Disruption of developmental enhancer and PRC2 function by K27M in childhood glioma
Diffuse Intrinsic Pontine Glioma (DIPG) is a universally fatal childhood brain tumour which frequently carries a mutation in genes encoding histone H3. These mutations lead to a lysine-to-methionine (K-to-M) substitution at position 27 (H3K27M) within the histone H3 tail and initiate global shifts in the abundance of Polycomb Repressive Complex 2 (PRC2) mediated H3K27 methylation (me) and P300/CBP mediated acetylation (ac). Acquisition of the H3K27M mutation is the founding genetic event in DIPG tumours, making it likely that these global shifts in H3K27me/ac are instrumental in promoting the early steps toward gliomagenesis. Here, we show that the H3.3K27M oncogene directly disrupts the function of tissue specific gene enhancers and increases Polycomb target gene repression limiting developmental potential of neural stem cells (NSCs). To study the initial functional consequences of H3K27M in glioma, we developed an isogenic human model system. To do this, we modelled the earliest stages of DIPG development by introducing either K27M or wildtype (WT) H3.3 into hindbrain derived NSC cultures. Importantly, this model faithfully recapitulated the global H3K27ac/me dynamics observed in patient samples. Moreover, epitope tagging of the K27M and WT histones allowed us to globally assess the localisation of K27M and WT H3.3. This for the first time facilitated a global analysis of H3.3K27M distribution, as it relates to the WT histone in a biologically relevant context. We found that the presence of the K27M mutation does not alter the localisation of the mutant histone, which is most abundant at enhancer elements with lower levels at gene promoters. Remarkably, the H3.3K27M oncogene limits the developmental potential of NSCs by directly impeding tissue specific enhancer function. Moreover, we found that PRC2 function is primarily altered outside of stably bound Polycomb target sites, with the majority of H3K27me3 lost outside of these regions. Finally, we provide in vivo evidence for sequestration of the PRC2 complex at a subset of Polycomb target promoters. Taken together, these findings provide important new mechanistic insights on the initial steps of DIPG development.  Overall design: RNA-Seq, Chip-RX (H3K27ac, H3K27me3, H3K27me2, H3K4me3 & SUZ12), ATAC-Seq and Chip-Seq (tagged H3.3WT-V5 & H3.3M-V5) of human hindbrain derived neural stem cells expressing wild-type or mutant H3.3.