Single-cell epigenetic analysis reveals principles of chromatin states in H3.3-K27M gliomas

Abstract

AbstractCancer cells are highly heterogeneous, both at the transcriptional level and in their epigenetic state. Methods to study epigenetic heterogeneity are limited in their throughput and the information obtained per cell. Here, we adapted Cytometry by Time of Flight (CyTOF) to analyze a wide panel of histone modifications and chromatin regulators in primary tumor-derived lines of Diffused Intrinsic Pontine Glioma (DIPG). DIPG is a lethal pediatric brain cancer, driven by a mutation in histone H3 leading to substitution of lysine 27 with methionine (H3-K27M mutation). We identified two epigenetically distinct subpopulations in DIGP, reflecting inherent heterogeneity in the expression levels of the mutant histone. These two epigenetic subpopulations are robust across tumor lines derived from different patients and show differential proliferation capacity as well as expression of stem-cell and differentiation markers. Moreover, we demonstrate the use of this single-cell high-dimensional data to elucidate potential interactions between histone modifications and epigenetic alterations during the cell-cycle. Our work establishes new concepts for the analysis of epigenetic heterogeneity and cross-talk in cancer that could be applied to diverse biological systems.