Abstract 4617: An alternatively spliced isoform of TMEM129 shows association with bladder cancer GWAS marker rs798766
Authors: Banday A. Rouf , Paquin Ashley , Middlebrooks Candace , Kiss Eniko , Prokunina-Olsson Ludmila 
Published: August 2015

Abstract
Genome-wide association studies (GWAS) have identified a number of single nucleotide polymorphisms (SNPs) associated with bladder cancer risk. Here, we explored the bladder cancer GWAS signal SNP rs798766 (C/T), which is located in the intron of TACC3 upstream of FGFR3 at 4p16.3 locus. This region represents a high linkage disequilibrium (LD) block and includes two more genes, TMEM129 and SLBP. Several SNPs in r2 = 1 with rs798766 are located within coding and non-coding regions of these genes; however, the coding SNPs are synonymous. Previously, genetic association of this GWAS marker has been shown by eQTL analysis with FGFR3 and TACC3 mRNA expression in adipose tissue. However, genetic association for all four genes and their several alternatively spliced isoforms remains largely unexplored in primary bladder normal and tumor tissue.
We used genotype and RNA-seq data from The Cancer Genome Atlas (TCGA), bladder cancer data set (n = 242). Within the 1000 Kb region surrounding rs798766 we imputed genotypes of 13,529 SNPs in the TCGA data set based on the 1000 Genomes reference panel. Next, we performed eQTL analysis of FGFR3, TACC3, SLBP and TMEM129 both at gene level and at individual isoform level with genotypes of GWAS and several other markers. For validation, we used an independent panel of 42 bladder tumor and 42 adjacent normal tissue samples, using TaqMan expression assays. Expression was analyzed by general linear regression based on an additive genetic model, adjusting for age, sex and race.
At the gene level in the TCGA data, we found significant association with TACC3 expression (p = 1.9 × 10−2unadj and p = 3.5 × 10−2 adj). The association was stronger for expression of an alternatively spliced isoform of TMEM129, designated TMEM129β, (p = 4.57×10−4unadj and p = 3.5 × 10−3adj). Computational annotation revealed that SNP rs2236786, r2 = 1 with GWAS marker, is located within a cassette exon that is an intron for isoform TMEM129β. Further analysis revealed that rs2236786 alleles affect a binding motif for alternative splicing factors SF2ASF, hnRNPF and CUG-BP. The functional exploration of this finding is underway.
In conclusion, we suggest that the molecular phenotype of the 4p16.3 bladder cancer GWAS signal could be associated with differential expression of more than one gene (FGFR3, TACC3, SLBP and TMEM129) and their alternatively spliced isoforms. We present the first evidence for possible association of alternative splicing of TMEM129 and bladder cancer GWAS signal.
Note: This abstract was not presented at the meeting.
Citation Format: A. Rouf Banday, Ashley Paquin, Candace Middlebrooks, Eniko Kiss, Ludmila Prokunina-Olsson. An alternatively spliced isoform of TMEM129 shows association with bladder cancer GWAS marker rs798766. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4617. doi:10.1158/1538-7445.AM2015-4617