Abstract LB-307: MTAP deletions in cancer create vulnerability to a MAT2A/PRMT5/RIOK1 axis

Abstract

Abstract Homozygous deletions of the CDKN2A tumor suppressor locus occur in approximately 15% of all cancer and represent a substantial therapeutic need(1). Targeted therapies selective for loss of CDKN2A have proven elusive, so we sought to evaluate whether the frequent co-deletion of the adjacent metabolic gene methylthioadenosine phosphorylase (MTAP) leads to collateral vulnerabilities. We conducted an shRNA screen in isogenic cells that vary only in their MTAP-deletion status, and identified an axis of targets that become vulnerable upon MTAP loss. Central in this axis is the arginine methyltransferase, PRMT5. Targeting PRMT5 with doxycycline-inducible shRNA impaired the growth of MTAP-deleted HCT116 colon carcinoma cells without impact on the growth of MTAP-wt HCT116 cells. Having identified this synthetic lethality between PRMT5 and MTAP, we sought next to elucidate the mechanistic basis for this relationship. Untargeted metabolomics revealed that MTA, the substrate of the MTAP enzyme reaction, accumulates dramatically in MTAP-deleted cancers. Biochemical profiling across the methyltransferase enzyme family revealed that MTA is a potent and selective inhibitor of PRMT5. Consistent with this in vitro finding, MTA accumulation in MTAP-deleted cancers led to reduced basal PRMT5 methylation. This selective vulnerability extends beyond PRMT5 to methionine adenosyltransferase 2, a (MAT2A), the metabolic enzyme upstream of PRMT5. MAT2A was the top hit in the shRNA screen, and targeting of MAT2A with inducible shRNA led to selective inhibition of growth in MTAP-deleted HCT116 cells in vitro and in vivo. Targeting of MAT2A led to substantial reduction of PRMT5 methylation activity in MTAP-deleted cells, indicating that PRMT5 activity is controlled by levels of substrate SAM and inhibitory metabolite MTA. To assess the therapeutic relevance of this axis in settings with endogenous deletion of the CDKN2A/MTAP locus, we depleted MAT2A in a panel of cancer cell lines and observed selective growth inhibition in the lines with endogenous deletion of CDKN2A/MTAP. Lastly, we noted that RIO Kinase 1 (RIOK1), a PRMT5-interacting protein(2), also scored in the shRNA screen. Doxycycline-inducible shRNA studies validated RIOK1 as an MTAP-selective target, and additional siRNA studies indicated that multiple PRMT5 co-complex members are selectively essential in MTAP-deleted cells. Thus, PRMT5 is the central node in an axis of targets that could be exploited therapeutically in cancers with deletion of CDKN2A/MTAP.