Arora, Shilpi

Abstract Abstract 229 Introduction: Optimal rational combination targets with Cytarabine (AraC) have not been identified. After the development of a high-throughput, small-interfering RNA (siRNA) platform for suspension cells, we performed the first RNAi sensitizer screen of the human kinome with AraC in myeloid cell lines. Herein we present the final data of this first siRNA-sensitizer screen in leukemias in combination with AraC. Our results include full validation of the selected targets as well as ex vivo data assessing the first in class clinically tested WEE1 inhibitor MK1775 with AraC providing a pre-clinical rationale for using the combination of AraC with WEE1 inhibitors in leukemias. RNAi Screens and siRNA Validation: In siRNA sensitizer screens, we silenced 572 kinases of the human kinome in combination with AraC. Few kinases strongly sensitized to AraC and the targets CHEK1 and the WEE1 related kinase PKMYT1 emerged as the most potent genes whose silencing sensitized leukemia cells to AraC. In secondary siRNA validation experiments, silencing of WEE1 kinase was found to be more potent than silencing of CHEK1, PKMYT1 or other kinases (i.e. ATR, BRCA, AURKB) in combination with AraC treatment. Importantly, the sensitizing activity observed with WEE1 inhibition was universal across all AML cell lines examined, whereas it was not for CHEK1 inhibition. siRNA assays were robust, exhibiting little (<10%) non-specific toxicity and siRNA silencing was specific for individual genes (i.e. WEE1 or CHEK1) as demonstrated by selective reduction of mRNA and protein level for the respective genes; confirming the validity of the siRNA assay. Pharmacological WEE1 Inhibitor Experiments In vitro and Ex vivo: In vitro treatment of eight AML, ALL and CML cell lines with commercial and the first clinically developed WEE1 kinase inhibitor MK1775, demonstrated strong sensitization to AraC up to 97-fold in individual cell lines. Ex vivo, MK1775 substantially reduced viability in 13 of 14 AML, MDS and CML patient samples compared to AraC alone. The optimal dose to achieve maximum sensitization was observed for AraC between ∼10–120 nM and for MK1775 between 200–400 nM. Synergy at these optimal concentrations was confirmed in all ex vivo samples tested for which sufficient data for analysis with CalcuSyn Software was available (n=7): with Combination Indices (CI) ranging from 0.21–0.45. At higher AraC and MK1775 concentrations antagonism was observed both ex vivo and in vitro. Thus, we have also established optimal suggested concentration dose ranges for the currently ongoing design of a clinical trial. Clinically relevant, WEE1 is expressed in primary AML, ALL and advanced CML specimens with a trend towards higher expression in relapsed samples. However, there was no direct correlation with WEE1 mRNA expression or TP53 status. Our initial in vitro experiments further suggest that inhibition of WEE1 with MK1775 in combination with AraC at optimal concentrations was associated with higher degree of caspase 3 cleavage, DNA damage induction as measured by gamma-H2AX, and greatest inhibition of proliferation. Thereby establishing a context of optimal drug concentration ranges with molecular correlates and anti-leukemic activity directly informing design of the clinical trial and correlative biomarkers. In conclusion, data from this first siRNA sensitizer screen of the kinome in leukemias identifies inhibition of WEE1 kinase as the most potent sensitizing target to AraC. Inhibiting WEE1 with pharmacological inhibitors in combination with AraC is a rational treatment strategy for myeloid and lymphoid leukemias that warrants clinical investigation. Furthermore, our RNAi loss-of-function genomics approach has high potential to rapidly identify and validate crucial genes whose inhibition modulate the response to cytotoxic agents. Establishment of the siRNA sensitizer platform allows accelerating the development of new rational combinations for leukemia therapy. Disclosures: Off Label Use: AraC in combination with the experimental Wee1 inhibitor MK1775. Mesa:NS Pharma: Research Funding; Astra Zeneca: Research Funding; SBio: Research Funding; Lilly: Research Funding; Incyte: Research Funding; Celgene: Research Funding. Demuth:Merck and CO: Employment.

Abstract Objective The prevalence and mortality for head and neck cancer (HNC) has not improved significantly in the last several decades. It is the sixth most common cancer with an estimated 600,000 new cases diagnosed worldwide every year and has ∼50% 5-year survival rate. Of these, 47000 new cases are diagnosed in the US annually. The most common risk factors for HNC are tobacco and alcohol use but a growing subset is also attributed to human papillomavirus (HPV) infection. Late stage HNCs are treated with a combination of surgery, radiation, and chemotherapy (often platinum-based), but the cancers treated with platinum-based chemotherapy often develop drug resistance. Identification of target genes using high-throughput RNAi (HT-RNAi) gene-silencing technology has become an increasingly popular method in the field of cancer research. The objective of our study is to use this functional genomics based approach to identify genes that, when silenced, increase the sensitivity of the platinum drugs. This would possibly help us in identifying potentiators of platinum-based drugs to more effectively treat HNC patients. Methods We performed drug dose response (DDR) experiments on nine HNC cell lines; including two are HPV-positive lines, to identify cisplatin-resistant and -sensitive cancer cell lines. To identify sensitizers of cisplatin response, we used a siRNA library targeting 572 kinases. Each kinase is represented by two different siRNA sequences in the library. Based on the data mined from published literature on head and neck cancer as well as genes thought to confer a functional relationship between HPV infection and HNC, a more focused siRNA library was also designed and included in the screening. Cell lines were reverse transfected with the siRNAs in a 384 well format, dosed with cisplatin after 24 hours and the plates were read 72 hours later. Results We calculated the inhibitory concentrations using DDR experiments for all the nine HNC cell lines and identified cisplatin-resistant (UMSCC47 and SCC9) and -sensitive (Cal27, UMSCC14C, and SCC090) HNC cell lines. HT-RNAi experiments have been performed on the cisplatin-resistant cell lines, one of which is HPV-positive. After data analysis, confirmation of silencing and validation of drug modulation will be done on a subset of candidate genes. Conclusions HNC patients with surgically non-resectable tumors could have improved treatment with chemotherapeutic drugs; however, acquired drug resistance often inhibits a successful treatment. Identification of sensitizing targets may provide hope for a better outcome, but may also allow for use of smaller doses of more toxic drugs, such as cisplatin. In addition, this study may also identify alternate genes that can be targeted in the subset of HPV-positive HNC. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5136. doi:1538-7445.AM2012-5136

AbstractTo identify rational therapeutic combinations with cytarabine (Ara-C), we developed a high-throughput, small-interference RNA (siRNA) platform for myeloid leukemia cells. Of 572 kinases individually silenced in combination with Ara-C, silencing of 10 (1.7%) and 8 (1.4%) kinases strongly increased Ara-C activity in TF-1 and THP-1 cells, respectively. The strongest molecular concepts emerged around kinases involved in cell-cycle checkpoints and DNA-damage repair. In confirmatory siRNA assays, inhibition of WEE1 resulted in more potent and universal sensitization across myeloid cell lines than siRNA inhibition of PKMYT1, CHEK1, or ATR. Treatment of 8 acute myeloid leukemia (AML), acute lymphoblastic leukemia (ALL), and chronic myeloid leukemia (CML) cell lines with commercial and the first-in-class clinical WEE1 kinase inhibitor MK1775 confirmed sensitization to Ara-C up to 97-fold. Ex vivo, adding MK1775 substantially reduced viability in 13 of 14 AML, CML, and myelodysplastic syndrome patient samples compared with Ara-C alone. Maximum sensitization occurred at lower to moderate concentrations of both drugs. Induction of apoptosis was increased using a combination of Ara-C and MK1775 compared with using either drug alone. WEE1 is expressed in primary AML, ALL, and CML specimens. Data from this first siRNA-kinome sensitizer screen suggests that inhibiting WEE1 in combination with Ara-C is a rational combination for the treatment of myeloid and lymphoid leukemias.