EZH1/2, SWI/SNF, and MLL2 Dependent Heterochromatin Formation and Abnormal Transcriptome in Hematological Malignancies

The neomorphic alteration of H3K27me3 patterning is a fundamental trait of cancers. We have developed a new clinical strategy; dual inhibition of EZH1 and EZH2 significantly reprogrammed the abnormal epigenome and restored the transcriptome in lymphomas (Blood, 2016; 58^th ASH, 2016; NCT02732275).

H3K27me3-associated chromatin regulation contributes to almost all human malignancies, yet the underlying mechanisms of gene silencing remain unclear, owing to a lack of data representing the action of EZH1/2 and other chromatin regulators in practical models. To analyze the dynamic processes of chromatin regulation, we treated H3K27me3-accumulated lymphoma cells with EZH2 inhibitors or EZH1/2 dual inhibitors and then profiled several epigenetic factors and histone marks using time-course chromatin immunoprecipitation (ChIP) and genome-wide ChIP assays. EZH2 single inhibition expelled the EZH2-containing polycomb repressive complex 2 (EZH2-PRC2) from methylated chromatin. This simultaneously triggered the acute recruitment of EZH1-PRC2 to a part of the loci, leading to homeostatic regulation of chromatin. In contrast, pharmacological EZH1/2 dual inhibition or EZH1 depletion prior to EZH2 inhibition resulted in the rapid removal of both PRC2 and PRC1 and their enzymatic products H3K27me3 and H2AK119ub. These initial changes were further accompanied by the recruitment of chromatin remolding factors (SWI/SNF, also called BAF complex), such as ARID1A, BRG1 (SMARCA4), and SNF5 (SMARCB1), histone H3K27 acetylation and H3K4 tri-methylation, formation of accessible focal chromatin, RNA PolII recruitment, and stable induction of transcription. We also found that hyperactivation of EZH1/2 by co-overexpression or EZH2 active mutation, as in a part of B-cell lymphoma, facilitated the eviction of the BAF complex and closed chromatin conformation. Thus, the opposing actions of EZH1/2-containing polycomb and SWI/SNF complexes are required for facultative heterochromatin formation.

Genetic lesions and transcriptional downregulation of epigenetic factors are frequently observed in general cancers, including hematological malignancies. We reconstructed the loss-of-function (LoF) models of major genetic targets ARID1A (9% in FL, 7% in BL) , SMARCA4 (21% in BL) , KDM6A (found in AML, CML, T-ALL, MM, HL) , and BAP1 and then analyzed them using epigenome/transcriptome profiling. Inactivation of the tumor-suppressive chromatin remodelers caused EZH1- and EZH2-dependent H3K27me3 accumulation and heterochromatin formation, leading to transcriptional silencing. The new EZH1/2 dual inhibitor effectively cancelled epigenetic abnormalities. The cell models lacking a functional BAF complex were sensitive to the EZH1/2 dual inhibitors compared with the EZH2 single inhibitor.

MLL2 (KMT2D)-mediated H3K4me3 regulation is frequently disrupted in DLBCL (~30%) and FL (~90%). MLL2 LoF enhanced cell growth in pre-tumorigenic LCLs, which could be cancelled by EZH1/2 dual inhibition. Genome-wide ChIP revealed that MLL2 LoF-dependent H3K4me3 downregulation is closely associated with EZH1- and EZH2-dependent H3K27me3 accumulation. Collectively, the EZH1/2 dual inhibitors may be promising for use in (1) EZH1/2 dual expressing tumors, such as ATL and other T- and B-cell lymphomas; (2) DLBCL/FL with actively mutated EZH2; and (3) additional cancer types (~20% of human malignancies) with mutations in the Trithorax and other epigenetic genes (ARID1A, SMARCA4, SMARCB1, KDM6A, BAP1, and MLL2).

The EZH1/2-dependent epigenetic pathway of cancer development is also initiated by viral infection (Curr. Opin. Oncol., 2017). Whole epigenome and transcriptome analyses revealed that infection by lymphotropic oncoviruses, HTLV-1 and EBV, reprogrammed global EZH1/2-H3K27me3 patterns and established unique transcriptomes in malignant progenitors. Low-dose EZH1/2 inhibitor selectively depleted the HTLV-1-infected cell population in asymptomatic carriers (31/35, 88.6%) and EBV-infected immortalized LCLs. Data integration with established lymphoma epigenome suggested that this heritable EZH1/2 dysfunctional state is epigenetically imprinted at the non-malignant, virus-infected step. The identification of this novel epigenetic pathway will lead to precision oncology and new therapeutic strategies in human malignancies, particularly for elimination of the founder cell populations.