Mutant EZH2 alters the epigenetic network and increases epigenetic heterogeneity in B cell lymphoma

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, alone or in combination, on the epigenetic landscape, we applied a single cell approach, based on Cytometry by Time of Flight (CyTOF), 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 dominant 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 analysis to reveal potential cross talk between various modifications in the epigenetic network, validated 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 MARS-seq (RNA) sequencing of cells lines - WT and CRISPR mutants. WT DLBCL cell line is OCI-Ly7 and over its background we generated mutants in either kmt2d, EZH2 GOF or a double mutant. We included three replicates of RNA from each cell line; 2m of cells were lysed and extracted for RNA with Nucleospin RNA kit, examined in tapestation and sequenced with Illumina NextSeq500