EZH2 inhibition as a targeted therapy for H3K27M mutant pediatric gliomas [RNA-Seq]

Diffuse intrinsic pontine glioma (DIPG) is a highly aggressive brain tumour that is located in the pons and primarily affects children. Whole-exome sequencing studies have identified recurrent driver mutations in H3F3A and HIST1H3B, leading to the expression of histone H3 in which lysine 27 is substituted with methionine (H3K27M) in nearly 80% of DIPGs. H3K27M inhibits Polycomb Repressive Complex 2 (PRC2) activity by binding to its catalytic subunit EZH2 and although DIPGs with H3K27M mutation show global loss of H3 with trimethylated lysine 27 (H3K27me3), several genomic loci are still H3K27me3 positive. Here, we describe a new mouse DIPG model in which H3K27M potentiates tumourigenesis. Using this model and primary patient-derived DIPG cell lines, we show that H3K27M expressing tumours require PRC2 for proliferation. Furthermore, we demonstrate that small molecule EZH2 inhibitors abolish in vitro and in vivo tumour cell growth through a mechanism involving induction of the tumour suppressor protein p16INK4A. In agreement with this, we show that tumour cells with inactivated p16INK4A function do not respond to EZH2 inhibitors. By analysing genome-wide H3K27me3 enrichment profile in mouse DIPG model, we highlight distinct features of the loci that lose or retain H3K27me3 in H3K27M expressing cells. Taken together these results show that residual PRC2 activity is required for the proliferation of H3K27M positive DIPGs, and we propose a therapeutic strategy for these tumours using EZH2 inhibitors and expression of p16INK4A as a marker for stratifying potential responding tumours.