Synergy Score Research Articles

ATRT-12. HYPERACTIVATING THE INTEGRATED STRESS RESPONSE WITH PROTEASOME INHIBITION IN AT/RT

Abstract Atypical teratoid/rhabdoid tumor (AT/RT) is an aggressive pediatric brain tumor with a poor prognosis. AT/RT has increased baseline activation of the integrated stress response (ISR), an evolutionarily conserved system that enables cells to tolerate various forms of stress. Elevated expression of ATF4 indicates activation of the ISR. Transient or low-level expression of this transcription factor protects cells from stress, while sustained, high-level activation results in cell death. Ixazomib is an orally bioavailable proteasome inhibitor that causes endoplasmic reticulum stress, which is a major upstream activator of the ISR. Because AT/RT has a high baseline level of ATF4, we hypothesized that this tumor would be susceptible to ISR activators such as ixazomib. After determining the IC50 of ixazomib, AT/RT cell lines were treated with increasing concentrations of the drug. Cleaved caspase-3 immunofluorescence showed a significant increase of apoptosis (CHLA06 p<0.0001 by ANOVA). We are currently testing ixazomib in combination with idarubicin, a brain-penetrant anthracycline, and gemcitabine, a brain-penetrant nucleoside analog. Synergy testing in CHLA06 showed an overall zero-interaction-potency (ZIP) synergy score of 23.464 with inhibitory concentrations of ixazomib and idarubicin in the low nanomolar range (scores of 10 or above indicate synergy). Similarly, ixazomib and gemcitabine synergized to suppress CHLA06 growth and induce apoptosis (67% Annexin V+ cells in combination compared to 14 and 24% Annexin V+ with single agent treatment). In the future, we will determine if ixazomib selectively kills AT/RT while sparing normal cells in iPSC brain organoids. We will also test ixazomib in orthotopic xenografts of AT/RT. These results suggest that ixazomib, especially in combination with idarubicin, gemcitabine or other ISR activators, has the potential to serve as an effective therapy for AT/RT.

Mind the Curve: Dose-Response Fitting Biases the Synergy Scores across Software Used for Chemotherapy Combination Studies.

Drug combinations are increasingly studied in the field of anticancer agents. Mathematical models, such as Loewe, Bliss, and HSA, are used to interpret drug combinations, while informatics tools help cancer researchers identify the most effective combinations. However, the different algorithms each software uses lead to results that do not always correlate. This study compared the performance of Combenefit (Ver. 2.021) and SynergyFinder (Ver. 3.6) in analyzing drug synergy by studying combinations involving non-steroidal analgesics (celecoxib and indomethacin) and antitumor drugs (carboplatin, gemcitabine, and vinorelbine) on two canine mammary tumor cell lines. The drugs were characterized, their optimal concentration-response ranges were determined, and nine concentrations of each drug were used to make combination matrices. Viability data were analyzed under the HSA, Loewe, and Bliss models. Celecoxib-based combinations showed the most consistent synergistic effect among software and reference models. Combination heatmaps revealed that Combenefit gave stronger synergy signals, while SynergyFinder produced better concentration-response fitting. When the average values of the combination matrices were compared, some combinations shifted from synergistic to antagonistic due to differences in the curve fitting. We also used a simulated dataset to normalize each software's synergy scores, finding that Combenefit tends to increase the distance between synergistic and antagonistic combinations. We conclude that concentration-response data fitting biases the direction of the combination (synergistic or antagonistic). In contrast, the scoring from each software increases the differences among synergistic or antagonistic combinations in Combenefit when compared to SynergyFinder. We strongly recommend using multiple reference models and reporting complete data analysis for synergy claiming in combination studies.

Abstract B015: HOXA9 promotes enzalutamide resistance in RB-p53 deficient prostate cancer

Abstract Introduction: Castration resistant prostate cancer (CRPC) cells can acquire resistance to the androgen receptor (AR) inhibitor enzalutamide (EZ). These cells can switch lineages from an adenocarcinoma to a neuroendocrine (NE) cell type that proliferate independently of the AR signaling pathway. Cancer genomic and molecular studies identified that co-deletion of the retinoblastoma (RB1) and TP53 genes can promote the acquisition of EZ resistance and neuroendocrine features. However, RB and p53 are both tumour suppressor and are therefore difficult to target pharmacologically. The purpose of this study is to identify an actionable molecular factor downstream of RB and p53 that drives EZ resistance in CRPC. Methods and Results: To characterize functional and molecular features of RB and p53 loss, CRISPR-Cas9 was used to generate a double knockout (DKO) line in LNCaP prostate cancer cells. Compared with LNCaP wild type (WT) cells, only DKOs formed distinct colonies over a 4-week colony forming assay under EZ treatment. RNA sequencing of DKO and WT cells, followed by gene ontology (GO) analysis, revealed NE and stemness genes, including HOXA9, were significantly upregulated in DKO cells. To categorize gene loss events in EZ-treated LNCaP cells, a genome-wide CRISPR knockout screen was performed. Pools of KO cells were treated with either EZ or DMSO and then analyzed by next generation sequencing to identify gene mutations that confer increased resistance or sensitivity to EZ. GO analysis of de-enriched genes following EZ treatment identified stemness genes, including HOXA9, highlighting the potential importance of a stem-like phenotype for acquiring EZ resistance EZ. To further investigate the functional significance of HOXA9 we analyzed EZ-resistant prostate tumour genomic data. HOXA9 is mutated or mis-expressed in 10% of cases. Importantly, HOXA9 is either amplified or overexpressed in virtually all these cases, and is associated with poorer prognosis, suggesting an oncogenic role for HOXA9 in CRPC. HOXA9 transcript levels were positively correlated with neuroendocrine features and negatively correlated with RB1expression in these tumour samples. LNCaP WT and DKO cells we then engineered to overexpress HOXA9 displayed increased IC50 values following a 6-day EZ treatment, compared with either parental line. DKO cells that overexpress HOXA9 also formed significantly more colonies following a 4-week EZ treatment, compared with parentals. In contrast, shRNA knockdown of HOXA9 caused a reduction in IC50 values and formed fewer drug resistant colonies compared with control cells. Finally, DKO and WT cells were co-treated with varying concentrations of the HOXA9 inhibitor DB818 and EZ. DKO cells were more sensitive to DB818 alone at high concentrations and displayed higher synergy as measured by a ZIP synergy score when co-treated with EZ. Conclusions: Overall, these results suggest that HOXA9 regulates EZ resistance in prostate cancer. Furthermore, HOXA9 inhibition may be of therapeutic benefit for treating EZ-resistant CRPC. Citation Format: Michael V. Roes, Fred A. Dick. HOXA9 promotes enzalutamide resistance in RB-p53 deficient prostate cancer [abstract]. In: Proceedings of the AACR Special Conference: Advances in Prostate Cancer Research; 2023 Mar 15-18; Denver, Colorado. Philadelphia (PA): AACR; Cancer Res 2023;83(11 Suppl):Abstract nr B015.

Systematic high-throughput combination drug screen to enhance poly (ADP-ribose) polymerase (PARP) inhibitor efficacy in ovarian cancer.

5546 Background: PARP inhibitors currently offer the greatest benefit to patients with loss-of-function BRCA1 or 2 mutations or other causes of homologous recombination deficiency (HRD). We hypothesized that combination therapy, possibly by augmenting or inducing an HRD phenotype, would enhance the efficacy of PARP inhibition in epithelial ovarian cancer. Methods: We performed a high-throughput screen of an informer set containing FDA-approved drugs, clinical candidates, and small-molecule probes to identify synergistic partners with olaparib in representative HRD and non-HRD human epithelial ovarian cancer cells. Single agent activity was described by area under the curve of the Hafner growth rate index (AUC_GRI) and synergy was ranked by cumulative difference from Bliss (ΔBliss). Analysis of the drug screen was performed using algorithms developed by the Gulf Coast Consortia’s Combinatorial Drug Discovery Program at the Texas A&M Institute of Bioscience and Technology. MTT assays were then independently performed to verify and characterize synergy between CT7439, an agent selected following the drug screen, and olaparib. MTT data were analyzed using the SynergyFinder Plus web application. Results: In an initial single agent screen, we identified 62 compounds with a mean AUC_GRI <0.75, indicating inhibitory activity. Prioritizing more potent agents and those of mechanistic interest, we selected 40 hits to validate and advance to a combination screen. Diverse mechanisms of action were represented among the hits, including many small molecule inhibitors of various cell cycle pathways. Following a combination screen with olaparib, the compounds selected for final validation were: AZD 7762 (CHK1/2 inhibitor), dinaciclib (pan-CDK inhibitor), onalespib (HSP90 inhibitor), and SN-38 (topoisomerase 1 inhibitor). The ΔBliss for these agents are presented in the table. Due to mechanistic rationale and concern for overlapping toxicities among the other candidates, we focused further study on CDK inhibitors. In MTT assays, we identified robust synergy between olaparib and CT7439, a next-generation oral CDK12/13 inhibitor, with a mean Bliss synergy score of 1.31 and scores as high as 22.03 at certain concentrations in the non-HRD model OVCAR-5. These findings were recapitulated in the HRD cell lines OVCAR-4 (mean Bliss synergy score 1.56) and OVCAR-8 (mean Bliss synergy score 5.69). Results from an in vivo model will be presented as well. Conclusions: Pairing a PARP inhibitor and CDK inhibitor, a strategy identified by a high-throughput drug screen and known to impair homologous recombination, resulted in robust synergy in both HRD and non-HRD ovarian cancer models. Clinical translation of this combination may enhance the efficacy of PARP inhibitors in patients with ovarian cancer. [Table: see text]

A powerful drug combination strategy targeting BRAF-mutant melanoma.

3152 Background: BRAF inhibitors, such as vemurafenib and dabrafenib, are effective in treating patients with melanoma harboring (V600E) BRAF mutations. These drugs block the activity of the mutated BRAF protein, which impacts the development and progression of melanoma. Despite initial efficacy, drug resistance reliably occurs leading to disease relapse. Here we show how BRAF inhibitors cause metabolic reprogramming in melanoma cells to achieve drug resistance and promote cell survival. Previously we demonstrated that wild-type isocitrate dehydrogenase 1 (wtIDH1) supports mitochondrial function and maintains redox homeostasis in melanoma, and that an FDA-approved mutant IDH1 inhibitor, ivosidenib (AG-120), is actually a potent wtIDH1 inhibitor. Thus, we hypothesized that wtIDH1 inhibition would synergize with BRAF inhibition. Methods: Metabolomic profiling using LC-MS determined the impact of BRAF inhibition on cellular metabolism. Cell viability was assessed by PicoGreen in drug combination assays. Synergism was calculated using the Bliss-Independence dose-response model for drug interaction. In vivo modeling of AG-120 in combination with BRAF inhibition used melanoma cell xenografts in athymic nude mice for tumor volume analyses, and survival studies were performed in both immunocompetent C57BL/6J mice (murine YUMM1.7 cells) and immunocompromised athymic nude mice (human A375 cells). Results: Metabolomics data suggest that BRAF-mutated melanoma cells treated with BRAF inhibitors increased oxidative metabolism and mitochondrial dependence (i.e., survival adaptations). These alterations suggest an opportunity for mitochondrial inhibitors to improve drug efficacy. Targeting wtIDH1 with AG-120 in combination with dabrafenib significantly reduced melanoma cell viability. A positive synergy score and Bliss score greater than 1 indicate that the combined treatment was more effective in reducing cell viability than either treatment alone. Further, the combination of AG-120 and dabrafenib was the most effective in vivo, reducing tumor growth in the BRAF-mutated melanoma xenograft model, and improving mouse survival compared to monotherapy controls. Mice tolerated combination therapy with no reduction in body weight observed. Conclusions: Our findings indicate that dual inhibition of mutated BRAF and wild-type IDH1 represents a novel treatment strategy for BRAF-mutated melanomas, with potential for application to other BRAF-mutated cancers (e.g., colon, hepatobiliary, thyroid, etc.).

Tumor sensitization to PARP inhibitors by DNA damaging synthetically lethal acylfulvenes.

e15123 Background: 20-30% of solid tumors (ovarian, breast, pancreatic, prostate cancers) harbor some level of deficiency in DNA Damage Repair (DDR) pathways. Such cancers become dependent on alternative DDR pathways to maintain genome integrity, making them selectively vulnerable to DNA damaging agents. The concept of synthetic lethality has been leveraged to treat subsets of such tumors. Clinically, PARP inhibitors (PARPi) have been successful in Homologous Recombination Deficiency (HRD) cancers. LP-100 and LP-184 are acylfulvene (AF) class small molecule prodrugs that are metabolized to active compounds by prostaglandin reductase 1 (PTGR1) that is often elevated in solid tumors. AF-induced DNA lesions are likely selectively processed by repair pathways including BRCA1/2 mediated Homologous Recombination (HR). Methods: Cell Titer Glo based 10 day cell viability assays were used to generate drug IC50 values in vitro. Bliss synergy scores were computed with scores ≥ 10 reflecting synergy. Drug-induced DNA double strand breaks (DSB) were detected and quantified with STRIDE (SensiTive Recognition of Individual DNA Ends) assay in cancer cells. A subcutaneous tumor xenograft model was used to determine tumor volumes in control and drug treated mice. Results: In a BRCA2 mutant ovarian cancer cell line OVCAR3, LP-184 and olaparib co-treatment in vitro showed synergistic effects (Bliss score 10). Similarly in a BRCA2 mutant prostate cancer cell line 22Rv1, LP-100 combination with rucaparib was synergistic (Bliss score 18). 400 nM LP-184 showed a time dependent increase in DNA DSB signals in vitro, 1.7X more so in BRCA2 mutant vs wild type (WT) DLD-1 isogenic colon cancer cell lines up to 24 hours. To validate the hypothesis that AF-induced DSBs remain unresolved if exposed to and further synergize with PARPi in vivo, we tested LP-100 plus olaparib in a DU145 (BRCA2 mutant) prostate cancer xenograft model. LP-100 + olaparib treatment resulted in sustained, durable tumor regression indicating in vivo synergy whereas either agent alone did not produce tumor shrinkage. Day 42 tumor growth inhibition was 66% for 2.5 mg/kg LP-100 alone, 34% for 40 mg/kg olaparib alone and 108% for the combination. Moreover, LP-184 treatment resulted in early onset and complete tumor regression in 7 PDX models of PARPi resistant triple negative breast cancers (TNBC) harboring BRCA1/2 loss whereas olaparib/ niraparib remained entirely ineffective in these. Conclusions: AF response is influenced by tumor DNA repair competence. LP-100 and LP-184 are synthetically lethal resulting from their abilities to cause unresolvable DNA damage where tumor cells express high PTGR1 and are deficient in the HR pathway. LP-184 single agent was superior to PARPi in TNBC and LP-100 combination made an olaparib resistant tumor highly sensitive, thereby facilitating a path to extend the opportunities for both AFs and PARPis and enhance the clinical utilization of PARPi.

Abstract A02: High-capacity drug screen identification of novel synergistic drug pairs with venetoclax in acute myeloid leukemia

Abstract Advancements in the development of targeted therapies have changed the therapeutic paradigm in acute myeloid leukemia (AML) in recent years. The orally available BCL-2 inhibitor venetoclax is effective and well tolerated in combination with either a hypomethylating agent (HMA) or low-dose cytarabine (LDAC). BCL-2 is a anti-apoptotic protein which binds to and sequesters pro-apoptotic proteins such as BAX, BAK, PUMA and NOXA and prevents pro-apoptotic proteins from initiating mitochondrial apoptosis leading to sustained survival in cancer cells. Venetoclax specifically antagonizes BCL-2 protein and allows unbound pro-apoptotic proteins to initiate apoptosis. Venetoclax antagonizes BCL-2 and allows pro-apoptotic proteins to initiate apoptosis. Venetoclax with HMA or LDAC received FDA approval in 2020 for the frontline treatment of AML patients unfit for standard chemotherapy. However, therapeutic resistance is common and there is an urgent need to improve the efficacy and durability of venetoclax in this setting. Combinatory drug approaches allow for targeting of multiple molecular drivers/pathogenic mutations, lower therapeutic concentrations, increased efficacy, and overcoming resistance. Here, we aimed to develop novel synergistic drug combinations with venetoclax to improve venetoclax safety, efficacy and overcome resistance in cell lines with potential clinical applications in AML. Venetoclax IC50 values in eight AML cell lines range from <0.01 µM to >5 µM highlighting differential response among the panel. THP-1 cells were identified as the most venetoclax resistant cell line with little response observed at any concentration up to 72 hours exposure. Western blot and qPCR analyses demonstrated BCL-2 is ubiquitously expressed across the cell lines. A single agent drug screen of 1,971 FDA approved compounds was performed at two concentrations (100 nM and 1 µM), in THP-1 cells at three timepoints (24, 48, and 72 hours). 364 of 1971 compounds (18.5%) induced >50% cell death and were identified as hits. A secondary screen was performed to investigate the top 180 most effective compounds in combination with venetoclax. Dose response matrices and cell viability data were used to calculate synergy scores. Combinations with synergy scores of >10 were considered synergistic. Many combinations were synergistic at one timepoint (n=117, 65%), others were synergistic at 2 timepoints (n=45, 25%) and few were synergistic at all 3 timepoints (n=5, 2.78%). Validation experiments are currently ongoing to investigate the synergistic relationship of top candidate combinations and identify an optimum dose for further investigations including additional validation experiments, mechanistic studies, and toxicity studies. Citation Format: Ruairidh Harrigan, Evangeline Johnston, Kyle B Matchett, Tony J Bjourson. High-capacity drug screen identification of novel synergistic drug pairs with venetoclax in acute myeloid leukemia [abstract]. In: Proceedings of the AACR Special Conference: Acute Myeloid Leukemia and Myelodysplastic Syndrome; 2023 Jan 23-25; Austin, TX. Philadelphia (PA): AACR; Blood Cancer Discov 2023;4(3_Suppl):Abstract nr A02.

Abstract A18: STC-15, a novel METTL3 inhibitor, and its combination with Venetoclax confer anti-tumour activity in AML models

Abstract N6-methyladenosine (m6A) is one of the most abundant RNA modifications, which influences mRNA and lncRNA localization, half-life, translation, and splicing. The majority of m6A modifications on cellular mRNAs are deposited by the RNA methyltransferase METTL3. To date, METTL3 has been implicated in the initiation and progression of multiple cancer types, with the highest expression of METTL3 mRNA observed in acute myeloid leukemia (AML). Currently, one line of standard of care therapy for AML patients is Venetoclax, which targets the anti-apoptotic protein BCL2. It was shown that m6A, deposited by METTL3 on BCL2 transcript, affects BCL2 mRNA stability and translation. Storm Therapeutics has developed potent and selective METTL3 inhibitors, including the clinical candidate STC-15. Here, we explore pharmacological inhibition of METTL3 as monotherapy or in combination with Venetoclax in AML models in vitro and in vivo. Sulforhodamine B and CellTiterGloTM assays were used to assess the viability of AML cell lines and patient-derived xenografts (PDXs), respectively, following METTL3 inhibition in vitro. BCL2 protein level was evaluated by Western blotting. SynergyFinder software was used to assess the degree of synergy between METTL3 inhibitors and Venetoclax. Intra-tibial implantation of human-derived AML cells (AML-PDXs) in NSG mice was used to determine single agent and combination therapy efficacy. Multiple AML cells lines and AML-PDXs were sensitive to pharmacological inhibition of METTL3 in vitro, as assessed by loss of viability. Treatment with METTL3 inhibitors led to downregulation of BCL2 protein level in several AML cell lines, as previously suggested by literature. Based on these results, the synergy between METTL3 inhibition and Venetoclax was assessed. Matrix-combination experiments have shown a high degree of synergy between the two drugs (defined by a synergy score >10) in THP-1 and MOLM-13 cell lines. To test METTL3 inhibition as a monotherapy and in combination with Venetoclax in vivo, three AML-PDX studies were initiated. Significantly lower spleen weight was observed in all animals treated with STC-15 or STC-15 + Venetoclax, and reduced number of circulating hCD45+ cells was observed in 2 out of the 3 models. In one of the models, STC-15 monotherapy outperformed Venetoclax (median survival 68 days vs 58 days, respectively), while the combination therapy extended median group survival to 85 days in comparison to 51.5 days in the vehicle group. In conclusion, we demonstrated that METTL3 inhibition results in anti-tumour effects across different AML models. Moreover, we demonstrated a synergistic effect between the novel METTL3 inhibitor STC-15 and Venetoclax, both in vitro and in vivo. These studies provide evidence for the utility of METTL3 inhibitor as a new therapeutic agent to treat AML. Currently, STC-15 is under clinical development (NCT05584111). Citation Format: Lina Vasiliauskaite, Yaara Ofir-Rosenfeld, Mark Albertella, Coralie Hoareau-Aveilla, Jerry McMahon, Oliver Rausch. STC-15, a novel METTL3 inhibitor, and its combination with Venetoclax confer anti-tumour activity in AML models [abstract]. In: Proceedings of the AACR Special Conference: Acute Myeloid Leukemia and Myelodysplastic Syndrome; 2023 Jan 23-25; Austin, TX. Philadelphia (PA): AACR; Blood Cancer Discov 2023;4(3_Suppl):Abstract nr A18.

Synergy between oxaliplatin and adenovirus initiates immunogenic cell death in human colorectal carcinoma cells

Abstract Externalization of Calreticulin (CALR) is the critical first step in the initiation of Immunogenic Cell Death. Since Oxaliplatin (OX) cooperates with an oncolytic chimeric human adenovirus Ad5/3-NP2.ADP (ADP) to induce adaptive immunity as well as regression of established cancer, we sought to determine whether the cooperation was additive or synergistic. Methods include immunohistochemistry (IHC) for Calreticulin expression in mice 11 days after intratumoral injection of the OX-ADP mixture. In vitro assays with limiting dilutions of OX and ADP on human Clone A colorectal carcinoma cell monolayers were cultured for 3 days and cytotoxicity, viral infectivity by GFP, and the expression of externalized CALR (ectoCALR) on Clone A cells measured by static cytometry. Synergy was measured using SynergyFinder 3.0 (Ianevski et al., PMC9252834) that creates 2-D interactive surfaces to measure synergy and antagonism. Areas of synergy have mean scores > 10. IHC revealed strong CALR expression in OX-ADP treated tumors, weak expression in tumors injected with OX or ADP alone and minimal in PBS treated controls. Mean Viral Infectivity synergy score was 27.2 for the area of (Ox μM, ADP MOI): (0.12μM, 4 MOI) to (12.5μM, 100 MOI) while mean synergy score for ectoCALR expression was 29.2 for OX/ADP (0.01μM, 0.16) to (0.12μM, 20 MOI). The role of oxidative and endoplasmic reticulum stress as the basis of synergy is under study. Oxaliplatin and adenovirus are synergistic in their ability to initiate ICD which is important for vaccine development.

Neddylation inhibition sensitises renal medullary carcinoma tumours to platinum chemotherapy.

Renal medullary carcinoma (RMC) is a highly aggressive cancer in need of new therapeutic strategies. The neddylation pathway can protect cells from DNA damage induced by the platinum-based chemotherapy used in RMC. We investigated if neddylation inhibition with pevonedistat will synergistically enhance antitumour effects of platinum-based chemotherapy in RMC. We evaluated the IC50 concentrations of the neddylation-activating enzyme inhibitor pevonedistat in vitro in RMC cell lines. Bliss synergy scores were calculated using growth inhibition assays following treatment with varying concentrations of pevonedistat and carboplatin. Protein expression was assessed by western blot and immunofluorescence assays. The efficacy of pevonedistat alone or in combination with platinum-based chemotherapy was evaluated in vivo in platinum-naïve and platinum-experienced patient-derived xenograft (PDX) models of RMC. The RMC cell lines demonstrated IC50 concentrations of pevonedistat below the maximum tolerated dose in humans. When combined with carboplatin, pevonedistat demonstrated a significant in vitro synergistic effect. Treatment with carboplatin alone increased nuclear ERCC1 levels used to repair the interstrand crosslinks induced by platinum salts. Conversely, the addition of pevonedistat to carboplatin led to p53 upregulation resulting in FANCD2 suppression and reduced nuclear ERCC1 levels. The addition of pevonedistat to platinum-based chemotherapy significantly inhibited tumour growth in both platinum-naïve and platinum-experienced PDX models of RMC (p<.01). Our results suggest that pevonedistat synergises with carboplatin to inhibit RMC cell and tumour growth through inhibition of DNA damage repair. These findings support the development of a clinical trial combining pevonedistat with platinum-based chemotherapy for RMC.

Abstract 1565: Targeting of KIF11 and AURKA to improve outcomes in Ewing sarcoma

Abstract Ewing Sarcoma (EWS) is a rare and aggressive pediatric malignancy of the bone and soft tissues. Despite intensive systemic combination chemotherapy and surgery/radiotherapy for local control, patients with metastatic disease have dismal prognosis (&amp;lt;30% overall survival rate). To identify better therapies for patients with refractory, recurrent and metastatic disease, we previously conducted in silico and drug re-purposing screens (PMID: 27863422; 31025088) that identified proteins essential for mitotic spindle formation and cell cycle progression such as Aurora Kinase A (AURKA), Kinesin Family Member 11 (KIF11), Kinesin Family Member 15 (KIF15) and its binding partner; targeting protein for Xklp2 (TPX2) that are upregulated by EWS-FLI1, the primary oncogenic driver of EWS, indicating their potential as therapeutic targets. KIF11 and KIF15 are mitotic motor kinesins essential for bipolar spindle formation, whereas AURKA is a mitotic kinase essential for centrosome maturation and mitotic spindle assembly. Though KIF11 and AURKA inhibitors have been extensively used in clinical trials before but have not been tested together in combination for any type of cancer. We hypothesized that targeting these two key proteins essential for mitotic progression provides a therapeutic vulnerability for Ewing Sarcoma by inducing G2/M arrest and mitotic catastrophe. Specific KIF11 (SB-743921) and AURKA (VIC-1911, VITRAC Therapeutics) inhibitors were used for targeting these proteins. We evaluated the in vitro activity of VIC-1911 and SB-743921 and synergy was measured by percentage inhibition of growth via SynergyFinder, that employs reference models (Bliss) to score synergy (scores &amp;gt;10 is synergistic). EWS showed strong synergistic interaction at physiologically relevant doses compared to control cell lines (e.g., mesenchymal stem cells and non-EWS tumor cells). This drug combination was effective in refractory EWS cells established post-chemotherapy (synergy score &amp;gt;24) and at much lower doses in cells established from pre-treatment tumor tissue (synergy score &amp;gt;27) indicating effectiveness at various clinical stages of EWS disease. Importantly, this therapy appeared preferential to EWS cells with an EWS-ETS fusion as compared to non-EWS cells. We observed zero colony formation in vitro with the combination treatment and increased percentage accumulation of cells in G2/M phase upon cell-cycle analysis indicating mitotic arrest. In vivo studies in EWS xenograft mouse models showed sustained tumor regression (NED at 30 days after ending therapy). The combination arm showed significant survival versus control (p≤ 0.001, HR=0.42, 95% CI=0.14-1.25), VIC-1911 (p≤ 0.001, HR=0.48, 95% CI=0.16-1.42) or SB-743921 (p ≤ 0.01, p≤ HR=0.71, 95% CI=0.21-2.34) alone. Efforts are underway to translate these preclinical studies into an early phase clinical trial of patients with histologically proven EWS who have failed standard of care therapy. Citation Format: Soumya M. Turaga, Vikalp Vishwakarma, Stacey Hembruff, Rajni Puri, Priya Sabu, Glenson Samuel, Andrew K. Godwin. Targeting of KIF11 and AURKA to improve outcomes in Ewing sarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1565.

Abstract 4278: Transcriptome-driven combination design: A computational approach

Abstract While rational drug combination design seeks to improve patient outcomes by leveraging biological synergy, outcomes from combination trials often fail. Only 12.4% of phase 1 trials eventually achieve regulatory approval. In vitro evidence has provided the rationale for the drug combinations in 36.6% of phase 1 combination trials, but none of those trials progressed past phase 3 (from a study by Paller CJ et al., 2019). A review of DrugCombDB, a publicly available database of experimental synergy results, supports the idea that such outcomes are mirrored in preclinical data. Analysis of the similarity of synergy scores within indication-specific subsets of cell lines from data in a 2022 paper by Douglass, et al. show that in both breast and lung cancer, combinations predicted to be synergistic in at least one cell line from that indication failed to be synergistic in the majority of indication cell lines more than half of the time. SHEPHERD’s Gene Cluster Voting Algorithm (GCVA) was adapted to improve upon current drug combination design and anticipate transcriptome changes as the result of drug treatment. GCVA relates drug sensitivity to the transcriptome by calculating a list of biomarkers that contribute to sensitivity and resistance for specific drugs, enabling the prediction of drug sensitivity on patient transcriptomic data captured via bulk RNAseq. Via this method, 15,137 publically available synergy data points in the Douglass paper were compared to predictions by our computational approach. For all synergy metrics contained within the dataset (ZIP, Bliss, Loewe, and HSA), the synergistic predictions made by application of GCVA have significantly higher synergy scores compared to the antagonistic predictions made by GCVA (p &amp;lt; .001). These test results support the potential for the application of GCVA to intelligent combination design with the ultimate goal of deployment on a patient-by-patient basis.In addition, analysis of GCVA’s drug efficacy predictions for the cell line DU145 showed that treatment with 9 kinase inhibitors consistently potentiated the predicted efficacy of between 5 and 11 additional drugs. Dasatinib, temsirolimus, and cabozantinib were newly predicted effective after treatment with each and every kinase inhibitor. This data suggests an avenue for the design of intelligent drug combinations based on anticipated transcriptomic changes that may improve on existing synergy prediction methods. Citation Format: Christina Gavazzi, Mikhail G. Grushko, Jeremy M. Goldstein, Mahta Samizadeh, Zakary Y. ElSeht, Katherine Arline. Transcriptome-driven combination design: A computational approach. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4278.

Abstract 5019: Next-generation DYRK1A inhibitors as a new therapeutic approach for the treatment of hematological malignancies

Abstract Background: The dual-specificity tyrosine-regulated kinase 1A (DYRK1A) can phosphorylate multiple targets involved in key cellular processes that have been associated with the hallmarks of cancer, including proliferation, survival, cell cycle regulation and the DNA damage response1. In addition, compounds that inhibit DYRK1A have demonstrated anti-tumor activity both in vitro and in vivo. However, until recently, there was a paucity of potent, specific, and bioavailable DYRK1A inhibitors that did not target the related cdc2-like kinases (CLKs) and glycogen synthase kinase 3β. In this study, we describe a set of next-generation DYRK1A inhibitors and used them to evaluate the specific contribution of DYRK1A activity to tumor biology and evaluate the therapeutic potential of DYRK1A inhibition in cancer. Methods: DYRK1A expression was analyzed in The Cancer Genome Atlas and Cancer Cell Line Encyclopedia databases. Cancer cell growth dependencies were evaluated by DepMap analysis. Cell-based target engagement (TE) was assessed by NanoBRETTM. Cell viability was assayed with CellTiter-Glo® following 4-day treatment with DYRK1A inhibitors. Synergy was calculated using Chalice software. Pharmacokinetics (PK) were evaluated in rodents and Tumor Growth Inhibition (TGI) in nude mice. Preliminary toxicology was assessed in a 14 day rat study. Results: DYRK1A expression and a systematic DYRK dependencies analysis in human cancers revealed that hematological malignancies, Small Cell Lung and Ovarian cancers rely on DYRK1A expression for their proliferation. A series of potent (biochemical IC50s 3nM to 10nM, TE 19 nM to 134 nM) and highly selective ATP-competitive DYRK1A inhibitors were designed with minimal inhibition of the rest of the kinome (1%-2.3% of kinases inhibited &amp;gt; 90%) Cancer cell lines (n=160) were treated with DYRK1A inhibitors and those belonging to hematological lineages were among the most sensitive (P&amp;lt;0.01). In vitro combination of DYRK1A inhibitors with the anti-leukemia agent venetoclax revealed high synergy in 3 out of the 5 AML cell lines tested (synergy score &amp;gt;20). Compounds that showed good oral bioavailability and plasma exposures in rodents were selected for further characterization in vivo. In the MV-4-11 xenograft model, mice treated daily with 25mg/kg, or 50mg/kg of 2 different DYRK1A showed 72-99% TGI compared to vehicle. Preclinical toxicity profile in rats showed next generation DYRK1A inhibitors were well tolerated. Concluding Remarks: these studies support further evaluation of DYRK1A inhibitors as a therapeutic strategy for some cancers, especially hematological malignancies including AML. 1 Boni, J.; Rubio-Perez, C.; López-Bigas, N.; Fillat, C.; de la Luna, S. The DYRK Family of Kinases in Cancer: Molecular Functions and Therapeutic Opportunities. Cancers 2020, 12, 2106. https://doi.org/10.3390/cancers12082106 Citation Format: Matthew C. Jarvis, Gopi Mittapalli, Emily Creger, Chelsea Nora, Maureen Ibanez, Deepti Bhat, Brian Hofilena, Josh Stewart, Elizabeth A. McMillan, Hadi Falahatpisheh, Chi-Ching Mak, Michael White, John S. Hill, Carine Bossard. Next-generation DYRK1A inhibitors as a new therapeutic approach for the treatment of hematological malignancies. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5019.

Abstract 3183: Combination of anti-EGFR antibody cetuximab with NKX101, an allogeneic NKG2D-L targeting NK cell therapy, enhances potency and in vitro cytotoxicity against solid tumors

Abstract Background: Antibody-dependent cellular cytotoxicity (ADCC) is a mechanism of cell-mediated immune defense against opsonized target cells wherein the Fc-fragment of an antibody binds to the CD16 Fc receptor (FcγRIIIa) on NK cells, triggering NK cell activation and targeted killing. Cetuximab is a human IgG1 antibody targeting epidermal growth factor receptor (EGFR) that is approved for the treatment of colorectal and head and neck cancers. Binding of cetuximab to EGRF+ cell lines has been shown to trigger ADCC mediated by NK cells. NKX101 is an investigational allogeneic NK cell therapy in development for the treatment of cancer. NKX101 is engineered to express an NKG2D-based chimeric antigen receptor (CAR) and membrane-bound IL-15. To investigate the combination of NKX101 and cetuximab, we developed in vitro assays to (i) demonstrate enhanced activity against cancer cells via CD16-mediated ADCC activity, (ii) compare ADCC activity of NKX101 cells generated from high-affinity CD16 and low-affinity CD16 donors, and (iii) evaluate the synergistic interaction between NKX101 and cetuximab. Methods: NKX101 cells were generated from peripheral blood leukopaks from healthy donors. NucRed-labeled EGFR+ NKG2D-L+ human cancer cell lines were pre-incubated with cetuximab or isotype control and co-cultured with NKX101. Specific cell killing of target cells was measured using an Incucyte instrument. For synergy assessments, a dose response matrix of NKX101 cells and cetuximab was used to generate cytotoxicity values. Synergy scores for combinations were determined using the Synergy Finder Plus web application. To determine donor CD16 V/F 158 genotypes, genomic DNA was isolated from each donor and assayed using a TaqMan CD16 genotyping kit. Results: We demonstrate that cetuximab increases the anti-tumor effect of NKX101 in a dose-dependent manner. Assessment of the interaction between NKX101 and cetuximab in vitro revealed that the two agents can combine to kill cancer cells in a synergistic manner. Blocking CD16 on NKX101 cells with a neutralizing antibody significantly decreased potency of the combination, suggesting that the improvement in potency observed is a direct result of CD16-mediated ADCC activity. To determine if common CD16 polymorphisms influence NKX101 ADCC activity, we compared NKX101 cells generated from CD16 158 V/V, V/F, and F/F donors. No significant differences in potency were observed with NKX101 cells expressing the high affinity CD16 158 V/V genotype compared with those derived from CD16 lower affinity 158 V/F or 158 F/F donors. In summary, we show that the combination of an engineered allogeneic NK cell therapy, NKX101, with cetuximab leads to an increase in the specific killing of cancer cells in vitro, supporting further investigation into this combination for the treatment of solid tumors. Citation Format: Cynthia Cho, Kyle Hansen, Max Zhang, Carmel Chan, James Trager. Combination of anti-EGFR antibody cetuximab with NKX101, an allogeneic NKG2D-L targeting NK cell therapy, enhances potency and in vitro cytotoxicity against solid tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3183.

Abstract 412: Drug combination screen identifies pemigatinib, an FGFR inhibitor, as a mechanism to overcome KRASG12C inhibitor resistance in lung cancer

Abstract Background: Lung cancer is one of the most common tumors, accounting for approximately 1.8 million deaths worldwide in 2020. KRAS is a frequently mutated oncogene, with mutations reported in roughly 20-25% of non-small cell lung cancer cases. Specifically, KRAS mutations at amino acid 12, resulting in a glycine to cysteine (G12C) substitution, occur in approximately 13% and 3% of lung and colon cancers, respectively, and less frequently in other solid tumors. Recently, the development of covalent KRASG12C inhibitors has shown meaningful anticancer activity in patients. However, many patients with KRASG12C do not respond and/or develop resistance to single-agent treatment. Here we investigate combination therapies that may overcome resistance and broaden patient response to KRASG12C inhibitors. Methods: In vitro preclinical KRASG12C models including lung and colon cancer cell lines were treated with a panel of small molecule and covalent KRASG12C inhibitors. The activity of single-agent versus combination treatments was measured in cell viability assays, and screen hits were validated by in vitro mechanism of action studies. Results: A curated set of 152 compounds was used in combination with screen monitoring cell-viability assays across 12 KRAS mutant lung and colon cancer cell lines. Compounds tested included kinase inhibitors targeting oncogenic signaling pathways, epigenetics modifiers, regulators of apoptosis, chemotherapeutics, and other anticancer agents. The screen identified synergy between covalent KRASG12C and several other inhibitors including those for FGFR, EGFR, and SHP2. Notably, pemigatinib, a potent and selective FGFR1-3 inhibitor, had a significantly high Bliss synergy score. Selectivity and siRNA knockdown experiments were performed to identify the specific FGFR isoform involved in synergistic anticancer activity. Inhibition of FGFR1 activity was shown to be essential, whereas an FGFR2-3 specific inhibitor demonstrated only modest activity in combination with KRASG12C inhibitors. Additionally, FGFR1 knockdown combined with KRASG12C inhibition resulted in increased drug sensitivity; in contrast, knockdown of other FGFR family members did not demonstrate similar increase in sensitivity to KRASG12C inhibition. Conclusions: Cell-viability combination screening identified strong synergy between KRASG12C covalent inhibitors and the FGFR1-3 inhibitor pemigatinib in KRASG12C cancer cell lines. The synergistic effect of pemigatinib and KRASG12C inhibition was notably strongest in mesenchymal cancer cell lines. This effect was further validated in in vitro selectivity and siRNA studies. Together, our results support pemigatinib as a promising agent for combination therapy with KRAS inhibitors in lung cancer. Citation Format: Angela Abdollahi, Margaret Favata, Darlise DiMatteo, Sean Schuette, Erika Boarder, Mark Rupar, Ricardo Macarron, Aidan Gilmartin, Hui Wang, Alejandro Amador-Arjona. Drug combination screen identifies pemigatinib, an FGFR inhibitor, as a mechanism to overcome KRASG12C inhibitor resistance in lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 412.

Abstract 674: CRISPR and drug screens identify ERK as the mediator of IFNg-induced melanoma growth inhibition

Abstract Interferon-gamma (IFNg) is critical for the success of immune checkpoint blockade therapy. Disruption of IFNg signaling makes tumors resistant to anti-PD-1/L1 treatment primarily by evasion of the growth inhibition (GI) induced by this cytokine. However, the pathways mediating IFNg-induced GI are largely unknown. We used two independent approaches to delineate the IFNg GI pathway, a chemical genomics screen and a whole genome targeting CRISPR/Cas9 screen in an IFNg GI-sensitive patient-derived melanoma (PDM) cell line. Drug screening revealed that treatment with RAF and ERK inhibitors disrupted IFNg GI in PDM cells. For the CRISPR screen, gene-level analysis showed that the magnitude of enrichment for guide RNAs targeting ERK2 in IFNg-treated cells was comparable to proximal IFNg signaling proteins like JAK1, STAT1, IFNGR2, and JAK2 (&amp;gt;26-fold enrichment for ERK2, p = 2.28e-07). Thus, results from both these experiments converged upon ERK as the primary downstream target of IFNg essential for GI induction. We validated the involvement of ERK by detecting a sustained increase in phospho-ERK1/2 levels following IFNg treatment. In live imaging experiments, we found that blocking ERK activity with the ERK inhibitor Ulixertinib blocks the induction of cell death after IFNg treatment in 17 of 23 (~74%) IFNg-sensitive PDM lines covering all the MAPK mutant and triple wildtype molecular subtypes of melanoma. Decreasing and increasing ERK activity levels using shRNA and overexpression approaches also led to a decrease and increase in IFNg-mediated GI, respectively. We have identified NOXA and DR5 as likely mediators of cell death through the IFNg-ERK GI pathway by comparing gene expression profiles of control and IFNg-treated PDM cells. Finally, phorbol 12-myristate 13-acetate (PMA), a known ERK activator, synergizes with IFNg treatment to induce increased GI in PDM cells (Bliss synergy score 16.87, p = 1.83e-123). In summary, the IFNg-ERK signaling axis mediates cell death downstream of IFNg treatment in melanoma cells. This pathway is active in all melanoma subtypes, making it an attractive target to enhance IFNg GI in tumor cells. Our results provide a new understanding of the IFNg GI pathway that will also be crucial to define mechanisms of GI resistance in tumor cells. Citation Format: Ameya S. Champhekar, Rachel Heymans, Cynthia Gonzalez, Guillem Turon Font, Daniel Karin, June Lee, Robert Damoiseaux, Antoni Ribas. CRISPR and drug screens identify ERK as the mediator of IFNg-induced melanoma growth inhibition [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 674.

Abstract 3858: Exploring Exportin-1 as a therapeutic vulnerability in squamous cell carcinoma

Abstract Introduction: Squamous cell carcinomas (LUSCs) account for 25-30% cases of non-small cell lung cancers, making them the second most common histology of lung cancer after adenocarcinomas. For the latter, molecular characterization has defined tumor subsets with discrete driver alterations sensitive to targeted inhibitors, leading to significant improvement in patient survival. However, for LUSCs, to date no specific drivers have been described that are amenable for pharmacological targeting and no targeted therapies are approved for use in this setting. Despite decades of research, LUSCs are still treated with cytotoxic chemotherapy, and now concomitant immunotherapy, which does not achieve durable responses in most patients. Thus, identification of targetable vulnerabilities in this setting remains a critical unmet clinical need. Preliminary data from our lab has identified the nuclear exporter exportin 1 as a therapeutic vulnerability in small cell lung carcinomas. Exportin 1 (XPO1) inhibition with Selinexor, a drug approved for clinical use in the setting of hematological malignancies, induces significant sensitivity in combination with cisplatin and irinotecan. Here, we explored the role of XPO1 as a therapeutic target in LUSC. Methods: We performed a comprehensive multi-omic molecular characterization of a library of LUSC patient-derived xenografts (PDXs) (N=28, with 17 clinical samples being matched pairs). IHC, RNA-seq and NGS via MSK-IMPACT were performed on 27 samples. To examine the potential of XPO1 inhibition as sensitizer to chemotherapy in LUSC, we performed genetic and pharmacological inhibition experiments in LUSC cell lines exhibiting high XPO1 expression. Results: Of the 28 models, 19 samples (68%) were from primary tumors and 9 samples (32%) from metastasis. The sample set were roughly split in half with regard to treatment status; 15 samples (54%) were treatment naïve and 13 sample were treated (46%).XPO1 is highly expressed in LUSCs clinical specimens compared to other tumor types, and its knockdown reduces tumorigenic features of LUSC cell lines with high XPO1 expression, including proliferation and anchorage-independent growth. Targeted XPO1 inhibition with selinexor induces chemotherapy sensitization to carboplatin and paclitaxel, drugs currently used in the treatment of LUSC, as depicted by high cytotoxic synergy scores of selinexor with either drug. Conclusion: Our data suggest that XPO1 expression may exert pro-oncogenic effects in LUSC, consistent with its upregulation in this tumor setting, and that its inhibition with selinexor may strongly sensitize to chemotherapy. Assessment of efficacy of combination therapies with selinexor in vivo will assess the potential of these combinations as a therapeutic approach for LUSC tumors. The clinical availability of selinexor would allow immediate clinical translation of the results generated in this project. Citation Format: Vidushi Durani, Rebecca Caeser, Charles M. Rudin, Alvaro Quintanal-Villalonga, Harsha Sridhar, Parvathy Manoj, Sam E. Tischfield, Marina Asher, Umeshkumar Bhanot, Jacklynn V. Egger, Nicholas D. Socci D. Socci, Nisargbhai S S. Shah, Elisa de Stanchina, Natasha Rekhtman. Exploring Exportin-1 as a therapeutic vulnerability in squamous cell carcinoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3858.

Abstract 6720: Using proteasome inhibition to hyperactivate the integrated stress response in aggressive pediatric brain tumors

Abstract H3K27-altered diffuse midline glioma (DMG) and atypical teratoid/rhabdoid tumor (AT/RT) are aggressive pediatric brain tumors with dismal outcomes. DMG and AT/RT have increased baseline activation of the integrated stress response (ISR), an evolutionarily conserved system that enables cells to tolerate various forms of stress. This activation is manifested by elevated levels of ATF4 and NRF2 in DMG and AT/RT, respectively. Transient or low-level expression of these transcription factors protect cells from stress, while sustained, high-level activation leads to cell death. Ixazomib is an orally bioavailable proteasome inhibitor that causes endoplasmic reticulum stress, which is a major upstream activator of the ISR. We hypothesized that the high baseline level of ATF4 in DMG and NRF2 in AT/RT would make these tumors susceptible to ISR activators such as ixazomib. After determining the IC50 of ixazomib, DMG and AT/RT cell lines (JHH-DIPG1, JHH-DIPG16A, and CHLA06) were treated with increasing concentrations of the drug. Cleaved caspase 3 immunofluorescence showed a significant increase of apoptosis in all cell lines (JHH-DIPG16A and CHLA06 p&amp;lt;0.0001, JHH-DIPG1 p=0.0008 by ANOVA). Additionally, western blots for cleaved PARP and phospho-Rb expression detected induction of apoptosis and suppression of cell proliferation in JHH-DIPG1 treated with ixazomib. We are currently testing ixazomib in combination with idarubicin, a brain-penetrant anthracycline, and gemcitabine, a brain-penetrant nucleoside analog. Synergy testing in CHLA06 showed an overall zero-interaction-potency (ZIP) synergy score of 23.464 with inhibitory concentrations of ixazomib and idarubicin in the low nanomolar range (scores of 10 or above indicate synergy). Similarly, ixazomib and gemcitabine synergized to suppress CHLA06 growth and induce apoptosis (67% Annexin V+ cells in combination compared to 14 and 24% Annexin V+ with single agent treatment). In the future, we will determine if ixazomib selectively kills DMG and AT/RT while sparing normal cells in iPSC brain organoids. We will also test ixazomib singly and in combination with traditional chemotherapy in orthotopic xenografts of AT/RT. These results suggest that ixazomib, especially in combination with idarubicin, gemcitabine or other ISR activators, has the potential to serve as an effective therapy for aggressive pediatric brain tumors. Citation Format: Orlandi Valencia Novak, Tyler Findlay, Jeffrey Rubens, Charles Eberhart, Eric H. Raabe. Using proteasome inhibition to hyperactivate the integrated stress response in aggressive pediatric brain tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6720.

Abstract 530: Preclinical evaluation of avutometinib (VS-6766; RAF/MEK clamp) in combination with EGFR inhibition in colorectal cancer patient-derived xenograft (PDX) models harboring KRAS mutations

Abstract Background KRAS mutation (mt) occurs in ~43% of patients with colorectal cancer (CRC) with KRAS G12D, G12V and G13D being most prevalent. Avutometinib (avuto, VS-6766) is a unique RAF/MEK clamp that inhibits MEK kinase activity and induces dominant negative RAF/MEK complexes preventing the re-activation of MEK by RAF. Preclinically, avuto inhibited proliferation of KRAS mt CRC cell lines. Clinically, avuto monotherapy produced clinical responses in gynecological cancers and KRAS mt non-small cell lung cancer. Methods 3D proliferation assays were used to quantify synergy between avuto and agents targeting other nodes in the MAPK pathway or parallel signaling pathways. We evaluated the antitumor effects of avuto alone or in combination with panitumumab in CRC PDX models with KRASG12V, concurrent KRASG12V and PIK3CA, or KRASG12D mutations. Mice bearing PDX tumors were randomized into groups of 6 mice treated with avuto alone or in combination with panitumumab for 21 days with tumor volume measured twice weekly. Results In 3D proliferation assays with a panel of KRAS mt CRC cell lines (including G12D, G12V and G13D mutations), the EGFR/ErbB family inhibitor afatinib showed the strongest synergy score with avuto relative to inhibitors of SHP2, ERK1/2, mTOR or CDK4/6. Based on the synergy of avuto with afatinib, the combination of avuto with the anti-EGFR antibody panitumumab was tested in KRAS mt CRC PDX models. In a KRASG12V PDX model, tumor regression (11%) was seen in 1/6 mice treated with avuto alone. No tumor regression was seen in mice treated with panitumumab monotherapy. The combination of avuto and panitumumab led to significant tumor regression (&amp;gt;40%) in 5/6 mice following 21 days of treatment. In a KRASG12V PDX model with concurrent PIK3CA mutations, no tumor regression was seen in mice treated with either avuto or panitumumab alone. The combination of avuto and panitumumab led to initial tumor stabilization followed by tumor growth in 3/6 mice. In a KRASG12D PDX model, tumor regression (17%) was seen in 1/6 mice treated with avuto and 0/6 with panitumumab. Tumor regression (13% and 18%) was noted in 2/6 mice treated with the combination of avuto and panitumumab. Conclusion In KRAS mt CRC cell lines, strong synergy was observed between avuto and afatinib. In KRAS mt CRC PDX models in vivo, avuto monotherapy showed tumor growth inhibition but limited tumor regression, and panitmumab monotherapy failed to show tumor regressions. The combination of avuto and panitumumab showed significant anti-tumor activity in a CRC PDX model harboring KRASG12V with less tumor regression observed in a KRASG12D PDX model or in a KRASG12V PDX model with concurrent PIK3CA mutation. These results support the ongoing clinical evaluation of avutometinib in combination with the anti-EGFR antibody cetuximab for treatment of KRAS mt CRC (NCT05200442). Citation Format: Chongkai Wang, Silvia Coma, Jonathan Pachter, Marwan Fakih. Preclinical evaluation of avutometinib (VS-6766; RAF/MEK clamp) in combination with EGFR inhibition in colorectal cancer patient-derived xenograft (PDX) models harboring KRAS mutations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 530.

Abstract 5509: The PI3K inhibitor Paxalisib combines synergistically with the MEK inhibitor Mirdametinib to target atypical teratoid/rhabdoid tumors

Abstract Atypical teratoid/rhabdoid tumors (AT/RT) are aggressive pediatric brain tumors and the most common malignant brain tumors of infancy. The four-year event-free survival rate is only 37%. For patients with relapsed AT/RT there are limited treatment options, but precision therapies may help improve survival for patients with this deadly disease. We have previously identified strong activation of the PI3K-AKT-mTOR (mTOR) signaling pathways in AT/RT. Paxalisib is a highly brain-penetrant PI3K inhibitor acting upstream of mTOR. We find that Paxalisib slows tumor growth in orthotopic xenograft models of AT/RT and extends median survival from 40 to 54 days (p=0.001, log-rank test). RNASeq after mTOR pathway inhibition identifies reflexive activation of the RAS-RAF-MEK-ERK (MAPK) pathway as a possible mechanism of therapy resistance (KEGG pathway analysis). The RAS-RAF-MEK-ERK (MAPK) pathway plays a pivotal role in regulating cell growth and survival and activation of the pathway contributes to the aggressive growth of numerous cancers. Mirdametinib is a small, allosteric MEK inhibitor currently used in clinical trials for both pediatric low- and high-grade gliomas (PD0325901). We find that dual inhibition of both the mTOR and MAPK pathways by Paxalisib and Mirdametinib synergize to reduce AT/RT growth and viability (Bliss synergy score 16.77). Paxalisib also combines with Mirdametinib to induce high levels of apoptosis and cell senescence (as determined by western blot: cPARP, pRB, P21, P16). Naïve treatments in mice bearing AT/RT orthotopic tumors suggests the combination therapy decrease mTOR and MAPK pathway activation (as determined by western blot). These data support the use of Paxalisib and Mirdametinib combination therapy as a promising novel combination therapy to treat relapsed AT/RT. Citation Format: Kristen J. Malebranche, Tyler Findlay, Anupa Geethadevi, Charles Eberhart, Eric Raabe, Jeffrey Rubens. The PI3K inhibitor Paxalisib combines synergistically with the MEK inhibitor Mirdametinib to target atypical teratoid/rhabdoid tumors. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5509.