Genome-wide chromatin accessibility change after PRC2 inhibition by MAK683 treatment

The methyltransferase Polycomb Repressive Complex 2 (PRC2), composed of EZH2, SUZ12, and EED subunits, is associated with transcriptional repression via tri-methylation of histone H3 on lysine 27 residue (H3K27me3). PRC2 is a validated drug target, as the EZH2 gain-of-function mutations identified in patient samples drive tumorigenesis. PRC2 inhibitors have been discovered and demonstrated anti-cancer efficacy in clinic. However, their pharmacological mechanisms are poorly understood. MAK683 is a potent EED inhibitor in clinical development. The overall goal of our study is to understand the molecular events leading to tumor regression after PRC2 inhibition. Our study revealed that multiple senescence-associated secretory phenotype (SASP) genes, such as Gata4, Mmp2/10, Itga2 and Gbp1, are derepressed upon PRC2 inhibition and contribute to decreased Ki67+, ECM reorganization, inflammation and tumor regression even in Cdkn2a/p16 knockout tumor. Overall design: We performed RNA-seq, ATAC-seq, whole genome bisulfide sequencing (WGBS) and H3K27me3 and H3K4me3 ChIP-seq with spike-in on MAK683-sensitive cancer cells G401 treated with DMSO or PRC2 inhibitor MAK683 at 3 µM. Two other MAK683-sensitive cells G402 and A2780 were also included in the cellular RNA-seq study. To reveal the p16-independent transcriptome change, we also constructed p16 KO G401 cell clone, build G401 and p16 KO cell-derived xenograft models in mice, and obtained the expression profiles of G401-derived xenograft tissues (WT or p16 knock out) after treatment with vehicle or 100 mg/kg MAK683 for 46 days.