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Wang Y, Gorlova OY, Gorlov IP, Zhu M, Dai J, Albanes D, Lam S, Tardon A, Chen C, Goodman GE, Bojesen SE, Landi MT, Johansson M, Risch A, Wichmann HE, Bickeboller H, Christiani DC, Rennert G, Arnold SM, Brennan P, Field JK, Shete S, Le Marchand L, Melander O, Brunnstrom H, Liu G, Hung RJ, Andrew AS, Kiemeney LA, Zienolddiny S, Grankvist K, Johansson M, Caporaso NE, Woll PJ, Lazarus P, Schabath MB, Aldrich MC, Stevens VL, Ma H, Jin G, Hu Z, Amos CI, Shen H. Association Analysis of Driver Gene-Related Genetic Variants Identified Novel Lung Cancer Susceptibility Loci with 20,871 Lung Cancer Cases and 15,971 Controls. Cancer Epidemiol Biomarkers Prev 2020; 29:1423-1429. [PMID: 32277007 PMCID: PMC8120681 DOI: 10.1158/1055-9965.epi-19-1085] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 11/10/2019] [Accepted: 04/07/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND A substantial proportion of cancer driver genes (CDG) are also cancer predisposition genes. However, the associations between genetic variants in lung CDGs and the susceptibility to lung cancer have rarely been investigated. METHODS We selected expression-related single-nucleotide polymorphisms (eSNP) and nonsynonymous variants of lung CDGs, and tested their associations with lung cancer risk in two large-scale genome-wide association studies (20,871 cases and 15,971 controls of European descent). Conditional and joint association analysis was performed to identify independent risk variants. The associations of independent risk variants with somatic alterations in lung CDGs or recurrently altered pathways were investigated using data from The Cancer Genome Atlas (TCGA) project. RESULTS We identified seven independent SNPs in five lung CDGs that were consistently associated with lung cancer risk in discovery (P < 0.001) and validation (P < 0.05) stages. Among these loci, rs78062588 in TPM3 (1q21.3) was a new lung cancer susceptibility locus (OR = 0.86, P = 1.65 × 10-6). Subgroup analysis by histologic types further identified nine lung CDGs. Analysis of somatic alterations found that in lung adenocarcinomas, rs78062588[C] allele (TPM3 in 1q21.3) was associated with elevated somatic copy number of TPM3 (OR = 1.16, P = 0.02). In lung adenocarcinomas, rs1611182 (HLA-A in 6p22.1) was associated with truncation mutations of the transcriptional misregulation in cancer pathway (OR = 0.66, P = 1.76 × 10-3). CONCLUSIONS Genetic variants can regulate functions of lung CDGs and influence lung cancer susceptibility. IMPACT Our findings might help unravel biological mechanisms underlying lung cancer susceptibility.
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Affiliation(s)
- Yuzhuo Wang
- Department of Epidemiology, International Joint Research Center on Environment and Human Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & Nanjing Medical University Affiliated Cancer Hospital, Nanjing, China
| | - Olga Y Gorlova
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
- Department of Medicine, Epidemiology Section, Institute for Clinical and Translational Research, Baylor Medical College, Houston, Texas
| | - Ivan P Gorlov
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire
- Department of Medicine, Epidemiology Section, Institute for Clinical and Translational Research, Baylor Medical College, Houston, Texas
| | - Meng Zhu
- Department of Epidemiology, International Joint Research Center on Environment and Human Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Department of Thoracic Surgery, Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & Nanjing Medical University Affiliated Cancer Hospital, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Juncheng Dai
- Department of Epidemiology, International Joint Research Center on Environment and Human Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Stephen Lam
- Department of Integrative Oncology, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Adonina Tardon
- Department of Public Health IUOPA, University of Oviedo, ISPA and CIBERESP, Oviedo, Spain
| | - Chu Chen
- Program in Epidemiology, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Gary E Goodman
- Public Health Sciences Division, Swedish Cancer Institute, Seattle, Washington
| | - Stig E Bojesen
- Department of Clinical Biochemistry, Copenhagen University Hospital, Copenhagen, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Mattias Johansson
- Genetic Epidemiology Group, International Agency for Research on Cancer, Lyon, France
| | - Angela Risch
- University of Salzburg, Department of Biosciences, Allergy-Cancer-BioNano Research Centre, Salzburg, Austria
- Division of Epigenomics and Cancer Risk Factors, DKFZ-German Cancer Research Center, Heidelberg, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC-H), German Center for Lung Research (DZL), Heidelberg, Germany
| | - Heunz-Erich Wichmann
- Institute of Medical Informatics, Biometry and Epidemiology, Chair of Epidemiology, Ludwig Maximilians University, Munich, Bavaria, Germany
- Helmholtz Zentrum Munchen, German Research Center for Environmental Health (GmbH), Institute of Epidemiology, Neuherberg, Germany
- Institute of Medical Statistics and Epidemiology, Technical University Munich, Munich, Germany
| | - Heike Bickeboller
- Department of Genetic Epidemiology, University Medical Center Goettingen, Goettingen, Germany
| | - David C Christiani
- Departments of Environmental Health and Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Gad Rennert
- Technion Faculty of Medicine, Carmel Medical Center, Haifa, Israel
| | - Susanne M Arnold
- Markey Cancer Center, University of Kentucky, Lexington, Kentucky
| | - Paul Brennan
- Genetic Epidemiology Group, International Agency for Research on Cancer, Lyon, France
| | - John K Field
- Molecular and Clinical Cancer Medicine, Roy Castle Lung Cancer Research Programme, The University of Liverpool Institute of Translational Medicine, Liverpool, United Kingdom
| | - Sanjay Shete
- Department of Epidemiology, The University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Loïc Le Marchand
- Epidemiology Program, University of Hawai'i Cancer Center, Honolulu, Hawai'i
| | - Olle Melander
- Clinical Sciences, Lund University, Lund, Sweden
- Department of Internal Medicine, Skåne University Hospital, Malmö, Sweden
| | | | - Geoffrey Liu
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Rayjean J Hung
- Prosseman Centre for Population Health Research, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Angeline S Andrew
- Department of Neurology, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
| | - Lambertus A Kiemeney
- Department for Health Evidence, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Kjell Grankvist
- Department of Medical Biosciences, Umeå University, Umea, Sweden
| | | | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Penella J Woll
- Academic Unit of Clinical Oncology, University of Sheffield, Sheffield, United Kingdom
| | - Philip Lazarus
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington
| | - Matthew B Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Melinda C Aldrich
- Department of Medicine (Division of Genetic Medicine), Vanderbilt University Medical Center, Nashville, Tennessee
| | - Victoria L Stevens
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
| | - Hongxia Ma
- Department of Epidemiology, International Joint Research Center on Environment and Human Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Guangfu Jin
- Department of Epidemiology, International Joint Research Center on Environment and Human Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Zhibin Hu
- Department of Epidemiology, International Joint Research Center on Environment and Human Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Christopher I Amos
- Department of Medicine, Epidemiology Section, Institute for Clinical and Translational Research, Baylor Medical College, Houston, Texas.
| | - Hongbing Shen
- Department of Epidemiology, International Joint Research Center on Environment and Human Health, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
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