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Polymorphisms of the Centrosomal Gene (FGFR1OP) and Lung Cancer

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Polymorphisms of the Centrosomal Gene (FGFR1OP) and Lung Cancer Carcinogenesis, 2016, Vol. 37, No. 3, 280–289 doi:10.1093/carcin/bgw014 Advance Access publication February 10, 2016 Original Manuscript original manuscript Polymorphisms of the centrosomal gene (FGFR1OP) and lung cancer risk: a meta-analysis of 14 463 cases and Downloaded from 44 188 controls Xiaozheng Kang1,2,3,†, Hongliang Liu1,4,†, Mark W.Onaitis1,2, Zhensheng Liu1,4, Kouros Owzar1,5,Younghun Han6, Li Su7,8, Yongyue Wei7,8, Rayjean J.Hung9, http://carcin.oxfordjournals.org/ Yonathan Brhane9, John McLaughlin10, Paul Brennan11, Heike Bickeböller12, Albert Rosenberger12, Richard S.Houlston13, Neil Caporaso14, Maria Teresa Landi14, Joachim Heinrich15, Angela Risch16, Xifeng Wu17, Yuanqing Ye17, David C.Christiani7,8, Christopher I.Amos6 and Qingyi Wei1,4,*; Transdisciplinary Research in Cancer of the Lung (TRICL) Research Team 1Duke Cancer Institute and 2Division of Cardiovascular and Thoracic Surgery, Department of Surgery, Duke University Medical Center, 905 S. LaSalle Street, Durham, NC 27710, USA, 3Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Thoracic Surgery I, Peking University Cancer Hospital and Institute, Beijing 100142, at Helmholtz Zentrum Muenchen on February 29, 2016 China, 4Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA, 5Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA, 6Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Hanover, NH 03755, USA, 7Massachusetts General Hospital, Boston, MA 02114, USA, 8Department of Environmental Health, Harvard School of Public Health, Boston, MA 02115, USA, 9Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Ontario, Canada, 10Public Health Ontario, Toronto, Ontario M5T 3L9, Canada, 11Genetic Epidemiology Group, International Agency for Research on Cancer (IARC), 69372 Lyon, France, 12Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, 37073 Göttingen, Germany, 13Division of Genetics and Epidemiology, the Institute of Cancer Research, London SW7 3RP, UK, 14Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA, 15Helmholtz Centre Munich, German Research Centre for Environmental Health, Institute of Epidemiology I, 85764 Neuherberg, Germany, 16Department of Molecular Biology, University of Salzburg, 5020 Salzburg, Austria and 17Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA *To whom correspondence should be addressed. Tel: +1 919 660 0562; Fax: +1 919 660 0178; Email: [email protected] †These authors contributed equally to this work. Abstract Centrosome abnormalities are often observed in premalignant lesions and in situ tumors and have been associated with aneuploidy and tumor development. We investigated the associations of 9354 single-nucleotide polymorphisms (SNPs) in 106 centrosomal genes with lung cancer risk by first using the summary data from six published genome-wide association studies (GWASs) of the Transdisciplinary Research in Cancer of the Lung (TRICL) (12 160 cases and 16 838 controls) and then conducted in silico replication in two additional independent lung cancer GWASs of Harvard University (984 cases and 970 controls) and deCODE (1319 cases and 26 380 controls). A total of 44 significant SNPs with false discovery rate (FDR) ≤ 0.05 were mapped to one novel gene FGFR1OP and two previously reported genes (TUBB and BRCA2). After combined the −6 results from TRICL with those from Harvard and deCODE, the most significant association (Pcombined = 8.032 × 10 ) was with Received: October 17, 2015; Revised: January 6, 2016; Accepted: January 25, 2016 © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: [email protected]. 280 X.Kang et al. | 281 Carcinogenesis, 2016, Vol. 37, No. 3, 280–289 doi:10.1093/carcin/bgw014 rs151606 within FGFR1OP. The rs151606 T>G was associated with an increased risk of lung cancer [odds ratio (OR) = 1.10, 95% Advance Access publication February 10, 2016 −6 confidence interval (95% CI) = 1.05–1.14]. Another significant tagSNP rs12212247 T>C (Pcombined = 9.589 × 10 ) was associated Original Manuscript with a decreased risk of lung cancer (OR = 0.93, 95% CI = 0.90–0.96). Further in silico functional analyzes revealed that rs151606 might affect transcriptional regulation and result in decreased FGFR1OP expression (Ptrend = 0.022). The findings shed some new light on the role of centrosome abnormalities in the susceptibility to lung carcinogenesis. Abbreviations Cancer Institute (NCI) GWAS, the International Agency for Research on Cancer (IARC) GWAS, Toronto study from Lunenfeld-Tanenbaum Research eQTL expression quantitative trait loci Institute study (Toronto) GWAS and the German Lung Cancer Study FDR false discovery rate (GLC) GWAS, Germany. The additional datasets of another two independ- GWASs genome-wide association studies ent GWASs of Caucasian populations were from Harvard Lung Cancer LD linkage disequilibrium Study (19) (984 cases and 970 controls) and Icelandic Lung Cancer Study SNPs single-nucleotide polymorphisms (deCODE) (1319 cases and 26 380 controls) (20) from the ILCCO. A written informed consent was obtained from each participant, and this study was Downloaded from approved by the institutional review boards for each of the participating institutions. Introduction Genotyping platforms and quality controls Lung cancer represents the number one cancer-related mor- For these GWASs, genotyping was performed using Illumina HumanHap tality worldwide, with more than 1.6 million cases diagnosed 317, 317+240S, 370Duo, 550, 610 or 1M arrays. Imputation was performed http://carcin.oxfordjournals.org/ and 1.3 million deaths per year (1). In the United States, it is by using data from the 1000 Genomes Project (phase I integrated release the primary cause of deaths from cancers in both men and 3, March 2012) (21) as reference and IMPUTE2 v2.1.1 (22), MaCH v1.0 (23) or women, leading to more deaths than from breast, colorec- minimac (version 2012.10.3) (24) software. Poorly imputed SNPs defined as tal and prostate cancers all combined. Although lung cancer an information score < 0.40 with IMPUTE2 or an r2 < 0.30 with MaCH were is commonly considered a disease caused by environmental excluded from the final analyses. Standard quality control on samples exposures, genetic factors also play a role in the etiology (2). was performed on all scans, excluding individuals with low call rate (< 90%) and extremely high or low heterozygosity (P < 1.0 × 10−4), as well as all Genomic regions at chromosomes 15q25.1 (3,4), 5p15.33 (4–6), individuals evaluated to be of non-European ancestry (using the HapMap 6p21.33 (4), 3q28 (4,7,8), 13q13.1 (8) and 22q12.1 (8) have been phase II CEU, JPT/CHB and YRI populations as a reference). identified to be associated with lung cancer susceptibility by genome-wide association studies (GWASs) in populations of Genes and SNPs selection at Helmholtz Zentrum Muenchen on February 29, 2016 European descent. Centrosomes are the pivotal regulating element of cell divi- The centrosomal genes were collected from the Molecular Signatures Database (http://software.broadinstitute.org/gsea/msigdb), which is a col- sion and act as a reaction center where the cell cycle key reg- lection of annotated gene sets for use with gene set enrichment analysis. ulating elements assemble and play an important role in cell Overall, 106 centrosomal genes located on autosomal chromosomes were polarization and ciliogenesis (9,10). Recent studies have revealed selected (Supplementary Table 1, available at Carcinogenesis Online). The that deregulation of centrosome-related proteins induce centro- genotyped or imputed common SNPs located within 2 kB up- and down- some abnormalities (11), which in turn result in tumor devel- stream of centrosomal genes were extracted from the GWAS datasets opment through the induction of chromosome instability and and the final meta-analysis included 9354 SNPs with genotyping call rate aneuploidy (12,13). A growing body of evidence has linked cen- ≥90%, minor allele frequency ≥5%, and Hardy Weinberg Equilibrium exact trosome abnormalities to the developments of solid tumors and P ≥ 10–5. As previously reported (8,25), SNPs from the 1000 Genomes project hematopoietic malignancies (10), and the underlying mecha- release Phase 1 integrated release version 3 and filtered with only SNPs nisms are now an active area of research (14–16). showing imputation accuracy > 0.3 were retained. The detailed workflow is shown in Supplementary Figure 1, available at Carcinogenesis Online. Centrosome abnormalities and chromosome instability are also frequently observed in human lung cancer (17). Genes In silico functional validation involved in centrosome dysregulation have emerged as the can- To predict the potential functions of risk-associated SNPs and their high- didate targets to study the mechanism of initiation and progres- linkage disequilibrium (LD) (r2 ≥ 0.60) variants, we used three in silico tools: sion of lung cancer. In this study, we hypothesized that genetic SNPinfo (26), RegulomeDB (27) and F-SNP (28). Expression quantitative variants of centrosomal genes are associated with lung cancer trait loci (eQTL) analysis was carried out using lymphoblastoid cell data risk. To test this hypothesis, we
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