Polycomb repressive complex 2 in the driver's seat of childhood and young adult brain tumours

Abstract

Deregulation of the epigenome underlies oncogenesis in numerous primary brain tumours in children and young adults. In this review, we describe how recurrent mutations in isocitrate dehydrogenases or histone 3 variants (oncohistones) in gliomas, expression of the oncohistone mimic enhancer of Zeste homologs inhibiting protein (EZHIP) in a subgroup of ependymoma, and epigenetic alterations in other embryonal tumours promote oncogenicity. We review the proposed mechanisms of cellular transformation, current tumorigenesis models and their link to development. We further stress the narrow developmental windows permissive to their oncogenic potential and how this may stem from converging effects deregulating polycomb repressive complex (PRC)2 function and targets. As altered chromatin states may be reversible, improved understanding of aberrant cancer epigenomes could orient the design of effective therapies.

Keywords: EZH inhibiting protein; epigenome; glioma; isocitrate dehydrogenases; polycomb repressive complex 2.

Figure 1.. Brain tumour subgroups associated with epigenetic remodeling.

Brain tumours are broadly stratified as glial or embryonal, and by regions of occurrence in the forebrain (blue), midbrain and pons (red) or cerebellum (yellow). Tumours arising in early development are located in the midbrain, pons and cerebellum events and are characterized by events altering the methylation of histone 3 lysine 27 (H3K27). H3 lysine 27-methione (H3K27M) mutations and EZHIP are likely functionally interchangeable yet associate with either oligodendroglial fates in midline high-grade glioma (HGGs) or radial glial progenitors in posterior fossa group A ependymomas (PFA-EPN). Low and High-Grade Glioma (L/HGG) subgroups of later childhood and young adults target the cortical hemispheres, and carry H3.3G34R/V, isocitrate dehydrogenase 1 or 2 mutations (IDH1-R132/IDH2-R172) and/or loss of SET domain containing 2 (SETD2) function. These events converge on altering higher methylation states at H3K36, with implications for altered polycomb complex distribution. Subgroup-specific lineage markers demarcate driver mutation associations with glial cell types. Atypical teratoid/rhabdoid tumours (ATRT) driven by SMARBC1 or occasionally SMARCA4 loss arise from early neural or mesenchymal progenitors in the brain. Embryonal tumours with multilayered rosettes (ETMR)present unique DNA methylation landscape likely tied to the TTYH1-C19MC fusion event, with their transcriptomes recapitulating a neuronal lineage. Four MB subgroups match different neuronal lineages from the cerebellum and carry a variety of mutations in epigenetic targets.

Figure 2.. Targets of chromatin modifiers altered in brain tumours

Appropriate differentiation of neural lineages requires remodeling of chromatin landscapes through the interplay of polycomb repressive complex 2 (PRC2), acting in opposition to BRG1/BRM associated factors (BAF) complexes and Complex Proteins associated with Set1 (COMPASS). Abnormal PRC2 occupancy at genomic loci involved in fate specification, and expression of stemness associated genes, can stall differentiation and promote tumorigenesis linked to enhanced self-renewal. In stem cells, polycomb targets are prone to acquisition of repressive 5 methyl-cytosine through the inhibition of histone and DNA demethylases. Restraining the spread of PRC2 through H3K27M or Enhancer of Zeste Homologs Inhibitory Protein (EZHIP) aberrant expression maintains repression of specific polycomb targets and an active chromatin at stemness-associated genes. Deposition of H3.3G34R/V mutant histone prevents SET Domain containing 2 (SETD2) deposition of H3K36me3, thereby facilitating PRC2 redistribution to genic regions. The loss of BAF and COMPASS functions further prevents the conversion from repressed PRC2 targets to an active state, and is associated with stalled neural differentiation.

Figure 3.. Epigenetic drivers potentiate tumour development in murine models

The introduction of epigenetic driver events in mice has revealed the dependencies of tumour formation on time windows, combinations of cooperating oncogenic stimuli, and cell type, lineage or brain region in which they are introduced. In H3K27M, added Trp53 loss is sufficient to induce HGGs. In other H3K27M mouse models, in addition to loss of p53 function, additional PDGFRA/PDGFB overexpression or activating mutations, or ACVR1-R206H appear needed to accelerate disease onset and induce features of human HGG. IDH1-R132H mutant cells also requires Trp53 loss for tumorigenicity and can promote tumours resembling human disease from late embryonic development to adulthood. Loss of Smarcb1 transforms neural progenitors either in combination with Trp53 loss, or on its own between embryonic development days 6–10.

Figure 4.. Manipulation of driver events determines reversibility of tumour epigenomes

The manipulation of driver events remodeling the epigenome serves to characterize the reversibility of their effects, and the dependence of transformed cells on their function to proliferate, self-renew, and form tumours. The inhibition of 2-HG production by IDH1-R132H using a small molecule drug elevates 5-hydroxymethylcytosine, diminishes histone methylation and promotes glial differentiation in vitro, while delaying tumour burden in xenografts. The knockout or knockdown of the H3F3A-K27M mutant allele in tumour-derived cell lines restores PRC2 activity and H3K27me2/3deposition, renders the cells capable of enhanced glial differentiation and delays or abolishes the potential to form xenograft tumours. Similar trends are observed upon knockout of EZHIP, variably diminishing cell proliferation in some contexts. The restoration of SMARCB1 expression in ATRT lines reversed the loss of H3K27ac to reactivate silenced genes and decrease proliferation.