Epigenomic Reprogramming as a Driver of Malignant Glioma

Abstract

Malignant gliomas are central nervous system tumors and remain among the most treatment-resistant cancers. Exome sequencing has revealed significant heterogeneity and important insights into the molecular pathogenesis of gliomas. Mutations in chromatin modifiers-proteins that shape the epigenomic landscape through remodeling and regulation of post-translational modifications on chromatin-are very frequent and often define specific glioma subtypes. This suggests that epigenomic reprogramming may be a fundamental driver of glioma. Here, we describe the key chromatin regulatory pathways disrupted in gliomas, delineating their physiological function and our current understanding of how their dysregulation may contribute to gliomagenesis.

Keywords: chromatin; epigenomics; glioma; transcription.

Figure 1.. Simplified molecular subgrouping of malignant gliomas defined by common somatic mutations.

Subtypes broadly defined by mutational status of H3 (in children), and IDH (in adults) with common accompanying molecular alterations for each subtype shown. Alterations in genes which regulate chromatin function shown in red. Subtypes were initially identified in either adults or children, though are distributed across age-groups at different frequencies e.g. H3 mutations were defined in children but also occurs in young adults. The designation ‘H3K27M-midline glioma’ is replacing ‘diffuse intrinsic pontine glioma or DIPG’ to reflect a variety of midline anatomical locations (e.g. pons, spinal cord) in which these mutations occur. IDH mutant subtype further defined by either ATRX loss (‘astrocytomas’) or 1p/19q co-deletion (‘oligodendrogliomas’). IDH wild-type group in adults and H3 wild-type group in children are highly heterogeneous and can be further subdivided based on DNA methylation analysis (reviewed in Sturm et al., 2014). Grade denotes typical grade at presentation, though tumors can present clinically at different points in their anaplastic evolution.

Figure 2.. Reprogramming of the H3K27 methylation landscape by H3K27M mutation and EZHIP.

(A) PRC2 establishes H3K27me3 through its enzymatic component EZH2. HK27me3 is recognized by a CBX ‘reader’ protein in the PRC1 complex, which compacts chromatin to repress genes. (B) PRC2 is unable to methylate methionine residue in H3K27M, but also has reduced methylation activity in ‘trans’ i.e. at nucleosomes which contain wildtype H3. Amino acid sequence adjacent to K-to-M mutation aligned with EZHIP sequence showing similarity: an example of ‘oncohistone mimicry’. (C) Schematic of genome-wide H3K27me3 landscape contrasting WT, H3K27M and PRC2 knockout cells. In H3K27M cells small areas of H3K27me3 are retained at PRC2 nucleation sites, in contrast to PRC2 knockout cells where H3K27me3 is totally ablated.

Figure 3.. Reprogramming of the H3K36me3 landscape by H3G34 and SETD2 mutations.

(A) H3K36me3 is coupled with transcription elongation and resides at gene bodies to recruit chromatin effectors to suppress cryptic transcripts (DNMT3B), and regulate splicing (MRG15), and DNA repair (MSH6, PHF1) (see text for details). (B) H3G34R/V sterically restricts access of SETD2 to H3K36 leading to loss of H3K36me3 in cis i.e. in nucleosomes where the mutant histone is incorporated, while SETD2 remains functional in trans on nucleosomes containing wild-type H3. (C) Loss-of-function mutations of SETD2 lead to global reduction in H3K36me3.

Figure 4.. Pleiotropic effects of IDH mutation on the epigenome and other alpha-ketoglutarate dependent pathways.

(A) Gain-of-function mutations in IDH leads enzyme to favor alpha-ketoglutarate as a substrate leading to production of oncometabolite 2-HG. 2-HG inhibits many alpha-ketoglutarate dependent enzymes including histone (KDMs) and DNA demethylases (TETs), leading to aberrant accumulation of methylation on chromatin. Some of these changes such as H3K9 methylation prevent appropriate gene activation required for normal differentiation (B) Mutant IDH induced DNA methylation at CTCF binding sites disrupts chromatin architecture allowing oncogenes such as PDGFRA to hijack enhancers in different TADs.

Figure 5:. Consequences of ATRX loss in different chromatin regions.

(A) ATRX acts in concert with DAXX as a chaperone to deposit the histone variant H3.3 into heterochromatic regions bearing H3K9me3 at telomeres and peri-centromeres, endogenous retroviral elements and some euchromatic sites. Loss of ATRX and H3.3. deposition at telomeres leads to ALT and supports cell immortalization. Consequences of ATRX loss in euchromatin are poorly defined but may affect gene expression.

Figure 6:. Putative hallmarks of chromatin factor mutations which drive gliomagenesis in young patients.

(A) Context dependent effects of chromatin may be oncogenic in a developmentally restricted cell of origin. (B) Developmentally active period may be more sensitive to perturbation in chromatin factors given their function in establishing and maintaining cell identity. (C) ‘Single-hit’ may disrupt multiple cancer hallmarks as chromatin factors reside at hundreds of different genes regulating distinct pathways.