Pfitzer, Jeremiah

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 (n>50) 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.

Mutations in genes that code for RAS isozymes (N- and K-) are the most common (40-50%) somatic variations in multiple myeloma (MM). While ~46% of patients with newly diagnosed MM carry a RAS/Raf mutation, >64% of patients with refractory/relapsed MM carry these mutations. RAS activation can also occur from upstream signaling through receptor tyrosine kinases (RTK) or loss-of-function mutations in GTPase-activating proteins (GAPs), which are prevalent in MM. Although covalent inhibitors targeting KRAS alleles are in various stages of clinical development, multiple mechanisms of resistance have been reported. We discovered and developed a novel, highly potent, and selective pan-RAS inhibitor, ADT-007, capable of suppressing MAPK/AKT signaling by blocking GTP activation of RAS. Here, we show that ADT-007 is effective against MM, particularly those MM cell lines harboring KRAS and NRAS mutations that are representative of relapsed/refractory myeloma (RRMM). For these studies, we compiled a panel of over 50 human myeloma cell lines (HMCLs) with broad biological and genetic heterogeneity that represent innate drug-response/resistance (refractory disease), as well as 10 pairs of parental and clonally-derived proteasome inhibitor (PI)- and immunomodulatory drug (IMD)- resistant HMCLs as models of acquired resistance (relapse). Using CRISPR-cas-directed gene editing, we also have generated clonal NRAS and KRAS mutants of drug-sensitive myeloma lines that initially had two wild-type alleles. All cell lines have been authenticated using the GenePrint 24 System and tested for mycoplasma contamination. First, we performed predictive analysis using single-cell RNA sequencing (scRNAseq; 10X Genomics) on all MM cell lines and demonstrated the potential efficacy of ADT-007 based on the subclonal expression of the target genes/pathways. Using in vitro chemosensitivity assays, ADT-007 was highly potent and effective in killing chemo-resistant and RAS-mutant myeloma cells as a single agent with IC50 values ranging from 0.76 to 12 nM with synergistic benefits if combined with PIs and IMDs. Combination indices (CI) were found to be consistently below 0.9, indicating a synergistic drug interaction. (Drug synergy was determined by CalcuSyn software based on Chou-Talalay's CI method and the isobologram algorithm). Caspase 3/7 assay and flow cytometry (Annexin V-FITC + propidium iodide) confirmed apoptosis induction by ADT-007. Furthermore, the in vitro efficacy of ADT-007 was significantly better (nM vs. µM IC50) than cyclorasin B4-27, a bicyclic peptidyl that has been reported as a potent pan-RAS inhibitor against several other cancers, and RMC-6236, a multi-selective noncovalent RAS(on) inhibitor which is in clinical trial for patients with advanced solid tumors harboring G12X, G13X, and Q61X mutations. Pre-vs-post-treatment bulk-RNA sequencing followed by pathway analysis (using Ingenuity Pathway Analysis and Gene Set Enrichment Analysis) showed that ADT-007 suppressed KRAS and NRAS in a dose-dependent manner. Immunoblotting analysis confirmed the dose-dependent reduction of protein markers implicated in cell survival and chemotherapeutic resistance in myeloma, including c-myc, Ki-67, NFkB, IRF4, IKZF1 (Ikaros) and IKZF3 (Aiolos). Finally, we performed pre-vs-post-treatment single-cell transcriptomics analysis, which revealed a distinct shift in clusters representing myeloma single-cell subpopulations following ADT-007 treatment. High-dimensional mass cytometry (cytometry by time of flight or CyTOF) analysis using heavy metal-conjugated proteins in RRMM patient bone marrow-derived primary myeloma cells is currently underway to confirm the cytotoxic effect of ADT-007 ex vivo. ADT-1004 is an orally bioavailable prodrug of ADT-007 designed to improve water solubility and metabolic stability. ADT-1004 has shown strong antitumor activity in highly aggressive and clinically relevant mouse models of pancreatic cancer at dosages, is well tolerated, and is being developed by the NCI Stepping Stones program. Next, we plan to evaluate the antitumor activity of ADT-1004 in mouse xenograft models of human myeloma using immunocompromised mice. Our research will lay the groundwork for future development efforts needed to advance ADT-1004 to clinical trials involving patients with RRMM.

Multiple myeloma is the second-most common hematological malignancy in the US that remains a challenging disease to cure despite recent advancements in treatment strategies. Drug resistance is a major cause of concern in myeloma chemotherapy. We have created an optimization-regularization-based computational prediction method called secDrug that identified several novel secondary drug (‘secDrug‘) combinations against drug-resistant myeloma (relapsed/refractory multiple myeloma or RRMM). Top among our predicted secDrugs includes the survivin inhibitor, YM155. Survivin is a member of the inhibitor of apoptosis protein (IAP) family that has dual roles in mitosis and apoptosis. YM155 inhibits survivin at the transcriptional level by inhibiting the survivin gene promoter. Several studies have demonstrated the efficacy of YM155 in solid tumors and heme malignancies, including myeloma. However, the precise mechanism of action is not yet known. MM cell lines express high levels of IAPs. We observed high in vitro cytotoxicity of YM155 as a single agent (IC 50 range 0.41 to 12.85nM) as well as in combination with the primary drugs like proteasome inhibitors and Immunomodulatory drugs (IMiDs) against >15 human myeloma cell lines representing innate/refractory and acquired/emerging (relapse) resistance. Next, we explored the molecular mechanisms underlying the efficacy of YM155 using pre-vs-post-treatment tumor whole-transcriptome analysis (RNAseq). The top differentially regulated genes include DDIT3 (CHOP), ATF3, TXNDC5 SEC24D, and DHX15 ( Figure 1A). Ingenuity Pathway Analysis (IPA) predicted that, in addition to regulating apoptosis, survivin inhibition in myeloma significantly upregulated unfolded protein response and downregulated vehicle trafficking and genes associated with immune cell function. Further, we performed single-cell transcriptomics (scRNAseq; 10X Genomics) analysis to explore treatment-induced changes to the subclonal architecture. Our scRNAseq results revealed a distinct shift in clusters representing myeloma single-cell subpopulations following YM155 treatment ( Figure 1B). For example, Cluster 1 (53.11%), characterized by high expression of cell survival markers Ki67 and MYC, was pre-dominant in untreated myeloma cells, while Cluster 4 (52.19%) was the primary subclone in post-treatment tumors. Cluster 3 was shared between the untreated and treated groups. Detailed distinctions between each single-cell cluster will be presented. Furthermore, our scRNAseq data alluded to the benefits of combining survivin-inhibitors and Hsp90-inhibitors based on the expression of drug target genes. Hsp90 inhibitors indirectly target survivin by disrupting the interaction between survivin and Hsp90, resulting in a destabilized survivin protein that ultimately results in survivin degradation. In fact, we have earlier shown the effectiveness of Hsp90 inhibitors (17-AAG, AICAR, and CCT018159) as potent secDrugs against RRMM. Finally, high-dimensional mass cytometry or CyTOF analysis using heavy metal-conjugated proteins in patient bone marrow-derived primary myeloma cells ( ex vivo model system) showed that YM155 induced dose-dependent reduction of several protein markers implicated in cell survival and chemotherapeutic resistance in multiple myeloma, including myc, Ki-67, CD28, CD81, and CD274 (PD-L1). Previous studies have shown that CD28 and CD81 are high-risk immunophenotypes associated with significantly worse prognosis in patients with myeloma. PD-L1 (Programmed death-ligand 1) is a cell-surface glycoprotein expressed in a large number of malignancies that is involved in the termination of immune response and immune evasion. An earlier study has shown that YM155 enhances daratumumab-mediated cellular lysis of multiple myeloma cells. Our RNAseq and CyTOF results thus suggest a potential basis of synergy between YM155 with immunotherapies approved for myeloma, which we will test further. Our approach thus integrates in silico prediction with single-cell multi-ome analysis to identify molecular mechanisms potentially underlying subclonal response to novel combination therapy candidates (secDrugs) for the treatment of RRMM.