Screening of predicted synergistic multi-target therapies in glioblastoma identifies new treatment strategies

Background

IDH-wildtype glioblastoma (GBM) is a highly malignant primary brain tumor with a median survival of 15 months after standard of care, which highlights the need for improved therapy. Personalized combination therapy has shown to be successful in many other tumor types and could be beneficial for GBM patients.

Methods

We performed the largest drug combination screen to date in GBM, using a high-throughput effort where we selected 90 drug combinations for their activity onto 25 patient-derived GBM cultures. 43 drug combinations were selected for interaction analysis based on their monotherapy efficacy and were tested in a short-term (3 days) as well as long-term (18 days) assay. Synergy was assessed using dose-equivalence and multiplicative survival metrics.

Results

We observed a consistent synergistic interaction for 15 out of 43 drug combinations on patient-derived GBM cultures. From these combinations, 11 out of 15 drug combinations showed a longitudinal synergistic effect on GBM cultures. The highest synergies were observed in the drug combinations Lapatinib with Thapsigargin and Lapatinib with Obatoclax Mesylate, both targeting epidermal growth factor receptor and affecting the apoptosis pathway. To further elaborate on the apoptosis cascade, we investigated other, more clinically relevant, apoptosis inducers and observed a strong synergistic effect while combining Venetoclax (BCL targeting) and AZD5991 (MCL1 targeting).

Conclusions

Overall, we have identified via a high-throughput drug screening several new treatment strategies for GBM. Moreover, an exceptionally strong synergistic interaction was discovered between kinase targeting and apoptosis induction which is suitable for further clinical evaluation as multi-targeted combination therapy.

Abstract 5645: BAL0891: A novel dual TTK/PLK1 mitotic checkpoint inhibitor (MCI) that drives aberrant tumor cell division resulting in potent anti-cancer activity

Background: BAL0891 is a dual inhibitor of threonine tyrosine kinase (TTK) and polo-like kinase 1 (PLK1). These kinases collaborate in activating the mitotic spindle assembly checkpoint (SAC) at the kinetochore (KT) to regulate chromosome alignment and segregation prior to mitotic exit. In vitro, BAL0891 has a combined prolonged effect on TTK and a transient effect on PLK1, leading to rapid disruption of the SAC that potentiates aberrant mitotic progression of tumor cells. In this work, efficacy of BAL0891 was investigated in mouse models of human triple negative breast cancer (TNBC) including evaluation of dose-dependency, drug exposure, target occupancy and a screen of activity across a panel of PDX models.

Methods: The MDA-MB-231 cell line was grown sc in nude mice and treated with BAL0891, administered IV weekly (QW) or twice-weekly (2QW). Thirteen sc TNBC PDX models were screened for BAL0891 response using 2QW administration. Efficacy was quantified as deltaT/C (treated/control tumors). Plasma and tumor were analyzed for drug levels or TTK target occupancy by LC-MS/MS. The latter used a biotinylated TTK-specific probe and streptavidin-mediated isolation of unoccupied TTK, trypsin digestion and quantification of TTK-representative peptides.

Results: BAL0891 efficacy was tested in the TNBC xenograft model MDA-MB-231 with QW or 2QW IV dosing schedules. All treatments were well tolerated, with no drug-related animal deaths. With MTD dosing, tumor regressions were observed, while different MTD fractions for both QW and 2QW schedules showed dose-dependent anti-tumor activity. The weekly MTD group was followed for an additional 20 days after treatment cessation on day 100. Strikingly, 3 of 8 tumors continued to shrink resulting in 2 (25%) pathologically confirmed cures. Consistent with the potent efficacy of intermittent MTD dosing, and prolonged tumor drug exposure, tumor TTK was fully drug-occupied for ≥ 6 days after the last administration; target occupancy was also dose-and drug exposure-dependent. To further evaluate BAL0891 anti-cancer activity in TNBC, a screen in 13 TNBC PDX models was conducted. Seven models exhibited deltaT/C < 50%, with regressions observed in 3. Of these, 2 models showed persistent regressions ≥ 70% vs. baseline. Interestingly, evaluation of TTK target occupancy in selected models showed high target occupancy independent of tumor response, indicating target dependency rather than drug availability is important for anti-cancer activity.

Conclusion: BAL0891 is a novel dual TTK/PLK1 mitotic checkpoint inhibitor with potent anti-cancer activity in TNBC models. Intermittent IV administration is well tolerated and associated with prolonged tumor drug exposure, prolonged TTK inhibition and notable anti-tumor efficacy. These data support further investigation of BAL0891 for the treatment of cancer patients (incl. TNBC).

Citation Format: Heidi A. Lane, Felix Bachmann, Elisa Zanini, Paul McSheehy, Karine Litherland, Nicole Forster-Gross, Luc Bury, Diep Vu-Pham, Jos de Man, Wilhelmina E. van Riel, Guido JR Zaman, Rogier C. Buijsman, Laurenz Kellenberger. BAL0891: A novel dual TTK/PLK1 mitotic checkpoint inhibitor (MCI) that drives aberrant tumor cell division resulting in potent anti-cancer activity [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 5645.

Abstract 5646: BAL0891: A novel, small molecule, dual TTK/PLK1 mitotic checkpoint inhibitor (MCI) that drives aberrant tumor cell division

Background: BAL0891 is a dual inhibitor of threonine tyrosine kinase (TTK) and polo-like kinase 1 (PLK1). These kinases collaborate in activating the mitotic spindle assembly checkpoint (SAC) at the kinetochore (KT) to regulate chromosome alignment and segregation prior to mitotic exit. In this work, kinase inhibition by BAL0891 was linked to effects on SAC integrity and aberrant mitotic progression in tumor cells. Comparison with a TTK-specific inhibitor (CFI-402257, CFI) allowed further evaluation of the contribution of dual TTK/PLK1 inhibition to anti-cancer activity, associated with a promising anti-proliferative profile across diverse tumor cell lines.

Methods: Kinase assays used a radiometric assay. Target residency was measured using surface plasmon resonance with recombinant kinase. Anti-proliferative activity was assessed with crystal violet or YO-PRO assay (5 days incubation), in-cell target inhibition by immunoblotting for phospho-TTK following drug wash-out. Effects on SAC integrity were followed by immunoprecipitation (IP) mitotic progression by flow cytometry/mitotic marker expression. Cells were blocked in mitosis using the microtubule-targeting agent nocodazole or the PLK1 inhibitor onvansertib. SAC KT accumulation was evaluated by immunofluorescence (IF) for co-localization of BubR1 with CENPC. Comparative studies with CFI used anti-proliferative IC50 concentrations.

Results: In vitro kinase profiling showed that BAL0891 has low nM IC50s against TTK and PLK1, with prolonged TTK (>12 h) and transient PLK1 (4 min) target residency. Prolonged TTK inhibition (≥38 h) was also observed in HT29 tumor cells. Consistent with a dominant TTK-targeting activity, BAL0891 treatment of HT29 cells blocked in mitosis with nocodazole or the PLK1 inhibitor onvansertib led to aberrant mitotic release and accumulation of polyploid cells. This was preceded by SAC disruption as visualized by IP assays. Effects on the SAC and mitotic exit were evaluated in comparative studies with CFI; BAL0891 exhibited faster kinetics for both parameters suggesting a contribution of PLK1 inhibition. This was confirmed by directly evaluating acute effects on SAC integrity at the KT by IF. Specifically, 1 h BAL0891 treatment of mitotic HT29 cells resulted in a highly reproducible and significant reduction in KT-associated SAC (p<0.0001) which was not observed with CFI in the same conditions. An extensive in vitro BAL0891 anti-proliferative screen indicated a broad anti-cancer potential, with low nM GI50s observed for most tumor lines and minimal activity on non-immortalized cells (GI50s >5 uM).

Conclusion: BAL0891 is a novel dual TTK/PLK1 mitotic checkpoint inhibitor. In tumor cells, prolonged effects on TTK and transient effects on PLK1 contribute to rapid SAC disruption and aberrant mitotic exit. This is associated with potent anti-proliferative activity in diverse tumor lines.

Citation Format: Elisa Zanini, Nicole Forster-Gross, Felix Bachmann, Nicole Willemsen-Seegers, Jos de Man, Guido J. Zaman, Rogier C. Buijsman, Anna Groner, Mila Roceri, Karin Burger, Paul McSheehy, Laurenz Kellenberger, Heidi A. Lane. BAL0891: A novel, small molecule, dual TTK/PLK1 mitotic checkpoint inhibitor (MCI) that drives aberrant tumor cell division [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 5646.

Abstract 1080: Altered response to BET-bromodomain inhibitors JQ1 and I-BET-762 targeting c-Myc in erdafitinib-resistant endometrial carcinoma cell line AN3 CA

The fibroblast growth factor receptors (FGFRs) 1-4 are receptor tyrosine kinases (RTKs) involved in activation of essential cellular processes such as differentiation, proliferation and migration. Since alterations in FGFRs are common in multiple cancers, including breast cancer, non-small cell lung cancer and endometrial cancer, several kinase inhibitors targeting FGFRs are in clinical development. Erdafitinib, a pan-FGFR inhibitor, has been approved as second-line treatment of locally advanced or metastatic urothelial carcinoma harboring genetic FGFR2 or FGFR3 alterations. Although erdafitinib is very effective against these tumors, progression-free survival lasts only a few months, indicating that resistance also develops fast. Insight into the evolved resistance mechanism is crucial for the development of improved therapies. In this study we generated cell lines resistant to erdafitinib by prolonged culturing of the endometrial carcinoma cell line AN3 CA, harboring FGFR2 gain-off-function mutation N549K, to increasing doses of erdafitinib. To gain insight into the developed resistance, the expression of genes that have previously been reported to be involved in resistance against FGFR inhibitors was analyzed by qPCR and immunoblot. In addition, anti-proliferative effects of target inhibition by small molecules was evaluated. To get an unbiased view on altered gene expression, RNA sequencing (RNA-seq) was performed, followed by Gene-Set-Enrichment Analysis (GSEA). Alterations in FGFR1-4 and cancer hotspot gene sequences were detected by DNA sequencing. Occurrence of resistance to erdafitinib was confirmed in proliferation assays by a decreased response of the erdafitinib-resistant cell lines compared to the parental line. In addition, cross-resistance to other FGFR inhibitors infigratinib, pemigatinib, derazantinib and AZD4547 was observed. Although mRNA expression was altered for several RTKs previously reported to be involved in resistance to FGFR inhibitors, such as EGFR, ERBB2/3 and c-MET, involvement in resistance to erdafitinib could be excluded, as no change in response was observed in proliferation assays with their associated targeted inhibitors. RNA-seq and GSEA indicated upregulation of c-Myc target genes in erdafitinib-resistant cell lines. The involvement of c-Myc in the developed resistance was further confirmed by increased response to BET-bromodomain inhibitors JQ1 and I-BET-762, which indirectly target c-Myc. Furthermore, DNA sequencing identified novel mutations in coding regions of FGFR1 and KRAS genes. In conclusion, we show that multiple factors contribute to the development of resistance against erdafitinib in an FGFR2-mutant endometrial carcinoma cell line. BET-bromodomain inhibitors are of potential interest as therapeutic agents to overcome resistance against FGFR inhibitors.

Citation Format: Wilhelmina E VAN RIEL, Janneke J. Melis, Demi H. Vogels, Winfried R. Mulder, Jeffrey J. Kooijman, Rogier C. Buijsman, Guido J. Zaman. Altered response to BET-bromodomain inhibitors JQ1 and I-BET-762 targeting c-Myc in erdafitinib-resistant endometrial carcinoma cell line AN3 CA [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 1080.

Abstract 1480: Comparative cancer cell panel profiling of kinase inhibitors approved for clinical use from 2018 to 2020

Kinases are the major anticancer drug target class of the 21st century with nearly sixty small molecule kinase inhibitors approved for clinical use in the first two decades. While there are more than 500 kinases encoded by the human genome, currently approved inhibitors act primarily through approximately twenty different targets. Key to the success of kinase inhibitor therapy has been the simultaneous development of biomarker assays to enable the selection of patients most likely to respond. Predictive drug response biomarkers can be identified with cancer cell panel profiling, which is the parallel testing of compounds on a large panel of cancer cell lines. By correlating drug sensitivity with genomic information of the cell lines, strategies for patient stratification or drug repurposing have been developed [1-3]. In two earlier studies [2,3], we compared the kinase selectivity and the cellular inhibition profiles of all kinase inhibitors approved by the FDA until May 2018. Here, we will present the cancer cell panel profiling of all twenty small molecule kinase inhibitors approved since then. Several of these inhibitors act through well-known targets, such as ALK (lorlatinib), BRAF (encorafenib), EGFR (dacomitinib) and MEK1 (binimetinib, selumetinib). Others act through kinases for which no small molecule inhibitors have been approved before, such as CSF1R (pexidartinib), FGFR (erdafitinib, pemigatinib), c-MET (capmatinib), RET (selpercatinib, pralsetinib) and TRK (larotrectinib, entrectinib). All compounds were profiled on a panel of 102 cancer cell lines, known as Oncolines, representing a wide range of solid tumors and hematological malignancies, and harboring mutant and wild-type versions of many major cancer driver genes [3]. To determine similarities in the mechanisms underlying the anti-proliferative activity of the inhibitors, their IC50 fingerprint in the cell proliferation assays were compared by hierarchical clustering [4]. Compounds that act through the same primary kinase clustered together in this analysis. Exceptions were investigated further by profiling of additional cell lines, representing cancer gene alterations that were not present in the 102 cell line panel, such as FLT3 mutation and TRK-gene fusions, which occur in relatively small cancer patient populations. To compare the genomic targeting of kinase inhibitors acting on the same biochemical target, the cancer cell lines were classified as either “mutant” or “wild-type” for specific cancer gene alterations and were grouped per cancer gene. The relationship between drug sensitivity and cancer gene mutation status was examined. Detailed genomic biomarker analyses and comparative profiling results of novel BTK, EGFR, FGFR, FLT3 and TRK kinase inhibitors will be presented.[1] Mol Cancer Ther 2017;26:2609-17; [2] PLoS ONE 2014;9:e92146; [3] Mol Cancer Ther 2019;18:470-81; [4] Mol Cancer Ther 2016;15:3097-109

Citation Format: Jeffrey J. Kooijman, Wilhelmina E. van Riel, Martine B. Prinsen, Jelle Dylus, Jeroen A. de Roos, Yvonne Grobben, Nicole Willemsen-Seegers, Michelle Muller, Jos de Man, Yugo Narumi, Yusuke Kawase, Rogier C. Buijsman, Suzanne J. van Gerwen, Guido J. Zaman. Comparative cancer cell panel profiling of kinase inhibitors approved for clinical use from 2018 to 2020 [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 1480.

Mapping Arginase Expression with 18F-Fluorinated Late-Generation Arginase Inhibitors Derived from Quaternary α-Amino Acids

Arginase hydrolyzes L-arginine and influences levels of polyamines and nitric oxide. Arginase overexpression is associated with inflammation and tumorigenesis. Thus, radiolabeled arginase inhibitors may be suitable PET tracers for staging arginase-related pathophysiologies. We report the synthesis and evaluation of 2 radiolabeled arginase inhibitors, ¹⁸F-FMARS and ¹⁸F-FBMARS, developed from α-substituted-2-amino-6-boronohexanoic acid derivatives. Methods: Arylboronic ester-derived precursors were radiolabeled via copper-mediated fluorodeboronation. Binding assays using arginase-expressing PC3 and LNCaP cells were performed. Autoradiography of lung sections from a guinea pig model of asthma overexpressing arginase and dynamic small-animal PET imaging with PC3-xenografted mice evaluated the radiotracers' specific binding and pharmacokinetics. Results: ¹⁸F-fluorinated compounds were obtained with radiochemical yields of up to 5% (decay-corrected) and an average molar activity of 53 GBq⋅μmol^-1 Cell and lung section experiments indicated specific binding that was blocked up to 75% after pretreatment with arginase inhibitors. Small-animal PET studies indicated fast clearance of the radiotracers (7.3 ± 0.6 min), arginase-mediated uptake, and a selective tumor accumulation (SUV, 3.0 ± 0.7). Conclusion: The new ¹⁸F-fluorinated arginase inhibitors have the potential to map increased arginase expression related to inflammatory and tumorigenic processes. ¹⁸F-FBMARS showed the highest arginase-mediated uptake in PET imaging and a significant difference between uptake in control and arginase-inhibited PC3 xenografted mice. These results encourage further research to examine the suitability of ¹⁸F-FBMARS for selecting patients for treatments with arginase inhibitors.

Pharmacological validation of TDO as a target for Parkinson's disease

Parkinson’s disease patients suffer from both motor and nonmotor impairments. There is currently no cure for Parkinson’s disease, and the most commonly used treatment, levodopa, only functions as a temporary relief of motor symptoms. Inhibition of the expression of the L‐tryptophan‐catabolizing enzyme tryptophan 2,3‐dioxygenase (TDO) has been shown to inhibit aging‐related α‐synuclein toxicity in Caenorhabditis elegans. To evaluate TDO inhibition as a potential therapeutic strategy for Parkinson’s disease, a brain‐penetrable, small molecule TDO inhibitor was developed, referred to as NTRC 3531‐0. This compound potently inhibits human and mouse TDO in biochemical and cell‐based assays and is selective over IDO1, an evolutionary unrelated enzyme that catalyzes the same reaction. In mice, NTRC 3531‐0 increased plasma and brain L‐tryptophan levels after oral administration, demonstrating inhibition of TDO activity in vivo. The effect on Parkinson’s disease symptoms was evaluated in a rotenone‐induced Parkinson’s disease mouse model. A structurally dissimilar TDO inhibitor, LM10, was evaluated in parallel. Both inhibitors had beneficial effects on rotenone‐induced motor and cognitive dysfunction as well as rotenone‐induced dopaminergic cell loss and neuroinflammation in the substantia nigra. Moreover, both inhibitors improved intestinal transit and enhanced colon length, which indicates a reduction of the rotenone‐induced intestinal dysfunction. Consistent with this, mice treated with TDO inhibitor showed decreased expression of rotenone‐induced glial fibrillary acidic protein, which is a marker of enteric glial cells, and decreased α‐synuclein accumulation in the enteric plexus. Our data support TDO inhibition as a potential therapeutic strategy to decrease motor, cognitive, and gastrointestinal symptoms in Parkinson’s disease.

Targeting Indoleamine 2,3-Dioxygenase in Cancer Models Using the Novel Small Molecule Inhibitor NTRC 3883-0

Indoleamine 2,3-dioxygenase (IDO1) is a key regulator of immune suppression by catalyzing the oxidation of L-tryptophan. IDO1 expression has been related to poor prognosis in several cancers and to resistance to checkpoint immunotherapies. We describe the characterization of a novel small molecule IDO1 inhibitor, NTRC 3883-0, in a panel of biochemical and cell-based assays, and various cancer models. NTRC 3883-0 released the inhibitory effect of IDO1 on CD8-positive T cell proliferation in co-cultures of IDO1-overexpressing cells with healthy donor lymphocytes, demonstrating its immune modulatory activity. In a syngeneic mouse model using IDO1-overexpressing B16F10 melanoma cells, NTRC 3883-0 effectively counteracted the IDO1-induced modulation of L-tryptophan and L-kynurenine levels, demonstrating its in vivo target modulation. Finally, we studied the expression and activity of IDO1 in primary cell cultures established from the malignant ascites of ovarian cancer patients. In these cultures, IDO1 expression was induced upon stimulation with IFNγ, and its activity could be inhibited by NTRC 3883-0. Based on these results, we propose the use of ascites cell-based functional assays for future patient stratification. Our results are discussed in light of the recent discontinuation of clinical trials of more advanced IDO1 inhibitors and the reconsideration of IDO1 as a valid drug target.

Chemotherapy sensitivity testing on ovarian cancer cells isolated from malignant ascites

BACKGROUND

In epithelial ovarian cancer (EOC), 15-20% of the tumors do not respond to first-line chemotherapy (paclitaxel with platinum-based therapy), and in recurrences this number increases. Our aim is to determine the feasibility of cell proliferation assays of tumor cells isolated from malignant ascites to predict in vitro chemotherapy sensitivity, and to correlate these results with clinical outcome.

MATERIALS AND METHODS

Ascites was collected from twenty women with advanced EOC. Cell samples were enriched for tumor cells and EOC origin was confirmed by intracellular staining of CK7, surface staining of CA125 and EpCAM, and HE4 gene expression. In vitro sensitivity to chemotherapy was determined in cell proliferation assays using intracellular ATP content as an indirect measure of cell number. In vitro drug response was quantified by calculation of the drug concentration at which cell growth was inhibited with 50%. Clinical outcome was determined using post-treatment CA125 level.

RESULTS

Cell samples of twenty patients were collected, of which three samples that failed to proliferate were excluded in the analysis (15%). Three other samples were excluded, because clinical outcome could not be determined correctly. In twelve of the fourteen remaining cases (86%) in vitro drug sensitivity and clinical outcome corresponded, while in two samples (14%) there was no correspondence.

CONCLUSIONS

Our study demonstrates the feasibility of drug sensitivity tests using tumor cells isolated from ascites of advanced EOC patients. Larger observational studies are required to confirm the correlation between the in vitro sensitivity and clinical outcome.

High-Throughput Fluorescence-Based Activity Assay for Arginase-1

Arginase-1, which converts the amino acid L-arginine into L-ornithine and urea, is a promising new drug target for cancer immunotherapy, as it has a role in the regulation of T-cell immunity in the tumor microenvironment. To enable the discovery of small-molecule Arginase-1 inhibitors by high-throughput screening, we developed a novel homogeneous (mix-and-measure) fluorescence-based activity assay. The assay measures the conversion of L-arginine into L-ornithine by a decrease in fluorescent signal due to quenching of a fluorescent probe, Arginase Gold. This way, inhibition of Arginase-1 results in a gain of signal when compared with the uninhibited enzyme. Side-by-side profiling of reference inhibitors in the fluorescence-based assay and a colorimetric urea formation assay revealed similar potencies and the same potency rank order among the two assay formats. The fluorescence-based assay was successfully automated for high-throughput screening of a small-molecule library in 384-well format with a good Z'-factor and hit confirmation rate. Finally, we show that the assay can be used to study the binding kinetics of inhibitors.

Abstract A141: Computational models of synergy contribute to efficient combination screening

Introduction: Combination drug treatment in cancer therapy aims to improve response rate and decrease the development of drug resistance. The discovery of novel drug combinations is constrained by the cost and effort of carrying out large unbiased screens and is hampered by poor translation towards the clinic. We investigate if computational models combined with screening can more efficiently reveal synergistic combinations and improve translation towards the clinic. The models are based on three different biological views of synergy. First, compounds that exploit similar vulnerabilities in cancer cells frequently show synergy in a particular genetic context (targeted synergy, model 1) [1,2]. Secondly, drugs with non-overlapping resistance mechanisms often yield clinically relevant drug combinations (model 2) [3]. Finally, drugs that mimic synthetic lethal interactions will often act synergistically (model 3) [4]. Experimental procedures Oncolines™ is a panel of 102 genetically characterized cell lines from diverse tumor origins, on which proliferation assays are run in parallel in nine-point dose-response curves. In this cell panel we profiled 162 different cancer therapeutics, including many standard of care, chemotherapeutic agents, epigenetic modulators, and approved and pre-clinical drugs such as CDK4/6, ALK and PI3K-inhibitors [5]. Cancer hotspot mutations and gene expression data were downloaded from the DepMap and CCLE databases. ANOVA and Pearson correlations were used to analyze the single agent response and genetic data in the statistical software R, to determine gene mutation (model 1) and resistance markers (model 2). For model 3, clinically relevant synthetic lethal pairs were combined with gene expression data [4]. The methods were used to predict results from published synergy screens, e.g. DREAM [6] and results from an independent experiment (NTRC SynergyScreen™) in which fixed concentrations of the poly-ADP ribose polymerase (PARP) inhibitor niraparib and the BET bromodomain inhibitor JQ1, were combined with nine-point dose-response curves of 150 anticancer agents. Synergies were quantified using curve-shift and CI-index. Results: Using a cancer cell line IC50 profile of a compound (such as Oncolines™), all three computational models of synergy prediction can be applied. Method 1 is successful in predicting combinations that augment a targeted effect, such as combining BRAF and MEK inhibitors in BRAF-mutant cancer [1]. Method 2 does not distinguish between additive or synergistic combinations but can identify clinically relevant combinations [3]. For method 3, a tool was developed that computationally assesses if drug pairs can pharmacologically mimic clinically validated synthetic lethal interactions [4]. This can predict DREAM data with a high AUC of 0.67 in a ROC curve. The tool successfully predicts synergy between niraparib and the SUMO inhibitor 2-D08, and niraparib and BCL2 inhibitors, which we observed in our screen. Conclusions: Computational tools for synergy have predictive value and can be useful to prioritize libraries for empirical combination screening. References: [1] Uitdehaag et al. (2015). PLoS ONE 10(5): e0125021. [2] Seashore-Ludlow et al. (2015) Cancer Discovery, 5: 1210-1223. [3] Palmer et al. (2017) Cell 171: 1678-1691. [4] Lee et al. (2018). Nature Communications 9: 2546. [5] Uitdehaag et al. (2016). Mol. Cancer Ther. 15: 3097-3109. [6] Menden et al. (2019) Nature Communications 10: 2674.

Citation Format: Joost C.M. Uitdehaag, Martine B.W. Prinsen, Derek W. van Tilborg, Jeffrey J. Kooijman, Jelle Dylus, Jeroen A.D.M. de Roos, Suzanne J.C. van Gerwen, Jos de Man, Rogier C. Buijsman, Guido J.R. Zaman. Computational models of synergy contribute to efficient combination screening [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 A141. doi:10.1158/1535-7163.TARG-19-A141

Abstract A044: A precision medicine platform to predict the clinical response to chemo- and immunotherapy for epithelial ovarian cancer

Introduction: Epithelial ovarian cancer (EOC) is the most lethal gynecologic malignancy. First-line therapy in advanced EOC is surgery in combination with platinum-based chemotherapy and paclitaxel. 15-20% of patients do not respond and in 80% of advanced cases, the disease recurs within three years. PARP inhibitors synergize with platinum therapy and have been approved for platinum sensitive EOC. Clinical trials with immunotherapies, such as PD-1/PD-L1 blockade, have so far not been successful. Currently, the only approved companion diagnostic is BRCA gene mutations for PARP inhibitors. More diagnostic assays to predict the clinical response to chemo- or immunotherapies are needed. We have developed a biomarker discovery platform using ascites of ovarian cancer patients. Experimental procedures Ascites was gathered from patients by punction or during debulking surgery. Cells were collected by centrifugation and characterized by flow cytometry using specific antibodies. Genomic DNA was sequenced using Illumina cancer gene panels. Gene expression was analyzed by quantitative PCR (qPCR). Cellular activity of the tryptophan metabolizing enzymes IDO1 and TDO was measured with NFK Green [1]. Levels of L-tryptophan and its metabolite L-kynurenine in ascites fluid and blood were determined with LC-MS/MS. In vitro data were related to tumor histopathology and clinical response data. Results: Low passage cell samples from twenty patients were profiled for sensitivity to various cytotoxic agents and targeted anti-cancer therapies in cell proliferation assays. In parallel the mutation status of fifty cancer genes including BRCA1 and 2 was assessed by DNA sequencing. The expression of genes implicated in resistance to chemotherapy (CCNE1, ABCB1) or immunotherapy (PD-L1, IDO1, TDO) was determined with qPCR. The immune status of ascites was analyzed by measuring the relative proportion of different immune cell populations, i.e., cytotoxic and regulatory T cells, monocytes, dendritic and natural killer cells. The expression of the immune suppressive markers PD-L1, IDO1 and TDO was related to the immune cell composition of the ascites, kynurenine-tryptophan ratio, and clinical response data. A tumor cell sample derived from a patient with low grade serous ovarian cancer (LGSOC) was heterozygous for an oncogenic NRAS mutation and was much more sensitive to MEK inhibitors than other samples not harboring the mutation. The cells also expressed IDO1 and high levels of PD-L1 at the cell surface. Two other samples derived from high grade serous ovarian cancer (HGSOC) expressed high PD-L1 and one also IDO1. Several HGSOC samples expressed TDO. One HGSOC sample showed high expression of the ABCB1 gene, encoding the multidrug transporter P-glycoprotein. The sample was relatively resistant to paclitaxel, a known substrate of P-glycoprotein Conclusion: Our study shows that in vitro drug sensitivity assays with primary patient samples can be used to confirm or identify predictive drug response biomarkers. In an ongoing study, in which hundred patients with HGSOC will be included, the in vitro drug response of tumor cells from ascites to first-line cytotoxic anti-cancer agents will be determined and compared to the clinical response of patients bearing specific genomic biomarkers. [1] Seegers et al. (2014) J Biomol Screen 19, 1266-1272

Citation Format: Guido J.R. Zaman, Judith E. den Ouden, Jelle Dylus, Antoon M. van Doornmalen, Winfried R. Mulder, Diep Vu-Pham, Suzanne J.C. van Gerwen, Joost C.M. Uitdehaag, Rogier C. Buijsman, Leon F. Massuger, Anne M. van Altena. A precision medicine platform to predict the clinical response to chemo- and immunotherapy for epithelial ovarian cancer [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 A044. doi:10.1158/1535-7163.TARG-19-A044

Abstract B060: Side-by-side comparison of small molecule IDO1 inhibitors in biochemical and cell-based assays and development of a IDO1-expressing mouse model to evaluate target modulation

Introduction: Indoleamine 2,3-dioxygenase (IDO1) is a heme-containing oxidoreductase enzyme that converts L-tryptophan (Trp) into N’-formylkynurenine (NFK). IDO1 is broadly expressed by tumor cells as well as immune cells in the tumor microenvironment of many cancers, which is often correlated with poor prognosis. Depletion of Trp and increased L-kynurenine (Kyn) levels induce immune tolerance by suppression of effector T-cell and natural killer cell functions, and activation of regulatory T-cells and myeloid-derived suppressor cells. Four small molecule inhibitors are currently investigated in phase III (linrodostat/BMS-986205), phase II (epacadostat/INCB024360) or phase I (MK7162 and LY3381916) clinical trials. Linrodostat, epacadostat and LY3381916 are reported as being selective for IDO1 over TDO, while details on MK7162 have not yet been disclosed. The compounds inhibit IDO1 with different mechanisms, with epacadostat binding to the heme-group in the catalytic center of IDO1, while linrodostat and LY3381916 bind to apo-IDO1 and compete with heme for the active site [1-3]. Experimental procedures Clinical and reference IDO1 inhibitors were characterized in biochemical assays for IDO1 and tryptophan 2,3-dioxygenase (TDO), a structurally different enzyme, which also catalyzes the conversion of Trp to NFK. Furthermore, the compounds were profiled in a panel of functional cell-based assays, including human cancer cell lines and assays based on IDO1- or TDO2-overexpressing HEK293 cells. A IDO1-expressing subline of the mouse B16F10 melanoma cell line was generated and used to develop a syngeneic mouse model at Charles River Laboratories (USA) to determine target modulation in vivo [4]. Stable gene expression was confirmed by qPCR and target modulation was examined by measurement of Trp and Kyn levels using LC-MS/MS. Results: Linrodostat has sub-nanomolar cellular potency, despite the absence of any biochemical activity on the timescale of our assays, which is consistent with its reported heme-competing mechanism of inhibition [1]. Linrodostat also inhibits different Cytochrome P450 enzymes with micromolar activity. In our biochemical assays, epacadostat was not selective for IDO1 over TDO, whereas in the IDO1- and TDO2-overexpressing HEK293 cell lines it was 2000 times selective for IDO1. High level expression of IDO1 in B16F10 cells did not result in enhanced tumor growth after grafting in syngeneic mice, which contrasts published data with a similar model [4]. Nonetheless, we observed strong modulation of Trp and Kyn levels in plasma and in tumors of the IDO1-overexpressing mouse model, compared to non-tumor bearing mice. Treatment of the B16F10-IDO1 model with epacadostat did not result in a reduction of tumor growth, though epacadostat did induce clear changes in Trp and Kyn in both plasma and tumor tissue. Conclusion: Our comparative study of the potencies and selectivities of IDO1 inhibitors, as well as our model for measuring in vivo target modulation, helps to identify strengths and weaknesses of current IDO1 inhibitors, and supports the development of new inhibitors. [1] Nelp et al. (2018) Proc. Natl. Acad. Sci. U.S.A. 115, 3249-3254; [2] Yue et al. (2017) ACS Med. Chem. Lett. 8, 486-491; [3] Dorsey et al. (2018) Proceedings: AACR Annual Meeting 2018, Abstract nr. 5245; [4] Holmgaard et al. (2015) Cell Rep. 13, 412-424.

Citation Format: Yvonne Grobben, Joost C.M. Uitdehaag, Antoon M. van Doornmalen, Nicole Willemsen-Seegers, Diep Vu-Pham, Jos de Man, Rogier C. Buijsman, Guido J.R. Zaman. Side-by-side comparison of small molecule IDO1 inhibitors in biochemical and cell-based assays and development of a IDO1-expressing mouse model to evaluate target modulation [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 B060. doi:10.1158/1535-7163.TARG-19-B060

Structural insights into human Arginase-1 pH dependence and its inhibition by the small molecule inhibitor CB-1158

Arginase-1 is a manganese-dependent metalloenzyme that catalyzes the hydrolysis of L-arginine into L-ornithine and urea. Arginase-1 is abundantly expressed by tumor-infiltrating myeloid cells that promote tumor immunosuppression, which is relieved by inhibition of Arginase-1. We have characterized the potencies of the Arginase-1 reference inhibitors (2S)-2-amino-6-boronohexanoic acid (ABH) and N ^ω-hydroxy-nor-L-arginine (nor-NOHA), and studied their pH-dependence and binding kinetics. To gain a better understanding of the structural changes underlying the high pH optimum of Arginase-1 and its pH-dependent inhibition, we determined the crystal structure of the human Arginase-1/ABH complex at pH 7.0 and 9.0. These structures revealed that at increased pH, the manganese cluster assumes a more symmetrical coordination structure, which presumably contributes to its increase in catalytic activity. Furthermore, we show that binding of ABH involves the presence of a sodium ion close to the manganese cluster. We also studied the investigational new drug CB-1158 (INCB001158). This inhibitor has a low-nanomolar potency at pH 7.4 and increases the thermal stability of Arginase-1 more than ABH and nor-NOHA. Moreover, CB-1158 displays slow association and dissociation kinetics at both pH 9.5 and 7.4, as indicated by surface plasmon resonance. The potent character of CB-1158 is presumably due to its increased rigidity compared to ABH as well as the formation of an additional hydrogen-bond network as observed by resolution of the Arginase-1/CB-1158 crystal structure.

Abstract 2158: Combining cell panel profiling and synthetic lethality data to efficiently screen for synergistic combinations

In cancer therapy, combination drug treatment aims to improve response rate and decrease the development of drug resistance. The discovery of new effective drug combinations is constrained by the cost and effort of carrying out large unbiased screens and by poor translation of results towards the clinic. Here we describe how focusing on the biological mechanisms underlying the activity of drug candidates may aid a priori selection of promising synergy candidates and help in translate synergistic combinations towards a clinical situation.

We have previously shown [1] that curve shift analysis as developed by Straetemans et al. [2] is a better method than combination-matrix screening. Also a dose based score such as the isobologram or the CI-index more robustly assesses synergy than an effect-based score such as the Bliss-additivity [1]. On this basis, we developed a two-step synergy screening approach, called SynergyScreen™. By distinguishing separate synergy screening and synergy confirmation stages, this setup capitalizes on insights from high throughput screening to discover robust and reproducible pharmacologically synergistic pairs.

To further improve the efficiency of synergy screening, we focused on pre-selecting compounds in our screening library according to their biological mechanism. We profiled a library of more than 160 anti-cancer agents in a cell panel of 102 cell lines from diverse tumor origins [3]. Agents were clustered according to response and so-called exemplars were collected into a focused library that represents the spectrum of biological mechanisms of current cancer therapy. This synergy screening library includes many standard of care chemotherapeutic agents, approved and pre-clinical kinase inhibitors, epigenetic modulators and compounds acting by other mechanisms.

Finally, we harnassed recent insights into the biology of synergy to understand and predict synergistic pairs. A tool was developed that uses the response of a compound in a 102 cell line panel to pick potential synergistic partners from the database of preprofiled compounds. It does this by computationally assessing if pairs can pharmacologically mimick clinically validated synthetic lethal interactions [4]. We optimized prediction accuracy using the results of internal and external synergy screens. The tool was applied to specifically enrich test libraries and to predict synergies at clinically relevant doses, including the results of a SynergyScreen™ with the poly-ADP ribose polymerase (PARP) inhibitor niraparib and the BET bromodomain inhibitor JQ1.

References [1] Uitdehaag et al. (2015). PLoS ONE 10(5): e0125021. [2] Straetemans et al. (2005). Biometrical J. 47, 299-308. [3] Uitdehaag et al. (2016). Mol. Cancer Ther. 15, 3097-3109. [4] Lee et al. (2018). Nature Communications 9, 2546.

Citation Format: Joost C. Uitdehaag, Derek W. van Tilborg, Martine B.W. Prinsen, Jeffrey J. Kooijman, Jelle Dylus, Jeroen A.D.M. de Roos, Suzanne J.C. van Gerwen, Jos de Man, Rogier C. Buijsman, Guido J.R. Zaman. Combining cell panel profiling and synthetic lethality data to efficiently screen for synergistic combinations [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 2158.

Abstract 279A: Cell panel profiling of 162 small molecule therapeutics identifies response biomarkers for PARP, BET-family and proteasome inhibitors

The collective effort of cancer research has resulted in a large diversity of small molecule therapeutics that are tested clinically as precision medicine in specific patient populations. The applications of these therapeutics could be further extended and refined by the identification of new genomic biomarkers that are predictive for response. One of the best ways to do this, is by in vitro profiling in cancer cell line panels.

Oncolines is a panel of 102 genetically characterized cell lines from diverse tumour origins, on which proliferation assays are run in parallel. Earlier analysis has shown that the Oncolines workflow generates highly reproducible data, as required for biomarker discovery [1]. In this cell panel, we profiled 162 different cancer therapeutics, including many standard of care chemotherapeutic agents, approved and pre-clinical kinase inhibitors, epigenetic modulators and compounds acting by other mechanisms.

Assays were based on ATP-lite read-out, with a nine-point duplicate dilution series of the compounds. Drug response was quantified by manual curve fitting. Response was associated with the genomic status of the cell lines as retrieved from the COSMIC and Cancer Cell Line Encyclopedia (CCLE) databases. Mutations in patient hotspot locations and copy number changes in well-characterized cancer genes were used as input for ANOVA tests. Basal gene expression levels of 383 clinically actionable genes and sets of perturbation-response genes were applied to pathway analysis.

Because various alternative metrics were proposed recently to quantify cell line response, we first investigated which metric resulted in the most sensitive identification of biomarkers. Responses were quantified as IC50, GI50, growth rate inhibition (GR50), DSS score, AUC and maximum effect. Known responder populations were analysed such as BRAF(V600E) mutant cell lines for BRAF inhibitors and EGFR amplified lines for EGFR inhibitors, to identify the optimal response metric for biomarker identification.

The full spectrum of cell line responses was analyzed with a variety of clustering and principal component methods to define groups of therapeutic agents based on common biological mechanisms. We further analyzed novel clusters of the Poly (ADP-ribose) polymerase (PARP) inhibitors olaparib, niraparib, rucaparib, and talazoparib, the proteasome inhibitors MG-132, bortezomib and carfilzomib, the ubiquitin activating enzyme inhibitor MLN-7243 (TAK-243) and the BET-family inhibitors JQ1 and I-BET-762 and identified several response biomarkers based on mutation, gene expression and pathway analysis.

References [1] Uitdehaag et al. (2016). Cell Panel Profiling Reveals Conserved Therapeutic Clusters and Differentiates the Mechanism of Action of Different PI3K/mTOR, Aurora Kinase and EZH2 Inhibitors.Mol. Cancer Ther. 15, 3097-3109.

Citation Format: Joost C. Uitdehaag, Jeffrey J. Kooijman, Jeroen A.D.M. de Roos, Martine B.W. Prinsen, Jelle Dylus, Nicole Willemsen-Seegers, Jos de Man, Suzanne J.C. van Gerwen, Rogier C. Buijsman, Guido J.R. Zaman. Cell panel profiling of 162 small molecule therapeutics identifies response biomarkers for PARP, BET-family and proteasome inhibitors [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 279A.

Abstract 2221: Chemotherapy sensitivity of tumor cells from ascites of ovarian cancer patients: Relationship with immune status and clinical response

Epithelial ovarian cancer (EOC) is the most lethal gynecologic malignancy. Standard treatment of advanced EOC is surgery in combination with chemotherapy, consisting of a platinum-based drug (carboplatin or cisplatin) and paclitaxel. Although most women show a good response to first line treatment, tumors do not respond in 15-20% of patients, whereas in 80% of cases of advanced EOC, the disease recurs within three years. Patients who have responded to first line treatment are referred to as ‘platinum sensitive’, and are treated with a PARP inhibitor in second line. Several other new targeted inhibitors are investigated in clinical trials, including PI3-kinase and bromodomain inhibitors. There is great need of new, more effective therapies with improved long-term treatment outcome, and diagnostic assays and biomarkers to predict chemotherapy response in the clinic. We have determined whether tumor cells isolated from ascites of patients with EOC can be used to develop in vitro cell proliferation assays. We also characterized the immune status of ascites by cytokine analysis and used flow cytometry to analyze the immune cell types in ascites. In a pilot study, ascites was gathered from 18 patients with advance stage EOC. Cells were isolated by centrifugation and tumor cells were separated from immune cells by adhering them to tissue culture plates. Sensitivity of tumor cells to platinum compounds, paclitaxel, PARP inhibitors, and other second line and investigational drugs, as well as drug combinations, was determined in cell proliferation assays, using intracellular ATP content as an indirect read-out of cell number [1]. The mutant status of a number of known oncogenes and tumor suppressor genes in the patient-derived cell samples was determined by DNA sequence analysis. Mutation status was related to histopathological data and in vitro drug response. We demonstrate that ascites from EOC patients contains many tumor cells and that these tumor cells can be used to perform drug sensitivity assays in vitro. In an ongoing study, in which ascites from hundred EOC patients will be included, the in vitro sensitivity to standard-of-care chemotherapy will be related to the immune status of the ascites and to the clinical outcome of the patient, which is defined by platinum sensitivity. An update of this study will be presented at the conference. [1] Uitdehaag et al. (2014) PLoS ONE 9(3): e92146

Citation Format: Guido Zaman, Judith E. den Ouden, Jelle Dylus, Antoon M. van Doornmalen, Rogier C. Buijsman, Astrid Eijkelenboom, Leon F. Massuger, Anne M. van Altena. Chemotherapy sensitivity of tumor cells from ascites of ovarian cancer patients: Relationship with immune status and clinical response [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 2221.

Combined Cellular and Biochemical Profiling to Identify Predictive Drug Response Biomarkers for Kinase Inhibitors Approved for Clinical Use between 2013 and 2017

Kinase inhibitors form the largest class of precision medicine. From 2013 to 2017, 17 have been approved, with 8 different mechanisms. We present a comprehensive profiling study of all 17 inhibitors on a biochemical assay panel of 280 kinases and proliferation assays of 108 cancer cell lines. Drug responses of the cell lines were related to the presence of frequently recurring point mutations, insertions, deletions, and amplifications in 15 well-known oncogenes and tumor-suppressor genes. In addition, drug responses were correlated with basal gene expression levels with a focus on 383 clinically actionable genes. Cell lines harboring actionable mutations defined in the FDA labels, such as mutant BRAF(V600E) for cobimetinib, or ALK gene translocation for ALK inhibitors, are generally 10 times more sensitive compared with wild-type cell lines. This sensitivity window is more narrow for markers that failed to meet endpoints in clinical trials, for instance CDKN2A loss for CDK4/6 inhibitors (2.7-fold) and KRAS mutation for cobimetinib (2.3-fold). Our data underscore the rationale of a number of recently opened clinical trials, such as ibrutinib in ERBB2- or ERBB4-expressing cancers. We propose and validate new response biomarkers, such as mutation in FBXW7 or SMAD4 for EGFR and HER2 inhibitors, ETV4 and ETV5 expression for MEK inhibitors, and JAK3 expression for ALK inhibitors. Potentially, these new markers could be combined to improve response rates. This comprehensive overview of biochemical and cellular selectivities of approved kinase inhibitor drugs provides a rich resource for drug repurposing, basket trial design, and basic cancer research.

Abstract 1944: High-throughput fluorescence-based assay for screening of Arginase I inhibitors for cancer immunotherapy

Arginase I (ArgI) is an important small molecule drug target in cancer immunotherapy. Arg1 converts L-arginine into L-ornithine and urea. Recruitment of ArgI-expressing myeloid-derived suppressor cells (MSDCs) at a tumor site results in the depletion of L-arginine, which causes reduced proliferation of T-cells and natural killer cells and inhibition of the antitumor immune response. In patient material, MSDC-induced T-cell suppression can be reverted by arginase inhibitors. ArgI inhibitors work synergistically with checkpoint inhibitor therapy in syngeneic mouse models.

In order to find novel inhibitors for ArgI, we developed a set of tools to enable screening and hit validation. The first is an activity assay that enables the high-throughput screening (HTS) of compound libraries. Previously reported arginase assays are poorly compatible with HTS due to the requirement of multiple reactions steps, harsh assay conditions, or the use of low-turnover substrates other than L-arginine.

We developed a novel ArgI activity assay, which has a homogenous format and requires only two addition steps before readout. The assay makes use of a fluorescence readout and has a high robustness (Z'-factor > 0.7). Progression of the assay can be followed in real time, allowing for kinetic experiments. To investigate the false positive hit rate, the assay was screened at the Pivot Park Screening Centre with a library consisting of 233 compounds with known interference in other assay formats. Using a simple background signal control, the number of false positives in this library was minimized to below 0.2%. The assay was subsequently used to accurately determine the dissociation constants and binding kinetics of the reference inhibitors ABH, NOHA and CB1158.

In order to validate the binding of screening hits to ArgI, we developed a thermal shift assay. We observed a shift in the ArgI melting temperature of up to 3.8°C after addition of the most potent inhibitors. In addition, we developed a Surface Plasmon Resonance binding assay. This showed that ABH and CB1158 have long residence times on ArgI.

To allow the development of novel inhibitors through rational drug design, we successfully crystallized human ArgI in a novel space group with higher symmetry (P63) compared to those previously reported (space group P3), and without the presence of hemihedral twinning. We determined a series of high resolution (< 1.7 Å) crystal structures at various pH values and with several ligands. These demonstrate that a series of peptide flips lies at the basis of the pH-dependent symmetry of ArgI and its unusually high pH optimum of 9.0 to 9.5.

Finally, to assess the cellular activity of ArgI inhibitors, we examined 102 cancer cell lines for ArgI activity and correlated the results to public gene expression profiles. The novel assay portfolio will help to deliver a new generation of ArgI inhibitors.

Citation Format: Yvonne Grobben, Joost C. Uitdehaag, Nicole Willemsen-Seegers, Werner W. Tabak, Martine B. Prinsen, Suzanne J. van Gerwen, Jan van Groningen, Johan Friesen, Helma Rutjes, Jos de Man, Rogier C. Buijsman, Guido J. Zaman. High-throughput fluorescence-based assay for screening of Arginase I inhibitors for cancer immunotherapy [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 1944.

Abstract 4907: Cell line panel profiling reveals novel drug response biomarkers for BTK and CDK4/6 inhibitors

Profiling of new drug candidates on cancer cell line panels is an important tool to identify candidate drug response biomarkers for clinical studies. We have set up a platform, called Oncolines™, that comprises 102 genetically well-characterized cell lines from diverse tumor tissues. The cell lines are screened in parallel in a high-throughput proliferation assay based on ATP-lite read-out with 9 point dose-response curves in duplicate and manual inspection of curve fitting. We have recently shown that this workflow leads to highly reproducible IC50s which are necessary for genomic biomarker discovery [1]. Here we apply this platform to investigate BTK and CDK4/6 inhibitors. In previous work [1,2] we correlated the IC50 profiles of small molecule inhibitors through Anova to curated databases of somatic mutations and copy numbers. To obtain a more comprehensive view of oncogenic signaling inside a cell, we calculated in this study correlations between the log IC50s and basal gene expression levels for more than 18,000 genes. To reduce the number of false positives, we first considered only genes with a known role in cancer biology or drug resistance. Secondly, correlations were corrected for the average correlations seen in an Oncolines™ database of more than 150 anti-cancer agents [1]. Thirdly, we looked at co-correlation of genes that interact on a protein level (StringDB) or at a pathway level (Gene Set Analysis). Our method, called GeneNominator™, was validated by profiling the microtubule binder vincristine, the EGFR inhibitor gefitinib, and the MDM2 antagonist nutlin, and confirmed known pharmacogenomic relations.In a first study we tested three CDK4/6 inhibitors, ribociclib, palbociclib and abemaciclib. Although their response patterns cluster together, they show significant differences. For instance, palbociclib is more active on cell lines that express the transcription factor GATA3, which is linked to cyclin signalling in neuroblastoma.In a second study we tested the BTK inhibitors ibrutinib and acalabrutinib. Both show very different inhibition profiles across the 102 cell lines. Ibrutinib shows considerable activity in cell lines that overexpress ERBB4, FGFR2 and ERBB2, reflecting its biochemical inhibition of these kinases. Acalabrutinib, which is more selective, is most active in cell lines that highly express IRF4, a known genetic driver in multiple myeloma. and the B-cell receptor subunit CD79B, of which mutations are often found in diffuse large B-cell lymphoma. When mutations and copy number changes are studied, acalabrutinib is particularly active in cell lines with CREBBP or EZH2 mutations, which occur in diffuse large B-cell lymphomas. Our data demonstrate that our in vitro cell panel screening method can uncover new mechanistic information on clinically used anti-cancer agents.

[1] Uitdehaag et al. (2016) Mol. Cancer Ther. 15, 3097-3109.[2] Uitdehaag et al. (2014) PLOS ONE 9: e92146

Citation Format: Joost C. Uitdehaag, Jeffrey J. Kooijman, Jeroen A.D.M. de Roos, Martine B.W. Prinsen, Jelle Dylus, Judith de Vetter, Nicole Willemsen-Seegers, Jos de Man, Suzanne J.C. van Gerwen, Rogier C. Buijsman, Guido J.R. Zaman. Cell line panel profiling reveals novel drug response biomarkers for BTK and CDK4/6 inhibitors [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 4907.

Stable aneuploid tumors cells are more sensitive to TTK inhibition than chromosomally unstable cell lines

Inhibition of the spindle assembly checkpoint kinase TTK causes chromosome mis-segregation and tumor cell death. However, high levels of TTK correlate with chromosomal instability (CIN), which can lead to aneuploidy. We show that treatment of tumor cells with the selective small molecule TTK inhibitor NTRC 0066-0 overrides the mitotic checkpoint, irrespective of cell line sensitivity. In stable aneuploid cells NTRC 0066-0 induced acute CIN, whereas in cells with high levels of pre-existing CIN there was only a small additional fraction of cells mis-segregating their chromosomes. In proliferation assays stable aneuploid cells were more sensitive than cell lines with pre-existing CIN. Tetraploids are thought to be an intermediate between diploid and unstable aneuploid cells. TTK inhibitors had the same potency on post-tetraploid and parental diploid cells, which is remarkable because the post-tetraploids are more resistant to mitotic drugs. Finally, we confirm that the reference compound reversine is a TTK inhibitor and like NTRC 0066-0, inhibits the proliferation of patient-derived colorectal cancer organoids. In contrast, treatment with TTK inhibitor did not reduce the viability of non-proliferating T cell acute lymphoblastic leukemia cells samples. Consequently, TTK inhibitor therapy is expected to spare non-dividing cells, and may be used to target stable aneuploid tumors.

Abstract B155: Combining cell panel screening with analysis of gene expression levels reveals features of drug response and resistance

Screening of new drugs on large cell panels is an important tool to study the biologic mechanism of drug response. From a combination of parallel in vitro tests and bio-informatics analysis, important conclusions can be drawn, for instance about drug selectivity in a cellular context, about resistance mechanisms, and about the patient population in which a drug is effective. This makes cell panel screening indispensable in modern drug discovery. We have set up a platform called Oncolines™ that comprises 102 cell lines from diverse tumor tissues. All cell lines are screened in parallel in high-throughput proliferation assays based on ATP-lite™. Compounds are tested with 9 point dose-response curves in duplicate. Curves are visually inspected. In the past, we have shown that this workflow leads to highly reproducible IC50s, which are necessary for genomic biomarker discovery [1]. For instance, the IC50s have been coupled to curated databases of somatic mutations and copy numbers (1). However, these changes only reflect a small percentage of oncogenic transformations. A more comprehensive view of oncogenic signaling inside a cell can be obtained from mRNA expression levels (2). Here, we describe a workflow to investigate drug response in the 102 cell line Oncolines™ panel based on basal gene expression levels. Correlations between gene expression levels and the log IC50s were calculated for more than 18,000 genes. To reduce the number of false-positive correlations, we considered only genes with a known biologic role in cancer or that were clinically actionable. Secondly, we filtered out genes that correlated indiscriminately with drug responses, by correcting for the average correlations seen in our profiling database of more than 150 inhibitors. This filtered gene list was structured graphically by combining it with information on protein-protein interactions (using the StringDB) or information on which genes are part of the same pathways (a method called Gene Set Analysis). Our method reveals that gene overexpression correlates with drug responses for a number of targets. For instance, EGFR, IGFR, or ALK kinase inhibitors have more potent effects in cell lines that overexpress EGFR, IGFR, or ALK, respectively, and the MDM2 antagonist nutlin is more active in MDM2-overexpressing cell lines. This is irrespective of the genomic alterations driving overexpression of these genes. The distinct response profiles of the spectrum-selective BTK/EGFR/ERBB2 inhibitor ibrutinib and the more selective BTK inhibitor alcalabrutinib could be distinguished as well. Finally, the analysis shows mechanisms of drug resistance. For instance, the response of vincristine strongly correlates to cellular ABCB1 expression, the P-glycoprotein/MDR1 drug transporter, but also to ABCC3, another ABC transporter. Combining basal gene expression levels with cell panel data therefore allows discovery of novel mechanisms of drug response and resistance. References: 1. Uitdehaag et al. Cell panel profiling reveals conserved therapeutic clusters and differentiates the mechanism of action of different PI3K/mTOR, Aurora kinase and EZH2 inhibitors. Mol Cancer Therap 2016;15:3097-3109. 2. Rees et al. Correlating chemical sensitivity and basal gene expression reveals mechanism of action. Nature Chem Biol 2016;12:109-16.

Citation Format: Joost C.M. Uitdehaag, Jeffrey Kooijman, Jeroen A.D.M. de Roos, Martine B.W. Prinsen, Jelle Dylus, Suzanne J.C. van Gerwen, Rogier C. Buijsman, Guido J.R. Zaman. Combining cell panel screening with analysis of gene expression levels reveals features of drug response and resistance [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 B155.

TTK Inhibitors as a Targeted Therapy for CTNNB1 (-catenin) Mutant Cancers

The spindle assembly checkpoint kinase TTK (Mps1) is a key regulator of chromosome segregation and is the subject of novel targeted therapy approaches by small-molecule inhibitors. Although the first TTK inhibitors have entered phase I dose escalating studies in combination with taxane chemotherapy, a patient stratification strategy is still missing. With the aim to identify a genomic biomarker to predict the response of tumor cells to TTK inhibitor therapy, we profiled a set of preclinical and clinical TTK inhibitors from different chemical series on a panel of 66 genetically characterized cell lines derived from different tumors (Oncolines). Cell lines harboring activating mutations in the CTNNB1 gene, encoding the Wnt pathway signaling regulator β-catenin, were on average up to five times more sensitive to TTK inhibitors than cell lines wild-type for CTNNB1 The association of CTNNB1-mutant status and increased cancer cell line sensitivity to TTK inhibition was confirmed with isogenic cell line pairs harboring either mutant or wild-type CTNNB1 Treatment of a xenograft model of a CTNNB1-mutant cell line with the TTK inhibitor NTRC 0066-0 resulted in complete inhibition of tumor growth. Mutations in CTNNB1 occur at relatively high frequency in endometrial cancer and hepatocellular carcinoma, which are known to express high TTK levels. We propose mutant CTNNB1 as a prognostic drug response biomarker, enabling the selection of patients most likely to respond to TTK inhibitor therapy in proof-of-concept clinical trials. Mol Cancer Ther; 16(11); 2609-17. ©2017 AACR.

Abstract 3457: Stable aneuploid cells are more sensitive to TTK inhibition than chromosome instable cell lines

Inhibition of the spindle assembly checkpoint kinase TTK causes chromosome mis-segregation and tumor cell death. High levels of TTK correlate with chromosomal instability (CIN), which can lead to aneuploidy. To investigate the potential relationship of CIN and sensitivity to TTK inhibition, we performed CIN analysis in human cancer cell lines from different tumor tissue origins and with different relative sensitivity to the selective TTK inhibitor NTRC 0066-0 [1]. By time lapse microscopy we observed that treatment with TTK inhibitor resulted in overriding of the mitotic checkpoint, irrespective of cell line sensitivity. Aneuploid but chromosomal stable cell lines were more sensitive than cell lines that already displayed high levels of CIN. In sensitive cell lines, treatment with TTK inhibitor induced acute chromosome mis-segregration. On the contrary, in populations of cells that already showed high levels of CIN, there was only a small additional fraction of cells mis-segregating their chromosomes. The resistant cell lines were all hypo-triploid instable cell lines, which are thought to be derived from cells with a double diploid genome (tetraploid cells) that have lost certain chromosomes. Next, we studied the effect of NTRC 0066-0 on three cell lines evolved via tetraploidization of the colorectal adenocarcinoma cell line HCT 116 referred as tetraploids. The tetraploids have low levels of CIN and were recently shown to display low level multidrug resistance against various cytotoxic agents and several targeted drugs. Proliferation of the tetraploids was inhibited with the same potency as the diploid parental cell line by three TTK inhibitors. Parental and tetraploids were also equally sensitive to reversine, a compound that is often used as a TTK reference inhibitor but whose selectivity has been disputed. In surface plasmon resonance binding experiments we measured a 800 times more potent binding of reversine to TTK over Aurora B. In a comparative cancer cell panel profiling study with 122 different anti-cancer agents [2], reversine clustered together with TTK inhibitors, demonstrating that in cells reversine acts as a TTK inhibitor. Finally, we show that NTRC 0066-0 inhibits the proliferation of primary human patient-derived colorectal cancer organoids with potencies similar to that of immortalized cancer cell lines. In contrast, treatment with TTK inhibitor did not reduce the viability T cell acute lymphoblastic leukemia cell samples, which are non-proliferating cells and very sensitive to classic chemotherapeutic agents, such as daunorubicin. These data is consistent with the function of TTK as a spindle assembly checkpoint kinase that is only active in proliferating cells. Consequently, TTK inhibitor therapy is expected to spare non-dividing cells, whereas it may be used to target stable aneuploid tumors. [1] Maia et al. (2015) Annals of Oncology; [2] Uitdehaag et al. (2016) Molecular Cancer Therapeutics.

Citation Format: Marion A.A. Libouban, Jeroen A.D.M. de Roos, Joost C.M. Uitdehaag, Nicole Willemsen-Seegers, Sara Mainardi, Jelle Dylus, Jos de Man, Bastiaan Tops, Jules P.P. Meijerink, Zuzana Storchová, Rogier C. Buijsman, René H. Medema, Guido J.R. Zaman. Stable aneuploid cells are more sensitive to TTK inhibition than chromosome instable cell lines [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 3457. doi:10.1158/1538-7445.AM2017-3457

Abstract 4185: NTRC 1501-0, a TTK kinase inhibitor selected for its long target residence time, completely inhibits tumor growth in the MDA-MB-231 xenograft model for triple-negative breast cancer

The protein kinase TTK is a critical component of the spindle assembly checkpoint (SAC), which regulates the proper attachment of sister chromatids during mitosis. TTK is essential for normal progression of the cell cycle and is upregulated in various aggressive cancers such as triple negative breast cancer (TNBC). Inhibition of TTK leads to an overriding of the SAC, premature progression of the cell cycle and mitotic catastrophe. TTK inhibition therefore contrasts with e.g. Aurora and PLK1 inhibition, which block the cell cycle [1]. Various studies have shown the clinical utility of TTK inhibition, particularly in combination therapy with paclitaxel [1,2]. In vivo, TTK inhibitor monotherapy has shown partial tumor growth inhibition without weight loss [1,2].

We have developed a novel class of TTK inhibitors based on a pyrimido-indolizine scaffold. These bind selectively and with high affinity to the ATP pocket of TTK and potently inhibit the proliferation of a variety of cell lines [1]. Previously we published a representative of this class, NTRC 0066-0, which has an IC50 of 0.6 nM in a biochemical assay for TTK activity and which is more than 200 times selective over a panel of 276 kinases [1]. NTRC 0066-0 has an average IC50 of 98 nM in proliferation assays in 66 different cell lines (Oncolines™ panel) [3].

To further improve the potency of the pyrimido-indolizine series, we determined the X-ray structures of a dozen of class representatives in complex with TTK. The results were compared to 3D complexes of other chemical scaffolds such as BAY-1161909, Mps-Bay2b, MPI-0479605, NMS-P715 and Mps1-IN1. The pyrimido-indolizine series uses an aromatic moiety to trap the catalytic lysine in the active site, enforcing a catalytically incompetent conformation of TTK. Thermal melting and surface plasmon resonance experiments demonstrate that this leads to a strong stabilization of the kinase domain and a slow dissociation rate for the compounds, which is one of the key determinants for potent cellular activity.

We took advantage of these structure-activity relationships to develop analogs of NTRC 0066-0 with increased residence time and cellular potency. One such analog, NTRC 1501-0, inhibits the proliferation of 66 cancer cell lines with an average IC50 of 18 nM, while retaining selectivity over the kinome. It has good pharmacokinetic properties and shows no cross-reactivity with drug safety targets in vitro. In a xenograft model of the human TNBC cell line MDA-MB-231, it completely inhibited tumor growth at a low oral dose, without effect on body weight, indicating good tolerability. These data show, for the first time, that TTK inhibition as monotherapy can achieve complete inhibition of tumor growth.

[1] Maia et al. (2015) Annals of Oncology 26, 2180-2192; [2] Wengner et al (2016) Mol. Canc. Therap. 15, 583-592; [3] Uitdehaag et al. (2016) Mol. Canc. Therap., in the press.

Citation Format: Joost C. Uitdehaag, Jos de Man, Marion Libouban, Nicole Willemsen-Seegers, Jan Gerard Sterrenburg, Joeri J. de Wit, Jeroen A.D de Roos, Martine B. Prinsen, Rogier C. Buijsman, Guido J. Zaman. NTRC 1501-0, a TTK kinase inhibitor selected for its long target residence time, completely inhibits tumor growth in the MDA-MB-231 xenograft model for triple-negative breast cancer [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 4185. doi:10.1158/1538-7445.AM2017-4185

Target Residence Time-Guided Optimization on TTK Kinase Results in Inhibitors with Potent Anti-Proliferative Activity

The protein kinase threonine tyrosine kinase (TTK; also known as Mps1) is a critical component of the spindle assembly checkpoint and a promising drug target for the treatment of aggressive cancers, such as triple negative breast cancer. While the first TTK inhibitors have entered clinical trials, little is known about how the inhibition of TTK with small-molecule compounds affects cellular activity. We studied the selective TTK inhibitor NTRC 0066-0, which was developed in our own laboratory, together with 11 TTK inhibitors developed by other companies, including Mps-BAY2b, BAY 1161909, BAY 1217389 (Bayer), TC-Mps1-12 (Shionogi), and MPI-0479605 (Myrexis). Parallel testing shows that the cellular activity of these TTK inhibitors correlates with their binding affinity to TTK and, more strongly, with target residence time. TTK inhibitors are therefore an example where target residence time determines activity in in vitro cellular assays. X-ray structures and thermal stability experiments reveal that the most potent compounds induce a shift of the glycine-rich loop as a result of binding to the catalytic lysine at position 553. This "lysine trap" disrupts the catalytic machinery. Based on these insights, we developed TTK inhibitors, based on a (5,6-dihydro)pyrimido[4,5-e]indolizine scaffold, with longer target residence times, which further exploit an allosteric pocket surrounding Lys553. Their binding mode is new for kinase inhibitors and can be classified as hybrid Type I/Type III. These inhibitors have very potent anti-proliferative activity that rivals classic cytotoxic therapy. Our findings will open up new avenues for more applications for TTK inhibitors in cancer treatment.

IL-7 Receptor Mutations and Steroid Resistance in Pediatric T cell Acute Lymphoblastic Leukemia: A Genome Sequencing Study

BACKGROUND

Pediatric acute lymphoblastic leukemia (ALL) is the most common childhood cancer and the leading cause of cancer-related mortality in children. T cell ALL (T-ALL) represents about 15% of pediatric ALL cases and is considered a high-risk disease. T-ALL is often associated with resistance to treatment, including steroids, which are currently the cornerstone for treating ALL; moreover, initial steroid response strongly predicts survival and cure. However, the cellular mechanisms underlying steroid resistance in T-ALL patients are poorly understood. In this study, we combined various genomic datasets in order to identify candidate genetic mechanisms underlying steroid resistance in children undergoing T-ALL treatment.

METHODS AND FINDINGS

We performed whole genome sequencing on paired pre-treatment (diagnostic) and post-treatment (remission) samples from 13 patients, and targeted exome sequencing of pre-treatment samples from 69 additional T-ALL patients. We then integrated mutation data with copy number data for 151 mutated genes, and this integrated dataset was tested for associations of mutations with clinical outcomes and in vitro drug response. Our analysis revealed that mutations in JAK1 and KRAS, two genes encoding components of the interleukin 7 receptor (IL7R) signaling pathway, were associated with steroid resistance and poor outcome. We then sequenced JAK1, KRAS, and other genes in this pathway, including IL7R, JAK3, NF1, NRAS, and AKT, in these 69 T-ALL patients and a further 77 T-ALL patients. We identified mutations in 32% (47/146) of patients, the majority of whom had a specific T-ALL subtype (early thymic progenitor ALL or TLX). Based on the outcomes of these patients and their prednisolone responsiveness measured in vitro, we then confirmed that these mutations were associated with both steroid resistance and poor outcome. To explore how these mutations in IL7R signaling pathway genes cause steroid resistance and subsequent poor outcome, we expressed wild-type and mutant IL7R signaling molecules in two steroid-sensitive T-ALL cell lines (SUPT1 and P12 Ichikawa cells) using inducible lentiviral expression constructs. We found that expressing mutant IL7R, JAK1, or NRAS, or wild-type NRAS or AKT, specifically induced steroid resistance without affecting sensitivity to vincristine or L-asparaginase. In contrast, wild-type IL7R, JAK1, and JAK3, as well as mutant JAK3 and mutant AKT, had no effect. We then performed a functional study to examine the mechanisms underlying steroid resistance and found that, rather than changing the steroid receptor's ability to activate downstream targets, steroid resistance was associated with strong activation of MEK-ERK and AKT, downstream components of the IL7R signaling pathway, thereby inducing a robust antiapoptotic response by upregulating MCL1 and BCLXL expression. Both the MEK-ERK and AKT pathways also inactivate BIM, an essential molecule for steroid-induced cell death, and inhibit GSK3B, an important regulator of proapoptotic BIM. Importantly, treating our cell lines with IL7R signaling inhibitors restored steroid sensitivity. To address clinical relevance, we treated primary T-ALL cells obtained from 11 patients with steroids either alone or in combination with IL7R signaling inhibitors; we found that including a MEK, AKT, mTOR, or dual PI3K/mTOR inhibitor strongly increased steroid-induced cell death. Therefore, combining these inhibitors with steroid treatment may enhance steroid sensitivity in patients with ALL. The main limitation of our study was the modest cohort size, owing to the very low incidence of T-ALL.

CONCLUSIONS

Using an unbiased sequencing approach, we found that specific mutations in IL7R signaling molecules underlie steroid resistance in T-ALL. Future prospective clinical studies should test the ability of inhibitors of MEK, AKT, mTOR, or PI3K/mTOR to restore or enhance steroid sensitivity and improve clinical outcome.

Cell Panel Profiling Reveals Conserved Therapeutic Clusters and Differentiates the Mechanism of Action of Different PI3K/mTOR, Aurora Kinase and EZH2 Inhibitors

Cancer cell line panels are important tools to characterize the in vitro activity of new investigational drugs. Here, we present the inhibition profiles of 122 anticancer agents in proliferation assays with 44 or 66 genetically characterized cancer cell lines from diverse tumor tissues (Oncolines). The library includes 29 cytotoxics, 68 kinase inhibitors, and 11 epigenetic modulators. For 38 compounds this is the first comparative profiling in a cell line panel. By strictly maintaining optimized assay protocols, biological variation was kept to a minimum. Replicate profiles of 16 agents over three years show a high average Pearson correlation of 0.8 using IC₅₀ values and 0.9 using GI₅₀ values. Good correlations were observed with other panels. Curve fitting appears a large source of variation. Hierarchical clustering revealed 44 basic clusters, of which 26 contain compounds with common mechanisms of action, of which 9 were not reported before, including TTK, BET and two clusters of EZH2 inhibitors. To investigate unexpected clusterings, sets of BTK, Aurora and PI3K inhibitors were profiled in biochemical enzyme activity assays and surface plasmon resonance binding assays. The BTK inhibitor ibrutinib clusters with EGFR inhibitors, because it cross-reacts with EGFR. Aurora kinase inhibitors separate into two clusters, related to Aurora A or pan-Aurora selectivity. Similarly, 12 inhibitors in the PI3K/AKT/mTOR pathway separated into different clusters, reflecting biochemical selectivity (pan-PI3K, PI3Kβγδ-isoform selective or mTOR-selective). Of these, only allosteric mTOR inhibitors preferentially targeted PTEN-mutated cell lines. This shows that cell line profiling is an excellent tool for the unbiased classification of antiproliferative compounds. Mol Cancer Ther; 15(12); 3097-109. ©2016 AACR.

Abstract 4635: Comparative cancer cell line profiling differentiates the mechanism of action of different PI3K/mTOR, Aurora kinase and EZH2 inhibitors

[purpose] Profiling of drug candidates in cell line panels is an important tool to compare the selectivity and targeting of new anti-cancer agents. In addition, comparative profiling may be used to repurpose established therapeutics by identifying new mechanisms of action or cross-selectivities.

[experimental procedures] A collection of more than 120 anti-cancer agents, targeting all important oncogenic signaling pathways, including classic cytotoxic agents as well as many targeted kinase inhibitors and epigenetic modulators, was profiled on a panel of 44 or 66 parallel cell line proliferation assays (Oncolines™) [1,2]. The Oncolines™ profiles of the compounds were compared by Pearson correlations of their inhibitor responses. Inhibitor sets were clustered using hierarchical trees. Response profiles were correlated to the genetic background of the cell lines by Analysis of Variance (Anova).

[results] Reproducibility of the NTRC Oncolines™ cell panel was validated by monitoring cell growth rate and the variation in IC50s of replicate profiles over a period of three years. The Pearson correlation between replicates ranged between 0.60 and 0.99 for 16 different inhibitors, depending on dose-response curve shape. Correlation analyses of the > 120 profiled anti-cancer agents revealed separate clusters of, a.o., taxanes, platins, topo-isomerase inhibitors, and EGFR, ABL, MEK and BRAF inhibitors. This demonstrates that the Oncolines™ profiles are an unbiased representation of the compound's mechanisms. The profile of the BTK inhibitor ibrutinib correlated with EGFR inhibitors. In biochemical experiments we showed that this due to its cross-reactivity with EGFR. The six Aurora kinase inhibitors profiled fall into two separate clusters, which are related to their biochemical selectivity. Thus, Aurora A-selective inhibitors are relatively more active in cell lines with mutations in cell cycle checkpoint-related genes such as TP53 and RB1; whereas pan-Aurora inhibitors are more active in cell lines with mutations in growth factor signaling pathways, such as NRAS. Profiling of eleven PI3 kinase and mTOR inhibitors revealed four distinct clusters. PI3Kalpha and PI3Kdelta isoform selective inhibitors each target genetically distinct subgroups of cell lines. Rapamycin-analogs, such as everolimus, specifically target PTEN-mutant cell lines. Finally, profiling of EZH2 inhibitors indicates that there are essentially two classes and that these have a cellular profile that is distinct from HDAC, DOT1L or BET inhibitors.

[conclusions] Comparative cancer cell line profiling is a powerful tool to rapidly explore the pharmacogenomics of drug action in cancer cells and to identify new or previously unnoted activities of compounds.

[references]: [1] Uitdehaag et al. (2014) PLOS ONE 9(3) e92146; [2] Uitdehaag et al. (2015) PLOS ONE 10(6) e0132230.

Citation Format: Joost C.M. Uitdehaag, Jeroen A.D.M. de Roos, Martine B.W. Prinsen, Judith R.F. de Vetter, Jelle Dylus, Antoon M. van Doornmalen, Suzanne J.C. van Gerwen, Jos de Man, Rogier C. Buijsman, Guido J.R. Zaman. Comparative cancer cell line profiling differentiates the mechanism of action of different PI3K/mTOR, Aurora kinase and EZH2 inhibitors. [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 4635.

Abstract 2646: The unique binding mode of NTRC 0066-0, a novel inhibitor of the spindle assembly checkpoint kinase TTK (Mps1), leads to long target residence time and potent antitumor activity

[purpose] An abnormal number of chromosomes, or ‘aneuploidy’, is a common feature of solid human tumors and a predictor of poor prognosis in breast, lung, brain and colorectal cancer. Aneuploidy is caused by malfunctioning of the Spindle Assembly Checkpoint (SAC), a surveillance mechanism that ensures the fidelity of chromosome segregation. The protein kinase TTK (commonly referred to as Mps1) is a component of the SAC. Inhibition of TTK gene expression by RNA interference and inhibition of TTK kinase activity by small molecule kinase inhibitors causes chromosome missegregation and cancer cell death.

[experimental procedures] A novel class of compounds was identified that potently inhibits TTK enzyme activity and cancer cell line proliferation [1]. Its binding mode and that of reference inhibitors was characterized by protein crystallography. Binding kinetics and target residence time were determined by surface plasmon resonance using Biacore T200. Anti-proliferative activity was measured on a broad panel of cancer cell lines [2].

[results] The clinical candidate, NTRC 0066-0, inhibits TTK with subnanomolar potency (IC50) in a kinase enzyme assay and is more than 200 times selective over 276 kinases examined, including mitotic and cell cycle dependent kinases (CDKs). X-ray structures of the TTK kinase domain in complex with NTRC 0066-0 and analogs indicate that this class of compounds induces a large conformational shift in the glycine-rich loop, invoking an inactive kinase conformation. In surface plasmon resonance experiments, NTRC 0066-0 exhibited slow dissociation kinetics, resulting in a long target residence time. Parallel surface plasmon resonance experiments with mitotic kinases confirmed the exquisite selectivity of NTRC 0066-0 for TTK over Aurora and Polo-like kinases. NTRC 0066-0 potently inhibited the proliferation of a wide variety of human cancer cell lines with potencies in the same range as marketed cytotoxic agents. The crystal structure, binding kinetics and cellular potency of NTRC 0066-0 were compared to that of other TTK inhibitors such as Mps1-IN-2, AZD-3146, Mps-BAY2b and Bay 1161909 as well as analogs from the NTRC 0066-0 series. This suggest that the unique binding mode of NTRC 0066-0 results in long target residence time which contributes to its strong anti-tumor activity. In subsequent mouse xenograft models of human cancer cell lines, NTRC 0066-0 inhibited tumor growth as a single agent after oral administration at 20 mg per kg.

[conclusions] NTRC 0066-0 is a novel TTK inhibitor with outstanding in vitro properties and potent anti-tumor activity in mouse xenograft models. Our data suggest that long target residence time corresponds with potent cellular activity for TTK inhibitors.

References

[1] Maia et al. (2015) Annals of Oncology 26, 2180-2192; [2] Uitdehaag et al. (2014) PLOS ONE 9(3) e92146.

Citation Format: Jos de Man, Joost C.M. Uitdehaag, Nicole Willemsen-Seegers, Jan Gerard Sterrenburg, Joeri J.P. de Wit, Jeroen A.D.M. de Roos, Martine B.W. Prinsen, Rogier C. Buijsman, Guido J.R. Zaman. The unique binding mode of NTRC 0066-0, a novel inhibitor of the spindle assembly checkpoint kinase TTK (Mps1), leads to long target residence time and potent antitumor activity. [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 2646.

Inhibition of the spindle assembly checkpoint kinase TTK enhances the efficacy of docetaxel in a triple-negative breast cancer model

BACKGROUND

Triple-negative breast cancers (TNBC) are considered the most aggressive type of breast cancer, for which no targeted therapy exists at the moment. These tumors are characterized by having a high degree of chromosome instability and often overexpress the spindle assembly checkpoint kinase TTK. To explore the potential of TTK inhibition as a targeted therapy in TNBC, we developed a highly potent and selective small molecule inhibitor of TTK, NTRC 0066-0.

RESULTS AND CONCLUSIONS

The compound is characterized by long residence time on the target and inhibits the proliferation of a wide variety of human cancer cell lines with potency in the same range as marketed cytotoxic agents. In cell lines and in mice, NTRC 0066-0 inhibits the phosphorylation of a TTK substrate and induces chromosome missegregation. NTRC 0066-0 inhibits tumor growth in MDA-MB-231 xenografts as a single agent after oral application. To address the effect of the inhibitor in breast cancer, we used a well-defined mouse model that spontaneously develops breast tumors that share key morphologic and molecular features with human TNBC. Our studies show that combination of NTRC 0066-0 with a therapeutic dose of docetaxel resulted in doubling of mouse survival and extended tumor remission, without toxicity. Furthermore, we observed that treatment efficacy is only achieved upon co-administration of the two compounds, which suggests a synergistic in vivo effect. Therefore, we propose TTK inhibition as a novel therapeutic target for neoadjuvant therapy in TNBC.

Selective Targeting of CTNBB1-, KRAS- or MYC-Driven Cell Growth by Combinations of Existing Drugs

The aim of combination drug treatment in cancer therapy is to improve response rate and to decrease the probability of the development of drug resistance. Preferably, drug combinations are synergistic rather than additive, and, ideally, drug combinations work synergistically only in cancer cells and not in non-malignant cells. We have developed a workflow to identify such targeted synergies, and applied this approach to selectively inhibit the proliferation of cell lines with mutations in genes that are difficult to modulate with small molecules. The approach is based on curve shift analysis, which we demonstrate is a more robust method of determining synergy than combination matrix screening with Bliss-scoring. We show that the MEK inhibitor trametinib is more synergistic in combination with the BRAF inhibitor dabrafenib than with vemurafenib, another BRAF inhibitor. In addition, we show that the combination of MEK and BRAF inhibitors is synergistic in BRAF-mutant melanoma cells, and additive or antagonistic in, respectively, BRAF-wild type melanoma cells and non-malignant fibroblasts. This combination exemplifies that synergistic action of drugs can depend on cancer genotype. Next, we used curve shift analysis to identify new drug combinations that specifically inhibit cancer cell proliferation driven by difficult-to-drug cancer genes. Combination studies were performed with compounds that as single agents showed preference for inhibition of cancer cells with mutations in either the CTNNB1 gene (coding for β-catenin), KRAS, or cancer cells expressing increased copy numbers of MYC. We demonstrate that the Wnt-pathway inhibitor ICG-001 and trametinib acted synergistically in Wnt-pathway-mutant cell lines. The ERBB2 inhibitor TAK-165 was synergistic with trametinib in KRAS-mutant cell lines. The EGFR/ERBB2 inhibitor neratinib acted synergistically with the spindle poison docetaxel and with the Aurora kinase inhibitor GSK-1070916 in cell lines with MYC amplification. Our approach can therefore efficiently discover novel drug combinations that selectively target cancer genes.

Abstract 2849: Analysis of the cancer gene targeting of clinical kinase inhibitor drugs by combining cellular and biochemical profiling

[Purpose] Kinase inhibitors are a prime example of the success of targeted therapy. Crucial to the development of targeted therapies is the ability to couple drug response to genetic markers, such as mutations in oncogenes and/or tumor suppressors, chromosomal rearrangements, and/or gene amplifications. The efficacy of response to such markers is linked with the biochemical characteristics of kinase inhibitors. However, it is poorly understood what profiles are required to achieve the best targeting. We have systematically compared the biochemical potency and selectivity profiles of all kinase inhibitor drugs in clinical use with their ability to inhibit cell proliferation in a panel of forty-four human cancer cell lines from diverse tumor tissue origins.[Experimental procedures] Proliferation assays were established for a panel of forty-four human cancer cell lines licensed from the American Type Culture Collection. The panel represents twenty-three of the most frequently identified genetic changes in the COSMIC Cell Lines (CCL) project in at least two cell lines. We profiled all twenty-five kinase inhibitors in clinical use on the cancer cell line panel, together with a number of classic cytotoxic agents for comparison. The proliferation assay data were linked to genetic data from the CCL database by Anova and volcano plot analysis. In parallel the biochemical profiles of all twenty-five kinase inhibitor drugs were determined on a panel of 313 protein kinase enzyme activity assays. The biochemical profiling data were used to interpret the cellular targeting compounds in terms of biochemical potency, selectivity and kinase poly-pharmacology.[Results] The suitability of the cell line panel was validated by confirming the known sensitivity of mutant B-RAF to vemurafenib, of BCR-ABL to imatinib, and EGFR overexpression to erlotinib. Mutation in SMAD4 was identified as a novel drug sensitivity marker for EGFR inhibitors, while mutation in the gene for β-catenin was identified as a sensitivity marker for MEK inhibitors, such as trametinib. When comparing compounds with similar mechanisms, dabrafenib is more efficient at selectively inhibiting BRAF-mutant transformed cells than vemurafenib. Of all ABL inhibitors, imatinib has the best targeting efficacy. The compound that most selectively inhibits growth of EGFR-overexpressing cell lines, is gefitinib.[Conclusions] Cancer cell line profiling can be used to identify novel sensitivity markers of drug response. Cancer cell line profiling in combination with biochemical kinase profiling revealed biochemical selectivity and potencies as prime determinants of on target efficacy of kinase inhibitor drugs, the extent of which is target-dependent. The combination of cell panel profiling and kinome profiling is an important tool for the development of optimal targeted therapies for kinases.

Citation Format: Guido J.R. Zaman, Joost C.M. Uitdehaag, Rogier C. Buijsman, Jeroen A.D.M. de Roos, Antoon M. van Doornmalen, Martine B.W. Prinsen, Jos de Man, Yusuke Kawase, Yoshinori Tanizawa, Kohichiro Yoshino. Analysis of the cancer gene targeting of clinical kinase inhibitor drugs by combining cellular and biochemical profiling. [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 2849. doi:10.1158/1538-7445.AM2014-2849

High-Throughput Fluorescence-Based Screening Assays for Tryptophan-Catabolizing Enzymes

Indoleamine 2,3-dioxygenase (IDO1) and tryptophan 2,3-dioxygenase (TDO) are two structurally different enzymes that have a different tissue distribution and physiological roles, but both catalyze the conversion of tryptophan to N-formylkynurenine (NFK). IDO1 has been clinically validated as a small-molecule drug target for cancer, while preclinical studies indicate that TDO may be a target for cancer immunotherapy and neurodegenerative disease. We have developed a high-throughput screening assay for IDO1 and TDO based on a novel chemical probe, NFK Green, that reacts specifically with NFK to form a green fluorescent molecule with an excitation wavelength of 400 nm and an emission wavelength of 510 nm. We provide the first side-by-side comparison of a number of published inhibitors of IDO1 and TDO and reveal that the preclinical IDO1 inhibitor Compound 5l shows significant cross-reactivity with TDO, while the relative selectivity of other published inhibitors was confirmed. The suitability for high-throughput screening of the assays was demonstrated by screening a library of 87,000 chemical substances in 384- or 1536-well format. Finally, we demonstrate that the assay can also be used to measure the capacity of cells to metabolize tryptophan and to measure the cellular potency of IDO1 and TDO inhibitors.

Comparison of the cancer gene targeting and biochemical selectivities of all targeted kinase inhibitors approved for clinical use

The anti-proliferative activities of all twenty-five targeted kinase inhibitor drugs that are in clinical use were measured in two large assay panels: (1) a panel of proliferation assays of forty-four human cancer cell lines from diverse tumour tissue origins; and (2) a panel of more than 300 kinase enzyme activity assays. This study provides a head-on comparison of all kinase inhibitor drugs in use (status Nov. 2013), and for six of these drugs, the first kinome profiling data in the public domain. Correlation of drug activities with cancer gene mutations revealed novel drug sensitivity markers, suggesting that cancers dependent on mutant CTNNB1 will respond to trametinib and other MEK inhibitors, and cancers dependent on SMAD4 to small molecule EGFR inhibitor drugs. Comparison of cellular targeting efficacies reveals the most targeted inhibitors for EGFR, ABL1 and BRAF(V600E)-driven cell growth, and demonstrates that the best targeted agents combine high biochemical potency with good selectivity. For ABL1 inhibitors, we computationally deduce optimized kinase profiles for use in a next generation of drugs. Our study shows the power of combining biochemical and cellular profiling data in the evaluation of kinase inhibitor drug action.

A guide to picking the most selective kinase inhibitor tool compounds for pharmacological validation of drug targets

To establish the druggability of a target, genetic validation needs to be supplemented with pharmacological validation. Pharmacological studies, especially in the kinase field, are hampered by the fact that many reference inhibitors are not fully selective for one target. Fortunately, the initial trickle of selective inhibitors released in the public domain has steadily swelled into a stream. However, rationally picking the most selective tool compound out of the increasing amounts of available inhibitors has become progressively difficult due to the lack of accurate quantitative descriptors of drug selectivity. A recently published approach, termed 'selectivity entropy', is an improved way of expressing selectivity as a single-value parameter and enables rank ordering of inhibitors. We provide a guide to select the best tool compounds for pharmacological validation experiments of candidate drug targets using selectivity entropy. In addition, we recommend which inhibitors to use for studying the biology of the 20 most investigated kinases that are clinically relevant: Abl (ABL1), AKT1, ALK, Aurora A/B, CDKs, MET, CSF1R (FMS), EGFR, FLT3, ERBB2 (HER2), IKBKB (IKK2), JAK2/3, JNK1/2/3 (MAPK8/9/10), MEK1/2, PLK1, PI3Ks, p38α (MAPK14), BRAF, SRC and VEGFR2 (KDR).

Synthetic heparin derivatives as new anticoagulant drugs

The journey towards a detailed mechanistic understanding of the anticoagulant action of heparin has resulted in synthetic mimetics with improved pharmacodynamic profiles. Inspired by the ternary complex formation of heparin with antithrombin III and thrombin, the active pentasaccharide fondaparinux has been succeeded by several clinical candidates, such as SR123781, that have tailor-made factor Xa and thrombin inhibitory activities combined with less aspecific binding (e.g. binding to platelet factor 4 involved in thrombocytopenia). Novel compounds with both antithrombin III-mediated inhibition of factor Xa and direct thrombin inhibition are emerging. Org42675 is one such compound, balancing dual inhibition of factor Xa and thrombin in one anticoagulant drug, with excellent pharmacokinetic properties and strong inhibitory activity toward clot-bound thrombin.

Non-Steroidal Steroid Receptor Modulators

The last ten years much attention has been focused on the finding of non-steroidal ligands for steroidal nuclear receptors for reasons such as diminishing cross-reactivity to eliminate side effect profiles, changing physicochemical properties which might cause different tissue distribution profiles and altering binding modes which influence the binding of cofactors. Compounds with a selective functionality profile are referred to as selective nuclear receptor modulators (e.g., SARMs or SPRMs). In the following paragraphs non-steroidal ligands which have full or partial agonistic activity will be described for the following receptors: PR, GR, AR, LXR and FXR.

Ruthenium-catalyzed olefin metathesis in ionic liquids

[reaction--see text] Ionic liquid 1-butyl-3-methylimidazoliumhexafluorophosphate ([bmim]PF(6)) is described as an effective medium for ring-closing metathesis (RCM) using Grubbs catalysts. When [bmim]PF(6) was used as solvent, the RCM showed high conversions and a broad substrate tolerance. [bmim]PF(6) and the ruthenium catalyst were recycled after extraction of the product in the organic phase for at least three cycles.

Synthesis of heparin-like antithrombotics having perphosphorylated thrombin binding domains

The synthesis of three heparin analogues (i.e. compounds VI-VIII) having perphosphorylated thrombin binding domains (TBDs) is reported. These compounds were tested in vitro for their antithrombin III (ATIII)-mediated anti-Xa and antithrombin activities. Conjugates VI and VIII show a remarkable increase in antithrombin activity compared to the structurally related conjugates with persulfated TBDs (i.e. compounds IV and V), whereas compound VII displays a diminished activity.

Design and synthesis of a novel synthetic NAPAP-penta-saccharide conjugate displaying a dual antithrombotic action

The synthesis of a novel antithrombotic consisting of a heparin pentasaccharide conjugated to the active site inhibitor N-(2-naphtalenesulfonyl)-glycyl-(D)-4-aminophenyl-alanyl-piperidin e (NAPAP) (i.e. compound I) is reported. This conjugate shows a unique pharmacological profile both in vitro and in vivo having direct anti-thrombin and ATIII-mediated anti-Xa activity. Furthermore, conjugate I has a prolonged in vivo half-life compared to NAPAP (1.5 h vs 9 min.).