Genome-Wide Association Studies Of Genetic Variants For Susceptibility To And Clinical Outcomes Of Esophageal Squamous-Cell Carcinoma And Small-Cell Lung Cancer

Genome-wide association studies developed in the recent years have assisted biomedical researchers to identify a number of genes or genetic loci that are associated with complex diseases or phenotypes. In the present study, we employed this powerful methodology to examine genetic variants for susceptibility to and clinical outcomes of esophageal squamous-cell carcinoma (ESCC) and small-cell lung cancer.A two-stage analysis (discovery stage and replication stage) was designed for this study. To identify genetic susceptibility loci for ESCC, we conducted a genome-wide association study on 2,031 ESCC cases and 2,044 controls using 666,141 autosomal single nucleotide polymorphisms (SNPs). Promising associations of SNPs found in the discovery stage were evaluated in additional 3,986 ESCC cases and 4,157 controls from northern, southern, eastern and central parts of China. We also conducted a two-stage analysis to identify prognostic loci associated with overall survival of ESCC patients. The discovery stage consisted of 800 patients and the replication stage consisted of 539 patients. Genome-wide scan of 440,093 SNPs was conducted to identify variants associated with response to first-line carboplatin or cisplatin plus etoposide chemotherapy and patients'overall survival in 245 patients with small-cell lung cancer and the results were replicated in another set of 183 patients for response and 305 for survival. PLINK was used to examine genome-wide associations of ESCC risk and Cox model was used to analyze genome-wide associations of overall survival. A series of biochemical assays was conducted to investigate the function of associated SNPs.We identified seven susceptibility loci for ESCC on chromosomes 5q11,6p21,10q23, 12q24 and 21q22 (P=7.48x10-12 to p=2.44x1O-31). Among them,3 variants in high linkage disequilibrium on 12q24 confer their risks to ESCC in a gene-lifestyle interaction manner, with more pronounced risk enhancement in tobacco smokers and alcohol drinkers. Furthermore, these variants had a cumulative association with ESCC risk (Ptrend=7.92xl0-56); individuals carrying 6 hazard genotypes had 4.60-fold [95%confident interval (CI), 2.73-7.74] increased risk for developing ESCC compared with those carrying≤1 hazard genotype. We also identified rs1050631 and rs7241481 SNPs located in the SLC39A6 gene on chromosome 18q12 were significantly associated with overall survival in patients with ESCC. The hazard ratio (HR) computed with Cox model for patients with the rs 1050631 CT or TT genotype was 1.28 (95%CI,1.08-1.51; P=0.0040) or 2.47 (95%CI,1.75-3.49; P=1.95x10-6) compared with the CC genotype. For rs7241481, the HRs for the AG and AA genotypes were 1.24 (95%CI,1.05-1.47; P=0.0100) and 1.51 (95%CI,1.27-1.79; P=1.98xlO-5) compared with the GG genotype. rs7242481 was located in the 5'-UTR and biochemical assays showed that the rs7241481A>G change creates a nuclear protein binding site and results in down-regulation of SLC39A6 expression.By set association analysis,20 SNPs were found to be associated with response to platinum-based chemotherapy in patients with small-cell lung cancer, with the odds ratios (ORs) ranging from 2.36 (95%CI,1.56-3.57) to 4.38 (95%CI,2.12-9.29) and these results were confirmed in the replication stage (Z transform,P=0.043). Most of these SNPs (14/20) were clustered on chromosomes 22p11.23,6q24.3, and 20pl2.2 containing the BTBD3, STXBP5 and BCR genes. We found that rs 1820453 within the promoter region of YAP I on 11q22 and rs716274 in the downstream region of DYNC2H1 on 11q22.3 were associated with survival of small-cell lung cancer patients treated with platinum-based regimen. The HR for patients with the rs1820453 TG or GG genotype was 1.49 (95%CI,1.19-1.85; P=0.0004) or 1.65 (95%CI,1.36-2.01;P=4.76x10-1) compared with the TT genotype; and for patients with the rs716274 AG or GG genotype was 1.83 (95%CI,1.47-2.29; P=8.74xlO-8) or 2.96 (95% CI,1.90-4.62; P=1.59x10-6) compared with the AA genotype. Functional analysis showed that the rs1820453 T>G change creates a transcriptional inhibitor binding site in the YAP1 promoter region and results in down-regulation of YAP1 expression.In conclusion, these findings highlight the involvement of multiple genetic loci and gene-environment interaction in the development of esophageal cancer. Genetic variations in some genes influence the effectiveness of platinum-based chemotherapy of small-cell lung cancer and, genetic variations may also be associated with cancer patients'survival. Our findings are of importance in better understanding the development of these two types of human cancer and may have potential utility in personalized prevention, chemotherapy, and clinical care of these two malignancies.