Combined inhibition of EZH2 and degradation of Ikaros has synergistic effects in germinal center B-cell diffuse large B-cell lymphoma [ChIP-seq]
To explore the therapeutic opportunities to enhance the clinical efficacy of EZH2 inhibitors in treating diffuse large B-cell lymphoma (DLBCL), a genome-wide drug sensitizing CRISPR/Cas9 screen was conducted in the presence of tazemetostat. We found that the loss of IKZF1 or IKZF3 augmented the potency of tazemetostat on DLBCL. Treating cells with lenalidomide, an immunomodulatory drug that degrades IKZF1 and IKZF3, in combination with tazemetostat, recapitulated the effects observed in the drug sensitizing screen. The combined drug treatment showed even higher synergistic effects, by triggering either cell cycle arrest or apoptosis, on a broader range of DLBCL cell lines, regardless of EZH2 mutation status. RNAseq analysis revealed strong upregulation of the interferon signaling and antiviral immune response signatures. Gene expression of key factors such as IRF7 and DDX58 were highly induced in cells treated with lenalidomide and tazemetostat, with a concomitant enrichment of H3K27 acetylation at their promoters as delineated in ChIPseq and ChIP qPCR analyses. Furthermore, transcriptome analysis and immunofluorescence staining demonstrated pronounced expression of a wide range of endogenous retroviruses (ERVs), with significant overlaps between the upregulated ERV loci and well-defined H3K27me3 enriched regions in EZH2-mutant lymphoma cell lines. Our data underscore the synergistic interplay between lenalidomide and tazemetostat on modulating epigenetic changes, resulting in upregulation of the interferon response and de-repression of ERVs, and ultimately to reduced growth of GCB-type DLBCL. Overall design: 1 cell lines, 4 conditions, 2 technical replicates per sample