Immune checkpoint blockade (ICB) with anti-PD1, anti-PD-L1 and anti-CTLA4 antibodies is an exciting and effective new treatment for metastatic melanoma. Unfortunately, ICB is effective in only 1/3 of the patients, and therefore advanced therapeutic approaches are urgently needed. This requires a fundamental understanding of why 2/3 of cases are not responsive to treatment. By examining the TCGA skin cutaneous melanoma (SKCM) dataset, we found that ~40% of metastatic melanoma cases exhibit prominent genome-wide DNA hypomethylation that correlates with upregulation of oncogenic signaling pathways and innate resistance to anti-PD1 immunotherapy. The hypomethylated epigenome of this melanoma subclass is also positively correlated with upregulation of Thymine DNA Glycosylase (TDG) and Ten Eleven Translocation enzymes that work sequentially to demethylate methyl-CpG sites. These observations raise the possibility that hypomethylation via elevated TET/TDG activity contributes to oncogenic activation and anti-PD1 resistance. We published that TDG knockdown in melanoma cells leads to DNA hypermethylation and stopped proliferation in culture and in xenografts. Importantly, CpG sites that became hypermethylated after TDG knockdown in melanoma cells significantly correlated with hypomethylated CpG sites in SKCM. This provides clinical relevance to our in vitro studies and suggests that inhibiting TDG can reverse the hypomethylated epigenome of metastatic melanomas, potentially suppressing oncogenic pathways and sensitizing them to ICB. This, combined with the fact that TDG is not essential in adult mice, suggests there is a potentially wide therapeutic window for TDG inhibitors between normal (adult) and cancer cells. We screened a virtual chemical library and identified a lead compound, MC1, with TDG inhibitory activity at moderate potency. Having validated our HTS assay, we propose screening campaigns to identify new leads with increased potency, specificity and chemical properties that will maximize our chances for future drug development. Here we will: 1) Screen chemical libraries for small molecule inhibitors of TDG, followed by stringent hit validation assays, to identify novel and more potent inhibitors of TDG. 2) Use computational methods to perform SAR studies on MC1, and to separately screen a >10 billion compound virtual library to identify potent new scaffolds with TDG inhibitory activity. Outcomes from this research will lead to the development of paradigm-shifting epigenetic therapy, based on TDG inhibitors as first-in-class DNA hypermethylating agents, that correct hypomethylated melanoma subclass and sensitize it to ICB.
TDG is a DNA repair enzyme that also promotes gene expression by removing DNA methylation that acts to block transcription. TDG is overexpressed in melanomas and other cancers whose genomes lack methylation, resulting in uncontrolled expression of pro-cancer genes and resistance to immunotherapy. We propose high- throughput chemical and virtual library screens to identify first-in-class inhibitors of TDG that can be used for future development of a novel personalized treatment for cancers that exhibit a hypomethylated epigenetic signature.
