EZH1-dependent H3K27me1 is an adaptive chromatin barrier that limits DNMT inhibitor response in colorectal cancer

Abstract

Abnormal DNA methylation patterning is a defining epigenetic hallmark of human cancer and is therapeutically targetable with DNA methyltransferase inhibitors (DNMTis). However, DNMTi-induced DNA hypomethylation promotes adaptive chromatin remodeling that limits molecular and therapeutic responses to these drugs. Here, we identify EZH1-dependent H3K27 mono-methylation (H3K27me1) as a previously unrecognized adaptive barrier to DNMTi response in colorectal cancer. While EZH2-selective inhibitors deplete H3K27me2 and H3K27me3, they preserve EZH1-dependent H3K27me1 at Polycomb-enriched genomic regions. In contrast, dual EZH1/2 inhibition eliminates all H3K27 methylation states and robustly synergizes with DNMTi to enhance transcriptional activation and growth suppression. Mechanistically, dual EZH1/2 inhibition induces a redistribution of p300/CBP-dependent H3K27 acetylation (H3K27ac), generating a therapy-associated bivalent chromatin state characterized by coexisting DNA methylation and H3K27ac. DNMT inhibition resolves this induced bivalency, enabling activation of tumor-suppressive transcriptional programs. At the same time, coordinated loss of H3K27me1 and gene-body DNA methylation, together with depletion of promoter-associated H3K27ac, suppresses MYC- and E2F-driven oncogenic transcription networks that define the cancer cell-intrinsic therapeutic response. Collectively, these findings establish EZH1-dependent H3K27me1 as a key mediator of adaptive epigenetic plasticity and provide mechanistic rationale for combining DNMT inhibitors with dual EZH1/2i inhibitors to reprogram chromatin and suppress oncogenic transcription in solid tumors. HighlightsO_LIEZH1-dependent H3K27me1 sustains an adaptive barrier to DNMT inhibitor response in colorectal cancer. C_LIO_LIDual EZH1/2 inhibition eliminates all H3K27 methylation states and remodels chromatin architecture. C_LIO_LIEZH inhibition induces a DNA methylation-H3K27ac bivalent chromatin state. C_LIO_LIDNMT and EZH1/2 co-inhibition reprograms enhancers and promoters to activate tumor-suppressive pathways. C_LIO_LICombination therapy suppresses MYC/E2F-driven oncogenic transcription, defining its cancer cell-intrinsic therapeutic efficacy. C_LI