Cancer cells are highly heterogeneous at the transcriptional level and epigenetic state. Methods to study epigenetic heterogeneity are limited in throughput and information obtained per cell. Here, we adapted cytometry by time-of-flight (CyTOF) to analyze a wide panel of histone modifications in primary tumor-derived lines of diffused intrinsic pontine glioma (DIPG). DIPG is a lethal glioma, driven by a histone H3 lysine 27 mutation (H3-K27M). We identified two epigenetically distinct subpopulations in DIPG, reflecting inherent heterogeneity in expression of the mutant histone. These two subpopulations are robust across tumor lines derived from different patients and show differential proliferation capacity and expression of stem cell and differentiation markers. Moreover, we demonstrate the use of these 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 in cancer that could be applied to diverse biological systems.

癌细胞在转录水平和表观遗传状态是高度异质的。研究表观遗传异质性的方法在通量和每个细胞获得的信息方面受到限制。在这里，我们采用飞行时间 (CyTOF) 流式细胞术来分析原发性肿瘤来源的弥漫性脑桥胶质瘤 (DIPG) 系中的一组广泛的组蛋白修饰。DIPG 是一种致命的神经胶质瘤，由组蛋白 H3 赖氨酸 27 突变 (H3-K27M) 驱动。我们在 DIPG 中鉴定了两个表观遗传上不同的亚群，反映了突变组蛋白表达的固有异质性。这两个亚群在来自不同患者的肿瘤系中是稳健的，并显示出不同的增殖能力以及干细胞和分化标志物的表达。而且，我们展示了使用这些高维数据来阐明细胞周期中组蛋白修饰和表观遗传改变之间的潜在相互作用。我们的工作为癌症表观遗传异质性分析建立了新概念，可应用于多种生物系统。