Targeting the Synthetic Lethality Interaction of MTAP and PRMT5 to Overcome Drug Resistance and Enhance Anti-Cancer Immunity in Mantle Cell Lymphoma

Background: Complex genetic, epigenetic alterations and metabolic reprogramming are among the hallmarks of mantle cell lymphoma, an aggressive B-cell type of non-Hodgkin's lymphoma. CDKN2A and MTAP are frequently co-deleted in human cancers including MCL. Deletion of MTAP gene results in the accumulation of methylthioadenosine (MTA), a selective inhibitor of protein arginine methyltransferase 5 (PRMT5), signifying a dependence of MTAP deleted tumors on PRMT5. PRMT5 plays an important role in normal cellular processes via epigenetic and post-translational modification of RNA splicing, DNA repair and cell cycle regulators. These pathways may be activated in response to targeted therapies to maintain tumor growth and survive chemotherapy. Sustained PRMT5 expression and activity could be therapeutically targeted in MTAP-deficient MCL. Mutations in RNA splicing factors are common in lymphoma and increase the susceptibility to perturbations in splicing events. Deregulated PRMT5 might induce alternative splicing, leading to loss of expression of proteins or epitopes, and subsequent immune evasion and failure of tumor specific immune therapy. Multiple mechanisms may co-exist.

Results: CDKN2A and MTAP were commonly co-deleted in ibrutinib-resistant MCL tumors (71%, p = 0.01). To corroborate with this finding, we found that PRMT5 was overexpressed in both primary ibrutinib-resistant MCL and cell lines, with its expression levels inversely correlated with the patient responses to ibrutinib treatment (p = 0.004). Metabolomics analysis revealed elevated S-Adenosyl-methionine (SAM) and S-Adenosyl-homocysteine (SAH) (t-test p <0.001 and p <0.05), PRMT5 cofactor and product, respectively, in ibrutinib-resistant MCL cell lines. PRMT5 plays an important role in the regulation of cell cycle progression. Consistently, treatment with PRMT5 inhibitors induced cell cycle arrest in MCL cell lines (20% and 47% reduction in S phase for JVM13 and JVM2 respectively). Interestingly, treatment with the catalytic inhibitors (GSK3226595 and EPZ015666) led to S-phase stasis in which MCL cells seem incapable of replication. Meanwhile, PRMT5 inhibition with these inhibitors prevented the growth of MCL cell lines as indicated by remarkable decreases in the cell viability (IC50 = 1-1.4 µM and 0.58-0.95µM, respectively). PRMT5 enzymatic activity is required for its function in promoting cell cycle progression and proliferation, as treatment with its inhibitors leads to dramatic reduction in the level of SDMA-containing proteins, especially that of H4R3me2s. More importantly, pharmacological blockade of PRMT5 with single agent GSK3226595 significantly inhibited tumor growth in ibrutinib-resistant MCL PDX models (n = 5, p <0.05), implicating PRMT5 as an actionable target in MCL. PRMT5-mediated alternative splicing may contribute to immune escape and immune suppression. Indeed, our preliminary results revealed that T cells from MCL specimen with high expression of PRMT5 displayed decreased glucose uptake (fold MFI <1-1.23 vs. 2.2), mitochondria mass (p <0.01) and ΔΨm (fold MFI <1-1.26 vs. 2.3), by flow cytometry. Strikingly, the same patient-derived cytotoxic T-lymphocytes (CTL) exhibit reduced cytotoxicity towards autologous lymphoma cells, compared to those derived from healthy donors (p <0.05), strongly implicating impaired T cell metabolic fitness plus immune escape and suppression diminished T cell effector function.

Conclusion: We presented evidence that MCL with MTAP deletion confers synthetic lethal dependence on PRMT5, making it an attractive therapeutic target. As an important metabolic and epigenetic regulator, loss of PRMT5 leads to malfunction of the constitutive splicing machinery that induces alternative splicing events, genetic instability and cell cycle arrest. Sustained PRMT5 expression and activity confers tumor aggressiveness and therapeutic resistance in MTAP-deficient MCL. Pharmacological blockade of PRMT5 may dramatically enhance T-cell immunity, while suppressing MCL cell proliferation and tumor growth in vivo. Further successful mechanistic studies would facilitate the identification of novel therapeutics and strategies to overcome resistance to targeted therapies and significantly improve the efficacy of immunotherapy for much better clinical outcomes of MCL.