Abstract LB137: Orally available, CDK9 selective, small molecule inhibitors shows promise in n-Myc-driven neuroendocrine prostate cancers (NEPC)

Introduction/Purpose: Amplification of N-MYC causes its overexpression in Neuroendocrine Prostate Cancer (NEPC) patients is prevalent, and it is a rare lethal subtype of cancer detected in 2% of all Prostate Cancers (PC)and over 10-17% of mCRPC (Metastatic Castration-Resistant PC) patients. N-MYC and activated CDK9 act as oncogenic drivers sufficient to transform human-derived prostate cancer cells to take on NEPC phenotypic changes resulting in a more aggressive disease identified in late-stage human PC patients. Additionally, N-MYC is required for tumor resistance, and its downregulation through CDK9 inhibitors lessens the tumor burden. Our efforts in this study have proven that the targeting of N-NYC as a driver of NEPC with CDK9 inhibitors such as BLX-3030 and its series could be a viable approach for therapeutic intervention of mCRPC and NEPCs.

Experimental Procedures: Utilizing our FIELDS fragment-based design strategies, we have developed and synthesized a series of novel small molecule CDK9 agents that reversibly bind to CDK9, competitively block the ATP site, and elicit pharmacological responses in N-MYC and other prostate cancer cells in vitro. CDK9 cell-free kinase binding, CDKs selectivity, pCDK9 inhibition assays were performed and confirmed its on-target efficacy and potency of lead CDK9 inhibitor BLX-3030.

Results and Summary: In these studies, our lead CDK9 kinase inhibitor BLX-3030 from over 60 plus analogs demonstrated potent activity with an IC50 of <5 nM in inhibiting CDK9. CDK9 and N-MYC expression has been detected in PC-3, DU-145, LNCaP, and in LASCPC-01, NCI-H660 and 22RV1 cell lines. HCI-3030 exhibited potent cellular efficacy with an IC50 of 22 to 590 nM in PC cell lines and in N-MYC expressed cells had an activity of 76, 470, and 132 nM respectively and reduced pCDK9, C-MYC, Mcl-1, N-MYC and its downstream RNA Pol II (Ser-2) and pAR (Ser-81) dose-dependently. Our preliminary results support the hypothesis that inhibition of CDK9 reinstates anti-tumor and blocks tumor progression in both mCRPC and NEPCs cellular models. BLX-3030 and a few of its analogs had excellent PK properties in mouse species in the range of 28-94% F, low clearance, and >3 hours half-life. BLX-3030 is nominated as a pre-clinical agent for additional 3D, FACS/apoptosis, cell migration, live-cell imaging including immunofluorescent studies along with in vivo prostate cancer mouse model efficacy studies as well and these results will be presented.

Conclusions: In summary, a series of BLX-3030, its analogs as CDK9 inhibitors, display a range of potency in prostate cancer and NEPC cells with ideal PK parameters, were identified. Within compounds of this profile, BLX-3030 was selected as a candidate CDK9 inhibitor upon in-depth evaluation of the in vitro and in Vivo PK properties further supporting our conclusion that BLX-3030 had the appropriate qualities for development as a pre-clinical candidate.

Citation Format: Kyle Medley, Zhaoliang Li, Saisha Vankayalapati, Sowmya Paritala, Dongqing Yan, Kimberly Coffman, Neeraj Agarwal, David J. Bearss. Orally available, CDK9 selective, small molecule inhibitors shows promise in n-Myc-driven neuroendocrine prostate cancers (NEPC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB137.

Abstract LB090: Targeting GCN2 kinase-driven stress response inactivation to restore immunity in AML Cancers

Introduction/Purpose: The most common leukemia in adults is Acute myeloid leukemia (AML) and the 5-year overall survival (OS) in all AML patients is approximately 24%. The highest of AML deaths in the US alone is among older patients at ages ≥ 65 emphasizing the need for better therapeutics. The older patients have more limited curative options available due to their inability to tolerate aggressive chemotherapy. Identifying ways to boost immunotherapy responses could change the paradigm of AML, a disease still difficult to treat despite several approved targeted immunotherapeutic. The development of effective small molecules would be significant since small molecules not only target immunosuppressive mechanisms like mAbs but can stimulate intracellular pathways where antibodies are unable to permeate. In addition, small molecules can provide optimal pharmacokinetics and pharmacodynamics for oral administration, amenable clinical dosing, and can induce relatively acute antitumor efficacy to avoid systemic immunogenicity, thus providing a superior therapeutic potential. The highly proliferative nature of tumor cells, along with infiltration of myeloid cells into the AML leads to depletion of nutrients such as functional/natural amino acids. A key meditator of this nutrient stress pathway, the cytoplasmic GCN2 (EIF2AK4) kinase, switches on reduction of amino acids, and this activity results in T-cell inactivation, T-cell death, regulatory T-cell expansion, and the potentiation of myeloid-derived suppressor cells (MDSCs). We have discovered a series of novel small molecule immunotherapeutic agents (HCI-1046) that reversibly bind to GCN2 kinase, competitively block the ATP site, and elicit responses in AML patient samples and cell lines.

Experimental Procedures: GCN2 cell-free kinase binding, EIF2α family selectivity, pGCN2 inhibition assays were performed and confirmed its on-target efficacy and potency of lead inhibitor HCI-1046. Additional experiments were conducted including CellTiterGlo, IncuCyte Live Cell Imaging, FACS Flow Cytometry, Cytotoxicity, Western Blot, ELISpot, and ELISA assays.

Results and Summary: GCN2 cell-free kinase binding, kinome selectivity, pGCN2, pEIF2α, ATF4 inhibition data confirmed on-target activities of our lead GCN2 inhibitor HCI-1046. HCI-1046 demonstrated potent activity, with an IC50 of 36 nM in inhibiting GCN2 kinase, and exhibited cellular efficacy with an IC50 of 0.1 to 0.5 μM range. Our preliminary results support the hypothesis that the inhibition of GCN2 reinstates anti-tumor immunity and blocks tumor progression in the AML cancer model in vivo. Our in vivo PK studies on HCI-1046 in rodent species showed excellent PK properties with 55% oral bioavailability, low clearance, and >5.0-hour half-life. Thus, HCI-1046 is nominated as a pre-clinical agent. Additional data regarding the evaluation of the effects of HCI-1046 on the MDSC-suppressive function on T-cells using ELISpot, ELISA assays in AML patient samples, and other mouse model efficacy studies results will be discussed.

Citation Format: Zhaoliang Li, Kyle Medley, Dongqing Yan, Kimberly Coffman, Tony Pomicter, David Lum, David J. Bearss, Hariprasad Vankayalapati. Targeting GCN2 kinase-driven stress response inactivation to restore immunity in AML Cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB090.

Abstract 2307: Elucidation of a unique regulatory mechanism for TNK1 provides potential therapeutic targeting opportunities in cancer

Sumitomo Dainippon Pharma Oncology (f/k/a Tolero Pharmaceuticals), Lehi, UTTNK1 is a poorly understood member of the ACK family of non-receptor tyrosine kinases with a unusual domain arrangement, but no known mechanism of regulation nor conclusive link to disease. We initially identified TNK1 as a mediator of cell survival in a subset of primary patient cancer samples. In an effort to understand how TNK1 is regulated, we discovered a MARK-mediated phosphorylation at S502 near the TNK1 C-terminus that mediates an interaction with 14-3-3. We found that 14-3-3 binding inhibitsTNK1 kinase activity, whereas disruption of this interaction renders TNK1 highly active and capable of driving tumor growth in vivo. In support of this idea, kinase substrate profiling at the proteome level revealed a variety of pro-growth and motility substrates for active TNK1. One unique feature of TNK1 is a ubiquitin-association domain (UBA) on its C-terminus, which sits adjacent to the 14-3-3 binding site. We found that the TNK1 UBA has a high affinity for a variety of poly-ubiquitin linkages—making TNK1the first kinase, to our knowledge, that directly interacts (non-covalently) with ubiquitin. Remarkably, point mutations within the UBA that disrupt ubiquitin binding inhibit TNK1 activation and oncogenic signaling, revealing a unique UBA-centric mechanism of tyrosine kinase regulation, in which TNK1toggles between 14-3-3-bound (inactive) and ubiquitin-bound (active) states. Finally, we used a structure-guided approach to identify novel small molecule TNK1 inhibitors with high potency and selectivity. One such compound, TP-5809, inhibits TNK1 dependent STAT5 phosphorylation in vitro and in vivo in L540, a Hodgkin lymphoma cell line with a TNK1-activating mutation. TP-5809 also potently inhibits the in vitro growth of mutant TNK1-driven pro-B cells and reduces disease burden and prolongs survival in mice with xenografted tumors. Together, our data elucidate the first mechanism of TNK1regulation and identify lead compounds for the development of a TNK1 inhibitor.

Citation Format: Tsz-Yin Chan, Christina Egbert, Logan Larsen, Jeremy Tsang, Julia Maxson, Eranga Roshan, Clifford J. Whatcott, Kim Wontak, Gaelle Mercenne, Savannah Free, Adam Siddiqui, Tetyana Forostyan, Ethika Tyagi, Kenneth A. Christensen, David J. Bearss, James Moody, Jeffrey Tyner, Jason M. Foulks, Steven L. Warner, Joshua Lyon Andersen. Elucidation of a unique regulatory mechanism for TNK1 provides potential therapeutic targeting opportunities in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2307.

Abstract 1345: Pharmacodynamic biomarkers for Pim inhibition with TP-3654 in patients with solid tumors

Proviral integration site for Moloney murine leukemia virus-1 (Pim-1) is a serine/threonine kinase downstream of Jak/Stat signaling which promotes cell growth, survival, and drug resistance. Pim-1 kinase is an important driver of tumorigenesis and tumor survival through its role in a number of downstream pathways, including inhibition of apoptosis through phosphorylation of the BH3-only protein BAD. Pim-1 is expressed at very low levels in most normal tissues, but is overexpressed in many cancers, such as prostate, colorectal, and many hematologic malignancies. Pim-1 kinase activity is constitutive and therefore directly proportional to protein expression. As such, Pim-1 is an attractive therapeutic target. TP-3654 is a second-generation, oral Pim inhibitor currently in Phase I clinical trials in solid tumors and myelofibrosis (NCT03715504 and NCT04176198). TP-3654 inhibits all three Pim kinases, with Ki values for Pim-1 (5nM), and Pim-2 and Pim-3 &lt250 nM in a biochemical assay. Treatment with TP-3654 in Jurkat and HEL cell lines showed dose-dependent modulation of the downstream targets of PIM, such as pS6K and pBad. A dose-dependent increase of TP-3654 Cmax was observed in plasma and subcutaneous PC-3 xenograft tumors in animals dosed orally at 50, 100 and 200 mg/kg with Tmax at 1 hour. Animals bearing HEL tumors were dosed similarly and Cmax values increased in a dose-dependent manner with Tmax at 2 hours. Plasma and tumor TP-3654 concentrations were above the measurement threshold out to 24 hours post dose. We further explored pharmacodynamic biomarkers of Pim inhibition (pBad, pS6K, and pS6RP) in flash frozen (FF) tumor tissue at various time points in both models by western blot and saw a maximum of 40% decrease in phosphorylated S6K at 2 hours, and an 80% decrease in pBad at 8 hrs in PC3 xenograft tumors in mice treated with 100 mg/kg of TP-3654. We hypothesized that treatment with TP-3654 would modulate Pim signaling in both cancer cells and peripheral blood mononuclear cells (PBMCs). This allows for detection of pharmacodynamic markers using repeated peripheral blood draws instead of invasive biopsies. We treated PBMCs from multiple healthy human donors with TP-3654 ex vivo at 0.3 and 3 µM to assess the movement of Pim biomarkers. Two phosphorylation markers, pS6K and pS6RP consistently exhibited dose-dependent decreases (30-70%) as measured by western blot. Inhibition of pBad was dependent on pretreatment phosphorylation state. These results were confirmed in an automated western blot system.

Citation Format: Curtis A. Allred, Yuta Matsumura, Ethika Tyagi, Mark Wade, Clifford Whatcott, Jason Foulks, Adam Siddiqui, David J. Bearss, Steven L. Warner. Pharmacodynamic biomarkers for Pim inhibition with TP-3654 in patients with solid tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1345.

Abstract 1959: CDK9 inhibition combined with hypomethylating agents target MCL-1 dependency in MDS and AML

Myelodysplastic syndrome (MDS) is a heterogeneous group of hematopoietic stem cell disorders. Approximately 70% of patients diagnosed with higher-risk (HR) MDS progress to acute myeloid leukemia (AML). Cyclin-dependent kinase 9 (CDK9) influences transcription through phosphorylation and activation of RNA polymerase II (RPB1), which increases the levels of key oncogenic survival genes like myeloid cell leukemia-1 (MCL-1). MCL-1 dependent malignancies can be identified through a functional assay by adding a NOXA mimetic MCL-1 antagonist peptide to patient samples and measuring the subsequent induction of apoptosis. The assay has been tested in bone marrow mononuclear cells (BMMCs) from AML and MDS patients to examine MCL-1 dependency prior to therapy with alvocidib. Approximately 25% of AML patient BMMCs and 60% of MDS patient BMMCs are MCL-1 dependent (data not shown). We hypothesized that the hypomethylating agents (HMAs) azacitidine and decitabine, which are currently approved for treatment of MDS, can increase MCL-1 dependency through re-expression of pro-apoptotic proteins like NOXA, normally repressed through DNA methylation in malignancies. In the MV-4-11 AML cell line and primary CD34+ MDS BMMCs, alvocidib treatment resulted in a dose dependent reduction in p-RPB1 and MCL-1. In cell viability assays using CellTiter-Glo, treatment with alvocidib and azacitidine resulted in IC50 values of ~100 nM and ~3000 nM, respectively in both cell types. Treatment with HMAs increased NOXA expression and alvocidib suppressed MCL-1 expression, whereas sequential treatment of azacitidine and alvocidib showed both NOXA induction and MCL-1 suppression. Sequential treatment of azacitidine and alvocidib showed synergistic apoptosis induction compared with either treatment alone. Azacitidine treatment sensitized MV-4-11 and MDS BMMCs to MCL-1 inhibition in an MCL-1 dependency assay. In an in vivo efficacy study using the MOLM13 AML xenograft model, the combination of alvocidib and azacitidine or decitabine inhibited tumor growth 71% and 84%, respectively. Alvocidib, azacitidine and decitabine alone showed 51%, 5.7% and 19% tumor growth inhibition (TGI), respectively. Pharmacodynamic analysis in a Phase 1 trial with alvocidib (clinicaltrials.gov, NCT03593915) showed DNA methylation of NOXA gene locus was reduced and NOXA gene expression was upregulated, while MCL-1 gene expression was suppressed in peripheral blood mononuclear cells (PBMCs) after azacitidine and alvocidib treatment. These pre-clinical and clinical data suggest that an alvocidib/HMA combination may constitute a viable therapeutic regimen whose rationale focuses on hypertargeting of NOXA/MCL-1. Taken together, these studies indicate that the combination of alvocidib and HMAs drives AML/MDS cells toward MCL-1 dependent apoptosis.

Citation Format: Yuta Matsumura, Ethika Tyagi, Satya Pathi, Dan D. Vo, Tianxiang Zhu, Suman Verma, Clifford J. Whatcott, Stephen P. Anthony, Adam Siddiqui, Jason M. Foulks, David J. Bearss, Steven L. Warner. CDK9 inhibition combined with hypomethylating agents target MCL-1 dependency in MDS and AML [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1959.

Abstract 5813: Pharmacodynamic biomarker strategies for CDK9 inhibition

Cyclin-dependent kinase 9 (CDK9) is a promising target for cancer therapy due to its regulation of RNA polymerase II (RPB1) and key downstream anti-apoptosis proteins such as myeloid cell leukemia-1 (MCL-1). TP-1287 is a novel oral prodrug of alvocidib, a potent CDK9 inhibitor, and is currently under clinical investigation in patients with advanced solid tumors (clinicaltrials.gov, NCT03604783). TP-1287 is converted to alvocidib by alkaline phosphatases. CDK9 mediates phosphorylation of RPB1 at Ser2 and subsequently drives transcription of key oncogenic signaling genes, such as MCL-1. MCL-1 is a critical factor for survival of tumor types including acute myeloid leukemia (AML), multiple myeloma (MM) and myelodysplastic syndromes (MDS). MCL-1 is also expressed in normal peripheral blood mononuclear cells (PBMCs), thus it was hypothesized that CDK9 inhibition can be assessed clinically using PBMCs as a surrogate biomarker at multiple time points. We hypothesized that alvocidib, the pharmaceutically active form of TP-1287, would modulate CDK9 signaling pathways in cancer cells, resulting in tumor growth inhibition. In cell viability assays using CellTiter-Glo to evaluate the in vitro anti-tumor activity of alvocidib, we observed an IC50 of around 100 nM in AML and MM cell lines: 53-78 nM in MOLM-13, MV-4-11, and HL-60 AML cell lines and 31-223 nM in NCI-H929 and RPMI-8226 MM cell lines. In flow cytometry analysis, alvocidib reduced phosphorylation of RPB1 (p-RPB1) and MCL-1 protein expression in RPMI-8226 and MV-4-11 cells in a dose and time-dependent manner. In a pharmacodynamic study using the RPMI-8226 xenograft model after a single oral administration of TP-1287, we observed a substantial decrease of p-RPB1 and MCL-1 in tumor tissues followed by induction of cleaved caspase-3, an indicator of apoptosis. Furthermore, in an in vivo efficacy study using the RPMI-8226 model, TP-1287 achieved tumor growth inhibition (%TGI), ranging from 17.3% at 0.5 mg/kg (QD) to 86.6% at 15 mg/kg (Q7D) at day 22 after treatment. We hypothesized that PBMCs could serve as a surrogate tissue to measure CDK9 inhibition. To assess this approach in PBMCs, we performed ex vivo assays using human PBMCs from multiple healthy donors. Alvocidib demonstrated dose-dependent p-RPB1 and MCL-1 inhibition after 24 hr treatment. Preliminary data from the Phase 1 trial with TP-1287 showed p-RPB1 suppression in PBMCs from multiple patients, suggesting the successful execution of this assay and evidence of target engagement in the clinical setting. Taken together, TP-1287 demonstrated potent cell and tumor growth inhibition in multiple hematological cell lines, including AML and MM. Furthermore, a newly established flow cytometry system for p-RPB1 and MCL-1 to evaluate CDK9 inhibition in human PBMCs was developed, which could be useful as a surrogate biomarker for TP-1287 in clinical trials and warrants further investigation.

Citation Format: Yuta Matsumura, Ethika Tyagi, Clifford J. Whatcott, Jason M. Foulks, Adam Siddiqui-Jain, David J. Bearss, Steven L. Warner. Pharmacodynamic biomarker strategies for CDK9 inhibition [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5813.

Abstract B29: AXL Inhibitor TP-0903 attenuates TGFβ-Hippo signaling in lung adenocarcinoma cells

Background: Non-small cell lung cancer (NSCLC) is a molecularly heterogeneous disease with a high propensity for drug resistance and metastasis. AXL, a member of the Tyro3-AXL-Mer (TAM) family of receptor tyrosine kinases, is a central regulator of epithelial-to-mesenchymal transition (EMT) and enables tumor cells to invade and acquire drug resistance. AXL is overexpressed in NSCLC and its expression correlates positively with tumor invasion, drug resistance, and negatively predicts overall survival. We mechanistically interrogated the effects of the AXL inhibitor, TP-0903, on EMT in NSCLC cells using transcriptomic and proteomic profiling.

Methods: Atomic force microscopy, Western blot analysis, RNA sequencing, and mass cytometry (CyTOF) were used to evaluate the phenotypic, transcriptomic, and proteomic profiles of A549 cells treated with 40 nM TP-0903 or shAXL knockdown. A549 and H1650 NSCLC xenograft models were used to explore the consequences of AXL inhibition in vivo.

Results: As expected, TP-0903 treatment attenuated AXL signaling and downstream phosphorylation in the A549 cells. Interestingly, the treatment also reduced gene expression responses to TGFβ-Hippo signaling by disrupting the transcriptional complexes formed by SMAD2/3, SMAD4, YAP1, and TAZ. Consistent with AXL inhibition, TP-0903 reversed the mesenchymal phenotype in A549 and H2009 cell lines and decreased their migratory potential in culture. The CyTOF analysis on TP-0903-treated cells identified resistant clones overexpressing TGFβ receptor II (TGFBR2) and TAZ proteins and displaying hybrid EMT phenotypes. TP-0903 was also active in suppressing A549 or H1650 tumor growth in vivo.

Conclusions: We are the first to report the interplay between AXL and TGFβ-Hippo signaling axis. TP-0903 has excellent therapeutic promise in NSCLC and we speculate that TP-0903 can target mesenchymal transitional states in NSCLC, possibly through the inhibition of the AXL-TGFβ-Hippo signaling axis.

Citation Format: Josephine A. Taverna, Chia-Nung Hung, Chun-Lin Lin, Pawel A. Osmulski, Maria E. Gaczynska, Chiou-Miin Wang, Nicholas D. Lucio, Meizhen Chen, Chih-Wei Chou, Alia Nazarullah, Shellye R. Lampkin, Lianquin Qiu, David J. Bearss, Steve Warner, Lars Mouritsen, Mark Wade, Daniel DeArmond, Ruben Mesa, Nameer Kirma, Tim H.-M. Huang. AXL Inhibitor TP-0903 attenuates TGFβ-Hippo signaling in lung adenocarcinoma cells [abstract]. In: Proceedings of the AACR Special Conference on the Hippo Pathway: Signaling, Cancer, and Beyond; 2019 May 8-11; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(8_Suppl):Abstract nr B29.

Single-Cell Proteomic Profiling Identifies Combined AXL and JAK1 Inhibition as a Novel Therapeutic Strategy for Lung Cancer

Cytometry by time-of-flight (CyTOF) simultaneously measures multiple cellular proteins at the single-cell level and is used to assess intertumor and intratumor heterogeneity. This approach may be used to investigate the variability of individual tumor responses to treatments. Herein, we stratified lung tumor subpopulations based on AXL signaling as a potential targeting strategy. Integrative transcriptome analyses were used to investigate how TP-0903, an AXL kinase inhibitor, influences redundant oncogenic pathways in metastatic lung cancer cells. CyTOF profiling revealed that AXL inhibition suppressed SMAD4/TGFβ signaling and induced JAK1-STAT3 signaling to compensate for the loss of AXL. Interestingly, high JAK1-STAT3 was associated with increased levels of AXL in treatment-naïve tumors. Tumors with high AXL, TGFβ, and JAK1 signaling concomitantly displayed CD133-mediated cancer stemness and hybrid epithelial-to-mesenchymal transition features in advanced-stage patients, suggesting greater potential for distant dissemination. Diffusion pseudotime analysis revealed cell-fate trajectories among four different categories that were linked to clinicopathologic features for each patient. Patient-derived organoids (PDO) obtained from tumors with high AXL and JAK1 were sensitive to TP-0903 and ruxolitinib (JAK inhibitor) treatments, supporting the CyTOF findings. This study shows that single-cell proteomic profiling of treatment-naïve lung tumors, coupled with ex vivo testing of PDOs, identifies continuous AXL, TGFβ, and JAK1-STAT3 signal activation in select tumors that may be targeted by combined AXL-JAK1 inhibition. SIGNIFICANCE: Single-cell proteomic profiling of clinical samples may facilitate the optimal selection of novel drug targets, interpretation of early-phase clinical trial data, and development of predictive biomarkers valuable for patient stratification.

Abstract B080: PKM2 activation modulates metabolism and enhances immune response in solid tumor models

Pyruvate kinase functions as the key enzyme in the final step of glycolysis. Cancer cells largely utilize the M2 isoform of pyruvate kinase (PKM2) due to the ability of PKM2 to be allosterically regulated between fully active (tetramer) and less active (dimer) forms of the enzyme. This dynamic regulation is associated with metabolic reprogramming of cancer cells creating a balance between energy needs and anabolic cellular requirements to support cell growth and division. Furthermore, the allosteric regulation creates an opportunity to design a small molecule activator to reverse the metabolic reprogramming favoring cancer growth and immune evasion. TP-1454 is a novel PKM2 activator with low nanomolar PKM2 activation in biochemical assays (AC50 = 10 nM) and in A549 epithelial lung carcinoma cells (AC50 < 20 nM). TP-1454 potently suppresses A549 cell viability (IC50 = 19 nM) and inhibits the tumor growth (60%) under serine auxotrophy conditions both in vitro and in vivo. PKM2 also plays a critical role in the regulation of the adaptive metabolism required to mount an innate immune response. We hypothesized that PKM2 activation may reverse the immune-suppressive microenvironment often observed in many cancers in part by decreasing tumor lactate levels and favoring glucose utilization by immune cells over cancer cells. To test this hypothesis, we explored the combination of TP-1454 with immunotherapy in both immune-suppressive and immune-permissive mouse syngeneic tumors. TP-1454 combination with α-PD1 and α-CTLA4 resulted in tumor regression in the MC38 syngeneic mouse colorectal cancer model with no adverse toxicity or effects on body weights. TP-1454 combination with α-PD1, α-CTLA4 or triple combination with α-PD1 and α-CTLA4 resulted in tumor growth inhibition (TGI) of 76%, 96% and 99% respectively, in the MC38 model. We observed increased levels of glucose and decreased levels of glucose 6-phosphate, phosphoglycerate, phosphoenolpyruvate and lactate in TP-1454 treated compared to vehicle treated MC38 tumors. Kaplan Meier survival analysis revealed 90% and 100% survival for TP-1454 combination with α-CTLA-4 or triple combination with α-PD1 and α-CTLA4 respectively, a vast improvement over the 10% survival of the vehicle group. TP-1454 or α-PD1 alone demonstrated <10% TGI in a CT26 colorectal syngeneic model but synergized in combination resulting in a 68% TGI. Potential downstream biomarkers, including metabolism, immune gene alterations and immune phenotyping are currently under evaluation using LC-MS/MS, NanoString and flow cytometry. These preclinical studies strongly suggest the potential novel therapeutic activity of TP-1454 in cancer models through metabolism and tumor microenvironment modulation. The immune-modulatory and metabolic alterations by TP-1454 offer a unique mechanism to potentially activate the immune response in cancer patients when combined with immunotherapy.

Citation Format: Satya Pathi, Peter Peterson, Ryan Mangelson, Ethika Tyagi, Jason M. Foulks, Clifford J. Whatcott, David J. Bearss, Steven L. Warner. PKM2 activation modulates metabolism and enhances immune response in solid tumor models [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr B080. doi:10.1158/1535-7163.TARG-19-B080

Abstract C081: Targeting CDK9 and MCL1 in castration-sensitive and resistant prostate cancer models

Prostate cancer is the most prevalent cancer in men, comprising 20% of all new cancer cases in United States, as per the Cancer Statistics, 2019. Many therapies for prostate cancer function by lowering androgen levels and include androgen deprivation therapy alone or in combination with surgical or chemical castration. Hormone therapy has been a mainstay treatment for prostate cancer, ultimately leading to progression free disease in over 80% of patients over short time periods. Unfortunately, these effects are not durable, and the majority of patients experience progressive disease. Ultimately, the disease progresses and becomes invasive and lethal in the form of castration-resistant prostate cancer (CRPC). Understanding the mechanism by which prostate cancer cells lose their inherent dependence on the canonical androgen signaling pathway for survival has been critical in developing new therapeutic options for patients with CRPC. CDK9 may constitute one such mechanism. CDK9 phosphorylates RNA polymerase II (RNA Pol II), resulting in gene transcription of anti-apoptotic proteins such as MCL1, that can influence prostate cancer cell survival. Additionally, CDK9 is known to phosphorylate the androgen receptor (AR) and both AR and RNA Pol II cooperate for transcription of key prostate cancer genes, including PSA. Therefore, inhibition of CDK9 has great potential to halt constitutive activity of both AR and the RNA Pol II -driven transcriptional program that drives CRPC. Here, we describe tumor growth inhibition in CRPC models using the CDK9 inhibitor TP-1287, an oral alvocidib prodrug, alone and in combination with docetaxel or venetoclax, a BCL-2 inhibitor that is currently being evaluated in a Phase II clinical trial for metastatic CRPC. The CDK9 inhibitor alvocidib demonstrates low nanomolar IC50 values in CRPC cell lines PC3, 22Rv1 and castration dependent PCa cell lines VCAP and LnCAP ranging from 25-175 nM. Alvocidib treatment inhibits RNA Pol II in 22Rv1 cells (~50%) at 80 and 160 nM, 3 and 24 hrs post treatment and regulates MCL-1 protein expression in PC3 cells (300 nM, 24 hrs). Alvocidib treatment also inhibited AR phosphorylation at Ser 81, reducing PSA gene expression (~50%) and inducing caspase activation in 22Rv1 cells (80-160 nM for 24 hrs). We explored the tumor growth inhibition of TP-1287, in several PCa xenograft models namely PC3, 22Rv1, LnCAP and C4-2 models. In androgen sensitive models, 1.25 mpk BID TP-1287 combined well with 10 mpk docetaxel, demonstrating 90% and 81% TGI in C4-2 and LnCAP models respectively. TP-1287 treatment (1.25 mpk BID) in combination with 100 mpk venetoclax demonstrated 64% tumor growth inhibition in the 22Rv1 CRPC model that was resistant to docetaxel, enzalutamide and venetoclax alone. These data support the potential of TP-1287 to be used in combination with currently available or novel therapies to achieve better efficacy for androgen sensitive and CRPC patients.

Citation Format: Tetyana V Forostyan, Evita Weagel, Yuta Matsumura, Ethika Tyagi, Jason M Foulks, Clifford J Whatcott, Adam Siddiqui-Jain, David J Bearss, Steven L Warner. Targeting CDK9 and MCL1 in castration-sensitive and resistant prostate cancer models [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr C081. doi:10.1158/1535-7163.TARG-19-C081

Abstract 2197: The AXL kinase inhibitor, TP-0903, demonstrates efficacy in preclinical models of colorectal cancer independent of KRAS mutation status

Colorectal cancer (CRC) is the third leading cause of cancer-related mortality in the US (2017). Most patients present with stage II or III disease at diagnosis, with the 5-year survival rate between 53-89%. Survival in patients with stage IV CRC, however, is a discouraging 11%. Metastasis in CRC is linked to a mesenchymal phenotype, which is associated with chemoresistance. AXL, a receptor tyrosine kinase, promotes the mesenchymal phenotype in cancer cells and its expression is associated with drug resistance and poor outcomes. TP-0903, a clinical-stage, investigational small molecule inhibitor of AXL has been shown to reverse the mesenchymal phenotype and restore drug sensitivity in cells that no longer respond to standard agents in preclinical models. TP-0903 is hypothesized to be an active agent in CRC through reversal of the mesenchymal phenotype. In cell viability assays of CRC lines, TP-0903 treatment resulted in IC50 values ranging from 4.5 – 123 nM. Notably, cell growth inhibition by TP-0903 was independent of KRAS mutation status; the KRAS mutant HCT-116 line was the most sensitive CRC cell line tested. Mesenchymal markers, including Snail, were suppressed by 7.6-fold (mRNA) and 4.9-fold (protein) in the HCT-116 line at 500 nM. TP-0903 activity was also assessed in vivo using two KRAS mutant CRC models: HCT-116 and a patient-derived xenograft (PDX) model. In the HCT-116 xenograft model, single agent TP-0903 treatment achieved 69% tumor growth inhibition (%TGI) with an oral dosing schedule at 40 mg/kg. In a KRAS-mutant PDX model, TP-0903 achieved 44% TGI when mice were dosed at 40 mg/kg. Pharmacodynamic analyses were performed on tissues from the HCT-116 and PDX models. The ligand for AXL, GAS6, was significantly upregulated in tissues after TP-0903 treatment in both CRC in vivo models while soluble AXL and GAS6 were significantly downregulated in plasma in the PDX model. Furthermore, Axin2, a Wnt/β-catenin regulated gene, was downregulated by TP-0903 in tumor tissue from the PDX model, suggesting inhibition of the Wnt/βcatenin pathway. These data support a potential role for AXL in the promotion of the mesenchymal phenotype in CRC, and showed that AXL inhibition by TP-0903 suppressed the mesenchymal phenotype and was effective against CRC cells regardless of KRAS mutation status. These observations support further clinical investigation of TP-0903 as a potential therapeutic agent in metastatic CRC. A Phase I trial with this investigational agent is ongoing, including patients with KRAS mutant CRC (clincaltrials.gov, NCT02729298).

Citation Format: Ryan Mangelson, Peter Peterson, Jason M. Foulks, Yuta Matsumura, Lars Mouritsen, Clifford J. Whatcott, David J. Bearss, Steven L. Warner. The AXL kinase inhibitor, TP-0903, demonstrates efficacy in preclinical models of colorectal cancer independent of KRAS mutation status [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 2197.

Abstract 3969: TP-0903, a potent AXL receptor tyrosine kinase inhibitor, enhances the activity of anti-PD-1 therapy in a metastatic preclinical syngeneic model of breast cancer

The high rate of non-responders to immune checkpoint inhibitors (ICI) represents significant challenges in the field of immune-oncology. Breast cancer has emerged as a cancer type that responds poorly to ICI. Therefore, there is an urgent need to better understand how cancer cells escape immune surveillance and resist immune attacks. Cancer cell clones with mesenchymal features seem to be less susceptible to attacks by immune cells. Hence, epithelial-to-mesenchymal transition (EMT) targeting agents such as TP-0903 are emerging as potential combination candidates to enhance immune checkpoint inhibition. AXL is overexpressed in a variety of cancers, often driving the pathogenesis and progression of disease. AXL overexpression induces cancer growth, invasion, metastasis, drug resistance, and mesenchymal characteristics. Aside from cancer cells, AXL is also expressed on several types of immune cells including macrophages and dendritic cells. Recently, it has been reported that AXL plays an important role as a negative regulator of immune response, contributing to an anti-tumor immune suppression. We have previously identified TP-0903 to be a potent small molecule inhibitor of AXL (IC50=14 nM) capable of reversing EMT. In this study, we evaluated whether TP-0903 could enhance the ICB effect in an ICB-resistant triple negative, metastatic breast cancer mouse model (4T1). In the 4T1 syngeneic model, anti-PD-1 monotherapy failed to inhibit tumor growth indicating that this tumor is resistant to anti-PD-1 treatment. The combination of TP-0903 and anti-PD-1 resulted in statistically significant tumor growth inhibition versus TP-0903 monotherapy (p<0.05). We hypothesized that the combination effect was influenced by potential CD8+ T cell depletion, and further investigated the effects of TP-0903 on immune cells in spleen and tumors. Tumor growth inhibition was found to be associated with a decrease in myeloid-derived suppressor cells (MDSC) in the spleen and an increase in infiltration and activation of dendritic cells (DCs) in the tumor. Gene expression analysis revealed that TP-0903 treatment decreased multiple immunosuppressive cytokines and chemokines including IL-6 and G-CSF in vivo. These results suggest that TP-0903 modulates the immune-suppressive tumor microenvironment (TME) to reinvigorate T cell immunity in anti-PD-1 resistant 4T1 tumors. In conclusion, AXL inhibition with TP-0903 modulates TME and enhances the anti-tumor effects of ICBs in an anti-PD-1 resistant, metastatic breast cancer mouse model. These findings support additional clinical testing of TP-0903 in combination with ICBs, which is currently being investigated in patients with advanced solid tumors in an ongoing clinical study (NCT02729298).

Citation Format: Yuka Kumagai, Jun Oishi, Megumi Nakamura, Jason M. Foulks, Clifford J. Whatcott, Steven L. Warner, David J. Bearss, Masashi Goto. TP-0903, a potent AXL receptor tyrosine kinase inhibitor, enhances the activity of anti-PD-1 therapy in a metastatic preclinical syngeneic model of breast cancer [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 3969.

Abstract 3166: Evaluation of genetic modulation of ACVR1 (aka ALK2) kinase gene as a clinical biomarker of the ACVR1 inhibitor TP-0184

The receptor kinase ALK2, the product of the ACVR1 gene, is a member of the bone morphogenic protein (BMP) receptor family and a type I receptor of the greater TGFβ family. Germline mutations in ACVR1, and specifically the R206H manifestation, are a driving factor in the development of fibrodysplasia ossificans progressiva (FOP). Additionally, the childhood brain tumor, diffuse intrinsic pontine glioma (DIPG), is also associated with mutations in the ACVR1 gene including R206H, but accounts for approximately only 25% of DIPG. In adult cancers, mutations in the ACVR1 gene are observed, yet their role is less established. TP-0184 is a small molecule inhibitor of ACVR1 which inhibits the kinase activity of wild-type and mutant forms of ALK2. We examined the genetic make-up of ACVR1 mutations across large data sets to evaluate which mutations may portend benefit with TP-0184 treatment. Using publicly available sequence databases (e.g. cBioPortal, Cosmic, TCGA) we searched for ACVR1 mutations in tissues of cancer patients. Results were compared to the known mutations of ACVR1 in the literature associated with various cancers or demonstrate gain-of-function activity. Multiple mutations were found within ACVR1. The FOP community has done extensive work to identify and understand mutations that can drive aberrant activation of ACVR1. These mutations include L196P, R206H, Q207E, R258S, G328E/R, and G356D to name a few. ACVR1 mutations identified in adult cancers include many of these FOP mutations, but also demonstrate more diversity in their ACVR1 mutational profile with fewer “hotspots” and many mutations of unknown significance. For example, 8.49% (45/530) of endometrial cancer patients in the TCGA database have ACVR1 mutations, yet these are represented by 52 different mutations. The most common ACVR1 mutation in endometrial cancer is the bona fide R206H mutation, but it only makes up 0.9% of the 8.49% of ACVR1 mutations in endometrial cancer. If all ACVR1 mutations of known significance are considered, 2.45% of endometrial cancers have validated gain-of-function mutations in ACVR1. The remaining ACVR1 mutations in endometrial cancer are of unknown significance. Similar results were observed in other types of cancer such as melanoma, prostate and breast cancer and in other publicly available databases. The results from surveying these rare mutations in multiple cancer types will be presented. Since the BMP and TGFβ pathways are frequently dysregulated in cancers, the importance of any mutation that regulates ACVR1 activity in cancer may be an important regulator of tumorigenesis and a target of ACVR1 inhibitors. A Phase I trial with TP-0184 is in progress and will assess the correlation of ACVR1 mutations and compound clinical activity (Clinical trial information: NCT03429218). Further studies are in progress to assess the consequences and causal impact of ACVR1 mutations in cancer.

Citation Format: Mark L. Wade, C Lars Mouritsen, Yuta Matsumura, Breeann V. Bryan, David J. Bearss, Steven L. Warner. Evaluation of genetic modulation of ACVR1 (aka ALK2) kinase gene as a clinical biomarker of the ACVR1 inhibitor TP-0184 [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 3166.

Abstract P2-06-05: TP-0903, an AXL kinase inhibitor, reduces inflammatory breast cancer aggressiveness and macrophage polarization through additional mechanisms that may include JAK2 and Aurora B

Background: Inflammatory breast cancer (IBC) is the most lethal and aggressive type of breast cancer; it accounts for 2-4% of breast cancer cases but causes 8-10% of breast cancer deaths. Novel targeted therapy to improve the outcomes of patients with IBC is urgently needed. The receptor tyrosine kinase AXL is a driver for metastasis and drug resistance in various cancers, including breast cancer. Our previous work showed that AXL signaling contributes to the aggressiveness of IBC. In addition, emerging evidence indicates that the tumor microenvironment components, particularly tumor-associated macrophages, are critical drivers of the IBC clinical phenotype and promote IBC metastasis. AXL signaling has been shown to modulate the tumor microenvironment. In the present study, we investigated the impact of TP-0903, a small-molecule AXL kinase inhibitor, with additional activity against Aurora B and Janus kinase 2 (JAK2), on IBC cells and macrophage polarization.

Methods: The effects of TP-0903 on IBC cell proliferation, migration/invasion, and mammosphere formation were analyzed. The effects of TP-0903 on the polarization of human monocytic cells THP-1 were tested in vitro. In addition, the signaling pathways involved in TP-0903-regulated M2 macrophage polarization were investigated using Western blotting.

Results: The half-maximal inhibitory concentration (IC50) of TP-0903 in an array of IBC cells (including SUM149, SUM190, BCX010, FC-IBC-02, MDA-IBC-3, and KPL4) ranged from 66 nM to 346 nM, suggesting a strong cell growth inhibitory effect. TP-0903 treatment decreased the migration, invasion, and mammosphere formation of IBC cells. In addition, TP-0903 inhibited both AXL signaling and Aurora B activation, which induced a G2/M cell cycle arrest in IBC cells. Based on the importance of AXL and JAK2 in the regulation of the tumor microenvironment, we showed that TP-0903 decreased expression of CD163/CD206 and the CCL17/CCL18 cytokine, and markers of M2 macrophages, suggesting that TP-0903 treatment inhibits the polarization of THP-1 cells to M2 macrophages in vitro. We also found that TP-0903 treatment decreased the phosphorylation of STAT6, a critical molecule in M2 polarization, and that knockdown of STAT6 expression decreased M2 macrophage polarization, indicating that TP-0903 may regulate macrophage polarization via STAT6 signaling.

Conclusion: Our results demonstrated the dual functions of TP-0903 targeting of both IBC cells and macrophages, possibly via the targeting of multiple kinases, including AXL and Aurora B. Examinations of the impact of TP-0903 on the cross-talk between IBC cells and macrophages in vitro and in vivo and the related mechanisms are ongoing and will be presented at the meeting.

Citation Format: Cheng Y, Funakoshi Y, Wang X, Warner SL, Bearss DJ, Ueno NT. TP-0903, an AXL kinase inhibitor, reduces inflammatory breast cancer aggressiveness and macrophage polarization through additional mechanisms that may include JAK2 and Aurora B [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P2-06-05.

Development of High-Throughput Screening Assays for Inhibitors of ETS Transcription Factors

ETS transcription factors from the ERG and ETV1/4/5 subfamilies are overexpressed in the majority of prostate cancer patients and contribute to disease progression. Here, we have developed two in vitro assays for the interaction of ETS transcription factors with DNA that are amenable to high-throughput screening. Using ETS1 as a model, we applied these assays to screen 110 compounds derived from a high-throughput virtual screen. We found that the use of lower-affinity DNA binding sequences, similar to those that ERG and ETV1 bind to in prostate cells, allowed for higher inhibition from many of these test compounds. Further pilot experiments demonstrated that the in vitro assays are robust for ERG, ETV1, and ETV5, three of the ETS transcription factors that are overexpressed in prostate cancer.

Abstract 4823: Alvocidib enhances the efficacy of cytarabine and daunorubicin (7+3) in non-clinical models of acute myeloid leukemia

The ‘7+3' induction regimen has been the standard of care for frontline acute myeloid leukemia (AML) for more than 30 years. There are still significant unmet needs for frontline patients, particularly those with high-risk features. Alvocidib, a potent CDK9 inhibitor, has shown clinical activity in multiple studies of frontline and relapsed/refractory AML. In some clinical studies, alvocidib has been administered as part of the ACM (alvocidib, cytarabine, and mitoxantrone) regimen. The ACM regimen has demonstrated greater clinical responses compared to 7+3 in frontline intermediate and high-risk AML patients. The ACM regimen is now being evaluated in a multi-institution, Phase II study using a MCL-1 dependency biomarker to select patients likely to be sensitive to the alvocidib-containing regimen. Alvocidib activity is primarily driven by its inhibition of CDK9/RNA-polymerase II and the subsequent suppression of key anti-apoptotic proteins, including MCL-1. Alvocidib induces apoptosis and potentiates the activity of apoptosis-inducing agents, such as cytarabine and mitoxantrone. The synergy of the ACM regimen led us to hypothesize that alvocidib may enhance the anti-leukemia activity of the 7+3 regimen in preclinical models as well. Cell viability and apoptosis measurements were made following treatment using the CellTiter-Glo and Caspase-Glo assays according to manufacturer protocol. MCL-1 mRNA expression and the expression of additional markers was determined using RT-qPCR. Protein expression was determined using standard immunoblotting techniques. Alvocidib and the 7+3 regimen were also tested in vivo in the MV4-11 AML xenograft model. Here, it was observed that the 72-hour viability assays yielded single agent IC50 values of alvocidib, cytarabine, or daunorubicin in cultured AML cells ranging from 2.2 nM to 567 nM. In apoptosis assays, a modest induction was observed with cytarabine, daunorubicin, or alvocidib. However, the three-drug combination more than doubled the induction of apoptosis compared to any of the agents alone. We also observed that MCL-1 was suppressed in the combination treatment. In a xenograft study, 21.1 and 48.5% tumor growth inhibition (TGI) was observed following either single agent treatment of daunorubicin (0.5 mg/kg) or cytarabine (60 mg/kg), respectively. Treatment of alvocidib (1.25 mg/kg) yielded 60.0% TGI. Combination treatment, however, resulted in tumor shrinkage, yielding 116.2% TGI. While we have reported previously that alvocidib synergizes with cytarabine and mitoxantrone preclinically in the ACM regimen, our data here demonstrates that alvocidib potentiates the activity of cytarabine and daunorubicin as well. Our results here provide additional scientific rationale for an investigational Phase Ib clinical study employing alvocidib in combination with 7+3 in frontline AML patients, which is currently ongoing.

Citation Format: Wontak Kim, Clifford J. Whatcott, Adam Siddiqui-Jain, David J. Bearss, Steven L. Warner. Alvocidib enhances the efficacy of cytarabine and daunorubicin (7+3) in non-clinical models of acute myeloid leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4823.

Abstract 2144: Enhanced expression of β-catenin and Axl receptor tyrosine kinase in chronic lymphocytic leukemia (CLL) B-cells with co-culture on marrow stromal cells: Implications for drug resistance

Our study in CLL delineated a unique mechanism of how bone marrow stromal cells (BMSCs), may influence CLL B-cell signaling and drug resistance via modifying β-catenin and Axl status in leukemic cells. Purified primary CLL B-cells (n= 31) from previously untreated CLL patients were cultured alone or co-cultured with primary BMSCs from either normal individuals (n=23) or CLL patients (n=12) at a 50:1 ratio in AIMV medium. After 48 hours, separated CLL B-cells or BMSCs were examined by immunoprecipitation/Western blot analyses and real-time PCRs. We observed significant increases in expression of Axl at both mRNA and protein levels in CLL B-cells co-cultured with BMSCs compared to CLL B-cells cultured alone. We also detected significantly increased expression of β-catenin at the protein level in co-cultured CLL B-cells. But, we did not see any significant change in β-catenin or Axl expression in BMSCs co-cultured with CLL B-cells. The CLL B-cells from co-culture had an upregulation in downstream P-ERK-1/2 but no change in P-AKT(Ser473). High nuclear active-β-catenin and P-ERK-1/2 levels were also detected in co-cultured CLL B-cells. ERK associates with and inactivates GSK-3β resulting in the up-regulation of β-catenin. We next checked for P-GSK-3β(Ser9) in co-cultured CLL B-cells. Upregulation in P-GSK-3β(Ser9) suggests inactivation of GSK-3β and β-catenin accumulation in co-cultured CLL B-cells. Additionally, we determined the phosphorylation status of Axl in CLL B-cells in co-culture compared with cultured alone. There was no change either at Y702 or total tyrosine phosphorylation in CLL B cells. Thus, we assume that the role of Axl in co-cultured leukemic B-cells is independent of its kinase activity. Next we determined the effect of Axl inhibitor TP-0903 on CLL B-cells in co-culture vs cultured alone. Interestingly, both Axl and β-catenin expression levels were further upregulated in CLL B-cells exposed to TP-0903 compared to CLL B-cells without TP-0903 in co-culture, indicating possible roles for both Axl and β-catenin in stromal mediated CLL B-cell drug resistance. However, TP-0903 decreased P-Axl(Y702) as well as an Axl downstream mediator, P-Akt(S473) and reduced Mcl-1 expression in CLL B-cells even in presence of BMSCs. This was associated with induction of cell death and overrode BMSC mediated protection. Treatments of fludarabine or chlorambucil also led to increase in expressions of both β-catenin and Axl in co-cultured CLL B-cells. Moreover, inhibition of P-ERK-1/2 with inhibitor PD98059 in CLL B-cells cultured with BMSCs inhibited β-catenin as well as Axl expression levels. Here we show that stroma mediated increased expression in both β-catenin and Axl likely contribute to the survival and drug resistance of B-cells from patients with CLL. Understanding their role in drug metabolism is underway.

Citation Format: Sutapa Sinha, Charla Secreto, Justin Boysen, Steven L. Warner, David J. Bearss, Asish Ghosh, Neil E. Kay. Enhanced expression of β-catenin and Axl receptor tyrosine kinase in chronic lymphocytic leukemia (CLL) B-cells with co-culture on marrow stromal cells: Implications for drug resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2144.

Abstract 883: Alvocidib-mediated inhibition of CDK9 upregulates BIM via suppression of miR17-92

The positive-transcription elongation factor (P-TEFb) complex is critical in stimulating the transcription of non-abortive transcripts by RNA polymerase II. The CDK9/cyclin-T heterodimer comprises the P-TEFb complex and promotes transcription elongation through phosphorylation of serine 2 of the heptapeptide repeats of the c-terminal domain of RNA Polymerase II (RNAPII-CTD). Alvocidib, a potent CDK9 inhibitor, has been shown to suppress expression of MCL-1 and Myc mRNAs, and clinical pharmacodynamic data suggest that alvocidib's activity is primarily mediated through the suppression of MCL-1 mRNA and protein expression. In addition to MCL-1 suppression, we hypothesized that CDK9 inhibition affects other RNA Polymerase II target RNAs, such as microRNAs. Recently, it was reported that inhibition of bromodomain and extraterminal domain (BET) protein by JQ1 suppresses miR17-92 expression. miR17-92 negatively regulates expression of the pro-apoptotic BH3-only protein, BIM, leading to suppression of BIM expression, thereby decreasing the cells' ability to induce apoptosis. It was hypothesized that CDK9 kinase activity is key to miR17-92 expression and suppression of BIM expression and that targeting CDK9 would lead to a decrease in miR17-92, and increases in BIM. MV4-11, OCI-AML3, MOLM13, and THP1 AML cell lines were used to determine the effects of alvocidib treatment on microRNAs. RT-qPCR was utilized to determine microRNA expression levels of miR17-92 and mRNA levels of BIM and other markers. Protein changes were determined using standard gel electrophoresis and immunoblotting technique. CellTiter-Glo and Caspase-Glo were used for all cell viability and apoptosis assays interrogating alvocidib. With CDK9 inhibition mediated via alvocidib, a dose- and time-dependent decrease in miR17-92 expression in MV4-11, OCI-AML3, MOLM13, and THP1 cells was observed. A decrease was observed even 3 hours post-treatment, persisting for up to 24 hours. MicroRNA suppression following treatment ranged in magnitude, with a maximal effect of between 3.3 to 4.2-fold suppression, depending on the cell line and timepoint. This suppression coincided with an increase in BIM mRNA and protein expression in the MV4-11, OCI-AML3, and MOLM13 cells. However, BIM protein increase was not observed in THP1 cells. Maximal increase in BIM mRNA levels reached 5.4-fold in the MV4-11 cell line. Our data suggest that CDK9 inhibition suppresses RNA Polymerase II-mediated expression of miR17-92, which in turn leads to increased expression of BIM. Combined with MCL-1 reduction, increased BIM protein expression mediated by alvocidib leads to enhanced apoptosis. Taken together, the data provide additional understanding of CDK9 as a potential therapeutic target, and are consistent with the hypothesis that CDK9 activity is necessary for miR17-92 expression.

Citation Format: Hillary Haws, Hubert F. Arokium, James L. Bogenberger, Adam Siddiqui-Jain, David J. Bearss, Raoul Tibes, Steven L. Warner, Clifford J. Whatcott. Alvocidib-mediated inhibition of CDK9 upregulates BIM via suppression of miR17-92 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 883.

Abstract B178: Targeting Myc in triple-negative breast cancer models through the dual inhibition of PIM kinases and CDK9

Of the more than 240,000 estimated new cases of breast cancer in 2016 (US), triple-negative breast cancer (TNBC) was expected to comprise roughly 12%. So named because of their lack of estrogen receptor, progesterone receptor, and human epidermal growth factor receptor 2 expression, TNBCs pose a unique therapeutic challenge, with only chemotherapeutic options currently available. New therapeutic options are desperately needed for patients with TNBC. Recent reports have identified a cellular addiction of TNBCs to PIM1, suggesting that the addiction is mediated by PIM regulation of Myc and BH3 proteins MCL-1 or BCL-2. The PIM family of serine/threonine kinases are highly conserved and the link between PIM and Myc function has been well studied. The second-generation PIM inhibitor, TP-3654, has been shown to suppress Myc expression in vitro. Additionally, CDK9 inhibitors are also known to suppress Myc expression. CDK9 inhibition mediates specific reductions in transcription of short-lived mRNAs such as Myc and MCL-1. The CDK9/cyclin T complex is a critical component of the P-TEFb complex, promoting productive RNA elongation through phosphorylation of serine 2 of the heptapeptide repeats of the C-terminal domain of RNA Polymerase II (RNAPII-CTD). We are developing a potent CDK9 inhibitor, alvocidib, and an oral prodrug form of alvocidib named TP-1287, and are investigating the potential clinical utility of CDK9 inhibition in acute myeloid leukemia (AML). We hypothesized that PIM and CDK9 inhibition would be an active combination in models of TNBC due to the added effect of targeting Myc through two independent mechanisms. In the TNBC cell line, MDA-MB-231, TP-3654 reduced relative Myc protein expression by 74%, while alvocidib reduced expression by 71%. The combination of TP-3654 and alvocidib reduced detectable expression 100%, as measured by standard immunoblotting, at concentrations of 100 nM with a 3-hour treatment. To test this hypothesis in vivo, TP-3654 and TP-1287 were tested in the MDA-MB-231 xenograft. Single-agent TP-3654 (150 mg/kg) reduced tumor growth (%TGI) 40.7%, while TP-1287 (3.75 mg/kg) reduced tumor growth 11.6%. The combined-treatment regimen reduced tumor growth by 58.3% at day 18 of treatment. These results support a rationale for further clinical investigation of PIM and CDK9 inhibitors for the suppression of Myc in patients with TNBC.

Citation Format: Hillary Haws, Wontak Kim, Adam Siddiqui-Jain, David J. Bearss, Steven L. Warner, Clifford J. Whatcott. Targeting Myc in triple-negative breast cancer models through the dual inhibition of PIM kinases and CDK9 [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr B178.

Abstract 1106: Alvocidib potentiates the activity of venetoclax in preclinical models of multiple myeloma

The proteasome inhibitor bortezomib is widely used in the treatment of patients with multiple myeloma (MM). The expression levels of many proteins increase as a result of bortezomib treatment, including the pro-apoptotic protein NOXA. NOXA functions to sequester the anti-apoptotic BCL-2 family member, MCL-1. High levels of MCL-1 and/or low levels of NOXA have been implicated in bortezomib resistance and negative patient outcomes, including short duration of treatment response. The BCL-2-specific BH3 mimetic venetoclax (ABT-199) has also been explored in multiple hematological malignancies, including the treatment of MM. Venetoclax induces apoptosis in a BCL-2 specific manner by directly inhibiting BCL-2 function. However, intrinsic resistance to venetoclax treatment observed in MM patient samples has been attributed to a low BCL-2-to-MCL-1 gene expression ratio, suggesting a central role for MCL-1 in cell survival in this context as well. Increased MCL-1 expression is a known resistance mechanism to venetoclax treatment in a variety of cell types including chronic lymphocytic leukemia and lymphomas. Considering the central role of MCL-1 to treatment efficacy in MM, we investigated the ability of an MCL-1-lowering agent, namely the CDK9 inhibitor alvocidib, to potentiate the activity of venetoclax in MM. Alvocidib suppresses MCL-1 expression via CDK9-mediated regulation of RNA polymerase II. Alvocidib has achieved robust improvements in the clinical response rates of high-risk, newly diagnosed acute myeloid leukemia (AML) patients as part of the time-sequential ACM regimen (alvocidib + cytarabine + mitoxantrone). We therefore hypothesized that alvocidib would potentiate the activity of venetoclax in MM through an MCL-1-dependent mechanism. In this report, we demonstrate that alvocidib inhibits the protein expression of MCL-1 in MM cells in a time-dependent fashion, up to 96 hours. In cell viability assays, the addition of up to 100 nM venetoclax resulted in a 2.8-fold reduction in the IC50 of alvocidib in the cultured OPM-2 cell line. Conversely, the potentiation of venetoclax activity with the addition of alvocidib resulted in a more than 500-fold decrease in IC50 in the relatively venetoclax-resistant OPM-2 cells. Additional studies are currently underway to investigate the efficacy of alvocidib and venetoclax in the context of bortezomib resistance where low NOXA may contribute to enhanced cell survival via MCL-1. Taken together, our data suggest that the combination of alvocidib with venetoclax may constitute a novel therapeutic regimen in the treatment of MM. Further, it suggests that CDK9-mediated targeting of MCL-1 may offer a clinical route to addressing intrinsic resistance in MM patients.

Citation Format: Mark Livingston, Wontak Kim, Hillary Haws, Peter Peterson, Clifford J. Whatcott, Adam Siddiqui-Jain, Steven Weitman, David J. Bearss, Steven L. Warner. Alvocidib potentiates the activity of venetoclax in preclinical models of multiple myeloma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1106. doi:10.1158/1538-7445.AM2017-1106

Are Accurins the cure for Aurora kinase inhibitors?

A nanoparticle formulation of an Aurora B inhibitor increases antitumor efficacy and reduces toxicity, which may be a precedent for the use of this technology with other small molecules (Ashton et al., this issue).

Abstract 3728: Targeting MCL-1 expression, through the inhibition of CDK9 and super enhancer driven transcription, offers multiple opportunities for rational drug combinations

Downregulating the expression and function of MCL-1 through the inhibition of cyclin-dependent kinase-9 (CDK9) has proven to be a valuable strategy to target this important pro-survival signal in malignant cells of numerous cancer types. This is exemplified by the ability of alvocidib, a potent CDK9 inhibitor, to inhibit the expression of MCL-1 at both the transcript and protein levels in multiple cell lines from both hematological and solid tumor origins. The timing and duration of MCL-1 knockdown varies between cell type; however, the knockdown is consistent and in some cell lines persistent after the removal of drug. Although alvocidib has demonstrated single agent activity in both the clinic and in nonclinical models, strategies that exploit MCL-1-dependent drug resistance, are allowing for the more rational use of alvocidib in combination with standard-of-care and investigational agents. Here, we demonstrate that treatment with alvocidib, followed by treatment with cytarabine and mitoxantrone (regimen called FLAM), is synergistic in nonclinical models of acute myeloid leukemia (AML). The FLAM regimen results in a significant increase in apoptosis in comparison to any of the single agents alone. This synergy correlates with the downregulation of MCL-1 expression by alvocidib treatment, which places the cancer cells into a heightened state to undergo apoptosis when induced by cytarabine and mitoxantrone treatments. Additionally, the FLAM regimen has demonstrated robust clinical activity in both front-line and relapsed/refractory AML patients. The knockdown of MCL-1 by alvocidib can also be exploited when used in combination with 5-azacytidine (5-aza). BCL-2 family members, including MCL-1 have been described as mechanisms of resistance to 5-aza. Treatment of cells with alvocidib, to repress MCL-1 expression prior to 5-aza treatment, reduced the 5-aza cell viability EC50 more than 2.5-fold, from 1.8 μM to 0.6 μM in MV4-11 cells. The alvocidib/5-aza combination also resulted in synergistic increases in caspase activity relative to either single agent within the combination, at multiple dose levels. MCL-1 dependence is a known mechanism of resistance to BCL-2-targeting agents, such as venetoclax (ABT-199). Alvocidib is an effective approach to targeting MCL-1 leading to the sensitization of cancer cells to venetoclax. Finally, the rational drug combinations described here are further supported by the finding that MCL-1-dependence, measured by NOXA priming, correlates with clinical benefit from treatment with an alvocidib-containing regimen (eg. FLAM) in AML patients. In conclusion, MCL-1 is a key downstream target of inhibiting CDK-9 with alvocidib. Combination strategies using alvocidib have emerged as a powerful solution for overcoming MCL-1 dependent drug resistance.

Citation Format: Wontak Kim, Katherine K. Soh, Ye Sol Lee, Peter Peterson, Clifford J. Whatcott, Adam Siddiqui-Jain, Steven Weitman, David J. Bearss, Steven L. Warner. Targeting MCL-1 expression, through the inhibition of CDK9 and super enhancer driven transcription, offers multiple opportunities for rational drug combinations. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3728.

Abstract C202: CDK9 inhibition synergizes with BRD4 inhibitor-mediated super enhancer transcriptional repression in multiple preclinical tumor models

The group of transcriptional regulatory proteins known collectively as the super enhancer complex (SEC) coordinate the expression of entire genetic programs directing cell fate. The SEC is also important in driving cancer progression mediated by transcription of key oncogenes such as c-Myc and Bcl-2. The SEC requires the interaction and coordination of many proteins, including cyclin-dependent kinases (CDK), bromodomain proteins (BRD), histone deacetylases (HDAC), and histone methyltransferases (HMT). Each of these proteins are the focus of significant development efforts for the treatment of cancer. SEC-regulated transcription requires recruitment of CDK9/cyclin T1 from the 7SK RNA/Hexim1 inhibitory complex by BRD4 to transcriptional start sites. CDK9 then phosphorylates RNA polymerase II, releasing it from the start site leading to productive transcriptional elongation and gene expression. Considering the close association of CDK9 and BRD4, we hypothesized that the combination of CDK9 and BRD4 inhibitors would have synergistic effects in cancer cells. Alvocidib is a potent CDK9 inhibitor with validated clinical activity in AML from multiple Phase II studies in over 400 patients. Additionally, BRD4 inhibitors have demonstrated early promise in clinical studies with a focus on hematologic malignancies. However, we have found that CDK9 inhibitors, combined with bromodomain inhibitors, produced a synergistic effect by inhibiting the SEC more effectively than either of these compounds alone. Cell viability studies with various combinations resulted in an increase in potency. This was observed with alvocidib combined with JQ-1 (BRD4 inhibitor) in A549 lung cancer cells. Furthermore, the combination of alvocidib with JQ-1 completely abrogated SEC function, as measured by c-Myc or Mcl-1 expression through RT-qPCR. Similar results were achieved with other combinations of CDK9 and BRD4 inhibitors. These data, primarily focused on alvocidib and JQ-1, suggest a strong rationale for combining CDK9 and BRD4 inhibitors as a treatment strategy for multiple tumor types, including lung cancer. Furthermore, these findings may be more broadly applied to additional therapeutic targets in the SEC. These strategies yield synergistic effects at inhibiting SEC function and are highly active in tumor growth studies of cancer, in vivo. Clinical studies utilizing these combination strategies will explore this therapeutic approach.

Citation Format: Ye Sol Lee, Wontak Kim, Katherine K. Soh, Peter Peterson, Clifford J. Whatcott, Adam Siddiqui-Jain, David J. Bearss, Steven L. Warner. CDK9 inhibition synergizes with BRD4 inhibitor-mediated super enhancer transcriptional repression in multiple preclinical tumor models. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr C202.

Abstract 3604: Targeting the PIM kinases in combination with BTK inhibition is synergistic in preclinical models of B-cell malignancies

BTK inhibitors (e.g. ibrutinib) have significantly impacted the treatment of B-cell malignancies in a positive way. Single agent response rates with ibrutinib are 65% or higher in B-cell lymphomas and chronic lymphocytic leukaemia with the majority of patients enjoying a prolonged duration of response. Continued clinical development is needed, however, as most patients achieve only a partial response from their treatment and ultimately patients become refractory to ibrutinib leading to relapse and disease progression. Targeted combinations with ibrutinib could potentially increase the number of patients undergoing complete remission and combat emergent resistant mechanisms. The PIM family (1, 2, and 3) are serine/threonine kinases that have proven to be oncogenic in-part due to their ability to suppress c-Myc induced apoptosis. The PIM kinases have emerged as important regulators of drug resistance in multiple cancer types. Tolero Pharmaceutical's second generation PIM Kinase inhibitor, TP-3654 has exhibited favorable activity in preclinical models of prostate cancer, AML, and lymphoma. Due to the signaling crosstalk between BTK and PIM through the STAT transcription factors, we hypothesized that synergies may arise through the simultaneous targeting of both kinases. Here, we report a significant increase in drug activity when a BTK inhibitor (ibrutinib) was combined with TP-3654 in various lymphoma cell lines. In Granta-519 cells, the IC50 of ibrutinib decreased 3.5-fold, from 0.7 μM to 0.2 μM, when cultured in combination with a subtoxic concentration of TP-3654 (300 nM). Similarly, the IC50 of TP-3654 decreased 6-fold, from 2.4 μM to 0.4 μM, when cells were cultured in combination with a subtoxic concentration of ibrutinib (100 nM). BTK is known to attenuate the activity of the transcription factor STAT3, a major regulator of PIM kinase levels in cells. Due to this, mechanistic studies focused on analyzing the STAT3 pathway are ongoing to determine the downstream effects of using ibrutinib and TP-3654 in combination. Several lymphoma xenograft studies are also ongoing to further explore this combination in vivo. These results provide a strong rationale that inhibitors of PIM and BTK could be used in combination for the treatment of B-cell malignancies and other B-cell mediated diseases.

Citation Format: Jeremiah J. Bearss, Brigham L. Bahr, Katie K. Soh, Peter W. Peterson, Clifford J. Whatcott, Adam Siddiqui-Jain, David J. Bearss, Steven L. Warner. Targeting the PIM kinases in combination with BTK inhibition is synergistic in preclinical models of B-cell malignancies. [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 3604. doi:10.1158/1538-7445.AM2015-3604

Abstract 3400: Mitochondrial profiling in AML patients treated with an Alvocidib containing regimen reveals MCL1 dependency in responder bone marrow

Background.  Molecular profiles may provide insights into the likelihood of responding to traditional cytotoxic chemotherapy as well as important clues to the success of novel targeted agents.  The anti-apoptotic BCL-2 family proteins have previously been shown to facilitate pro-survival and resistance to chemotherapy in AML, multiple myeloma, as well as in other types of cancer. Measuring the function of these proteins using BH3 profiling has proven to provide useful information in predicting AML treatment response with traditional ara-c based treatment. Here, we sought to determine if such an approach might detect response with the addition of Alvocidib to ara-c-based chemotherapy. Mitochrondrial apoptosis signaling was assessed in AML patients treated with Alvocidib, ara-c and mitoxantrone (FLAM).  Methods.  Pretreatment peripheral blood mononuclear cell and bone marrow specimens from 63 patients treated with FLAM were measured for mitochondrial outer membrane permeabilization following incubation with BH3 peptides as a surrogate for BCL-2 protein family function. Results.  Analysis of the priming states (mitochondrial depolarization) in the patients who underwent complete remission (CR), compared with those who did not (NR), revealed that NOXA priming was significantly higher in CR bone marrow samples (median 44.5%) compared with NR samples (median 5.2%, p = 0.006). NOXA is known to interact most directly with MCL1, suggesting that these cancer cells may be MCL1 dependent. An additional multi-peptide algorithm using three BH3 members was also identified (involving BAD, PUMA, and BIM), which may also indirectly support MCL1 dependency. These BH3 priming profiles were both additive to known risk factors associated with clinical response to chemotherapy, including cytogenetic risk factors. Receiver operating characteristic (ROC) curve analysis of NOXA priming plus cytogenetics and MDS history indicated that these variables were highly predictive of response to FLAM (AUC-0.92, p = 0.0002). This correlation is distinct from our previous work which showed that the priming due to the BIM peptide predicts response to traditional ara-c based treatment. This work provides a basis for further studies into the MCL1 dependent action of Alvocidib, as well as a potential biomarker for identification of patients likely to respond to FLAM.

Citation Format: Elisha J. Dettman, Steven L. Warner, Camille Doykan, Melissa Arn, Noel Blake, David J. Bearss, Michael Cardone, Bruce D. Smith. Mitochondrial profiling in AML patients treated with an Alvocidib containing regimen reveals MCL1 dependency in responder bone marrow. [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 3400. doi:10.1158/1538-7445.AM2015-3400

Abstract 3579: Identification of biomarkers of AXL-mediated drug resistance in head and neck squamous cell carcinoma

Background:

Head and neck squamous cell carcinoma (HNSCC) is the fifth most common cancer. In 2013, there were ∼53,000 newly diagnosed cases and ∼11,000 deaths related to HNSCC in the USA. Overexpression of EGFR is seen in 90% HNSCC; but, only ∼10% of patients treated with the anti-EGFR antibody cetuximab show increased response rates to cetuximab and these eventually gain resistance by poorly-characterized mechanisms. We showed an association between EMT and resistance to EGFR inhibitors in lung cancers (LC) and HNSCC using a 76-gene EMT signature. AXL was identified as a therapeutic candidate linking EMT and drug resistance, showing significantly higher expression in erlotinib resistant cell lines. Other groups have linked AXL to drug resistance in HNSCC, LC and breast cancers. Here we identify signaling pathways that are regulated by AXL, mediate drug resistance, and identify potential therapeutic targets to combine with AXL inhibition.

Methods:

Using 6 clinical cohorts including The Cancer Genome Atlas (TCGA N = 493) and PROSPECT (N = 142) across 3 cancer types, we identified genes whose mRNA expression was highly correlated with AXL. Protein profiling by reverse phase protein array (RPPA) to analyze total and phospho-proteins in HNSCC cell lines, pre- and post-AXL inhibitor treatment was used to identify pathways altered upon AXL inhibition. The response to AXL inhibition was assayed in HNSCC cell lines by proliferation assays and correlated to mRNA and protein expression.

Results:

Using gene-expression and RPPA analysis we saw the highest association of AXL with pathways involved in EMT (TGF-β, Rho GTPases), autophagy and immune response. Following treatment with an AXL inhibitor, we observed a decrease in phospho-proteins in the PI3K-AKT pathway, increased expression of markers associated with apoptosis, an epithelial phenotype, and p-EGFR. Using an AXL knockdown model system in HNSCC cell lines, we validated an increase in EGFR signaling (EGFR and p-Erk), epithelial (E-cadherin), apoptotic (cleaved PARP and caspase-7) and DNA repair proteins (RAD51, ku-80 and PARP) and a decrease in Slug, Twist and ZEB-1, indicating that AXL may be directly involved in mediating EMT. AXL knockdown reduced proliferation of HNSCC cell lines and AXL inhibition was able to re-sensitize resistant HNSCC cell lines to erlotinib, an EGFR tyrosine kinase inhibitor.

Conclusions:

In summary, we identified potential therapeutic targets that are upregulated with AXL expression in HNSCC and LC patient tumors and cell lines. Using AXL inhibitor and knockdown in HNSCC cell lines, we validated biomarkers involved in EMT, EGFR signaling and apoptosis that are altered upon AXL inhibition. AXL inhibition led to an epithelial phenotype in cells and re-sensitized resistant cells to erlotinib. Studies are ongoing to validate the mechanisms of AXL-mediated drug resistance and to identify potential combination treatments that can synergize with AXL-inhibition.

Citation Format: Kavitha Balaji, Robert Cardnell, Lixia Diao, Pan Tong, Milena Mak, You Hong Fan, Fatemeh Masrorpour, Steven L. Warner, David J. Bearss, Ignacio Wistuba, Gordon B. Mills, John Heymach, Khandan Keyomarsi, Jing Wang, Lauren Averett Byers. Identification of biomarkers of AXL-mediated drug resistance in head and neck squamous cell carcinoma. [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 3579. doi:10.1158/1538-7445.AM2015-3579

Targeted Axl Inhibition Primes Chronic Lymphocytic Leukemia B Cells to Apoptosis and Shows Synergistic/Additive Effects in Combination with BTK Inhibitors

PURPOSE

B-cell chronic lymphocytic leukemia (CLL) is an incurable disease despite aggressive therapeutic approaches. We previously found that Axl receptor tyrosine kinase (RTK) plays a critical role in CLL B-cell survival. Here, we explored the possibility of using a high-affinity Axl inhibitor as a single agent or in combination with Bruton's tyrosine kinase (BTK) inhibitors for future clinical trial to treat patients with CLL.

EXPERIMENTAL DESIGN

Expression/activation status of other members of the TAM (e.g., Tyro3, Axl, and MER) family of RTKs in CLL B cells was evaluated. Cells were treated with a high-affinity orally bioavailable Axl inhibitor TP-0903 with or without the presence of CLL bone marrow stromal cells (BMSCs). Inhibitory effects of TP-0903 on the Axl signaling pathway were also evaluated in CLL B cells. Finally, cells were exposed to TP-0903 in combination with BTK inhibitors to determine any synergistic/additive effects of the combination.

RESULTS

CLL B cells overexpress Tyro3, but not MER. Of interest, Tyro3 remains as constitutively phosphorylated and forms a complex with Axl in CLL B cells. TP-0903 induces massive apoptosis in CLL B cells with LD50 values of nanomolar ranges. Importantly, CLL BMSCs could not protect the leukemic B cells from TP-0903-induced apoptosis. A marked reduction of the antiapoptotic proteins Mcl-1, Bcl-2, and XIAP and upregulation of the proapoptotic protein BIM in CLL B cells was detected as a result of Axl inhibition. Finally, combination of TP-0903 with BTK inhibitors augments CLL B-cell apoptosis.

CONCLUSIONS

Administration of TP-0903 either as a single agent or in combination with BTK inhibitors may be effective in treating patients with CLL.

Abstract 907: Bcl-xL dependence predicts response to alvocidib in chronic lymphocytic leukemia patients

Introduction. Chronic lymphocytic leukemia (CLL) patients may benefit from personalized strategies targeting specific therapies to individuals with favorable molecular profiles. Many therapeutics exhibit response in a subset of patients, and factors such as age or cytogenetics are insufficient to predict treatment success with high accuracy. We assessed mitochondrial functionality in apoptosis signaling for identification of CLL patients likely to exhibit clinical response to treatment with alvocidib. Effects of this agent have been shown to involve pathways of apoptosis, providing the rationale for our study. Patients and Methods. Relapsed/refractory patients comprising OSU0055 and Sanofi EFC6663 clinical trials were analyzed. Pretreatment peripheral blood mononuclear cell (PBMC) specimens were divided into training and validation sets for response-correlative assessment. Blinded to outcomes, we analyzed specimens by flow cytometry-based BH3 profiling, indirectly measuring induction of mitochondrial outer membrane permeabilization in response to treatment with BH3-only peptides (Bim, Noxa, Bad, Bmf, Hrk) as surrogates for Bcl-2 family functions. Findings were correlated with disease characteristics and treatment outcome in the proof-of-principal set and tested for confirmation in the validation set. Results. Response data were available for 62 patients; training and test sets comprised 30 and 32 patients, respectively. Regression analyses indicated a correlation between clinical response (ordered 3 categories; PD, SD, PR) and priming in training set with Bim(0.1) (p=.014) and Hrk (p=.0098), that later validated in the test set for both markers (p=.0051 and p=.015, respectively). In total (n=62), Bim regression displayed a p=.0027 and Hrk regression a p=.00046. When analyzed as PD/SD vs PR, the combined cohort yielded Bim p=.04, and Hrk p=.0039 by logistic regression. Using area under the receiver operating curve (AUC) to quantify the accuracy of outcome prediction, Bim AUC = 0.73 (CI[.60-.85]; p=.0004) and Hrk AUC = .73 (CI[.61-.86]; p=.0002). Hrk benefitted from adjustment for trisomy12 status (AUC=0.83; CI[.71-.95]; p<.0001). Analysis of BH3 profiling and tumor lysis syndrome (TLS) indicated correlation between TLS and Bad priming (p=.012 log regression; AUC=.75; CI[.60-.89]; p=.0007) that benefitted from inclusion of ECOG status and patient age (AUC=.85; CI[.73-.97]; p<.0001). Conclusion. Bim and Hrk are significantly associated with response and, thus, engaging Bcl-xL dependence may be a component of response to alvocidib in relapsed CLL patients. Interestingly, TLS is predicted by a distinct BH3 profiling peptide readout, Bad, consistent with alvocidib-associated TLS driven by Bcl-2-dependency. Taken together, these biomarkers may predict patient response to investigational CDK inhibitors in CLL and concurrently identify patients at risk for treatment-related toxicity.

Citation Format: William E. Pierceall, Steven L. Warner, Ryan J. Lena, Camille Doykan, Noel Blake, Michael Elashoff, Daniel D. Von Hoff, David J. Bearss, Michael H. Cardone, Michael Grever, Mark C. Lanasa, John C. Byrd, Amy J. Johnson. Bcl-xL dependence predicts response to alvocidib in chronic lymphocytic leukemia patients. [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 907. doi:10.1158/1538-7445.AM2014-907

A small-molecule inhibitor of PIM kinases as a potential treatment for urothelial carcinomas

The proto-oncogene proviral integration site for moloney murine leukemia virus (PIM) kinases (PIM-1, PIM-2, and PIM-3) are serine/threonine kinases that are involved in a number of signaling pathways important to cancer cells. PIM kinases act in downstream effector functions as inhibitors of apoptosis and as positive regulators of G₁-S phase progression through the cell cycle. PIM kinases are upregulated in multiple cancer indications, including lymphoma, leukemia, multiple myeloma, and prostate, gastric, and head and neck cancers. Overexpression of one or more PIM family members in patient tumors frequently correlates with poor prognosis. The aim of this investigation was to evaluate PIM expression in low- and high-grade urothelial carcinoma and to assess the role PIM function in disease progression and their potential to serve as molecular targets for therapy. One hundred thirty-seven cases of urothelial carcinoma were included in this study of surgical biopsy and resection specimens. High levels of expression of all three PIM family members were observed in both noninvasive and invasive urothelial carcinomas. The second-generation PIM inhibitor, TP-3654, displays submicromolar activity in pharmacodynamic biomarker modulation, cell proliferation studies, and colony formation assays using the UM-UC-3 bladder cancer cell line. TP-3654 displays favorable human ether-à-go-go-related gene and cytochrome P450 inhibition profiles compared with the first-generation PIM inhibitor, SGI-1776, and exhibits oral bioavailability. In vivo xenograft studies using a bladder cancer cell line show that PIM kinase inhibition can reduce tumor growth, suggesting that PIM kinase inhibitors may be active in human urothelial carcinomas.

Activators of PKM2 in cancer metabolism

Pyruvate kinase converts phosphoenolpyruvate to pyruvate, catalyzing the rate-limiting step of glycolysis. The M1 isoenzyme of pyruvate kinase (PKM1) is found in adult tissues; whereas, PKM2 is a splicesome variant found in embryonic and cancer cells. PKM2 expression in malignant cells is a result of the tumor microenvironment and is responsible for maintaining a glycolytic phenotype. PKM2 has other nonmetabolic functions in malignant cells, including transcriptional coactivation and protein kinase activity. PKM2 activators have antitumor properties by inducing tetramerization of two PKM2 dimers causing PKM2 to function like PKM1. Restoring PKM2 to PKM1-like levels of activity causes reversal of the Warburg effect in cancer cells. PKM2 activators have therapeutic potential in the treatment of cancer and other metabolic diseases.

Discovery of Novel Putative Inhibitors of UDP-GlcNAc 2-Epimerase as Potent Antibacterial Agents

We present the discovery and optimization of a novel series of inhibitors of bacterial UDP-N-acetylglucosamine 2-epimerase (called 2-epimerase in this paper). Starting from virtual screening hits, the activity of various inhibitory molecules was optimized using a combination of structure-based and rational design approaches. We successfully designed and identified a 2-epimerase inhibitor (compound 12-ES-Na, that we named Epimerox) which blocked the growth of methicillin-resistant Staphylococcus aureus (MRSA) at 3.9 μM MIC (minimum inhibitory concentration) and showed potent broad-range activity against all Gram-positive bacteria that were tested. Additionally a microplate coupled assay was performed to further confirm that the 2-epimerase inhibition of Epimerox was through a target-specific mechanism. Furthermore, Epimerox demonstrated in vivo efficacy and had a pharmacokinetic profile that is consonant with it being developed into a promising new antibiotic agent for treatment of infections caused by Gram-positive bacteria.

TIG1 promotes the development and progression of inflammatory breast cancer through activation of Axl kinase

Inflammatory breast cancer (IBC) is the most lethal form of breast cancer, but the basis for its aggressive properties are not fully understood. In this study, we report that high tumoral expression of TIG1 (RARRES1), a functionally undefined membrane protein, confers shorter survival in patients with IBC. TIG1 depletion decreased IBC cell proliferation, migration, and invasion in vitro and inhibited tumor growth of IBC cells in vivo. We identified the receptor tyrosine kinase, Axl, as a TIG1-binding protein. TIG1 interaction stablilized Axl by inhibiting its proteasome-dependent degradation. TIG1-depleted IBC cells exhibited reduced Axl expression, inactivation of NF-κB, and downregulation of matrix metalloproteinase-9, indicating that TIG1 regulates invasion of IBC cells by supporting the Axl signaling pathway in IBC cells. Consistent with these results, treatment of IBC cells with the Axl inhibitor SGI-7079 decreased their malignant properties in vitro. Finally, TIG1 expression correlated positively with Axl expression in primary human IBC specimens. Our findings establish that TIG1 positively modifies the malignant properties of IBC by supporting Axl function, advancing understanding of its development and rationalizing TIG1 and Axl as promising therapeutic targets in IBC treatment.

Abstract 4413: Mechanisms of sensitivity to treatment with the PDK1 inhibitors HCI-1680 and HCI-1708

The phosphoinositide-dependent kinase-1 (PDK1) is a serine/threonine kinase that has been considered a promising potential oncology drug target because of its role as an important regulator in the PI3K/AKT/mTOR pathway. PDK1 phosphorylates highly conserved Ser or Thr residues in the activation loop of several AGC super family kinases including PKC, SGK, PKB/Akt, p70S6K, and PDK1 itself. Approximately, 40-50% of all tumors involve mutations in the phosphatase and tensin homolog (PTEN) protein, which results in elevated levels of PIP3 and enhanced activation of PKB/AKT, p70S6K, and SGK. It has been proposed that inhibitors of PDK1 could provide a valuable therapeutic approach to targeting cancer, particularly those with PTEN deficiencies. Using a fragment-based design strategy, we screened a collection of 1100 low molecular weight (< 250 MW) fragments against the PDK1 kinase and identified 9 fragments with moderate inhibitory activity against PDK1 (IC50 values from 45-82 μM). Subsequent molecular docking studies using a crystal structure of PDK1 allowed for the structural rationalization of how these fragments bound in the ATP-binding pocket (hydrogen bonding to S160/A162 hinge residues) and provided insight for further optimization. Synthesis and follow-up screening led to the discovery of HCI-1680 and a related compound SGI-1708, as potent PDK1 inhibitors with IC50 values of 80 and 94 nM, respectively. We used a large cell line panel of over 100 cancer cell lines to examine the ability of these compounds to kill cancer cells. Both HCI-1680 and SGI-1708 demonstrated remarkable selectivity for cell killing in several cell lines (KATO3, KG-1, MV4-11, Kasumi-1, MFE296 and AN3CA) in the low nanomolar range compared to all of the remaining cell lines in which the compounds showed low micromolar activity. Based on the known mutations in these cell lines we determined that HCI-1680 and SGI-1708 were more active in cells with PTEN deletion/silencing as well as activation of PIK3CA through activating mutations in PIK3CA or Ras proteins. Our compounds from this series were also shown to inhibit the activation of AKT and other downstream signaling molecules. We have explored the effects on gene expression Moreover, the lead compounds had high ligand efficiency with promising solubility and permeability parameters. Early animal studies examining pharmacokinetics and efficacy in xenograft models of human cancers have suggested that HCI-1680 and SGI-1708 have properties and activity to be developed as potential clinical candidates. We hypothesize that tumors, which have inactivated PTEN through mutations or silencing and also harbor mutations that activate PI3K define a population of cancer cells that are uniquely sensitive to PDK1 Inhibition. By inhibiting PDK1 activity we will block signaling from the PI3K pathway and lead to inhibition of cell proliferation and survival of these cancer cells.

Citation Format: Brian Walker, Sorna Venkataswamy, Steven Warner, Lee Call, Hariprasad Vankayalapati, Sunil Sharma, David J. Bearss. Mechanisms of sensitivity to treatment with the PDK1 inhibitors HCI-1680 and HCI-1708. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4413. doi:10.1158/1538-7445.AM2013-4413

Abstract LB-303: Small molecule inhibitor of the BTK pathway disrupts BCR signaling and demonstrates antitumor efficacy in a xenograft model

Despite the recent advances made in the treatment and management of B cell malignancies, these diseases are not curable and overall survival is limited. Bruton's Tyrosine Kinase (BTK) is a member of the Tec family of intracellular kinases first identified for its signaling via the B-cell Receptor (BCR) and its role in the immune system. More recently, BTK was found to play an important role in B cell malignancies and select solid tumors. Preclinical and clinical results with selective irreversible BTK inhibitors provide validation for BTK as a therapeutic target in B cell malignancies.

Aiming to leverage the contribution of the BTK signaling pathway to tumor growth, and its role in progression and drug resistance, we have developed a series of relatively selective, reversible, small molecule BTK inhibitors and evaluated their activity in enzyme, cell-based, and in vivo studies. Data obtained with the orally available MKC4659 compound illustrates our findings. In biochemical assays, compound MKC4659 demonstrated a relatively select targeting profile focused on a narrow group of PTKs including significant activity against BTK with IC50 less than 25 nM. In cellular assays the compound demonstrated significant in vitro potency against B cell lymphoma cell lines, inhibiting the growth of several B cell tumor cell lines including ones unresponsive to currently known BTK inhibitors. Importantly, MKC4659 showed a differential effect on B cell lymphoma, with no significant activity detected in control cells lacking detectable BTK expression. In vitro mode of action studies demonstrated that MKC4659 induces apoptosis and PARP cleavage in B cell lymphoma but not in control cells. Assays evaluating the in vitro on-target effect of compounds showed significant inhibition of the B cell receptor-mediated activation of the BTK pathway. In addition to inhibiting the phosphorylation of BTK, MKC4659 inhibited the phosphorylation of PLCγ in several B cell lymphoma cell lines. With in vitro potency demonstrated, and PK and ADMET profiles amenable to in vivo dosing, MKC4659 was evaluated for in vivo efficacy in a xenograft model of B cell lymphoma. In vivo dosing of MKC4659 inhibited growth of DOHH2 xenograft tumors in a dose dependent manner.

In summary, our team has identified BTK pathway inhibitors with demonstrated on-target and anti-tumor activity in cellular assays, and efficacy in a preclinical model of B cell malignancy. This effort provides a platform for compound development and evaluation for the treatment of hematologic malignancies. Optimization efforts on the MKC4659 series are ongoing and have yielded potent and drug-like preclinical candidates that are now moving into advanced animal studies.

Citation Format: Mary Faris, Uriel M. Malyankar, Victor Tam, Colleen Schweitzer, Diljeet Joea, Alexis Mollard, Bret Stephens, Steven L. Warner, David J. Bearss, Qingping Zeng. Small molecule inhibitor of the BTK pathway disrupts BCR signaling and demonstrates antitumor efficacy in a xenograft model. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-303. doi:10.1158/1538-7445.AM2013-LB-303

Abstract 2174: Small molecule iInhibitors of PIM kinases as potential treatments for urothelial carcinomas

The proto-oncogene PIM kinases (PIM-1, PIM-2, PIM-3) are serine/threonine kinases that have been shown to be involved in a number of signaling pathways important to cancer cells. PIM kinases act as downstream effectors as inhibitors of apoptosis and as positive regulators of G1-S phase progression through the cell cycle. PIM kinases are upregulated in multiple cancer indications, including lymphoma, leukemia, multiple myeloma, prostate, gastric, and head & neck cancers. Overexpression of one or more PIM family members in patient tumors frequently correlates with poor prognosis. The aim of this investigation was to evaluate PIM expression in low- and high-grade urothelial carcinoma, and to assess for expression that may contribute to disease progression and serve as a potential site for targeted therapy. Seventy-two cases of urothelial carcinoma were included in this retrospective study of surgical biopsy and resection specimens from the University of Utah Department of Pathology (retrieved from 2008-2011). Tissue was stained with commercially available antibodies against PIM-1, PIM-2, and PIM-3. Cases were divided into three groups (invasive high grade urothelial carcinoma (n=49), non-invasive urothelial carcinoma/carcinoma in situ (n=16), and non-invasive low grade urothelial carcinoma (n=7)). Individual cases were then given a score (0-4) based upon a percentage of cells staining positive for each antibody (<5%=0; 5-25%=1; 26-50%=2; 51-75%=3; >75%=4). A score of 2 or greater was considered expressed. PIM-1, PIM-2 and PIM-3 expression was noted in 29% (2/7), 43% (3/7) and 86% (6/7) cases of non-invasive low-grade urothelial carcinoma; 44% (7/16), 50% (8/16), 44% (7/16) cases of non-invasive high-grade urothelial carcinoma; 10% (5/49), 27% (13/49), and 18% (9/49) cases of invasive high-grade urothelial carcinoma, respectively. These results suggest that expression of PIM-1, PIM-2 and PIM-3 is present in a significant percentage of urothelial carcinomas and may serve as a source for targeted PIM-kinase inhibition. We have developed PIM inhibitors exhibiting 4-10 fold improved potency against the PIM kinase family compared to our original PIM inhibitor SGI-1776. Our PIM inhibitors display sub-μM activity in pharmacodynamic marker modulation, proliferation and 2D colony formation assays using the UM-UC-3 bladder cancer cell line. These PIM kinase inhibitors also are potent inducers of apoptosis in T24, RT4, and UM-UC-3 bladder cancer cell lines. These compounds have favorable hERG and CYP inhibition profiles compared with SGI-1776, and demonstrate excellent oral bioavailability. In vivo xenograft studies using bladder cancer cell line models show that PIM kinase inhibition can reduce the tumor growth of these tumor models suggesting that PIM kinase inhibitors may be active in human urothelial carcinomas.

Citation Format: Kent J. Carpenter, Rachel Brog, Christopher Moreno, Daniel J. Albertson, Jared J. Bearss, Ting Liu, Steven Warner, David J. Bearss. Small molecule iInhibitors of PIM kinases as potential treatments for urothelial carcinomas. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2174. doi:10.1158/1538-7445.AM2013-2174

Abstract 904: TP-0413 is a dual-specific inhibitor against Jak2 and Alk2 with therapeutic potential for treating anemia of chronic disease

Anemia of chronic disease is a debilitating condition commonly found in cancer patients. Studies suggest that this syndrome is largely the result of the body's production of hepcidin, a master regulator of human iron metabolism. TP-0413 is a small molecule that targets two important components of the hepcidin pathway, Janus Kinase 2 (Jak2) and Activin A receptor, type I (Alk-2). Jak2 facilitates hepcidin function by phosphorylating ferroportin upon hepcidin binding, inducing its degradation and thus preventing iron entry into plasma. Alk2 on the other hand, is a component of the signal transduction pathway that leads to hepcidin expression. Here we report on recent efforts aimed at further characterization of TP-0413. In biochemical assays TP-0413 inhibits Jak2 and Alk2 at 3.11 nM and 70 nM, respectively (IC50). In cell culture, HepG2 cells treated with TP-0413 exhibit reduced hepcidin levels, and TP-0413 is able to inhibit BMP-2 induction of hepcidin. Furthermore, TP-0413 ameliorates hypoferremia induced by LPS treatment in mice, and modulates cytokine levels in these animals. TP-0413 shows favorable drug-like properties in pharmacokinetic models, and further studies are being undertaken to advance TP-0413 towards clinical trials.

Citation Format: Bret J. Stephens, Alexis Mollard, Lingyao Meng, David J. Bearss, Steven L. Warner. TP-0413 is a dual-specific inhibitor against Jak2 and Alk2 with therapeutic potential for treating anemia of chronic disease. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 904. doi:10.1158/1538-7445.AM2013-904

Chemical genetic screen reveals a role for desmosomal adhesion in mammary branching morphogenesis

During the process of branching morphogenesis, the mammary gland undergoes distinct phases of remodeling to form an elaborate ductal network that ultimately produces and delivers milk to newborn animals. These developmental events rely on tight regulation of critical cellular pathways, many of which are probably disrupted during initiation and progression of breast cancer. Transgenic mouse and in vitro organoid models previously identified growth factor signaling as a key regulator of mammary branching, but the functional downstream targets of these pathways remain unclear. Here, we used purified primary mammary epithelial cells stimulated with fibroblast growth factor-2 (FGF2) to model mammary branching morphogenesis in vitro. We employed a forward chemical genetic approach to identify modulators of this process and describe a potent compound, 1023, that blocks FGF2-induced branching. In primary mammary epithelial cells, we used lentivirus-mediated knockdown of the aryl hydrocarbon receptor (AHR) to demonstrate that 1023 acts through AHR to block branching. Using 1023 as a tool, we identified desmosomal adhesion as a novel target of AHR signaling and show that desmosomes are critical for AHR agonists to block branching. Our findings support a functional role for desmosomes during mammary morphogenesis and also in blocking FGF-induced invasion.

Mechanism and relevance of EWS/FLI-mediated transcriptional repression in Ewing sarcoma

Ewing sarcoma provides an important model for transcription-factor mediated oncogenic transformation because of its reliance on the ETS-type fusion oncoprotein EWS/FLI. EWS/FLI functions as a transcriptional activator and transcriptional activation is required for its oncogenic activity. Here we demonstrate that a previously less-well characterized transcriptional repressive function of the EWS/FLI fusion is also required for the transformed phenotype of Ewing sarcoma. Through comparison of EWS/FLI transcriptional profiling and genome-wide localization data, we define the complement of EWS/FLI direct downregulated target genes. We demonstrate that LOX is a previously undescribed EWS/FLI-repressed target that inhibits the transformed phenotype of Ewing sarcoma cells. Mechanistic studies demonstrate that the NuRD co-repressor complex interacts with EWS/FLI, and that its associated histone deacetylase and LSD1 activities contribute to the repressive function. Taken together, these data reveal a previously unknown molecular function for EWS/FLI, demonstrate a more highly coordinated oncogenic transcriptional hierarchy mediated by EWS/FLI than previously suspected, and implicate a new paradigm for therapeutic intervention aimed at controlling NuRD activity in Ewing sarcoma tumors.

An epithelial-mesenchymal transition gene signature predicts resistance to EGFR and PI3K inhibitors and identifies Axl as a therapeutic target for overcoming EGFR inhibitor resistance

PURPOSE

Epithelial-mesenchymal transition (EMT) has been associated with metastatic spread and EGF receptor (EGFR) inhibitor resistance. We developed and validated a robust 76-gene EMT signature using gene expression profiles from four platforms using non-small cell lung carcinoma (NSCLC) cell lines and patients treated in the Biomarker-Integrated Approaches of Targeted Therapy for Lung Cancer Elimination (BATTLE) study.

EXPERIMENTAL DESIGN

We conducted an integrated gene expression, proteomic, and drug response analysis using cell lines and tumors from patients with NSCLC. A 76-gene EMT signature was developed and validated using gene expression profiles from four microarray platforms of NSCLC cell lines and patients treated in the BATTLE study, and potential therapeutic targets associated with EMT were identified.

RESULTS

Compared with epithelial cells, mesenchymal cells showed significantly greater resistance to EGFR and PI3K/Akt pathway inhibitors, independent of EGFR mutation status, but more sensitivity to certain chemotherapies. Mesenchymal cells also expressed increased levels of the receptor tyrosine kinase Axl and showed a trend toward greater sensitivity to the Axl inhibitor SGI-7079, whereas the combination of SGI-7079 with erlotinib reversed erlotinib resistance in mesenchymal lines expressing Axl and in a xenograft model of mesenchymal NSCLC. In patients with NSCLC, the EMT signature predicted 8-week disease control in patients receiving erlotinib but not other therapies.

CONCLUSION

We have developed a robust EMT signature that predicts resistance to EGFR and PI3K/Akt inhibitors, highlights different patterns of drug responsiveness for epithelial and mesenchymal cells, and identifies Axl as a potential therapeutic target for overcoming EGFR inhibitor resistance associated with the mesenchymal phenotype.

Abstract 2776: Inhibition of Nek2 by novel small molecules affects proteasome activity

Nek2 is a serine/threonine kinase that has been associated with centrosome function and cell cycle progression. Nek2 overexpression has been reported in several tumor types including breast and lung cancers. We have previously shown that elevated expression of Nek2 in clinical samples of multiple myeloma (MM) correlates with bortezomib resistance. Furthermore, the overexpression of Nek2 in MM cell lines decreases sensitivity to bortezomib and knockdown with RNAi sensitizes bortezomib resistant cells. Due to the proteaseome inhibitory activity of bortezomib, we hypothesized that Nek2 overexpression may increase proteasome activity. 26S proteasomes were isolated by ultracentrifugation from stably transfected Hela cells (+Nek2 or +GFP) and Nek2 was shown to be involved in the 26S proteasome complex by western blot. Proteasome activity assays were performed both biochemically and in cell culture demonstrating that proteasome activity in Hela+Nek2 is significantly higher than in Hela+GFP. Furthermore, the isolated 26S proteasomes were incubated with novel Nek2 inhibitors (HCI-2184 and HCI-2389) resulting in a significant reduction in proteasome function when used as single agents or in combination with bortezomib. HCI-2184, a reversible inhibitor of Nek2, demonstrated an IC50 value in the range of 13-38 nM, and HCI-2389, an irreversible inhibitor of Nek2, showed an IC50 value between 8-26 nM. Similarly, both compounds significantly increased the efficacy of bortezomib in inhibiting the proteasome activity. These results were confirmed in multiple cancer cell lines, including ARP1 (human MM cell line), H299 (human lung cancer cell line) and K28 (mouse Leydig tumor cell line). The effect of inhibiting Nek2 on cell cycle was also investigated. The expression levels of cyclinB1 and cdc2, proteins degraded by the proteasome for cells to exit mitosis, were increased in HCI-2389 treated Hela+Nek2 and to a lesser extent Hela+GFP treated cells. While Nek2 overexpression leads to the down-regulation of cyclinB1 and cdc2, HCI-2389 treatment successfully rescued this effect. Flow cytometry data showed that both treatments of HCI-2184 and HCI-2389 significantly arrested Hela+Nek2 and Hela+GFP in G2/M phase after 24 hours at concentration as low as 10nM. In conclusion, we have discovered a novel biological function of Nek2 related to elevated proteasome activity. We also demonstrated that our novel Nek2 inhibitors efficiently inhibit Nek2 function, resulting in reduced proteasome activity. These Nek2 inhibitors have the potential to be applied clinically for treatment of the MM patients resistant to bortezomib.

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 2776. doi:1538-7445.AM2012-2776

Abstract 1045: Activity of the LSD1 inhibitor HCI-2509 in ER-negative breast cancer cells

Lysine-specific demethylase 1 (LSD1/AOF2/KDM1A) is a flavin-dependent histone demethylase that catalyzes the post-translational oxidative demethylation of mono- and di-methylated lysines on histones. Methylation of lysine residues on histones can signal transcriptional activation or repression depending on the specific residue involved. H3K4me2 is a transcription-activating chromatin mark at gene promoters and demethylation of this mark by LSD1 is thought to prevent expression of tumor suppressor genes important in human cancer. In contrast, methylation of H3K9 is a repressive mark and LSD1 activity has been shown to upregulate tumor promoting pathways. High LSD1 protein levels have been reported in tissue specimens from estrogen receptor (ER)-negative breast cancers and high expression of LSD1 in these tumors correlates with aggressive biology. Thus, LSD1 is emerging as an important target for the development of specific inhibitors as a new class of antitumor drugs. Only a few existing compounds, most of which are monoamine oxidase inhibitors, have been shown to act as inhibitors of LSD1. More potent and specific inhibitors of LSD1 lacking the monoamine oxidase activity are needed to advance LSD1 biology and test for potential efficacy in tumor models. We have previously reported using a structure-based drug discovery approach using solved 3-D crystal structures of LSD1 to computationally dock more than 10 million virtual compounds into the active site of the protein. From the docking experiments, we physically screened a selected group of compounds in an LSD1 biochemical assay. Initial hits from the screen were optimized utilizing a structure-based synthetic design strategy and a lead was identified as a potent inhibitor of LSD1 enzymatic activity, with an IC50 of 13 nM. To evaluate inhibitor specificity, our lead compounds were tested against 5 closely related flavin-dependent enzymes and showed minimal inhibition in these assays. Additionally, cell lines treated with our lead, HCI-2509, show increased levels of H3K4 methylation. To examine the cell-based activity of various cancer cell lines to our lead, a large panel of cancer cell lines was tested for sensitivity to HCI-2509 using a cell viability assay. Among the most sensitive cell lines are several derived from ER-negative breast cancers. We further demonstrated potent activity of HCI-2509 in cells taken directly from ER-negative breast cancer patients. Using gene expression analysis after treatment of highly sensitive and less sensitive breast cancer cell lines we have developed a gene expression signature associated with sensitivity to HCI-2509. Our efforts are now focused on examining HCI-2509 potential as novel therapeutic targeting LSD1 for treatment of ER-negative breast cancers using mouse models of breast cancer.

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 1045. doi:1538-7445.AM2012-1045

Design, Synthesis and Biological Evaluation of a Series of Novel Axl Kinase Inhibitors

The receptor tyrosine kinase AXL has emerged in recent years as an potential oncology target due to its over expression in several types of cancers coupled with its ability to promote tumor growth and metastasis. In order to identify small molecule inhibitors of AXL, we built a homology model of its catalytic domain to virtually screen and identify scaffolds displaying an affinity for AXL. Further computational and structure-based design resulted in the synthesis of a series of 2,4,5-trisubstitued pyrimidines which demonstrated potent inhibition of AXL in vitro (IC(50) 19 nM) and strongly inhibited the growth of several pancreatic cell lines.

Targeting Axl and Mer kinases in cancer

Receptor tyrosine kinases (RTK) are cell-surface transmembrane receptors that contain regulated kinase activity within their cytoplasmic domain and play an important role in signal transduction in both normal and malignant cells. The mammalian TAM RTK family includes 3 closely related members: Tyro-3, Axl, and Mer. Overexpression or ectopic expression of the TAM receptors has been detected in a wide array of human cancers. Growth arrest-specific gene 6 has been identified as the major ligand for these TAM RTKs, and its binding to the receptors has been shown to promote proliferation and survival of cancer cells in vitro. Abnormal expression and activation of Axl or Mer can provide a survival advantage for certain cancer cells. Inhibition of Axl and Mer may enhance the sensitivity of cancer cells to cytotoxic agents and would potentially be a therapeutic strategy to target cancer cells. This review elucidates the role of Axl and Mer in normal cellular function and their role in oncogenesis. In addition, we review the potential to inhibit these RTKs for the development of therapeutic targets in treatment of cancer.

Abstract 3609: Homology structure-based design, synthesis and biological evaluation of a series of novel Axl and Mer kinase inhibitors

Axl and Mer kinases belong to the TAM family that was first identified as a transforming gene in chronic myeloid leukemia. Its intracellular region has the typical receptor tyrosine kinase (RTK) structure and its extracellular domain is similar to cadherin-type adhesion molecules in that it is composed of fibronectin type II and immunoglobulin (Ig) motifs. Axl binds various growth factors, with vitamin K-dependent protein growth-arrest-specific gene 6 (GAS6) being the best studied. Axl is involved in mesenchymal and neuronal development as well as in cell survival, adhesion and blood vessel function. High levels of Axl are found in various tumors, including malignant glioma and metastatic colon, ovarian and breast cancers, and it plays a role in cancer invasion. Recent development of Axl inhibitors suggested that inhibition of Axl activity may be impact both tumor angiogenesis and tumor growth. We describe here the design, synthesis, molecular modeling, and biological evaluation of a series of small molecule, inhibitors of Axl and Mer kinases. Our initial lead compound was identified via cross-docking experiments utilizing the homology model of Axl kinase and screening of a diverse in-house chemical library. We subsequently carried out structure-activity relationship studies and optimized the lead structure which has 2 to 6.1 μM inhibition activity to 2-fold improvement in the Axl and Mer kinase activities to 730 nM. As a starting point for further optimization, it was considered that the modest of these series could be improved by introducing a spacer at the aryl piperazine moiety and focused on maximizing the in vitro potency, addressing the SAR and molecular properties. We further explored Leu620, hydrophobic, Gly543, Phe547 and DFG motif sites through scaffold hoping lead to the identification of an electron-withdrawing functional groups lead to the compound HCI-2084 and HCI-2091 which exhibited potent Axl kinase inhibition activity of 7 and 12 nM in Axl kinase assay and 30-50 nM is panel of cancer cell lines. These novel series of compounds were synthesized in two-step procedure via a standard cross-coupling reaction or with various substituted aryl amine derivatives under amination conditions. In a subsequent step we employed Buchwald-Hartwig amination reaction to prepare target molecules. Due to the ready synthesis accessibility, we extensively investigated the SAR improving the RO5, solubility and permeability parameters. The details of these results will be presented.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3609. doi:10.1158/1538-7445.AM2011-3609

Abstract 2788: Design, optimization, and biological evaluation of potent irreversible inhibitors of BTK kinase

Bruton's tyrosine kinase (BTK) is a cytoplasmic nonreceptor tyrosine kinase belonging to the Tec family of kinases. Critical for its function, BTK contains a pleckstrin homology (PH) domain and Src homology SH3 and SH2 domains. It signals downstream of the B-cell receptor (BCR) and is centrally involved in B-cell development. Activation of B-cells by various ligands is accompanied by the translocation of BTK to the cell membrane where it binds phosphatidylinositol-3,4,5-trisphosphate through its PH domain. Activation of BTK results in downstream signaling through the PI3K/AKT, PLCγ, NFκB, and other signaling pathways important for B-cell development and function. Recent reports have shown the aberrant expression and function of BTK in some cancers, including B-cell malignancies. We describe here the design, synthesis, molecular modeling, and biological evaluation of a series of small molecule, inhibitors of BTK kinase. Our initial lead compounds were identified via cross-docking experiments utilizing the crystal structure of BTK kinase and screening a previously in-house explored kinase inhibitor scaffold. We subsequently carried out structure-activity relationship studies and optimized the lead structures, which have IC50 activities in the range of 1 to 10μM against BTK. A critical step in the optimization of this chemical series against BTK was to explore the possibility of adding a Michael's acceptor group to react with Cys481 in the ATP-binding pocket of BTK. Optimization efforts yielded the currently best leads, HCI-1684 and HCI-1685, which inhibit BTK with IC50 values of 12 and 45 nM, respectively. Modeling data suggest these compounds irrepressibly bind in the ATP-binding pocket of BTK. HCI-1684, HCI-1685 and other lead compounds were further evaluated in cell-based assays and were demonstrated to inhibit BTK function downstream of BCR activation. This series of BTK inhibitors were shown to decrease phospho-PLCγ1/2 levels and other downstream phosphorylation events in malignant B-cell cell lines, such as Ramos B. Compound optimization and biological evaluation of this chemical series and evaluation in animal pharmacodynamic endpoint studies will be presented. Taken together, these results suggest BTK is a potential therapeutic target in cancer and that HCI-1684 is an exciting agent to potentially treat B-cell malignancies

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2788. doi:10.1158/1538-7445.AM2011-2788