Histone tail analysis reveals H3K36me2 and H4K16ac as epigenetic signatures of diffuse intrinsic pontine glioma

Abstract

Background Diffuse intrinsic pontine glioma (DIPG) is an aggressive pediatric brainstem tumor. Most DIPGs harbor a histone H3 mutation, which alters histone post-translational modification (PTM) states and transcription. Here, we employed quantitative proteomic analysis to elucidate the impact of the H3.3K27M mutation, as well as radiation and bromodomain inhibition (BRDi) with JQ1, on DIPG PTM profiles. Methods We performed targeted mass spectrometry on H3.3K27M mutant and wild-type tissues (n = 12) and cell lines (n = 7). Results We found 29.2 and 26.4% of total H3.3K27 peptides were H3.3K27M in mutant DIPG tumor cell lines and tissue specimens, respectively. Significant differences in modification states were observed in H3.3K27M specimens, including at H3K27, H3K36, and H4K16. In addition, H3.3K27me1 and H4K16ac were the most significantly distinct modifications in H3.3K27M mutant tumors, relative to wild-type. Further, H3.3K36me2 was the most abundant co-occurring modification on the H3.3K27M mutant peptide in DIPG tissue, while H4K16ac was the most acetylated residue. Radiation treatment caused changes in PTM abundance in vitro, including increased H3K9me3. JQ1 treatment resulted in increased mono- and di-methylation of H3.1K27, H3.3K27, H3.3K36 and H4K20 in vitro. Conclusion Taken together, our findings provide insight into the effects of the H3K27M mutation on histone modification states and response to treatment, and suggest that H3K36me2 and H4K16ac may represent unique tumor epigenetic signatures for targeted DIPG therapy.

A novel proteomics approach to epigenetic profiling of circulating nucleosomes

“…Given their key involvement in carcinogenesis, histone PTMs are emerging as potential biomarkers in clinical diagnostics and prognostics of cancer as well as therapeutic targets 23 . While most work studying histone PTMs are carried out on tumor resection or cells lines 24 – 26 , we propose here a new method to identify and quantify epigenetic alterations directly from the blood of patients. Using the combination of the capture of circulating nucleosomes and the underlying analysis of histone PTMs by tandem mass spectrometry, we significantly reduced the abundance of blood proteins, allowing the characterization of histone PTMs in plasma.…”

The Long Non-Coding RNA H19 Drives the Proliferation of Diffuse Intrinsic Pontine Glioma with H3K27 Mutation

“…DIPG tumours bearing H3K27M induce a dramatic reduction in the global levels of H3K27me3 in DIPG cells [4]. Recently, other PTMs were identified, including H3K26me2 and H416ac [31]. Herein, we did not have the bioinformatics tools to determine the association between histone PTMs and H19 expression, but this would be very interesting and the objective of future studies.…”

“…These mutations are not common, but have been suggested to be associated with DIPG-H3K27M; however, their implication in DIPG progression and their link with H3K27M are poorly understood [4,21]. Other chromatin changes are controlled by dynamic post-translational modifications (PTMs) on the histone N-terminal tail, which influence the structure of chromatin and, hence, gene expression [31]. DIPG tumours bearing H3K27M induce a dramatic reduction in the global levels of H3K27me3 in DIPG cells [4].…”

The Advances in Epigenetics for Cancer Radiotherapy

“…Radiotherapy combined with histone methyltransferase G9a inhibitor was designed to reduce H3K9me3 levels and DSB repair. Radiotherapy can induce some histone-modified cell-specific and peptide-specific changes, which should be paid attention to when using modifiers [ 50 ]. It has been suggested that radiation kills a large number of cancer cells and induces radiation resistance and more aggressive epigenetic phenotypes.…”