Bogenberger, James M.

Abstract Purpose: Cholangiocarcinoma (CCA) is a highly lethal malignancy that often presents at advanced stages. Gemcitabine/cisplatin (GP) represents the standard-of-care but provides only a modest response rate and survival benefit. Loss of the CDK4/6 inhibitor CDKN2A is a prevalent genetic event in CCA, thus CDK4/6 inhibitors, FDA-approved in some breast cancer regimens, are hypothesized to have a role in treating CCA. Clinical challenges to target cell cycle dysregulation and exploit cytotoxic chemotherapy include predictive biomarkers for selecting patients most likely to respond. We hypothesized autophagy is involved in therapeutic resistance to CDK4/6 inhibitors, and plays a role in the activity of GP in CCA. Thus, we investigated CDK4/6 inhibitors as monotherapy, and combined with GP in CCA, measuring multiple readouts pertaining to drug synergy, putative pathway biomarkers and autophagy. Methods: The activity of 3 FDA approved CDK4/6 inhibitors, palbociclib, ribociclib and abemaciclib, as monotherapy (N=24), and combined with GP (N=10), was assessed in CCA cell lines by measuring relative cell number with Cell TiterGlo, and apoptosis with Annexin/PI and cleaved caspase3 quantification via flow cytometry. To characterize RB status for biomarker potential, protein levels of CCND1, CDK4, CDK6, RB, and CDKN2A were measured by western blot. Autophagy was measured using an autophagy flux assay, LysoTracker confocal staining, and by quantifying protein levels of LC3B, p62 and Beclin1A. Results: 22/24 (92%) of CCA cell lines were found to have at least one defect likely relevant to CDK4/6 inhibition: CDKN2A (92%), Rb1 (63%), CDK4 (23%) and cyclin D1 (32%). Protein levels of CDKN2A and RB1 showed moderate correlation with CDK4/6 inhibitor activity. Abemaciclib was the most potent CDK inhibitor in vitro (IC50≤0.5uM; palbociclib IC50>1uM; ribociclib IC50>5uM). Combined abemaciclib and GP showed higher cytotoxicity and synergy at lower doses compared to chemotherapy alone or single-agent abemaciclib. Compared to CDK4/6 inhibitors or chemotherapy alone, combination therapy enhanced growth inhibition, cell cycle arrest and caspase-dependent apoptotic cell death. Abemaciclib triggered autophagy mediated by significant increases in reactive oxygen species (ROS). Combination therapy reduced ROS production and thus autophagy, as seen by reduced autophagic flux, reduced LysoTracker mean fluorescence intensity, a decrease in the expression of LC3B-II, Beclin1A and an increase in p62. Conclusion: These results suggest CDK4/6 inhibitors interact synergistically with GP in CCA and mechanistically disrupt autophagy. This suggests potential to further explore CDKN2A and RB as biomarkers for preclinical sensitivity in CCA. Pre-clinical data supports ongoing clinical studies of this concept, as well as planned clinical studies of GP and alternative CDK4/6 inhibitors. Citation Format: Mansi Arora, James Bogenberger, Nagalo Bolni, Yumei Zhou, Latha Kannan, Jan Egan, Raquel Yokoda, Daniel H. Ahn, Mitesh J. Borad. Synergy of cyclin dependentkinase 4/6 inhibitors with cytotoxic chemotherapy in cholangiocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4417.

Key Points KMT2C mutations occur in 15% and 25% of patients with cHCL and vHCL, respectively, along with CCND3 and U2AF1 mutations each in 13% of vHCLs. NF1, NF2, N/KRAS, and IRS1 alterations contribute to clinical resistance to vemurafenib treatment in patients with cHCL.

Abstract The lysine deacetylase inhibitor suberoylanilide acid (SAHA) has shown promising but limited activity in the treatment of acute myeloid leukemia (AML). To identify potential targets for rational combination therapies that increase the efficacy of SAHA in AML, we used a functional RNA-interference (RNAi) screening approach to identify genes, that when inhibited, potentiate the in vitro anti-leukemic activity of SAHA. A total of 901 kinase, phosphatase and associated signaling genes were silenced, with four different siRNA sequences per gene, in combination with SAHA treatment. Log2 values of the ratio [(siRNA + SAHA)/(siRNA alone)] were calculated, with median and standard deviation determined on a per-plate basis. Hits were defined as ≥ 2 standard deviations from the log2 ratio median. Hit lists for each cell line were over-laid on an integrated functional relationship network. We applied a community detection algorithm to this sub-network and identified siRNA sensitive modules. Each module represents a highly connected set of genes in the integrated network. To identify the pathways represented by each module, we evaluated enrichment using the National Cancer Institute (NCI) Protein Interaction Database (PID) pathways. Several novel sensitizing targets, grouped into a small number of pathways, emerged from these screens. Some hits exhibit little to no anti-leukemic activity when silenced alone, indicative of synthetic lethal interaction with SAHA treatment. Initial validation experiments with siRNA and novel small molecule inhibitors confirm RNAi screen results and pharmacological sensitization is observed. The first reported large-scale HDAC inhibitor RNAi screen in leukemias has identified a novel rational combination that can be translated into design of a clinical trial. Citation Format: James M. Bogenberger, James E. Rudd, Donald Chow, Michelle Kassner, Holly Yin, Casey S. Greene, Raoul Tibes. Identification of HDAC inhibitor potentiating targets in acute myeloid leukemia cells by large-scale RNA-interference. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr A28.

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.

Abstract In order to identify novel targets and clinically exploitable vulnerabilities, we performed high-throughput RNA-interference (RNAi) synthetic lethality screening using myeloid cell lines TF-1 and ML-2 in combination with the hypomethylating agent 5-Azacytidine. A custom small interfering RNA (siRNA) library targeting nearly 1000 cancer-associated genes, including the human kinome, was utilized. Bcl-XL emerged as the strongest 5-Azacytidine sensitizing target in the erythroid cell line TF-1 but not in ML-2 cells. Additional siRNA sequences targeting Bcl-XL were transfected into a panel of myeloid cell lines and tested in drug dose response experiments using a ten-point serial dilution of 5-Azacytidine. The erythroid differentiated myeloid cell lines TF-1 and HEL both exhibited a 3 to 4-fold reduction in the IC50 of 5-Azacytidine upon knockdown of Bcl-XL, whereas IC50 values for non-erythroid, myeloid cell lines ML-2, THP-1 and MDS-L were unchanged. Furthermore, we tested lentiviral delivery of short-hairpin RNA (shRNA) targeting Bcl-XL in additional cell lines. Lentiviral knockdown of Bcl-XL confirmed 2 to 3-fold 5-Azacytidine sensitization in TF-1 and HEL cells while U937, HL-60, ML-2, THP-1 and MDS-L were not sensitized by Bcl-XL knockdown. Interestingly, while Bcl-XL knockdown with shRNA potentiated the effects of 5-Azacytidine in TF-1 and HEL, Bcl-XL knockdown alone resulted in considerable reductions in cell viability in TF-1 and HEL cells. These results demonstrate erythroid lineage-specific responses to Bcl-XL knockdown and suggest that Bcl-XL may represent an erythroid lineage-specific therapeutic vulnerability. To begin to explore this possibility we examined the putative BH3 mimetics Gossypol, Obatoclax and ABT-737 with 5-Azacytidine drug dose response experiments in myeloid cell lines. Neither Gossypol nor Obatoclax potentiated the effects of 5-Azacytdine. In striking contrast, ABT-737 resulted in a 2 to 4-fold reduction in the IC50 of 5-Azacytidine in all cell lines tested to date (TF-1, HEL, ML-2 and THP-1). ABT-737 sensitization to 5-Azacytidine was dose dependent. Furthermore, Combination Index (CI) values calculated with Calcusyn software demonstrate synergy between ABT-737 and 5-Azacytidine at clinically relevant concentrations. These results suggest that inhibition of anti-apoptotic Bcl-2 family members with a BH3 mimetic may represent an effective strategy for 5-Azacytidine combination therapy that can be directly translated into design of combination clinical trials in patients with myeloid leukemias. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr LB-128.