ALBERT

Description: INTRODUCTION: Multiple myeloma (MM) is a biologically and clinically heterogeneous disease. Different recurrent driver genomic events have been reported, but to date no unifying feature has been identified in MM evolution. The recent interest in signatures of mutational processes through analysis of whole-exome sequencing data has led to initial insights into what generates MM mutational repertoire (Bolli et al, Nat Com 2014). Here, taking advantage of the increased power provided by whole genome sequencing (WGS), we analyzed 22 paired samples from 11 patients first at the smoldering (SMM)/MGUS stage and subsequently at the time of progression to symptomatic MM to gain a deeper understanding of the full landscape of mutational processes operative in MM, especially during their evolution over time. MATERIAL AND METHODS: DNA from bone marrow CD138+ cells underwent WGS along with a matched normal sample using HiSeq X Ten machines (Illumina, Inc.). Mutational signature extraction was performed running non-negative matrix factorization (NMF) as previously described (Alexandrov et al, Nature 2013). RESULTS: We have observed and utilized a median number of 5780 (range 2599-7760) substitutions per patient at the asymptomatic stage and 5954 (ranges 2824-8227) at progression to MM stage to extract mutational signatures. NMF extracted 5 main signatures (http://cancer.sanger.ac.uk/cosmic/signatures). Specifically, APOBEC- (signature #2) and age-related signatures (signatures #1 and #5) accounted for 13% (1-21%) and 23% (3.2-40%) of all substitutions, respectively. In addition, we found two known signatures that were not implicated in MM so far: non-canonical AID (Signature #9), contributing to 28% of all substitutions (17-55%); and signature #8, accounting for 28% of all substitutions (13-45%) and pertaining to a yet unknown mutational process. Finally, the fifth signature did not match any of the previously described ones, representing a potential novel process which we defined as MM-1 (7%, range (1-16%). Interestingly, we found a differential contribution of processes in non-coding and intronic regions where AID was more prevalent, while exonic regions where APOBEC and age signatures were more prevalent. In intronic regions we found widespread regions of kataegis (9/11 patients), reflective of localized hypermutation. In our patients, kataegis was associated with rearrangements in 60% of cases, and was present in both the SMM and MM sample in 84% of cases, suggestive of an early event during tumor development. Contrary to what is observed in solid cancers, APOBEC signature was only responsible for 25% of kataegis variants, vs 70% for AID, suggesting a causative role of aberrant AID activity in shaping the early mutational repertoire of neoplastic plasma cells. To confirm this, we looked at serial samples in our cohort. While the percent contribution of each signature varied in each patient, confirming genomic heterogeneity of MM, it did not change when paired SMM and MM samples from the same patient were compared. This shows that mutational processes required for the development of symptomatic MM act early, and have been already operative at the SMM stage. However, by clustering substitutions as clonal (early variants present at the time of tumor initiation) or subclonal (late variants arisen closer to the time of sampling) using a Bayesian hierarchical Dirichlet process (Bolli et al, Nature Comms 2014), we could analyze processes operative before SMM was diagnosed. NMF analysis of these clusters reported striking differences. Specifically, AID and age were the predominant mutational processes in early substitutions in all patients, contributing to a median of 35% (25-54%) and 30% (15-43%) of variants respectively. Conversely the contribution of AID was minimal among late substitutions (5%, 1-22%), where instead APOBEC, Signature #8 and MM-1 activity was prominent [19% (1-43), 38% (8-73%), 16% (2-50%) respectively]. CONCLUSION: WGS data allowed the identification of mutational processes operative well before MM becomes clinically evident. Our observation that all samples have signs of aberrant AID at the time of tumor initiation supports a unifying model where MM precursors are initially transformed with the contribution of AID, providing a fertile ground for other later processes (i.e APOBEC and signature #8) to act and shape the final genomic landscape of overt multiple myeloma. Disclosures No relevant conflicts of interest to declare.

Description: Multiple myeloma (MM) is a complex hematological malignancy characterized by gene pathway deregulations. Initial sequencing approaches have failed to identify any single frequent (〉25%) mutation in the coding genome. We, therefore performed a deep (average coverage 〉 80X) whole genome sequencing (WGS) on 260 MM samples (208 newly diagnosed and 52 first relapse after uniform treatment) to comprehensively identify recurrent somatic alterations in non-coding regions. We have identified the most frequently involved genes affected by perturbation in neighboring non-coding region and integrate their expression using our matching deep RNA-seq data from the same patients. One of the most prominent examples is mutations in the 5' untranslated region and intron 1 of the BCL7A gene in 76% of myeloma patients. Integration of WGS with RNA-seq data confirmed significant downregulation of its expression (p values 〈 1e-5) in the MM cells as compared to normal plasma cells (PC). This led us to investigate the consequences of BCL-7A loss in MM. To evaluate the role of BCL7A in MM, using gain of- (GOF) and loss-of-function (LOF) approaches, we have utilized a large panel of MM cell lines with differential expression of BCL7A at the RNA and protein levels. Ectopic expression of BCL7A in a panel of 3 MM cell lines with low basal levels of BCL7a significantly reduced cell viability and colony formation over time. Inhibition of cell viability was associated with induction of apoptotic cell death in the BCL7A overexpressing cells compared to control cells. LOF studies in 3 MM cell lines with relatively higher expression of BCL7a using 3 BCL7A-specific shRNA constructs showed a more proliferative phenotype, with increased growth and viability and enhanced colony formation. The effects of BCL7A loss in MM cells were further confirmed using CRISPR-Cas9 system. BCL7a-KO cells had higher proliferative rate compared to WT cells and add back of lentiviral BCL7a plasmid reversed this effect. BCL7A is part of the SWI/SNF chromatin remodeling complex. Mutations in the genes encoding m-SWI/SNF subunits are found in more than 20% of human cancers, with subunit- and complex-specific functions. We confirmed that when expressed, BCL7A interacts with BCL11A into the SWI/SNF complex in MM cells. Comparative, mass spectrometry analysis in fact revealed SMARCC2 (BAF170), an integral subunit of SWI/SNF complex, to bind with BCL7A-BCL11A complex. However, BCL7A loss causes decreased SMARCC2 incorporation into SWI/SNF, thus suggesting that presence of BCL7A is crucial in the formation of SWI/SNF complex in MM cells and might play an important role in chromatin remodeling. Interestingly, oncogenes DEK (DNA binding oncogene) and TPD52 (tumor protein D52) involved in cancer cell proliferation and chromatin remodeling formed complex with BCL11A in BCL7A KO MM cells. Additionally, several anti-apoptotic proteins such as ANXA-1 and BCL2 are in complex with BCL11A when BCL7A is lost, suggesting the formation of an anti-apoptotic complex with consequences on MM cell survival. Currently ongoing studies are investigating the molecular mechanism of non-coding mutations impacting BCL7A expression and pathways affected by its downregulation with impact on MM cell growth and survival. In conclusion, we report biological consequences of a frequent (〉75% patients) non-coding mutation in MM with cellular and molecular effects of BCL7A loss in which implicates a functional role of the m-SWI/SNF complex in driving a MM cell proliferative phenotype. Disclosures Anderson: Gilead Sciences: Other: Advisory Board; Janssen: Other: Advisory Board; Sanofi-Aventis: Other: Advisory Board; C4 Therapeutics: Other: Scientific founder ; OncoPep: Other: Scientific founder . Munshi:Abbvie: Consultancy; Abbvie: Consultancy; Amgen: Consultancy; Amgen: Consultancy; Adaptive: Consultancy; Adaptive: Consultancy; Celgene: Consultancy; Janssen: Consultancy; Janssen: Consultancy; Takeda: Consultancy; Takeda: Consultancy; Oncopep: Consultancy; Oncopep: Consultancy; Celgene: Consultancy.

Description: Dysregulated translational control and high protein turnover is a feature of multiple myeloma (MM) cells; as a result, proteasome inhibitors (PI), triggering a misfolded protein stress and death response, have been extremely successfully in MM therapy. But despite success of PIs and other novel therapeutic approaches, majority of patients progress; thus, investigating the mechanisms driving the drug sensitivity and/or resistance is important. We here report a novel chaperone protein 14-3-3ε with significant impact on MM cell pathobiology and patient outcome. 14-3-3 proteins are a family of master regulators of intracellular signaling that influence several cellular processes through binding to specific serine/threonine-phosphorylated residues on a diverse array of cellular proteins. With known interaction of 14-3-3 proteins with several functionally diverse molecules and well recognized chaperon function, we sought to evaluate their role in impacting proteasome activity. We compared the sensitivity of 14 MM cell lines to two proteasome inhibitors, Bortezomib (BTZ) and Carfilzomib (CFZ) with expression of all 14-3-3 proteins at both mRNA and protein levels. We compared the measured drug activity and individual 14-3-3 gene expression across all cell lines by Pearson correlation coefficients and observed that the expression level of only YWHAE (coding gene for the isoform 14-3-3ε) showed a significant negative correlation with both BTZ and CFZ response. We therefore evaluated its expression in primary MM cells and found its lower expression to be associated with poor outcome in MM patients receiving a bortezomib (Btz)-based therapy. To elucidate the underlying molecular mechanism responsible for 14-3-3ε contribution to PIs sensitivity, we performed integrated analysis of protein interactome and transcriptomic changes following 14-3-3ε gene modulation. These studies showed that 14-3-3ε impacts mTORC1 signaling in MM cells by binding to serine-phosphorylated residues on mTOR and its upstream negative regulator TSC2, resulting in mTORC1 activation. Conversely, depletion of 14-3-3ε inhibits TSC2 phosphorylation, causing a subsequent inhibition of mTORC1 signaling. One major conserved function of mTORC1 is to promote mRNA translation and therefore protein synthesis via activation of S6 kinase 1 (S6K1) as well as inhibition of the eukaryotic initiation factor 4E (eIF4E) binding protein (4E-BP). We have therefore assessed the impact of 14-3-3ε on translational efficiency in MM cells. In the viable MM cell population, 14-3-3ε depletion caused up to 50% reduction of protein synthesis in three MM cell lines, whereas 14-3-3ε overexpression in the KMS20 cell line or addback in YWHAE-KO cells (H929 and KMS11) resulted in a marked upregulation of protein synthesis. As MM is characterized by excess production of monoclonal immunoglobulins, we evaluated impact of 14-3-3ε perturbation on intracellular and secretion light chains production. We observed a significant decrease in the intracellular abundance and secretion of the light chains with 14-3-3ε KD in all MM cell lines tested. These observations were corroborated by gain-of-function studies where ectopic overexpression of 14-3-3ε in MM cells was associated with increased protein load (and an enhanced sensitivity to PIs) in vitro as well as in vivo. Importantly, we confirmed a significant correlation between 14-3-3ε expression, PIs sensitivity and protein load (evaluated as M protein production) in primary MM cells from two independent datasets. Moreover, MM patients with del17p, where 14-3-3ε is located, have lower 14-3-3ε expression and decreased monoclonal protein level, providing an explanation for inability of BTZ to overcome high-risk feature associated with del17p. In conclusion, we here report for the first time a unique function for 14-3-3ε in modulating the sensitivity to PIs through regulation of protein synthesis and M protein load in MM cells. Altogether these observations suggest that 14-3-3ε is a predictor of clinical outcome and may serve as a potential target to modulate PIs sensitivity in MM. Disclosures Anderson: Sanofi-Aventis: Other: Advisory Board; OncoPep: Other: Scientific founder ; C4 Therapeutics: Other: Scientific founder ; Janssen: Other: Advisory Board; Gilead Sciences: Other: Advisory Board. Munshi:Takeda: Consultancy; Takeda: Consultancy; Oncopep: Consultancy; Abbvie: Consultancy; Abbvie: Consultancy; Adaptive: Consultancy; Amgen: Consultancy; Amgen: Consultancy; Celgene: Consultancy; Oncopep: Consultancy; Adaptive: Consultancy; Janssen: Consultancy; Celgene: Consultancy; Janssen: Consultancy.

Description: Uncontrolled proliferation is a hallmark of tumorigenesis and is associated with perturbed transcriptional profiles. The proliferative program in Multiple myeloma (MM), a complex disease with heterogeneous genetic changes, is controlled by transcription factors (TFs) and chromatin-associated factors. The dependency on these transcriptional regulators, leading to the dysregulated proliferation, is not predicted by genetic changes, making the tumor cells more sensitive to inhibition of these regulators than normal cells.The relationship between promoter proximal transcription factor-associated gene expression and super-enhancer-driven transcriptional programs is not well-defined. However, their distinct genomic occupancy suggests a mechanism for specific and separable gene control. Our genome-wide epigenomic profile in myeloma has identified the existence of two non-overlapping regulatory axes controlled by promoter and enhancer-driven processes, governing distinct biological functions. We have utilized E2F1 as promoter proximal transcription factor, and evaluated its transcriptional and functional interrelationship with enhancer-associated factors, such as BET bromodomain transcriptional co-activators. We identified that the transcription factor E2F1 and its heterodimerization partner DP1 represent a dependency in MM cells. Global chromatin analysis revealed two distinct regulatory axes, with E2F and MYC predominantly localized to active gene promoters of growth/proliferation genes and CDK9 and BETs disproportionately at enhancer-regulated tissue-specific genes. This divergent BRD4 enhancer and E2F promoter axes is also observed in diffuse large B-cell lymphoma, suggesting a more broader transcriptome control process. Dual inhibition of E2F and BETs displays a superior activity against MM cell growth and viability, both in vitro and in vivo, compared to single perturbation alone providing an important molecular mechanism for combination therapy. Moreover, at low doses of BRD4 inhibitor JQ1, the addition of E2F1 depletion down-regulates the promoter controlled proliferation gene expression axis. As for many TFs, direct pharmacologic inhibition of E2F remains a difficult challenge in drug discovery. However, E2F is not entirely "undruggable" as inhibitors of upstream regulators of the pRB-E2F axis are available. For example, a number of Cyclin dependent kinases (CDK) 4/6 inhibitors, including Palbociclib are now being investigated in clinical trials in in fact approved by the FDA in select malignancies. CDKs are serine threonine kinases that modulate cell cycle progression. CDK4 and CDK6 together with D-type cyclins and cyclin E/CDK2 complexes control the commitment to cell cycle entry from quiescence and the G1 phase. These kinase complexes can phosphorylate RB, releasing E2F to modulate the expression of E2F target genes that are required for S phase entry. We investigated combination of low doses of JQ1 and Palbociclib and observed a profound effect on E2F promoter driven transcriptional activity, and was highly synergistic with JQ1 in a large panel of MM cell lines and primary MM cells from newly diagnosed and relapsed patients. Cell cycle analysis revealed complete G1 arrest after treatment. Importantly, the combination regimen was not effective in healthy donor PBMCs activated with PHA, suggesting a favorable therapeutic index. Transcriptomic changes to assess the impact on promoter and SE-driven processes are ongoing and will be presented. In conclusion, these data implicates the existence of a sequestered cellular functional control that may be perturbed in cancer to maintain the tumor cell state. Simultaneous targeting of non-overlapping promoter and enhancer vulnerabilities impairs the myeloma proliferative program, with potential for development of a promising therapeutic strategy in MM and other malignancies. Disclosures Young: Omega Therapeutics: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Syros Pharmaceuticals: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Camp4 Therapeutics: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees. Anderson:Bristol Myers Squibb: Consultancy; C4 Therapeutics: Equity Ownership, Other: Scientific founder; Celgene: Consultancy; Millennium Takeda: Consultancy; Gilead: Membership on an entity's Board of Directors or advisory committees; OncoPep: Equity Ownership, Other: Scientific founder. Munshi:OncoPep: Other: Board of director.

Description: Somatic alterations including single nucleotide variants (SNVs), copy number alterations (CNAs) and structural variants (SVs) are an important component and the hallmark of Multiple Myeloma (MM) with certain alterations having clinical implications. Recently, the chronological order of such events was explained in detailed studies however previous study has compared the frequency and clonality of such events in early stage plasma cell disorder (MGUS or SMM) and their comparison with MM.Here we performed whole genome (WGS) and RNA sequencing (RNAseq) on 67 samples (8 Unique paired samples from patients with MGUS and when progressed to MM, 10 paired samples at SMM stage and then progressed to MM, as well as non-progressor SMM (NP-SMM) patients who have not progressed after at least 5 years of follow-up. In addition, we profiled CNAs and their clonality level in 164 MGUS, 147 SMM and 336 newly diagnosed MM patients to construct the clonal structure and frequency of somatic alterations.We did not observe significant difference in overall frequency of mutations at MGUS (median=5662 SNVs, IQR= [5252 - 7864]) and SMM stage (median=5308 SNVs, IQR=[4236 - 6125] ) and at progression to MM (median= 5983 SNVs, IQR=[5097 - 8916]). Overall mutational load increased from precursor stage to MM by only 5% with no recurrent change and the difference was not statistically significant (p 〉 0.05). Similar trend was also observed for SVs [median=36, IQR= [25.25 -40.75] at MGUS, median=34, IQR= [12-52] at SMM, median=27, IQR= [27-41] at MM]. In fact, some of the samples had lower SNV and SV load in MM compared to precursor stages even though that had increased cancer cell fraction. Copy number analysis on paired samples also showed 〉90% similarity only with few non-recurrent focal CNAs. We have compared WGS data from non-progressor SMM with progressor SMM and newly-diagnosed MM. The non-progressor SMM patients showed identical CNAs and not significantly different Ig translocation frequencies to both other groups. Except for NRAS mutations, mutation frequency in NP-SMM was similar to others. Finally, by using data from 647 patients at three stages (MGUS, SMM and MM), we compared the frequency of CNAs at each time point. Similar to MM, we observed almost equal frequency of hyperdiploid and non-hyperdiploid SMM cases. In hyperdiploid SMM, clonal copy number gain was observed in 95% of patients involving two of the three chromosomes 9, 15 and 19. Moreover, a similar pattern was observed in other hyperdiploid chromosomes including chromosomes 3,5,7,11 and 21. The observed event frequency and clonality levels in SMM were identical to one observed in MM as well as MGUS. Non-hyperdiploid SMM group had early and clonal events targeting chromosome 13 deletion with gain of 1q, 11 and/or 9 at the same frequency level as in MM. The only significant difference was observed in subclonal deletions targeting some of the infrequent deletion events observed in HMM and NHMM. In conclusion, our data from longitudinal analysis of paired precursor and symptomatic MM samples as well as cross sectional data highlight lack of significant differences in genomic changes between precursor conditions and symptomatic myeloma. This lack of progressive and unique genomic change suggests the need for additional transcriptomic, epigenomic or tumor micro environment changes to accelerate the tumor development. Disclosures Bolli: Celgene: Honoraria; Gilead: Other: travel expenses; Novartis: Honoraria. Moreau:Amgen: Consultancy, Honoraria; Takeda: Consultancy, Honoraria; AbbVie: Consultancy, Honoraria; Celgene: Consultancy, Honoraria; Janssen: Consultancy, Honoraria. Anderson:Sanofi-Aventis: Other: Advisory Board; Bristol-Myers Squibb: Other: Scientific Founder; Oncopep: Other: Scientific Founder; Janssen: Consultancy, Speakers Bureau; Takeda: Consultancy, Speakers Bureau; Celgene: Consultancy, Speakers Bureau; Amgen: Consultancy, Speakers Bureau. Munshi:Celgene: Consultancy; Oncopep: Consultancy; Janssen: Consultancy; Takeda: Consultancy; Amgen: Consultancy; Adaptive: Consultancy; Abbvie: Consultancy.

Description: The APOBEC family of cytidine deaminases include AID (activity induced deaminase) and 10 related APOBEC enzymes (A1,A2,A3A,A3B,A3C,A3D,A3F,A3G,A3H and A4). AID is well studied for its role in somatic hyper mutation and class switch recombination of immunoglobulin genes. APOBECs (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like) have been shown to have roles in mRNA editing and in antiviral immunity. Recently, a causal role for the AID/APOBECs in inducing somatic mutations in myeloma has been proposed and we have previously published that APOBEC signature mutations as a frequent event in Myeloma. We have also observed that APOBEC-mediated mutations may account for mutations associated with progression of smoldering myeloma to MM. We further investigated the role of APOBEC in genomic changes in MM and observed that APOBEC expression and activity is elevated in myeloma cell lines as well as patient samples. Using knockdown and over expression approaches, we showed that depletion of APOBECs in myeloma cell lines reduces genomic instability. Following APOBEC3G knock down we observed decreased DNA damage (by g-H2AX), decrease in acquisition of new copy number events over time, and reduced mutational load, strongly suggesting that inhibiting APOBECs could be a potential approach to reduce genome evolution in MM. We next investigated the effect of APOBEC inhibition on myeloma cell proliferation. We observed that Sh-RNA-based APOBEC knock down in MM1S and H929 MM cell lines, led to significant inhibition of MM cell proliferation, and induction of apoptotic cell death. Associated with APOBEC knockdown, we also observed increased levels of Cyclin-dependent kinase inhibitor 1B (p27Kip1) at both RNA and protein level. By immunoprecipitation we found that APOBEC3G interacts and inhibits the RNA binding protein DEAD-END 1 (DND1), thereby preventing it from inhibiting miR-221-mediated targeting of p27 transcripts. Knockdown of DND1, or over-expression of miR-221 in APOBEC-depleted cells rescued the cell proliferation defects with concomitant decrease in p27 levels. These results show that APOBCs bind to and sequester DND1, leading to miR-221-mediated depletion of p27. In the absence of APOBEC, DND1 prevents the degradation of p27 mRNA, leading to elevated p27 levels and inhibition of cell cycle, suggesting a role for APOBECs in regulating MM cell proliferation that might be independent of its RNA/DNA mutator function. Taken together, these results indicate a significant functional role for APOBECs both in genome evolution as well as cell growth in myeloma and may constitute an important therapeutic target. Disclosures Munshi: OncoPep: Other: Board of director.

Description: Bidirectional interaction between MM cells and accessory cells regulates tumor development on the one hand, while transforming the BM microenvironment into a tumor promoting and immune suppressive milieu on the other. Recent developments in targeted therapies have indicated that generation of the most effective therapeutic strategies requires not only targeting tumor or stroma, but also methods to overcome blockade of anti-tumor immune responses. Tumor associated immune suppressor cells such as Treg and myeloid derived suppressor cells (MDSC) can effectively block anti-tumor immune responses, thereby representing an important obstacle for immunotherapy. Co-inhibitory molecules programmed cell death-1 (PD-1) and its ligand (PD-L1) play a fundamental role in tumor immune escape by inhibiting immune effector functions. Since PD-1/PD-L1 signaling promotes tumor growth while inhibiting effector cell mediated anti-tumor immune responses, we here assessed the impact of PD-1/PD-L1 blockade, alone or in combination with lenalidomide (Len), on accessory and immune cells function, as well as tumor cell growth of MM in the BM milieu. Methods: PD-L1 gene expression was determined in IFM MM data set (n=170). Cell surface expression of PD-L1 in CD138+ MM cells, stroma, and MDSCs; as well as PD-1 expression on effector cells (CD4T, CD8T, NK, NKT and monocytes/macrophages) were determined in the bone marrow (BM) and peripheral blood (PB) of patients with MGUS (n=3), newly diagnosed (ND-MM, n=5) and relapsed/refractory (RR-MM, n=11) compared to healthy donors (HD, n=10). PD-1/PD-L1 signaling was assessed in the autologous cocultures of patient MM cells or MM cell lines with stroma (BMSC) or MDSCs and effector cells, in the presence or absence of PD-1/PD-L1 blockade and Len. Len effect on PD-1 expression on effector cells and PD-L1 expression on tumor, BMSC and MDSCs was determined by flow cytometry analysis. BMSC and MDSC induced MM growth/viability was measured by MTT, 3H-Thy and CFSE flow cytometry analysis. Effector cell-mediated MM cytotoxicity was measured by CFSE/PI flow cytometry. The effect of PD-1/PD-L1 blockade with or without Len on cytokine pattern was determined by intracellular cytokine flow cytometry analysis. Results: Statistical analysis of IFM MM data demonstrated that the majority of patient MM cells have increased PD-L1 mRNA compared to HD (p=0.0064). Cell surface expression of PD-L1 was also significantly increased in ND-MM cells (median 65%) and even higher in RR-MM cells. Correspondingly, there was a significant increase in PD-1 expression on CD8T and NK cells in ND-MM and RR-MM. Moreover, PD-L1 expression was significantly higher on both mMDSC and nMDSC than APCs in ND-MM and RR-MM. Coculture with BMSC significantly increased expression of PD-L1 on MM cells. PD-1/ PD-L1 blockade overcame BMSC-induced tumor cell growth in both patient MM cells and MM cell lines. Importantly, Len significantly reduced PD-L1 expression on MM cells; and combined blockade of PD-1/PD-L1 with Len further decreased BMSC-induced MM growth. Immunomodulatory effects of PD-1/PD-L1 blockade were also evaluated in autologous cocultures of immune effector cells with MM cells. Even though there was no change in effector cell proliferation, PD-1/PD-L1 blockade significantly induced cytotoxic activity of autologous T cells, NK cells, and macrophages cultured with MM cells; and Len further enhanced effector cell-mediated cytotoxicity. PD-1/PD-L1 blockade induced intracellular expression of cytotoxic cytokines IFNg and Granzyme B (Gzm B) in CD4T cells, CD8T cells, NK cells and Macrophages. Furthermore, MDSC-mediated MM growth was significantly decreased by PD-1/ PD-L1 blockade. Finally, PD-1/PD-L1 blockade induced intracellular expression of IFNg and Gzm B in T cells, NK cells and NKT cells cultured with autologous MDSC; and Len further enhanced this effector cell activation. Conclusion: Our data demonstrated that immune checkpoint signaling plays an important role in providing the tumor promoting, immune suppressive microenvironment in MM. Blockade of PD-1/PD-L1 signaling induces anti-MM immune responses that can be enhanced by Len. Targeting checkpoint signaling using PD-1 and PD-L1 blocking antibodies, particularly in combination with Len, therefore represents a promising novel immune-based therapeutic strategy to both inhibit tumor cell growth and restore host immune function in MM. Disclosures Kikuchi: The ITO Foundation for the Promotion of Medical Science: Research Funding. Hideshima:Acetylon Pharmaceuticals: Consultancy. Raje:novartis, Amgen, Celgene, Millenium, Onyx: Consultancy; Eli Lilly, Acetylon: Research Funding. Anderson:Celgene: Consultancy; Onyx: Consultancy; Gilead Sciences: Consultancy; Sanofi-Aventis US: Consultancy; Acetylon: Scientific Founder Other; Oncoprep: Scientific Founder Other.

Description: Genomic instability is a hallmark of several types of solid and hematologic malignancies, including multiple myeloma (MM). Although structural and numerical chromosomal abnormalities are common features of MM cells, the underlying molecular basis of MM genomic instability is still largely unknown. To this aim, we have investigated the activity of non-homologous end joining (NHEJ), which represents the most important mechanism of double-strand breaks (DSBs) repair, in MM cells. First, we developed and validated a dual gene plasmid-based assay utilizing Luciferase (LUC) as a test gene which measures end joining, and Alkaline Phosphatase (SEAP) as a reporter gene to control for transfection efficiency, in either intact cells (in vivo assay) or in cell free extracts (in vitro assay). The first one is a chemiluminescent assay which allows for direct measurement of LUC and SEAP in the supernatant of the cells 24h after electroporation with the plasmid, while the cell free extract method is a customized TaqMan® approach based on a quantitative evaluation of the plasmid rejoining. Both assays revealed a significant increase in NHEJ in all 6 MM cell lines tested compared to normal peripheral blood mononuclear cells (PB-ND) and bone marrow stromal cells (BMSC). We further confirmed the hyper-activation of the NEHJ pathway by analyzing the binding activity of ku86, a key NHEJ-related protein involved in the recognition of the broken DNA ends and in the initiation of the DSBs repair process. Six out of 9 MM cell lines showed a significant increase in ku86-binding activity respect to normal cells. We also found a higher phosphorylation at Ser 2056 of DNA-PK, a ku86-partner whitch plays a key role in NHEJ. Next, we evaluated the NHEJ activity in 35 patient samples using the cell free assay. Interestingly, level of NHEJ activity divided patients into two different groups: one with an NHEJ activity similar to normal cells and the other to the MM cell lines. Preliminary correlation analysis between NHEJ activity and the clinical features of the patients indicated that the MGUS and Smoldering MM subgroup fall into the normal cluster while relapsed/refractory disease to the cell lines one. Finally, using the French (IFM) and the Arkansas (GSE2658) dataset, we demonstrate a significant association between NHEJ pathway-related gene expression and overall survival by the Globaltest analysis. We were also able to find a common NHEJ signature of 6 genes whose expression significantly correlates with patient survival in both the datasets. In conclusion, our data indicate an aberrant activation of NHEJ in MM, highlighting its role in the progression of the disease and suggesting this pathway as an important new prognostic marker in myeloma. Disclosures: No relevant conflicts of interest to declare.

Description: Transcriptome modifiers such as alternative pre-mRNA splicing (AS), long non-coding RNA and microRNA (miRNA) need to be considered in order to provide a more accurate genomic framework for clinical correlation, as well as for high value therapeutic target discovery. Aberrant splicing of numerous genes has been reported in other malignancies, including a small number of genes reported in MM. We have evaluated AS in MM by analyzing clinically annotated high throughput RNA-seq data from 410 newly-diagnosed patients and 18 normal donor plasma cells. We observed a profound and significant AS in MM with over 600 genes showing significant changes in relative isoform abundances (isoform switching) between MM and normal samples. Importantly, unsupervised analysis identified clinically relevant MM subgroups with high and low splicing index respectively and showed significant impact of alternate splicing on overall clinical outcome. Based on these data, we next focused on understanding the molecular mechanisms driving aberrant alternate splicing in myeloma. Several studies provide evidence that an abnormally expressed splicing factor (SF) can have oncogenic properties by impacting alternative splicing of cancer-associated genes. We detected dysregulated expression of several SFs, including SF3B1, Fox2, SRSF1, NONO, in patients with MM compared to normal plasma cells with impact on outcome, highlighting for the first time the prognostic significance of splicing related factors in myeloma. We further observed that overexpression of some of these SFs increased cell proliferation, enhanced anchorage independent growth in semi-solid medium, and affected tumorigenic potential. We have further investigated role of Serine/Arginine Splicing Factor 1 (SRSF1) in MM by gain of- and loss of- function studies. Enforced expression of SRSF1 in MM cells significantly increased proliferation, especially in the presence of bone marrow stromal cells. Conversely, transient or stable downregulation of SRSF1 with specific siRNA and shRNAs respectively, significantly inhibited MM cell proliferation and cell survival. We have also investigated a small molecular inhibitor of SRSF1 (TG003) and observed inhibition of MM cell growth and survival. The impact of this inhibitor on allelic isoforms of specific gene targets is undergoing. To dissect the mechanisms involved in the SRSF1-mediated MM growth induction, we used SRSF1 mutants lacking either of the two RNA-recognition motifs (ΔRRM1 or ΔRRM2 mutants) or the serine/argine-rich C-terminal domain (ΔRS mutant) involved in protein-protein interactions, subcellular localization, and recruitment of spliceosome components. We also used a C-terminal fusion of SRSF1 with the nuclear-retention signal of SRSF2 (NRS1 mutant), to force SRSF1 retention in the nucleus and assess the role of its nuclear versus cytoplasmic functions. We surprisingly found that only NRS1 mutant failed to promote MM growth, suggesting an important role of cytoplasmic SRSF1 in promoting MM cells proliferation. Finally, using genome wide chromatin and transcription landscape mapping techniques, we have found SRSF1 to be under the transcriptional control of E2F1, a transcription factor with significant impact on MM cell growth and survival. A significant reduction in SRSF1 at mRNA and protein levels was observed after E2F1 and/or E2F1 heterodimerization partner Dp1 gene silencing. Moreover, peptide-based strategy to abrogate interaction between Dp1-E2F1 led to decreased SRSF1 expression levels. These results indicate a functional role and clinical significance of a gene involved in regulation of alternate splicing in MM. The study highlights the need to further understand the splicing pattern in myeloma and also supports the emerging concept that splicing programs, together with transcriptional programs participate in the altered cellular function during tumor initiation and progression. Disclosures Munshi: onyx: Membership on an entity's Board of Directors or advisory committees; celgene: Membership on an entity's Board of Directors or advisory committees; millenium: Membership on an entity's Board of Directors or advisory committees; novartis: Membership on an entity's Board of Directors or advisory committees.

Description: Alternative splicing is an important post-translational change that alters gene function. Misregulation of alternative splicing has been implicated in number of disease processes including cancer. Here we have analyzed alternative splicing in myeloma using high throughput RNA-seq. Our analytic pipeline for RNA-seq data used in this investigation not only provides information on expression levels for genes, but also provides information on the expression of known splice variants of genes (isoforms), and can identify novel exon level events across individuals (i.e. exon skipping events). We conducted a study of 328 newly-diagnosed patients with multiple myeloma treated homogeneously with novel agent combination containting lenalidomide, bortezomib and dexamethsone with or without high-dose melphalan followed by lenalidomide maintenance in the IFM/DFCI study. RNA isolated from purified CD138+ MM cells collected at the time of diagnosis and from 18 normal donor plasma cells were processed by RNA-seq (100 million paired end reads on Illumina HiSeq) and analyzed using a custom computational and statistical pipeline. Following read alignment to hg19, we utilized RSEM to quantify both gene-level and isoform-level expression of known ENSEMBL transcripts. We then implemented a novel testing approach based on compositional regression to discover genes that show significant isoform switching between the 328 MM samples and 18 Normal Plasma Cell (NPC) samples from healthy donors. Using various programs and their modifications, we also identified novel alternative splicing events, such as exon skipping and mutually exclusive exon usage, among others. Patient data for MM characteristics, cytogenetic and FISH as well as clinical survival outcomes were also analyzed and correlated with genomic data. We observed over 600 genes showing significant changes in relative isoform abundances (isoform switching) between MM and normal samples. A number of previously characterized genes including MYCL1 (adj. p = 0.0014) and CCND3 (adj. p = 0.0013), and MAP kinase-related genes (MAP3K8, MAPKAPK2, MAPKAPK3, MAP4K4) exhibited significant isoform switching compared to normal, in addition to some not well characterized genes. Genes showing the greatest magnitude of isoform switching include MEFV (adj. p = 2.7 x 10-5), showing a two fold change in the relative major isoform abundance compared to normal, and has been previously shown to have a role in lymphoid neoplasms. We applied hierarchical clustering to the isoforms showing significant changes in isoform-switching and identified 4 distinct clusters, which are currently being investigated for correlation with clinical subtypes of MM. Exon level analyses of alternative splicing events, such as exon skipping, are currently underway. Clinical data including MM characteristics, cytogenetics, FISH and survival outcomes was available for a subset of 265 patients. We found that 109 genes showed significant isoform switching between t(4;14) and non-t(4;14) patients, such as CD44 (adj. p =1.8 x 10-6) and WHSC1 (adj. p =5.1 x 10-28). Comparing del17p (28 in total) and non del17p patients, we found no significant splicing changes after multiple testing adjustment. Of these genes, only a subset (40%) were shown to be differentially expressed in terms of total gene expression, suggesting the importance of examining alternative splicing events in addition to total gene expression. With respect to treatment response, we compared the expression of gene isoforms between patients achieving complete response (CR) versus others and identified 38 isoforms associated with response to treatment (adj. p value 〈 0.05), with SEPT9, SLC2A5, and UBX6 having the strongest associations (adj. p-value 〈 3 x 10-4). Using a univariate cox regression model, 4 spliced isoforms relating to 3 genes were identified as having significant correlation with event-free survival (EFS) (FDR-adjusted cox p value 〈 0.05). We are in the process of now integrating the gene expression data with altered splicing data to develop an integrated survival model. In summary, this study highlights the significant frequency, biological and clinical importance of alternative splicing in MM and points to the need for evaluation of not only the expression level of genes but also post-translational modifications. The genes identified here are important targets for therapy as well as possible immune modulation. Disclosures Moreau: Celgene Corporation: Honoraria, Membership on an entity's Board of Directors or advisory committees.