CyTOF antibodies used in this study.

Diffuse large B cell lymphomas and follicular lymphomas show recurrent mutations in epigenetic regulators; among these are loss-of-function mutations in KMT2D and gain-of-function mutations in EZH2. To systematically explore the effects of these mutations on the wiring of the epigenetic network, we applied a single-cell approach to probe a wide array of histone modifications. We show that mutant-EZH2 elicits extensive effects on the epigenome of lymphomas, beyond alterations to H3K27 methylations, and is epistatic over KMT2D mutations. Utilizing the single-cell data, we present computational methods to measure epigenetic heterogeneity. We identify an unexpected characteristic of mutant-EZH2, but not KMT2D, in increasing heterogeneity, shedding light on a novel oncogenic mechanism mediated by this mutation. Finally, we present tools to reconstruct known interactions within the epigenetic network, as well as reveal potential novel cross talk between various modifications, supported by functional perturbations. Our work highlights novel roles for mutant-EZH2 in lymphomagenesis and establishes new concepts for measuring epigenetic heterogeneity and intra-chromatin connectivity in cancer cells.

弥漫性大B细胞淋巴瘤与滤泡性淋巴瘤的表观遗传调控因子中存在复发性突变；其中包括KMT2D的功能丧失突变，以及EZH2的功能获得突变。为系统性探究此类突变对表观遗传网络调控通路的影响，我们采用单细胞方法对多种组蛋白修饰进行检测。本研究证实，突变型EZH2不仅会改变H3K27甲基化水平，还会对淋巴瘤细胞的表观基因组产生广泛影响，且该突变对KMT2D突变具有上位性。依托单细胞数据，我们开发了用于量化表观遗传异质性的计算方法。我们发现了突变型EZH2（而非KMT2D）可增加异质性这一意外特征，为该突变介导的新型致癌机制提供了新的研究视角。最后，我们提出了可重构表观遗传网络内已知相互作用的工具，并经功能扰动实验验证，揭示了不同组蛋白修饰间潜在的新型串扰通路。本研究阐明了突变型EZH2在淋巴瘤发生过程中的全新作用，并为量化癌细胞的表观遗传异质性与染色质内部连接建立了全新的研究范式。