EZH2 cooperates with DNA methylation to downregulate key tumour suppressors and interferon gene signatures in melanoma

The histone methylase EZH2 is frequently dysregulated in melanoma and is associated with DNA methylation and silencing of genes involved in tumor suppression. In the present study we used ChIP-seq to identify key suppressor genes that are silenced by histone methylation (H3K27me3) in constitutively active EZH2 mutant melanoma and assessed whether these regions were also sites of DNA methylation. The genes identified were validated by their re-expression after treatment with EZH2 and DNA methyltransferase (DNMT) inhibitors. Expression of putative EZH2 target genes were shown to be highly relevant to survival of melanoma patients in clinical datasets. To determine correlates of response to EZH2 inhibitors we screened a panel of 53 melanoma cell lines for drug sensitivity. We compared RNAseq profiles of sensitive to resistant melanoma cells and performed pathway analysis. Sensitivity was associated with strong downregulation of interferon gamma and alpha gene signatures that were reversed by treatment with EZH2 inhibitors. This is consistent with EZH2-driven dedifferentiated, invasive states associated with treatment resistance and defects in antigen presentation. These results suggest that EZH2 inhibitors may be most effectively targeted to immunologically "cold" melanoma to induce both direct cytotoxicity and increase immune responses in the context of checkpoint inhibitor immunotherapy