Associations between candidate SNPs in 15 q 25 and risk of lung cancer in a Chinese population

Recent three genome-wide association studies have mapped a lung cancer susceptibility locus to chromosome 15q25 in Caucasians. However, the reported risk single nucleotide polymorphisms (SNPs) are extremely rare in Asians, arguing against any of these being causative variants. This study sought to identify other variants on 15q25 associated with lung cancer susceptibility in Chinese. Two-stage case-control studies were conducted in subjects derived from both Northern and Southern China. The first-stage, consisting of 576 cases and 576 controls, was to discover novel risk variants using a haplotype-tagging SNP approach, and these variants were then replicated in the second-stage, consisting of 2,989 cases and 2,880 controls. Associations were estimated by logistic regression models, and function of the variants was examined by biochemical assays. We found that the three risk SNPs reported in Caucasians were not associated with lung cancer risk in Chinese. However, we identified four novel SNPs (rs2036534C>T, rs667282C>T, rs12910984G>A, and rs6495309T>C) that were associated with significantly increased lung cancer risk and smoking behavior, which were all confirmed in the replication analyses [odds ratios (95% confidence intervals) in the dominant model: 1.39 (1.23–1.57; P = 2.3 × 10), 1.52 (1.35–1.71; P = 2.0 × 10), 1.44 (1.28–1.63; P = 2.7 × 10), and 1.43 (1.27– 1.61; P = 2.6 × 10), respectively]. We characterized the rs6495309T>C change in the CHRNA3 promoter as a functional variant because it affected the Oct-1 binding ability, resulting in increased CHRNA3 expression. These results support 15q25 as a susceptibility region for lung cancer in Chinese but underscore the difference in genetic markers among different ethnic populations. [Cancer Res 2009;69(12):5065–72] Introduction Lung cancer is the leading cause of cancer-related deaths all over the world. In many countries, including China, the morbidity and mortality of lung cancer have been increasing rapidly in recent years, which is believed to be mainly due to continuous increase in tobacco consumption (1, 2). Although over 80% of lung cancer are tobacco related (3), accumulating evidence supports that genetic factors are also risk factors for lung cancer because only a small fraction of smokers (usually <20%) develop this disease. Efforts have been made to discover the potential biomarkers (4–6), but lung cancer still lacks specific biomarkers for risk assessment, early detection, and prognosis. Recently, three genome-wide association studies (GWAS) in Caucasian populations have mapped a lung cancer susceptibility locus to chromosome 15q25 containing nicotinic acetylcholine receptor genes CHRNA3, CHRNA5, and CHRNB4 (7–9). Nicotinic acetylcholine receptors expressed in the key regions of the brain play an important role in controlling smoking behavior (10, 11). These receptors are also expressed in epithelial cells of the lung, where they execute signal transduction upon binding to nicotine and/ or its carcinogenic derivatives [e.g., 4-(methylnitrosamino)-1-(3pyridyl)-1-butanone, NNK], resulting in cell proliferation and neoplastic transformation (12–15). Therefore, it seems plausible that genetic variations, such as single nucleotide polymorphisms (SNP) in nicotinic acetylcholine receptors that affect the gene expression or protein function, would be associated with smoking behavior and the risk of smoking-related lung cancer. The exciting results in the GWAS encouraged us to investigate the association between the SNPs reported in Caucasians (7–9) and lung cancer risk in Chinese populations. By examining the HapMap data, however, we found that the risk SNPs, rs8034191, rs1051730, and rs16969968 identified in previous GWAS are extremely rare in Asians, suggesting that the role these SNPs play in risk of lung cancer in Asian populations, if any, may not be as important as they do in Caucasians. We thus hypothesized that if chromosome 15q25 also plays a role in susceptibility to lung cancer in Chinese populations, there must be other risk variants. To test this hypothesis, we conducted a two-stage case-control studies of 3,565 cases with lung cancer and 3,456 controls derived from both Northern and Southern China. We discovered four novel SNPs associated with lung cancer risk in Chinese populations, which are different from those reported in the GWAS in Caucasian populations. In addition, we characterized a SNP in the promoter region of CHRNA3 as a potential causative SNP because it affected the transcriptional factor Oct-1 binding ability, resulting in alteration of CHRNA3 expression. Note: Supplementary data for this article are available at Cancer Research Online (http://cancerres.aacrjournals.org/). C. Wu and Z. Hu contributed equally to this work. Requests for reprints: Hongbing Shen, Department of Epidemiology and Biostatistics, Cancer Center, Nanjing Medical University, Nanjing 210029, China. E-mail: hbshen@njmu.edu. cn or Dongxin Lin, Departments of Etiology and Carcinogenesis, Cancer Institute and Hospital, Chinese Academy of Medical Sciences, Beijing 100021, China. E-mail: lindx72@cicams.ac. cn. ©2009 American Association for Cancer Research. doi:10.1158/0008-5472.CAN-09-0081 5065 Cancer Res 2009; 69: (12). June 15, 2009 www.aacrjournals. org Published Online First on June 2, 2009 as 10.1158/0008-5472.CAN-09-0081 Research. on January 6, 2018. © 2009 American Association for Cancer cancerres.aacrjournals. org Downloaded from Published OnlineFirst June 2, 2009; DOI: 10.1158/0008-5472.CAN-09-0081