Abstract 3521: Combined targeting of DNA and histone methylation improves the efficacy and specificity of epigenetic therapy

Simultaneous treatment of cancer cells with DNA methyltransferase and HDAC inhibitors leads to synergistic increases of gene expression, indicating that certain genes require targeting of multiple modes of epigenetic regulation to be fully reactivated. However, a major obstacle facing the use of epigenetic therapies such as HDAC inhibitors in cancer is the lack of specificity in reactivating gene expression. Combined targeting of DNA and histone methylation is an unexplored and promising alternative to current therapies due to the role of both modifications in silencing of various tumor suppressor genes in cancer. To address this possibility, we performed a genome wide gene expression study of a DNA methyltransferase inhibitor (DAC) in combination with a LSD1 inhibitor (S2101), G9a inhibitor (UNC0638), EZH2 inhibitor (GSK343) or a HDAC inhibitor (Depsipeptide) in colon cancer (SW48) and breast cancer (MCF7) models. The trends of gene expression changes in response to the inhibitors were similar in both cancer models. S2101, UNC0638, and GSK343 treatment by themselves induced limited gene upregulation in comparison to DAC and especially Depsipeptide. Interestingly, UNC0638 along with DAC had a strong preference to upregulate genes that had high levels of DNA methylation in their promoters. DAC in combination with S2101, UNC0638, or GSK343 was able to synergistically or additively upregulate many DAC target genes compared to levels achieved by DAC alone, demonstrated limited overlap between the upregulated genes (only 4.42% of genes commonly upregulated in SW48, 0.32% in MCF7), and formed distinct clusters in a hierarchical cluster analysis. Each DAC+inhibitor combination also induced a significant number of novel genes that were only upregulated with the combination therapy and not with DAC or inhibitor alone (>490 genes for each inhibitor combination in both cancer models), and there was again limited overlap between the upregulated genes (only 7.64% of genes commonly upregulated in SW48, 7.31% in MCF7). IPA analysis demonstrated that genes induced uniquely by the inhibitor combinations are enriched in critical cancer regulation pathways such as cell proliferation, cell death, and cell movement. Overall, these results demonstrate that effectiveness of combined targeting of DNA and histone methylation is achieved through two mechanisms: 1) Increase effectiveness of DAC by further upregulation of DAC target genes, and 2) Reactivate novel target genes unable to be induced by DAC or the inhibitors alone. These results also demonstrate a promising ability to target specific, non-overlapping sets of genes through different inhibitor combinations, contrary to the nonspecific effect observed with traditional epigenetic therapies. Combined targeting of DNA and histone methylation is a promising novel epigenetic therapy that may allow for the targeting of specific tumor types based on their gene expression profiles. Citation Format: Takahiro Sato, Matteo Cesaroni, Jaroslav Jelinek, Jean-Pierre Issa. Combined targeting of DNA and histone methylation improves the efficacy and specificity of epigenetic therapy. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3521. doi:10.1158/1538-7445.AM2015-3521