Stewart, A. Keith

Abstract Cyclin Ds are key regulators of the cell cycle that are frequently over-expressed in multiple myeloma and leukemia and act to promote the phosphorylation of Rb, thereby facilitating the transition from G1 to S phase. Over-expression of cyclin Ds increases cell proliferation and chemoresistance. In contrast, reducing cyclin Ds levels directly or indirectly through G1 arrest can decrease cellular proliferation and induce apoptosis. To identify novel pharmaceutical inhibitors of cyclin D transactivation, we screened the LOPAC and Prestwick libraries of drugs and natural compounds (n = 2400) using NIH 3T3 cells stably expressing the Cyclin D2 promoter-driving a luciferase reporter gene. From this library screen and subsequent validation experiments we identified Cyproheptadine as a novel inhibitor of Cyclin D2 transactivation. Cyproheptadine has been used previously for the treatment of atopic dermatitis and anorexia, but its ability to inhibit cyclin D expression has not previously been reported. By immunoblotting, Cyproheptadine decreased expression of cyclin D1, D2 and D3 proteins in human myeloma and leukemia cell lines at low micromolar concentrations. Consistent with effects on the cyclin Ds, Cyproheptadine arrested cells in the G1 phase at concentrations associated with reduction in cyclin D expression. Decreased cyclin D expression and G1 arrest can induce apoptosis, so we tested the effects of Cyproheptadine on cell viability. Myeloma and leukemia cell lines were treated with increasing concentrations of Cyproheptadine and viability was measured by the MTS assay. Cyproheptadine reduced the viability of 7/10 myeloma and 7/8 AML cells lines with an IC50 ranging from 10–25μM. In contrast, it was less toxic to HeLa or NIH3T3 cells with IC20 > 50 μM. Cyproheptadine also reduced the viability of primary myeloma (8/8) and AML patient samples (7/9) with an IC50 <25 μM, but was less toxic to normal hematopoietic cells (IC20 > 50 μM). In a MDAY-D2 mouse model of leukemia, treatment with Cyproheptadine (50mg/kg/d) abolished formation of malignant leukemic ascites without untoward toxicity. Cyproheptadine-induced cell death was associated with reductions in mitochondrial membrane potential. Furthermore, reductions of pro-caspases -3 and -9 were observed prior to the reduction in pro-caspase-8, indicating that Cyproheptadine activates the mitochondrial pathway of caspase activation. Cyproheptadine is a known H1 histamine and serotonin receptor inhibitor, but pre-incubation with histamine, serotonin, or a combination of histamine and serotonin did not abrogate Cyproheptadine-induced cell death. Moreover, the structurally related H1 receptor inhibitor loratadine did not decrease cyclin D expression or reduce cell viability. Therefore, the pro-apoptotic activity of Cyproheptadine is not due to a competitive inhibition of the H1 and/or serotonin receptors, suggesting that Cyproheptadine has additional targets. In summary, Cyproheptadine arrests cells in G1, reduces cyclin D expression, and induces apoptosis via the mitochondrial pathway of caspase activation. Given the prior safety and toxicity record of Cyproheptadine, this drug could be rapidly advanced into clinical trial for the treatment of hematologic malignancies.

Abstract Background: Chronic myelogenous leukemia (CML) is a BCR-ABL1 driven myeloid neoplasm, with excellent response rates to tyrosine kinase inhibitors (TKI). TKI such as imatinib (IM), dasatinib (DAS), nilotinib (NIL), bosutinib (BOS), and ponatinib (PON) currently US FDA approved, have dramatically changed survival outcomes. That being said, two main challenges exist; suboptimal responses and TKI intolerance. The reason why some patients tolerate/respond to TKI better than others is unknown, but is potentially explainable based on drug metabolism. The field of pharmacogenomics (PGX) is rapidly evolving, with commercial panel's rapidly assessing metabolic pathways such as cytochrome P450 (CYP), UGTA1A, p-glycoprotein/ABCB1. We carried out this study using a 22 gene-PGX panel to assess potential causes of TKI related intolerance and suboptimal responses in compliant patients. Methods: Twenty-nine Mayo Clinic patients with CML were prospectively recruited after informed consent. Buccal swabs were utilized for PGX testing to assess variations/polymorphisms involving CYP3A4/5, 1A2, 2C9, UGT1A1, amongst others (www.Oneome.com). Three groups of patients were recruited, those with i) TKI intolerance, ii) suboptimal responses by ELN criteria, iii) and newly diagnosed cases, to assess if PGX testing could explain TKI intolerance or resistance, or alter choice of therapy in newly diagnosed cases. A pharmacology review was obtained to interpret reports in all cases. Results: 29 patients with CML were prospectively enrolled, median age 64 years, 15 (52%) male. At last follow up (median 21 months), 3 (10%) deaths and no disease progressions were documented. 82% received first line IM, whereas 18% received first line DAS. Major metabolic pathways assessed for IM included, CYP3A4 and 5, while minor pathways included 2C19, 2C9 and 2D6. Majority (83%) of IM patients had normal major pathways with 17% being intermediate-normal. With regards to the minor pathways, 25% were rapid metabolizers for 2C19, whereas 29% were intermediate and 4% poor metabolizers for 2C9 and 50% and 16% were intermediate and poor metabolizers for 2D6. In all IM treated patients PGX testing did not completely explain intolerance or resistance and did not change clinical decision making. Front line DAS was used in 18% and the major pathway assessed was CYP 3A4, with 80% being normal and 20% being intermediate metabolizers. Once again PGX testing did not completely explain intolerance/resistance and no therapeutic changes were based on PGX analysis. Seventeen (59%) patients received second line TKI therapy (50% each for intolerance and resistance), with DAS (58%) and NIL (29%), being the two most common. Once again for DAS, 90% had normal 3A4 metabolism while 10% were intermediate and for NIL 80% were normal and 20% intermediate. Only one of 2 NIL treated patients with UGTA1A polymorphisms developed indirect hyperbilirubinemia (grade 1). In the second line setting, PGX testing did not completely explain or alter treatment decisions. BOS was used as a third line agent in 3 (>10%) patients, 2 who remained refractory and one with intolerance, and all three were normal CYP3A4 metabolizers. None of these patients developed diarrhea a common side effect of BOS. PON was used in one patient with intermediate CYP3A4 metabolism as a 5th line agent and the patient continues to have refractory disease with no thrombotic events. In all cases, no changes were made to concomitant medications based on PGX testing. Conclusion: In conclusion, while PGX testing has rapidly evolved and become commercially available, in the context of TKI therapy for CML, while it offers useful insights on minor metabolic derangements and side effects like NIL induced hyperbilirubinemia, in our study, currently limited by a small sample size, it did not completely explain TKI intolerance or resistance. Recruitment of additional patients (n=100) and correlations with plasma drug levels are currently ongoing. Table. Table. Disclosures Al-Kali: Novartis: Research Funding. Stewart:Amgen Inc., Celgene, Roche, Seattle Genetics: Research Funding; Amgen Inc., BMS, Celgene, Takeda, Roche, Seattle Genetics, Janssen, Ono: Consultancy.

Abstract Abstract 3854 Poster Board III-790 Background Primary systemic amyloidosis (AL) is an incurable plasma cell disorder. Lenalidomide, especially in conjunction with dexamethasone, has been shown to be active in patients with multiple myeloma. Pomalidomide is a derivative of thalidomide that acts as an immunomodulator. Preliminary data in multiple myeloma demonstrate that this agent is highly active and well tolerated. Methods Eligible patients were accrued into an IRB approved treatment trial with pomalidomide and dexamethasone after signing informed consent. Pomalidomide (2 mg) and dexamethasone (40 mg) were scheduled to be taken orally, the former on a continuous schedule and the latter once weekly. All patients were instructed to take an aspirin daily. Patients were eligible if they had previously treated, biopsy proven, symptomatic AL. Patients were required to have measurable hematologic disease, defined as either a serum M-protein greater than 1 g/dL, a urinary M-protein greater than 200 mg/24-hours, or a serum immunoglobulin free light chain greater than 10 mg/dL. Other eligibility criteria included an ECOG PS>=2, adequate hematologic reserve (ANC>=1000/uL, platelets>=75/uL) and adequate renal function (creatinine <=2.5 mg/dL). They also were required to comply with contraceptive requirements. Patients were excluded if they had uncontrolled infection, another active malignancy, NYHA classification III or IV, a serum troponin T >0.1 ng/mL, >=grade 3 peripheral neuropathy, untreated active thrombosis, or other chemotherapy within 2 weeks of study enrollment. Thirty-four patients are to be enrolled to allow for 2 possible cancels and to provide 90% power to detect a true hematologic response rate of at least 20%. Between 11/24/08-7/28/09, 20 patients have been enrolled. Baseline characteristics and adverse events are available for 17 of the 20 enrolled patients. Results Median age was 63 years (range 52 78), with 60% male. The median time from diagnosis to study entry was 45 months (range 4.5-103). Eighty-two percent had cardiac involvement; 41% renal involvement; 18% peripheral nerve involvement; and 12% autonomic nerve involvement. The cardiac biomarker staging breakdown was: I, 13%; II, 56%; and III, 31%. Patients were heavily treated, with 100% having received prior alkylator (including prior transplant in 9), 44% prior lenalidomide, 31% prior thalidomide, and 37% prior bortezomib. Thirty-three percent of patients had non-hematological adverse events (AEs) >=grade 3 (severe) that were deemed to be at least possibly related to therapy. Thirty-three percent had >=grade 3 hematologic AEs. Neutropenia was most the most common severe hematologic AE; severe thrombocytopenia was observed in only 1 patient, and there was no severe anemia. The most common severe non-hematologic AE was fatigue, which was observed in 3 patients. The only other severe AEs, each of which was observed in one subject each, were pneumonia, weakness, dyspnea, and ascites. As of 8/14/09, 17 patients remain on active therapy. Median time on study is only 3.7 months (range 0.2-8.1). Three patients have discontinued therapy: two progressions; and one death 5 days into treatment, presumably due to cardiac amyloidosis. At the time of this writing response rates could not be calculated given the short follow-up, but hematologic responses have been observed, and details on efficacy will be presented at the meeting. Conclusions Pomalidomide is well tolerated in previously treated AL patients. More information about its activity will be provided at the meeting. Disclosures: Dispenzieri: Celgene: Research Funding. Gertz:Celgene: Honoraria. Kumar:Celgene: Research Funding. Rajkumar:Celgene: Research Funding. Witzig:Novartis: Research Funding. Greipp:Celgene: Research Funding. Fonseca:Celgene: Consultancy. Bergsagel:Celgene: Consultancy. Mikhael:Celgene: Research Funding. Roy:Celgene: Research Funding. Lacy:Celgene: Research Funding.

Abstract Introduction: Partial loss of chromosome arm 1p frequently occurs in multiple myeloma (MM), and is associated with a poor prognosis. Several minimally altered regions on 1p have been identified, including 1p32.3, 1p31.3, 1p22.1-1p21.3, and 1p12. Cytoband 1p12 was deleted in 19% of cases, and this deletion was associated with shorter overall survival (OS) in univariate analysis. The target of homozygous deletion 1p12 was FAM46C. In addition, mutations of FAM46C were identified in 3.4% to 13% of primary MM tumors and 25% of 16 human myeloma cell lines (HMCLs), implying its potential pathogenic relevance. In other work we have suggested that FAM46C mutation is a progression event and have shown that it is rarely seen in newly diagnosed del17 patients, inferring some overlap in function. However, there is no published functional annotation of FAM46C and its role in MM remains unknown. In the present study, we aimed to identify the biological role of FAM46C in myeloma cells. Materials/Method: The expression of FAM46C in HMCLs was analyzed by western blot. Lentiviral constructs expressing wild type and mutated FAM46C were generated and transduced into HMCLs, followed by cell viability assay and cell cycle analysis. Cells were harvested and processed to measure gene expression and cell signaling changes after introduction of FAM46C by mRNAseq, pathway analysis and immunoblotting assay. Results: The expression of FAM46C protein is generally low in most HMCLs. Introduction of wild type FAM46C in HMCLs induced a substantial cell growth inhibition and apoptosis, especially in two HMCLs including MM1.S and KMS11. Cell viability of KMS11 and MM1.S was reduced by 50% to 80% at day 6 after introduction of FAM46C, compared to 0-30% growth retardation detected in HMCLs and non-myeloma cell lines that do not carry FAM46C deletion. We identified 88 genes whose mRNA expression was significantly altered after enforced expression of FAM46C in MM1.S cells. Pathway analysis revealed that FAM46C-regulated genes are enriched in the canonical pathways associated with unfolded protein response, cell cycle control and DNA damage repair. Critical MM genes that are downregulated by FAM46C expression include IRF4 and MYC, which are also downstream targets of immunomodulatory drugs (IMiDs). Consistently, some HMCLs such as KMS11 and OPM2 show an enhanced sensitivity to lenalidomide after introduction of FAM46C. Next, lentiviral constructs expressing various FAM46C mutants were generated in order to understand the consequence of FAM46C mutation. The mutant constructs mimic mutations identified in MM patients or HMCLs. Those mutants and wild type FAM46C were transduced and tested together in MM1.S cells. We found that three published misssense mutations, one frame-shift mutation and deletion of the sequence between aa172 and aa186 of FAM46C (which has been found in previous studies as a hot spot of mutation) all abolished FAM46C-mediated anti-myeloma activity, thus would be expected to confer a MM cell survival advantage. Conclusion: Our data demonstrated that enforced FAM46C expression in myeloma cells induced myeloma growth inhibition and apoptosis. Mutations in FAM46C and TP53 in newly diagnosed patients seem mutually exclusive but not in relapsed patients from our patients sequencing studies, suggesting it may associate with disease progression. Together, these studies suggest that FAM46C may function as a tumor suppressor in myeloma. We also found that published mutations of FAM46C confer a survival advantage to MM cells, and that FAM46C overexpression downregulates IRF4 and MYC and is thus associated with loss of myeloma cell survival. Disclosures Stewart: Novartis: Consultancy; Oncospire Inc.: Equity Ownership; Celgene: Consultancy; BMS: Membership on an entity's Board of Directors or advisory committees.

Abstract Abstract 2801 Poster Board II-777 To provide a rationale basis for targeted drug development for multiple myeloma patients, we have conducted high-throughput genome-scale RNA interference (RNAi) synthetic lethality studies in human myeloma cell lines (HMCL) to generate a comprehensive map of critical genes and molecular vulnerabilities in human myeloma tumor cells. KMS11 human myeloma cells were screened with a 13,982-oligo library targeting the ‘druggable' genome (6,991 genes) using optimized conditions that resulted in >95% transfection efficiency. Each gene was screened with 2 or more distinct oligos, in duplicate, using a single-siRNA-per-well format, testing >34,000 wells. Replicate high throughput experiments yielded highly reproducible results (R2=0.82). Viability was measured at 96h by ATP-dependent luminescence. Universally lethal siRNA and non-targeted siRNA were employed as controls. The specificity (FDR) of lethal RNAi was evaluated by custom-developed statistical methods based on RNAi result concordancy. From screening, 5.8% of druggable genome siRNA caused statistically relevant reductions in HMCL viability (greater than three standard deviations from control samples treated with non-silencing siRNA, compared with an anticipated rate due to chance of only 0.135%). Of these, two hundred and nineteen genes, targeted by the most lethal siRNA, were forwarded to validation studies. Validation high-throughput RNAi studies, using 4 oligos per gene, were conducted in order to verify target gene vulnerability. Ultimately, seventy two genes were validated as highly critical for myeloma cell survival (each with multiple concordant siRNA hits plus high reproducibility of R2 =0.94). Among top-ranked lethal molecular vulnerabilities in KMS11 myeloma cells we recurrently identified the proteasome (8 PSM subunits were independently identified as highly vulnerable); and BCL2 family member MCL1; both known therapeutic targets, validating a functional genomics approach to target discovery. In addition, a number of novel, equally lethal, molecular vulnerabilities were identified in KMS11 including WEE1, kinetochore complex component KNTC2, the aurora kinases, polo-like kinase 1, a previously uncharacterized DNA methyl transferase, ribonucleotide reductase, ribosomal protein L38, leptin receptor overlapping transcript LEPROT and SLC25A23 (a carrier responsible for mitochondrial adenine nucleotide flux). Various ubiquitous cellular proteins involved in RNA or protein processing (e.g. SF3a, SNW1, SNRPA1, EIF3s8, amongst others) were also identified as non redundant and critical for cellular viability. Thirty nine top-ranked molecular vulnerabilities in KMS11 were evaluated for comparative vulnerability in a second myeloma cell line, JJN3, and in A549 and 293 epithelial cells. A majority were vulnerable in JJN3. While 25 genes proved equally lethal on silencing in A549 and 293 epithelial cells, several, notably including MCL1 and three proteasome subunits, appear differentially susceptible in myeloma cells versus epithelial cells. From this genome scale study, MCL1 ranks third as a target capable of inducing cell death in myeloma cells, highlighting the potent vulnerability of myeloma cell viability to alterations in this anti-apoptosis regulator. Moreover, from active comparative studies of molecular vulnerability in myeloma versus epithelial cell lines, MCL1 as an RNAi target demonstrates perhaps the greatest cytotoxic selectivity between myeloma and epithelial cell lines of all targets examined. Gene expression studies indicate that MCL1 is highly expressed in myeloma tumor cells but is absent or only weakly expressed in human primary somatic tissues. Overall, therefore, from an unsupervised genome-scale screening approach, our data support MCL1 as an optimal Achilles heel molecular target in multiple myeloma, potentially offering greater specificity and deeper cytotoxic effect than proteasome inhibition. Disclosures: No relevant conflicts of interest to declare.

Abstract Background: It is now well established that the immune modulator (IMiD) drugs thalidomide (Thal), lenalidomide (Len) and pomalidomide (Pom) bind a specific pocket in the protein, cereblon (CRBN) that is required for MM cytotoxicity after IMiD treatment. Recently, we reported 46 CRBN binding proteins which were altered by Len, two of which were the transcription factors Ikaros (IKZF1) and Aiolis (IKZF3), important regulators of B and T cell development. Others had previously reported the same finding and went further by demonstrating that following binding of IMiD drugs, CRBN accumulates and accentuates the ubiquitination and subsequent proteasomal degradation of these two binding proteins. The resulting degradation and depletion of IKZF proteins has the simultaneous effect of downregulating IRF4 and MYC leading to MM cell death while simultaneously enhancing transcription of interleukin 2 and activating the immune compartment. Methods: To further explore this phenomenon and its relationship to drug sensitivity we first created two stable MM cell lines (H929IKZF1Luc, 8226IKZF1Luc) expressing an IKZF1-luciferase (luc) fusion gene and tested for sensitivity to Len alone and in combination with dexamethasone (Dex), bortezomib (Bor) or the histone deacetylase inhibitor SAHA. Next, we constructed an adenoviral vector expressing IKZF1-luc and used this to transfect 16 MM cell lines, confirmed expression and tested sensitivity to Len by MTT (Figure 1). Results: We first examined the stable cell lines and measured luc expression after exposure to all three IMiD drugs. With all IMiD drugs luc dramatically decreased in sensitive H929 cells. IKZF1 depletion was both time and dose dependent. Using this surrogate marker cell line assay, luc is most efficiently degraded by Pom which is twice as potent as Len, but a thousand times more potent than Thal (Concentration of drug required to reduce luc expression by 50%, Pom: 4.9nM, Len: 10.2 nM, and Thal: 4,795 nM). We then tested all 16 cell lines with Len 2uM for 5 hours and show a strong correlation of IKZF-luc depletion with sensitivity. Figure 1: Luc levels 5 hours after Len treatment at 2uM. We divided the cell lines into three groups: 1) Len resistant: 8226, KMS12PE, My5, SKMM2, JJN3, FR4, H112; 2) Len intermediate response: EJM, OPM2, U266, KMS18; 3) Len sensitive: H929, MM1.S, MM1.R, KMS11, XG1; Figure 1:. Luc levels 5 hours after Len treatment at 2uM. We divided the cell lines into three groups: 1) Len resistant: 8226, KMS12PE, My5, SKMM2, JJN3, FR4, H112; 2) Len intermediate response: EJM, OPM2, U266, KMS18; 3) Len sensitive: H929, MM1.S, MM1.R, KMS11, XG1; We next performed western blots on 9 MM cell lines and demonstrate that IKZF1 levels were lowest in 3 of 5 resistant MM cell lines and normal in all 4 sensitive lines studied. The cell line (FR4) with the lowest levels of IKZF1 harbors a damaging mutation of IZKF1 as well as a translocation which upregulates IRF4, an IKZF target. Of the remaining two resistant lines one has low levels of Cereblon. In one line the mechanism of IMiD resistance could not be established. Finally, we were curious about the dichotomy of the IMiD biology which seemingly has an absolute requirement for a functional proteasome for successful IMiD cytotoxicity which is at variance with clinical reports of synergy between the IMiDs and the proteasome inhibitors (PIs) Bor and carfilzomib (Car). To explore this, we treated the 8226IKZF1Luc cell line with Len alone or in combination with increasing concentrations of Bor (6 nM) or Car (40nM) and found that both totally blocked IKZF1 fusion protein degradation promoted by Len, beginning as soon as 1 hour at 100nM Bor or after 3 hours at 40nM treatment. Conversely, in low concentration of Bor (<4nM) no IKZF1 degradation blocking was observed in the Luc assay and Bor remained lethal to the MM cells. In that light with lower levels of Bor (<3nM) even varying the sequencing of MM cell exposure to the two drug classes did not block cytotoxicity. Other MM active drug Dex or SAHA, blocking the aggresome, had no significant inhibition for Len-induced IKZF1 fusion protein degradation. Conclusion: These results validate the central role for the CRBN-IKZF-IRF4 axis proteins in IMiD response and show a strong correlation of IZKF1 expression and the ability to degrade IKZF1 with sensitivity. Our data provide interesting and perhaps disconcerting biologic data suggesting that the timing and dosing of clinical use of IMiDs and PI treatment in combination should be carefully evaluated to prevent antagonism of effect but suggest in vitro that a therapeutic window exists at which proteasome inhibitors can be active without blocking IMiD activity. Disclosures Stewart: Sanofi: Consultancy; Array BioPharma: Consultancy; Bristol Myers Squibb: Consultancy; Celgene: Consultancy; Novartis: Consultancy; Takeda Pharmaceuticals International Co.: Research Funding.

463 Background: The genomic assessment of cancer has been revolutionized by next-generation sequencing and is increasingly being applied in the clinic to guide therapeutic decision-making. Time to reporting of results, specimen quantity, and analyte quality have constrained initial clinical applications to gene panels and whole exome based strategies. Methods: Patients underwent surgical resection, excisional or core biopsies, or bone marrow biopsy. Samples were analyzed by whole genome or exome sequencing and RNA sequencing, bioinformatics analysis, and therapeutic target prioritization by a multi-disciplinary Clinical Genomics Board. All prioritized targets were CLIA validated using Sanger sequencing, RT-qPCR, FISH, or IHC as appropriate. Treatment was delivered using off-label FDA approved drugs, clinical trials, or single patient INDs. Results: We have enrolled 40 patients with advanced, treatment-refractory cancers of whom sequencing data is available on 33. The initial 6 patients were evaluated in a non-CLIA pilot phase and 27 in the CLIA enabled phase. Upon availability of the initial report, identified targets of putative therapeutic relevance were then prioritized by the CGB in 22/27 patients (81%) for subsequent CLIA validation. Eleven patients have been treated with genomically selected therapy with partial response in 3/10 assessed patients. A testicular cancer patient had aberrations in two testes specific genes, a copy number gain in TSSK6 and a novel gene fusion between thyroid hormone receptor associated protein 3 (THRAP3) and Tektin 2 (TEKT2). Additionally, a case of papillary renal cell carcinoma had an amplification of YAP1 and a previously unreported P287T mutation in CCND1, suggesting potential benefit with a CDK4/6 inhibitor. Treatment is ongoing and results will be reported. Conclusions: Integrated whole genome analysis in a CLIA setting is feasible. Integration of SNV, copy number and transcriptional data may allow for selection of putative driver genes to enhance targeted therapy decisions. Barriers for future broader implementation include the need for reduced time from biopsy to report and availability of therapies.

AbstractPatients with indolent non‐Hodgkin lymphoma (NHL) have multiple treatment options yet there is no consensus as to the best initial therapy. Lenalidomide, an immunomodulatory agent, has single agent activity in relapsed lymphoma. This trial was conducted to assess feasibility, efficacy, and safety of adding lenalidomide to rituximab, cyclophosphamide, and dexamethasone (LR‐CD) in untreated indolent NHL patients requiring therapy. This was a single institution phase II trial. Treatment consisted of IV rituximab 375 mg/m2 day 1; oral lenalidomide 20 mg days 1–21; cyclophosphamide 250 mg/m2 days 1, 8, and 15; and dexamethasone 40 mg days 1, 8, 15, and 22 of a 28‐day cycle. Treatment continued 2 cycles beyond best response for a maximum of 12 cycles without rituximab maintenance. Thirty‐three patients were treated. Median age was 68 (43–83 years). 39% had stage IV disease. Histologic subtypes included 8 follicular lymphoma (FL), 7 marginal zone lymphoma (MZL) (1 splenic, 2 extranodal, and 4 nodal), 15 Waldenström's macroglobulinemia (WM), 1 lymphoplasmacytic lymphoma, 1 small lymphocytic lymphoma, and 1 low‐grade B‐cell lymphoma with plasmacytic differentiation (unable to be classified better as MZL or LPL). Hematologic toxicity was the most common adverse event. Median time of follow‐up was 23.4 months (range 1.8–50.9). The overall response rate was 87.9%, with 30.3% complete response. The median duration of response was 38.7 months. The median progression free survival was 39.7 months, while median overall survival (OS) has not yet been reached. Lenalidomide can be safely added to a simple regimen of rituximab, oral cyclophosphamide, and dexamethasone and is an effective combination as initial therapy for low‐grade B‐cell NHL.

Abstract Background: Genomic assessment of cancer has been revolutionized by Next-Generation sequencing and is increasingly being applied to guide clinical prognostic and therapeutic decision-making. Initial clinical applications have been limited to gene panels and whole exome based strategies due to challenges with time to reporting of results, specimen quantity, analyte quality, and ethical-legal-social issues (ELSI). Methods: Excisional or core tumor biopsies or bone marrow biopsies were obtained from consenting participants. Nucleic acid was extracted from fresh or frozen samples followed by WGS/WES/RNASeq on the Illumina HiSeq2000 or HiSeq2500 and bioinformatics analysis. Therapeutic targets were then prioritized by a multi-disciplinary Genomic Tumor Board (GTB) and CLIA validated using Sanger sequencing, RT-qPCR, FISH and/or IHC. Treatment was delivered using on/off-label FDA approved drugs, available clinical trials and single patient INDs. Results: We consented 64 and enrolled 35 patients with advanced, treatment-refractory cancers. Median age was 59 (range 27-91) with 62% male. The majority had ECOG scores of 1 (94%). A median of 79 (range 28-8891) potentially functional somatic point mutations were identified in each case. One to two mutations/case were further identified as therapeutically targetable in 60% of the cases. The median time from tissue acquisition to CLIA validated results was 116 days (range 42-282) with CLIA validation of targets achieved in 21 of 22 patients. Genomic, target directed treatment was ultimately instituted in 13 patients utilizing: on/off label FDA approved drugs (n = 9), clinical trial (n = 3) and single patient IND (n = 1). Preliminary clinical efficacy was noted in 5 patients (2 PR, 3 SD). Integration of WES, long-insert WGS and RNA-Seq identified a case with an ERRFI1 mutant allele present in only 11% of the DNA reads while 82% of the RNA-Seq reads had the mutant transcript. The patient was treated with erlotinib and achieved a partial response by RECIST criteria. In another case, a fusion between FGFR2-MGEA5 was observed in WES and RNA-Seq data leading to prioritization as a drug target. Reasons for patients not receiving targeted therapy included: inability to access treatment (n = 1), death prior to intended treatment (n = 3), results returned after death (n = 3), no targets identified (n = 2) and decision to pursue alternate therapy (n = 5). Conclusions: Integrating whole genome analysis in a CLIA setting is not only feasible, but also valuable, in the prioritization and selection of potential targeted therapies for patients with advanced tumors. Continued barriers to broad application include the need for shorter time to reporting as well as broad availability of therapies through basket studies. Citation Format: Mitesh J. Borad, Jan Egan, Mia Champion, Katherine Hunt, Robert McWilliams, Ann McCullough, Jessica Aldrich, Sara Nasser, Winnie Liang, Michael Barrett, David Craig, Ramesh Ramanathan, John Carpten, A. Keith Stewart, Alan Bryce. Implementation of CLIA enabled integrated whole genome (WGS)/exome (WES)/transcriptome (RNAseq) next-gen sequencing to identify therapeutically relevant targets in advanced cancer patients. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr CT112. doi:10.1158/1538-7445.AM2015-CT112

Abstract Background: Whole genome/exome/RNA sequencing has revolutionized the ability to assess the genomic landscape of cancer and is increasingly being utilized for clinical decision-making. Initial clinical applications have been constrained by specimen quantity, analyte quality and the time from sample acquisition to results report. Methods: Patients with advanced cancers underwent surgical resection, excisional/core biopsies, or bone marrow biopsy. Samples were analyzed by whole genome or exome sequencing in addition to RNA sequencing, bioinformatics analysis, and therapeutic target prioritization by a multi-disciplinary Clinical Genomics Board. All prioritized targets were CLIA validated using Sanger sequencing, RT-qPCR, FISH, or IHC as appropriate. Treatment was delivered using off-label FDA approved drugs, clinical trials, or single patient INDs. Results: We have enrolled 40 patients for whom sequencing data is available on 33. The initial 6 patients were evaluated in a non-CLIA pilot phase and 27 in a CLIA-enabled phase. Tumor types in the CLIA-enabled phase with the highest enrollment were pancreatic cancer (n=8) and cholangiocarcinoma (n=8). We sought to quantify the targets identified along with clinical benefit, defining these as the “Actionable Index” (AI) (proportion of patients with ≥ 1 putative drug target) and “Utility Index” (UI) (proportion of patients who derive clinical benefit). Putative therapeutic targets were identified in 7/8 (AI=0.88) cholangiocarcinoma (CC) patients and in 5/8 (AI=0.63) pancreatic cancer (PC) patients. All 3 CC patients who received target directed treatment achieved a partial response (UI=0.38). In contrast, none of the 4 PC patients who received target directed therapy had treatment response (UI=0.0). Interestingly no actionable targets were identified in 1 CC and in 2 PCs. One CC with an identified target was unable to access the drug and subsequently died. A CC patient and a PC patient, each with identified targets, expired prior to the initiation of therapy. Conclusions: While whole genome/exome/RNA sequencing is providing unparalleled detail of tumor genomes, the application to the clinic must be carefully considered. Actionability of targets will eventually need to be defined in close relation to eventual clinical utility and appropriate refinements to disease-gene-drug databases implemented. Preliminary observations in pancreatic cancer and cholangiocarcinoma demonstrate disparity in correlation between utility indices and actionable indices. Application of these tools in larger cohorts and types of tumors will need to be conducted to ascertain more precise estimates. Additional measures that are organ-site agnostic but pertain to specific targets (e.g. BRAF) will also need to be developed in order to facilitate more judicious application of sequencing in the clinical setting. Citation Format: Jan B. Egan, Alan H. Bryce, Mia D. Champion, Winnie S. Liang, Rafael Fonseca, Ann E. McCullough, Michael T. Barrett, Katherine Hunt, Rachel M. Condjella, Robert R. McWilliams, Stephen D. Mastrian, Janine LoBello, Daniel Von Hoff, David W. Craig, A. Keith Stewart, John D. Carpten, Mitesh J. Borad. Indices of actionability and clinical utility in a CLIA-enabled study of whole genome/exome/RNA sequencing in 33 cancer patients: Actionable vs. utility. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4694. doi:10.1158/1538-7445.AM2014-4694