PI-resistant Cell Lines Research Articles

Abstract 7191: Targeting IGF1R/INSR pathway with approved ALK inhibitors inhibits AKT signaling and overcomes proteasome inhibitor resistance in multiple myeloma

Abstract Background: Resistance to proteasome inhibitors (PI) bortezomib (BTZ) and carfilzomib (CFZ) is a major obstacle to the successful treatment of multiple myeloma (MM); thus, identification of novel therapeutic options is an unmet medical need. ALK inhibitors have been shown to exhibit anti-MM activity in monotherapy or in combination with CFZ. Our data showed that MM cells were negative for ALK; thus, we aimed to identify the mechanism of action of the ALK inhibitor ceritinib in MM cells and the mechanism of synergy between ceritinib and CFZ. Methods: A set of PI-naïve and PI-resistant MM cells was used in this study. Genome-wide CRISPR/Cas9-based screening using the Brunello library was performed in the AMO-1 cell line. Kinase inhibitor selectivity data were retrieved from ChEMBL, v30 database. RNA sequencing was used to determine expression changes after treatment, and RNA-seq data from patients included in the CoMMpass study were analyzed. Western blotting was performed to assess the levels of total and phosphorylated protein. Unbiased LC-MS/MS was performed to determine the effects of ceritinib and CFZ on the intracellular metabolites. An in vivo mouse model based on the orthotopic injection of AMO-BTZ cells into the femur of NSG mice was used to determine the effect of the drug combination in vivo. Results: Among approved ALK inhibitors, ceritinib has been identified as the most synergistic cytotoxic combination with CFZ in PI-naïve and PI-resistant MM cells. An in silico search of the ChEMBL database identified InsR and IGF1R as receptor tyrosine kinase that are inhibited by ceritinib. PI-naïve, PI-resistant cell lines, as well as MM patients were negative for ALK, but positive for InsR and IGF1R expression. CRISPR/Cas9-screening identified genes involved in the negative regulation of mTORC signaling (DDIT4, NPRL2/3, TSC1/2) and the transcription factor FOXO1 as the major resistance candidates to ceritinib. Subsequently, FOXO1 inhibition using a selective chemical inhibitor protected the cells from ceritinib-induced cytotoxicity. Next, ceritinib inhibited mTORC signaling and induced the expression of genes related to cell cycle arrest, which are downstream of FOXO1. Likewise, ceritinib, by targeting the InsR/IGF1R, impaired purine-pyrimidine and amino acid homeostasis, suggesting metabolic and proliferation shut-down and amino acid starvation due to downstream mTORC and Akt inhibition and FOXO1 induction. The combination of ceritinib and CFZ was superior to CFZ in PI-resistant MM in vivo and showed strong synergistic cytotoxicity in primary cells from MM patients progressing under or after PI-containing therapy. Conclusion: Ceritinib, an FDA-approved drug, overcomes PI resistance in MM by inhibiting InsR/IGF1R and downstream Akt signaling. Therefore, ceritinib is a promising treatment option for PI-resistant MM. Supported by the project National Institute for Cancer Research (Programme EXCELES, ID Project No. LX22NPO5102) - Funded by the European Union - Next Generation EU. Citation Format: Andrej Besse, Tiberiu Totu, Marianne Kraus, Anthonius P. Janssen, Jana Veprkova, Max Mendez Lopez, Ondrej Slaby, Marija Buljan, Mario van der Stelt, Christoph Driessen, Lenka Besse. Targeting IGF1R/INSR pathway with approved ALK inhibitors inhibits AKT signaling and overcomes proteasome inhibitor resistance in multiple myeloma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7191.

Targeting IGF1R/Insr Pathway with Approved ALK-Inhibitors Overcomes Proteasome Inhibitor Resistance in Multiple Myeloma

Background: The treatment of multiple myeloma (MM) has advanced rapidly with the discovery of proteasome inhibitors (PIs) bortezomib (BTZ) and carfilzomib (CFZ). PIs disrupt the equilibrium between production and disposal of excess and/or misfolded proteins in MM cells, leading to apoptosis. However, despite this success, essentially all patients with MM eventually develop resistance to PIs. Therefore, identifying strategies to overcome PIs resistance is clinically important. ALK inhibitors exhibit anti-MM activity ex vivo. Previously, the ALK inhibitor ceritinib has been shown to inhibit IGF1R/InsR signaling. Signaling through the IGF1/IGF1R axis contributes to acquired resistance to BTZ, and PI activity is reduced in the presence of IGF1, suggesting that IGF1R inhibitors may enhance the cytotoxic effect of PIs. To date, IGF1R/InsR inhibitors have not been successful as single agents in clinical trials and no formally approved drugs are available. Importantly, the drug repurposing approach offers a promising strategy for drug development, particularly for MM. Therefore, we aimed to identify i) whether ALK inhibitors are cytotoxic in MM by targeting the IGF1R/InsR pathway, and ii) whether they can be combined with PIs to overcome PI resistance in vitro and in vivo. Methods: A set of PI-naïve and PI-resistant cells was used in this study. The cytotoxicity of drugs was determined by CCK8 assay in cell lines and by CellTiter-Glo assay in primary cells. Genome-wide CRISPR/Cas9-based loss-of-function screening using the Brunello library was performed in the AMO-1 cell line to identify the mechanism of action of ceritinib. Kinase inhibitor selectivity data were retrieved from ChEMBL, v30. Western blotting was performed to assess the levels of total and phosphorylated proteins. RNA sequencing was used to determine the number of transcripts in PI-sensitive and PI-resistant cells, and RNA-seq data from patients included in the CoMMpass study were analyzed. Unbiased LC-MS/MS was performed to determine the effects of ceritinib and carfilzomib on intracellular metabolites. An in vivo mouse model based on orthotopic injection of AMO-BTZ cells into the femur of NSG mice was used to determine the effect of the drug combination in vivo. Results: Initially, seven ALK inhibitors were tested in PI-naïve and PI-adapted MM cell lines. Based on IC 50 values, the most effective ALK inhibitors to induce cytotoxicity in MM were ceritinib > brigatinib > entrectinib. The combination of ceritinib, brigatinib, and entrectinib showed synergistic cytotoxicity with PI BTZ and CFZ and overcame PI-resistance in four different sets of PI-adapted cells. The strongest synergistic cytotoxicity was observed between ceritinib and CFZ in CFZ-adapted cells. CRISPR/Cas9-screening identified genes involved in the negative regulation of mTORC signaling (DDIT4, NPRL2/3, TSC1/2) and transcription factor FOXO1 as the major resistance candidates to ceritinib. Subsequently, ceritinib treatment significantly inhibited mTORC signaling and impaired purine-pyrimidine and amino acid production pathways, suggesting a metabolic and proliferation shut-down and amino acid starvation due to targeting of the upstream receptor tyrosine kinases (RTK), which are essential for cell viability and thus not identified by CRISPR screening. Further search in the ChemBL database identified InsR and IGF1R, as RTK that was potently inhibited by ceritinib. PI-naïve and PI-resistant cell lines as well as MM patients were negative for ALK, but positive for InsR and IGF1R expression. Accordingly, co-treatment of PI-resistant cells with a combination of InsR/IGF1R inhibitors and CFZ induced strong synergistic cytotoxicity, resembling the synergistic cytotoxicity observed for ceritinib and CFZ, whereas InsR/IGF1R inhibitors did not show any synergistic cytotoxicity with ceritinib, suggesting targeting the same pathway. Importantly, the combination of ceritinib and CFZ was superior to CFZ in an orthotopic mouse model bearing PI-resistant MM cells and showed strong synergistic cytotoxicity in primary cells from MM patients progressing under or after PI-containing therapy. Conclusion: Ceritinib, an FDA-approved drug, overcomes PI resistance in MM by targeting InsR/IGF1R signaling, which is essential for PI resistance in MM. Therefore, ceritinib represents a promising, potential option for the treatment of PI-resistant MM.

Acid Ceramidase (ASAH1) Is a Key Mediator of Drug Resistance in Refractory Multiple Myeloma

Despite the growing armamentarium of treatments including proteasome inhibitors (PIs), immunomodulatory imides (IMiDs) and cellular and non-cellular immunotherapies MM remains incurable, due to the emergence of drug resistance that causes patient relapse. To develop therapies that significantly extend overall survival, a clearer understanding of the mechanisms driving drug-resistance is urgently required. Analysis of RNA-seq data derived from 672 MM Moffitt patients revealed that sphingolipid metabolism genes and in particular acid ceramidase (ASAH1), are significantly enriched in relapse MM (RMM). Further, high levels of ASAH1 in RMM patients predicted poorer overall survival when patients were treated with any PI-containing regimen (median overall survival 552 vs 1226 days). These findings were corroborated in the Multiple Myeloma Research Foundation CoMMpass dataset (IA17). Next, we queried potential mechanisms of treatment resistance using gene-set enrichment analysis (GSEA). ASAH1 High patients displayed upregulation of gene signatures involved in metabolism of lipids, sphingolipids and regulation of apoptosis. Further, PI-resistant cell lines (U266-PSR, RPMI8226-B25, and ANBL6-V10R) displayed elevated levels of ASAH1, and total and phosphorylated levels of anti-apoptotic proteins MCL-1 and BCL-2 compared to PI-sensitive parental cells (U266, RPMI8226 and ANBL6). Genetic (shRNA) and pharmacological (ceranib-2) inhibition of ASAH1 significantly decreased MM viability and reduced MCL-1/BCL-2 expression. Further, ASAH1 inhibition resensitized resistant MM cells to PI treatment. Importantly, we recapitulated our findings in CD138+ patient MM cells ex vivo (EMMA platform), with ceranib-2/PI treatment being synergistic in the majority (>75%) of patient samples tested. In vivo, ceranib-2 treatment limited PI-resistant U266-PSR MM tumor growth and extended overall survival of NSG mice. Further, ASAH1 depletion (shRNA) resensitized MM cells to PI treatment in vivo and loss of MCL-1 and BCL-2 expression was confirmed ex vivo. To understand the mechanism through which ASAH1 mediates PI-resistance we performed total and pSTY proteomic profiling (LC-MS/MS). Proteomic analyses revealed inhibition of the endogenous phosphatase PP2A inhibitor, I2PP2A as a candidate mechanism. Notably, I2PP2A was elevated in PMRC RMM patient samples, correlating with ASAH1 expression, and predicting poorer overall survival. In conclusion, in vitro, in vivo and patient ex vivo data demonstrate ASAH1 is a novel, clinically relevant and tractable target for the treatment of PI-resistant MM. Future studies to develop novel and potent ASAH1 inhibitors for the treatment resistant MM, in combination with current standard of care therapies are on-going and we believed warranted based on our emerging data.

Gene Expression Profiling of Kinetic Response to Proteasome Inhibitors in Innate and Acquired Resistant Multiple Myeloma

Extensive inter-individual variation in response to chemotherapy is a serious cause of concern in the treatment of multiple myeloma (MM). Drug resistance may be categorized into innate resistance already present in drug-naive refractory patients or emerging (acquired) resistance where a patient's tumor ultimately undergoes relapse in course of treatment despite initial response.Using a panel of human myeloma cell lines (HMCLs), we have earlier presented a gene expression signature that could not only distinguish good and poor Proteasome inhibitor (PI)-response in the HMCL panel, but was also successful in stratifying exceptional response to PI-based chemotherapy in MM clinical datasets.In this study, we used six (6) most PI-sensitive and six (6) most PI-resistant HMCLs representing innate PI response and clonally-derived PI-resistant (R) cell lines and PI-sensitive (P) HMCLs representing acquired PI-response to identify kinetic changes in gene expression patterns following test dosing with the 2nd generation PI drug Ixazomib. High quality RNA was extracted from untreated/baseline/0Hr and treated/24hrs post-treatment myeloma cell lines and RNA sequencing was performed on llumina's HiSeq 2000 using 50bp paired-end protocol with depth of >20million reads-per-sample. Transcriptome profiles were then compared to characterize differences in kinetic response to PIs.Our analysis revealed, at FDR<0.05, 74 genes changed significantly post-treatment in Ix-sensitive lines, with a |fold-change|> 1.5 while no gene showed any significant kinetic change in Ix-resistant cell lines. When our kinetic innate Ix-response profile was compared to Shaughnessy's 80-gene kinetic signature derived from Bz test-dosing, 16 genes were found similar, including PSMD4 that was identified earlier as novel high-risk feature in MM patients on Bz-based clinical trial. On the other hand, kinetic expression analysis of the clonally-related PI-sensitive parental and PI-resistant cell line pairs representing acquired PI-resistance revealed 651 genes were significantly differentially expressed in the sensitive/parental cell lines compared to 21 in clonally-derived resistant cell lines. Further, we observed that the gene signatures of kinetic innate PI-response were different from the signature of acquired PI-response. We also observed strikingly lower number of genes that significantly changed post-treatment in both innate and acquired PI-resistant cell lines when compared to the PI-sensitive cell lines. Ingenuity Pathway Analysis (IPA) identified the proteasome ubiquitination pathway, NRF2-mediated oxidative stress response pathway, oxidative stress response and Glutathione depletion/ Glutathione redox reactions as top canonical pathways associated with the most differentially regulated kinetic response genes. Several of these genes, including CCND1 (cyclin D1) and E2F, have been earlier shown involved in proliferative activity as well as susceptibility to chemotherapy.Our results thus provide key insights into the phenomenon of kinetic PI response in MM and highlights the notable differences between innate and acquired drug response. We are currently validating our in vitro findings using ex vivo kinetic transcriptome analysis in primary myeloma cells derived from drug-naive newly diagnosed MM patients representing variation in PI-response. DisclosuresKumar:Celgene, Millennium, BMS, Onyx, Janssen, Noxxon, AbbVie, Amgen, Merck, Oncopeptides, Skyline Diagnostics, Takeda: Consultancy; Celgene, Millennium/Takeda, Onyx, AbbVie, Janssen, Sanofi, Novartis, Amgen, Genentech, Merck, Oncopeptides, Roche, Skyline Diagnostics: Research Funding; Skyline: Honoraria.

Repurposing Clofazimine As a Novel Drug for the Treatment of PI-Resistant Stem Cell-like Subclones in Myeloma

Multiple myeloma (MM) is the second-most common hematopoietic malignancy in the United States with estimated new reported cases of 32,110 and deaths of 12,960 in 2019. Despite recent improvement in therapies, including proteasome inhibitors (PIs) - the standard-of-care drug, MM still remains a difficult-to-cure disease with significant complexity and heterogeneity at the molecular level. Recent studies have shown that the presence of cell sub populations with potential cancer stem cell-like properties (MM-CSCs), including CD19- CD138- quiescent stem cells, dormant cells, ALDH+ cells and side populations/SP, in drug-resistant tumors significantly contribute to the development of PI resistance in myeloma. However, no study so far has attempted to develop drugs specifically targeting MM-CSCs involved in drug resistance. Further, the gene signature underlying these sub cellular populations are yet to be revealed. We have previously demonstrated that Clofazimine (CFZ), an anti-leprosy drug, could be successfully repurposed for the treatment of Chronic myeloid leukemia (CML) by specifically targeting quiescent stem cell population (CD34+CD38-, CFSE-bright) in drug resistant patient samples. Here, we hypothesized that we will repurpose CFZ as a novel drug for the treatment of PI-resistant MM by targeting the sub-cellular stem cell-like subclones. Therefore, in the current study we utilized our panel of &gt;50 human myeloma cell lines (HMCLs) representing innate PI-response/resistance and &gt;10 pairs (parental and PI-resistant lines generated using dose escalation over a period of time) of clonally derived PI-resistant HMCLs representing acquired resistance to repurpose CFZ for the management of PI-resistant MM. Cells were treated with CFZ and the PIs Bortezomib (Bz), Carfilzomib (Cz), Ixazomib (Ix) and Oprozomib (Opz) as single agents or in combination and in vitro cytotoxicity was determined using CellTiter-Glo assay. Synergy between CFZ and PIs was analyzed by Calcusyn software based on Chou-Talalay's combination index (CI) theorem. Drug-induced apoptosis, ROS generation, mitochondrial membrane potential and cell cycle arrest were evaluated by Flow cytometry. Sub-cellular stem cell-like populations were isolated using cell sorting by Flow Cytometry (FCM/FACS). Tumorigenic potential of purified MM-CSCs was determined using colony forming assay, carboxyfluorescein succinimidyl ester (CFSE) assay, Aldeflour activity and analysis of side population in resistant MM cells. We found very promising preliminary results where CFZ alone showed very potent inhibition of cell viability in HMCLs. Further, treatment with CFZ + PIs significantly improved the therapeutic index of PI administration to the cells. Similar results were observed in parental (P) vs clonally derived PI-resistant (VR) cell lines. We next evaluated if CFZ alone or in combination with PIs could erode quiescent CD138+ cells in parental-P/clonally derived PI-resistant cells-VR. Hence, we labelled RPMI-8226 (parental cells), RPMI8226-VR with CFSE and treated them with drugs for 96h. While PIs failed to reduce CFSE-bright (non-dividing) cells, CFZ alone or in combination with Ixazomib significantly reduced their number and increased CFSE-dim (dividing cell) population. Evaluation of apoptosis in these cells revealed that CFZ alone caused apoptosis in both CFSE-bright and CFSE-dim cells while combining CFZ +PI caused a more robust effect amounting to their near-obliteration. We next assessed side populations/SP in resistant cells. We found that % SP was higher in resistant cells as compared to parental cells. CFZ alone or in combination (CFZ+PI) reduced %SP in PI- resistant cell lines. Based on these results, we propose that CFZ may have strong potential to increase the therapeutic efficacy of PIs when used in combination by specifically targeting MM-CSCs sub cellular population in MM - which we are investigating further. Currently, we are: 1) validating the potency of CFZ (alone or CFZ+PI combination therapy) in primary myeloma cells/PMCs from newly diagnosed patients, followed by 2) bulk mRNA sequencing and 3) single-cell transcriptomic analysis of MM-CSCs in HMCLs and PMCs to evaluate molecular pathways involved in stem-cell based PI-resistance and to characterize PI-resistant sub-cellular stem cell populations based on gene expression signatures using our prediction analysis software SCATTome. Disclosures No relevant conflicts of interest to declare.

Abstract 285: Ixazomib combined with the nuclear export inhibitors selinexor or eltanexor for the treatment of multiple myeloma

Abstract Introduction In the past decade, response and survival rates in multiple myeloma (MM) patients have been greatly increased by newer therapies. Nevertheless, most patients with MM eventually die from relapsed/refractory disease. Previous studies in our lab and in others have shown that exportin 1 inhibitors (XPO1i) are potent anti-MM drugs, whether used as single agents or in combination with proteasome inhibitors (PIs), immunomodulator drugs (IMiDs), anthracyclines, or alkylating agents. Ixazomib (IXA), an orally available PI, has been shown to be effective when combined with IMiDs, dexamethasone, alkylating agents, and/or prednisone for the treatment of patients with MM. We investigated whether the clinical XPO1i selinexor (SEL) or eltanexor (ELT) combined with IXA could overcome PI resistance in MM cell lines and in ex vivo bone marrow aspirates from PI-refractory patients. Materials and Methods PI-resistant MM cell lines 8226B25 and U226PSR and their respective parental cell lines, 8226 and U266, were treated in vitro and in vivo (mice) with SEL/IXA or ELT/IXA combinations or with each drug as a single agent. Bone marrow aspirates from newly diagnosed and PI-refractory MM patients were treated ex vivo with SEL/IXA or ELT/IXA and assayed for apoptosis. Mechanistic studies included NFkB and IkBα protein assays, immunofluorescence microscopy, ImageStream flow-cytometry, and proximity-ligation assay. IkBα knockdown and NFkB transcriptional activity were measured in SEL/IXA- or ELT/IXA-treated MM cells. Results SEL and ELT each sensitized parental and, to a lesser extent, PI-resistant MM cells to IXA, as measured by apoptosis. XPO1i/IXA treatments inhibited U266 and 8226 MM tumor growth and increased survival in mice; however, PI-resistant tumors were not sensitized by XPO1i/IXA treatment. Myeloma cells isolated from both newly diagnosed and PI-refractory MM patients were sensitized by XPO1i to IXA, as compared to untreated and single agent-treated MM cells, without affecting non-MM cells. Immunofluorescence microscopy, Western blot, and ImageStream analyses of MM cells showed increased nuclear IkBα with the XPO1i/PI treatments. Proximity ligation found increased IkBα-NFkB complexes in treated MM cells. IkBα knockdown abrogated XPO1i/PI-induced cytotoxicity in MM cells. XPO1i/PI treatment decreased NFkB transcriptional activity. Conclusions In previous studies, we found that SEL sensitized PI-resistant cell lines to carfilzomib and bortezomib; however, IXA was less effective in these same MM cells. SEL or ELT used in combination with IXA have the potential to overcome PI drug resistance in MM patients. Sensitization may be due to inactivation of the NFkB pathway by IkBα. Further investigation is underway to examine these mechanisms. The results presented in this study support combinatorial clinical trials in relapsed and refractory MM patients who use PI therapies. Citation Format: Joel G. Turner, Jana Dawson, Alexis Bauer, Juan Gomez, Erkan Baloglu, Yosef Landesman, Daniel M. Sullivan. Ixazomib combined with the nuclear export inhibitors selinexor or eltanexor for the treatment of multiple myeloma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 285.

IdentificationofLongNon-CodingRNAs DeregulatedinMultipleMyelomaCellsResistantto ProteasomeInhibitors.

While the clinical benefit of proteasome inhibitors (PIs) for multiple myeloma (MM) treatment remains unchallenged, dose-limiting toxicities and the inevitable emergence of drug resistance limit their long-term utility. Disease eradication is compromised by drug resistance that is either present de novo or therapy-induced, which accounts for the majority of tumor relapses and MM-related deaths. Non-coding RNAs (ncRNAs) are a broad class of RNA molecules, including long non-coding RNAs (lncRNAs), that do not encode proteins but play a major role in regulating the fundamental cellular processes that control cancer initiation, metastasis, and therapeutic resistance. While lncRNAs have recently attracted significant attention as therapeutic targets to potentially improve cancer treatment, identification of lncRNAs that are deregulated in cells resistant to PIs has not been previously addressed. We have modeled drug resistance by generating three MM cell lines with acquired resistance to either bortezomib, carfilzomib, or ixazomib. Genome-wide profiling identified lncRNAs that were significantly deregulated in all three PI-resistant cell lines relative to the drug-sensitive parental cell line. Strikingly, certain lncRNAs deregulated in the three PI-resistant cell lines were also deregulated in MM plasma cells isolated from newly diagnosed patients compared to healthy plasma cells. Taken together, these preliminary studies strongly suggest that lncRNAs represent potential therapeutic targets to prevent or overcome drug resistance. More investigations are ongoing to expand these initial studies in a greater number of MM patients to better define lncRNAs signatures that contribute to PI resistance in MM.

Abstract 153: Long non-coding RNAs deregulated in Multiple Myeloma impact therapeutic response to proteasome inhibitors

Abstract Multiple Myeloma (MM) is a complex disease that frequently leads to fatal outcome and accurate risk classification to optimize the choice of therapy may have impact on clinical outcomes. MM stratification based upon cytogenetic abnormalities and protein-coding gene expression does not adequately correlate with the depth or durability of therapeutic response. Therefore, the new class of molecular effectors, non-coding RNAs (ncRNAs), may enhance the basic understanding of myelomagenesis, drug resistance and provide better stratification of myeloma subtypes. NcRNAs include long ncRNAs (lncRNAs) and microRNAs (miRNAs) that may act as positive or negative regulators of gene expression to control cell proliferation, apoptosis and drug resistance. We hypothesized that lncRNAs commonly deregulated in the 3 resistant cell lines would have significant overlap to the deregulated lncRNA in MM patients. To investigate the role of lncRNAs in resistance to proteasome inhibitors (PIs), we compared global lncRNA profiling in drug-naïve cells to cells with acquired resistance to the PIs bortezomib, carfilzomib and ixazomib. RPMI 8226 cells resistant to each of the three PIs were generated through successive exposure to bortezomib, carfilzomib or ixazomib. Total RNA was isolated and genome-wide ncRNA expression profiling was performed using Affymetrix 3.0 microarray chips LncRNA expression profiles from drug-resistant cells were compared to that of drug-naïve cells treated with vehicle alone. MM patients’ bone marrow aspirates were obtained after UCCOM IRB-approval. Bioinformatic analysis identified a panel of 18 lncRNAs that were significantly (&amp;gt;100-fold) deregulated in all three drug-resistant cell lines relative to drug-naïve cells. Strikingly, the majority of the deregulated lncRNAs exhibited a similar expression pattern in all 3 PI-resistant cell lines (Figure 2a). RPMI 8226 cells carry a t(14,16) and none of the deregulated lncRNAs detected localized to chromosomes 14 or 16, suggestive of a cytogenetic-independent mechanism of drug resistance. We also identified lncRNAs deregulated in MM patient samples relative to plasma cells from healthy age-matched individuals. We found a significant overlap (&amp;gt;90%) between deregulated lncRNAs in PI-resistant cells and MM cells. The lncRNA COL4A-2A was upregulated &amp;gt;5,000-fold in resistant cells and displayed extensive sequence complementarity to miRNA-29 that was downregulated in resistant cells. Taken together, we identified a curated panel of deregulated lncRNAs in common within myeloma cells generated with acquired resistant to three different clinically-relevant proteasome inhibitors and MM patients. Further investigation is warranted to shed light on the role of these lncRNAs in the development of MM, to identify their targets and to define their role in drug resistance. Note: This abstract was not presented at the meeting. Citation Format: Ehsan Malek, Rebekah Karns, Anil G. Jegga, Sajjeev Jagannathan, Nikhil Vad, Mohamed A.Y Abdel Malek, James J. Driscoll. Long non-coding RNAs deregulated in Multiple Myeloma impact therapeutic response to proteasome inhibitors. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 153. doi:10.1158/1538-7445.AM2015-153

Correlation of Non-Coding RNA Expression with Response to Proteasome Inhibitors in Multiple Myeloma

Background: Multiple myeloma (MM) is a heterogeneous diseaseand there is an increased need for more accurate risk classification methods to improve treatment decision-making because of its high impact on clinical outcomes. Here, we demonstrate evidence to support the prognostic value of non-coding RNAs (ncRNAs) as newly discovered genetic biomarkers of drug-resistant and/or high-risk forms of MM. NcRNAs, e.g., long ncRNAs (lncRNAs) and microRNAs (miRNAs), act as positive or negative regulators of gene expression to control cell proliferation, apoptosis and drug resistance. NcRNAs have been shown to play a role in both solid and hematological tumors. Stratification of MM based upon cytogenetic abnormalities and protein-coding gene signatures does not adequately correlate with the depth and durability of response to novel agents such as bortezomib. Therefore, ncRNAs as new class of molecular effectors may enhance the basic understanding of myelomagenesis and provide better stratification of myeloma subtypes. To investigate the role of ncRNAs in resistance to proteasome inhibitors (PIs), we compared global ncRNA profiling in drug-naïve cells to cells with acquired resistance to the PIs bortezomib, carfilzomib and ixazomib. We hypothesized that ncRNAs commonly deregulated in the 3 resistant cell lines would yield a ncRNA signature and novel therapeutic targets.Experimental Procedures: RPMI 8226 cells resistant to PIs were generated through successive exposure to bortezomib, carfilzomib or ixazomib over a period of 6 months. Total RNA was isolated and genome-wide ncRNA expression profiling was performed using Affymetrix3.0 microarray chips that contained nearly 40,000 miRNA and 13,300 lncRNA probes. NcRNA expression profiles from drug-resistant cells were compared to that of drug- naïve parental cells treated with vehicle alone using the same treatment algorithm. Housekeeping genes were used for log expression normalization. MM patients’ bone marrow aspirates were obtained from patients after University of Cincinnati Institutional Review Board approval. Results: Bioinformatic analysis of the ncRNA profiles identified a panel of 87 lncRNAs and ~40 miRNAs that were significantly (>100-fold) deregulated in all three drug-resistant cell lines relative to drug- naïve parental cells. Strikingly, ~90% of the deregulated lncRNAs exhibited a similar expression pattern in all 3 PI-resistant cell lines. Twenty lncRNAs were deregulated > 1000-fold in all 3 resistant cell lines (Figure 1). RPMI 8226 cells carry a chromosomal (14,16) translocation. Interestingly, none of the deregulated lncRNAs detected here localized to chromosome 14 or 16, suggestive of a cytogenetic-independent mechanism of drug resistance. The lncRNA COL4A-2A was upregulated >5,000-fold in resistant cells and displayed extensive sequence complementarity to miRNA-29 that was downregulated in resistant cells. Also, our microarray-based studies have identified ncRNAs deregulated in MM patient tumor samples relative to normal plasma cells from healthy age-matched individuals. A significant number of the deregulated ncRNAs between drug- naïve and drug resistant cells were also deregulated in normal plasma cells relative to myeloma cells. Studies are correlating the ncRNA patterns seen in drug-sensitive and drug-resistant cell lines with ncRNA patterns obtained from malignant plasma cells of patients currently receiving bortezomib-based therapy. Updated results to correlate ncRNA expression with myeloma patient response to bortezomib will be presented.Conclusions: Taken together, we have identified a curated panel of ncRNAs deregulated in common within myeloma cells generated with acquired resistant to three different clinically-relevant proteasome inhibitors. Ongoing studies will correlate ncRNA expression patterns from resistant cells with patterns generated from patients with monoclonal gammopathy of unknown significance (MGUS), Smoldering MM, newly diagnosed MM, refractory disease and plasma cell leukemia. In addition, ncRNA patterns will be generated based upon MM patient response to bortezomib. Further investigation is warranted to shed light on the role of these ncRNAs in the development of MM, to identify their targets and to define their role in drug resistance. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.