Abstract 2259: Identifying causative genes and prognostic markers for bladder cancer
Authors: Van Tilborg Angela A.G. , Quist Jelmar , Kompier Lucie C. , Lurkin Irene , van Helvoirt Miriam , Burger Maximilian , Hartmann Arndt , Zwarthoff Ellen C. 
Published: June 2012

Abstract
Upon presentation 70% of the bladder tumors are confined to the epithelial (stage pTa) and stromal layers (stage pT1) of the bladder. These non-muscle invasive tumors (NMI-BC) frequently recur and 10-15% will eventually invade the detrusor muscle and may cause metastases. The management of these tumors is characaterized by the difficult choice between transurethral resection (TURB) or total bladder removal by cystectomy. Our first objective was to identify DNA copy number changes as biomarkers predicting tumor progression in high grade NMI-BC to aid decision making. A set of 18 DNA samples isolated from fresh frozen high grade NMI-BC was hybridized on Illumina SNP arrays. Analysis of alterations was done with Nexus software. Hierarchical clustering of significantly differing SNPs showed that tumors that progressed and those that did not clustered separately. A comparison of the differential alterations between tumor groups resulted in many chromosomal locations encompassing chromosome 1p, 2-6, 8-10, 12p, 13q, 17q, 18p and 22q that were fit for inclusion in a validation assay. A custom Agilent 15K array was designed to include probes for these locations. We collected a retrospective series of 96 high grade NMI-BC paraffin embedded tumors with a median follow-up of 5 years. Half of these samples were from patients who developed a muscle-invasive tumor at a later time. Preliminary results show an interesting region on chromosome 8 with the best independent prognostic value. This region and the genes therein will be studied in more detail. This and other validated regions will be used to design a definitive prognostic assay.
Complex losses on chromosome 9 characterize bladder tumors regardless of stage. We hypothesized that the complex rearrangements on this chromosome in BC are the results of attempts of the tumor cell to loose tumor suppressor genes whilst struggling to retain other (onco)genes. Therefore, the second aim was to identify pivotal tumor suppressor and/or oncogenes on chromosome 9 for development of bladder cancer, with the aim to exploit these genes or the pathways in which they function as potential targets for therapy for tumors from all stage categories. A custom Agilent 44K array was designed, containing probes for all genes on chromosome 9 (and 8p). DNA from a series of 144 tumors from different stages was hybridized to the arrays. Analysis of alterations was done with Nexus software. We found many regions of loss as expected but also a region that appeared amplified in most tumors. Several candidate regions were validated of their copy number status with specific MLPA assays. Two potential candidate genes from chromosome 9 were selected for mutational and functional analysis. In one of those genes we found several mutations affecting protein function, suggesting that this gene is a new tumor suppressor gene for bladder cancer.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2259. doi:10.1158/1538-7445.AM2011-2259