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

Ashot S Harutyunyan,Peter W Lewis,Warren A Cheung,Brian Krug,Leonie G Mikael,Carol C.l Chen ,Shriya Deshmukh,Melissa K Mcconechy ,Claudia L Kleinman,Nada Jabado,Damien Faury,Tomi Pastinen,Manav Pathania,Jad I Belle ,Dylan M Marchione,Alexander G Weil,Nicolas Jay ,Michele Zeinieh,Paolo Salomoni,Denise Béchet ,Simon Papillon‐Cavanagh ,Benjamin Ellezam,Benjamin A García ,Gaël Cagnone ,Rui Li,Siddhant Jain ,Bo Hu,Hamid Nikbakht,Haifen Chen,Chao Lü ,Abdulshakour Mohammadnia,Alexandre Montpetit,Jacek Majewski

doi:10.1038/s41467-019-09140-x

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.

Highlights

Lys-27-Met mutations in histone 3 genes (H3K27M) characterize a subgroup of deadly gliomas and decrease genome-wide H3K27 trimethylation
The H3K27me[2] mark showed a broader distribution in K27M, resembling the distribution of H3K27me[3] in wildtype High-Grade Gliomas (HGG), while in these cells not carrying the mutation this mark spread as expected genome-wide largely outside H3K27me[3] domains (Fig. 1b, c)
We observe non-random decrease of H3K27me[3] in the presence of the mutation, with residual deposition confined to large unmethylated CpG islands (CGIs) enriched for PRC2

Summary

Introduction

Lys-27-Met mutations in histone 3 genes (H3K27M) characterize a subgroup of deadly gliomas and decrease genome-wide H3K27 trimethylation. HGG have molecular signatures distinct from those of adult HGG2–4 They frequently harbor somatic mutations in histone 3 (H3) genes[5,6,7]. The most frequent oncohistone, H3K27M, specifies diffuse midline gliomas, which include deadly diffuse intrinsic pontine gliomas (DIPG) and represents a newly recognized molecular HGG entity in the 2016 World Health Organization classification[11] This somatic heterozygous mutation is present in all tumor cells at diagnosis, tumor spread, and in autopsy samples, and is recognized to be the major oncogenic driver in these HGGs1,6,10,12,13. Non-canonical (H3.3) histone variants, contributes to only a fraction of the total H3 pool (3–17%)[14] It has a dominant effect as it drastically reduces overall levels of the repressive H3K27me[3] mark in cells[14,15,16].

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Conclusion