PRMT5 inhibition alters cellular chromatin landscape and drives vulnerability to BH3 mimetics in mantle cell lymphoma

Background: Mantle cell lymphoma (MCL) is a rare and incurable blood cancer, comprising 10% of Non-Hodgkin lymphomas. Especially in relapse settings, there remains a crucial need for novel treatments. The enzyme protein arginine methyltransferase 5 (PRMT5) is an oncogenic driver in MCL which targets both histones and non-histone proteins for posttranslational symmetric arginine dimethylation (me2s). BCL2 family proteins govern apoptosis and their dysregulation is a hallmark of MCL, but treatment with pharmacological inhibitors (BH3 mimetics) has had limited success. We hypothesized that transcriptional and epigenomic perturbations via PRMT5 inhibitors (PRMT5i) will sensitize MCL cells to BH3 mimetics for synergistic drug action. Methods: Plate- and flow-cytometry-based BH3 profiling was used to read out the apoptotic priming state of n=5 MCL cell lines and n=2 primary patient samples. Effects of the small molecule PRMT5i PRT382 were assessed via BH3 profiling, transcriptomics (RNA sequencing) and genome-wide histone modification profiling (CUT&RUN sequencing for H3K4me3, H3K27me3, H3K27ac and two me2s marks H3R8me2s and H4R3me2s). Drug combination effects of PRT382 and BH3-mimetics (navitoclax, A852/A-1331852, PRT1419) were tested in MCL cell lines (n=5). Efficacy of navitoclax and PRT808, a related PRMT5i, was assessed alone or in combination in a murine patient-derived xenograft (PDX) model of aggressive, relapsed MCL. Results: Global analysis of histone modifications and RNA expression revealed strong association around transcription start sites (adjusted p<0.0001), including for PRMT5-mediated H4R3me2s (adjusted p<0.0001), but revealed no pronounced global loss of histone arginine methylation under PRT382. Epigenomic responses to PRT382 were highly distinct in MCL models Z-138 and CCMCL1, with the latter revealing lowered global H3K4me3 (p<0.0001) at loci specifically enriched for cell cycle pathways (adjusted p<0.0001). BH3 profiling revealed vulnerabilities to mitochondrial insults in cell lines, PDX cells, and patient samples, which was correlated with pro-survival BCL2 family RNA- and protein expression (p<0.01). Pronounced sensitization to depolarization with PRT382 in Z-138, but not CCMCL1, was reflective of transcriptomic differences in these models. We observed strong synergistic reduction in cell viability with n=16 distinct PRMT5i/BH3 mimetic combinations (p<0.01). In our PDX model, the PRT808/navitoclax combination outperformed single treatment cohorts in survival (median 93 vs. 65/75 days for PRT808/navitoclax alone, p<0.01) and circulating disease (p<0.01). Conclusions: Our study showed the broad synergistic potential of combining PRMT5i and BH3 mimetics both in vitro and in vivo. PRMT5i lead to epigenome-wide modulation of chromatin states with potential to create vulnerabilities to targeted agents.