Abstract 2166: Identification of novel epigenetically silenced genes by a global reactivation screen of prostate cancer

Abstract

Abstract The epigenetic alteration of aberrant DNA methylation of CpG island in the promoter region is a common mechanism of inactivation of tumor suppressor genes in cancer cells and a number of other cancer genes have been identified as hypermethylated with associated loss of expression in prostate cancer. By definition, a candidate gene approach has resulted in the examination of only a limited number of genes for epigenetic alteration. Many other tumor suppressor and cancer genes important in prostate tumorigenesis likely remain to be identified. A global approach to the identification of epigenetically silenced genes in prostate tumor cells could provide methylation signatures for early detection and for prognostic and predictive classification studies, identify novel targets for therapy, and lead to further elucidation of the biology of this disease. One global approach to the identification of epigenetically silenced genes in tumor cells is based on the reversal of epigenetic silencing by drugs such as 5-aza-2 deoxycytidine resulting in re-expression analyzed by well-annotated gene expression arrays. This approach can preferentially identify re-expression of epigenetically silenced genes over methylated CpG islands that do not affect transcription. A proportion of the reexpressed genes will have been silenced by promoter hypermethylation in the untreated tumor cell lines. In this study we performed a demethylating drug-based global epigenetic reactivation screen with an expression microarray on 4 well-established prostate cancer cell lines (LNCaP, DU-145, PC-3 and MDA2b) to identify new methylated genes in prostate cancer. A total of 2998 genes were found to have at least 2-fold upregulation of expression after drug treatment in one or more of four prostate tumor cell lines. Using qMSP and bisulfite sequencing, we studied the first 45 upregulated genes that were prioritized by examination of expression status in the normal cell counterpart compared to the tumor cell and the presence and location of a CpG island in the promoter region. Validation studies revealed several novel genes hypermethylated in primary prostate tumors compared to normal prostate that may have utility in methylation-based detection of prostate cancer tests. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2166.