Abstract B42: Decitabine specifically targets genes that gain DNA methylation and lose expression in cancer and can be combined with histone methylation inhibitors for increased efficacy
Authors: Sato Takahiro , Cesaroni Matteo , Tran Anthony , Madzo Jozef , Okamoto Yasuyuki , Zhang Hanghang , Panjarian Shoghag , Jelinek Jaroslav , Issa Jean-Pierre 
Published: May 2016

A major question facing the use of epigenetic therapies in cancer is the specificity in reactivating gene expression. In addition, combined targeting of DNA and histone methylation remains largely unexplored despite the promising synergistic effects observed from combining DNA methyltransferase inhibitors with HDAC inhibitors.

To address these questions, we performed RNA-seq in colon cancer (SW48) and breast cancer (MCF7) models treated with a DNA methyltransferase inhibitor (Decitabine/DAC) either alone or in combination with a LSD1 inhibitor (S2101), G9a inhibitor (UNC0638), EZH2 inhibitor (GSK343) or a HDAC inhibitor (Depsipeptide). Additionally, we performed ChIP-seq (H3K4me2, H3K9me2, and H3K27me3) and DNA methylation analysis (DREAM) on SW48 cells. Both low dose (100nM) and intermediate dose (1uM) DAC were very specific in upregulating genes with high levels of DNA methylation (86% and 78% of upregulated genes in SW48 cells, respectively). DAC alone and in combination with S2101, UNC0638, or GSK343 preferentially upregulated genes that were expressed in normal colon and silenced in SW48 cells (443, 718, 728, 1095 genes, respectively) compared to genes that didn't change expression (194, 343, 424, 479 genes, respectively). Additionally, the combination therapies specifically upregulated genes that were not DNA methylated in normal colon but gained methylation in cancer (91%, 85%, 87%, and 79% of upregulated genes, respectively). The combination therapies also preferentially upregulated genes that lost expression in cancer and were silenced by H3K9me2 and/or H3K27me3 (121, 204, 277, 380 genes, respectively) compared to genes that didn't change expression in cancer but were silenced by histone methylation (42, 82, 163, 167 genes, respectively). In contrast, Depsipeptide and the combination of Depsipeptide with DAC induced major expression changes in all genes (2167 and 2938 genes upregulated that were expressed in normal colon and silenced in SW48, compared to 1807 and 2389 genes upregulated with no change in expression, respectively).

Furthermore, DAC in combination with S2101, UNC0638, or GSK343 induced a significant number of synergistic genes that were only upregulated with the combination therapy and not with either monotherapy (&gt;490 genes for each inhibitor combination in both cancer models). These synergistic genes showed limited overlap between the three combination therapies (only 7.64% of genes commonly upregulated in YB5, 7.31% in MCF7), and formed distinct clusters in a hierarchical cluster analysis. IPA analysis demonstrated that these genes are enriched in critical cancer regulation pathways such as cell proliferation, cell death, and cell movement. Consistent with this analysis, the combination therapies were able to decrease cancer cell proliferation more effectively than monotherapy.

Overall, these results demonstrate that DNA methyltransferase inhibitors preferentially target cancer relevant genes, and can be combined with epigenetic inhibitors targeting histone methylation to increase efficacy while still maintaining specificity.

Citation Format: Takahiro Sato, Matteo Cesaroni, Anthony Tran, Jozef Madzo, Yasuyuki Okamoto, Hanghang Zhang, Shoghag Panjarian, Jaroslav Jelinek, Jean-Pierre Issa. Decitabine specifically targets genes that gain DNA methylation and lose expression in cancer and can be combined with histone methylation inhibitors for increased efficacy. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr B42.