Abstract 3012: Genome-wide analysis of CpG island methylation in bladder cancer identifies novel biomarkers for diagnosis, prediction of progression and survival
Authors: Kandimalla Raju , van Tilborg Angela A. G. , Kompier Lucie C. , Stumpel Dominique J.P.M. , Bangma Chris H. , Zwarthoff Ellen C. 
Published: June 2012

Abstract
Cancers of the urinary bladder (BC) present as muscle-invasive (MI) or non-muscle invasive (NMI). Major problems with NMI-BC are that 70% of the tumors will recur and 10-20% will eventually progress to MI-BC. These patients require life-long surveillance by cystoscopy. Over 50% of patients with primary or secondary MI-BC die of their disease. Epigenetic modifications have been shown to contribute to the pathogenesis of various cancers including bladder cancer. Hypermethylation is often found in CGIs in the 5’ regions of genes overlapping promoter regions. Methylation of these CGIs negatively affects gene expression and consequently DNA modifications may serve as useful biomarkers, both for diagnostic and prognostic purposes. We aimed to identify DNA methylation markers as a prognostic tool to predict progression, survival and to enable detection of recurrent tumors in urine. In this study, we performed a genome wide screening for DNA methylation in different subtypes of bladder cancer with the aid of differential methylation hybridization (DMH) coupled with Agilent 244k human CpG island microarrays. We have found 731 significant probes to be more methylated in bladder tumors than in blood, which represents 392 unique CGIs. The adjacent CpG dinucleotides within a CGI were co-methylated in most of the significantly methylated CGIs. In contrast, CGIs neighboring a methylated island were usually not methylated. Extensive methylation indicative of a CGI methylator phenotype was observed in FGFR3 wild-type NMI-BC. Most de novo methylated genes in bladder cancer are known targets of repression by polycomb group proteins in embryonic stem cells. CGI markers for the detection of recurrences and prediction of progression and survival were validated in an independent set of 90 FFPE tumors on a 384-plex custom Illumina Golden Gate Methylation Assay (GGMA). We identified 110 CGIs that are differentially methylated between tumor cells and control urine and 20 of these were further validated for the detection of recurrent and primary tumors in voided urine. Methylation of 34 CGIs was significantly associated with progression, with 22/34 prediction no progression and 13 predicting progression. Methylation of 7/13 CGIs was inversely associated with survival, while 8 were positively correlated with survival. These results imply that therapies targeting DNA methylation in bladder tumors should not be used without further studies.
In summary, DNA methylation markers were identified that will help to predict disease progression and help to stratify patients for personalized follow-up. In addition, a vast number of markers were selected to employ in urine-based tests in order to reduce cystoscopy frequency.
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 3012. doi:10.1158/1538-7445.AM2011-3012