Abstract 4257: Genome-wide CpG island methylation analysis identifies tumor specifically methylated genes in non-small cell lung cancer patients.
Authors: Heller Gerwin , Babinsky Valerie , Ziegler Barbara , Weinzierl Marlene , Noll Christian , Altenberger Corinna , Muellauer Leonhard , Dekan Gerhard , Grin Yuliya , Lang Gyoergy , End-Pfützenreuter Adelheid , Steiner Irene , Zehetmayer Sonja , Doeme Balazs , Arns Madeleine , Fong Kwun M. , Wright Casey M. , Yang Ian A. , Klepetko Walter , Posch Martin , Zielinski Christoph C. , Zoechbauer-Mueller Sabine 
Published: August 2014

DNA methylation is part of the epigenetic gene regulation complex and it has been shown that methylation of certain genes occurs frequently in non-small cell lung cancers (NSCLC). We performed a genome-wide search for methylated CpG islands in primary tumors and corresponding non-malignant lung tissue samples of 101 stage I-III NSCLC patients by combining methylated DNA immunoprecipitation and microarray analysis using NimbleGen's 385K Human CpG Island plus Promoter arrays (MeDIP-chip). To test for differences in methylation between tumors and corresponding non-malignant lung tissues, we calculated paired t-statistics with permutation adjusted p-values for step down multiple testing. Overall, we identified 2.414 genomic positions differentially methylated between tumor and corresponding non-malignant lung tissue samples by MeDIP-chip analyses. Ninety-seven % of them were found to be tumor-specifically methylated. Annotation of these genomic positions resulted in the identification of 477 tumor-specifically methylated genes. These genes were classified according to Gene Ontology (GO) categories and over-representation of certain GO terms was calculated. Interestingly, we found that a large number of tumor-specifically methylated genes act as regulators of gene expression or mediate homophilic cell adhesion. Tumor-specific methylation of selected genes was confirmed by methylation-sensitive high-resolution melting analysis and ROC curve analyses revealed that primary tumors may be distinguished from non-malignant lung tissue samples by methylation of certain genes. In addition, in the majority of tumors methylation of certain genes was associated with loss of their protein expression determined by immunohistochemistry. Moreover, treatment of NSCLC cells with epigenetically active drugs resulted in upregulated expression of many tumor-specifically methylated genes analysed by gene expression microarrays. In conclusion, we identified a large number of tumor-specifically methylated genes in NSCLC patients. Expression of many of them is regulated by methylation. Overall, our findings emphasize the impact of methylation on the pathogenesis of NSCLCs.

Citation Format: Gerwin Heller, Valerie Babinsky, Barbara Ziegler, Marlene Weinzierl, Christian Noll, Corinna Altenberger, Leonhard Muellauer, Gerhard Dekan, Yuliya Grin, Gyoergy Lang, Adelheid End-Pfützenreuter, Irene Steiner, Sonja Zehetmayer, Balazs Doeme, Madeleine Arns, Kwun M. Fong, Casey M. Wright, Ian A. Yang, Walter Klepetko, Martin Posch, Christoph C. Zielinski, Sabine Zoechbauer-Mueller. Genome-wide CpG island methylation analysis identifies tumor specifically methylated genes in non-small cell lung cancer patients. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4257. doi:10.1158/1538-7445.AM2013-4257