry and imaging variables. These phenotypes are highly predictive of disease, and family studies have shown that spirometric phenotypes are heritable. OBJECTIVES To assess the heritability and coheritability of four major COPD-related phenotypes (measurements of FEV1, FEV1/FVC, percent emphysema, and percent gas trapping), and COPD affection status in smokers of non-Hispanic white and African American descent using a population design. METHODS Single-nucleotide polymorphisms from genome-wide association studies chips were used to calculate the relatedness of pairs of individuals and a mixed model was adopted to estimate genetic variance and covariance. MEASUREMENTS AND MAIN RESULTS In the non-Hispanic whites, estimated heritabilities of FEV1 and FEV1/FVC were both about 37%, consistent with estimates in the literature from family-based studies. For chest computed tomography scan phenotypes, estimated heritabilities were both close to 25%. Heritability of COPD affection status was estimated as 37.7% in both populations. CONCLUSIONS This study suggests that a large portion of the genetic risk of COPD is yet to be discovered and gives rationale for additional genetic studies of COPD. The estimates of coheritability (genetic covariance) for pairs of the phenotypes suggest considerable overlap of causal genetic loci.
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Affiliation(s)
- Jin J Zhou
- 1 Biostatistics Department, Harvard School of Public Health, Boston, Massachusetts
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270
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Cheng DT, Kim DK, Cockayne DA, Belousov A, Bitter H, Cho MH, Duvoix A, Edwards LD, Lomas DA, Miller BE, Reynaert N, Tal-Singer R, Wouters EFM, Agustí A, Fabbri LM, Rames A, Visvanathan S, Rennard SI, Jones P, Parmar H, MacNee W, Wolff G, Silverman EK, Mayer RJ, Pillai SG. Systemic soluble receptor for advanced glycation endproducts is a biomarker of emphysema and associated with AGER genetic variants in patients with chronic obstructive pulmonary disease. Am J Respir Crit Care Med 2013; 188:948-57. [PMID: 23947473 DOI: 10.1164/rccm.201302-0247oc] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
RATIONALE Emphysema in chronic obstructive pulmonary disease (COPD) can be characterized by high-resolution chest computed tomography (HRCT); however, the repeated use of HRCT is limited because of concerns regarding radiation exposure and cost. OBJECTIVES To evaluate biomarkers associated with emphysema and COPD-related clinical characteristics, and to assess the relationships of soluble receptor for advanced glycation endproducts (sRAGE), a candidate systemic biomarker identified in this study, with single-nucleotide polymorphisms (SNPs) in the gene coding for RAGE (AGER locus) and with clinical characteristics. METHODS Circulating levels of 111 biomarkers were analyzed for association with clinical characteristics in 410 patients with COPD enrolled in the TESRA study. sRAGE was also measured in the ECLIPSE cohort in 1,847 patients with COPD, 298 smokers and 204 nonsmokers. The association between 21 SNPs in the AGER locus with sRAGE levels and clinical characteristics was also investigated. MEASUREMENTS AND MAIN RESULTS sRAGE was identified as a biomarker of diffusing capacity of carbon monoxide and lung density in the TESRA cohort. In the ECLIPSE cohort, lower sRAGE levels were associated with increased emphysema, increased Global Initiative for Chronic Obstructive Lung Disease stage, and COPD disease status. The associations with emphysema in both cohorts remained significant after covariate adjustment (P < 0.0001). One SNP in the AGER locus, rs2070600, was associated with circulating sRAGE levels both in TESRA (P = 0.0014) and ECLIPSE (7.07 × 10(-16)), which exceeded genome-wide significance threshold. Another SNP (rs2071288) was also associated with sRAGE levels (P = 0.01) and diffusing capacity of carbon monoxide (P = 0.01) in the TESRA study. CONCLUSIONS Lower circulating sRAGE levels are associated with emphysema severity and genetic polymorphisms in the AGER locus are associated with systemic sRAGE levels. Clinical trial registered with www.clinicaltrials.gov (NCT 00413205 and NCT 00292552).
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271
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Liao SY, Lin X, Christiani DC. Gene-environment interaction effects on lung function- a genome-wide association study within the Framingham heart study. Environ Health 2013; 12:101. [PMID: 24289273 PMCID: PMC3882096 DOI: 10.1186/1476-069x-12-101] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Accepted: 11/22/2013] [Indexed: 05/19/2023]
Abstract
BACKGROUND Previous studies in occupational exposure and lung function have focused only on the main effect of occupational exposure or genetics on lung function. Some disease-susceptible genes may be missed due to their low marginal effects, despite potential involvement in the disease process through interactions with the environment. Through comprehensive genome-wide gene-environment interaction studies, we can uncover these susceptibility genes. Our objective in this study was to explore gene by occupational exposure interaction effects on lung function using both the individual SNPs approach and the genetic network approach. METHODS The study population comprised the Offspring Cohort and the Third Generation from the Framingham Heart Study. We used forced expiratory volume in one second (FEV1) and ratio of FEV1 to forced vital capacity (FVC) as outcomes. Occupational exposures were classified using a population-specific job exposure matrix. We performed genome-wide gene-environment interaction analysis, using the Affymetrix 550 K mapping array for genotyping. A linear regression-based generalized estimating equation was applied to account for within-family relatedness. Network analysis was conducted using results from single-nucleotide polymorphism (SNP)-level analyses and from gene expression study results. RESULTS There were 4,785 participants in total. SNP-level analysis and network analysis identified SNP rs9931086 (P(interaction) =1.16 × 10(-7)) in gene SLC38A8, which may significantly modify the effects of occupational exposure on FEV1. Genes identified from the network analysis included CTLA-4, HDAC, and PPAR-alpha. CONCLUSIONS Our study implies that SNP rs9931086 in SLC38A8 and genes CTLA-4, HDAC, and PPAR-alpha, which are related to inflammatory processes, may modify the effect of occupational exposure on lung function.
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Affiliation(s)
- Shu-Yi Liao
- Harvard School of Public Health, 665 Huntington Avenue, Boston, MA 02115, USA
| | - Xihong Lin
- Harvard School of Public Health, 665 Huntington Avenue, Boston, MA 02115, USA
| | - David C Christiani
- Harvard School of Public Health, 665 Huntington Avenue, Boston, MA 02115, USA
- Harvard Medical School, 665 Huntington Ave, Boston, MA 02115, USA
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272
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Reardon BJ, Hansen JG, Crystal RG, Houston DK, Kritchevsky SB, Harris T, Lohman K, Liu Y, O'Connor GT, Wilk JB, Mezey J, Gao C, Cassano PA. Vitamin D-responsive SGPP2 variants associated with lung cell expression and lung function. BMC MEDICAL GENETICS 2013; 14:122. [PMID: 24274704 PMCID: PMC3907038 DOI: 10.1186/1471-2350-14-122] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 11/08/2013] [Indexed: 12/05/2022]
Abstract
Background Vitamin D is associated with lung health in epidemiologic studies, but mechanisms mediating observed associations are poorly understood. This study explores mechanisms for an effect of vitamin D in lung through an in vivo gene expression study, an expression quantitative trait loci (eQTL) analysis in lung tissue, and a population-based cohort study of sequence variants. Methods Microarray analysis investigated the association of gene expression in small airway epithelial cells with serum 25(OH)D in adult non-smokers. Sequence variants in candidate genes identified by the microarray were investigated in a lung tissue eQTL database, and also in relation to cross-sectional pulmonary function in the Health, Aging, and Body Composition (Health ABC) study, stratified by race, with replication in the Framingham Heart Study (FHS). Results 13 candidate genes had significant differences in expression by serum 25(OH)D (nominal p < 0.05), and a genome-wide significant eQTL association was detected for SGPP2. In Health ABC, SGPP2 SNPs were associated with FEV1 in both European- and African-Americans, and the gene-level association was replicated in European-American FHS participants. SNPs in 5 additional candidate genes (DAPK1, FSTL1, KAL1, KCNS3, and RSAD2) were associated with FEV1 in Health ABC participants. Conclusions SGPP2, a sphingosine-1-phosphate phosphatase, is a novel vitamin D-responsive gene associated with lung function. The identified associations will need to be followed up in further studies.
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Affiliation(s)
- Brian J Reardon
- Division of Nutritional Sciences, Cornell University, 209 Savage Hall, Ithaca, NY 14853, USA.
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Hofman A, Darwish Murad S, van Duijn CM, Franco OH, Goedegebure A, Ikram MA, Klaver CCW, Nijsten TEC, Peeters RP, Stricker BHC, Tiemeier HW, Uitterlinden AG, Vernooij MW. The Rotterdam Study: 2014 objectives and design update. Eur J Epidemiol 2013; 28:889-926. [PMID: 24258680 DOI: 10.1007/s10654-013-9866-z] [Citation(s) in RCA: 259] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 11/08/2013] [Indexed: 02/06/2023]
Abstract
The Rotterdam Study is a prospective cohort study ongoing since 1990 in the city of Rotterdam in The Netherlands. The study targets cardiovascular, endocrine, hepatic, neurological, ophthalmic, psychiatric, dermatological, oncological, and respiratory diseases. As of 2008, 14,926 subjects aged 45 years or over comprise the Rotterdam Study cohort. The findings of the Rotterdam Study have been presented in over a 1,000 research articles and reports (see www.erasmus-epidemiology.nl/rotterdamstudy ). This article gives the rationale of the study and its design. It also presents a summary of the major findings and an update of the objectives and methods.
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Affiliation(s)
- Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands,
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274
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Qiao D, Cho MH, Fier H, Bakke PS, Gulsvik A, Silverman EK, Lange C. On the simultaneous association analysis of large genomic regions: a massive multi-locus association test. ACTA ACUST UNITED AC 2013; 30:157-64. [PMID: 24262215 DOI: 10.1093/bioinformatics/btt654] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
MOTIVATION For samples of unrelated individuals, we propose a general analysis framework in which hundred thousands of genetic loci can be tested simultaneously for association with complex phenotypes. The approach is built on spatial-clustering methodology, assuming that genetic loci that are associated with the target phenotype cluster in certain genomic regions. In contrast to standard methodology for multilocus analysis, which has focused on the dimension reduction of the data, our multilocus association-clustering test profits from the availability of large numbers of genetic loci by detecting clusters of loci that are associated with the phenotype. RESULTS The approach is computationally fast and powerful, enabling the simultaneous association testing of large genomic regions. Even the entire genome or certain chromosomes can be tested simultaneously. Using simulation studies, the properties of the approach are evaluated. In an application to a genome-wide association study for chronic obstructive pulmonary disease, we illustrate the practical relevance of the proposed method by simultaneously testing all genotyped loci of the genome-wide association study and by testing each chromosome individually. Our findings suggest that statistical methodology that incorporates spatial-clustering information will be especially useful in whole-genome sequencing studies in which millions or billions of base pairs are recorded and grouped by genomic regions or genes, and are tested jointly for association. AVAILABILITY AND IMPLEMENTATION Implementation of the approach is available upon request.
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Affiliation(s)
- Dandi Qiao
- Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston, MA 20115, USA, Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA, Department of Genomic Mathematics, University of Bonn, 53113 Bonn, Germany and Department of Thoracic Medicine, Haukeland University Hospital and Section for Respiratory Medicine Institute of Medicine, University of Bergen, 5006 Bergen, Norway
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275
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Goh F, Shaw JG, Savarimuthu Francis SM, Vaughan A, Morrison L, Relan V, Marshall HM, Dent AG, O'Hare PE, Hsiao A, Bowman RV, Fong KM, Yang IA. Personalizing and targeting therapy for COPD: the role of molecular and clinical biomarkers. Expert Rev Respir Med 2013; 7:593-605. [PMID: 24160750 DOI: 10.1586/17476348.2013.842468] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is a heterogeneous disease characterized by persistent airflow limitation. It is the third leading cause of death worldwide, and there are currently no curative strategies for this disease. Many factors contribute to COPD susceptibility, progression and exacerbations. These include cigarette smoking, environmental and occupational pollutants, respiratory infections and comorbidities. As the clinical phenotypes of COPD are so variable, it has been difficult to devise an individualized treatment plan for patients with this complex chronic disease. This review will highlight how potential clinical, inflammatory, genomic and epigenomic biomarkers for COPD could be used to personalize treatment, leading to improved disease management and prevention for our patients.
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Affiliation(s)
- Felicia Goh
- Department of Thoracic Medicine, The Prince Charles Hospital, Brisbane, Australia
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276
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Tang W, Bentley AR, Kritchevsky SB, Harris TB, Newman AB, Bauer DC, Meibohm B, Cassano PA. Genetic variation in antioxidant enzymes, cigarette smoking, and longitudinal change in lung function. Free Radic Biol Med 2013; 63:304-12. [PMID: 23688726 PMCID: PMC4060265 DOI: 10.1016/j.freeradbiomed.2013.05.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 04/08/2013] [Accepted: 05/10/2013] [Indexed: 12/25/2022]
Abstract
Antioxidant enzymes play an important role in the defense against oxidative stress in the lung and in the pathogenesis of chronic obstructive pulmonary disease (COPD). Sequence variation in genes encoding antioxidant enzymes may alter susceptibility to COPD by affecting longitudinal change in lung function in adults. We genotyped 384 sequence variants in 56 candidate genes in 1281 African American and 1794 European American elderly adults in the Health, Aging, and Body Composition study. Single-marker associations and gene-by-smoking interactions with rate of change in FEV₁ and FEV₁/FVC were evaluated using linear mixed-effects models, stratified by race/ethnicity. In European Americans, rs17883901 in GCLC was statistically significantly associated with rate of change in FEV₁/FVC; the recessive genotype (TT) was associated with a 0.9% per year steeper decline (P = 4.50 × 10(-5)). Statistically significant gene-by-smoking interactions were observed for variants in two genes in European Americans: the minor allele of rs2297765 in mGST3 attenuated the accelerated decline in FEV₁/FVC in smokers by 0.45% per year (P = 1.13 × 10(-4)); for participants with greater baseline smoking pack-years, the minor allele of rs2073192 in IDH3B was associated with an accelerated decline in FEV₁/FVC (P = 2.10 × 10(-4)). For both genes, nominally significant interactions (P < 0.01) were observed at the gene level in African Americans (P = 0.007 and 4.60 × 10(-4), respectively). Nominally significant evidence of association was observed for variants in SOD3 and GLRX2 in multiple analyses. This study identifies two novel genes associated with longitudinal lung function phenotypes in both African and European Americans and confirms a prior finding for GCLC. These findings suggest novel mechanisms and molecular targets for future research and advance the understanding of genetic determinants of lung function and COPD risk.
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Affiliation(s)
- Wenbo Tang
- Division of Nutritional Sciences, Cornell University, Ithaca, NY 14853, USA
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277
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Collins SA, Lucas JSA, Inskip HM, Godfrey KM, Roberts G, Holloway JW. HHIP, HDAC4, NCR3 and RARB polymorphisms affect fetal, childhood and adult lung function. Eur Respir J 2013; 41:756-7. [PMID: 23456936 DOI: 10.1183/09031936.00171712] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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278
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Obeidat M, Miller S, Probert K, Billington CK, Henry AP, Hodge E, Nelson CP, Stewart CE, Swan C, Wain LV, Artigas MS, Melén E, Ushey K, Hao K, Lamontagne M, Bossé Y, Postma DS, Tobin MD, Sayers I, Hall IP. GSTCD and INTS12 regulation and expression in the human lung. PLoS One 2013; 8:e74630. [PMID: 24058608 PMCID: PMC3776747 DOI: 10.1371/journal.pone.0074630] [Citation(s) in RCA: 42] [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: 05/02/2013] [Accepted: 08/05/2013] [Indexed: 12/29/2022] Open
Abstract
Genome-Wide Association Study (GWAS) meta-analyses have identified a strong association signal for lung function, which maps to a region on 4q24 containing two oppositely transcribed genes: glutathione S-transferase, C-terminal domain containing (GSTCD) and integrator complex subunit 12 (INTS12). Both genes were found to be expressed in a range of human airway cell types. The promoter regions and transcription start sites were determined in mRNA from human lung and a novel splice variant was identified for each gene. We obtained the following evidence for GSTCD and INTS12 co-regulation and expression: (i) correlated mRNA expression was observed both via Q-PCR and in a lung expression quantitative trait loci (eQTL) study, (ii) induction of both GSTCD and INTS12 mRNA expression in human airway smooth muscle cells was seen in response to TGFβ1, (iii) a lung eQTL study revealed that both GSTCD and INTS12 mRNA levels positively correlate with percent predicted FEV1, and (iv) FEV1 GWAS associated SNPs in 4q24 were found to act as an eQTL for INTS12 in a number of tissues. In fixed sections of human lung tissue, GSTCD protein expression was ubiquitous, whereas INTS12 expression was predominantly in epithelial cells and pneumocytes. During human fetal lung development, GSTCD protein expression was observed to be highest at the earlier pseudoglandular stage (10-12 weeks) compared with the later canalicular stage (17-19 weeks), whereas INTS12 expression levels did not alter throughout these stages. Knowledge of the transcriptional and translational regulation and expression of GSTCD and INTS12 provides important insights into the potential role of these genes in determining lung function. Future work is warranted to fully define the functions of INTS12 and GSTCD.
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Affiliation(s)
- Ma’en Obeidat
- Division of Respiratory Medicine, University of Nottingham, Queen’s Medical Center, Nottingham, United Kingdom
- James Hogg Research Centre, Institute for Heart and Lung Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Suzanne Miller
- Division of Respiratory Medicine, University of Nottingham, Queen’s Medical Center, Nottingham, United Kingdom
| | - Kelly Probert
- Division of Respiratory Medicine, University of Nottingham, Queen’s Medical Center, Nottingham, United Kingdom
| | - Charlotte K. Billington
- Division of Respiratory Medicine, University of Nottingham, Queen’s Medical Center, Nottingham, United Kingdom
| | - Amanda P. Henry
- Division of Respiratory Medicine, University of Nottingham, Queen’s Medical Center, Nottingham, United Kingdom
| | - Emily Hodge
- Division of Respiratory Medicine, University of Nottingham, Queen’s Medical Center, Nottingham, United Kingdom
| | - Carl P. Nelson
- Division of Respiratory Medicine, University of Nottingham, Queen’s Medical Center, Nottingham, United Kingdom
| | - Ceri E. Stewart
- Division of Respiratory Medicine, University of Nottingham, Queen’s Medical Center, Nottingham, United Kingdom
| | - Caroline Swan
- Division of Respiratory Medicine, University of Nottingham, Queen’s Medical Center, Nottingham, United Kingdom
| | - Louise V. Wain
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | - María Soler Artigas
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, United Kingdom
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet and Sachs’ Children’s Hospital, Stockholm, Sweden
| | - Kevin Ushey
- James Hogg Research Centre, Institute for Heart and Lung Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ke Hao
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, United States of America
| | - Maxime Lamontagne
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec City, Canada
| | - Yohan Bossé
- Department of Molecular Medicine, Laval University, Québec City, Canada
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Québec City, Canada
| | - Dirkje S. Postma
- Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Martin D. Tobin
- Genetic Epidemiology Group, Department of Health Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health Research (NIHR) Leicester Respiratory Biomedical Research Unit, Glenfield Hospital, Leicester, United Kingdom
| | - Ian Sayers
- Division of Respiratory Medicine, University of Nottingham, Queen’s Medical Center, Nottingham, United Kingdom
| | - Ian P. Hall
- Division of Respiratory Medicine, University of Nottingham, Queen’s Medical Center, Nottingham, United Kingdom
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279
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Klimentidis YC, Vazquez AI, de los Campos G, Allison DB, Dransfield MT, Thannickal VJ. Heritability of pulmonary function estimated from pedigree and whole-genome markers. Front Genet 2013; 4:174. [PMID: 24058366 PMCID: PMC3766834 DOI: 10.3389/fgene.2013.00174] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 08/22/2013] [Indexed: 11/13/2022] Open
Abstract
Asthma and chronic obstructive pulmonary disease (COPD) are major worldwide health problems. Pulmonary function testing is a useful diagnostic tool for these diseases, and is known to be influenced by genetic and environmental factors. Previous studies have demonstrated that a substantial proportion of the variation in pulmonary function phenotypes can be explained by familial relationships. The availability of whole-genome single nucleotide polymorphism (SNP) data enables us to further evaluate the extent to which genetic factors account for variation in pulmonary function and to compare pedigree- to SNP-based estimates of heritability. Here, we employ methods developed in the animal breeding field to estimate the heritability of forced expiratory volume in one second (FEV1), forced vital capacity (FVC), and the ratio of these two measures (FEV1/FVC) among subjects in the Framingham Heart Study dataset. We compare heritability estimates based on pedigree-based relationships to those based on genome-wide SNPs. We find that, in a family-based study, estimates of heritability using SNP data are nearly identical to estimates based on pedigree information, and range from 0.50 for FEV1 to 0.66 for FEV1/FVC. Therefore, we conclude that genetic factors account for a sizable proportion of inter-individual differences in pulmonary function, and that estimates of heritability based on SNP data are nearly identical to estimates based on pedigree data. Finally, our findings suggest a higher heritability for FEV1/FVC compared to either FEV1 or FVC.
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Affiliation(s)
- Yann C. Klimentidis
- Division of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, University of ArizonaTucson, AZ, USA
| | - Ana I. Vazquez
- Department of Biostatistics, Section on Statistical Genetics, University of Alabama at BirminghamBirmingham, AL, USA
| | - Gustavo de los Campos
- Department of Biostatistics, Section on Statistical Genetics, University of Alabama at BirminghamBirmingham, AL, USA
| | - David B. Allison
- Office of Energetics, School of Public Health, University of Alabama at BirminghamBirmingham, AL, USA
| | - Mark T. Dransfield
- Allergy and Critical Care Medicine, Department of Medicine, Division of Pulmonary, University of Alabama at BirminghamBirmingham, AL, USA
| | - Victor J. Thannickal
- Allergy and Critical Care Medicine, Department of Medicine, Division of Pulmonary, University of Alabama at BirminghamBirmingham, AL, USA
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Ong BA, Li J, McDonough JM, Wei Z, Kim C, Chiavacci R, Mentch F, Caboot JB, Spergel J, Allen JL, Sleiman PMA, Hakonarson H. Gene network analysis in a pediatric cohort identifies novel lung function genes. PLoS One 2013; 8:e72899. [PMID: 24023788 PMCID: PMC3759429 DOI: 10.1371/journal.pone.0072899] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 07/15/2013] [Indexed: 01/06/2023] Open
Abstract
Lung function is a heritable trait and serves as an important clinical predictor of morbidity and mortality for pulmonary conditions in adults, however, despite its importance, no studies have focused on uncovering pediatric-specific loci influencing lung function. To identify novel genetic determinants of pediatric lung function, we conducted a genome-wide association study (GWAS) of four pulmonary function traits, including FVC, FEV1, FEV1/FVC and FEF25–75% in 1556 children. Further, we carried out gene network analyses for each trait including all SNPs with a P-value of <1.0×10−3 from the individual GWAS. The GWAS identified SNPs with notable trends towards association with the pulmonary function measures, including the previously described INTS12 locus association with FEV1 (pmeta = 1.41×10−7). The gene network analyses identified 34 networks of genes associated with pulmonary function variables in Caucasians. Of those, the glycoprotein gene network reached genome-wide significance for all four variables. P-value range pmeta = 6.29×10−4 - 2.80×10−8 on meta-analysis. In this study, we report on specific pathways that are significantly associated with pediatric lung function at genome-wide significance. In addition, we report the first loci associated with lung function in both pediatric Caucasian and African American populations.
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Affiliation(s)
- Bruce A. Ong
- Division of Pulmonary Medicine and Cystic Fibrosis Center, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Jin Li
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Joseph M. McDonough
- Division of Pulmonary Medicine and Cystic Fibrosis Center, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Zhi Wei
- Department of Computer Science, New Jersey Institute of Technology, Newark, New Jersey, United States of America
| | - Cecilia Kim
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Rosetta Chiavacci
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Frank Mentch
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Jason B. Caboot
- Division of Pediatric Pulmonology, Madigan Army Medical Center, Tacoma, Washington, United States of America
| | - Jonathan Spergel
- Center for Pediatric Eosinophilic Disorders, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- Division of Allergy and Immunology, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Julian L. Allen
- Division of Pulmonary Medicine and Cystic Fibrosis Center, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Patrick M. A. Sleiman
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail: (HH); (PMAS)
| | - Hakon Hakonarson
- Division of Pulmonary Medicine and Cystic Fibrosis Center, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail: (HH); (PMAS)
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Causal and synthetic associations of variants in the SERPINA gene cluster with alpha1-antitrypsin serum levels. PLoS Genet 2013; 9:e1003585. [PMID: 23990791 PMCID: PMC3749935 DOI: 10.1371/journal.pgen.1003585] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 05/08/2013] [Indexed: 11/29/2022] Open
Abstract
Several infrequent genetic polymorphisms in the SERPINA1 gene are known to substantially reduce concentration of alpha1-antitrypsin (AAT) in the blood. Since low AAT serum levels fail to protect pulmonary tissue from enzymatic degradation, these polymorphisms also increase the risk for early onset chronic obstructive pulmonary disease (COPD). The role of more common SERPINA1 single nucleotide polymorphisms (SNPs) in respiratory health remains poorly understood. We present here an agnostic investigation of genetic determinants of circulating AAT levels in a general population sample by performing a genome-wide association study (GWAS) in 1392 individuals of the SAPALDIA cohort. Five common SNPs, defined by showing minor allele frequencies (MAFs) >5%, reached genome-wide significance, all located in the SERPINA gene cluster at 14q32.13. The top-ranking genotyped SNP rs4905179 was associated with an estimated effect of β = −0.068 g/L per minor allele (P = 1.20*10−12). But denser SERPINA1 locus genotyping in 5569 participants with subsequent stepwise conditional analysis, as well as exon-sequencing in a subsample (N = 410), suggested that AAT serum level is causally determined at this locus by rare (MAF<1%) and low-frequent (MAF 1–5%) variants only, in particular by the well-documented protein inhibitor S and Z (PI S, PI Z) variants. Replication of the association of rs4905179 with AAT serum levels in the Copenhagen City Heart Study (N = 8273) was successful (P<0.0001), as was the replication of its synthetic nature (the effect disappeared after adjusting for PI S and Z, P = 0.57). Extending the analysis to lung function revealed a more complex situation. Only in individuals with severely compromised pulmonary health (N = 397), associations of common SNPs at this locus with lung function were driven by rarer PI S or Z variants. Overall, our meta-analysis of lung function in ever-smokers does not support a functional role of common SNPs in the SERPINA gene cluster in the general population. Low levels of alpha1-antitrypsin (AAT) in the blood are a well-established risk factor for accelerated loss in lung function and chronic obstructive pulmonary disease. While a few infrequent genetic polymorphisms are known to influence the serum levels of this enzyme, the role of common genetic variants has not been examined so far. The present genome-wide scan for associated variants in approximately 1400 Swiss inhabitants revealed a chromosomal locus containing the functionally established variants of AAT deficiency and variants previously associated with lung function and emphysema. We used dense genotyping of this genetic region in more than 5500 individuals and subsequent conditional analyses to unravel which of these associated variants contribute independently to the phenotype's variability. All associations of common variants could be attributed to the rarer functionally established variants, a result which was then replicated in an independent population-based Danish cohort. Hence, this locus represents a textbook example of how a large part of a trait's heritability can be hidden in infrequent genetic polymorphisms. The attempt to transfer these results to lung function furthermore suggests that effects of common variants in this genetic region in ever-smokers may also be explained by rarer variants, but only in individuals with hampered pulmonary health.
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Yao TC, Du G, Han L, Sun Y, Hu D, Yang JJ, Mathias R, Roth LA, Rafaels N, Thompson EE, Loisel DA, Anderson R, Eng C, Arruabarrena Orbegozo M, Young M, Klocksieben JM, Anderson E, Shanovich K, Lester LA, Williams LK, Barnes KC, Burchard EG, Nicolae DL, Abney M, Ober C. Genome-wide association study of lung function phenotypes in a founder population. J Allergy Clin Immunol 2013; 133:248-55.e1-10. [PMID: 23932459 DOI: 10.1016/j.jaci.2013.06.018] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 04/18/2013] [Accepted: 06/12/2013] [Indexed: 02/04/2023]
Abstract
BACKGROUND Lung function is a long-term predictor of mortality and morbidity. OBJECTIVE We sought to identify single nucleotide polymorphisms (SNPs) associated with lung function. METHODS We performed a genome-wide association study (GWAS) of FEV1, forced vital capacity (FVC), and FEV1/FVC in 1144 Hutterites aged 6 to 89 years, who are members of a founder population of European descent. We performed least absolute shrinkage and selection operation regression to select the minimum set of SNPs that best predict FEV1/FVC in the Hutterites and used the GRAIL algorithm to mine the Gene Ontology database for evidence of functional connections between genes near the predictive SNPs. RESULTS Our GWAS identified significant associations between FEV1/FVC and SNPs at the THSD4-UACA-TLE3 locus on chromosome 15q23 (P = 5.7 × 10(-8) to 3.4 × 10(-9)). Nine SNPs at or near 4 additional loci had P < 10(-5) with FEV1/FVC. Only 2 SNPs were found with P < 10(-5) for FEV1 or FVC. We found nominal levels of significance with SNPs at 9 of the 27 previously reported loci associated with lung function measures. Among a predictive set of 80 SNPs, 6 loci were identified that had a significant degree of functional connectivity (GRAIL P < .05), including 3 clusters of β-defensin genes, 2 chemokine genes (CCL18 and CXCL12), and TNFRSF13B. CONCLUSION This study identifies genome-wide significant associations and replicates results of previous GWASs. Multimarker modeling implicated for the first time common variation in genes involved in antimicrobial immunity in airway mucosa that influences lung function.
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Affiliation(s)
- Tsung-Chieh Yao
- Department of Human Genetics, University of Chicago, Chicago, Ill; Division of Allergy, Asthma, and Rheumatology, Department of Pediatrics, Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Taoyuan, Taiwan.
| | - Gaixin Du
- Department of Human Genetics, University of Chicago, Chicago, Ill
| | - Lide Han
- Department of Human Genetics, University of Chicago, Chicago, Ill
| | - Ying Sun
- Department of Human Genetics, University of Chicago, Chicago, Ill
| | - Donglei Hu
- Department of Medicine, University of California, San Francisco, Calif
| | - James J Yang
- Department of Public Health Sciences, Henry Ford Health System, Detroit, Mich
| | - Rasika Mathias
- Division of Allergy and Clinical Immunology, Department of Medicine, The Johns Hopkins University, Baltimore, Md
| | - Lindsey A Roth
- Department of Medicine, University of California, San Francisco, Calif
| | - Nicholas Rafaels
- Division of Allergy and Clinical Immunology, Department of Medicine, The Johns Hopkins University, Baltimore, Md
| | - Emma E Thompson
- Department of Human Genetics, University of Chicago, Chicago, Ill
| | - Dagan A Loisel
- Department of Human Genetics, University of Chicago, Chicago, Ill
| | - Rebecca Anderson
- Department of Human Genetics, University of Chicago, Chicago, Ill
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, Calif
| | | | - Melody Young
- Department of Pediatrics, University of Chicago, Chicago, Ill
| | | | | | | | | | - L Keoki Williams
- Center for Health Services Research and Department of Internal Medicine, Henry Ford Health System, Detroit, Mich
| | - Kathleen C Barnes
- Division of Allergy and Clinical Immunology, Department of Medicine, The Johns Hopkins University, Baltimore, Md
| | - Esteban G Burchard
- Department of Medicine, University of California, San Francisco, Calif; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, Calif
| | - Dan L Nicolae
- Department of Human Genetics, University of Chicago, Chicago, Ill; Department of Pediatrics, University of Chicago, Chicago, Ill; Department of Statistics, University of Chicago, Chicago, Ill
| | - Mark Abney
- Department of Human Genetics, University of Chicago, Chicago, Ill
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, Ill.
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283
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Hodge E, Nelson CP, Miller S, Billington CK, Stewart CE, Swan C, Malarstig A, Henry AP, Gowland C, Melén E, Hall IP, Sayers I. HTR4 gene structure and altered expression in the developing lung. Respir Res 2013; 14:77. [PMID: 23890215 PMCID: PMC3750317 DOI: 10.1186/1465-9921-14-77] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 07/23/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Meta-analyses of genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) spanning the 5-hydroxytryptamine receptor 4 (5-HT₄R) gene (HTR4) associated with lung function. The aims of this study were to i) investigate the expression profile of HTR4 in adult and fetal lung tissue and cultured airway cells, ii) further define HTR4 gene structure and iii) explore the potential functional implications of key SNPs using a bioinformatic approach. METHODS Following reverse transcription (RT)-PCR in human brain, 5' rapid amplification of cDNA ends (5' RACE) was used to examine the exonic structure of HTR4 at the 5' end. Quantitative (Q)-PCR was used to quantify HTR4 mRNA expression in total RNA from cultured airway cells and whole lung tissue. Publically available gene microarray data on fetal samples of estimated gestational age 7-22 weeks were mined for HTR4 expression. Immunohistochemistry (IHC; in adult and fetal lung tissue) and a radioligand binding assay (in cultured airway cells) were used to analyze 5-HT₄R protein expression. RESULTS IHC in adult lung, irrespective of the presence of chronic obstructive pulmonary disease (COPD), suggested low level expression of 5-HT₄R protein, which was most prominent in alveolar pneumocytes. There was evidence of differential 5-HT₄R protein levels during gestation in fetal lung, which was also evident in gene expression microarray data. HTR4 mRNA expression, assessed by Q-PCR, was <0.5% relative to brain in total adult lung tissue and in human airway smooth muscle (HASM) and bronchial epithelial cells (HBEC) derived from adult donors. Radioligand binding experiments also indicated that HBEC and HASM cells did not express a significant 5-HT₄R population. 5' RACE in brain identified a novel N-terminal variant, containing an extended N-terminal sequence. The functional significance of key HTR4 SNPs was investigated using the encyclopedia of DNA elements consortium (ENCODE) dataset. These analyses identified multiple alterations in regulatory motifs for transcription factors implicated in lung development, including Foxp1. CONCLUSIONS Taken together, these data suggest a role for HTR4 in lung development, which may at least in part explain the genetic association with lung function.
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Affiliation(s)
- Emily Hodge
- Division of Respiratory Medicine, University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK
| | - Carl P Nelson
- Division of Respiratory Medicine, University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK
| | - Suzanne Miller
- Division of Respiratory Medicine, University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK
| | - Charlotte K Billington
- Division of Respiratory Medicine, University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK
| | - Ceri E Stewart
- Division of Respiratory Medicine, University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK
| | - Caroline Swan
- Division of Respiratory Medicine, University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK
| | - Anders Malarstig
- Precision Medicine Unit, Pfizer Global Research and Development, Cambridge, UK
| | - Amanda P Henry
- Division of Respiratory Medicine, University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK
| | - Catherine Gowland
- Division of Respiratory Medicine, University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet and Sachs’ Children’s Hospital, Stockholm, Sweden
| | - Ian P Hall
- Division of Respiratory Medicine, University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK
| | - Ian Sayers
- Division of Respiratory Medicine, University of Nottingham, Queen’s Medical Centre, Nottingham NG7 2UH, UK
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284
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Rietveld CA, Medland SE, Derringer J, Yang J, Esko T, Martin NW, Westra HJ, Shakhbazov K, Abdellaoui A, Agrawal A, Albrecht E, Alizadeh BZ, Amin N, Barnard J, Baumeister SE, Benke KS, Bielak LF, Boatman JA, Boyle PA, Davies G, de Leeuw C, Eklund N, Evans DS, Ferhmann R, Fischer K, Gieger C, Gjessing HK, Hägg S, Harris JR, Hayward C, Holzapfel C, Ibrahim-Verbaas CA, Ingelsson E, Jacobsson B, Joshi PK, Jugessur A, Kaakinen M, Kanoni S, Karjalainen J, Kolcic I, Kristiansson K, Kutalik Z, Lahti J, Lee SH, Lin P, Lind PA, Liu Y, Lohman K, Loitfelder M, McMahon G, Vidal PM, Meirelles O, Milani L, Myhre R, Nuotio ML, Oldmeadow CJ, Petrovic KE, Peyrot WJ, Polašek O, Quaye L, Reinmaa E, Rice JP, Rizzi TS, Schmidt H, Schmidt R, Smith AV, Smith JA, Tanaka T, Terracciano A, van der Loos MJ, Vitart V, Völzke H, Wellmann J, Yu L, Zhao W, Allik J, Attia JR, Bandinelli S, Bastardot F, Beauchamp J, Bennett DA, Berger K, Bierut LJ, Boomsma DI, Bültmann U, Campbell H, Chabris CF, Cherkas L, Chung MK, Cucca F, de Andrade M, De Jager PL, De Neve JE, Deary IJ, Dedoussis GV, Deloukas P, Dimitriou M, Eiriksdottir G, Elderson MF, Eriksson JG, Evans DM, Faul JD, Ferrucci L, Garcia ME, Grönberg H, Gudnason V, Hall P, Harris JM, Harris TB, Hastie ND, Heath AC, Hernandez DG, Hoffmann W, Hofman A, Holle R, Holliday EG, Hottenga JJ, Iacono WG, Illig T, Järvelin MR, Kähönen M, Kaprio J, Kirkpatrick RM, Kowgier M, Latvala A, Launer LJ, Lawlor DA, Lehtimäki T, Li J, Lichtenstein P, Lichtner P, Liewald DC, Madden PA, Magnusson PKE, Mäkinen TE, Masala M, McGue M, Metspalu A, Mielck A, Miller MB, Montgomery GW, Mukherjee S, Nyholt DR, Oostra BA, Palmer LJ, Palotie A, Penninx B, Perola M, Peyser PA, Preisig M, Räikkönen K, Raitakari OT, Realo A, Ring SM, Ripatti S, Rivadeneira F, Rudan I, Rustichini A, Salomaa V, Sarin AP, Schlessinger D, Scott RJ, Snieder H, Pourcain BS, Starr JM, Sul JH, Surakka I, Svento R, Teumer A, Tiemeier H, Rooij FJA, Van Wagoner DR, Vartiainen E, Viikari J, Vollenweider P, Vonk JM, Waeber G, Weir DR, Wichmann HE, Widen E, Willemsen G, Wilson JF, Wright AF, Conley D, Davey-Smith G, Franke L, Groenen PJF, Hofman A, Johannesson M, Kardia SL, Krueger RF, Laibson D, Martin NG, Meyer MN, Posthuma D, Thurik AR, Timpson NJ, Uitterlinden AG, van Duijn CM, Visscher PM, Benjamin DJ, Cesarini D, Koellinger PD. GWAS of 126,559 individuals identifies genetic variants associated with educational attainment. Science 2013; 340:1467-71. [PMID: 23722424 PMCID: PMC3751588 DOI: 10.1126/science.1235488] [Citation(s) in RCA: 484] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A genome-wide association study (GWAS) of educational attainment was conducted in a discovery sample of 101,069 individuals and a replication sample of 25,490. Three independent single-nucleotide polymorphisms (SNPs) are genome-wide significant (rs9320913, rs11584700, rs4851266), and all three replicate. Estimated effects sizes are small (coefficient of determination R(2) ≈ 0.02%), approximately 1 month of schooling per allele. A linear polygenic score from all measured SNPs accounts for ≈2% of the variance in both educational attainment and cognitive function. Genes in the region of the loci have previously been associated with health, cognitive, and central nervous system phenotypes, and bioinformatics analyses suggest the involvement of the anterior caudate nucleus. These findings provide promising candidate SNPs for follow-up work, and our effect size estimates can anchor power analyses in social-science genetics.
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Affiliation(s)
- Cornelius A. Rietveld
- Department of Applied Economics, Erasmus School of Economics, Erasmus University Rotterdam, 3000 DR Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
| | - Sarah E. Medland
- Queensland Institute of Medical Research, 300 Herston Road, Brisbane, Queensland 4006, Australia
| | - Jaime Derringer
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO 80309–0447, USA
| | - Jian Yang
- University of Queensland Diamantina Institute, The University of Queensland, Princess Alexandra Hospital, Brisbane, Queensland 4102, Australia
| | - Tõnu Esko
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Nicolas W. Martin
- Queensland Institute of Medical Research, 300 Herston Road, Brisbane, Queensland 4006, Australia
- School of Psychology, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Harm-Jan Westra
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Konstantin Shakhbazov
- University of Queensland Diamantina Institute, The University of Queensland, Princess Alexandra Hospital, Brisbane, Queensland 4102, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Abdel Abdellaoui
- Department of Biological Psychology, VU University Amsterdam, 1081 BT Amsterdam, The Netherlands
| | - Arpana Agrawal
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Eva Albrecht
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Behrooz Z. Alizadeh
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Najaf Amin
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, the Netherlands
| | - John Barnard
- Heart and Vascular and Lerner Research Institutes, Cleveland Clinic, Cleveland, OH 44195, USA
| | | | - Kelly S. Benke
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario M5G 1X5, Canada
| | - Lawrence F. Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109–2029, USA
| | - Jeffrey A. Boatman
- Division of Biostatistics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Patricia A. Boyle
- Rush University Medical Center, Rush Alzheimer’s Disease Center, Chicago, IL 60612, USA
| | - Gail Davies
- Centre for Cognitive Aging and Cognitive Epidemiology, The University of Edinburgh, Edinburgh EH8 9JZ, Scotland, UK
| | - Christiaan de Leeuw
- Department of Functional Genomics, VU University Amsterdam and VU Medical Center, 1081 HV Amsterdam, The Netherlands
| | - Niina Eklund
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland
- Public Health Genomics Unit, Department of Chronic Disease Prevention, The National Institute for Health and Welfare, Helsinki 00014, Finland
| | - Daniel S. Evans
- California Pacific Medical Center Research Institute, San Francisco, CA 94107–1728, USA
| | - Rudolf Ferhmann
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Krista Fischer
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Håkon K. Gjessing
- Department of Genes and Environment, Division of Epidemiology, Norwegian Institute of Public Health, Nydalen, N-0403 Oslo, Norway
| | - Sara Hägg
- Molecular Epidemiology, Department of Medical Sciences, Uppsala University, 751 85 Uppsala, Sweden
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Jennifer R. Harris
- Department of Genes and Environment, Division of Epidemiology, Norwegian Institute of Public Health, Nydalen, N-0403 Oslo, Norway
| | - Caroline Hayward
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Christina Holzapfel
- Else Kroener-Fresenius-Centre for Nutritional Medicine, Technische Universität München, 81675 Munich, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Carla A. Ibrahim-Verbaas
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, the Netherlands
- Department of Neurology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
| | - Erik Ingelsson
- Molecular Epidemiology, Department of Medical Sciences, Uppsala University, 751 85 Uppsala, Sweden
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Bo Jacobsson
- Department of Genes and Environment, Division of Epidemiology, Norwegian Institute of Public Health, Nydalen, N-0403 Oslo, Norway
- Department of Obstetrics and Gynecology, Institute of Public Health, Sahlgrenska Academy, Sahgrenska University Hospital, Gothenburg, 413 45, Sweden
| | - Peter K. Joshi
- Centre for Population Health Sciences, The University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Astanand Jugessur
- Department of Genes and Environment, Division of Epidemiology, Norwegian Institute of Public Health, Nydalen, N-0403 Oslo, Norway
| | - Marika Kaakinen
- Institute of Health Sciences, University of Oulu, Oulu 90014, Finland
- Biocenter Oulu, University of Oulu, Oulu 90014, Finland
| | - Stavroula Kanoni
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Juha Karjalainen
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Ivana Kolcic
- Faculty of Medicine, University of Split, 21000 Split, Croatia
| | - Kati Kristiansson
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland
- Public Health Genomics Unit, Department of Chronic Disease Prevention, The National Institute for Health and Welfare, Helsinki 00014, Finland
| | - Zoltán Kutalik
- Department of Medical Genetics, University of Lausanne, 1005 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Jari Lahti
- Institute of Behavioral Sciences, University of Helsinki, Helsinki 00014, Finland
| | - Sang H. Lee
- Queensland Institute of Medical Research, 300 Herston Road, Brisbane, Queensland 4006, Australia
| | - Peng Lin
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Penelope A. Lind
- Queensland Institute of Medical Research, 300 Herston Road, Brisbane, Queensland 4006, Australia
| | - Yongmei Liu
- Department of Epidemiology & Prevention, Division of Public Health Sciences, Wake Forest University Health Sciences, Winston-Salem, NC 27157–1063, USA
| | - Kurt Lohman
- Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest University Health Sciences, Winston-Salem, NC 27157–1063, USA
| | - Marisa Loitfelder
- Division for Neurogeriatrics, Department of Neurology, Medical University of Graz, Graz 8036, Austria
| | - George McMahon
- School of Social and Community Medicine, University of Bristol, Bristol BS8 2PR, UK
| | - Pedro Marques Vidal
- Institute of Social and Preventive Medicine, Lausanne University Hospital, 1005 Lausanne, Switzerland
| | - Osorio Meirelles
- National Institute on Aging, National Institutes of Health, Baltimore, MD 20892, USA
| | - Lili Milani
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Ronny Myhre
- Department of Genes and Environment, Division of Epidemiology, Norwegian Institute of Public Health, Nydalen, N-0403 Oslo, Norway
| | - Marja-Liisa Nuotio
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland
- Public Health Genomics Unit, Department of Chronic Disease Prevention, The National Institute for Health and Welfare, Helsinki 00014, Finland
| | - Christopher J. Oldmeadow
- Hunter Medical Research Institute and Faculty of Health, University of Newcastle, Newcastle, NSW 2308, Australia
| | - Katja E. Petrovic
- Division of General Neurology, Department of Neurology, General Hospital and Medical University of Graz, Graz 8036, Austria
| | - Wouter J. Peyrot
- Department of Psychiatry, VU University Medical Center, 1081 HL Amsterdam, The Netherlands
| | - Ozren Polašek
- Faculty of Medicine, University of Split, 21000 Split, Croatia
| | - Lydia Quaye
- Department of Twin Research and Genetic Epidemiology, King’s College London, London SE1 7EH, UK
| | - Eva Reinmaa
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - John P. Rice
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Thais S. Rizzi
- Department of Functional Genomics, VU University Amsterdam and VU Medical Center, 1081 HV Amsterdam, The Netherlands
| | - Helena Schmidt
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Graz 8036, Austria
| | - Reinhold Schmidt
- Division for Neurogeriatrics, Department of Neurology, Medical University of Graz, Graz 8036, Austria
| | - Albert V. Smith
- Icelandic Heart Association, Kopavogur 201, Iceland
- Department of Medicine, University of Iceland, Reykjavik 101, Iceland
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109–2029, USA
| | - Toshiko Tanaka
- National Institute on Aging, National Institutes of Health, Baltimore, MD 20892, USA
| | - Antonio Terracciano
- National Institute on Aging, National Institutes of Health, Baltimore, MD 20892, USA
- College of Medicine, Florida State University, Tallahassee, FL 32306–4300, USA
| | - Matthijs J.H.M. van der Loos
- Department of Applied Economics, Erasmus School of Economics, Erasmus University Rotterdam, 3000 DR Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
| | - Veronique Vitart
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald 17489, Germany
| | - Jürgen Wellmann
- Institute of Epidemiology and Social Medicine, University of Muenster, 48129 Muenster, Germany
| | - Lei Yu
- Rush University Medical Center, Rush Alzheimer’s Disease Center, Chicago, IL 60612, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109–2029, USA
| | - Jüri Allik
- Department of Psychology, University of Tartu, Tartu 50410, Estonia
| | - John R. Attia
- Hunter Medical Research Institute and Faculty of Health, University of Newcastle, Newcastle, NSW 2308, Australia
| | | | - François Bastardot
- Department of Internal Medicine, University Hospital, 1011 Lausanne, Switzerland
| | | | - David A. Bennett
- Rush University Medical Center, Rush Alzheimer’s Disease Center, Chicago, IL 60612, USA
| | - Klaus Berger
- Institute of Epidemiology and Social Medicine, University of Muenster, 48129 Muenster, Germany
| | - Laura J. Bierut
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dorret I. Boomsma
- Department of Biological Psychology, VU University Amsterdam, 1081 BT Amsterdam, The Netherlands
| | - Ute Bültmann
- Department of Health Sciences, Community & Occupational Medicine, University Medical Center Groningen, 9700 AD Groningen, The Netherlands
| | - Harry Campbell
- Centre for Population Health Sciences, The University of Edinburgh, Edinburgh EH8 9AG, UK
| | | | - Lynn Cherkas
- Department of Twin Research and Genetic Epidemiology, King’s College London, London SE1 7EH, UK
| | - Mina K. Chung
- Heart and Vascular and Lerner Research Institutes, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica, CNR, Monserrato, 09042, Cagliari, Italy
- Dipartimento di Scienze Biomediche, Università di Sassari, 07100 SS, Italy
| | - Mariza de Andrade
- Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA
| | - Philip L. De Jager
- Program in Translational Neuropsychiatric Genomics, Department of Neurology, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Jan-Emmanuel De Neve
- School of Public Policy, University College London, London WC1H 9QU, UK
- Centre for Economic Performance, London School of Economics, London WC2A 2AE, UK
| | - Ian J. Deary
- Centre for Cognitive Aging and Cognitive Epidemiology, The University of Edinburgh, Edinburgh EH8 9JZ, Scotland, UK
- Department of Psychology, The University of Edinburgh, Edinburgh EH8 9JZ, Scotland, UK
| | - George V. Dedoussis
- Department of Nutrition and Dietetics, Harokopio University of Athens, Athens 17671, Greece
| | - Panos Deloukas
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Maria Dimitriou
- Department of Nutrition and Dietetics, Harokopio University of Athens, Athens 17671, Greece
| | | | - Martin F. Elderson
- LifeLines Cohort Study, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, The Netherlands
| | - Johan G. Eriksson
- Department of General Practice and Primary Health Care, University of Helsinki, Helsinki 00014, Finland
- Unit of General Practice, Helsinki University Central Hospital, Helsinki 00280, Finland
- Folkhälsan Research Center, Helsinki 00250, Finland
- Vaasa Central Hospital, Vaasa 65130, Finland
| | - David M. Evans
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Bristol BS8 2PR, UK
| | - Jessica D. Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48106, USA
| | - Luigi Ferrucci
- National Institute on Aging, National Institutes of Health, Baltimore, MD 20892, USA
| | - Melissa E. Garcia
- National Institute on Aging, National Institutes of Health, Baltimore, MD 20892, USA
| | - Henrik Grönberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur 201, Iceland
- Department of Medicine, University of Iceland, Reykjavik 101, Iceland
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Juliette M. Harris
- Department of Twin Research and Genetic Epidemiology, King’s College London, London SE1 7EH, UK
| | - Tamara B. Harris
- National Institute on Aging, National Institutes of Health, Baltimore, MD 20892, USA
| | - Nicholas D. Hastie
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Andrew C. Heath
- Division of Biology and Biomedical Sciences, Washington University, St. Louis, MO 63110–1093, USA
| | - Dena G. Hernandez
- National Institute on Aging, National Institutes of Health, Baltimore, MD 20892, USA
| | - Wolfgang Hoffmann
- Institute for Community Medicine, University Medicine Greifswald, Greifswald 17489, Germany
| | - Adriaan Hofman
- Faculty of Behavioral and Social Sciences, University of Groningen, 9747 AD Groningen, The Netherlands
| | - Rolf Holle
- Institute of Health Economics and Health Care Management, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Elizabeth G. Holliday
- Hunter Medical Research Institute and Faculty of Health, University of Newcastle, Newcastle, NSW 2308, Australia
| | - Jouke-Jan Hottenga
- Department of Biological Psychology, VU University Amsterdam, 1081 BT Amsterdam, The Netherlands
| | - William G. Iacono
- Department of Psychology, University of Minnesota, Minneapolis, MN 55455–0344, USA
| | - Thomas Illig
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
- Hannover Unified Biobank, Hannover Medical School, 30625 Hannover, Germany
| | - Marjo-Riitta Järvelin
- Institute of Health Sciences, University of Oulu, Oulu 90014, Finland
- Biocenter Oulu, University of Oulu, Oulu 90014, Finland
- Department of Epidemiology and Biostatistics, MRC-HPA Centre for Environment and Health, Imperial College London, London W2 1PG, UK
- Unit of Primary Care, Oulu University Hospital, Oulu 90220, Finland
- Department of Children and Young People and Families, National Institute for Health and Welfare, Oulu 90101, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital and University of Tampere School of Medicine, Tampere 33520, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland
- Department of Public Health, University of Helsinki, 00014 Helsinki, Finland
- Department of Mental Health and Substance Abuse Services, National Institute for Health and Welfare, 00300 Helsinki, Finland
| | | | - Matthew Kowgier
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Antti Latvala
- Department of Public Health, University of Helsinki, 00014 Helsinki, Finland
- Department of Mental Health and Substance Abuse Services, National Institute for Health and Welfare, 00300 Helsinki, Finland
| | - Lenore J. Launer
- National Institute on Aging, National Institutes of Health, Baltimore, MD 20892, USA
| | - Debbie A. Lawlor
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Bristol BS8 2PR, UK
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere University Hospital, Tampere 33520, Finland
| | - Jingmei Li
- Human Genetics, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Paul Lichtenstein
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Peter Lichtner
- Institute of Human Genetics, Helmholtz Centre Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - David C. Liewald
- Centre for Cognitive Aging and Cognitive Epidemiology, The University of Edinburgh, Edinburgh EH8 9JZ, Scotland, UK
| | - Pamela A. Madden
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Patrik K. E. Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Tomi E. Mäkinen
- Department of Health, Functional Capacity and Welfare, National Institute for Health and Welfare, Helsinki 00271, Finland
| | - Marco Masala
- Istituto di Ricerca Genetica e Biomedica, CNR, Monserrato, 09042, Cagliari, Italy
| | - Matt McGue
- Department of Psychology, University of Minnesota, Minneapolis, MN 55455–0344, USA
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Andreas Mielck
- Institute of Health Economics and Health Care Management, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Michael B. Miller
- Department of Psychology, University of Minnesota, Minneapolis, MN 55455–0344, USA
| | - Grant W. Montgomery
- Queensland Institute of Medical Research, 300 Herston Road, Brisbane, Queensland 4006, Australia
| | - Sutapa Mukherjee
- Western Australia Sleep Disorders Research Institute, Sir Charles Gairdner Hospital, Perth, Western Australia 6009, Australia
- Department of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Women’s College Research Institute, University of Toronto, Toronto, Ontario M5G 1N8, Canada
| | - Dale R. Nyholt
- Queensland Institute of Medical Research, 300 Herston Road, Brisbane, Queensland 4006, Australia
| | - Ben A. Oostra
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, the Netherlands
| | - Lyle J. Palmer
- Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Aarno Palotie
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
- Department of Medical Genetics, University of Helsinki, 00014 Helsinki, Finland
| | - Brenda Penninx
- Department of Psychiatry, VU University Medical Center, 1081 HL Amsterdam, The Netherlands
| | - Markus Perola
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland
- Public Health Genomics Unit, Department of Chronic Disease Prevention, The National Institute for Health and Welfare, Helsinki 00014, Finland
| | - Patricia A. Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109–2029, USA
| | - Martin Preisig
- Department of Internal Medicine, University Hospital, 1011 Lausanne, Switzerland
| | - Katri Räikkönen
- Institute of Behavioral Sciences, University of Helsinki, Helsinki 00014, Finland
| | - Olli T. Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku 20520, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku 20520, Finland
| | - Anu Realo
- Department of Psychology, University of Tartu, Tartu 50410, Estonia
| | - Susan M. Ring
- School of Social and Community Medicine, University of Bristol, Bristol BS8 2PR, UK
| | - Samuli Ripatti
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland
- Public Health Genomics Unit, Department of Chronic Disease Prevention, The National Institute for Health and Welfare, Helsinki 00014, Finland
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Fernando Rivadeneira
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
| | - Igor Rudan
- Centre for Population Health Sciences, The University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Aldo Rustichini
- Department of Economics, University of Minnesota, Minneapolis, MN 55455–0462, USA
| | - Veikko Salomaa
- Chronic Disease Epidemiology Unit, Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki 00271, Finland
| | - Antti-Pekka Sarin
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland
| | - David Schlessinger
- National Institute on Aging, National Institutes of Health, Baltimore, MD 20892, USA
| | - Rodney J. Scott
- Hunter Medical Research Institute and Faculty of Health, University of Newcastle, Newcastle, NSW 2308, Australia
| | - Harold Snieder
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Beate St Pourcain
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Bristol BS8 2PR, UK
- School of Oral and Dental Sciences, University of Bristol, Bristol BS1 2LY, UK
| | - John M. Starr
- Centre for Cognitive Aging and Cognitive Epidemiology, The University of Edinburgh, Edinburgh EH8 9JZ, Scotland, UK
- Alzheimer Scotland Dementia Research Centre, The University of Edinburgh, Edinburgh EH8 9JZ, Scotland, UK
| | - Jae Hoon Sul
- Department of Computer Science, University of California, Los Angeles, CA 90095, USA
| | - Ida Surakka
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland
- Public Health Genomics Unit, Department of Chronic Disease Prevention, The National Institute for Health and Welfare, Helsinki 00014, Finland
| | - Rauli Svento
- Department of Economics, Oulu Business School, University of Oulu, Oulu 90014, Finland
| | - Alexander Teumer
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Greifswald 17487, Germany
| | | | - Henning Tiemeier
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
- Department of Child and Adolescent Psychiatry, Erasmus Medical Center, 3000 CB Rotterdam, The Netherlands
| | - Frank JAan Rooij
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
| | - David R. Van Wagoner
- Heart and Vascular and Lerner Research Institutes, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Erkki Vartiainen
- Division of Welfare and Health Promotion, National Institute for Health and Welfare, Helsinki 00271, Finland
| | - Jorma Viikari
- Department of Medicine, Turku University Hospital, Turku 20520, Finland
| | - Peter Vollenweider
- Department of Internal Medicine, University Hospital, 1011 Lausanne, Switzerland
| | - Judith M. Vonk
- Department of Epidemiology, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | - Gérard Waeber
- Department of Internal Medicine, University Hospital, 1011 Lausanne, Switzerland
| | - David R. Weir
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI 48106, USA
| | - H.-Erich Wichmann
- Institute of Medical Informatics, Biometry and Epidemiology, Chair of Epidemiology, Ludwig-Maximilians-Universität, 81377 Munich, Germany
- Klinikum Grosshadern, 81377 Munich, Germany
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany
| | - Elisabeth Widen
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki 00014, Finland
| | - Gonneke Willemsen
- Department of Biological Psychology, VU University Amsterdam, 1081 BT Amsterdam, The Netherlands
| | - James F. Wilson
- Centre for Population Health Sciences, The University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Alan F. Wright
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Dalton Conley
- Department of Sociology, New York University, New York, NY 10012, USA
| | - George Davey-Smith
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Bristol BS8 2PR, UK
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Patrick J. F. Groenen
- Econometric Institute, Erasmus School of Economics, Erasmus University Rotterdam, Rotterdam 3000 DR, The Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
| | - Magnus Johannesson
- Department of Economics, Stockholm School of Economics, Stockholm 113 83, Sweden
| | - Sharon L.R. Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109–2029, USA
| | - Robert F. Krueger
- Department of Psychology, University of Minnesota, Minneapolis, MN 55455–0344, USA
| | - David Laibson
- Department of Economics, Harvard University, Cambridge, MA 02138, USA
| | - Nicholas G. Martin
- Queensland Institute of Medical Research, 300 Herston Road, Brisbane, Queensland 4006, Australia
| | - Michelle N. Meyer
- Petrie-Flom Center for Health Law Policy, Biotechnology, & Bioethics, Harvard Law School, Cambridge, MA 02138, USA
- Nelson A. Rockefeller Institute of Government, State University of New York, Albany, NY 12203–1003, USA
| | - Danielle Posthuma
- Department of Functional Genomics, VU University Amsterdam and VU Medical Center, 1081 HV Amsterdam, The Netherlands
- Department of Child and Adolescent Psychiatry, Erasmus Medical Center, 3000 CB Rotterdam, The Netherlands
- Department of Clinical Genetics, VU University Medical Centrer, 1081 BT Amsterdam, The Netherlands
| | - A. Roy Thurik
- Department of Applied Economics, Erasmus School of Economics, Erasmus University Rotterdam, 3000 DR Rotterdam, The Netherlands
- Panteia, Zoetermeer 2701 AA, Netherlands
- GSCM-Montpellier Business School, Montpellier 34185, France
| | - Nicholas J. Timpson
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Bristol BS8 2PR, UK
| | - André G. Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
| | - Cornelia M. van Duijn
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, the Netherlands
- Centre for Medical Systems Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Peter M. Visscher
- Queensland Institute of Medical Research, 300 Herston Road, Brisbane, Queensland 4006, Australia
- University of Queensland Diamantina Institute, The University of Queensland, Princess Alexandra Hospital, Brisbane, Queensland 4102, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | | | - David Cesarini
- Center for Experimental Social Science, Department of Economics, New York University, New York, NY 10012, USA
- Division of Social Science, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, UAE
- Research Institute of Industrial Economics, Stockholm 102 15, Sweden
| | - Philipp D. Koellinger
- Department of Applied Economics, Erasmus School of Economics, Erasmus University Rotterdam, 3000 DR Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam 3000 CA, The Netherlands
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Perzlmaier AF, Richter F, Seufert W. Translation initiation requires cell division cycle 123 (Cdc123) to facilitate biogenesis of the eukaryotic initiation factor 2 (eIF2). J Biol Chem 2013; 288:21537-46. [PMID: 23775072 DOI: 10.1074/jbc.m113.472290] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The eukaryotic translation initiation factor 2 (eIF2) is central to the onset of protein synthesis and its modulation in response to physiological demands. eIF2, a heterotrimeric G-protein, is activated by guanine nucleotide exchange to deliver the initiator methionyl-tRNA to the ribosome. Here we report that assembly of the eIF2 complex in vivo depends on Cdc123, a cell proliferation protein conserved among eukaryotes. Mutations of CDC123 in budding yeast reduced the association of eIF2 subunits, diminished polysome levels, and increased GCN4 expression indicating that Cdc123 is critical for eIF2 activity. Cdc123 bound the unassembled eIF2γ subunit, but not the eIF2 complex, and the C-terminal domain III region of eIF2γ was both necessary and sufficient for Cdc123 binding. Alterations of the binding site revealed a strict correlation between Cdc123 binding, the biological function of eIF2γ, and its ability to assemble with eIF2α and eIF2β. Interestingly, high levels of Cdc123 neutralized the assembly defect and restored the biological function of an eIF2γ mutant. Moreover, the combined overexpression of eIF2 subunits rescued an otherwise inviable cdc123 deletion mutant. Thus, Cdc123 is a specific eIF2 assembly factor indispensable for the onset of protein synthesis. Human Cdc123 is encoded by a disease risk locus, and, therefore, eIF2 biogenesis control by Cdc123 may prove relevant for normal cell physiology and human health. This work identifies a novel step in the eukaryotic translation initiation pathway and assigns a biochemical function to a protein that is essential for growth and viability of eukaryotic cells.
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Panasevich S, Melén E, Hallberg J, Bergström A, Svartengren M, Pershagen G, Nyberg F. Investigation of novel genes for lung function in children and their interaction with tobacco smoke exposure: a preliminary report. Acta Paediatr 2013; 102:498-503. [PMID: 23409998 DOI: 10.1111/apa.12204] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Revised: 12/20/2012] [Accepted: 02/12/2013] [Indexed: 01/06/2023]
Abstract
AIM To replicate newly reported single nucleotide polymorphism (SNP) associations with adult lung function in a cohort of children and to investigate interactions with tobacco smoke exposure on lung function. METHODS Of 37 reported SNPs in adults, 21 were available in our genome-wide association study data set, either directly genotyped or as proxy SNPs. We tested for association with lung function (FEV1 , FVC, FEV1 /FVC%) in 8-year-old children and analysed interaction with tobacco smoke exposure both prenatally and/or during infancy, as well as at the age of 8 years. RESULTS SNPs in TNS1, ADAM19, THSD4 and ADCY2 showed significant association with lung function in children, although ADCY2 variants not in the expected direction. For example, variant allele A in THSD4 rs12899618 was associated with 50.2 mL higher FEV1 (p = 0.007) and variant allele C in ADAM19 rs2277027 with 1% unit lower FEV1 /FVC% (p = 0.03) per allele. DAAM2 rs2395730 showed interaction with current tobacco smoke exposure, with variant C allele associated with 1.3% unit decrease in FEV1 /FVC% in exposed children, but not in unexposed (p for interaction 0.04). CONCLUSION Our data replicate in children an association for TNS1, ADAM19, THSD4 and ADCY2 gene variants with lung function and suggest that interaction with tobacco smoke exposure may be of importance.
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Affiliation(s)
| | | | | | - Anna Bergström
- Institute of Environmental Medicine; Karolinska Institutet; Stockholm; Sweden
| | - Magnus Svartengren
- Department of Public Health Sciences; Karolinska Institutet; Stockholm; Sweden
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Genome-wide association study identifies multiple susceptibility loci for pulmonary fibrosis. Nat Genet 2013; 45:613-20. [PMID: 23583980 PMCID: PMC3677861 DOI: 10.1038/ng.2609] [Citation(s) in RCA: 566] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 03/18/2013] [Indexed: 12/14/2022]
Abstract
We performed a genome-wide association study in non-Hispanic white subjects with fibrotic idiopathic interstitial pneumonias (N=1616) and controls (N=4683); replication was assessed in 876 cases and 1890 controls. We confirmed association with TERT and MUC5B on chromosomes 5p15 and 11p15, respectively, the chromosome 3q26 region near TERC, and identified 7 novel loci (PMeta = 2.4×10−8 to PMeta = 1.1×10−19). The novel loci include FAM13A (4q22), DSP (6p24), OBFC1 (10q24), ATP11A (13q34), DPP9 (19p13), and chromosomal regions 7q22 and 15q14-15. Our results demonstrate that genes involved in host defense, cell-cell adhesion, and DNA repair contribute to the risk of fibrotic IIP.
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Loth DW, Ittermann T, Lahousse L, Hofman A, Leufkens HGM, Brusselle GG, Stricker BH. Normal spirometry values in healthy elderly: the Rotterdam Study. Eur J Epidemiol 2013; 28:329-34. [PMID: 23539359 DOI: 10.1007/s10654-013-9800-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2012] [Accepted: 03/20/2013] [Indexed: 10/27/2022]
Abstract
Although many different reference values for spirometry are available from various studies, the elderly are usually underrepresented. Therefore, our objective was to assess reference values in a sample of healthy participants from a prospective population-based cohort study, including a large proportion of elderly. We included spirometry measurements of healthy, never smokers, from the Rotterdam Study and excluded participants with respiratory symptoms or prescriptions for respiratory medication. Age- and height-specific curves for the 5th (lower limit of normal) and the 50th (median) percentile of Forced Expiratory Volume in 1 s (FEV1), Forced Vital Capacity (FVC), and the ratio (FEV1/FVC) were calculated by quantile regression models. The group of healthy elderly study subjects consisted of 1,125 individuals, with a mean age of 68 years, ranging from 47 to 96 years of age. Sex stratified equations for the median and the lower limit of normal were calculated adjusted for age and height. In this study, we report age- and height-dependent reference limits for FEV1, FVC, and FEV1/FVC in a large population, and prediction equations for the lower limit of normal and median values for a sample containing a large proportion of healthy elderly.
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Affiliation(s)
- Daan Willem Loth
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands.
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Li X, Hawkins GA, Ampleford EJ, Moore WC, Li H, Hastie AT, Howard TD, Boushey HA, Busse WW, Calhoun WJ, Castro M, Erzurum SC, Israel E, Lemanske RF, Szefler SJ, Wasserman SI, Wenzel SE, Peters SP, Meyers DA, Bleecker ER. Genome-wide association study identifies TH1 pathway genes associated with lung function in asthmatic patients. J Allergy Clin Immunol 2013; 132:313-20.e15. [PMID: 23541324 DOI: 10.1016/j.jaci.2013.01.051] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 12/18/2012] [Accepted: 01/18/2013] [Indexed: 11/17/2022]
Abstract
BACKGROUND Recent meta-analyses of genome-wide association studies in general populations of European descent have identified 28 loci for lung function. OBJECTIVE We sought to identify novel lung function loci specifically for asthma and to confirm lung function loci identified in general populations. METHODS Genome-wide association studies of lung function (percent predicted FEV1 [ppFEV1], percent predicted forced vital capacity, and FEV1/forced vital capacity ratio) were performed in 4 white populations of European descent (n = 1544), followed by meta-analyses. RESULTS Seven of 28 previously identified lung function loci (HHIP, FAM13A, THSD4, GSTCD, NOTCH4-AGER, RARB, and ZNF323) identified in general populations were confirmed at single nucleotide polymorphism (SNP) levels (P < .05). Four of 32 loci (IL12A, IL12RB1, STAT4, and IRF2) associated with ppFEV1 (P < 10(-4)) belong to the TH1 or IL-12 cytokine family pathway. By using a linear additive model, these 4 TH1 pathway SNPs cumulatively explained 2.9% to 7.8% of the variance in ppFEV1 values in 4 populations (P = 3 × 10(-11)). Genetic scores of these 4 SNPs were associated with ppFEV1 values (P = 2 × 10(-7)) and the American Thoracic Society severe asthma classification (P = .005) in the Severe Asthma Research Program population. TH2 pathway genes (IL13, TSLP, IL33, and IL1RL1) conferring asthma susceptibility were not associated with lung function. CONCLUSION Genes involved in airway structure/remodeling are associated with lung function in both general populations and asthmatic subjects. TH1 pathway genes involved in anti-virus/bacterial infection and inflammation modify lung function in asthmatic subjects. Genes associated with lung function that might affect asthma severity are distinct from those genes associated with asthma susceptibility.
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Affiliation(s)
- Xingnan Li
- Center for Genomics and Personalized Medicine Research, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA.
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Kerr SM, Campbell A, Murphy L, Hayward C, Jackson C, Wain LV, Tobin MD, Dominiczak A, Morris A, Smith BH, Porteous DJ. Pedigree and genotyping quality analyses of over 10,000 DNA samples from the Generation Scotland: Scottish Family Health Study. BMC MEDICAL GENETICS 2013; 14:38. [PMID: 23521772 PMCID: PMC3614907 DOI: 10.1186/1471-2350-14-38] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Accepted: 03/14/2013] [Indexed: 11/27/2022]
Abstract
Background Generation Scotland: Scottish Family Health Study (GS:SFHS) is a family-based biobank of 24,000 participants with rich phenotype and DNA available for genetic research. This paper describes the laboratory results from genotyping 32 single nucleotide polymorphisms (SNPs) on DNA from over 10,000 participants who attended GS:SFHS research clinics. The analysis described here was undertaken to test the quality of genetic information available to researchers. The success rate of each marker genotyped (call rate), minor allele frequency and adherence to Mendelian inheritance are presented. The few deviations in marker transmission in the 925 parent-child trios analysed were assessed as to whether they were likely to be miscalled genotypes, data or sample handling errors, or pedigree inaccuracies including non-paternity. Methods The first 10,450 GS:SFHS clinic participants who had spirometry and smoking data available and DNA extracted were selected. 32 SNPs were assayed, chosen as part of a replication experiment from a Genome-Wide Association Study meta-analysis of lung function. Results In total 325,336 genotypes were returned. The overall project pass rate (32 SNPs on 10,450 samples) was 97.29%. A total of 925 parent-child trios were assessed for transmission of the SNP markers, with 16 trios indicating evidence of inconsistency in the recorded pedigrees. Conclusions The Generation Scotland: Scottish Family Health Study used well-validated study methods and can produce good quality genetic data, with a low error rate. The GS:SFHS DNA samples are of high quality and the family groups were recorded and processed with accuracy during collection of the cohort.
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Affiliation(s)
- Shona M Kerr
- Centre for Molecular Medicine, University of Edinburgh, Institute of Genetics and Molecular Medicine, Western General Hospital, Crewe Road, Edinburgh, UK.
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Zhang R, Zhao Y, Chu M, Mehta A, Wei Y, Liu Y, Xun P, Bai J, Yu H, Su L, Zhang H, Hu Z, Shen H, Chen F, Christiani DC. A large scale gene-centric association study of lung function in newly-hired female cotton textile workers with endotoxin exposure. PLoS One 2013; 8:e59035. [PMID: 23527081 PMCID: PMC3602449 DOI: 10.1371/journal.pone.0059035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 02/08/2013] [Indexed: 02/02/2023] Open
Abstract
Background Occupational exposure to endotoxin is associated with decrements in pulmonary function, but how much variation in this association is explained by genetic variants is not well understood. Objective We aimed to identify single nucleotide polymorphisms (SNPs) that are associated with the rate of forced expiratory volume in one second (FEV1) decline by a large scale genetic association study in newly-hired healthy young female cotton textile workers. Methods DNA samples were genotyped using the Illumina Human CVD BeadChip. Change rate in FEV1 was modeled as a function of each SNP genotype in linear regression model with covariate adjustment. We controlled the type 1 error in study-wide level by permutation method. The false discovery rate (FDR) and the family-wise error rate (FWER) were set to be 0.10 and 0.15 respectively. Results Two SNPs were found to be significant (P<6.29×10−5), including rs1910047 (P = 3.07×10−5, FDR = 0.0778) and rs9469089 (P = 6.19×10−5, FDR = 0.0967), as well as other eight suggestive (P<5×10−4) associated SNPs. Gene-gene and gene-environment interactions were also observed, such as rs1910047 and rs1049970 (P = 0.0418, FDR = 0.0895); rs9469089 and age (P = 0.0161, FDR = 0.0264). Genetic risk score analysis showed that the more risk loci the subjects carried, the larger the rate of FEV1 decline occurred (Ptrend = 3.01×10−18). However, the association was different among age subgroups (P = 7.11×10−6) and endotoxin subgroups (P = 1.08×10−2). Functional network analysis illustrates potential biological connections of all interacted genes. Conclusions Genetic variants together with environmental factors interact to affect the rate of FEV1 decline in cotton textile workers.
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Affiliation(s)
- Ruyang Zhang
- Department of Epidemiology and Biostatistics and Ministry of Education (MOE) Key Lab for Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China
- Section of Clinical Epidemiology, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Cancer Center, Nanjing Medical University, Nanjing, China
| | - Yang Zhao
- Department of Epidemiology and Biostatistics and Ministry of Education (MOE) Key Lab for Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Minjie Chu
- Department of Epidemiology and Biostatistics and Ministry of Education (MOE) Key Lab for Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China
- Section of Clinical Epidemiology, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Cancer Center, Nanjing Medical University, Nanjing, China
| | - Amar Mehta
- Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Yongyue Wei
- Department of Epidemiology and Biostatistics and Ministry of Education (MOE) Key Lab for Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Yao Liu
- Department of Epidemiology and Biostatistics and Ministry of Education (MOE) Key Lab for Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China
- Section of Clinical Epidemiology, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Cancer Center, Nanjing Medical University, Nanjing, China
| | - Pengcheng Xun
- Department of Epidemiology and Biostatistics, School of Public Health, Indiana University Bloomington, Bloomington, Indiana, United States of America
| | - Jianling Bai
- Department of Epidemiology and Biostatistics and Ministry of Education (MOE) Key Lab for Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Hao Yu
- Department of Epidemiology and Biostatistics and Ministry of Education (MOE) Key Lab for Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Li Su
- Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Hongxi Zhang
- Putuo District Peoples Hospital, Shanghai Second Medical University, Shanghai, China
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics and Ministry of Education (MOE) Key Lab for Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China
- Section of Clinical Epidemiology, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Cancer Center, Nanjing Medical University, Nanjing, China
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics and Ministry of Education (MOE) Key Lab for Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China
- Section of Clinical Epidemiology, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Cancer Center, Nanjing Medical University, Nanjing, China
| | - Feng Chen
- Department of Epidemiology and Biostatistics and Ministry of Education (MOE) Key Lab for Modern Toxicology, School of Public Health, Nanjing Medical University, Nanjing, China
- * E-mail: (FC); (DCC)
| | - David C. Christiani
- Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Pulmonary and Critical Care Unit, Department of Medicine, Massachusetts General Hospital/Harvard Medical School, Boston, Massachusetts, United States of America
- * E-mail: (FC); (DCC)
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292
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Bossé Y. Research Highlights: Highlights from the latest articles in chronic obstructive pulmonary disease genetics. Per Med 2013; 10:123-125. [DOI: 10.2217/pme.13.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Yohan Bossé
- Laval University, Department of Molecular Medicine, Institut universitaire de cardiologie et de pneumologie de Québec, Pavillon Marguerite-d’Youville, Y4190, 2725 Chemin Sainte-Foy, Québec, Canada
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Bai C. Respiratory diseases call for special attention from clinical and translational science. TRANSLATIONAL RESPIRATORY MEDICINE 2013; 1:1. [PMID: 27234383 PMCID: PMC6733423 DOI: 10.1186/2213-0802-1-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 10/02/2012] [Indexed: 02/01/2023]
Abstract
Respiratory diseases will become one of the top 3 leading causes of estimated mortality in 2020 and become about one third of total causes of estimated mortality. The journal of Translational Respiratory Medicine is a truly international, peer-reviewed journal devoted to the publication of articles on outstanding work with translational potentials between basic research and clinical application to understanding respiratory disease. Translational respiratory medicine will more focus on biomarker identification and validation in pulmonary diseases in combination with clinical informatics, targeted proteomics, bioinformatics, systems medicine, or mathematical science; on different translational strategies of cell-based therapy to clinical application to treat lung diseases; on targeted therapies in combination with personalized medicine; and on distant electronic medicine to monitor a large population of people’s health. Translational Respiratory Medicine is an additional but unique opportunity for scientists and clinicians who work on pulmonary diseases to publish their outstanding findings, initiative results, and critical and perceptive opinions in the journal.
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Affiliation(s)
- Chunxue Bai
- Shanghai Respiratory Research Institute, Respiratory Research Institute, Department of Respiratory Medicine, Zhongshan Hospital, Fudan University Shanghai School of Medicine, Shanghai, China.
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294
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Hwang JY, Lee SH, Go MJ, Kim BJ, Kou I, Ikegawa S, Guo Y, Deng HW, Raychaudhuri S, Kim YJ, Oh JH, Kim Y, Moon S, Kim DJ, Koo H, Cha MJ, Lee MH, Yun JY, Yoo HS, Kang YA, Cho EH, Kim SW, Oh KW, Kang MI, Son HY, Kim SY, Kim GS, Han BG, Cho YS, Cho MC, Lee JY, Koh JM. Meta-analysis identifies a MECOM gene as a novel predisposing factor of osteoporotic fracture. J Med Genet 2013; 50:212-9. [PMID: 23349225 DOI: 10.1136/jmedgenet-2012-101156] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND Osteoporotic fracture (OF) as a clinical endpoint is a major complication of osteoporosis. To screen for OF susceptibility genes, we performed a genome-wide association study and carried out de novo replication analysis of an East Asian population. METHODS Association was tested using a logistic regression analysis. A meta-analysis was performed on the combined results using effect size and standard errors estimated for each study. RESULTS In a combined meta-analysis of a discovery cohort (288 cases and 1139 controls), three hospital based sets in replication stage I (462 cases and 1745 controls), and an independent ethnic group in replication stage II (369 cases and 560 for controls), we identified a new locus associated with OF (rs784288 in the MECOM gene) that showed genome-wide significance (p=3.59×10(-8); OR 1.39). RNA interference revealed that a MECOM knockdown suppresses osteoclastogenesis. CONCLUSIONS Our findings provide new insights into the genetic architecture underlying OF in East Asians.
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Affiliation(s)
- Joo-Yeon Hwang
- Center for Genome Science, National Institute of Health, Chungcheongbuk-do, Republic of Korea
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295
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Affiliation(s)
- Erik Melén
- Institute of Environmental Medicine and Centre for Allergy Research, Karolinska Institutet, Stockholm,
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296
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Hancock DB, Artigas MS, Gharib SA, Henry A, Manichaikul A, Ramasamy A, Loth DW, Imboden M, Koch B, McArdle WL, Smith AV, Smolonska J, Sood A, Tang W, Wilk JB, Zhai G, Zhao JH, Aschard H, Burkart KM, Curjuric I, Eijgelsheim M, Elliott P, Gu X, Harris TB, Janson C, Homuth G, Hysi PG, Liu JZ, Loehr LR, Lohman K, Loos RJF, Manning AK, Marciante KD, Obeidat M, Postma DS, Aldrich MC, Brusselle GG, Chen TH, Eiriksdottir G, Franceschini N, Heinrich J, Rotter JI, Wijmenga C, Williams OD, Bentley AR, Hofman A, Laurie CC, Lumley T, Morrison AC, Joubert BR, Rivadeneira F, Couper DJ, Kritchevsky SB, Liu Y, Wjst M, Wain LV, Vonk JM, Uitterlinden AG, Rochat T, Rich SS, Psaty BM, O'Connor GT, North KE, Mirel DB, Meibohm B, Launer LJ, Khaw KT, Hartikainen AL, Hammond CJ, Gläser S, Marchini J, Kraft P, Wareham NJ, Völzke H, Stricker BHC, Spector TD, Probst-Hensch NM, Jarvis D, Jarvelin MR, Heckbert SR, Gudnason V, Boezen HM, Barr RG, Cassano PA, Strachan DP, Fornage M, Hall IP, Dupuis J, Tobin MD, London SJ. Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function. PLoS Genet 2012; 8:e1003098. [PMID: 23284291 PMCID: PMC3527213 DOI: 10.1371/journal.pgen.1003098] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 10/01/2012] [Indexed: 01/20/2023] Open
Abstract
Genome-wide association studies have identified numerous genetic loci for spirometic measures of pulmonary function, forced expiratory volume in one second (FEV(1)), and its ratio to forced vital capacity (FEV(1)/FVC). Given that cigarette smoking adversely affects pulmonary function, we conducted genome-wide joint meta-analyses (JMA) of single nucleotide polymorphism (SNP) and SNP-by-smoking (ever-smoking or pack-years) associations on FEV(1) and FEV(1)/FVC across 19 studies (total N = 50,047). We identified three novel loci not previously associated with pulmonary function. SNPs in or near DNER (smallest P(JMA = )5.00×10(-11)), HLA-DQB1 and HLA-DQA2 (smallest P(JMA = )4.35×10(-9)), and KCNJ2 and SOX9 (smallest P(JMA = )1.28×10(-8)) were associated with FEV(1)/FVC or FEV(1) in meta-analysis models including SNP main effects, smoking main effects, and SNP-by-smoking (ever-smoking or pack-years) interaction. The HLA region has been widely implicated for autoimmune and lung phenotypes, unlike the other novel loci, which have not been widely implicated. We evaluated DNER, KCNJ2, and SOX9 and found them to be expressed in human lung tissue. DNER and SOX9 further showed evidence of differential expression in human airway epithelium in smokers compared to non-smokers. Our findings demonstrated that joint testing of SNP and SNP-by-environment interaction identified novel loci associated with complex traits that are missed when considering only the genetic main effects.
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Affiliation(s)
- Dana B. Hancock
- Behavioral Health Epidemiology Program, Research Triangle Institute International, Research Triangle Park, North Carolina, United States of America
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, U.S. Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - María Soler Artigas
- Departments of Health Sciences and Genetics, University of Leicester, Leicester, United Kingdom
| | - Sina A. Gharib
- Center for Lung Biology, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Amanda Henry
- Division of Therapeutics and Molecular Medicine, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
- Department of Public Health Sciences, Division of Biostatistics and Epidemiology, University of Virginia, Charlottesville, Virginia, United States of America
| | - Adaikalavan Ramasamy
- Respiratory Epidemiology and Public Health, Imperial College London, London, United Kingdom
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
- Department of Medical and Molecular Genetics, King's College London, Guy's Hospital, London, United Kingdom
| | - Daan W. Loth
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Inspectorate of Healthcare, The Hague, The Netherlands
| | - Medea Imboden
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Beate Koch
- Department of Internal Medicine B, University Hospital Greifswald, Greifswald, Germany
| | - Wendy L. McArdle
- ALSPAC, School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Albert V. Smith
- Icelandic Heart Association, Kopavogur, Iceland
- University of Iceland, Reykjavik, Iceland
| | - Joanna Smolonska
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Akshay Sood
- Department of Medicine, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Wenbo Tang
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, United States of America
| | - Jemma B. Wilk
- Division of Aging, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
- The National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts, United States of America
| | - Guangju Zhai
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | - Jing Hua Zhao
- MRC Epidemiology Unit, Institute of Metabolic Science, Cambridge, United Kingdom
| | - Hugues Aschard
- Program in Molecular and Genetic Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Kristin M. Burkart
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, New York, United States of America
| | - Ivan Curjuric
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Mark Eijgelsheim
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
- MRC-HPA Centre for Environment and Health, Imperial College London, London, United Kingdom
| | - Xiangjun Gu
- Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Tamara B. Harris
- National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Christer Janson
- Department of Medical Sciences, Respiratory Medicine, Uppsala University, Uppsala, Sweden
| | - Georg Homuth
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Pirro G. Hysi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Jason Z. Liu
- Department of Statistics, University of Oxford, United Kingdom
| | - Laura R. Loehr
- Gillings School of Global Public Health, Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Kurt Lohman
- Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Ruth J. F. Loos
- MRC Epidemiology Unit, Institute of Metabolic Science, Cambridge, United Kingdom
| | - Alisa K. Manning
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Kristin D. Marciante
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Ma'en Obeidat
- Division of Therapeutics and Molecular Medicine, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom
| | - Dirkje S. Postma
- Department of Pulmonology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- GRIAC Research Institute, University Medical Center Groningen, Groningen, The Netherlands
| | - Melinda C. Aldrich
- Department of Thoracic Surgery and Division of Epidemiology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Guy G. Brusselle
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Ting-hsu Chen
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, Veterans Administration Boston Healthcare System, Boston, Massachusetts, United States of America
- The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | | | - Nora Franceschini
- Gillings School of Global Public Health, Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Joachim Heinrich
- Institute of Epidemiology I, Helmholtz Zentrum München, Munich, Germany
| | - Jerome I. Rotter
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - O. Dale Williams
- Department of Biostatistics, Robert Stempel College of Public Health and Social Work, Florida International University, Miami, Florida, United States of America
| | - Amy R. Bentley
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Cathy C. Laurie
- Department of Biostatistics, University of Washington, Seattle, Washington, United States of America
| | - Thomas Lumley
- Department of Statistics, University of Auckland, Auckland, New Zealand
| | - Alanna C. Morrison
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Bonnie R. Joubert
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, U.S. Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
| | - Fernando Rivadeneira
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
- Netherlands Genomics Initiative (NGI)–sponsored Netherlands Consortium for Healthy Aging (NCHA), Leiden, The Netherlands
| | - David J. Couper
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Stephen B. Kritchevsky
- Sticht Center on Aging, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Yongmei Liu
- Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Matthias Wjst
- Institute of Lung Biology and Disease, Comprehensive Pneumology Center, Helmholtz Zentrum München, Neuherberg, Germany
- Institute for Medical Statistics and Epidemiology (IMSE), Technical University Munich, Munich, Germany
| | - Louise V. Wain
- Departments of Health Sciences and Genetics, University of Leicester, Leicester, United Kingdom
| | - Judith M. Vonk
- GRIAC Research Institute, University Medical Center Groningen, Groningen, The Netherlands
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- The LifeLines Cohort Study, Groningen, The Netherlands
| | - André G. Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
- Netherlands Genomics Initiative (NGI)–sponsored Netherlands Consortium for Healthy Aging (NCHA), Leiden, The Netherlands
| | - Thierry Rochat
- Division of Pulmonary Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, United States of America
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit and Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Departments of Medicine and Health Services, University of Washington, Seattle, United States of America
- Group Health Research Institute, Group Health Cooperative, Seattle, Washington
| | - George T. O'Connor
- The National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts, United States of America
- The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Kari E. North
- Gillings School of Global Public Health, Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Daniel B. Mirel
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Bernd Meibohm
- College of Pharmacy, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Lenore J. Launer
- National Institute on Aging, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kay-Tee Khaw
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Anna-Liisa Hartikainen
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Oulu, Oulu, Finland
| | - Christopher J. Hammond
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Sven Gläser
- Department of Internal Medicine B, University Hospital Greifswald, Greifswald, Germany
| | | | - Peter Kraft
- Departments of Epidemiology and Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Nicholas J. Wareham
- MRC Epidemiology Unit, Institute of Metabolic Science, Cambridge, United Kingdom
| | - Henry Völzke
- Institute for Community Medicine, Study of Health In Pomerania (SHIP)/Clinical Epidemiological Research, University of Greifswald, Greifswald, Germany
| | - Bruno H. C. Stricker
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Inspectorate of Healthcare, The Hague, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Medical Informatics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Timothy D. Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
| | - Nicole M. Probst-Hensch
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Deborah Jarvis
- Respiratory Epidemiology and Public Health, Imperial College London, London, United Kingdom
- MRC-HPA Centre for Environment and Health, Imperial College London, London, United Kingdom
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, United Kingdom
- MRC-HPA Centre for Environment and Health, Imperial College London, London, United Kingdom
- Department of Children, Young People, and Families, National Institute for Health and Welfare, Oulu, Finland
- Institute of Health Sciences, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Susan R. Heckbert
- Cardiovascular Health Research Unit and Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Group Health Research Institute, Group Health Cooperative, Seattle, Washington
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- University of Iceland, Reykjavik, Iceland
| | - H. Marike Boezen
- GRIAC Research Institute, University Medical Center Groningen, Groningen, The Netherlands
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- The LifeLines Cohort Study, Groningen, The Netherlands
| | - R. Graham Barr
- Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, New York, United States of America
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Patricia A. Cassano
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, United States of America
- Department of Public Health, Weill Cornell Medical College, New York, New York, United States of America
| | - David P. Strachan
- Division of Population Health Sciences and Education, St. George's University of London, London, United Kingdom
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Ian P. Hall
- Division of Therapeutics and Molecular Medicine, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom
| | - Josée Dupuis
- The National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, Massachusetts, United States of America
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Martin D. Tobin
- Departments of Health Sciences and Genetics, University of Leicester, Leicester, United Kingdom
| | - Stephanie J. London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, U.S. Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
- Laboratory of Respiratory Biology, National Institute of Environmental Health Sciences, National Institutes of Health, U.S. Department of Health and Human Services, Research Triangle Park, North Carolina, United States of America
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297
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Wain LV, Soler Artigas M, Tobin MD. What can genetics tell us about the cause of fixed airflow obstruction? Clin Exp Allergy 2012; 42:1176-82. [PMID: 22805464 DOI: 10.1111/j.1365-2222.2012.03967.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is a major cause of chronic morbidity and mortality worldwide with smoking being the most important risk factor of the disease. However, lung function and COPD are known to also have a genetic component and a deeper knowledge of the genetic architecture of the disease could lead to further understanding of predisposition to COPD and also to development of new therapeutic interventions. Genetic linkage studies and candidate gene association studies have not provided evidence to convincingly identify the genes underlying lung function or COPD. However, recent large genome-wide association studies (GWAS) including tens of thousands of individuals have identified 26 variants at different loci in the human genome that show robust association with quantitative lung function measures in the general population. A growing number of these variants are being shown to be associated with COPD. Following the identification of these new lung function loci, the challenge now lies in refining the signals to identify the causative variants underlying the association signals and relating these signals to the molecular pathways that underlie lung function.
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Affiliation(s)
- L V Wain
- Department of Health Sciences, University of Leicester, Leicester, UK
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Wang X, Ward PA. Opportunities and challenges of disease biomarkers: a new section in the Journal of Translational Medicine. J Transl Med 2012; 10:240. [PMID: 23217078 PMCID: PMC3543303 DOI: 10.1186/1479-5876-10-240] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Accepted: 11/01/2012] [Indexed: 11/10/2022] Open
Abstract
Disease biomarkers are defined to diagnose various phases of diseases, monitor severities of diseases and responses to therapies, or predict prognosis of patients. Disease-specific biomarkers should benefit drug discovery and development, integrate multidisciplinary sciences, be validated by molecular imaging. The opportunities and challenges in biomarker development are emphasized and considered. The Journal of Translational Medicine opens a new Section of Disease Biomarkers to bridge identification and validation of gene or protein-based biomarkers, network biomarkers, dynamic network biomarkers in human diseases, patient phenotypes, and clinical applications. Disease biomarkers are also important for determining drug effects, target specificities and binding, dynamic metabolism and pharmacological kinetics, or toxicity profiles.
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Affiliation(s)
- Xiangdong Wang
- Department of Respiratory Medicine, Biomedical Research Center, Zhongshan Hospital Qing-Pu Branch, Fudan University, Shanghai, China.
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Gertow K, Sennblad B, Strawbridge RJ, Ohrvik J, Zabaneh D, Shah S, Veglia F, Fava C, Kavousi M, McLachlan S, Kivimäki M, Bolton JL, Folkersen L, Gigante B, Leander K, Vikström M, Larsson M, Silveira A, Deanfield J, Voight BF, Fontanillas P, Sabater-Lleal M, Colombo GI, Kumari M, Langenberg C, Wareham NJ, Uitterlinden AG, Gabrielsen A, Hedin U, Franco-Cereceda A, Nyyssönen K, Rauramaa R, Tuomainen TP, Savonen K, Smit AJ, Giral P, Mannarino E, Robertson CM, Talmud PJ, Hedblad B, Hofman A, Erdmann J, Reilly MP, O'Donnell CJ, Farrall M, Clarke R, Franzosi MG, Seedorf U, Syvänen AC, Hansson GK, Eriksson P, Samani NJ, Watkins H, Price JF, Hingorani AD, Melander O, Witteman JCM, Baldassarre D, Tremoli E, de Faire U, Humphries SE, Hamsten A. Identification of the BCAR1-CFDP1-TMEM170A locus as a determinant of carotid intima-media thickness and coronary artery disease risk. CIRCULATION. CARDIOVASCULAR GENETICS 2012; 5:656-65. [PMID: 23152477 DOI: 10.1161/circgenetics.112.963660] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
BACKGROUND Carotid intima-media thickness (cIMT) is a widely accepted marker of subclinical atherosclerosis. To date, large-scale investigations of genetic determinants of cIMT are sparse. METHODS AND RESULTS To identify cIMT-associated genes and genetic variants, a discovery analysis using the Illumina 200K CardioMetabochip was conducted in 3430 subjects with detailed ultrasonographic determinations of cIMT from the IMPROVE (Carotid Intima Media Thickness [IMT] and IMT-Progression as Predictors of Vascular Events in a High Risk European Population) study. Segment-specific IMT measurements of common carotid, bifurcation, and internal carotid arteries, and composite IMT variables considering the whole carotid tree (IMT(mean), IMT(max), and IMT(mean-max)), were analyzed. A replication stage investigating 42 single-nucleotide polymorphisms for association with common carotid IMT was undertaken in 5 independent European cohorts (total n=11,590). A locus on chromosome 16 (lead single-nucleotide polymorphism rs4888378, intronic in CFDP1) was associated with cIMT at significance levels passing multiple testing correction at both stages (array-wide significant discovery P=6.75 × 10(-7) for IMT(max); replication P=7.24×10(-6) for common cIMT; adjustments for sex, age, and population substructure where applicable; minor allele frequency 0.43 and 0.41, respectively). The protective minor allele was associated with lower carotid plaque score in a replication cohort (P=0.04, n=2120) and lower coronary artery disease risk in 2 case-control studies of subjects with European ancestry (odds ratio [95% confidence interval] 0.83 [0.77-0.90], P=6.53 × 10(-6), n=13 591; and 0.95 [0.92-0.98], P=1.83 × 10(-4), n=82 297, respectively). Queries of human biobank data sets revealed associations of rs4888378 with nearby gene expression in vascular tissues (n=126-138). CONCLUSIONS This study identified rs4888378 in the BCAR1-CFDP1-TMEM170A locus as a novel genetic determinant of cIMT and coronary artery disease risk in individuals of European descent.
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Affiliation(s)
- Karl Gertow
- Atherosclerosis Research Unit, Karolinska University Hospital Solna, Center for Molecular Medicine, Stockholm, Sweden.
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Velez Edwards DR, Naj AC, Monda K, North KE, Neuhouser M, Magvanjav O, Kusimo I, Vitolins MZ, Manson JE, O'Sullivan MJ, Rampersaud E, Edwards TL. Gene-environment interactions and obesity traits among postmenopausal African-American and Hispanic women in the Women's Health Initiative SHARe Study. Hum Genet 2012. [PMID: 23192594 DOI: 10.1007/s00439-012-1246-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Genome-wide association studies (GWAS) of obesity measures have identified associations with single nucleotide polymorphisms (SNPs). However, no large-scale evaluation of gene-environment interactions has been performed. We conducted a search of gene-environment (G × E) interactions in post-menopausal African-American and Hispanic women from the Women's Health Initiative SNP Health Association Resource GWAS study. Single SNP linear regression on body mass index (BMI) and waist-to-hip circumference ratio (WHR) adjusted for multidimensional-scaling-derived axes of ancestry and age was run in race-stratified data with 871,512 SNPs available from African-Americans (N = 8,203) and 786,776 SNPs from Hispanics (N = 3,484). Tests of G × E interaction at all SNPs for recreational physical activity (m h/week), dietary energy intake (kcal/day), alcohol intake (categorical), cigarette smoking years, and cigarette smoking (ever vs. never) were run in African-Americans and Hispanics adjusted for ancestry and age at interview, followed by meta-analysis of G × E interaction terms. The strongest evidence for concordant G × E interactions in African-Americans and Hispanics was for smoking and marker rs10133840 (Q statistic P = 0.70, beta = -0.01, P = 3.81 × 10(-7)) with BMI as the outcome. The strongest evidence for G × E interaction within a cohort was in African-Americans with WHR as outcome for dietary energy intake and rs9557704 (SNP × kcal = -0.04, P = 2.17 × 10(-7)). No results exceeded the Bonferroni-corrected statistical significance threshold.
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Affiliation(s)
- Digna R Velez Edwards
- Center for Human Genetics Research, Vanderbilt Epidemiology Center Institute of Medicine and Public Health, Vanderbilt University, 2525 West End Avenue, Suite 600 6th fl, Nashville, TN 37203, USA
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