Abstract B44: Identification of epigenomic changes induced by H3 K27M mutation in glioblastoma using patient-derived and CRISPR/Cas9 edited cell lines
Authors: Harutyunyan Ashot S. , Krug Brian , Papillon-Cavanagh Simon , Chen Haifen , Deshmukh Shriya , Cheung Warren A. , Li Rui , Belle Jad , Bechet Denise , Jay Nicolas De , Zeinieh Michele , Gayden Tenzin , Russo Caterina , Mikael Leonie , Faury Damien , Kleinman Claudia , Pastinen Tomi , Majewski Jacek , Jabado Nada 
Published: February 2019

Abstract
Background: Glioblastoma is a grade IV malignant brain tumor with poor prognosis and rapid disease progression. Recurrent somatic mutations in histone H3 genes have been identified in the majority of pediatric glioblastoma cases. The K27M mutation in H3.1 and H3.3 histones globally inhibits lysine methylation at the K27 position, whereas H3.3 G34R/V possibly affects histone lysine methylation at the K36 position. H3 K27M mutation has been shown to dramatically decrease the total levels of H3K27me3 and H3K27me2 marks and increase H3K27ac levels. However, the effect of H3 K27M on global epigenomic changes is not fully characterized. Furthermore, standard profiling of histone marks by chromatin immunoprecipitation combined with next-generation sequencing (ChIP-seq) is not quantitative, a significant caveat when global levels of histone marks change so drastically.
Methods: We assembled a collection of H3 K27M mutant and wild-type cell lines derived from the glioblastoma patients. The epigenomes of these cell lines were comprehensively characterized by profiling for six histone marks (H3K4me1, H3K4me3, H3K27ac, H3K27me3, H3K36me2, H3K36me3) using ChIP-seq. In addition, we derived isogenic cell lines overexpressing H3.3 K27M, as well as cell lines with knockin or knockout of the K27M mutation using the CRISPR/Cas9 genome editing system. These cell lines were profiled for H3K27me3 mark by ChIP-seq. We used a modified ChIP-seq protocol, chromatin immunoprecipitation with exogenous reference genome (ChIP-Rx), which allows quantitation of histone mark abundance by normalization to proportions of added Drosophila chromatin in the ChIP reaction. RNA sequencing was performed on both primary and isogenic cell lines.
Results: The most striking difference we observed between H3 K27M and wild-type cells was in H3K27me3 mark. Using ChIP-Rx, we observe significantly lower levels of H3K27me3 mark in H3 K27M cell lines, both in primary cells and isogenic contexts. Despite very low total levels of H3K27me3 mark, K27M mutant cells display enrichment of the mark in certain regions, at comparable levels to wild-type cell lines. Using our isogenic cell line models, we show that K27M mutation is indeed responsible for those genome-wide changes in the epigenome. Correlating H3K27me3 distribution with transcriptome data, we show that expression changes mainly among the genes that are lowly expressed in these cells. Pathway analysis of differentially expressed genes shows enrichment for neural development and differentiation that suggests links to disease pathogenesis.
Conclusions: Despite the fact that primary cell lines have different origins and a variety of additional driver mutations, their epigenomes appears to be remarkably similar, due to being shaped predominantly by the effects of histone mutations, as demonstrated in isogenic cell line systems. Global changes in H3K27me3 levels and distribution in H3 K27M mutant cells lead to specific changes in gene expression. The changes induced by K27M mutations also appear to be specific to the cell type and/or developmental context of origin. This may help better understand the effect they have in reshaping the epigenome to promote oncogenesis.
Citation Format: Ashot S. Harutyunyan, Brian Krug, Simon Papillon-Cavanagh, Haifen Chen, Shriya Deshmukh, Warren A. Cheung, Rui Li, Jad Belle, Denise Bechet, Nicolas De Jay, Michele Zeinieh, Tenzin Gayden, Caterina Russo, Leonie Mikael, Damien Faury, Claudia Kleinman, Tomi Pastinen, Jacek Majewski, Nada Jabado. Identification of epigenomic changes induced by H3 K27M mutation in glioblastoma using patient-derived and CRISPR/Cas9 edited cell lines [abstract]. In: Proceedings of the AACR Special Conference: Pediatric Cancer Research: From Basic Science to the Clinic; 2017 Dec 3-6; Atlanta, Georgia. Philadelphia (PA): AACR; Cancer Res 2018;78(19 Suppl):Abstract nr B44.