Search

PDF file - 116K

The NEDD8-activating enzyme is upstream of the 20S proteasome in the ubiquitin/proteasome pathway and catalyzes the first step in the neddylation pathway. NEDD8 modification of cullins is required for ubiquitination of cullin-ring ligases that regulate degradation of a distinct subset of proteins. The more targeted impact of NEDD8-activating enzyme on protein degradation prompted us to study MLN4924, an investigational NEDD8-activating enzyme inhibitor, in preclinical multiple myeloma models. In vitro treatment with MLN4924 led to dose-dependent decrease of viability (EC50 = 25–150 nmol/L) in a panel of human multiple myeloma cell lines. MLN4924 was similarly active against a bortezomib-resistant ANBL-6 subline and its bortezomib-sensitive parental cells. MLN4924 had submicromolar activity (EC50 values + multiple myeloma patient cells and exhibited at least additive effect when combined with dexamethasone, doxorubicin, and bortezomib against MM.1S cells. The bortezomib-induced compensatory upregulation of transcripts for ubiquitin/proteasome was not observed with MLN4924 treatment, suggesting distinct functional roles of NEDD8-activating enzyme versus 20S proteasome. MLN4924 was well tolerated at doses up to 60 mg/kg 2× daily and significantly reduced tumor burden in both a subcutaneous and an orthotopic mouse model of multiple myeloma. These studies provide the framework for the clinical investigation of MLN4924 in multiple myeloma. Mol Cancer Ther; 11(4); 942–51. ©2012 AACR.

Supplementary Data from Interactions of the Hdm2/p53 and Proteasome Pathways May Enhance the Antitumor Activity of Bortezomib

Purpose: p53 is inactivated in many human malignancies through missense mutations or overexpression of the human homologue of Mdm2 (Hdm2), an E3 ubiquitin ligase that ubiquitinates p53, thereby promoting its proteasomal degradation. The cis-imidazoline nutlin-3 can disrupt the p53-Hdm2 interaction and activate p53, inducing apoptosis in vitro in many malignancies, including multiple myeloma (MM).Experimental Design: We hypothesized that suppression of Hdm2-mediated p53 ubiquitination may augment sequelae of p53 accumulation caused by proteasomal inhibition. We compared the response of MM cells versus several epithelial cancer models to the proteasome inhibitor bortezomib in combination with nutlin-3.Results: The combination of sublethal concentrations of bortezomib plus nutlin-3 induced additive cytotoxicity against bortezomib-sensitive MM cell lines. Importantly, however, in breast, prostate, colon, and thyroid (papillary, follicular, anaplastic, and medullary) carcinoma cell lines, this combination triggered synergistic cytotoxicity, and increased expression of p53, p21, Hdm2, Bax, Noxa, PUMA, and cleavage of caspase-3 and poly ADP ribose polymerase. Coculture with bone marrow stromal cells attenuated MM cell sensitivity to nutlin-3 monotherapy and was associated with evidence of suppression of p53 activity in MM cells, whereas combined bortezomib-nutlin-3 treatment maintained cytotoxicity even in the presence of bone marrow stromal cells.Conclusions: This differential response of MM versus epithelial carcinomas to combination of nutlin-3 with bortezomib sheds new light on the role of p53 in bortezomib-induced apoptosis. Concurrent Hdm2 inhibition with bortezomib may extend the spectrum of bortezomib applications to malignancies with currently limited sensitivity to single-agent bortezomib or, in the future, to MM patients with decreased clinical responsiveness to bortezomib-based therapy. (Clin Cancer Res 2009;15(23):7153–60)

Background: In normal cells, homologous recombination (HR) is tightly regulated and plays an important role in the maintenance of genomic integrity and stability through precise repair of DNA damage. RAD51 is a recombinase that mediates homologous base pairing and strand exchange during DNA repair by HR. Our previous data in multiple myeloma and esophageal adenocarcinoma (EAC) show that dysregulated HR mediates genomic instability. Purpose of this study was to investigate role of HR in genomic instability, chemoresistance and immune dysregulation in solid tumors including colon and breast cancers. Methods: The GEO dataset were used to investigate correlation of RAD51 expression with patient survival and expression of various immune markers in EAC, breast and colorectal cancers. RAD51 was inhibited in cancer cell lines using shRNAs and a small molecule inhibitor. HR activity was evaluated using a plasmid-based assay, DNA breaks assessed by evaluating expression of γ-H2AX (a marker of DNA breaks) and p-RPA32 (a marker of DNA end resection) using Western blotting. Genomic instability was monitored by investigating micronuclei (a marker of genomic instability). Impact of RAD51 inhibitor and/or a DNA-damaging agent was assessed on viability and apoptosis in EAC, breast and colon cancer cell lines in vitro and in a subcutaneous tumor model of EAC. Impact of RAD51 inhibitor on expression profile was monitored by RNA sequencing. Results: Elevated RAD51 expression correlated with poor survival of EAC, breast and colon cancer patients. RAD51 knockdown in cancer cell lines inhibited DNA end resection and strand exchange activity (key steps in the initiation of HR) as well as spontaneous DNA breaks, whereas its overexpression increased DNA breaks and genomic instability. Treatment of EAC, colon and breast cancer cell lines with a small molecule inhibitor of RAD51 inhibited DNA breaking agent-induced DNA breaks and genomic instability. RAD51 inhibitor potentiated cytotoxicity of DNA breaking agent in all cancer cell types tested in vitro as well as in a subcutaneous model of EAC. Evaluation by RNA sequencing demonstrated that DNA repair and cell cycle related pathways were induced by DNA breaking agent whereas their induction either prevented or reversed by RAD51 inhibitor. In addition, immune-related pathways such as PD-1 and Interferon Signaling were also induced by DNA breaking agent whereas their induction prevented by RAD51 inhibitor. Consistent with these observations, elevated RAD51 expression also correlated with that of genes involved in inflammation and other immune surveillance. Conclusions: Elevated expression of RAD51 and associated HR activity is involved in spontaneous and DNA damaging agent-induced DNA breaks and genomic instability thus contributing to chemoresistance, immune dysregulation and poor prognosis in cancer. Therefore, inhibitors of RAD51 have great potential as therapeutic agents for EAC, colon, breast and probably other solid tumors.

Genomic instability contributes to cancer progression and is at least partly due to dysregulated homologous recombination. Here, we show that an elevated level of ABL1 kinase overactivates the HR pathway and causes genomic instability in multiple myeloma (MM) cells. Inhibiting ABL1 with either shRNA or a pharmacological inhibitor (nilotinib) inhibits HR activity, reduces genomic instability, and slows MM cell growth. Moreover, inhibiting ABL1 rescues the HR dysregulation and genomic instability caused by melphalan, a chemotherapeutic agent used in MM treatment, and increases melphalan’s efficacy and cytotoxicity in vivo in a subcutaneous tumor model. In these tumors, nilotinib inhibits endogenous as well as melphalan-induced HR activity. These data demonstrate that inhibiting ABL1 using the clinically approved drug nilotinib reduces MM cell growth, promotes genome stability, increases the cytotoxicity of melphalan (and similar chemotherapeutic agents), and can potentially prevent or delay progression in MM patients.

Genomic instability fuels genomic alterations that befit cancer cells with necessary adaptations to keep proliferating and overcome the impact of host anti-tumor immunity and cytotoxic therapy. Since DNA breaks are required for genomic rearrangements to take place, we hypothesized that dysregulated nuclease activity mediates genomic instability in cancer. Using an integrated genomics protocol, we identified a four gene deoxyribonuclease signature correlating with genomic instability in six human cancers which included adenocarcinomas of esophagus (EAC), lung, prostate, stomach, pancreas and triple negative breast cancer. Functional screens confirmed the role of these nucleases in genomic instability and growth of cancer cells. Apurinic/apyrimidinic nuclease 1 (APE1), identified as top nuclease in functional screen, was further investigated in five cell lines representing four solid tumors (EAC, lung, prostate and breast cancer). We demonstrate that chemical as well as transgenic suppression of APE1 impaired growth/colony formation and increased cytotoxicity of chemotherapeutic agent, whereas inhibited spontaneous as well as chemotherapy-induced DNA breaks, homologous recombination (HR) activity and genomic instability in all cancer cell types tested. Treatment with APE1 inhibitor also impaired tumor growth and significantly increased efficacy of a chemotherapeutic agent in a subcutaneous mouse model of EAC. Overexpression of APE1 in normal esophageal epithelial cells increased DNA breaks and HR activity, leading to massive mutational, copy number as well as karyotypic instability. Evaluation of by whole genome sequencing identified HR as the top mutational process activated by APE1. Normal cells overexpressing APE1 grew as tumors in mice and tumors removed from mice displayed additional karyotypic changes, providing evidence of genomic instability in vivo. Overall, our data demonstrate that elevated APE1 dysregulates HR activity, G2/M checkpoint and genome stability thus contributing to tumorigenesis and chemoresistance in cancer. Therefore, inhibitors of APE1 have potential to inhibit growth and increase cytotoxicity of chemotherapeutic agents while minimizing spontaneous as well as chemotherapy-induced genomic damage and instability in EAC and other solid tumors.

Esophageal adenocarcinoma (EAC) is associated with a marked genomic instability, which underlies disease progression and development of resistance to treatment. In this study, we used an integrated genomics approach to identify a genomic instability signature. Here we show that elevated expression of this signature correlates with poor survival in EAC as well as three other cancers. Knockout and overexpression screens establish the relevance of these genes to genomic instability. Indepth evaluation of three genes (TTK, TPX2 and RAD54B) confirms their role in genomic instability and tumor growth. Mutational signatures identified by whole genome sequencing and functional studies demonstrate that DNA damage and homologous recombination are common mechanisms of genomic instability induced by these genes. Our data suggest that the inhibitors of TTK and possibly other genes identified in this study have potential to inhibit/reduce growth and spontaneous as well as chemotherapy-induced genomic instability in EAC and possibly other cancers., Subodh Kumar et al. identify a gene signature correlated with genomic instability and poor survival in esophageal adenocarcinoma (EAC), using a combination of integrative genomic analysis of patient data and laboratory validation in cell line models and mice. They find that inhibitors of some of the identified proteins, including TTK, could be used to reduce genomic evolution as well as inhibit growth of EAC cells.

Background We have previously reported the identification of FEN1 a driver of genomic instability in myeloma (MM) as well as esophageal adenocarcinoma (EAC) cells. We demonstrated that FEN1 is overexpressed in MM cell lines and in clinical datasets of MM and several other cancers including EAC, and FEN1-knockdown inhibited spontaneous DNA breaks, homologous recombination (HR) activity as well as genomic instability in MM cells. We now show that FEN1-overexpression in non-cancerous (normal fibroblasts and bone marrow/stroma HS5) cells increases DNA breaks and genomic instability, as assessed by micronucleus assay. Methods In order to further evaluate the impact on genomic instability, control and FEN1-overexpressing cells were cultured for three weeks and new genomic changes acquired in cultured relative to “day 0” cells (representing baseline genome), were identified using single nucleotide polymorphism (SNP) arrays. Results Overall, the acquisition of amplification and deletion events were increased by ~ 3-fold in FEN1-overexpressing relative to control cells. Evaluation by RNA sequencing in two different non-cancerous cell types showed that FEN1-overexpression was associated with upregulation of several interconnected pathways including DNA double strand break repair, cell cycle, mitotic G2 M phases, TP53, homologous DNA pairing and strand exchange. Top downregulated pathways included several metabolic pathways and an apoptosis pathway. These data demonstrate a significant role and the impact of FEN1 on DNA repair and genome maintenance, especially HR. We next identified FEN1-interacting proteins from two different MM cell lines (MM1S, RPMI8226) by mass spectrometry. Forty-one proteins interacted with FEN1 in both MM cell lines including two helicases (ASCC3, RUVBL2) and several proteins involved in DNA damage response and recruitment. To investigate the functional relevance of FEN1-ASCC3 interaction, FEN1 was overexpressed in non-cancerous (stromal HS5) cells and ASCC3 was suppressed in control as well as FEN1-overexpressed cells, and impact on different parameters of genome stability (HR activity, micronuclei) and growth (cell viability and DNA replication) monitored. FEN1-overexpression increased HR activity, whereas ASCC3-knockdown inhibited spontaneous as well as FEN1-induced HR activity. Consistent with these data, FEN1-overexpression also increased genomic instability, whereas ASCC3-knockdown inhibited spontaneous as well as FEN1-induced genomic instability as assessed by micronucleus assay. Importantly, FEN1-overexpression also increased DNA replication (as assessed by BrdU-labelling), whereas ASCC3-knockdown inhibited spontaneous as well as FEN1-induced DNA replication in these cells. Conclusion These data suggest that helicase activity of ASCC3 is coupled to endonuclease activity of FEN1 to cause genomic instability and cancer cell proliferation, and is currently being investigated in MM and other cancer models to develop translational application.

Administration of posttransplant cyclophosphamide (PTCy) has significantly expanded the number of patients undergoing HLA-haploidentical hematopoietic cell transplantation (haplo-HCT). To examine immune reconstitution in these patients, we monitored T- and natural killer (NK)-cell recovery in 60 patients receiving bone marrow or peripheral blood stem cell (PBSC) grafts after haplo-HCT with PTCy and 35 patients receiving HLA-matched donor PBSC grafts with standard graft-versus-host disease (GVHD) prophylaxis. Compared with HLA-matched recipients, early T-cell recovery was delayed in haplo-HCT patients and skewed toward effector memory T cells with markedly reduced naive T cells. We found higher regulatory T (Treg)-cell/conventional T (Tcon)-cell ratios early after HCT and increased PD-1 expression on memory T cells. Within the haplo-HCT, patients who did not develop chronic GVHD (cGVHD) had higher PD-1 expression on central and effector memory CD4+ Treg cells at 1 month after transplant. These findings suggest an immunologic milieu that promotes immune tolerance in haplo-HCT patients. NK cells were decreased early after haplo-HCT with preferential expansion of immature CD56brightCD16− NK cells compared with matched donor transplants. One month after transplant, mass cytometry revealed enrichment of immature NK-cell metaclusters with high NKG2A, low CD57, and low killer-cell immunoglobulin-like receptor expression after haplo-HCT, which partially recovered 3 months post-HCT. At 2 months, immature NK cells from both groups were functionally impaired, but interleukin-15 priming corrected these defects in vitro. Increased immature/mature NK-cell ratios were associated with cytomegalovirus reactivation and increased incidence of cGVHD after haplo-HCT. These homeostatic imbalances in T- and NK-cell reconstitution after haplo-HCT reveal opportunities for early immune-based interventions to optimize clinical outcomes.

Identification of genes driving genomic evolution can provide novel targets for cancer treatment and prevention. Here we show identification of a genomic instability gene signature, using an integrated genomics approach. Elevated expression of this signature correlated with poor survival in esophageal adenocarcinoma (EAC) as well as three other human cancers. Knockout and overexpression screens confirmed the relevance of this signature to genomic instability. Indepth evaluation of TTK (a kinase), TPX2 (spindle assembly factor) and RAD54B (recombination protein) further confirmed their role in genomic instability and tumor growth. Mutational signatures identified by whole genome sequencing and functional studies demonstrated that DNA damage and homologous recombination were common mechanisms of genomic instability induced by these genes. Consistently, a TTK inhibitor impaired EAC cell growth in vivo, and increased chemotherapy-induced cytotoxicity while inhibiting genomic instability in surviving cells. Thus inhibitors of TTK and other genes identified in this study have potential to inhibit/delay genomic evolution and tumor growth. Such inhibitors also have potential to increase chemotherapy-induced cytotoxicity while reducing its harmful genomic impact in EAC and possibly other cancers.

Background: In normal cells, RAD51-mediated homologous recombination (HR) is a precise DNA repair mechanism which plays a key role in the maintenance of genomic integrity and stability. However, elevated (dysregulated) RAD51 is implicated in genomic instability and is a potential target for treatment of certain cancers, including Barrett’s adenocarcinoma (BAC). In this study, we investigated genomic impact and translational significance of moderate vs. strong suppression of RAD51 in BAC cells. Methods: BAC cells (FLO-1 and OE33) were transduced with non-targeting control (CS) or RAD51-specific shRNAs, mediating a moderate (40-50%) suppression or strong (80-near 100%) suppression of the gene. DNA breaks, spontaneous or following exposure to DNA damaging agent, were examined by comet assay and 53BP1 staining. Genomewide expression was monitored by microarrays (Affymetrix). Genomic instability was evaluated by Alu-PCR and Homologous recombination (HR) and single strand annealing (SSA) activities measured using plasmid based assays. Results: We previously showed that suppression of RAD51 significantly reduces the acquisition of genomic changes over time, as assessed by SNP arrays (Affymetrix). Here, we show that although moderate suppression consistenly inhibits/reduces HR activity, the strong suppression is associated with increase in HR activity (by ~15 - ³ 50% in various experiments), suggesting activation of RAD51-independent pathway. Contrary to moderate suppression, a strong suppression of RAD51 is associated with a significant increase in spontaneous as well as UV-induced DNA breaks as well as altered expression of genes involved in detection/processing of DNA breaks and apoptosis. Stronger RAD51 suppression was also associated with mutagenic single strand annealing mediated HR with evidence of increased genomic instability. Suppression of RAD51C inhibited RAD51-independent (SSA-mediated) HR, indicating its role in this process. Conclusion: Elevated (dysregulated) RAD51 in BAC is implicated in both the repair of DNA breaks as well as ongoing genomic rearrangements. Moderate suppression of this gene reduces HR activity, whereas strong or near complete suppression of this gene activates RAD51C-dependent HR involving a mechanism known as single strand annealing (SSA). SSA-mediated HR, which is a mutagenic HR pathway, further disrupts genomic integrity by increasing DNA breaks and acquisition of new genomic changes in BAC cells. We, therefore, conclude that inhibition of RAD51C, alone or in combination with RAD51 suppression, has potential to make BAC cells static.

Dysregulated homologous recombination (HR) contributes to the acquisition of genomic changes and development of drug resistance over time in multiple myeloma (MM). We have now further investigated the molecular intermediates that may play an important role in HR process. We observe that ABL kinase, which regulates RAD51 through its phosphorylation, contributes to increased HR activity and genomic instability in myeloma. Moreover, Cellular response after DSBs involves nuclear re-localization of ABL1 upon DNA damage. A cellular localization of ABL1 has been confirmed in MM. Consistently, we observe that ABL kinase inhibitor reduces HR activity and genomic instability (as assessed by micronucleus assay) in MM cells. Based on our observation that melphalan increases genomic instability (as assessed by micronuclei assay and by whole genome sequencing), we sought to investigate impact of melpahalan on HR and role of ABL1 kinase in this process. We show that treatment with melphalan leads to increase in RAD51 expression and HR activity in MM cells in a dose-dependent manner. Evaluation by RNA sequencing showed that treatment of MM1S cells with melphalan is associated with upregulation of p53 signaling (containing multiple genes involved in DNA damage, detection of damaged sites, recombination/repair and genomic instability) as the topmost pathway. These findings suggest that melphalan-induced DNA damage leads to a concerted overexpression of genes involved in DNA damage response, recombination, genomic instability and chemoresistance. With the role of ABL1-kinase following DSB, we investigated and report that treatment with melphalan induces micronuclei formation, whereas nilotinib significantly reduces both the basal and melphlalan-induced micronuclei in all MM cell lines tested. We have now confirmed these observations by evaluating copy number alterations using single nucleotide polymorphism (SNP) arrays. To evaluate the impact of nilotinib, melphalan and their combination on genomic instability, we cultured MM cells in the presence of nilotinib (2.5 µM), melphalan (1 µM) and combination of both drugs for three weeks and investigated the acquisition of new copy number events, relative to "day 0" cells (serving as baseline genome), using SNP arrays. Treatment with melphalan led to massive increase in the acquisition of amplification and deletion events, whereas nilotinib not only reduced the acquisition of copy number events under spontaneous condition but also almost completely reversed/prevented those induced by melphlalan. Importantly, the treatment with nilotinib could also significantly sensitized MM cell lines and bone marrow plasma cells from relapsed MM patients to melphalan treatment. These data confirm that ABL1 inhibition reduces spontaneous and melphalan-induced genomic instability in MM cells. Since components of cell cycle play critical role in the maintenance of genome stability and growth, we investigated the impact of ABL1-inhibitor nilotinib, alone and in combination with melphalan, on cell cycle. Treatment of MM1S cells with melphalan for 48hrs led to 2.5-fold increase in the accumulation of cells in S-phase, suggesting an increase in replication stress by melphalan. Nilotinib reduced both the spontaneous and melphalan-induced fraction of S-phase cells by 27% (±2%) and 30% (±1%), respectively. Combined treatment with nilotinib and melphalan also increased sub G1 fraction of cells by 2.3-fold compared to those treated with melphalan alone, suggesting increased apoptosis in these cells. These data are consistent with our observation that treatment of MM cells with melphalan increase the phosphorylation of RPA32, a marker of replication stress while nilotinib reduces both the endogenous and melphalan-induced phosphorylated RPA32 level, suggesting that nilotinib might also be helpful in combating replication stress-mediated genomic instability. Taken together, these data demonstrate the critical role of ABL1-kinase in both spontaneous and drug (melphalan)-induced genomic instability and its inhibition could reduce/delay genomic evolution while enhancing cytotoxicity in multiple myeloma. Disclosures Fulciniti: NIH: Research Funding. Munshi:Takeda: Consultancy; Karyopharm: Consultancy; AbbVie: Consultancy; Amgen: Consultancy; Legend: Consultancy; Adaptive: Consultancy; Janssen: Consultancy; C4: Current equity holder in private company; OncoPep: Consultancy, Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees, Patents & Royalties; BMS: Consultancy.

Multiple myeloma (MM) is a genomically heterogenous malignancy characterized by a number of copy number alterations (CNA). Moreover, there is a clear evolution of genomic changes that may affect prognosis. To identify the drivers of this inherent genomic instability, we applied an integrated genomics approach utilizing genomic data for copy number changes and transcriptomic profile. We first identified genes whose expression correlated with total copy number events in a patient dataset (gse26863, n=246). We then applied those genes to identify the genes whose elevated expression correlated with both overall and event free survival in two different datasets (IFM70, n=170; gse2408, n=559). Elevated expression of this 30 gene signature also correlated with poor overall as well as event free survival in a third myeloma dataset (MMRF; P In summary, we demonstrate that elevated ATAD2 contributes to dysregulation of DNA repair and genome stability and is required for MM cell survival, indicating that it is a promising target to inhibit growth and reduce genomic evolution in myeloma. Disclosures Munshi: BMS: Consultancy; OncoPep: Consultancy, Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees, Patents & Royalties; C4: Current equity holder in private company; Janssen: Consultancy; Adaptive: Consultancy; Legend: Consultancy; Amgen: Consultancy; AbbVie: Consultancy; Karyopharm: Consultancy; Takeda: Consultancy.

BACKGROUND In normal cells, RAD51-mediated homologous recombination (HR) is a precise DNA repair mechanism which plays a key role in the maintenance of genomic integrity and stability. However, elevated (dysregulated) RAD51 is implicated in genomic instability and is a potential target for treatment of certain cancers, including Barrett’s adenocarcinoma (BAC). In this study, we investigated genomic impact and translational significance of moderate vs. strong suppression of RAD51 in BAC cells. METHODS BAC cells (FLO-1 and OE33) were transduced with non-targeting control (CS) or RAD51-specific shRNAs, mediating a moderate (40–50%) suppression or strong (80-near 100%) suppression of the gene. DNA breaks, spontaneous or following exposure to DNA damaging agent, were examined by comet assay and 53BP1 staining. Gene expression was monitored by microarrays (Affymetrix). Homologous recombination (HR) and single strand annealing (SSA) activities were measured using plasmid based assays. RESULTS We show that although moderate suppression consistenly inhibits/reduces HR activity, the strong suppression is associated with increase in HR activity (by ~15 – ≥ 50% in various experiments), suggesting activation of RAD51-independent pathway. Contrary to moderate suppression, a strong suppression of RAD51 is associated with a significant induced DNA breaks as well as altered expression of genes involved in detection/processing of DNA breaks and apoptosis. Stronger RAD51 suppression was also associated with mutagenic single strand annealing mediated HR. Suppression of RAD51C inhibited RAD51-independent (SSA-mediated) HR in BAC cells. CONCLUSION Elevated (dysregulated) RAD51 in BAC is implicated in both the repair of DNA breaks as well as ongoing genomic rearrangements. Moderate suppression of this gene reduces HR activity, whereas strong or near complete suppression of this gene activates RAD51C-dependent HR involving a mechanism known as single strand annealing (SSA). SSA-mediated HR, which is a mutagenic HR pathway, further disrupts genomic integrity by increasing DNA breaks in BAC cells.

Identification of mechanisms underlying genomic instability is necessary to understand disease progression, including development of drug resistance. Our previous data demonstrates that dysregulation of DNA repair and maintenance/modification activities (including homologous recombination (HR), apurinic/apyrimidinic nuclease and APOBEC) significantly contribute to genomic instability in multiple myeloma (MM). However, how these and other pathways involved in genomic instability are dysregulated, remains to be explored. Since kinases play a critical role in the regulation of the maintenance of genomic integrity, we have performed a genome-wide kinome profiling to identify those involved in genomic instability in cancer. First, we analyzed genomic database for ten human cancers (including MM) from TCGA with both tumor cell gene expression and SNP/CGH array-based copy number information for each patient.We assessed genomic instability in each patient based on the total number of amplification and deletion events. We next interrogated all 550 kinases expressed in humans and identified those whose expression correlated with copy number alteration (based on FDR ≤ 0.05) in all tumor types. We identified six kinases whose elevated expression correlated with increased genomic instability defined by genomic amplification/deletion events in all ten cancers, including MM. To demonstrate functional relevance of these kinases, we conducted a CRISPR-based loss of function screen (using 3 guides per gene) in MM cells and evaluated the impact of each gene-knockout on micronuclei, a marker of ongoing genomic rearrangements and instability. For all six kinases, at least one guide resulted in ≥ 65% inhibition of micronuclei formation. Moreover, for five out of the six kinases, at least two guides showed ≥ 60% inhibition of micronuclei. All together, these data establishes a strong relevance of these kinases with genomic instability in MM. PDZ Binding Kinase (PBK) was among top kinases impacting genome stability in this data set with 2 out of 3 guides causing > 88% and 3rdguide causing 35% inhibition of micronuclei formation. We further report that inhibition of PBK, by knockdown or small molecule, inhibits DNA breaks, RAD51 recombinase expression and homologous recombination in MM cells. We further investigated molecular mechanisms involved in PBK-mediated genomic instability in MM. Expression profiling using RNA sequencing of MM cells treated with a specific PBK inhibitor showed that top ten pathways downregulated by treatment were mostly DNA repair/recombination followed by replication and G2/M checkpoint. Interestingly, we identified a notable overlap between PBK-regulated genes with FOXM1 target genes. FOXM1 is a major transcriptional regulator of genes involved in DNA repair, G2/M regulation and chromosomal stability. We, therefore, investigated PBK/FOXM1 interaction and show that PBK interacts with FOXM1 in MM cells. Moreover, the inhibition of PBK, by knockdown or small molecule, inhibits phosphorylation of FOXM1 as well as downregulates FOXM1-regulated HR and cell cycle genes RAD51, EXO1 and CDC25A. These results suggest that PBK-dependent phosphorylation of FOXM1 activity controls transcriptional networks involved in genomic instability in MM. Ongoing work is investigating role of PBK and other kinases in progression of MGUS/SMM to active MM and their impact on ongoing genomic changes with influence on multiple DNA repair pathways including HR. In conclusion, we describe a kinase panel that may have significant role in maintaining genome stability, and their perturbation may allow to improve genome stability in MM. Disclosures Munshi: Adaptive: Consultancy; Amgen: Consultancy; Celgene: Consultancy; Janssen: Consultancy; Abbvie: Consultancy; Oncopep: Consultancy; Takeda: Consultancy.

BCL-2 antagonist venetoclax combined with hypomethylating agents or low-dose cytarabine is a new standard of care for treatment-naive elderly or unfit AML patients. Despite the striking overall response of 70%, only 30% achieved MRD negative status with a short remission duration of 11.3 months. This highlights the need for new agents that can overcome venetoclax resistance. We exploited mitochondrial functional assay called BH3 profiling to identify predictors of clinical responses and to discover combination partners of venetoclax. BH3 profiling measures apoptotic priming of a cell (proximity to the apoptotic threshold) by measuring mitochondrial response to a standardized panel of pro-apoptotic BH3 oligopeptides. By using pretreatment myeloblasts of patients (N=16) from clinical trial of venetoclax and azacitidine, we found that response to HRK + MS1 peptides (infers BCL-XL and MCL-1 dependency, respectively) inversely correlates with the achievement of remission. The serial sampling on treatment revealed the emergence of differential patterns of anti-apoptotic dependency that correlated with patient response. Of note, mitochondrial sensitivity to the MS-1 peptide, an indication of MCL-1 dependence, increased from 0% at diagnosis to 40% at relapse, suggesting an opportunity for MCL-1 antagonism in the relapsed setting. First, we exposed 6 AML cell lines with a BCL-2 (venetoclax) and MCL-1 antagonist (S63845). As previously reported, combination treatment resulted in synergistic cell line killing. Venetoclax treatment (within an hour) led to a dynamic increase in mitochondrial sensitivity to the MCL-1 selective MS-1 peptide, while S63845 caused increased mitochondrial susceptibility to the BCL-2 and BCL-XL selective BAD peptide. There was a correlation between % of priming caused by MS-1 and BAD peptide with Loewe synergy score (Spearman r=0.79, p We next investigated combination MCL-1 and BCL-2 antagonism in vivo in venetoclax resistant AML PDXs. We transplanted NSG mice with human AML cells and started them on venetoclax (100mg/kg, PO) until leukemia relapsed (N=6 models). We subjected resistant myeloblasts to BH3 profiling and identified dependency on BCL-2 and MCL-1 to guide therapeutic choices. As a single agent, S63845 showed limited activity in venetoclax resistance models (p Next, we applied the dynamic BH3 profiling technique that measures drug-induced changes in mitochondrial priming to discover additional agents that may overcome venetoclax resistance. We compared mitochondrial priming signals of 40 targeted agents in isolated parental and resistant cells. Although venetoclax resistant cells gained cross resistance to most of the agents, inhibitors of the FLT-3 pathway, including quizartinib, crenolanib, and gilteritinib retained similar priming responses as in parental cells. To validate this, we re-transplanted venetoclax resistant cells and found that quizartinib treatment maintained anti-leukemia efficacy compared to venetoclax or vehicle-treated mice (p In conclusion, our study illustrates the power of mitochondrial measurements as a predictive biomarker for BH3 mimetic based therapy. We provide an evidence for the persistent activity of FLT-3 inhibitors in venetoclax resistance settings, a discovery made possible by dynamic BH3 profiling. Disclosures Ryan: Vivid Biosciences: Consultancy. Erick:Novartis: Employment. Weinstock:Celgene: Research Funding. Garcia:Abbvie: Research Funding; Genentech: Research Funding. Letai:Novartis: Research Funding; Flash Therapeutics: Equity Ownership; Abbvie: Consultancy, Research Funding; Vivid Bioscience: Equity Ownership; Astrazeneca: Research Funding.

Introduction We have previously shown that increased numbers of plasmacytoid dendritic cells (pDCs) in bone marrow (BM) of multiple myeloma (MM) patients promote tumor cell growth, survival, and drug resistance; as well as suppress T and NK cell mediated anti-MM immunity (Chauhan et al, Cancer Cell 2009, 16:309-323; Ray et al, Leukemia 2015, 29:1441-1444). Here, we analyzed genetic changes in MM cells triggered by coculture with pDCs using next generation sequencing (NGS). Functional validation of NGS data was performed in our coculture models of pDC-T-MM cells to assess impact on tumor cell surface phenotype, growth, survival, and drug resistance; as well as cytotoxic T lymphocyte (CTL) activity against MM. We identified and validated the metabolic ectoenzyme CD73/NT5E, implicated in cancer metabolism and immunosuppression via nucleotide degradation pathway, as a novel therapeutic target in MM. Methods Purified MM patient pDCs were cocultured with autologous MM cells or allogeneic MM cell lines (1pDC/5MM) for 48h, followed by separation of MM cells from pDCs using flow cytometry. Total RNA from MM cells was subjected to RNAseq analysis using Illumina Next Generation Sequencing (NGS). Raw sequence data were analyzed using VIPER workflow generating differential expression (DEseq2) and KEGG pathway. Statistical significance: log2FC (fold change) values in coculture vs control, with an FDR (False Discovery Rate) value of 95). Linear model for RNAseq analysis (Limma) and its GUI (Glimma) were also utilized for the visualization of data. Results RNA-seq data was analyzed using negative binomial distribution (DEseq2) and linear (Limma) models. Results showed 9200 and 9250 genes were differentially expressed (p < 0.05). MM cells cultured with or without pDCs clustered into two distinct groups, based upon pDC-MM contact-dependent transcriptional changes. Pathway enrichment analysis showed that pDCs interaction with MM cells regulates multiple physiological processes in MM cells including DNA replication/repair, purine/pyrimidine metabolism, and cell cycle. Hierarchical clustering showed increased expression of genes in MM cells after coculture with pDCs (log2FC range: ± 6.0): TLR7/9 (0.5; p=0.02), HDAC6 (0.65; p=0.00002), CD274 (0.6; p=0.02), or IL3Rα/CD123(0.1; p Conclusions Our RNA-seq and NGS analysis of pDCs-triggered transcriptome changes in MM cells identifies genes and pathways mediating tumor growth and immunosuppression, which therefore represent targets for novel therapeutics to improve patient outcome. Disclosures Chauhan: C4 Therapeutics.: Equity Ownership; Stemline Therapeutics: Consultancy. Anderson:Sanofi-Aventis: Other: Advisory Board; Bristol-Myers Squibb: Other: Scientific Founder; Oncopep: Other: Scientific Founder; Amgen: Consultancy, Speakers Bureau; Janssen: Consultancy, Speakers Bureau; Takeda: Consultancy, Speakers Bureau; Celgene: Consultancy, Speakers Bureau.

Homologous recombination (HR), a mechanism to accurately repair DNA in normal cells, is deregulated in cancer. Elevated/deregulated HR is implicated in genomic instability and telomere maintenance, which are critical lifelines of cancer cells. We have previously shown that HR activity is elevated and significantly contributes to genomic instability in Barrett's esophageal adenocarcinoma (BAC). The purpose of this study was to evaluate therapeutic potential of HR inhibition, alone and in combination with telomerase inhibition, in BAC. We demonstrate that telomerase inhibition in BAC cells increases HR activity, RAD51 expression, and association of RAD51 to telomeres. Suppression of HR leads to shorter telomeres as well as markedly reduced genomic instability in BAC cells over time. Combination of HR suppression (whether transgenic or chemical) with telomerase inhibition, causes a significant increase in telomere attrition and apoptotic death in all BAC cell lines tested, relative to either treatment alone. A subset of treated cells also stain positive for β-galactosidase, indicating senescence. The combined treatment is also associated with decline in S-phase and a strong G2/M arrest, indicating massive telomere attrition. In a subcutaneous tumor model, the combined treatment resulted in the smallest tumors, which were even smaller (P=0.001) than those that resulted from either treatment alone. Even the tumors removed from these mice had significantly reduced telomeres and evidence of apoptosis. We therefore conclude that although telomeres are elongated by telomerase, elevated RAD51/HR assist in their maintenance/stabilization in BAC cells. Telomerase inhibitor prevents telomere elongation but induces RAD51/HR, which contributes to telomere maintenance/stabilization and prevention of apoptosis, reducing the efficacy of treatment. Combining HR inhibition with telomerase renders telomeres more vulnerable to degradation and significantly increases/expedites their attrition, leading to apoptosis. We therefore demonstrate that a therapy targeting HR and telomerase has the potential to prevent both tumor growth and genomic evolution in BAC.

A prominent feature of most cancers including Barrett’s adenocarcinoma (BAC) is genetic instability, which is associated with development and progression of disease. In this study, we investigated the role of recombinase (hsRAD51), a key component of homologous recombination (HR)/repair, in evolving genomic changes and growth of BAC cells. We show that the expression of RAD51 is elevated in BAC cell lines and tissue specimens, relative to normal cells. HR activity is also elevated and significantly correlates with RAD51 expression in BAC cells. The suppression of RAD51 expression, by short hairpin RNA (shRNA) specifically targeting this gene, significantly prevented BAC cells from acquiring genomic changes to either copy number or heterozygosity (P

As in all cancers, genomic instability leads to ongoing acquisition of new genetic changes in multiple myeloma (MM). This adaptability underlies the development of drug resistance and progression in MM. This genomic instability is driven by cellular processes, mainly related with DNA repair and perturbed by functional changes in limited number of genes. Since kinases play a critical role in the regulation of biological processes, including DNA damage/repair signaling and are relatively easy to screen for inhibitors, we investigated for novel genes involved in the acquisition of new genomic changes in MM. Using a large genomic database which had both the gene expression and CGH array-based copy number information (gse26863, n=246), we first identified a total of 890 expressed kinases in MM and correlated their expression with genomic instability defined as a change in ≥3 and/or 5 consecutive amplification and/or deletion events. We identified 198 kinases whose elevated expression correlated with increased genomic instability (based on FDR ≤ 0.05). Amongst these kinases, using univariate Cox survival analysis, elevated expression of 15 kinases correlated with poor overall as well as event free survival (P ≤0.05) in two MM datasets (IFM70, n=170; gse24080; n=559). We further confirmed the correlation of these 15 genes in both EFS and OS in additional two MM datasets (MMRF CoMMpass Study, IFM-DFCI 2009) as well as in additional solid tumor datasets from TCGA from patients with lung and pancreatic adenocarcinoma (P values ranging from 0.01 to To investigate the relevance of these genes with genomic instability, we performed a functional siRNA screen to evaluate impact of their suppression on homologous recombination (HR). PDZ Binding Kinase (PBK) was one of the top genes whose knockdown caused the maximal inhibition of HR activity in initial screen. To investigate it further in detail, we suppressed PBK in MM cells using shRNA and confirmed that its suppression significantly reduces HR activity. PBK-knockdown also reduced gH2AX levels (marker of DNA breaks) measured by Western blotting and decreased number of micronuclei (a marker of ongoing genomic rearrangements and instability) as assessed by flow cytometry . A small molecule inhibitor of PBK also confirmed a similar reduction in gH2AX levels as well as micronuclei, indicating inhibition of spontaneous DNA breaks and genomic instability. Using mass spectrometry and co-immunoprecipitation, we identified that PBK interacts with FEN1, a nuclease with roles in base excision repair and HR pathways. We confirmed that PBK induces phosphorylation of FEN1 and that inhibition of PBK, suppressed the phosphorylation of FEN1, RAD51 expression and gH2AX levels and it reversed FEN1-induced HR activity. These results confirm that phosphorylation of FEN1 nuclease by PBK contributes to its ability to impact DNA breaks, HR and genome stability in MM. PBK inhibition also significantly sensitized MM cells to melphalan and inhibited cell viability in a panel of MM cell lines (IC50 in MM cell lines ~20-30 nM vs ~100 nM in normal PBMCs) at the same time also reversed melphalan-induced genomic instability, as assessed by micronucleus assay. These data identify PBK as an important target affecting genomic instability, and its inhibitor as a potential drug, to inhibit genomic evolution and MM cell growth. Disclosures Munshi: OncoPep: Other: Board of director.

Introduction We identified an integral role of bone marrow (BM) plasmacytoid dendritic cells (pDCs) in multiple myeloma (MM) pathogenesis. Specifically, we found increased numbers pDCs in MM BM vs normal BM. pDCs protect tumor cells from therapy-induced cytotoxicity; promote tumor growth and survival, as well as suppress immune responses (Chauhan et al, Cancer Cell 2009, 16:309-323). Aberrant pDC function is evidenced in their interactions not only with MM cells, but also with immune effector T cells and NK cells in the MM BM milieu (Ray et al, Leukemia 2015, 29:1441-1444). Directly targeting pDC interactions with MM and immune effector cells in the MM BM milieu will be required to enhance both anti-tumor immunity and cytotoxicity. To further characterize the role of pDCs in MM pathogenesis, we utilized our pDC/MM co-culture model and analyzed genetic changes in MM cells after coculture with pDCs using next generation sequencing (NGS). NGS data was confirmed using flow cytometry analysis, and functionally validated in cocultures of pDC-MM-T cells, as well as cytotoxic T lymphocyte assays. Based on our NGS study, we have identified the metabolic ectoenzyme NT5E/CD73 as a promising novel therapeutic target in MM; primarily for its role in cancer metabolism and immunosuppression via nucleotide degradation pathway. Methods. Patient BM/PB pDC and MM cells were evaluated by flow cytometry following immunomagnetic separation (purity> 95%). pDCs were cocultured with autologous MM cells or allogeneic MM cell lines (pDC/MM; 1:5) for 48h, followed by separation of MM cells from pDCs using FACS. Total RNA from MM cells was subjected to RNAseq analysis using Illumina Next Generation Sequencing (NGS). Raw sequence data were subjected to VIPER workflow generating differential expression (DEseq2) and KEGG pathway analyses. For RNAseq analysis, log2FC (fold change) values in coculture vs single control, with an FDR (False Discovery Rate) value of 95). Linear model for RNAseq analysis (Limma) and its GUI (Glimma) were used for the visualization of data. Results A total of 19,569 and 25,436 transcripts were analyzed through negative binomial (DEseq2) and linear (Limma) models, respectively. We found that 9200 (47.01%) and 9250 (36.36%) genes were differentially expressed (p < 0.05). The sample-sample correlation analysis showed that MM cells cultured with or without pDCs fall into 2 different groups with distinct clustering properties (n=3), suggesting that pDCs trigger genetic alterations in MM cells. Furthermore, pathway analysis showed that pDCs interaction with MM cells modulates various physiological processes in MM cells including Cell cycle, DNA replication/repair (Fanconi anemia) and Purine/Pyrimidine metabolism. Hierarchical cluster analysis demonstrated upregulation or downregulation of several genes in MM after coculture with pDCs (log2FC range: ± 6.0). For example, pDCs trigger upregulation of CD274 (0.6; p=0.02), IL3Rα/CD123(0.1; p Conclusions Collectively, our RNAseq NGS analysis of pDCs-induced gene changes in MM cells validates our previously published findings (Ray et al Leukemia 2014; 28(8): 1716-1724; Leukemia 2015; Leukemia 2017; 31:2652-2660; Leukemia 2018,32:843-846) that these accessory cells induce growth, survival and drug resistance in tumor cells. Importantly, these studies delineate novel genes and pathways mediating these sequelae which represent targets for future therapies. Disclosures Anderson: Gilead: Membership on an entity's Board of Directors or advisory committees; C4 Therapeutics: Equity Ownership; Bristol Myers Squibb: Consultancy; Takeda Millennium: Consultancy; Celgene: Consultancy; Oncopep: Equity Ownership.

Purpose: p53 is inactivated in many human malignancies through missense mutations or overexpression of the human homologue of Mdm2 (Hdm2), an E3 ubiquitin ligase that ubiquitinates p53, thereby promoting its proteasomal degradation. The cis-imidazoline nutlin-3 can disrupt the p53-Hdm2 interaction and activate p53, inducing apoptosis in vitro in many malignancies, including multiple myeloma (MM). Experimental Design: We hypothesized that suppression of Hdm2-mediated p53 ubiquitination may augment sequelae of p53 accumulation caused by proteasomal inhibition. We compared the response of MM cells versus several epithelial cancer models to the proteasome inhibitor bortezomib in combination with nutlin-3. Results: The combination of sublethal concentrations of bortezomib plus nutlin-3 induced additive cytotoxicity against bortezomib-sensitive MM cell lines. Importantly, however, in breast, prostate, colon, and thyroid (papillary, follicular, anaplastic, and medullary) carcinoma cell lines, this combination triggered synergistic cytotoxicity, and increased expression of p53, p21, Hdm2, Bax, Noxa, PUMA, and cleavage of caspase-3 and poly ADP ribose polymerase. Coculture with bone marrow stromal cells attenuated MM cell sensitivity to nutlin-3 monotherapy and was associated with evidence of suppression of p53 activity in MM cells, whereas combined bortezomib-nutlin-3 treatment maintained cytotoxicity even in the presence of bone marrow stromal cells. Conclusions: This differential response of MM versus epithelial carcinomas to combination of nutlin-3 with bortezomib sheds new light on the role of p53 in bortezomib-induced apoptosis. Concurrent Hdm2 inhibition with bortezomib may extend the spectrum of bortezomib applications to malignancies with currently limited sensitivity to single-agent bortezomib or, in the future, to MM patients with decreased clinical responsiveness to bortezomib-based therapy. (Clin Cancer Res 2009;15(23):7153–60)

The AID/APOBEC family of cytidine deaminase proteins includes AID (activity induced deaminase), and 10 related APOBEC enzymes (A1, A2, A3A, A3B, A3C, A3D, A3F, A3G, A3H and A4). AID has been well-studied for its role in somatic hyper mutation and class switch recombination of immunoglobulin genes whereas APOBECs (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like) have been shown to have roles in mRNA editing and in antiviral immunity. Dysregulated activity of APOBECs causes C >T transitions or C>G, C>A transversions in DNA. We have recently shown APOBEC signature mutation pattern in multiple myeloma (MM) genomes (Bolli et al Nat. Comm. 2014), and interestingly, the APOBEC mutation signature correlates with sub clonal diversity in myeloma. A role for the AID/APOBECs in generation of somatic mutations has also been proposed in a variety of other cancers based on identification of APOBEC signature mutations In order to understand which APOBECs are dysregulated in myeloma, we performed RNA sequencing analysis of primary myeloma cells from 409 newly-diagnosed MM patients and myeloma cell lines. Our analysis showed elevated expression of several APOBEC family members; mainly A3A, A3B, A3C, and A3G. We then optimized a plasmid-based functional assay and found high cytidine deaminase activity in extracts from a number of myeloma cell lines and patient derived CD138+ cells compared to CD138+ cells from healthy donors, suggesting that APOBECs are dysregulated in myeloma. We then investigated the impact of elevated APOBEC expression/function on overall genome maintenance and acquisition of genomic changes (such as amplifications, deletions) overtime. We used shRNA-mediated knockdown of specific APOBEC proteins in myeloma cell lines and investigated the acquisition of genomic changes in control and knockdown cells during their growth in culture, using SNP (Single Nucleotide Polymorphism) arrays and WGS (whole genome sequencing) platforms. Our results with both approaches showed significant reduction in the accumulation of copy number changes (both amplifications and deletions) and overall mutation load after APOBEC knockdown. Evaluation with both the SNP and WGS showed that when control and APOBEC knockdown cells were cultured for three weeks, the acquisition of new copy number and mutational changes throughout genome were reduced by ~50%. We next investigated the relationship between APOBEC expression/activity in MM and other DNA repair pathways. Using an in vitro HR activity assay, we measured HR activity in extracts from control and APOBEC knockdown cells. Depletion of APOBEC proteins resulted in 50-80% reduction in in vitro HR activity of the extracts. We also evaluated correlation between HR activity and gene expression using RNA-seq data from myeloma cells derived from 100 patients at diagnosis and identified the genes whose expression correlated with HR activity. Elevated expression of APOBECs 3D, 3G and 3F significantly correlated with high HR activity (R=0.3; P≤0.02), suggesting their relevance to HR. Analyzing genomic copy number information for each patient we have also observed significant correlation between higher expression of A3G and increased genomic instability in this dataset (P=0.0045). In summary, our study shows that dysregulated APOBECs induce mutations and genomic instability, and inhibiting APOBEC activity could reduce the rate of accumulation of ongoing genomic changes. This data sheds light on biology of the disease as well as clonal evolution. Disclosures Munshi: Amgen: Consultancy; Oncopep: Patents & Royalties; Celgene: Consultancy; Janssen: Consultancy; Takeda: Consultancy; Merck: Consultancy; Pfizer: Consultancy.

The NEDD8-activating enzyme is upstream of the 20S proteasome in the ubiquitin/proteasome pathway and catalyzes the first step in the neddylation pathway. NEDD8 modification of cullins is required for ubiquitination of cullin-ring ligases that regulate degradation of a distinct subset of proteins. The more targeted impact of NEDD8-activating enzyme on protein degradation prompted us to study MLN4924, an investigational NEDD8-activating enzyme inhibitor, in preclinical multiple myeloma models. In vitro treatment with MLN4924 led to dose-dependent decrease of viability (EC50 = 25–150 nmol/L) in a panel of human multiple myeloma cell lines. MLN4924 was similarly active against a bortezomib-resistant ANBL-6 subline and its bortezomib-sensitive parental cells. MLN4924 had submicromolar activity (EC50 values

Genomic instability leads to acquisition of mutational changes which underlie development and progression of cancer, including development of drug resistance and poor clinical outcome. Understanding mechanisms of genomic instability is therefore necessary to develop promising strategies for prevention and treatment of disease. Homologous recombination (HR), the most precise DNA repair mechanism, has been previously described to be dysregulated in multiple myeloma (MM) mediating genomic instability. Since nuclease activity, by producing free ends of DNA, can induce DNA recombination leading to genomic rearrangements, we investigated prognostic significance of nuclease activity and nuclease gene expression in MM. We first developed a nuclease gene signature correlating with both the genomic instability and survival in myeloma patients. We used two different myeloma patient datasets (gse26863, n=246 and IFM 170 patient dataset) which had both the gene expression and SNP/CGH array-based copy number information for each patient. Genomic instability in each patient was determined by counting the total number of amplification and/or deletion events; an event was defined as a change in ≥3 and/or 5 consecutive SNPs/probes. We identified 34 nucleases whose elevated expression correlated with increased genomic instability in gse26863 dataset. Of these, the elevated expression of 21 nucleases also correlated with increased genomic instability in 170 dataset. Elevated expression of seven of these genes also correlated with poor overall survival (p=0.00005) as well as event free survival (P=0.0003) in myeloma patients (n=170). We further tested one of these nucleases (APEX2) in both the loss and gain of function studies and found that its suppression significantly reduces DNA breaks and dysregulated HR, an important activity underlying ongoing genomic rearrangements and instability in myeloma. Upregulation of APEX2 was associated with excessive DNA breaks, dysregulation of HR, acquisition of new genomic changes over time in myeloma cells. We also investigated the prognostic significance of nucleolytic activity in cell lines and patient samples using a plasmid degradation assay in which supercoiled DNA is converted to open circular and linear forms by the MM cell lystae prepared from purified CD138+ patient MM cells or MM cell lines. The ratio of supercoiled to total DNA per lane was graphed across successive time points (0, 3, 6, 12, 24 minutes) and analyzed via nonlinear regression using PRISM (statistical software) to calculate a half-life and k-constant. The longer half life suggests lower nuclease activity in MM cells. This assay was able to differentiate MGUS and smoldering myeloma (SMM) patients with long half-life of plasmid (9499 minutes) versus newly diagnosed MM (9 minutes) in which there was variability with some patients with plasmid degradation pattern closer to SMM versus some with significantly higher activity. A large number of (N = 410) clinically annotated sample patients are currently being evaluted for both functional and clinical correlation of nuclease activity. In summary, we show correlation between nucleases activity and genomic instability with impact on survival in MM. The genes in this signature not only provide novel markers to predict clinical outcome but also potential targets for prevention/reduction of genomic evolution. Investigation of the role of each of the seven genes, separately and in combination, in the overall nucleolytic activity, genomic instability, and pathways involved in the regulation of cell cycle, DNA repair/maintenance checkpoints, apoptosis and survival is currently ongoing. Disclosures Avet-Loiseau: jansen: Membership on an entity's Board of Directors or advisory committees; millenium: Membership on an entity's Board of Directors or advisory committees; onyx: Membership on an entity's Board of Directors or advisory committees; BMS: Membership on an entity's Board of Directors or advisory committees; celgene: Membership on an entity's Board of Directors or advisory committees; jansen: Membership on an entity's Board of Directors or advisory committees; millenium: Membership on an entity's Board of Directors or advisory committees; onyx: Membership on an entity's Board of Directors or advisory committees; BMS: Membership on an entity's Board of Directors or advisory committees.

Telomerase has multiple functions. We here reported that besides telomere maintenance, telomerase is also involved in the repair of DNA breaks in myeloma (MM) cells. By sequence analyses of “TTAGGG” enriched genomic fragments, we also mapped the interstitial telomeric repeat sequences (ITS) and demonstrate that telomerase mediated repair involves the insertion of ITS within cancer genome. More importantly, we show that such insertions which occur at higher frequency in cancer vs. normal cells, are reduced in the presence of telomerase inhibitor (TI). We hypothesized that if the ITS if inserted in large numbers following massive DNA breaks, induced by a genotoxic agent, could become substrates for recombination (which is elevated in myeloma) leading to increased genomic instability. To investigate if repair of induced DNA breaks by telomerase would contribute to genomic instability, DNA breaks in RPMI cells were induced by UV, cells cultured in the presence of TI or control oligo for four 4 days, drug was then withdrawn and cells continued in culture for 30 days. Cells were harvested at days 10, 20 and 30 and their genomic DNA evaluated for copy number changes using SNP6.0 arrays. Genome of day 10 for each sample was used as baseline to identify genomic changes in corresponding day 20 and day 30 samples. We observed a gradual increase in deletion events in UV treated control cells from 14-fold at day 20 to 147-fold at day 30, relative to corresponding changes in UV-TI samples at respective time points. Likewise, the amplifications were massively increased (by 500-fold) at day 30, relative to changes in UV-TI cells at the respective time points. When we compared the fold changes in copy number in these samples relative to UV unexposed baseline control cells, changes in TI-treated cells remained close to the baseline till day 30. However, there was a sharp rise in copy number changes in UV treated control cells at corresponding time point. These data indicate that a brief telomerase inhibition during induced DNA damage may prevent late genomic instability. We have further evaluated the translational significance of these findings. We investigated if inhibition of telomerase mediated repair could sensitize cancer cells to DNA damaging chemotherapeutic agents. RPMI MM cells, pretreated with TI or control oligo for 60 hours, were incubated with melphalan at various concentrations for 48 hrs and cell viability assessed. Cell death in cells pretreated with TI was significantly higher than control cells at each dose level suggesting that TI pretreatment sensitizes cells to DNA damaging agents. Telomerase mediated repair involving insertion of telomeric repeats at interstitial break sites prevents immediate genomic loss, and inhibition of this repair sensitizes MM calls to DNA damaging agent. We conclude that presence of a TI during treatment with a DNA damaging agent would not only enhance the efficacy of treatment but may also protect cancer cells against therapy induced late genomic instability and evolution of aggressive malignant clones. Disclosures No relevant conflicts of interest to declare.

Abstract 1820 Proteasome inhibitors such as Bortezomib (Bort) represent a key drug class for the therapeutic management of multiple myeloma (MM). However, MM patients, even those who initially achieve complete clinical and biochemical remission with bortezomib-based regimens eventually relapse, and bortezomib-refractory disease is associated with short overall survival. Identifying the molecular basis of resistance to bortezomib is therefore crucial for the rational development of novel therapies to hopefully improve clinical outcome for advanced MM. To address this question, we generated an isogenic cell line model of bortezomib resistance by successive rounds of in vitro exposure of bortezomib-sensitive MM.1R cells to progressively increasing bortezomib concentrations. Serial dose-response analyses confirmed the generation of several clones with variable reduction in bortezomib-sensitivity (IC50 range 40–80nM vs. Disclosures: Hayes: Pfizer: Research Funding; Amgen: Research Funding. van de Donk:Celgene: Research Funding. Richardson:Johnson & Johnson: Advisory Board; Millennium: Advisory Board; Celgene: Advisory Board; Bristol-Myers Squibb: Advisory Board; Novartis: Advisory Board. Anderson:Millennium: Consultancy, Research Funding. Mitsiades:Millennium Pharmaceuticals: Consultancy, Honoraria; Celgene: Consultancy, Honoraria; Novartis Pharmaceuticals: Consultancy, Honoraria; Bristol-Myers Squibb: Consultancy, Honoraria; Merck &Co.: Consultancy, Honoraria; Kosan Pharmaceuticals: Consultancy, Honoraria; Pharmion: Consultancy, Honoraria; Centocor: Consultancy, Honoraria; Amnis Therapeutics: Consultancy, Honoraria; PharmaMar.: Licensinig royalties; OSI Pharmaceuticals: Research Funding; Amgen Pharmaceuticals: Research Funding; AVEO Pharma: Research Funding; Sunesis: Research Funding; Gloucester Pharmaceuticals: Research Funding; Genzyme: Research Funding; Johnson & Johnson: Research Funding.

activity. Exposure to 15mmHg increased extracellular pressure stimulated serine phosphorylation of FAK (p-FAK) in Caco-2 and primary human colon cancer cells isolated from surgical specimens. This pressure-induced increase in serine p-FAK was blocked by Akt inhibitor and by siRNA silencing of Akt1 but not by silencing Akt2. Co-precipitation demonstrated that Akt associates directly with FAK. Akt-FAK association was increased by pressure and this increased association was blocked by inhibiting FAK or silencing Akt1 but not Akt2. Scanning the FAK sequence with Scansite software revealed three serine-containing consensus sequences for AKT phosphorylation in the FAK sequence. We therefore constructed a FAK non-phosphorylatable mutant with point mutations (S®A) at these three putative serine phosphorylation sites (S517/601/695) of FAK by Akt to investigate their relevance to pressurestimulated cell adhesion and tyrosine p-FAK. Indeed, overexpression of the triple mutant of FAK (S517/601/695®A) in Caco-2 cells, in contrast to wild type FAK, prevented the increase in p-FAK at Y397 and cancer cell adhesion induced by extracellular pressure. These results suggest that Akt regulates pressure-induced cancer cell adhesion by binding directly to and phosphorylating FAK at S509/601/695. This serine phosphorylation, in turn, permits the pressure-dependent tyrosine autophosphorylation of p-FAK at Y397, the conventional initiator of FAK activation. Although Akt is therefore required for FAK activation in response to pressure, further studies demonstrated that FAK also potentiates Akt activation. Blocking or silencing FAK by three different FAK-specific siRNA sequences prevented the increases in serine p-Akt (S473) and tyrosine p-FAK(Y397) induced by increased pressure. Thus, FAK and Akt bind directly and potentiate each other's activation. This novel mechanism of FAKAkt interaction suggests that FAK and Akt1 may be important dual therapeutic targets for preventing cancer cell adhesion, and eventually cancer metastasis.

Abstract 730 Multi-targeted kinase inhibitors, when associated with manageable toxicity, offer the therapeutically desirable option of targeting, through a single chemical entity, several pathways that may contribute to the complexity and heterogeneity of molecular lesions harbored by neoplasias such as multiple myeloma (MM). However, intractable questions often emerge while prioritizing for preclinical studies different multi-targeted agents with extensive and/or only partially overlapping of sets of known targets. We have hypothesized that the potential therapeutic relevance of a multi-targeted inhibitor may be reflected on the prognostic relevance of its targets' transcriptional signature. We applied this concept in the case of the orally bioavailable multi-targeted kinase inhibitor AS703569, which targets (with IC50 in low nM range) all 3 Aurora kinase (AK) isoforms as well as various other kinases (e.g. cSRC, FGFR1, Flt3, Fyn, Lyn, Rsk1-3, Yes, Axl, et.c.) and evaluated the transcriptional signature of AS703569 kinase targets (with IC50 Disclosures: Laubach: Novartis: Consultancy, Honoraria. Rastelli:EMD Serono: Employment. Clark:EMD Serono: Employment. Sarno:EMD Serono: Employment. Richardson:Millenium: (Speakers' Bureau up to 7/1/09), Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Celgene: (Speakers' Bureau up to 7/1/09), Membership on an entity's Board of Directors or advisory committees, Speakers Bureau. Anderson:Millennium: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; Novartis: Consultancy, Honoraria, Research Funding; Celgene: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding. Mitsiades:Millennium: Consultancy, Honoraria; Novartis : Consultancy, Honoraria; Bristol-Myers Squibb : Consultancy, Honoraria; Merck & Co: Consultancy, Honoraria; Kosan Pharmaceuticals: Consultancy, Honoraria; Pharmion: Consultancy, Honoraria; PharmaMar: Patents & Royalties; Amgen: Research Funding; AVEO Pharma: Research Funding; EMD Serono : Research Funding; Sunesis Pharmaceuticals: Research Funding.

Abstract 605 Despite therapeutic advances and high response rates, most if not all patients with multiple myeloma (MM) develop drug resistance and relapse and curative outcomes remain elusive. A prominent feature of MM is striking genomic instability that evolves with the progression of disease. This genomic instability is considered responsible for development of aggressive phenotype associated with relapsed disease and for development of drug resistance. The molecular basis for the generation of this genetic diversity in cancer cells thus has important implication in understanding cancer progression and therapy. However the genomic evolution in MM patient samples has not been documented. Here, we have utilized single nucleotide polymorphism (SNP) arrays to monitor genome-wide changes in heterozygosity and copy number, in two CD138+ MM cell samples collected 6 months apart from 14 MM patients. Genomic changes acquired in the late tumor samples were identified using early samples as baseline. We defined an event as detectable change in heterozygosity/copy number in three or more consecutive SNPs. All 14 MM patients acquired new genomic change in the later sample at a frequency ranging from 0.021 - 2.674 % (i.e. per 100 informative loci investigated). Although the rate of mutation varied, 12 out of 14 patients had acquired >100 mutational events. Chromosomes 1, 13, and × showed large areas of copy number change in several patients. We also evaluated if genomic changes correlate with changes in expression of corresponding genes. Selecting larger areas of genome, we observed that copy number changes correlate well with the change in expression of genes in these areas. As expected, we also observed a correlation among changes in copy number, heterozygosity, and gene expression at several chromosomal loci. In a number of instances frequently recurrent changes were observed. For example, recurrent copy number changes in areas spanning 1q42.13-1q44 and 1p12-1p12 of chromosome 1 were seen in majority (12 out of 14 and 13 out of 14) patients, whereas copy number changes in the p arm of chromosome × were present in all patients. Similarly the region of chromosome × spanning xq42.13-xq44 showed change in heterozygosity in majority of patients. We also observed that some of the newly acquired changes in late samples correlated with genomic markers of poor clinical outcome. We evaluated prognostic significance of these changes in 192 uniformly treated patients with MM with genomic gains and losses data from SNP array and survival information. Changes in chromosomal regions 1p12 and xp22.1-xp22.33 frequently observed in late samples were significantly (p = 0.017 and 0.037) associated with poor survival in these patients. These data suggest that MM cells acquire changes associated with aggressive phenotype and shorter survival. In conclusion we observe that MM patients acquire genomic changes at a very high rate; and certain chromosomal regions are more vulnerable predicting poor clinical outcome. These data also suggest a need to target mechanisms mediating genomic instability for therapeutic application. Disclosures: Richardson: Keryx Biopharmaceuticals: Honoraria. Anderson:Millenium: Consultancy, Honoraria, Research Funding; Celgene: Consultancy, Honoraria, Research Funding; Novartis: Consultancy, Honoraria, Research Funding.

Abstract 2846 Poster Board II-822 Background: A prominent feature of most cancers is striking genetic instability and ongoing accrual of mutational changes associated with tumor progression, including acquisition of invasiveness, drug resistance, and metastasis. Methods: We first utilized single nucleotide polymorphism (SNP) arrays (Affymetrix) to evaluate genome-wide gains and losses in copy number and heterozygosity in CD138+ multiple myeloma (MM) cells collected from 14 patients at two time points at least 6 months apart. To estimate the extent of genomic instability in each patient, the number of events leading to copy number or heterozygosity changes throughout the genome were calculated. An event was defined as detectable change in copy number or heterozygosity in three or more consecutive SNPs. Two cases were also investigated for genome-wide rearrangements utilizing a paired-end approach on next generation sequencing. Results: In a period of six months, all MM patients analyzed acquired multiple new mutational events including changes in copy number and heterozygosity, ranging from 0.021 - 2.674 %, indicating a wide range of genetic instability. Although the rate of mutation varied, the majority (71%) of MM patients had acquired > 100 mutational events within the six months period, thus indicating a striking genetic instability. Chromosomes 1, 13, and X were unique with respect to copy number changes and showed large areas of change, spanning the entire length of a chromosome in several patient samples analyzed. Chromosomes 1 and 13 also showed large areas of loss or gain of heterozygosity in several patients, indicating areas of recurrent changes. We were also able to correlate genomic changes with changes in expression of corresponding genes. In two cases, we investigated genome-wide rearrangements utilizing a massively parallel sequencing approach. Short insert (400bp) libraries from two samples collected 6 months apart were constructed and subjected to paired-end sequencing utilizing 37bp readlengths on the Illumina GAII instrument. Approximately 80 million reads were generated for each of the 4 samples. Read pairs were mapped back to the reference genome, and those mapping aberrantly (incorrect orientation, different chromosomes, incorrect genomic distance) were further analyzed. Bespoke PCR assays defining each breakpoint were designed and used to verify the somatic nature of the mapped rearrangement. Further, PCR fragments spanning somatic genomic rearrangements were sequenced to generate base-pair resolution of breakpoints. To date, 29 somatic rearrangements have been sequenced, including three that were present only in the second sample. One of these was on chromosome 13. Breakpoint sequencing revealed a 64.9Kb homozygous (no wild-type readpairs found) deletion removing the first two exons of the RB1 gene. No reads spanning this breakpoint were found in the matching sample taken six months earlier. Conclusions: This is the first study utilizing massively parallel sequencing to investigate the MM genome and provides important insight into the pathogenesis of disease progression .as well as confirms the potential of whole genome sequencing to inform biology of the disease that may affect the therapeutic approach in future. Disclosures: Munshi: Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Millennium: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Novartis : Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau. Richardson:Celgene: Consultancy, Membership on an entity's Board of Directors or advisory committees; Millennium Pharmaceuticals, Inc.: Consultancy, Membership on an entity's Board of Directors or advisory committees, Research Funding. Anderson:Celgene: Consultancy, Honoraria, Research Funding; Millennium: Consultancy, Honoraria, Research Funding; Novartis : Consultancy, Honoraria, Research Funding.

Abstract 1105 Poster Board I-127 Genetic recombination plays a critical role in telomere maintenance, chromosomal translocation, and gene amplification, and may therefore underlie the chromosomal aberrations observed with high frequency in number of malignancies. The molecular mechanism/s inducing genomic instability remains ill-defined and their elucidation may provide methods to prevent tumor progression and development of drug resistance. Our earlier work has demonstrated that homologous recombination (HR) activity is elevated in multiple myeloma (MM) cells and leads to increased rate of mutation and progressive accumulation of genetic variation over time. We have further demonstrated that the inhibition of HR activity in MM cells by siRNAs targeting recombinase leads to significant reduction in the acquisition of new genetic changes in the genome; and conversely, induction of HR activity leads to significant elevation in the number of new mutations over time, and development of drug resistance in MM cells. Here we have evaluated a PI3K inhibitor Wortmaninin which has significant inhibitory activity against both HR and non-HR (nHR) pathways. Exposure of MM cells (OPM1, ARP and RPMI 8226) to wortmannin (WM) led to reduced expression of recombinase (hsRAD51) and nearly complete inhibition of HR activity, within 24 hrs as determined by a plasmid based assay in which generation of active gene product by recombination is measured. Similarly nHR was evaluated by measuring generation of intact gene product from a linearized plasmid. We evaluated effect of WM on nHR by 3 hours preincubation before transfecting the plasmid followed by cell culture for 72 hrs at 37° C. Cells were harvested and analyzed for nHR as previously described. Treatment with WM led to >40% reduction in nHR, indicating that WM affects both HR and NHR pathways. Downregulation of these pathways by wortmannin was also associated with a reduced growth rate of myeloma cells in culture by 20-25% at 48 hours. Importantly, WM treatment markedly decreased the acquisition of new genomic changes in MM as measured by genome-wide loss of heterozygosity assay as an indicator of genomic stability. To evaluate the impact of WM on in vivo tumor growth, OPM1 cells were injected subcutaneously in SCID mice and following appearance of palpable tumors, mice were treated with WM at 0.75 mg/kg, injecting daily intraperitoneally. Treatment with WM was associated with almost complete inhibition of tumor growth in vivo. Long term exposure of myeloma cells to WM was consistently associated with reduced telomere length, probably by blocking HR dependent ALT pathway. These data identifies dysregulated recombination activity as a key mediator of DNA instability and progression of MM, and WM as a potential therapeutic agent for prevention of myeloma progression and possibly drug resistance. Disclosures Anderson: Millenium: Consultancy, Honoraria, Research Funding; Celgene: Consultancy, Honoraria, Research Funding; Novartis: Consultancy, Honoraria, Research Funding. Munshi:Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Millennium: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau; Novartis : Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau.

Multiple myeloma (MM) cells present with significant genetic abnormality. This genetic instability is considered responsible for not only development of malignant phenotype but also progression of myeloma as well as development of drug resistance. We have previously demonstrated that MM cell lines have elevated homologous recombination activity that leads to acquisition of new genomic changes over time and is associated with development of drug resistance (Blood2004; 104: 3409). However, such genomic evolution in patient samples has not been documented. Here, we have performed a genome wide loss of heterozygosity (LOH) assay, using high-density oligonucleotide arrays capable of measuring up to 500K single nucleotide polymorphisms (SNP) loci, and identify areas of amplification and losses to determine ongoing development of new changes that may reflect instability. We have evaluated 17 MM patients with purified myeloma cells obtained at two time points, at least six months apart. CD138–expressing myeloma cells from these patients were purified and their peripheral blood mononuclear cells were also obtained. Genomic DNA from these cells was digested with StyI, PCR amplified and hybridized to 250K SNP array. Results from CD138+ myeloma cells from two time points or more were compared with each other using the dChip software for LOH and copy number analysis. During the LOH analysis, we have adapted a tumor vs. tumor comparison to track all the new SNPs affected. We have observed that myeloma cells acquired new LOH loci in the subsequent samples. These new areas of genetic changes were recurrent; for example on chromosome 13, an average area of recurrent LOH of 87 Mb was found to be present among three patients. We were able to observe recurrence of significant copy changes on several chromosomes with/without LOH. The reproducible area of new acquisition of LOH and/or significant copy changes interestingly involved areas on chromosomes 1p, 1q, 8p, 9q, 13q, 15, 16q, 20p, 21q, and X that may have significant role in the pathogenesis and progression of the disease. We are currently analyzing the gene expression profile from these time points to identify expression changes correlating with the observed genomic changes on follow up samples. In summary we demonstrate continued acquisition of new genomic changes in vivo in MM over time and provide a molecular basis for evolution of more aggressive disease able to escape therapeutic interventions. The mechanism governing such evolution is an important target to not only inhibit progression of the disease but also development of drug resistance.