Abstract 4828: Genome-wide DNA methylation analysis identifies tumor-specifically methylated genes in non-small cell lung cancer patients

Abstract

Abstract Epigenetic changes largely contribute to the regulation of gene expression in cancer cells. DNA methylation is part of this epigenetic gene regulation complex and it has been shown that methylation of certain genes occurs frequently in non-small cell lung cancers (NSCLC). So far, in primary NSCLCs mainly studies investigating methylation of small numbers of genes have been performed. Thus, we performed a genome-wide search for methylated CpG islands in primary tumors and corresponding non-malignant lung tissue samples of 100 stage I-III NSCLC patients by combining methylated DNA immunoprecipitation (MeDIP) and microarray analysis (MeDIP-chip). 385K Human CpG Island plus Promoter arrays from NimbleGen which cover ∼28,000 CpG islands were used. To test for differences in methylation between tumors and corresponding non-malignant lung tissues we calculated paired t-statistics and performed a multiplicity adjusted permutation test. By this approach we identified 303 tumor-specifically methylated genes. These genes include 263 well characterized protein encoding genes and 40 predicted genes. Tumor-specifically methylated genes were classified according to Gene Ontology (GO) categories and over-representation of certain GO terms was calculated. This analysis demonstrated that a large number of tumor-specifically methylated genes act as regulators of gene expression (including members of homeobox, forkhead box and paired box gene clusters) or mediate homophilic cell adhesion (including members of protocadherin alpha and gamma gene clusters). To confirm our results obtained by MeDIP-chip analysis we additionally performed methylation-sensitive high-resolution melting (MS-HRM) analysis of selected genes (e.g. HOXA2, SHOX2 and TAL1). These results corresponded with the results obtained by MeDIP-chip analysis. A comparison of our methylation results obtained by MeDIP-chip analysis and clinico-pathological characteristics of the patients will be performed. In conclusion, using a genome-wide approach we identified a large number of tumor-specifically methylated genes in NSCLC patients. From many of these genes epigenetic regulation was unknown so far. Moreover, our data suggest that transcriptional regulation and cell adhesion are frequently affected by DNA methylation in NSCLC. Overall, our results stress the importance of DNA methylation for the pathogenesis of NSCLC. 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 4828. doi:10.1158/1538-7445.AM2011-4828