Drug Resistance In Myeloma Research Articles

Research Advances of Exosomes in Pathogenesis of Multiple Myeloma --Review

Research on the participation of exosomes in pathogenesis and prognosis of multiple myeloma (MM) has made encouraging progress. However, the specific mechanism has not yet been clarified. Recently, domestic and foreign researchers have pressed forward on deeper study on exosomes. This article mainly summarizes the role of exosomes in the pathophysiological processes, such as bone marrow microenvironment changes, immunosuppression, myeloma bone disease generation and myeloma drug resistance, so as to provide new reference for further clinical research of exosomes as potential biomarkers for MM.

CDK6 protein expression is associated with disease progression and treatment resistance in multiple myeloma.

Multiple myeloma (MM) is a heterogeneous malignancy of plasma cells. Despite improvement in the prognosis of MM patients after the introduction of many new drugs in the past decades, MM remains incurable since most patients become treatment-resistant. Cyclin-dependent kinase 6 (CDK6) is activated in many types of cancer and has been associated with drug resistance in MM. However, its association with disease stage, genetic alterations, and outcomehas not been systematically investigated in large cohorts. Here, we analyzed CDK6 expression using immunohistochemistry in 203 formalin-fixed paraffin-embeddedsamples of 146 patients and four healthy individuals. We found that 61.5% of all MM specimens express CDK6 at various levels. CDK6 expression increased with the progression of disease with a median of 0% of CDK6-positive plasma cells in monoclonal gammopathy of undetermined significance (MGUS) (n = 10) to 30% in newly diagnosed MM (n = 78)and up to 70% in relapsed cases (n = 55). The highest median CDK6 was observed in extramedullary myeloma (n = 12), a highly aggressive manifestation of MM. Longitudinal analyses revealed that CDK6 is significantly increased in lenalidomide-treated patients but not in those who did not receive lenalidomide. Furthermore, we observed that patients who underwent lenalidomide-comprising induction therapy had significantly shorter progression-free survival when their samples were CDK6 positive. These data support that CDK6 protein expression is a marker for aggressive and drug-resistant disease and describes a potential drug target in MM.

Enhanced Expression of DNp73 Promotes Drug Resistance and Immune Evasion in Multiple Myeloma By Targeting the MYC and MYCN Pathways

Background Multiple myeloma (MM) is an incurable haematological malignancy with high chromosome instability and is highly dependent on the immunosuppressive bone marrow microenvironment. TP53 mutations and deletions are uncommon in MM patients, with other types of mechanisms involved in the abrogation of TP53 pathway activity. DNp73, an inhibitor of the p53 tumour suppressor family, drives drug resistance and cancer progression in several solid malignancies. However, the biological functions of DNp73, the molecular mechanisms underlying these actions and their correlations with aberrant TP53 expression in myelomagenesis remain unclear. In this study, we investigated the role of DNp73 in the drug resistance of MM, and disclosed the corresponding mechanism of how DNp73 promotes the immune escape of MM cells. Aims To disclose the role of DNp73 in promoting drug resistance and immune evasion in MM, and explore the therapeutic strategy based on the mechanism research. Methods We constructed DNp73 overexpression and sh-RNA interference plasmids to obtain stable cell lines. The effects of DNp73 on proliferation and drug sensitivity were determined by CCK8, flow cytometry and xenotransplantation model. To identify mechanisms of drug resistance, we here perform RNA-seq and CHIP-seq analyses in MM cell lines, while Western blot and RT-PCR were used to confirm the results. The DNA damage repair and invasion ability of MM cells were detected by immunofluorescence and transwell assay. To validate the role of DNp73 in immune escape, we also performed phagocytosis assays in vitro. Results Our previous study revealed that the miRNA-15a is a tumour suppressor involved in aggressive MM cell proliferation and drug resistance. Here, we found that miRNA-15a downregulation in MM cells activated NF-κB-p65, which upregulated the expression of DNp73 at the transcriptional level. In addition, the level of miR-15a was negatively correlated with the expression of DNp73 in MM cells of patients (r=-0.672, p<0.05). Enforced expression of DNp73 promoted aggressive proliferation and multidrug resistance in MM cells (p<0.001). Bulk RNA sequencing data showed that the levels of MYCN, MYC and CDK7 were increased in cells with enforced DNp73 expression. Furthermore, a ChIP-qPCR assay revealed that DNp73 bound to the MYCN gene promoter and upregulated MYCN expression. The MM cell immune evasion rate was notable when DNp73 expression was high because of CD47 and PD-L1 upregulation. Blockade of the CD47/SIRPα and PD-1/PD-L1 signalling pathways by the SIRPα-Fc fusion protein IMM01 and monoclonal antibody atezolizumab significantly re-established the anti-MM function of macrophages and T cells in the MM microenvironment, respectively (p<0.01). Notably, DNp73 dysregulation and its pathogenetic function in MM cells were found to be independent of TP53 expression. Conclusion Altogether, our study demonstrates that DNp73 is a potential oncogene involved in MM pathogenesis and promotes MM cell proliferation and immune evasion by targeting the MYC and MYCN pathways.

Single-Cell Multi-Ome Analysis Reveals Novel Molecular Mechanisms Underlying Subclonal Response to Survivin Inhibition in Relapsed/Refractory Multiple Myeloma

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.

Inhibition of Rho-Associated Coiled-Coil Containing Protein Kinases with Belumosudil Mesylate Shows Anti-Tumor and Immune Modulatory Properties in Models of Multiple Myeloma

Background: Myeloma patient outcomes have continuously improved with the introduction of proteasome inhibitors (PIs), immunomodulatory drugs (IMiDs), monoclonal antibodies (mAbs) recognizing cell surface proteins and, most recently, B-cell maturation antigen (BCMA)-targeted bispecifics and chimeric antigen receptor (CAR)-guided T-cells. However, the prognosis in triple-class refractory (TCR) disease that is refractory to PIs, IMiDs, and CD38 mAbs remains poor and, since BCMA-targeted CAR-Ts and bispecifics are not curative, quadruple-class refractory (QCR) disease that progresses during or after these therapies is an emerging challenge, indicating a persistent need for novel agents. Rho-associated coiled-coil containing protein kinases (ROCK1 and ROCK2) may represent novel potential targets since ROCK1 has been associated with a plasma cell leukemia-like transcriptional profile and as a myeloma dependency. Moreover, ROCK2 mediates expression of Interferon regulatory factor 4 (IRF4) and c-MYC, as well as Th17 responses that may contribute to an immune suppressive microenvironment. Methods: To examine the central hypothesis that targeting ROCK1/2 could be a novel and effective approach to myeloma therapy, we performed pre-clinical studies with the ROCK1/2 inhibitor belumosudil mesylate using drug-naïve and drug-resistant myeloma cell lines in vitro. Also, in vivo studies with immune correlates were performed in the Vk*MYC immune-competent syngeneic myeloma model, which has been reported to have a 67% positive predictive value for clinical efficacy in humans. Results: Belumosudil mesylate as a single agent reduced the viability of a panel of myeloma cell lines representing different molecular subtypes in a time- and concentration-dependent manner, with median inhibitory concentrations from 618 to 1,114 nM at 72 hours. These represent clinically relevant concentrations as the mean steady state C max for belumosudil mesylate given with food in studies of chronic graft-versus-host disease patients was 4.36 mM. Staining of myeloma cells with Annexin V and propidium iodide (PI) demonstrated that belumosudil induced appearance first of Annexin +/PI - (early apoptotic) cells, followed later by Annexin +/PI + (late apoptotic) and Annexin -/PI + (necrotic) cells, in a concentration-dependent manner. Studies of myeloma resistance mechanisms showed belumosudil largely overcame adhesion-mediated drug resistance, and was active against MM.1S and RPMI 8226 cells that are considered daratumumab-resistant. Moreover, belumosudil showed equal or even, in some cases, higher potency against bortezomib-, carfilzomib-, dexamethasone-, iberdomide-, lenalidomide-, melphalan-, and mezigdomide-resistant cell lines compared to their drug-naïve counterparts. Belumosudil induced in vitro killing of myeloma cells in a time- and dose-dependent manner independent of the presence of natural killer (NK) cells. Notably, when used in combination with the CD38 mAb isatuximab and in the presence of NK cells, belumosudil enhanced myeloma cell killing and prevented isatuximab-induced loss of CD38 expression. Mechanistically, belumosudil induced a reduction in c-MYC, IRF4, and phospho-STAT3 levels, consistent with its action on the IRF4/c-MYC axis. Dosing of belumosudil in vivo at 50 mg/kg twice weekly for three weeks in Vk*MYC mice with paraprotein levels consistent with active myeloma produced a consistent decline in disease burden as determined by serum protein electrophoresis monitoring ( A) compared to vehicle controls. NanoString analysis of tumor samples from these mice ( B) found down-regulation of XBP1 (X-box binding protein 1) and SLAMF7 (Signaling lymphocytic activation molecule family member 7), consistent with the anti-tumor efficacy of belumosudil mesylate. In addition, up-regulation was seen of c- JUN and c- FOS, consistent with promotion of T-cell activation and clonal expansion, as well as effector differentiation of antigen-activated CD8 + T cells. Conclusions: These pre-clinical in vitro and in vivo data support the hypothesis that targeting of ROCK1 and ROCK2 with belumosudil mesylate may be a promising strategy for relapsed/refractory myeloma and provide a rationale for its translation to the clinic. Currently, clinical trials of belumosudil are planned.

The Resistance Mechanism to BET-Protac in Multiple Myeloma

Objective ：Explore the resistance mechanism of BET protein degradation targeting chimera (BET-PROTAC) in multiple myeloma (MM) cells, and find strategies to enhance the efficacy of BET-PROTAC. So as to provide new theoretical basis for the treatment of multiple myeloma. Methods ：The changes of TCF7 and c-Myc mRNA level were detected by RT-qPCR after BET-PROTAC (ARV-771) treatment of RPMI-8226 cells, the transcriptional activity of β-catenin in ARV-771 tolerant cells was detected by double luciferase reporter assay. Constructing lentiCRISPR-v2 vector to knockout β-catenin in RPMI-8226 cells, and detecting the sensitivity changes to ARV-771 and the formation of drug-resistant clones; MM cell lines resistant to ARV-771 were induced by dose escalation method, and detect the sensitivity of drug-resistant cells to other BET inhibitors and anti-tumor drugs; RNA-seq was used to detect the significantly changed genes and signal modules in drug-resistant cells, and verify this in drug-resistant cells; The drug resistant cells were treated with inhibitors or knockout the resistance gene to observe whether the drug resistance was reversible; The CRISPR knockout gene library was used to screen the candidate genes related to the up-regulation of drug resistance genes in drug-resistant cells, the expression of candidate genes was interfered, and the expression of drug resistance proteins was detected. The correlation between these candidate genes and the prognosis of MM patients was analyzed through public databases. Results ： In ARV-771 tolerant RPMI-8226 cells, the mRNA expression of TCF7 was significantly elevated, but the expression of c-Myc was still at a low level. TOPFlash assay showed activation of β-catenin signal in tolerant cells; Knockout of β-catenin in RPMI-8226 cells by CRISPR/cas9 increased apoptosis induced by ARV-771. Colony formation assay showed that there was no significant difference in the formation rate and number of drug-resistant clones after β-catenin knockout. ARV-771 resistant RPMI-8226 cells were successfully induced by dose increasing method, and three drug-resistant clones (AR1, AR2 and AR3) were obtained, the IC50 of these cells were 80, 120 and 8 times higher than the parental cells, respectively. The drug-resistant cells were cultured in drug-free medium for another 6 months, but the sensitivity did not recover. AR1 and AR2 cells showed decreased sensitivity to ARV-825, MZ-1, OTX-015, I-BET151, Daunorubicin and Epirubicin. RNA-seq showed that ABCB1 was significantly up-regulated in drug-resistant cells, and we verified the up-regulation of ABCB1 at mRNA and protein levels in all drug-resistant cells. Combined use of ABCB1 inhibitors (verapamil, cyclosporin A, Elacridar) or knockout of ABCB1 could significantly reduce the IC50 of drug-resistant cells, increase the apoptosis rate after ARV-771 treatment, and increase the degradation of BRD4 and the down-regulation of c-Myc. Using CRISPR/Cas9 library screening technology, we preliminarily selected 39 genes that may be involved in the regulation of ABCB1 expression, among which the downregulation of 14 genes could reduce the protein expression of ABCB1 in drug-resistant cells. Further through public databases, we found that C1orf112, CCDC167 and CRIP2 are significantly correlated with the prognosis of myeloma patients and are highly expressed in a variety of tumor tissues. These three genes will be the focus of subsequent studies. Conclusions ：Our results showed that BET-PROTAC resistance in MM cells wasindependent of β-catenin activation. The up-regulation of ABCB1 expression was the key mechanism mediating the resistance of myeloma cells to BET-PROTAC. C1orf112, CCDC167 and CRIP2 might be associated with drug resistance in myeloma and could affect prognosis, and their mechanisms in myeloma need to be further investigated. Keywords ：Multiple myeloma; BET; Protein degradation targeting chimera; Drug resistance; CRISPR library; ABCB1

Deacetylation induced nuclear condensation of HP1γ promotes multiple myeloma drug resistance

Acquired chemoresistance to proteasome inhibitors is a major obstacle in managing multiple myeloma but key regulators and underlying mechanisms still remain to be explored. We find that high level of HP1γ is associated with low acetylation modification in the bortezomib-resistant myeloma cells using SILAC-based acetyl-proteomics assay, and higher HP1γ level is positively correlated with poorer outcomes in the clinic. Mechanistically, elevated HDAC1 in the bortezomib-resistant myeloma cells deacetylates HP1γ at lysine 5 and consequently alleviates the ubiquitin-mediated protein degradation, as well as the aberrant DNA repair capacity. HP1γ interacts with the MDC1 to induce DNA repair, and simultaneously the deacetylation modification and the interaction with MDC1 enhance the nuclear condensation of HP1γ protein and the chromatin accessibility of its target genes governing sensitivity to proteasome inhibitors, such as CD40, FOS and JUN. Thus, targeting HP1γ stability by using HDAC1 inhibitor re-sensitizes bortezomib-resistant myeloma cells to proteasome inhibitors treatment in vitro and in vivo. Our findings elucidate a previously unrecognized role of HP1γ in inducing drug resistance to proteasome inhibitors of myeloma cells and suggest that targeting HP1γ may be efficacious for overcoming drug resistance in refractory or relapsed multiple myeloma patients.

HNRNPA2B1-mediated m6A modification of TLR4 mRNA promotes progression of multiple myeloma

BackgroundMultiple myeloma (MM) is a malignancy of plasma cells that remains incurable. Toll-like receptor 4 (TLR4) acts as a stress-responsive signal, protecting mitochondria during proteasome inhibitor (PI) exposure, maintaining mitochondrial metabolism and increasing drug resistance in MM. However, the mechanism of TLR4 regulation remains elusive.AimsThe purpose of this study was to investigate the methylation pattern of multiple myeloma and its effect on the expression of HNRNPA2B1 and downstream targets.MethodsThe methylation level in MM and normal bone marrow specimens was detected using a colorimetric assay. HNRNPA2B1 gene knockdown was achieved in RPMI 8226 MM cells via adenovirus transfection. CCK8 and flow cytometric assays were used to detect proliferation and apoptosis, respectively. Transcriptome sequencing and m6A methylation MeRIP sequencing were applied, and differentially expressed genes (DEGs) were detected. Three independent NCBI GEO datasets were applied to examine the effects of HNRNPA2B1 and TLR4 expression on MM patient survival.ResultsHNRNPA2B1 promoted MM progression. Clinical data from database revealed that HNRNPA2B1 was adverse prognostic factor for survival among MM patients. Furthermore, transcriptome sequencing and methylation sequencing showed that HNRNPA2B1 recognized and was enriched at the m6A sites of TLR4 and TLR4 was down-regulated of both the m6A level and transcription level in HNRNPA2B1-knockdown MM cells. Moreover, TLR4 was an adverse survival prognostic factor based on database analysis.ConclusionOverall, our study implies that the RNA-binding protein HNRNPA2B1 increases cell proliferation and deregulates cell apoptosis in MM through TLR4 signaling. Our study suggests HNRNPA2B1 as a potential therapeutic target for MM.

Validation of a Novel Rac1 Inhibitor As Potent Secdrug Against Activating Ras Mutant and Drug-Resistant Multiple Myeloma

Multiple myeloma is the second-most common hematopoietic malignancy in the United States. Although several drugs have so far been approved by the FDA, myeloma still remains an incurable disease with dose-limiting toxicities and resistance to primary drugs like proteasome inhibitors (PIs) and Immunomodulatory drugs (IMiDs). Furthermore, activating Ras gene (NRAS, KRAS, and HRAS) mutations are known to occur in >50% of myeloma patients, which are also associated with greater tumor burden, cancer aggressiveness, high recurrence rates, and poor survival. We have recently established a novel drug development/re-purposing pipeline called secDrug that incorporates a pharmacogenomics data-driven computational algorithm to introduce several new drug candidates (secDrugs), including EHT1864 (a Rac1 (Ras superfamily GTPase) inhibitor), CCT018159 (Hsp90 inhibitor), and CP466722 (a reversible ATM inhibitor) as synergistic partners of primary drugs against drug-resistant myeloma. The overall objective of this study is to validate EHT1864 using in vitro and ex vivo models of relapsed and refractory myeloma (RRMM) patients. First, we used single-cell RNA sequencing (scRNAseq) as a novel screening tool to demonstrate that EHT1864 is potentially effective against myeloma subclones based on the enrichment of target genes (Figure 1). For in vitro validation, we used a human myeloma cell line (HMCL) panel representing drug-sensitive (FLAM76), innate/refractory resistance (LP1), and acquired/relapsed resistance (parental and clonally derived PI-resistant and IMiD-resistant HMCL pairs U266 P/VR, RPMI P/VR, MM1S P/VR/LenR). FLAM76 KRas (FLAM76-K12) and FLAM76 Nras (FLAM76-N12) cell lines were generated using Adeno-associated viral (AAV) vector-mediated delivery of CRISPR-Cas9 for genome editing in humans. Ras mutations were confirmed using Sanger DNA sequencing method. Cell viability measured using CellTiter-Glo luminescent cell viability assay showed the potency of EHT1864 as a single-agent (IC50 range 15-40µM) as well as in combination with PIs (represented by Ixazomib) and IMiDs (represented by Lenalidomide). Combination index (CI) values calculated using Chou-Talalay's CI theorem were consistently less than 0.9, while all the four synergy scores (HSA, Bliss, Loewe, and ZIP) were higher than 5, demonstrating high synergy. Cell death due to apoptosis was confirmed using flow cytometry (Annexin-V-Propidium Iodide staining), Caspase 3/7 activity assay, and immunoblotting. Interestingly, EHT1864 was most potent against drug-resistant and Ras-mutant HMCLs. Further, we showed that EHT1864 treatment also affects ROS generation and mitochondrial membrane potential, indicating that EHT1864 induces apoptosis via mitochondria-mediated pathway. Finally, we performed pre-vs-post-treatment genome-wide transcriptome analysis (tumor mRNAseq) and single-cell multi-ome analysis (single-cell RNA sequencing/scRNAseq + single-cell Assay of Transposase Accessible Chromatin sequencing/scATACseq) analysis to derive molecular signatures and pathways representing the basis of (on-target and off-target) efficacy of EHT1864 and drug synergy at the bulk tumor and subclonal levels. Finally, we will perform single-cell proteomics (high-dimensional immunophenotyping using mass cytometry/CyTOF/Cytometry time of flight) in CD138+ bone marrow cells derived from newly-diagnosed and relapsed myeloma patients (ex vivo) to demonstrate efficacy in RRMM. Thus, our work lays a framework to establish EHT1864 as a clinical trial-ready therapeutic option for the management of drug-resistant myeloma. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Multiple myeloma metabolism - a treasure trove of therapeutic targets?

Multiple myeloma is an incurable cancer of plasma cells that is predominantly located in the bone marrow. Multiple myeloma cells are characterized by distinctive biological features that are intricately linked to their core function, the assembly and secretion of large amounts of antibodies, and their diverse interactions with the bone marrow microenvironment. Here, we provide a concise and introductory discussion of major metabolic hallmarks of plasma cells and myeloma cells, their roles in myeloma development and progression, and how they could be exploited for therapeutic purposes. We review the role of glucose consumption and catabolism, assess the dependency on glutamine to support key metabolic processes, and consider metabolic adaptations in drug-resistant myeloma cells. Finally, we examine the complex metabolic effects of proteasome inhibitors on myeloma cells and the extracellular matrix, and we explore the complex relationship between myeloma cells and bone marrow adipocytes.

Single-Cell Proteomics and Tumor RNAseq Identify Novel Pathways Associated With Clofazimine Sensitivity in PI- and IMiD- Resistant Myeloma, and Putative Stem-Like Cells.

Multiple myeloma (MM) is an incurable plasma cell malignancy with dose-limiting toxicities and inter-individual variation in response/resistance to the standard-of-care/primary drugs, proteasome inhibitors (PIs), and immunomodulatory derivatives (IMiDs). Although newer therapeutic options are potentially highly efficacious, their costs outweigh the effectiveness. Previously, we have established that clofazimine (CLF) activates peroxisome proliferator-activated receptor-γ, synergizes with primary therapies, and targets cancer stem-like cells (CSCs) in drug-resistant chronic myeloid leukemia (CML) patients. In this study, we used a panel of human myeloma cell lines as in vitro model systems representing drug-sensitive, innate/refractory, and clonally-derived acquired/relapsed PI- and cereblon (CRBN)-negative IMiD-resistant myeloma and bone marrow-derived CD138+ primary myeloma cells obtained from patients as ex vivo models to demonstrate that CLF shows significant cytotoxicity against drug-resistant myeloma as single-agent and in combination with PIs and IMiDs. Next, using genome-wide transcriptome analysis (RNA-sequencing), single-cell proteomics (CyTOF; Cytometry by time-of-flight), and ingenuity pathway analysis (IPA), we identified novel pathways associated with CLF efficacy, including induction of ER stress, autophagy, mitochondrial dysfunction, oxidative phosphorylation, enhancement of downstream cascade of p65-NFkB-IRF4-Myc downregulation, and ROS-dependent apoptotic cell death in myeloma. Further, we also showed that CLF is effective in killing rare refractory subclones like side populations that have been referred to as myeloma stem-like cells. Since CLF is an FDA-approved drug and also on WHO’s list of safe and effective essential medicines, it has strong potential to be rapidly re-purposed as a safe and cost-effective anti-myeloma drug.

SecDrug: a pipeline to discover novel drug combinations to kill drug-resistant multiple myeloma cells using a greedy set cover algorithm and single-cell multi-omics

Multiple myeloma, the second-most common hematopoietic malignancy in the United States, still remains an incurable disease with dose-limiting toxicities and resistance to primary drugs like proteasome inhibitors (PIs) and Immunomodulatory drugs (IMiDs).We have created a computational pipeline that uses pharmacogenomics data-driven optimization-regularization/greedy algorithm to predict novel drugs (“secDrugs”) against drug-resistant myeloma. Next, we used single-cell RNA sequencing (scRNAseq) as a screening tool to predict top combination candidates based on the enrichment of target genes. For in vitro validation of secDrugs, we used a panel of human myeloma cell lines representing drug-sensitive, innate/refractory, and acquired/relapsed PI- and IMiD resistance. Next, we performed single-cell proteomics (CyTOF or Cytometry time of flight) in patient-derived bone marrow cells (ex vivo), genome-wide transcriptome analysis (bulk RNA sequencing), and functional assays like CRISPR-based gene editing to explore molecular pathways underlying secDrug efficacy and drug synergy. Finally, we developed a universally applicable R-software package for predicting novel secondary therapies in chemotherapy-resistant cancers that outputs a list of the top drug combination candidates with rank and confidence scores.Thus, using 17AAG (HSP90 inhibitor) + FK866 (NAMPT inhibitor) as proof of principle secDrugs, we established a novel pipeline to introduce several new therapeutic options for the management of PI and IMiD-resistant myeloma.

Pyrroline-5-Carboxylate Reductase 1: a novel target for sensitizing multiple myeloma cells to bortezomib by inhibition of PRAS40-mediated protein synthesis

BackgroundMultiple myeloma (MM) remains an incurable cancer despite advances in therapy. Therefore, the search for new targets is still essential to uncover potential treatment strategies. Metabolic changes, induced by the hypoxic bone marrow, contribute to both MM cell survival and drug resistance. Pyrroline-5-carboxylate reductase 1 and 2 (PYCR1 and PYCR2) are two mitochondrial enzymes that facilitate the last step in the glutamine-to-proline conversion. Overexpression of PYCR1 is involved in progression of several cancers, however, its’ role in hematological cancers is unknown. In this study, we investigated whether PYCR affects MM viability, proliferation and response to bortezomib.MethodsCorrelation of PYCR1/2 with overall survival was investigated in the MMRF CoMMpass trial (653 patients). OPM-2 and RPMI-8226 MM cell lines were used to perform in vitro experiments. RPMI-8226 cells were supplemented with 13C-glutamine for 48 h in both normoxia and hypoxia (< 1% O2, by chamber) to perform a tracer study. PYCR1 was inhibited by siRNA or the small molecule inhibitor pargyline. Apoptosis was measured using Annexin V and 7-AAD staining, viability by CellTiterGlo assay and proliferation by BrdU incorporation. Differential protein expression was evaluated using Western Blot. The SUnSET method was used to measure protein synthesis. All in vitro experiments were performed in hypoxic conditions.ResultsWe found that PYCR1 and PYCR2 mRNA expression correlated with an inferior overall survival. MM cells from relapsed/refractory patients express significantly higher levels of PYCR1 mRNA. In line with the strong expression of PYCR1, we performed a tracer study in RPMI-8226 cells, which revealed an increased conversion of 13C-glutamine to proline in hypoxia. PYCR1 inhibition reduced MM viability and proliferation and increased apoptosis. Mechanistically, we found that PYCR1 silencing reduced protein levels of p-PRAS40, p-mTOR, p-p70, p-S6, p-4EBP1 and p-eIF4E levels, suggesting a decrease in protein synthesis, which we also confirmed in vitro. Pargyline and siPYCR1 increased bortezomib-mediated apoptosis. Finally, combination therapy of pargyline with bortezomib reduced viability in CD138+ MM cells and reduced tumor burden in the murine 5TGM1 model compared to single agents.Conclusions This study identifies PYCR1 as a novel target in bortezomib-based combination therapies for MM.

Induction of m6A methylation in adipocyte exosomal LncRNAs mediates myeloma drug resistance

BackgroundTherapeutic resistance occurs in most patients with multiple myeloma (MM). One of the key mechanisms for MM drug resistance comes from the interaction between MM cells and adipocytes that inhibits drug-induced apoptosis in MM cells; MM cells reprogram adipocytes to morph into different characterizations, including exosomes, which are important for tumor-stroma cellular communication. However, the mechanism by which exosomes mediate the cellular machinery of the vicious cycle between MM cells and adipocytes remains unclear.MethodsAdipocytes were either isolated from bone marrow aspirates of healthy donors or MM patients or derived from mesenchymal stem cells. Co-culturing normal adipocytes with MM cells was used to generate MM-associated adipocytes. Exosomes were collected from the culture medium of adipocytes. Annexin V-binding and TUNEL assays were performed to assess MM cell apoptosis. Methyltransferase activity assay and dot blotting were used to access the m6A methylation activity of methyltransferase like 7A (METTL7A). RIP, MeRIP-seq, and RNA–protein pull down for assessing the interaction between long non-cording RNAs (LncRNAs) and RNA binding proteins were performed. Adipocyte-specific enhancer of zeste homolog 2 (EZH2) knockout mice and MM-xenografted mice were used for evaluating MM therapeutic response in vivo.ResultsExosomes collected from MM patient adipocytes protect MM cells from chemotherapy-induced apoptosis. Two LncRNAs in particular, LOC606724 and SNHG1, are significantly upregulated in MM cells after exposure to adipocyte exosomes. The raised LncRNA levels in MM cells are positively correlated to worse outcomes in patients, indicating their clinical relevancy in MM. The functional roles of adipocyte exosomal LOC606724 or SNHG1 in inhibition of MM cell apoptosis are determined by knockdown in adipocytes or overexpression in MM cells. We discovered the interactions between LncRNAs and RNA binding proteins and identified methyltransferase like 7A (METTL7A) as an RNA methyltransferase. MM cells promote LncRNA package into adipocyte exosomes through METTL7A-mediated LncRNA m6A methylation. Exposure of adipocytes to MM cells enhances METTL7A activity in m6A methylation through EZH2-mediated protein methylation.ConclusionThis study elucidates an unexplored mechanism of how adipocyte-rich microenvironment exacerbates MM therapeutic resistance and indicates a potential strategy to improve therapeutic efficacy by blocking this vicious exosome-mediated cycle.

Loss of COP9 Signalosome Gene-Containing 2q Region Is Associated with Lenalidomide and Pomalidomide Resistance in Myeloma Patients

IntroductionIdentification of the causes of, and biomarkers for, drug resistance in myeloma is important for understanding treatment failures, and for future instigation of targeted therapeutics for myeloma. Using the largest set of whole genome sequencing (WGS) of advanced and drug resistant multiple myelomas to date, we reported that even heterozygous loss of the 3p region, which harbours immunomodulatory drug (IMiD) and CRBN E3 ligase modulator drug (CELMoD)-binding protein Cereblon (CRBN), undergoes strong therapeutic selection on lenalidomide (LEN) and/or pomalidomide (POM) treatment (Gooding et al 2021, PMC7893409). We hypothesized that copy loss of other genes required for IMiD activity may also have clinical relevance. Several groups have reported pharmacogenetic screens identifying genes essential for IMiD sensitivity in vitro, particularly genes required for the maintenance of the CUL4-DDB1-CRBN E3 Ubiquitin Ligase, such as members of the COP9 signalosome complex, function of which prevents CRBN protein degradation. However, loss of these genes has hitherto not been reported in myeloma.Methods and resultsWe identified candidate genes whose loss may favor IMiD drug resistance from published pharmacogenetic screens (n=5), and shortlisted genes consistently identified as essential for LEN or POM function in ≥2 screens (n=23). In our WGS dataset of 455 patients (cohorts: newly diagnosed (ND) n = 198, LEN-refractory n = 203; and LEN-then-POM-refractory n = 54), the incidence of mutation of shortlisted LEN/POM-essential genes in drug-refractory cohorts was rare (<5% combined), as found with CRBN. We next identified all those with overall incidence of >10% copy loss at the LEN-then-POM-refractory state, plus incidence of copy loss that increased from ND to LEN-then-POM-refractory states by ≥1.5-fold. This delivered 3 copy loss regions for further investigation: a) 3p, which we had already reported; b) 17p, loss of which is known to be strongly selected in myeloma as the site of TP53; and c) 2q, previously unidentified as relevant in myeloma, but whose minimal common region contained two members of the COP9 signalosome (COPS7B, COPS8). Proportion of loss of this region increased between ND (5.5%), LEN-refractory (9.8%) and LEN-then-POM-refractory states (16.6%), p=0.009. Those patients who had lost a copy of these genes also demonstrated a significant reduction in COPS7B/COPS8 gene expression (p<0.01 both genes).In a separate cohort of myeloma patients (n=24) with sequential sample WGS analysis before and after LEN and/or POM resistance acquisition, we traced acquisition of CNA-defined subclones. 5/24 (21%) patients had acquired either clonal or subclonal loss of the 2q region containing COPS7B and COPS8 at IMID resistance, which had been either absent or below limit of detection pre-IMiD exposure. No other CNA newly-emerged in such a high proportion during IMiD treatment. Relative decrease in even one COP9 signalosome gene has been shown to cause CRBN protein level to fall, and reduce LEN efficacy (Sievers et al 2018, PMC6148446). We are now analysing CRBN protein levels in sequential biopsies from these cases.ConclusionCopy number aberrations have not previously been shown to drive a therapy-specific clonal advantage in myeloma in the clinic. We have now identified a second novel CNA, 2q loss, which increases in incidence through LEN- and POM-refractory states to emerge as a marker of dominant clones in advanced, IMiD-resistant disease. Whether these CNAs will mark resistance to novel CELMoDs remains to be seen. The CRBN protein is key to the function of these drugs, and many novel proteolysis targeting chimeras (PROTACs) in development, but whether the kinetics of their CRBN binding are as sensitive to relative CRBN protein loss remains a key question. CNAs may be easily and cost-effectively detected in the clinic by targeted sequencing approaches, and may prove valuable in future therapeutic decision making. DisclosuresGooding: Bristol Myers Squibb: Research Funding. Ansari-Pour: Bristol Myers Squibb: Consultancy. Karagoz: h.: Research Funding. Ortiz Estevez: Bristol Myers Squibb: Current Employment, Current equity holder in publicly-traded company. Towfic: Bristol Myers Squibb: Current Employment, Current equity holder in publicly-traded company. Flynt: BMS: Current Employment, Current equity holder in publicly-traded company. Pierceall: BMS: Current Employment, Current equity holder in publicly-traded company. Yong: Sanofi: Honoraria, Research Funding; Janssen: Honoraria, Research Funding; Takeda: Honoraria; GSK: Honoraria; Amgen: Honoraria; BMS: Research Funding; Autolus: Research Funding. Vyas: Astellas: Consultancy, Honoraria; Takeda: Honoraria; Janssen: Honoraria; Novartis: Honoraria; Pfizer: Honoraria; Daiichi Sankyo: Honoraria; Bristol Myers Squibb: Consultancy, Honoraria, Research Funding; Gilead: Honoraria; Jazz: Honoraria; AbbVie: Consultancy, Honoraria. Thakurta: Bristol Myers Squibb: Current Employment, Current equity holder in publicly-traded company, Patents & Royalties.

Establishing a Novel Pipeline That Combines in-Silico Prediction with in-Vitro and Ex-Vivo Validation to Discover Secondary Drug Combinations Against Relapsed and/or Refractory Multiple Myeloma

Multiple myeloma (MM) is the second-most common hematological malignancy in the US. MM is an incurable, age-dependent plasma cell neoplasm with a 5-year survival rate of less than 50%. Extensive inter-individual variation in response to standard-of-care drugs like proteasome inhibitors (PIs) and immunomodulatory drugs (IMiDs), drug resistance, and dose-limiting toxicities are critical problems for the treatment of MM. Clinical success in anti-myeloma treatment, therefore, warrants continuous development of novel combination therapy strategies with the explicit goal to improve the therapeutic efficacy by concomitantly targeting multiple signaling pathways.Previously, we have reported the development of an in-house computational pipeline called secDrug that applies greedy algorithm-based set-covering computational optimization method followed by a regularization technique to predict secondary drugs that can be repurposed as novel synergistic partners of standard-of-care drugs for the management of refractory/ resistant MM. Top among these secondary drugs (secDrugs) were the HSP90 inhibitor 17-AAG.In this study, we used 17-AAG as a proof of principle to establish a pipeline that integrates our in silico predictions with in vitro and ex vivo validation as well as multi-omics technologies to identify, validate, and characterize therapeutic agents that could be used either alone or in combination with standard-of-care drugs for the treatment of R/R MM patients (Figure 1).To screen and validate our in silico prediction results, we performed in vitro cytotoxicity assays using 17-AAG on a panel of human myeloma cell lines (HMCLs; in vitro model systems) that captures a wide range of biological and genetic heterogeneity representing the complexities encountered in clinical settings. These cell lines include HMCLs representing innate sensitive/resistance, >10 pairs of parental and clonally-derived PI- and IMiD-resistant pairs (P vs VR or LenR; representing acquired/emerging resistance/relapse), NRAS mutants which leads to the constitutive activation of oncogenic Ras signaling, and CRISPR-edited HSP90 knockdown cell line. Our results showed that 17-AAG has high synergistic activity in combination with PI in inducing apoptosis even in innate and acquired PI-resistant HMCLs and significantly reduces the effective dose of PI required to achieve IC 50 (Chou-Talalay's Dose Reduction Index or DRI 7±1.4). Moreover, 17-AAG+IMiD showed synergistic cell killing activity in clonally-derived IMiD resistant HMCL. Further, 17-AAG induced cell death was comparable with Hsp90 knockdown as evident from the cytotoxicity assay using PI and 17-AAG in combination in RPMI8226-wild type and RPMI-HSP90AA1 knocked down cell line. Notably, 17-AAG was strikingly effective against the NRAS-mutant cell line indicating an additional niche (NRas mutant myeloma) where 17-AAG could be most effective.Next, we performed RNA sequencing to elucidate the molecular mechanisms behind 17-AAG drug action, drug synergy, 17-AAG-induced cell death. Our gene expression profiling (GEP) followed by Ingenuity Pathway Analysis (IPA) analysis revealed protein ubiquitination, aryl hydrocarbon receptor signalling pathway as the top canonical pathways. 17-AAG induced apoptosis via mitochondrial mediated pathway in myeloma. 17-AAG exerts its cytotoxic effect by activating intrinsic pathway of apoptosis which we further confirmed through the increase in reactive oxygen species generation and decrease in mitochondrial membrane potential. 17-AAG was also effective in reducing the expression of hallmarks of MM such as p65/NF-kB, IRF4, c-Myc. Finally, we performed mass cytometry (CyTOF; Cytometry by time of flight) on primary bone-marrow cells (PMCs) from myeloma patients for further validation of proteomic signatures at the single-cell level. CyTOF analysis confirmed 17-AAG-induced cell death and key changes in MM-specific proteomic markers. 17-AAG treated PMCs showed elevated cleaved caspase levels and down-regulation of IRF4 and phospho-STAT3. GEP and CyTOF results were confirmed using immunoblotting assays.Together, our study demonstrates a unique pipeline for drug repositioning that has the potential to revolutionize clinical decision-making by minimizing the number of drugs required for discovering successful combination chemotherapy regimens against drug-resistant myeloma. [Display omitted] DisclosuresKumar: BMS: Consultancy, Research Funding; Abbvie: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Amgen: Consultancy, Research Funding; Takeda: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Tenebio: Research Funding; Beigene: Consultancy; Oncopeptides: Consultancy; Antengene: Consultancy, Honoraria; Carsgen: Research Funding; Janssen: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; KITE: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Merck: Research Funding; Astra-Zeneca: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding; Novartis: Research Funding; Roche-Genentech: Consultancy, Research Funding; Bluebird Bio: Consultancy; Celgene: Membership on an entity's Board of Directors or advisory committees, Research Funding; Adaptive: Membership on an entity's Board of Directors or advisory committees, Research Funding; Sanofi: Research Funding.

Mechanism of exosomal miR-155 derived from bone marrow mesenchymal stem cells on stemness maintenance and drug resistance in myeloma cells

ObjectiveThis study was to explore the effect of exosomal miR-155 derived from bone marrow mesenchymal stem cells (BMSCs) on stemness maintenance and drug resistance in MPC-11 multiple myeloma cells.MethodsMPC-11 cells were transfected with mimics or inhibitors of miR-155. miR-155 expression was detected by qRT-PCR, cell condition was observed, and the expression of stemness maintenance markers OCT-4 and Nanog was observed by immunofluorescence. The expression of proteins associated with the Hedgehog signaling pathway and drug resistance was evaluated by western blot. To investigate whether exosomes affect cell behavior by horizontal delivery of miR-155, MPC-11 cells were co-cultured with exosomes isolated from BMSCs that were transfected with mimics or inhibitors of miR-155. Cell proliferation and the expression of proteins related to stemness maintenance protein and drug resistance were examined.ResultsIn function assays, after miR-155-mimics transfection, the expression levels of proteins related to stemness maintenance marker, Hedgehog signaling, and drug resistance were increased in MPC-11 cells. BMSC-derived exosomes carrying miR-155 inhibited apoptosis, promoted cell division, and upregulated the expression of protein associated with stemness maintenance, Hedgehog signaling, and drug resistance.ConclusionTherefore, our findings indicate that exosomal delivery of miR-155 exerted the same effect as transfection did on the stemness maintenance and drug resistance of multiple myeloma cells.

DKK1 activates noncanonical NF-κB signaling via IL-6–induced CKAP4 receptor in multiple myeloma

AbstractProteasome inhibitors, such as bortezomib (BTZ), represent the key elements in chemotherapy regimens for multiple myeloma (MM), whereas acquired chemoresistance and ultimately relapse remain a major obstacle. In the current study, we screened differently expressed cytokines in bortezomib-resistant MM cells and found that Dickkopf-1 (DKK1) level was remarkably augmented, whereas CD138 level was significantly suppressed. DKK1 in vitro specifically enhanced the resistance of myeloma cells to bortezomib treatment, and excessive DKK1 drove CD138 downregulation via inhibition of canonical Wnt signaling. Notably, DKK1 mainly induced drug resistance in MM cells via the receptor of CKAP4. Mechanistically, CKAP4 transduced DKK1 signal and evoked NF-κB pathway through recruiting and preventing cullin associated and neddylation dissociated 1 from hampering the assembly of E3 ligase-mediated ubiquitination of IκBα. In addition, we found that interleukin-6 (IL-6) stimulated CKAP4 expression to generate drug resistance, and disturbance of DKK1-CKAP4 axis improved sensitivity to BTZ treatment of MM and attenuated bone destruction in a mouse model. Collectively, our study revealed the previously unidentified role of DKK1 in myeloma drug resistance via Wnt signaling dependent and independent manners, and clarified the importance of antagonism of DKK1-IL-6 loop in bone marrow microenvironment.

Novel Peptide-drug Conjugate Melflufen Efficiently Eradicates Bortezomib-resistant Multiple Myeloma Cells Including Tumor-initiating Myeloma Progenitor Cells.

Introduction of the proteasome inhibitor bortezomib has dramatically improved clinical outcomes in multiple myeloma. However, most patients become refractory to bortezomib-based therapies. On the molecular level, development of resistance to bortezomib in myeloma cells is accompanied by complex metabolic changes resulting in increased protein folding capacity, and less dependency on the proteasome. In this study, we show that aminopeptidase B, encoded by the RNPEP gene, is upregulated in bortezomib-resistant myeloma cell lines, and in a murine in vivo model. Moreover, increased RNPEP expression is associated with shorter survival in multiple myeloma patients previously treated with bortezomib-containing regimens. Additionally, expression is increased in plasma cell precursors, a B-lymphoid compartment previously associated with myeloma stem cells. We hypothesized that increased aminopeptidase B expression in aggressive myeloma clones may be used therapeutically toward elimination of the cells via the use of a novel peptide-drug conjugate, melphalan flufenamide (melflufen). Melflufen, a substrate of aminopeptidase B, efficiently eliminates bortezomib-resistant myeloma cells in vitro and in vivo, and completely suppresses clonogenic myeloma growth in vitro at subphysiological concentrations. Thus, melflufen represents a novel treatment option that is able to eradicate drug-resistant myeloma clones characterized by elevated aminopeptidase B expression.

IL-32γ Induces M2 Macrophage Polarization with Enhanced Ability of Macrophage-Mediated Drug Resistance in Myeloma Cells through STAT3 and NF-κB Activation

Background: Macrophages(MΦs) are an abundant and important component of multiple myeloma (MM) microenvironment, and support the survival of MM cells and promote their resistance to chemotherapy. It has been proposed that MΦs have great plasticity and can differentiate into 2 major polarized states, M1 (“classically activated”) and M2 (“alternatively activated”). M1 macrophages are considered to be anti-tumoural and pro-inflammatory, whereas M2 macrophages are characterized by efficient activity of tumour promotion and suppression of adaptive immunity.IL-32, a novel proinflammatory cytokine, has been found to play a crucial role in a variety of inflammatory diseases and cancers. In this study, we investigated the immunomodulatory effects and underlying mechanisms of IL-32γ on macrophage polarization and MΦ-mediated drug resistance in myeloma cells.Results: First, we found that both bone marrow supernatant and peripheral blood supernatant of MM patients showed significantly higher levels of IL-32 as compared with those of healthy controls. We also detected IL-32 in MM cell lines and M-CSF-induced MØs by qRT-PCR and Western blot, which showed that IL-32 expression was higher in MM cell lines than in MØs. We next investigated the polarization profiles and functional activities of IL-32γ-treated MØs. After stimulated with recombinant IL-32γ,MØs exhibited upregulated expression of cell-surface molecules and cytokines associated with M2 polarization(CD206,Dectin-1, and IL-10), while M1-polarizing marker(CD86) were down-regulated.Further, Western blot was applied to detect the inflammation molecular pathway in MØs, which showed that IL-32γ treatment activated the JAK-STAT3 pathway and NF-κB pathway. This pro-M2MØ polarization effect of IL-32γ was inhibited by the addition of specific inhibitors of STAT3 and NF-kB. Moreover, co-culture experiments revealed that IL-32γ-educated MØs provided a survival benefit to myeloma cells, as tested with several anti-myeloma agents including bortezomib and doxorubicin. The pro-survival effect was associated with less cleavage of caspase-3 and PARP in myeloma cells, and thus less apoptosis. The STAT3 and NF-κB inhibitors partially inhibited the observed IL-32γ-induced and MØs -mediated resistance to bortezomib in MM cells.Conclusions:IL-32γ could effectively induce the polarization of M2 MØs, leading to enhanced MØ-mediated drug resistance in myeloma cells as the result of activating the JAK-STAT3 and NF-κB pathways in MØs. DisclosuresNo relevant conflicts of interest to declare.