H3K27M induces defective chromatin spread of PRC2-mediated repressive H3K27me2/me3 and is essential for glioma tumorigenesis

Abstract

Lys-27-Met mutations in histone 3 genes (H3K27M) characterize a subgroup of deadly gliomas and decrease genome-wide H3K27 trimethylation. Here we use primary H3K27M tumor lines and isogenic CRISPR-edited controls to assess H3K27M effects in vitro and in vivo. We find that whereas H3K27me3 and H3K27me2 are normally deposited by PRC2 across broad regions, their deposition is severely reduced in H3.3K27M cells. H3K27me3 is unable to spread from large unmethylated CpG islands, while H3K27me2 can be deposited outside these PRC2 high-affinity sites but to levels corresponding to H3K27me3 deposition in wild-type cells. Our findings indicate that PRC2 recruitment and propagation on chromatin are seemingly unaffected by K27M, which mostly impairs spread of the repressive marks it catalyzes, especially H3K27me3. Genome-wide loss of H3K27me3 and me2 deposition has limited transcriptomic consequences, preferentially affecting lowly-expressed genes regulating neurogenesis. Removal of H3K27M restores H3K27me2/me3 spread, impairs cell proliferation, and completely abolishes their capacity to form tumors in mice.

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

“…has shown that H3K27M reduces the level of EZH2 automethylation, which decreases PRC2 methyltransferase activity in a manner that most dramatically affects the conversion of H3K27me2 to me3 . This is consistent with the relative effects of H3K27M on H3K27me2 vs. H3K27me3 quantity and deposition .…”

“…The same H3F3A knockdown did not alter survival time of an H3WT paediatric midline HGG. A second study utilized the CRISPR/Cas‐9 methodology in H3.3K27M DIPG xenografts to generate clones completely lacking the H3K27M mutation and compared tumourigenicity of these clones to both an unedited clone and the parental PDX . Here, clones lacking the H3K27M mutation were not able to generate tumours, while both the parental and unedited clones were.…”

“…In addition to effects on tumour growth and self‐renewal, H3K27M alters differentiation programs. Gene ontology analysis of genes differentially expressed in response to H3K27M frequently show enrichment for lists associated with neural lineage differentiation . In cultured cells, expression of H3K27M blocked astrocytic and impaired oligodendrocytic differentiation of hNPCs expressing constitutively active PDGFRA with p53 loss .…”

“…While the loss of H3K27me3 is a hallmark of the H3K27M mutation, regions exist that are able to retain or even gain H3K27me3 in H3K27M cells. These loci represent strong PRC2 targets and may be of critical importance in H3K27M tumourigenicity (Figure C ). To target these loci, several small molecule inhibitors of EZH2 (EZH2i) have been used to deplete the remaining H3K27me3 in H3K27M cells, but the impact on cell growth has been somewhat inconsistent.…”

Glioblastoma Stem Cells: Driving Resilience through Chaos

“…making cancer networks distinct from their normal counterparts [27,29,41]. Although conventional tumor genetics categorize mutations into oncogenes and tumor-suppressor genes, recent genetic analyses of gliomas and other malignancies have detected dysregulation of chromatin regulators, which may lead to plasticity in the epigenetic cell state [42][43][44][45]. When analyzed in this context, cancer networks reside at a net higher entropy than do corresponding normal tissues, and display distinct energy relationships between stem and non-stem populations [29].…”