PFA ependymoma-associated protein EZHIP inhibits PRC2 activity through a H3 K27M-like mechanism

Abstract

Posterior fossa type A (PFA) ependymomas exhibit very low H3K27 methylation and express high levels of EZHIP (Enhancer of Zeste Homologs Inhibitory Protein, also termed CXORF67). Here we find that a conserved sequence in EZHIP is necessary and sufficient to inhibit PRC2 catalytic activity in vitro and in vivo. EZHIP directly contacts the active site of the EZH2 subunit in a mechanism similar to the H3 K27M oncohistone. Furthermore, expression of H3 K27M or EZHIP in cells promotes similar chromatin profiles: loss of broad H3K27me3 domains, but retention of H3K27me3 at CpG islands. We find that H3K27me3-mediated allosteric activation of PRC2 substantially increases the inhibition potential of EZHIP and H3 K27M, providing a mechanism to explain the observed loss of H3K27me3 spreading in tumors. Our data indicate that PFA ependymoma and DIPG are driven in part by the action of peptidyl PRC2 inhibitors, the K27M oncohistone and the EZHIP ‘oncohistone-mimic’, that dysregulate gene silencing to promote tumorigenesis.

Automethylation of PRC2 promotes H3K27 methylation and is impaired in H3K27M pediatric glioma

“…7). Given the unique role of H3K27me3 in gene repression and disease pathogenesis (Wigle et al 2011;Yap et al 2011;Lee et al 2018b;Oksuz et al 2018;Hübner et al 2019;Jain et al 2019), it is telling that automethylation of PRC2 mainly participates in the rate-limiting process of attaining the highest H3K27 methylation state (Fig. 7).…”

Diffuse intrinsic pontine glioma-like tumor with EZHIP expression and molecular features of PFA ependymoma

“…EZHIP bears a methionine residue, similar to the H3 lysine-to-methionine (K27M) mutation, that is critical for mediating global H3K27me3 reduction [6,7,13]. The genomic distribution of H3K27me3 in H3K27M DIPGS and PFAs show remarkable similarities suggesting that these two tumors may be epigenetically related and share similar pathogenic mechanisms [2,7]. Indeed, in support of this hypothesis,~4% of PFAs demonstrate H3K27M mutations that are mutually exclusive from EZHIP mutations [11].…”

“…Additionally, three independent groups have demonstrated that EZHIP mimics the H3K27M "oncohistone" to cause global H3K27me3 reduction. EZHIP bears a methionine residue, similar to the H3 lysine-to-methionine (K27M) mutation, that is critical for mediating global H3K27me3 reduction [6,7,13]. The genomic distribution of H3K27me3 in H3K27M DIPGS and PFAs show remarkable similarities suggesting that these two tumors may be epigenetically related and share similar pathogenic mechanisms [2,7].…”

Invited Review: Emerging functions of histone H3 mutations in paediatric diffuse high‐grade gliomas

“…CXORF67, now termed EZH1/2 Inhibitory Protein (EZHIP), is normally expressed predominantly in gonads, where it limits PRC2 enzymatic activity . EZHIP contains an amino acid sequence with similarities to the K27M mutant histone H3 tail and also places a methionine in the lysine‐binding pocket of EZH2, resulting in even more potent inhibition of PRC2 . In agreement with this proposed overlap of mechanism, H3K27M mutations are found with low frequency in PFA ependymomas and are always mutually exclusive with high expression of EZHIP .…”