BIRC5 inhibition as a novel approach to target RAS mutant and drug-resistant multiple myeloma

Abstract Multiple myeloma (MM) is the second-most common hematological malignancy in the United States. Myeloma tumors have significant genetic heterogeneity that impacts disease progression and promotes resistance to treatment. RAS is a key oncogenic driver that activates the mitogen-activated protein kinase (MAPK) and the phosphatidylinositol 3-kinase (PI3K)/AKT pathways..Mutations in genes that code for RAS isozymes, KRAS, HRAS, or NRAS, lead to increased levels of activated GTP-RAS and are associated with the most aggressive forms of cancer. Mutations in the RAS family of genes are most common (40-50%) in myeloma. We and others have reported that RAS mutations may not be disease-initiating but rather arise during disease progression and relapse or as subclonal events that impart selective growth advantage and emerging drug resistance. In addition, non-mutant RAS can also be hyperactivated from upstream signaling (like receptor tyrosine kinases) or loss-of-function mutations in GTPase-activating proteins (GAPs). Given the importance of RAS mutations, allele-specific RAS inhibitors have long been considered an attractive strategy for myeloma treatment. However, multiple studies have reported various mechanisms of resistance to allele-specific RAS inhibitors as well as isoform-specific pan-RAS inhibitors, including newly acquired activating RAS mutations, RAS amplification, unchecked activation of co-expressed wild-type RAS (WT-RAS) isozymes, or acquired bypass mechanisms like new oncogenic fusions. Since MM remains incurable, we sought to improve upon currently available treatments by developing small-molecule inhibitors that preferentially inhibit myeloma cells with activated RAS isozymes. We have created NRasQ61X and KRasG12X mutations by CRISPR-Cas directed edits in a single endogenous RAS allele in human myeloma cell lines (HMCLs) that initially had two wild-type alleles. We found that these mutant-NRAS and mutant-KRAS edited cells have increased proliferation compared to cells with WT-RAS, as well as acquired resistance to several commonly used therapeutics. In this study, we used a triangulation method that combines our drug combination candidate prediction algorithm called ‘secDrug’ and the ‘Direct to Drug’ screening platform that evaluated 84 FDA-approved oncology drugs and emerging therapeutics in these RAS mutant myeloma lines. We identified BIRC5 as a potential target for RAS-mutant myeloma. BIRC5 expression is a key mechanism for the evasion of apoptosis. Notably, oncogenic RAS has been shown to promote MYC stabilization via upregulation of BIRC5. Earlier studies suggested that BIRC5 inhibitors are potent in targeting drug-resistant subclones in hematological malignancies. We performed in vitro cytotoxicity studies and cell-based assays using an in-house panel of HMCLs (n50) representing WT- and mutant-RAS, as well as innate and acquired response/resistance to the standard of care drugs, proteasome inhibitors (PIs) and immunomodulatory drugs (IMiDs), to confirm the potency of novel selective BIRC5 inhibitors, as single agent (IC50 range 0.22-15.30 nM; Mean 4.431±1.041 nM) and in combination with PIs and IMiDs (Chou-Talalay's Combination Index or CI 0.3, indicating strong synergism). Further, we used bulk and single-cell whole-transcriptomics, siRNA-mediated gene knockdown studies, and functional validation to characterize the treatment-induced genes and molecular pathways underpinning the mechanism of action and drug synergy at the subclone level. Finally, we compared the efficacy of these BIRC5 inhibitors against several RAS inhibitors, including cyclorasin B4-27, a bicyclic peptidyl pan-RAS inhibitor, RMC-6236, a multi-selective noncovalent RAS(on) inhibitor, and ADT-007, a novel, highly potent, and selective pan-RAS inhibitor that we have synthesized, and observed comparable effects on cell death and apoptosis. Ex vivo analysis in bone marrow-derived CD138+ cells from myeloma patients using high-throughput Mass Cytometry (CyTOF or Cytometry by Time-Of-Flight) confirmed the dose-dependent reduction of MCL1, Ki-67, CCND1, c-KIT, and MYC. We will present these results that demonstrate the clinical potential of BIRC5 inhibitors as novel candidates in curbing progression and drug resistance in RAS-mutant myeloma.