The genetic signatures of pediatric high-grade glioma: no longer a one-act play

Abstract

Advances in understanding pediatric high-grade glioma (pHGG) genetics have revealed key differences between pHGG and adult HGG and have uncovered unique molecular drivers among subgroups within pHGG. The 3 core adult HGG pathways, the receptor tyrosine kinase-Ras-phosphatidylinositide 3-kinase, p53, and retinoblastoma networks, are also disrupted in pHGG, but they exhibit a different spectrum of effectors targeted by mutation. There are also similarities and differences in the genomic landscape of diffuse intrinsic pontine glioma (DIPG) and pediatric nonbrainstem (pNBS)-HGG. In 2012, histone H3 mutations were identified in nearly 80% of DIPGs and ~35% of pNBS-HGG. These were the first reports of histone mutations in human cancer, implicating novel biology in pediatric gliomagenesis. Additionally, DIPG and midline pNBS-HGG vary in the frequency and specific histone H3 amino acid substitution compared with pNBS-HGGs arising in the cerebral hemispheres, demonstrating a molecular difference among pHGG subgroups. The gene expression signatures as well as DNA methylation signatures of these tumors are also distinctive, reflecting a combination of the driving mutations and the developmental context from which they arise. These data collectively highlight unique selective pressures within the developing brainstem and solidify DIPG as a specific molecular and biological entity among pHGGs. Emerging studies continue to identify novel mutations that distinguish subgroups of pHGG. The molecular heterogeneity among pHGGs will undoubtedly have clinical implications moving forward. The discovery of unique oncogenic drivers is a critical first step in providing patients with appropriate, targeted therapies. Despite these insights, our vantage point has been largely limited to an in-depth analysis of protein coding sequences. Given the clear importance of histone mutations in pHGG, it will be interesting to see how aberrant epigenetic regulation contributes to tumorigenesis in the pediatric context. New mechanistic insights may allow for the identification of distinct vulnerabilities in this devastating spectrum of childhood tumors.

Figure 1. The p53/RB and RTK/Ras/PI3K pathways are dysregulated in pHGG

a. The p53 and RB pathways regulate G1 cell cycle checkpoints. Mitogenic signaling activates the cyclin D-dependent kinases CKD4 or CKD6, coupled with cyclin D family members (CCND1/2/3). This complex phosphorylates pRB, releasing E2F and promoting transcription of genes responsible for G1/S cell cycle progression. Gene amplifications of CDK4, CDK6, or any of the three Cyclin D family members are found in pHGG, with greater frequency in DIPG. The tumor suppressor locus CDKN2A encodes two different proteins through translation of two different reading frames, p16INK4A and p19ARF. P16INK4A inhibits the activity of the cyclin D-dependent kinases CKD4 and CKD6. Oncogenic signals, DNA damage, or induction of P19ARF induce p53, leading to cell cycle arrest, apoptosis or senescence. Homozygous deletions of CDKN2A occur almost exclusively in NBS-HGGs; whereas TP53 mutations are common in both pNBS-HGG and DIPG. b. Mutations in the RTK/RAS/PI3K pathway transduce unregulated signals for cell proliferation, growth and survival. RTK signaling begins when growth factor ligand binding leads to receptor dimerization. In pediatric HGG, PDGFRα is the RTK most frequently targeted by amplification and/or mutation. Upon dimerization, RTKs trans-phosphorylate one another at tyrosine residues in their cytosolic tails. p85, the regulatory subunit of PI3K, can then either directly bind to these phosphor-tyrosine residues or connect to RTKs through adaptor molecules and Ras. PI3K is comprised of catalytic (p110) and regulatory (p85) subunits, both of which are targeted by mutation, usually in a mutually exclusive pattern, in pHGG.

Figure 2. Hotspot histone mutations occur in nearly 80% of DIPGs and ∼35% of NBS-HGGs

a. The basic unit of chromatin is the nucleosome; DNA wrapped around a histone octamer consisting of two copies of H2A, H2B, H3, and H4. The N-terminal tails of histones undergo post-translational modifications (PTMs), represented by yellow and blue circles, which in turn alter chromatin accessibility and recruitment of effector proteins, together influencing transcriptional permissiveness. This is accomplished because PTMs can 1) themselves alter the strength of DNA-histone interactions 2) facilitate recruitment of chromatin remodeling complexes or histone PTM-binding effector proteins. b. p.K27M substitutions occur in histone H3.1 and H3.3; p.G34R/V substitutions occur in H3.3. Histone H3.1/3.3 p.K27M exerts a dominant effect, preventing the accumulation of H3K27me2/3 on the wild-type histone H3 expressed in the same cell. p.G34R/V mutations do not exert the same effect on H3K27me3, but p.K27M and p.G34R/V histone mutations are associated with distinct genome-wide DNA methylation and gene expression tumor signatures. c. Table summarizing the functional consequences of histone mutations.

Figure 3. Histone mutations are strongly associated with anatomical location

Midsagittal (a) and coronal (b) MR images demonstrating that p.K27M mutations occur predominantly in tumors involving midline structures (such as the brainstem, cerebellum, and thalamus); while p.G34R/V mutations mainly occur in tumors arising in the cerebral hemispheres.