RNA-seq on DMSO or MAK683 treated cancer cells and xenograft tumor samples

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 BMP-ACVR1 signaling pathway as a critical component for the anti-lymphoma efficacy of PRC2 inhibitor. We performed RNA-seq, H3K27me3 and H3K4me3 ChIP-seq with spike-in on MAK683-sensitive cancer cells WSU-DLCL2 treated with DMSO or PRC2 inhibitor MAK683 (3 μM for ChIP-seq, 5 μM for RNA-seq). To reveal the ACVR1-independent transcriptome change, we also constructed ACVR1 KO WSU-DLCL2 cell clone, NT and ACVR1 knock out cells that treated with DMSO or MAK683 (5 μM) were also included in the cellular RNA-seq study. Finally, we build WSU-DLCL2 and ACVR1 KO cell-derived xenograft models in mice, and obtained the expression profiles of WSU-DLCL2-derived xenograft tissues (NT or ACVR1 knock out) after treatment with vehicle or 100 mg/kg MAK683 for 28 days.