Simultaneous disruption of PRC2 and enhancer function underlies histone H3.3-K27M oncogenic activity in human hindbrain neural stem cells

Abstract

Driver histone H3-K27M mutations are frequent in pediatric midline brain tumors. However, the precise mechanisms by which H3-K27M causes tumor initiation remain unclear. Here, we use human hindbrain neural stem cells to model the consequences of H3.3-K27M on the epigenomic landscape in a relevant developmental context.Genome-wide mapping of epitope-tagged histone H3.3 reveals that both wildtype and K27M-mutant incorporate abundantly at pre-existing active enhancers and promoters, and to a lesser extent at PRC2-bound regions. At active enhancers, H3.3-K27M leads to focal H3K27ac loss, decreased chromatin accessibility, and reduced transcriptional expression of nearby neurodevelopmental genes. In addition, H3.3-K27M deposition at a subset of PRC2 target genes leads to increased PRC2 and PRC1 binding and augmented transcriptional repression that can be partially reversed by PRC2 inhibitors. Our work suggests that rather than imposing de novo transcriptional circuits, H3.3-K27M drives tumorigenesis by locking initiating cells in their pre-existing, immature epigenomic state, via disruption of PRC2 and enhancer functions.

New Developments in the Pathogenesis, Therapeutic Targeting, and Treatment of H3K27M-Mutant Diffuse Midline Glioma

“…H3K27M mutation globally reduces H3K27 trimethylation (H3K27me3), leading to elevated expression of gliomagenesis genes [ 7 , 34 , 35 ]. Thus, research focused on reversing the H3K27 mutation effects through targeted upstream target inhibition or epigenetic therapy remains a viable treatment option [ 36 , 37 , 38 ].…”

“…Somatic ACVR1 mutations are nearly exclusively limited to H3K27M-mutant diffuse midline glioma, occurring on only 0.3% of all other tumor types. These mutations induce hyperactive bone morphogenic protein (BMP) signaling, which arrests oligodendrocyte differentiation and increases tumorigenicity [ 36 , 37 ]. Specifically, Hoeman et al found that mouse tumor models with ACVR1 R206H plus H3.1K27M mutation had significantly shorter survival than tumor models with H3.1K27M mutations and no ACVR1 mutation [ 39 ].…”

“…Specifically, Hoeman et al found that mouse tumor models with ACVR1 R206H plus H3.1K27M mutation had significantly shorter survival than tumor models with H3.1K27M mutations and no ACVR1 mutation [ 39 ]. These findings suggest tumor-selective molecular therapy targeting ACVR1 mutations may decrease tumor aggressiveness and improve patients’ H3K27 mutant DMG life expectancy [ 37 , 41 ].…”

“…Although both studies suggest that suppression of EZH2 is a promising therapeutic strategy, additional studies that singularly target EZH2 and not multiple targets are needed to gauge better whether EZH2 suppression alone is a viable strategy to arrest tumor proliferation and disease progression. Additionally, since polycomb repressive complex 2 (PRC2) has recently been implicated in H3K27M gliomas, targeting EZH2, the main enzymatic subunit of PRC2, may also be an attractive option for PRC2-directed therapy [ 37 ].…”

Polycomb‐mediated gene regulation in human brain development and neurodevelopmental disorders

“…While global H3K27me2/3 levels were found to be decreased in DIPG expressing H3K27M, individual genes exhibit dramatically increased levels of the repressive H3K27me3 mark (Chan et al., 2013; Mohammad et al., 2017). This aberrant epigenetic profile might be explained by a confinement of PRC2 at its initial binding sites mediated by strong interaction of the mutant histone with EZH2, in turn leading to impaired spreading of the H3K27me3 mark (Brien et al., 2021; Chan et al., 2013; Voigt & Reinberg, 2013).…”