Genetic variation in the prostate stem cell antigen gene PSCA confers susceptibility to urinary bladder cancer

Abstract

We conducted a genome-wide association study on 969 bladder cancer cases and 957 controls from Texas. For fast-track validation, we evaluated 60 SNPs in three additional US populations and validated the top SNP in nine European populations. A missense variant (rs2294008) in the PSCA gene showed consistent association with bladder cancer in US and European populations. Combining all subjects (6,667 cases, 39,590 controls), the overall P-value was 2.14 x 10(-10) and the allelic odds ratio was 1.15 (95% confidence interval 1.10-1.20). rs2294008 alters the start codon and is predicted to cause truncation of nine amino acids from the N-terminal signal sequence of the primary PSCA translation product. In vitro reporter gene assay showed that the variant allele significantly reduced promoter activity. Resequencing of the PSCA genomic region showed that rs2294008 is the only common missense SNP in PSCA. Our data identify rs2294008 as a new bladder cancer susceptibility locus.

Figure 1

The 8q24 locus encompassing rs2294008. (a) Results of SNP association from the genome-wide screen. Observed results from genotyped SNPs are in red and imputed results are in black. All known genes in this region are also shown. (b) LD structure of this region. Red arrow, position of rs2294008. Represented in each location is the square of the correlation coefficient (r²) derived from phase 2 genotypes in Haploview software (version 4.1), with darker shading indicating greater extent of LD between two SNPs. Triangles represent LD blocks identified by Haploview software.

Figure 2

In vitro reporter assay of the four most frequent haplotypes of the PSCA 5′ upstream region (nucleotides −3236 to +28). (a) The four SNPs that comprise these haplotypes are rs2976387, rs6471587, rs13262164 and rs2294008. The frequencies of top four haplotypes in our population were wild-type (G-C-C-C), 58%; UP-H1 (A-C-T-T), 25%; UP-H2 (A-C-C-T), 16%; and UP-H3 (G-G-C-T), 1%, respectively. (b) Three bladder cell lines were transfected with a luciferase (Luc) reporter gene driven by PSCA upstream sequences containing these four haplotypes. In all three cell lines, the wild-type sequence (containing C at rs2294008) showed significantly higher promoter activity than the other three (all containing T at rs2294008) (P < 0.001). (c) Substitution of a single nucleotide (rs2294008 C to T) in the wild-type haplotype significantly reduced promoter activity, whereas a single substitution (rs2294008 T to C) in UP-H1 increased promoter activity to a level comparable to that in wild-type in UC1 cells.