Abstract B56: DNA demethylation in gene bodies is of therapeutic significance

Abstract Reversal of aberrant promoter hypermethylation and associated gene silencing has been the primary focus of epigenetic therapy. Recently, gene body methylation has been implicated as having a functional role in the regulation of gene expression; however it is unclear how gene body methylation changes might contribute to the therapeutic effects of epigenetic therapy. To investigate the role of DNA demethylation in inducing gene expression changes in a comprehensive way, we treated the HCT116 colon cancer cell line with 5-Aza-2′-deoxycytidine (5-Aza-CdR) transiently for 24 hours and monitored changes in gene expression and DNA methylation levels at gene bodies and promoters for up to 42 days after treatment using 450K Infinium DNA methylation arrays and expression arrays. We observed that probes that became demethylated and subsequently regained methylation did at different rates. As we expected, demethylation of methylated promoters is negatively correlated with expression (R2≤ -0.75) and considerable demethylation of promoters (485) and the associated gene reactivation could be maintained for up to 42 days after drug treatment. Most of these genes are de novo methylated and their expression is down-regulated in primary colon cancers in the TCGA database. Strikingly, a group of genes shows a positive correlation between demethylation of gene bodies and down-regulation of gene expression after treatment (R2≥ 0.75). Four hundred ninety eight have fast rebound methylation kinetics and decreased expression and they are enriched for genes involved in metabolic process which are over-expressed in primary colon cancer tissues. Furthermore, 494 genes with sustained down-regulation of gene expression maintained their demethylated status and those are enriched for de novo methylation targets and over-expressed genes in colon cancer. Our results demonstrate that DNA demethylation at gene bodies induced by 5-Aza-CdR can be of therapeutic significance by resulting in the down-regulation of genes that are overexpressed in cancers. Our findings also confirm that demethylation treatment could potentially cause prolonged reactivation of genes that are silenced by promoter methylation while simultaneously down-regulating genes that are overexpressed and have body methylation. Together, demethylation of gene bodies may confer therapeutic benefit in addition to demethylation of gene promoters. Citation Format: Han Han Zhang, Xiaojing Yang, Daniel D. De Carvalho, Peter A. Jones, Gangning Liang. DNA demethylation in gene bodies is of therapeutic significance. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr B56.