Abstract 6657: Phase I trial of first-in-class anti-PVR mAb NTX1088: Restoration of DNAM1 expression as MOA for enhanced antitumor immunity

NTX1088, a first-in-class anti-PVR (CD155) monoclonal antibody (mAb), is currently evaluated in a Phase 1, open-label, multi-center study (NCT05378425), initiated at MD Anderson Cancer center. Study objectives are safety, dose-finding, and efficacy with focus on pharmacokinetics, pharmacodynamics, and biomarker discovery. NTX1088 will be investigated as a single agent and combined with the anti-PD1 mAb, pembrolizumab (Keytruda) in patients with locally advanced and metastatic solid malignancies. NTX1088 is a humanized, IgG4-S228P mAb that binds PVR with sub-nM affinity and blocks all known interacting receptors with a single nM EC50. PVR, is a membranal protein, highly upregulated on tumor cells, across multiple cancer types. PVR expression has been associated with worse patient outcomes, due to its role in immune suppression. PVR’s impact on immune cells is mediated through interaction with the key stimulatory receptor, DNAM1 (CD226), on T and NK cells, leading to internalization and degradation of DNAM1. Additionally, PVR is the ligand for the inhibitory immune checkpoint receptors, TIGIT, CD96 and KIR2DL5A. Blocking PVR by NTX1088, therefore, has a multi-faceted immune-stimulating role, through restoration of DNAM1 expression and its immune activation function, while simultaneously neutralizing TIGIT, CD96 and KIR2DL5A inhibitory signals in immune cells. Importantly, DNAM1 downmodulation was recently identified as a key resistance mechanism to approved immune checkpoint inhibitors (ICIs), and its restoration by NTX1088 is a novel MoA, not demonstrated by other therapies. In vitro, as a monotherapy, NTX1088 significantly increased immune cell activation, and was superior to TIGIT, CD112R, and PD1 antibody blockade, leading to greater immune-mediated tumor cell killing, IFNγ secretion, and CD137 induction. Importantly, only NTX1088 was able to restore DNAM1 to the surface of immune cells in all experimental settings. Synergy was observed when NTX1088 was combined with PD1 blockers, or with the anti-CD112R mAb, NTX2R13, in line with the restoration of DNAM1 expression. Numerous humanized murine xenograft models were investigated. NTX1088 exhibited robust tumor growth inhibition as a standalone and in combination with PD1 blockade. Syngeneic models of PVRK.O resulted in complete immune-mediated tumor regression, including hard to treat colorectal tumors. In conclusion, PVR blockade by NTX1088 has a remarkable pre-clinical efficacy, suggesting a potential clinical breakthrough, based on the ability of simultaneously overcome multiple tumor escape mechanisms. First-in-human (FIH) trial is currently ongoing and biomarker data is analyzed to assess clinical impact of the drug and prepare for patient stratification.

Citation Format: Anas Atieh, Akram Obiedat, Alon Vitenshtein, Guy Cinamon, Keren Paz, Tihana lenac, Paola Kucan, Marija Mazor, Ofer Mandelboim, Stipan Jonji, Pini Tsukerman. Phase I trial of first-in-class anti-PVR mAb NTX1088: Restoration of DNAM1 expression as MOA for enhanced antitumor immunity [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 6657.

Abstract 5534: NTX-1088, a first-in-class anti-PVR mAb mediates DNAM1-dependent antitumor immunity

Poliovirus receptor (PVR, CD155), expressed on the surface of cancer cells, represents a resistance mechanism to approved immune checkpoint inhibitors (ICIs). It is a key regulator of immune activation, that modifies function through multiple mechanisms. Increased PVR expression levels have been associated with resistance to anti-PD-(L)1 therapy, while loss of PVR led to reduced tumor growth. Targeting PVR using mAbs offers an intriguing therapeutic approach for patients with advanced cancers, who are not responding to other ICIs.NTX-1088 is a potent, first-in-class, anti-PVR mAb, developed for the treatment of patients with locally advanced and metastatic solid tumors. The antibody binds PVR with high affinity, blocks its interactions with TIGIT and CD96, and preventing their inhibitory signaling. Moreover, NTX-1088 block the critical interaction between PVR and DNAM1 (CD226). This blockade prevents internalization of DNAM1, restores its expression on the surface of immune cells and results in a robust antitumor activity.NTX-1088 was thoroughly investigated in vitro and in vivo. Various cancer cell lines were co-cultured with immune effector cells from healthy human donors, in the presence of NTX-1088, alone and in combination with anti-PD-1 mAb (pembrolizumab). NTX-1088 significantly increased immune cell activation, as measured by IFN-gamma release from activated polyclonal CD8+ T cells, induction of CD137 and killing of tumor cells. When tested in combination with pembrolizumab, NTX-1088 further improved all measured activation parameters. Synergistic effect was obtained when NTX-1088 was combined with the anti-CD112R mAb, NTX-2R13. The effect surpassed that of TIGIT and CD112R combined inhibition. When compared to anti-TIGIT mAb (tiragolumab), NTX-1088 demonstrated clear superiority in activating T and NK cells as a single agent. Furthermore, NTX-1088 in combination with pembrolizumab, was superior to the combination of pembrolizumab with tiragolumab. Importantly, NTX-1088 was the only intervention that significantly restored DNAM1 levels, leading to an enhanced antitumor immune surveillance. Numerous humanized murine models, including pembrolizumab-insensitive models, confirmed the above observations; NTX-1088 exhibited a robust tumor growth inhibition, accompanied by significantly higher prevalence of CD137+, DNAM1+, CD8+ T cells within the tumor bed, compared to mice treated by other ICIs. This is the first report of drug-induced DNAM1 restoration and immune activation. NTX-1088 shows, for the first time, exclusive triple mechanism of action, whereby simultaneous and effective blockade of TIGIT and CD96 is complemented by the efficient restoration of DNAM1. This is a step change in antitumor immune activation that provides a remarkable and differentiated addition to the armamentarium available to patients and their treating oncologists. An IND will be open during 2Q2022.

Citation Format: Akram Obiedat, Anas Atieh, Guy Cinamon, Keren Paz, Paola Kucan Brilc, Lea Hirsl, Tihana Lenac Roviš, Ofer Mandelboim, Stipan Jonjic, Pini Tsukerman. NTX-1088, a first-in-class anti-PVR mAb mediates DNAM1-dependent antitumor immunity [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 5534.

Abstract P075: NTX-1088, a potent first-in-class, anti-PVR mAb, restores expression and function of DNAM1 for optimal DNAM1-mediated antitumor immunity

The poliovirus receptor (PVR, CD155) represents a resistance mechanism to approved immune checkpoint inhibitors (ICIs). It is a key regulator of immune activation, that modifies immune function through multiple mechanisms. Increased levels of PVR expression on tumor cells have been associated with resistance to anti-PD-(L)1 therapy in clinical settings, while loss of PVR led to reduced tumor growth in multiple pre-clinical models. Targeting PVR using blocking mAbs offers an attractive therapeutic approach for patients with advanced cancer. NTX-1088 is a first-in-class, potent, anti-PVR mAb being developed for the treatment of solid tumors. The antibody binds to PVR with high affinity, blocks its interactions with TIGIT and CD96, and thus interrupt their immunosuppressive signaling. However, NTX-1088 forte is manifested through its ability to block the critical interaction between PVR and the costimulatory receptor DNAM1 (CD226). This blockade prevents internalization of DNAM1, restores its expression on the surface of immune cells and results in a robust antitumor activation. NTX-1088 was tested using several tumor and immune cell co-culture systems. Various cancer cell lines were co-incubated with relevant immune effector cells from healthy human donors, in the presence of NTX-1088, as a single agent and in combination with anti-PD-1 mAb (pembrolizumab). NTX-1088 significantly increased immune cell activation, as measured by IFNg release from activated polyclonal CD8+ T cells, induction of CD137 and killing of tumor cells. When tested in combination with pembrolizumab, NTX-1088 further increased all measured activation parameters, suggesting a potential synergistic effect. When compared to anti-TIGIT mAb (tiragolumab), NTX-1088 demonstrated clear superiority in its ability to activate T and NK cells. Furthermore, NTX-1088 in combination with pembrolizumab was significantly superior to the combination of pembrolizumab with anti-TIGIT mAb. Interestingly, NTX-1088 as a single agent showed a comparable effect to that of the combined blockade of TIGIT and CD112R, and further synergized with anti-CD112R for maximal activity. NTX-1088 was the only intervention that significantly restored DNAM1 levels, whereas blockade of DNAM1 reduced the activity of NTX-1088 to levels comparable to that of anti-TIGIT mAb. Humanized murine models confirmed the above observations; NTX-1088 exhibited strong efficacy, inducing a robust tumor growth inhibition, accompanied by significantly higher prevalence of CD137+, DNAM1+, CD8+ tumor infiltrating cells, compared to control treated mice. This is the first report of drug-induced DNAM1 restoration and immune activation. NTX-1088 shows, for the first time, exclusive triple mechanism of action, whereby simultaneous and effective blockade of TIGIT and CD96 is complemented by the efficient restoration of DNAM1. This is a step change in antitumor immune activation, which will soon be tested in the clinic.

Citation Format: Pini Tsukerman, Anas Atieh, Akram Obeidat, Keren Paz, Guy Cinamon, Tihana Lenac Rovis, Paola Kucan Brlic, Lea Hirsl, Stipan Jonjić, Ofer Mandelboim. NTX-1088, a potent first-in-class, anti-PVR mAb, restores expression and function of DNAM1 for optimal DNAM1-mediated antitumor immunity [abstract]. In: Abstracts: AACR Virtual Special Conference: Tumor Immunology and Immunotherapy; 2021 Oct 5-6. Philadelphia (PA): AACR; Cancer Immunol Res 2022;10(1 Suppl):Abstract nr P075.

Abstract P102: NTX-1088, A potent first-in-class, anti-PVR mAb, restores expression and function of DNAM1 for optimal DNAM1-mediated antitumor immunity

The poliovirus receptor (PVR, CD155) represents a resistance mechanism to approved immune checkpoint inhibitors (ICIs). It is a key regulator of immune activation, that modifies immune function through multiple mechanisms. Increased levels of PVR expression on tumor cells have been associated with resistance to anti-PD-(L)1 therapy in clinical settings, while loss of PVR led to reduced tumor growth in multiple pre-clinical models. Targeting PVR using blocking mAbs offers an attractive therapeutic approach for patients with advanced cancer. NTX-1088 is a first-in-class, potent, anti-PVR mAb being developed for the treatment of solid tumors. The antibody binds to PVR with high affinity, blocks its interactions with TIGIT and CD96, and thus interrupt their immunosuppressive signaling. However, NTX-1088 forte is manifested through its ability to block the critical interaction between PVR and the costimulatory receptor DNAM1 (CD226). This blockade prevents internalization of DNAM1, restores its expression on the surface of immune cells and results in a robust antitumor activation. NTX-1088 was tested using several tumor and immune cell co-culture systems. Various cancer cell lines were co-incubated with relevant immune effector cells from healthy human donors, in the presence of NTX-1088, as a single agent and in combination with anti-PD-1 mAb (pembrolizumab). NTX-1088 significantly increased immune cell activation, as measured by IFNg release from activated polyclonal CD8+ T cells, induction of CD137 and killing of tumor cells. When tested in combination with pembrolizumab, NTX-1088 further increased all measured activation parameters, suggesting a potential synergistic effect. When compared to anti-TIGIT mAb (tiragolumab), NTX-1088 demonstrated clear superiority in its ability to activate T and NK cells. Furthermore, NTX-1088 in combination with pembrolizumab was significantly superior to the combination of pembrolizumab with anti-TIGIT mAb. Interestingly, NTX-1088 as a single agent showed a comparable effect to that of the combined blockade of TIGIT and CD112R, and further synergized with anti-CD112R for maximal activity. NTX-1088 was the only intervention that significantly restored DNAM1 levels, whereas blockade of DNAM1 reduced the activity of NTX-1088 to levels comparable to that of anti-TIGIT mAb. Humanized murine models confirmed the above observations; NTX-1088 exhibited strong efficacy, inducing a robust tumor growth inhibition, accompanied by significantly higher prevalence of CD137+, DNAM1+, CD8+ tumor infiltrating cells, compared to control treated mice. This is the first report of drug-induced DNAM1 restoration and immune activation. NTX-1088 shows, for the first time, exclusive triple mechanism of action, whereby simultaneous and effective blockade of TIGIT and CD96 is complemented by the efficient restoration of DNAM1. This is a step change in antitumor immune activation, which will soon be tested in the clinic.

Citation Format: Pini Tsukerman, Anas Atieh, Akram Obeidat, Keren Paz, Guy Cinamon, Tihana Lenac Roviš, Lea Hirsl, Paola Kucan Brilc, Stipan Jonjic, Ofer Mandelboim. NTX-1088, A potent first-in-class, anti-PVR mAb, restores expression and function of DNAM1 for optimal DNAM1-mediated antitumor immunity [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P102.

254 NTX-1088, a potent anti-PVR Mab induces DNAM1-mediated antitumor immunity

Background

Poliovirus receptor (PVR, CD155) represents a resistance mechanism to approved immune checkpoint inhibitors (ICIs). It is a key regulator of immune activation, that modifies function through multiple mechanisms. Increased PVR expression levels on tumor cells have been associated with resistance to anti-PD-(L)1 therapy, while loss of PVR led to reduced tumor growth. Targeting PVR using mAbs offers an attractive therapeutic approach for patients with advanced cancer, who are not responding to other ICIs.NTX-1088 is a first-in-class, anti-PVR mAb developed for the treatment of solid tumors and will enter clinical trials early 2022. The antibody binds PVR with high affinity, blocks its interactions with TIGIT and CD96, preventing their inhibitory signaling. Moreover, NTX-1088 forte is manifested through its ability to block the critical interaction between PVR and DNAM1 (CD226). This blockade prevents internalization of DNAM1, restores its expression on the surface of immune cells and results in a robust antitumor activity.

Methods

NTX-1088 was rigorously tested in vitro and in-vivo. Various cancer cell lines were incubated with immune effector cells from healthy human donors, in the presence of NTX-1088, alone and in combination with anti-PD-1 mAb (pembrolizumab).

Results

NTX-1088 significantly increased immune cell activation, as measured by IFNg release from activated polyclonal CD8+ T cells, induction of CD137 and killing of tumor cells. When tested in combination with pembrolizumab, NTX-1088 further increased all measured activation parameters, suggesting a potential synergistic effect. A synergistic effect was obtained when NTX-1088 was combined with the anti-CD112R mAb, NTX-2R13, superior to TIGIT-CD112R combinations. When compared to anti-TIGIT mAb (tiragolumab), NTX-1088 demonstrated clear superiority in activating T and NK cells as stand-alone agent. Furthermore NTX-1088 in combination with pembrolizumab, was superior to the combination of pembrolizumab with anti-TIGIT.Importantly, NTX-1088 was the only intervention that significantly restored DNAM1 levels, whereas DNAM1 blockade reduced the activity of NTX-1088 to levels comparable to that of anti-TIGIT mAb.Humanized murine models confirmed the above observations; NTX-1088 exhibited a robust tumor growth inhibition, accompanied by significantly higher prevalence of CD137+, DNAM1+, CD8+ T cells, compared to mice treated by other ICIs.

Conclusions

This is the first report of drug-induced DNAM1 restoration and immune activation. NTX-1088 shows, for the first time, exclusive triple mechanism of action, whereby simultaneous and effective blockade of TIGIT and CD96 is complemented by the efficient restoration of DNAM1. This is a step change in antitumor immune activation, which will be validated in the clinic starting early 2022.

Regulation of Cellular Heterogeneity and Rates of Symmetric and Asymmetric Divisions in Triple-Negative Breast Cancer

Differentiation events contribute to phenotypic cellular heterogeneity within tumors and influence disease progression and response to therapy. Here, we dissect mechanisms controlling intratumoral heterogeneity within triple-negative basal-like breast cancers. Tumor cells expressing the cytokeratin K14 possess a differentiation state that is associated with that of normal luminal progenitors, and K14-negative cells are in a state closer to that of mature luminal cells. We show that cells can transition between these states through asymmetric divisions, which produce one K14⁺ and one K14^- daughter cell, and that these asymmetric divisions contribute to the generation of cellular heterogeneity. We identified several regulators that control the proportion of K14⁺ cells in the population. EZH2 and Notch increase the numbers of K14⁺ cells and their rates of symmetric divisions, and FOXA1 has an opposing effect. Our findings demonstrate that asymmetric divisions generate differentiation transitions and heterogeneity, and identify pathways that control breast cancer cellular composition.

Patient-derived xenografts effectively capture responses to oncology therapy in a heterogeneous cohort of patients with solid tumors

Background

While patient-derived xenografts (PDXs) offer a powerful modality for translational cancer research, a precise evaluation of how accurately patient responses correlate with matching PDXs in a large, heterogeneous population is needed for assessing the utility of this platform for preclinical drug-testing and personalized patient cancer treatment.

Patients and methods

Tumors obtained from surgical or biopsy procedures from 237 cancer patients with a variety of solid tumors were implanted into immunodeficient mice and whole-exome sequencing was carried out. For 92 patients, responses to anticancer therapies were compared with that of their corresponding PDX models.

Results

We compared whole-exome sequencing of 237 PDX models with equivalent information in The Cancer Genome Atlas database, demonstrating that tumorgrafts faithfully conserve genetic patterns of the primary tumors. We next screened PDXs established for 92 patients with various solid cancers against the same 129 treatments that were administered clinically and correlated patient outcomes with the responses in corresponding models. Our analysis demonstrates that PDXs accurately replicate patients' clinical outcomes, even as patients undergo several additional cycles of therapy over time, indicating the capacity of these models to correctly guide an oncologist to treatments that are most likely to be of clinical benefit.

Conclusions

Integration of PDX models as a preclinical platform for assessment of drug efficacy may allow a higher success-rate in critical end points of clinical benefit.

Alveolar rhabdomyosarcoma: morphoproteomics and personalized tumor graft testing further define the biology of PAX3-FKHR(FOXO1) subtype and provide targeted therapeutic options

Alveolar rhabdomyosarcoma (ARMS) represents a block in differentiation of malignant myoblasts. Genomic events implicated in the pathogenesis of ARMS involve PAX3-FKHR (FOXO1) or PAX7-FKHR (FOXO1) translocation with corresponding fusion transcripts and fusion proteins. Commonalities in ARMS include uncontrollable proliferation and failure to differentiate. The genomic-molecular correlates contributing to the etiopathogenesis of ARMS incorporate PAX3-FKHR (FOXO1) fusion protein stimulation of the IGF-1R, c-Met and GSK3-β pathways. With sequential morphoproteomic profiling on such a case in conjunction with personalized tumor graft testing, we provide an expanded definition of the biology of PAX3-FKHR (FOXO1) ARMS that integrates genomics, proteomics and pharmacogenomics. Moreover, therapies that target the genomic and molecular biology and lead to tumoral regression and/or tumoral growth inhibition in a xenograft model of ARMS are identified.

Establishment and characterization of a platinum- and paclitaxel-resistant high grade serous ovarian carcinoma cell line

High grade serous ovarian cancer (HGSOC) patients have a high recurrence rate after surgery and adjuvant chemotherapy due to inherent or acquired drug resistance. Cell lines derived from HGSOC tumors that are resistant to chemotherapeutic agents represent useful pre-clinical models for drug discovery. Here, we describe establishment of a human ovarian carcinoma cell line, which we term WHIRC01, from a patient-derived mouse xenograft established from a chemorefractory HGSOC patient who did not respond to carboplatin and paclitaxel therapy. This newly derived cell line is platinum- and paclitaxel-resistant with cisplatin, carboplatin, and paclitaxel half-maximal lethal doses of 15, 130, and 20 µM, respectively. Molecular characterization of this cell line was performed using targeted DNA exome sequencing, transcriptomics (RNA-seq), and mass spectrometry-based proteomic analyses. Results from exomic sequencing revealed mutations in TP53 consistent with HGSOC. Transcriptomic and proteomic analyses of WHIRC01 showed high level of alpha-enolase and vimentin, which are associated with cell migration and epithelial-mesenchymal transition. WHIRC01 represents a chemorefractory human HGSOC cell line model with a comprehensive molecular profile to aid future investigations of drug resistance mechanisms and screening of chemotherapeutic agents.

Comparative mutational landscape analysis of patient-derived tumour xenografts

Background:

Screening of patients for cancer-driving mutations is now used for cancer prognosis, remission scoring and treatment selection. Although recently emerged targeted next-generation sequencing-based approaches offer promising diagnostic capabilities, there are still limitations. There is a pressing clinical need for a well-validated, rapid, cost-effective mutation profiling system in patient specimens. Given their speed and cost-effectiveness, quantitative PCR mutation detection techniques are well suited for the clinical environment. The qBiomarker mutation PCR array has high sensitivity and shorter turnaround times compared with other methods. However, a direct comparison with existing viable alternatives are required to assess its true potential and limitations.

Methods:

In this study, we evaluated a panel of 117 patient-derived tumour xenografts by the qBiomarker array and compared with other methods for mutation detection, including Ion AmpliSeq sequencing, whole-exome sequencing and droplet digital PCR.

Results:

Our broad analysis demonstrates that the qBiomarker's performance is on par with that of other labour-intensive and expensive methods of cancer mutation detection of frequently altered cancer-associated genes, and provides a foundation for supporting its consideration as an option for molecular diagnostics.

Conclusions:

This large-scale direct comparison and validation of currently available mutation detection approaches is extremely relevant for the current scenario of precision medicine and will lead to informed choice of screening methodologies, especially in lower budget conditions or time frame limitations.

Screening of Conditionally Reprogrammed Patient-Derived Carcinoma Cells Identifies ERCC3-MYC Interactions as a Target in Pancreatic Cancer

PURPOSE

Even when diagnosed prior to metastasis, pancreatic ductal adenocarcinoma (PDAC) is a devastating malignancy with almost 90% lethality, emphasizing the need for new therapies optimally targeting the tumors of individual patients.

EXPERIMENTAL DESIGN

We first developed a panel of new physiologic models for study of PDAC, expanding surgical PDAC tumor samples in culture using short-term culture and conditional reprogramming with the Rho kinase inhibitor Y-27632, and creating matched patient-derived xenografts (PDX). These were evaluated for sensitivity to a large panel of clinical agents, and promising leads further evaluated mechanistically.

RESULTS

Only a small minority of tested agents was cytotoxic in minimally passaged PDAC cultures in vitro Drugs interfering with protein turnover and transcription were among most cytotoxic. Among transcriptional repressors, triptolide, a covalent inhibitor of ERCC3, was most consistently effective in vitro and in vivo causing prolonged complete regression in multiple PDX models resistant to standard PDAC therapies. Importantly, triptolide showed superior activity in MYC-amplified PDX models and elicited rapid and profound depletion of the oncoprotein MYC, a transcriptional regulator. Expression of ERCC3 and MYC was interdependent in PDACs, and acquired resistance to triptolide depended on elevated ERCC3 and MYC expression. The Cancer Genome Atlas analysis indicates ERCC3 expression predicts poor prognosis, particularly in CDKN2A-null, highly proliferative tumors.

CONCLUSIONS

This provides initial preclinical evidence for an essential role of MYC-ERCC3 interactions in PDAC, and suggests a new mechanistic approach for disruption of critical survival signaling in MYC-dependent cancers. Clin Cancer Res; 22(24); 6153-63. ©2016 AACR.

MEK inhibitors block growth of lung tumours with mutations in ataxia-telangiectasia mutated

Lung cancer is the leading cause of cancer deaths, and effective treatments are urgently needed. Loss-of-function mutations in the DNA damage response kinase ATM are common in lung adenocarcinoma but directly targeting these with drugs remains challenging. Here we report that ATM loss-of-function is synthetic lethal with drugs inhibiting the central growth factor kinases MEK1/2, including the FDA-approved drug trametinib. Lung cancer cells resistant to MEK inhibition become highly sensitive upon loss of ATM both in vitro and in vivo. Mechanistically, ATM mediates crosstalk between the prosurvival MEK/ERK and AKT/mTOR pathways. ATM loss also enhances the sensitivity of KRAS- or BRAF-mutant lung cancer cells to MEK inhibition. Thus, ATM mutational status in lung cancer is a mechanistic biomarker for MEK inhibitor response, which may improve patient stratification and extend the applicability of these drugs beyond RAS and BRAF mutant tumours.

RET Fusion Lung Carcinoma: Response to Therapy and Clinical Features in a Case Series of 14 Patients

BACKGROUND

RET (rearranged during transfection) fusions have been reported in 1% to 2% of lung adenocarcinoma (LADC) cases. In contrast, KIF5B-RET and CCDC6-RET fusion genes have been identified in 70% to 90% and 10% to 25% of tumors, respectively. The natural history and management of RET-rearranged LADC are still being delineated.

MATERIALS AND METHODS

We present a series of 14 patients with RET-rearranged LADC. The response to therapy was assessed by the clinical response and an avatar model in 2 cases. Patients underwent chemotherapy, targeted therapy, and immunotherapy.

RESULTS

A total of 14 patients (8 women; 10 never smokers; 4 light smokers; mean age, 57 years) were included. KIF5B-RET and CCDC6-RET variants were diagnosed in 10 and 4 cases, respectively. Eight patients had an early disseminated manifestation, seven with KIF5B-RET rearranged tumor. The features of this subset included bilateral miliary lung metastases, bone metastases, and unusual early visceral abdominal involvement. One such patient demonstrated an early and durable complete response to cabozantinib for 7 months. Another 2 patients treated with cabozantinib experienced a partial response, with rapid significant clinical improvement. Four patients with tumors harboring CCDC6-RET and KIF5B-RET fusions showed pronounced and durable responses to platinum-based chemotherapy that lasted for 8 to 15 months. Two patients' tumors showed programmed cell death ligand 1-positive staining but did not respond to pembrolizumab. The median overall survival was 22.8 months.

CONCLUSION

RET-rearranged LADC in our series tended to occur as bilateral disease with early visceral involvement, especially with KIF5B fusion. Treatment with cabozantinib achieved responses, including 1 complete response. However, further studies are required in this group of patients.

Abstract A21: Accurate molecular fidelity of patient-derived xenograft (PDX) models to original human tumors and to The Cancer Genome Atlas (TCGA)

Background: Patient-derived xenograft (PDX) models, also known as Champions TumorGraft® models, maintain the complex intra-tumoral biology of the primary tumor. Over 250 of the Champions models, ranging over a wide variety of solid tumors and passaging generations, have been analyzed using whole exome sequencing (WES) and RNA sequencing (RNAseq). SNPs, InDels and copy number alterations (CNAs) data have been generated for each model, following the Genome Analysis Toolkit (GATK). While several publications compare small numbers of PDX models and human tumors on the molecular level, this is the first known comprehensive analysis whereby the molecular fidelity of the PDX platform is corroborated across several cancer types and throughout different mouse generations.

Method and Results: First, we compared PDXs to their human original counterparts using a preliminary group of four PDX models with available matching human patient WES data. Patient tumor source included dedifferentiated liposarcoma, synovial sarcoma, renal cell carcinoma and squamous cell carcinoma of the lung. PDX passages ranged from 2 to 4. We compared called mutations and a high percentage of identified human tumor mutations were present in the PDX models (42-82%), with the lowest scoring model also showing signs of normal contamination in the human tumor sample. For CNAs in oncogenic sites, we saw an average of 65% of human tumor alterations recurring in the PDX models. This was observed, despite inherent difficulties due to exome- based CNA analysis methods.

Encouraged by the individual patient results, we subjected our largest (per cancer type) PDX cohorts to a molecular comparison with the equivalent TCGA cohorts. More than 200 of the sequenced models, grouped into colorectal adenocarcinoma (COADREAD), lung adenocarcinoma (LUAD), breast carcinoma (BRCA), head and neck squamous cell carcinoma (HNSC) and ovarian serous carcinoma (OV) cohorts were compared. We applied mutation category (MC) and significantly mutated genes (SMG) analysis, as well as comparison of mutation population frequencies for TCGA SMG. Results showed high correlation between the TCGA and the Champions PDX cohorts, although the level of matching varied between cancer types. For instance, COADREAD was highly correlative, while other cancer types, such as BRCA, showed bias toward CpG site mutations. In SMG analysis and population frequency analysis, major SMGs recur across the cohorts, while, as expected, weaker signals from the TCGA were often missed in the smaller cohorts.

Conclusions: Detailed comparison of several PDX models to the human tumor counterpart demonstrated high fidelity, not only at the gene level but also the mutation and CNA level. Cohort comparisons were correlative as well, but a certain bias was discerned in both MC and SMG analyses. There could be several causes for this, including statistical artifacts due to small cohort sizes, clinical and demographic differences between the Champions and TCGA patient profiles, or biological factors such as clonal selection and engraftment pressure. Further analysis is ongoing to better understand the model at a molecular level and maximize its utility as a robust translational research tool.

Citation Format: Ido Sloma, Ido Ben-zvi, Tin Khor, Daniel Ciznadija, Amanda Katz, David Vasquez, Jennifer Jaskowiak, Lindsay Ryland, Angela Davies, David Sidransky, Keren Paz. Accurate molecular fidelity of patient-derived xenograft (PDX) models to original human tumors and to The Cancer Genome Atlas (TCGA). [abstract]. In: Proceedings of the AACR Special Conference: Patient-Derived Cancer Models: Present and Future Applications from Basic Science to the Clinic; Feb 11-14, 2016; New Orleans, LA. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(16_Suppl):Abstract nr A21.

Abstract A40: The ImmunoGraftTM: A humanized mouse model for translational assessment of immunotherapy in solid tumors

Background: Therapeutics reactivating the immune system have demonstrated promise, with durable objective responses in patients with a variety of solid tumors. Despite these successes, current animal models do not reliably identify immunotherapeutic targets with the greatest clinical potential, due in part to differences between human and murine immune systems. Hence, development of robust preclinical tools to test such drugs against human tumors in the context of an allogeneic immune system remains an imperative. We have previously demonstrated the generation of its ImmunoGraft platform, whereby two technologies, the patient-derived xenograft (PDX) and humanized mice (immunodeficient mice reconstituted with a human immune system), are combined in a single platform. We now report on the utility of the ImmunoGraft for assessing the effect of immune-modulating agents in solid tumors.

Materials and Methods: Immune-compromised NOG (PrkdcscidIl2rgtm1Sug) mice were reconstituted with human CD34+ cells and monitored for the expansion of human immune cells (humanized). Humanized mice were engrafted with solid tumors that had been subjected to histocompatibility typing and characterized for a number of molecular markers, including PD-L1 expression. Tumor growth in the ImmunoGrafts was compared against non-humanized counterparts, as well as the level of immune reconstitution. Finally, ImmunoGrafts were treated with drugs blocking the immune checkpoints CTLA4 and PD1 and human immune activation and tumor growth inhibition evaluated.

Results: Mature human CD45+ cells comprised close to 50% of the leukocytes detected in the circulation and lymphoid organs of humanized mice. Solid tumors, including NSCLC, melanoma, and head and neck cancer, were successfully engrafted in the humanized mice. Moderate to high expression of PD-L1 was found in approximately 80% of these tumors. ImmunoGrafts treated with anti-CTLA4 or anti-PD1 antibodies exhibited systemic immune responses characterized by robust proliferation of splenic and circulating huCD3+ T cells, as well as activated huCD4+ Th1 cells. There was also an increase in tumor-infiltrating huCD8+ cytotoxic T lymphocytes and huCD68+ macrophages, along with elevated secretion of human-specific cytokines. Tumor growth inhibition, and in some instances tumor regression, was demonstrated in treated ImmunoGrafts. The magnitude of growth inhibition correlated with the level of immune activation.

Conclusion : The ImmunoGraft is an innovative pre-clinical model enabling immunotherapeutic agents to be evaluated for efficacy in solid tumors. This platform is more reflective of the human tumor microenvironment (both immune and non-immune cell-based) and may be one of the most translationally-relevant models to date for screening therapies targeting the immune system. To gauge the clinical potential of the ImmunoGraft, a retrospective analysis is currently ongoing using PDX models developed from patients treated with immuno-oncology drugs. The ImmunoGraft has the potential to revolutionize translational drug discovery and development for immunotherapeutic agents in oncology.

Citation Format: Gilson Baia, David Vasquez, David Cerna, Daniel Ciznadija, David Sidransky, Jennifer Jaskowiak, Lindsay Ryland, Angela Davies, Amanda Katz, Keren Paz. The ImmunoGraftTM: A humanized mouse model for translational assessment of immunotherapy in solid tumors. [abstract]. In: Proceedings of the AACR Special Conference: Patient-Derived Cancer Models: Present and Future Applications from Basic Science to the Clinic; Feb 11-14, 2016; New Orleans, LA. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(16_Suppl):Abstract nr A40.

Abstract B40: Mouse clinical trials: integrating PDX models of sarcoma subtypes with genomics to replicate patient responses to cancer therapeutics

Objective: Sarcomas are clinically and genetically heterogeneous tumors that are often difficult to treat. Patient-derived xenograft (PDX or TumorGraft) models have been shown to accurately reflect the characteristics of patient tumors and may be useful tools for developing personalized treatment strategies and deployment in mouse clinical trials assessing novel therapies. We evaluated the accuracy of PDX models in reproducing clinical responses to standard and experimental drugs used for sarcoma treatment.

Methods: Fresh tumor tissue (comprising 172 distinct explants) was collected by surgery or biopsy from 150 patients with sarcoma and implanted into immunodeficient mice. Tumors successfully engrafting were screened using next-generation sequencing technology to identify key genomic alterations with therapeutic implications. PDX sensitivity to standard of care and experimental agents was evaluated and tumor growth inhibition/regression values and clinical RECIST outcomes determined. Drug screening results were correlated with individual patient outcomes.

Results: Of the 172 implanted tumors, 145 have completed the implantation process, with 86 (59%) successfully establishing a PDX model. Engraftment rate depended on sarcoma subtype and specimen origin (surgical explant versus biopsy). Next generation sequencing of models from major sarcoma subtypes (Ewing sarcoma, leiomyosarcoma, liposarcoma, osteosarcoma, and rhabdomyosarcoma) highlighted alterations in 454 genes, including those informing treatment selection such as PIK3CA, MET, and CDK4. A total of 26 PDX models from 25 patients across the major sarcoma subtypes were screened in 148 drug tests employing 64 FDA-approved drugs/combinations such as ifosfamide, and gemcitabine/docetaxel, and 26 experimental therapies in clinical trial. In 13/13 (100%) cases with available data, a significant correlation between patient clinical response and PDX model outcome was noted (p=0.0004; Fisher's exact test).

Conclusions: Given the close match between patient clinical responses and PDX model outcomes, these results validate the concept of mouse clinical trials for determining the efficacy of novel therapies in sarcoma prior to broad application in expensive human trials. Moreover, the retention of alterations in key genes influencing therapeutic decision-making suggests a use for PDX models in functionally validating genomic hypotheses in a pre-clinical setting.

Citation Format: Amanda Katz, Raphael E. Pollock, Leonard H. Wexler, Carlos Rodriguez-Galindo, Jonathan C. Trent, Robert Maki, Jennifer Jaskowiak, Lindsay Ryland, Daniel Ciznadija, Angela Davies, Keren Paz. Mouse clinical trials: integrating PDX models of sarcoma subtypes with genomics to replicate patient responses to cancer therapeutics. [abstract]. In: Proceedings of the AACR Special Conference: Patient-Derived Cancer Models: Present and Future Applications from Basic Science to the Clinic; Feb 11-14, 2016; New Orleans, LA. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(16_Suppl):Abstract nr B40.

Milk derived colloid as a novel drug delivery carrier for breast cancer

Triple negative breast cancer has an extremely poor prognosis when chemotherapy is no longer effective. To overcome drug resistance, novel drug delivery systems based on nanoparticles have had remarkable success. We produced a novel nanoparticle component 'MDC' from milk-derived colloid. In order to evaluate the anti-cancer effect of MDC, we conducted in vitro and in vivo experiments on cancer cell lines and a primary tumor derived breast xenograft. Doxorubicin (Dox) conjugated to MDC (MDC-Dox) showed higher cancer cell growth inhibition than MDC alone especially in cell lines with high EGFR expression. In a mouse melanoma model, MDC-Dox significantly suppressed tumor growth when compared with free Dox. Moreover, in a primary tumor derived breast xenograft, one of the mice treated with MDC-Dox showed partial regression, while mice treated with free Dox failed to show any suppression of tumor growth. We have shown that a novel nanoparticle compound made of simple milk-derived colloid has the capability for drug conjugation, and serves as a tumor-specific carrier of anti-cancer drugs. Further research on its safety and ability to carry various anti-cancer drugs into multiple drug-resistant primary breast models is warranted.

Abstract A8: The ImmunoGraft: A humanized mouse model for translational assessment of immunotherapy in solid tumors

Background: Therapeutics reactivating the immune system have demonstrated promise, with durable objective responses in patients with a variety of solid tumors. Despite these successes, current animal models do not reliably identify immunotherapeutic targets with the greatest clinical potential, due in part to differences between human and murine immune systems. Hence, development of robust preclinical tools to test such drugs against human tumors in the context of an allogeneic immune system remains an imperative. We have previously demonstrated the generation of its ImmunoGraftTM platform, whereby two technologies, the patient-derived xenograft (PDX) and humanized mice (immunodeficient mice reconstituted with a human immune system), are combined in a single platform. We now report on the utility of the ImmunoGraftTM for assessing the effect of immune-modulating agents in solid tumors.

Materials and Methods: Immune-compromised NOG (PrkdcscidIl2rgtm1Sug) mice were reconstituted with human CD34+ cells and monitored for the expansion of human immune cells (humanized). Humanized mice were engrafted with solid tumors that had been subjected to histocompatibility typing and characterized for a number of molecular markers, including PD-L1 expression. Tumor growth in the ImmunoGraftsTM was compared against non-humanized counterparts, as well as the level of immune reconstitution. Finally, ImmunoGraftsTM were treated with drugs blocking the immune checkpoints CTLA4 and PD1 and human immune activation and tumor growth inhibition evaluated.

Results: Mature human CD45+ cells comprised close to 50% of the leukocytes detected in the circulation and lymphoid organs of humanized mice. Solid tumors, including NSCLC, melanoma, and head and neck cancer, were successfully engrafted in the humanized mice. Moderate to high expression of PD-L1 was found in approximately 80% of these tumors. ImmunoGraftsTM treated with anti-CTLA4 or anti-PD1 antibodies exhibited systemic immune responses characterized by robust proliferation of splenic and circulating huCD3+ T cells, as well as activated huCD4+ Th1 cells. There was also an increase in tumor-infiltrating huCD8+ cytotoxic T lymphocytes and huCD68+ macrophages, along with elevated secretion of human-specific cytokines. Tumor growth inhibition, and in some instances tumor regression, was demonstrated in treated ImmunoGraftsTM. The magnitude of growth inhibition correlated with the level of immune activation.

Conclusion: The ImmunoGraftTM is an innovative pre-clinical model enabling immunotherapeutic agents to be evaluated for efficacy in solid tumors. This platform is more reflective of the human tumor microenvironment (both immune and non-immune cell-based) and may be one of the most translationally-relevant models to date for screening therapies targeting the immune system. To gauge the clinical potential of the ImmunoGraftTM, a retrospective analysis is currently ongoing using PDX models developed from patients treated with immuno-oncology drugs. The ImmunoGraftTMhas the potential to revolutionize translational drug discovery and development for immunotherapeutic agents in oncology.

Citation Format: Gilson Baia, David Vasquez, David Cerna, Daniel Ciznadija, David Sidransky, Amanda Katz, Keren Paz. The ImmunoGraft: A humanized mouse model for translational assessment of immunotherapy in solid tumors. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr A8.

Abstract A14: Molecular fidelity of patient derived xenograft (PDX) models to original human tumor and to the cancer genome atlas (TCGA)

Background

Patient-derived xenograft (PDX) models, also known as Champions TumorGraft® models, maintain the complex intra-tumoral biology of the primary tumor. Over 250 of the Champions models, ranging over a wide variety of solid tumors and passaging generations, have been analyzed using whole exome sequencing (WES) and RNA sequencing (RNAseq). SNPs, InDels and copy number alterations (CNAs) data have been generated for each model, following the Genome Analysis Toolkit (GATK). While several publications compare small numbers of PDX models and human tumors on the molecular level, this is the first known comprehensive analysis whereby the molecular fidelity of the PDX platform is corroborated across several cancer types and throughout different mouse generations.

Method and Results

First, we compared PDXs to their human original counterparts using a preliminary group of four PDX models with available matching human patient WES data. Patient tumor source included dedifferentiated liposarcoma, synovial sarcoma, renal cell carcinoma and squamous cell carcinoma of the lung. PDX passages ranged from 2 to 4. We compared called mutations and a high percentage of identified human tumor mutations were present in the PDX models (42-82%), with the lowest scoring model also showing signs of normal contamination in the human tumor sample. For CNAs in oncogenic sites, we saw an average of 65% of human tumor alterations recurring in the PDX models. This was observed, despite inherent difficulties due to exome based CNA analysis methods.

Encouraged by the individual patients results, we subjected our largest (per cancer type) PDX cohorts to a molecular comparison with the equivalent TCGA cohorts. More than 200 of the sequenced models, grouped into colorectal adenocarcinoma (COADREAD), lung adenocarcinoma (LUAD), breast carcinoma (BRCA), head and neck squamous cell carcinoma (HNSC) and ovarian serous carcinoma (OV) cohorts were compared. We applied mutation category (MC) and significantly mutated genes (SMG) analysis, as well as comparison of mutation population frequencies for TCGA SMG. Results showed high correlation between the TCGA and the Champions PDX cohorts, although the level of matching varied between cancer types. For instance, COADREAD was highly correlative, while other cancer types, such as BRCA, showed bias toward CpG site mutations. In SMG analysis and population frequency analysis, major SMGs recur across the cohorts, while, as expected, weaker signals from the TCGA were often missed in the smaller cohorts.

Conclusion

Detailed comparison of several PDX models to the human tumor counterpart demonstrated high fidelity, not only at the gene level but also the mutation and CNA level. Cohort comparisons were correlative as well, but a certain bias was discerned in both MC and SMG analyses. There could be several causes for this, including statistical artifacts due to small cohort sizes, clinical and demographic differences between the Champions and TCGA patient profiles, or biological factors such as clonal selection and engraftment pressure. Further analysis is ongoing to better understand the model at a molecular level and maximize its utility as a robust translational research tool.

Citation Format: Ido Ben-Zvi, Ido Sloma, Tin Khor, Daniel Ciznadija, Amanda Katz, David Vasquez, David Sidransky, Keren Paz. Molecular fidelity of patient derived xenograft (PDX) models to original human tumor and to the cancer genome atlas (TCGA). [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr A14.

Abstract 3219: A patient-centric repository of PDX models for translational oncology research

Patient-derived xenograft (PDX) models maintain the complex intra-tumoral biology and heterogeneity of an intact malignancy, as well as the interplay with stromal components and other cells fluxing into the tumor environment. This intrinsic cross-talk between different elements of the tumor makes PDX models a superior tool for translational drug discovery research and personalized oncology studies. Champions PDX models were originally developed for personalizing cancer treatments through the different Champions clinical programs. These models accurately reflect the population of patients enrolling in clinical trials. We describe herein our extensive TumorBank of PDX models, a valuable resource for translational oncology research to predetermine target populations for intervention with novel therapeutics in specific cancer subtypes.

Tumor tissue from over 950 patients with a variety of primary and metastatic solid malignancies, across all ages and ethnicities and encompassing both treatment-naïve and heavily-pretreated individuals, has been implanted into immunodeficient mice with successful engraftment observed in ∼72% of cases. Comprehensive and translational-relevant clinical annotations have been maintained for these PDX models, including patient demographics, disease stage, anatomic location, tumor grade and histology, and treatment history. Importantly, whole exome and RNA sequencing, tissue histopathology, and protein immunohistochemistry have all been applied to 297 of these models. Finally, 70 of the models were screened against the corresponding patient's treatment used in the clinic, demonstrating a sensitivity of 98%, specificity of 76%, positive predictive value of 89% and negative predictive value of 96%. This wealth of information can be accessed through the Champions TumorGraft Database. The combination of extensive molecular and clinical annotation, together with opportunities for unlimited prospective preclinical testing, makes Champions TumorBank a pioneering resource for pharmaceutical companies seeking to identify target populations for therapeutic intervention.

Citation Format: Tin O. Khor, Ido Ben Zvi, Amanda Katz, David Vasquez-Dunddel, Ido Sloma, Daniel Ciznadija, David Sidransky, Keren Paz. A patient-centric repository of PDX models for translational oncology research. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3219. doi:10.1158/1538-7445.AM2015-3219

Humanized immune system mice: Improving the predictability of mouse models in immuno-oncology drug development (TUM3P.1044)

Mouse models are widely used in preclinical oncology research but species differences can limit efficacy predictions for clinical translation. Taconic Biosciences, Inc. is leveraging the super immunodeficient status of the CIEA NOD.Cg-Prkdcscid Il2rgtm1Sug/JicTac (NOG) mouse, which allows it so support the engraftment of human cells and tissues, to accelerate efficacy and safety testing of novel immunotherapies. We have optimized this model for efficient engraftment of the human immune system, and co-engraftment of patient derived xenografts (PDX). In a collaboration with Champions Oncology, the PDX engrafted humanized NOG mouse responded to immune checkpoint inhibition, by activating T cells which are able to infiltrate the tumor. An overview of Taconic's humanization program will be presented, including data showing the utility of humanized mice in PDX applications for immuno-oncology drug development, and recent advances in the development of next generation humanized mice

Abstract P3-06-31: Patient-derived xenografts accurately predict patient response in breast cancer patients

PURPOSE/OBJECTIVES: A growing body of evidence demonstrates that patient-derived xenografts (PDXs) represent living tumor models that accurately reflect the biology of the primary patient tumor. More importantly, we have previously shown that PDX models show responses to therapeutic agents that are concordant with patient clinical response and can be used to direct personalized cancer treatments (Stebbing, 2014). Here we report the ability of PDX models to predict for patient response to drug treatment in a cohort of breast cancer patients.

MATERIALS/METHODS: Tumors were resected from patients with either primary or metastatic breast cancer and implanted into immunodeficient mice to establish PDX models. Successfully engrafted PDX models were expanded and randomized for drug sensitivity testing. Tumor growth inhibition and tumor regression were captured and results were correlated with a patient’s clinical response. In some cases, PDX results were used to personalize cancer treatment and some patients used PDX-directed treatments over multiple lines of therapy.

RESULTS: A total of 42 tumors from 40 patients were implanted resulting in 21 successfully engrafted PDX models (50% engraftment rate). Notably, engraftment rates were much higher for patients with triple negative breast cancer (TNBC) and resulted in 7 successful PDX models from 8 TNBC patients (87.5% engraftment rate). Drug sensitivity testing was offered to patients with established PDX models. Drugs and drug combinations tested included standard and nonstandard chemotherapy as well as biologics. At that time of this publication, 4 patients (3 TNBC and 1 HER2+) with completed drug sensitivity tests also had clinical data available resulting in 7 clinical correlations; 4 retrospective and 3 prospective. In all 7 cases, the PDX model accurately predicted patient clinical response demonstrating an accuracy of 100%. Five of the drug tests predicted drug sensitivity and 2 tests predicted resistance, indicating the potential of the PDX platform to predict for both sensitivity and resistance to therapy. The 3 prospective correlations resulted in concordant clinical benefit in 2 patients for duration greater than 6 months each.

CONCLUSIONS: These data support the use of the personalized PDX model as a platform for therapeutic decision making that can guide treatment for patients with breast cancer. A prospective clinical trial in TNBC is currently underway.

Citation Format: Lisa Stow, Amanda Katz, Hanna Irie, Elisa Port, Justin Stebbing, Daniel Ciznadija, Angela Davies, Keren Paz. Patient-derived xenografts accurately predict patient response in breast cancer patients [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P3-06-31.

Pathway activation strength is a novel independent prognostic biomarker for cetuximab sensitivity in colorectal cancer patients

Cetuximab, a monoclonal antibody against epidermal growth factor receptor (EGFR), was shown to be active in colorectal cancer. Although some patients who harbor K-ras wild-type tumors benefit from cetuximab treatment, 40 to 60% of patients with wild-type K-ras tumors do not respond to cetuximab. Currently, there is no universal marker or method of clinical utility that could guide the treatment of cetuximab in colorectal cancer. Here, we demonstrate a method to predict response to cetuximab in patients with colorectal cancer using OncoFinder pathway activation strength (PAS), based on the transcriptomic data of the tumors. We first evaluated our OncoFinder pathway activation strength model in a set of transcriptomic data obtained from patient-derived xenograft (PDx) models established from colorectal cancer biopsies. Then, the approach and models were validated using a clinical trial data set. PAS could efficiently predict patients’ response to cetuximab, and thus holds promise as a selection criterion for cetuximab treatment in metastatic colorectal cancer.

Elevated AKAP12 in paclitaxel-resistant serous ovarian cancer cells is prognostic and predictive of poor survival in patients

A majority of high-grade (HG) serous ovarian cancer (SOC) patients develop resistant disease despite high initial response rates to platinum/paclitaxel-based chemotherapy. We identified shed/secreted proteins in preclinical models of paclitaxel-resistant human HGSOC models and correlated these candidate proteins with patient outcomes using public data from HGSOC patients. Proteomic analyses of a HGSOC cell line secretome was compared to those from a syngeneic paclitaxel-resistant variant and from a line established from an intrinsically chemorefractory HGSOC patient. Associations between the identified candidate proteins and patient outcome were assessed in a discovery cohort of 545 patients and two validation cohorts totaling 795 independent SOC patients. Among the 81 differentially abundant proteins identified (q < 0.05) from paclitaxel-sensitive vs -resistant HGSOC cell secretomes, AKAP12 was verified to be elevated in all models of paclitaxel-resistant HGSOC. Furthermore, elevated AKAP12 transcript expression was associated with worse progression-free and overall survival. Associations with outcome were observed in three independent cohorts and remained significant after adjusted multivariate modeling. We further provide evidence to support that differential gene methylation status is associated with elevated expression of AKAP12 in taxol-resistant ovarian cancer cells and ovarian cancer patient subsets. Elevated expression and shedding/secretion of AKAP12 is characteristic of paclitaxel-resistant HGSOC cells, and elevated AKAP12 transcript expression is a poor prognostic and predictive marker for progression-free and overall survival in SOC patients.

Abstract B25: KRAS mutation status is associated with enhanced dependency on purine biosynthesis and related pathways in non small cell lung cancer cells

KRAS gene mutation is linked to poor prognosis and resistance to oncology therapeutics in Non Small Cell Lung Cancer (NSCLC). We have explored the possibility of exploiting inherent differences in KRAS mutant cell metabolism to enhance the efficacy of treatment. We have identified a greater dependency on purine biosynthesis and related pathways in KRAS mutant compared to KRAS wild type NSCLC cell lines. Purine synthesis requires factors generated from other metabolic reactions including ribose-5-phosphate from the pentose phosphate pathway, THF cofactors from folate metabolism and glycine / amide nitrogen groups from glutamine and aspartate metabolism. In this study, microarray gene expression and biological pathway analysis identified higher expression of purine synthesis and accessory pathways such as folate metabolism, 5-aminoimidazole ribonucleotide biosynthesis and glycine synthesis pathways in KRAS mutant NSCLC cells compared to wildtype counterparts. KRAS knockdown and overexpression studies demonstrated the ability of KRAS to regulate expression of genes that comprise purine synthesis and folate metabolism pathways. Moreover, pathway analysis and knockdown studies suggest a role for MYC, an oncogene previously recognized to be associated with KRAS mutant tumors, in the regulation of these pathways in KRAS mutant NSCLC cells. Proliferation studies demonstrated higher responsiveness to antifolates such as methotrexate and pemetrexed in KRAS mutant NSCLC cells, both of which may interfere indirectly with purine biosynthesis. In vivo analysis of NSCLC tumorgraft models in nude mice also identified an association between KRAS mutant tumor status and response to pemetrexed. The expression of a KRAS driven folate/purine synthesis gene, Methylenetetrahydrofolate Dehydrogenase 2 (MTHFD2), was also correlated with antifolate activity suggesting its use as a possible biomarker of response to antifolates. We propose that KRAS mutation drives increased purine synthesis activity and as a result an elevated dependency on the factors needed to feed this biosynthetic pathway such as those generated by folate metabolism. Thus, antifolates can indirectly inhibit purine synthesis through the depletion of folate cofactors which may account for the stronger response to these agents in KRAS mutant cells. We are currently expanding this study to examine alternative inhibitors of purine synthesis as possible therapeutics in KRAS mutant NSCLC and other cancers. Collectively, our findings highlight that a better understanding of the molecular mechanisms underlying the dependency of cancer cells on specific metabolic pathways may result in more effective metabolic targeting and new approaches in treating specific cancers.

Citation Format: Diarmuid M. Moran, Patricia B. Trusk, Karen Pry, Keren Paz, David Sidransky, Sarah S. Bacus. KRAS mutation status is associated with enhanced dependency on purine biosynthesis and related pathways in non small cell lung cancer cells. [abstract]. In: Proceedings of the AACR Special Conference on RAS Oncogenes: From Biology to Therapy; Feb 24-27, 2014; Lake Buena Vista, FL. Philadelphia (PA): AACR; Mol Cancer Res 2014;12(12 Suppl):Abstract nr B25. doi: 10.1158/1557-3125.RASONC14-B25

Abstract 4410: KRAS mutation status is associated with enhanced dependency on purine biosynthesis and related pathways in non small cell lung cancer cells

KRAS gene mutation is linked to poor prognosis and resistance to oncology therapeutics in Non Small Cell Lung Cancer (NSCLC). We have explored the possibility of exploiting inherent differences in KRAS mutant cell metabolism to enhance the efficacy of treatment. We have identified a greater dependency on purine biosynthesis and related pathways in KRAS mutant compared to KRAS wild type NSCLC cell lines. Purine synthesis requires factors generated from other metabolic reactions including ribose-5-phosphate from the pentose phosphate pathway, THF cofactors from folate metabolism and glycine / amide nitrogen groups from glutamine and aspartate metabolism. In this study, microarray gene expression and biological pathway analysis identified higher expression of purine synthesis and accessory pathways such as folate metabolism, 5-aminoimidazole ribonucleotide biosynthesis and glycine synthesis pathways in KRAS mutant NSCLC cells compared to wildtype counterparts. KRAS knockdown and overexpression studies demonstrated the ability of KRAS to regulate expression of genes that comprise purine synthesis and folate metabolism pathways. Moreover, pathway analysis and knockdown studies suggest a role for MYC, an oncogene previously associated with KRAS mutant tumors, in the regulation of these pathways in KRAS mutant NSCLC cells. Proliferation studies demonstrated higher responsiveness to antifolates such as methotrexate and pemetrexed in KRAS mutant NSCLC cells, both of which may interfere indirectly with purine biosynthesis. In vivo analysis of NSCLC tumorgraft models in nude mice also identified an association between KRAS mutant tumor status and response to pemetrexed. The expression of a KRAS driven folate/purine synthesis gene, Methylenetetrahydrofolate Dehydrogenase 2 (MTHFD2), was also correlated with antifolate activity suggesting its use as a possible biomarker of response to antifolates. We propose that KRAS mutation drives increased purine synthesis activity and as a result an elevated dependency on the factors needed to feed this biosynthetic pathway such as those generated by folate metabolism. Thus, antifolates can indirectly inhibit purine synthesis through the depletion of folate cofactors which may account for the stronger response to these agents in KRAS mutant cells. We are currently expanding this study to examine alternative inhibitors of purine synthesis as possible therapeutics in KRAS mutant NSCLC and other cancers. Collectively, our findings highlight that a better understanding of the molecular mechanisms underlying the dependency of cancer cells on specific metabolic pathways may result in more effective metabolic targeting and new approaches in treating specific cancers.

Citation Format: Diarmuid M. Moran, Patricia B. Trusk, Karen Pry, David Sidransky, Keren Paz, Sarah S. Bacus. KRAS mutation status is associated with enhanced dependency on purine biosynthesis and related pathways in non small cell lung cancer cells. [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 4410. doi:10.1158/1538-7445.AM2014-4410

Abstract 1187: The Champions TumorGraft Bank: A demographically-rich repository of preclinical TumorGraft models

Many oncology pharmaceuticals fail during phased clinical trials, having been advanced based on research using flawed preclinical models that do not accurately replicate human tumor biology. For example, numerous models are based on genetically-engineered mice, which are often generated from limited numbers of genetic aberrations. As such, they may not accurately represent either the chaotic heterogeneity that exists within intact human tumors or throughout the clinical population. TumorGrafts, in which patient-derived tumor tissue is directly engrafted into immunodeficient mice, offer a step forward in this unresolved issue. These models maintain the complex intra-tumoral heterogeneity and biology of an intact malignancy, as well its 3-dimensional interplay with stromal components and other cells fluxing into the immediate environment. The intrinsic cross-talk between the different compartments of the tumor is also retained.

We wanted to generate a repository of these tumor models and make them available to the research community for use in pharmaceutical development and basic research processes. Here we describe our extensive bank of live TumorGrafts comprising a range of different tumor types, from more common cancers, including lung, colon, and breast, to a number of rare subtypes such as adenoid cystic carcinoma. These models were originally developed for personalizing cancer treatments and are derived from patient populations across all ages and ethnicities, encompassing both treatment-naïve and heavily-treated individuals. Furthermore, because of our distinct patient-focus, we maintain detailed clinical histories, as well as molecular data where available. Hence, the bank is a reasonable surrogate of the population from which treatment groups are typically drawn for clinical trials and could potentially be of value for predetermining target populations for therapeutic intervention. The Champions TumorGraft Bank provides superior pre-clinical models that faithfully capture all the biological and molecular features of cancer and can serve basic and clinical research groups as an increasingly valuable source for drug development and biomarker discovery.

Citation Format: Tin Khor, David Vasquez, Amanda Katz, Gilson Baia, Daniel Ciznadija, David Sidransky, Keren Paz. The Champions TumorGraft Bank: A demographically-rich repository of preclinical TumorGraft models. [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 1187. doi:10.1158/1538-7445.AM2014-1187

Abstract 1190: Multifactorial biological processes govern engraftment of patient-derived tumor tissue in immunodeficient mice

TumorGrafts (also known as patient-derived xenografts) are a valuable tool for the personalization of oncology treatment, as well as development of new cancer therapeutics. Tumor explants are engrafted into immunodeficient mice and allowed to develop prior to screening against a panel of drugs or drug combinations to assess which best inhibit tumor growth. These models capture the chaotic heterogeneity, histopathology, and biology of the original tumor, as well its 3-dimensional interaction with the surrounding stroma and other cells migrating into the tumor environment. TumorGrafts will serve basic and clinical research groups as an increasingly valuable preclinical model of cancer. One important variable governing the generation of these models is the take rate, or the percentage of patient tumors that successfully engraft and grow in the mice. This is a potentially critical limitation to applying these preclinical models for improving patient treatment and advancing novel drug regimens to the clinic. Hence, there is a need to understand and exploit the mechanisms that influence take rate in order to ensure that the majority of tumor explants readily engraft and expand. We describe here our experience in optimizing the engraftment of patient tumor tissue in immunodeficient mice. We found a number of factors contribute to take rate including tumor type, tissue quantity and quality, engraftment site, oxygenation state, neovascularization and the presence of extracellular stromal components and cells. We have also uncovered a correlation between the growth rate of tumors in the mice and the clinical aggressiveness of the original malignancy, information that may be useful in guiding clinical management. Moreover, we describe how we are now able to consistently use biopsy material rather than surgical explants to establish TumorGrafts, a crucial step forward that allows this technology to benefit patients diagnosed with early-stage cancers or where surgery is not indicated. Although engraftment of patient tumor tissue in immunodeficient mice is a complex process, with multiple factors impacting success, we have effectively optimized this process, improving our take rate and at the same time, reducing the time to obtaining drug screening results, all without compromising tumor integrity.

Citation Format: David M. Vasquez-Dunddel, Gilson Baia, Amanda Katz, Daniel Ciznadija, David Sidransky, Keren Paz. Multifactorial biological processes govern engraftment of patient-derived tumor tissue in immunodeficient mice. [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 1190. doi:10.1158/1538-7445.AM2014-1190

Abstract 1674: Humanized mouse models for personalized preclinical testing of monoclonal antibodies targeting immune checkpoints

The blockade of immune checkpoints with monoclonal antibodies (mAbs) is a promising therapeutic avenue, with durable objective responses observed in patients with solid tumors, particularly melanoma, non-small cell lung cancer (NSCLC) and renal cell carcinoma. Preclinical models that recapitulate a functional human immune system will therefore be essential tools for the continued investigation of immunotherapy approaches. Champions Oncology is engaged in advanced personalized solutions and our TumorGraft models have been developed and extensively characterized as a platform for use in personalizing cancer patient care, as well as pharmaceutical development. However, because TumorGrafts are established by engrafting patient tumors into immune-deficient mice, the therapeutic efficacy of immune-modulatory drugs cannot be directly examined. To circumvent this limitation, we reconstituted the human immune system by engrafting human hematopoietic cells (HLA-A2; CD34+) into immune-compromised mice (PrkdcscidIl2rgtm1Sug) carrying the scid mutation and a targeted mutation of the Il2r-gamma gene. Ten to twelve weeks later, mature CD45+ human T cells could be detected in these mice, at which time TumorGrafts were established, followed by drug-sensitivity testing with various mAbs targeting the immune system. Fifty six well-established melanoma, colorectal, breast and lung TumorGraft models were characterized and selected with regard to their HLA type and other molecular characteristics such as BRAF mutation status (in melanoma) and KRAS mutation status (in colorectal and lung cancer) as well as expression of PD-L1. With the present study, we demonstrated the potential of combining the humanized mouse with Champions TumorGraft to generate a preclinical platform for assessing the therapeutic value of mAbs targeting immune checkpoints in various solid tumors.

Citation Format: Gilson S. Baia, David Vasquez, Daniel Ciznadija, Brandy Wilkinson, David Sidransky, Amanda Katz, Keren Paz. Humanized mouse models for personalized preclinical testing of monoclonal antibodies targeting immune checkpoints. [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 1674. doi:10.1158/1538-7445.AM2014-1674

Patient-derived xenografts for individualized care in advanced sarcoma

BACKGROUND

Patients with advanced, metastatic sarcoma have a poor prognosis, and the overall benefit from the few standard-of-care therapeutics available is small. The rarity of this tumor, combined with the wide range of subtypes, leads to difficulties in conducting clinical trials. The authors previously reported the outcome of patients with a variety of common solid tumors who received treatment with drug regimens that were first tested in patient-derived xenografts using a proprietary method ("TumorGrafts").

METHODS

Tumors resected from 29 patients with sarcoma were implanted into immunodeficient mice to identify drug targets and drugs for clinical use. The results of drug sensitivity testing in the TumorGrafts were used to personalize cancer treatment.

RESULTS

Of 29 implanted tumors, 22 (76%) successfully engrafted, permitting the identification of treatment regimens for these patients. Although 6 patients died before the completion of TumorGraft testing, a correlation between TumorGraft results and clinical outcome was observed in 13 of 16 (81%) of the remaining individuals. No patients progressed during the TumorGraft-predicted therapy.

CONCLUSIONS

The current data support the use of the personalized TumorGraft model as an investigational platform for therapeutic decision-making that can guide treatment for rare tumors such as sarcomas. A randomized phase 3 trial versus physician's choice is warranted.

A human monoclonal antibody targeting the stem cell factor receptor (c-Kit) blocks tumor cell signaling and inhibits tumor growth

Stem cell factor receptor (c-Kit) exerts multiple biological effects on target cells upon binding its ligand stem cell factor (SCF). Aberrant activation of c-Kit results in dysregulated signaling and is implicated in the pathogenesis of numerous cancers. The development of more specific and effective c-Kit therapies is warranted given its essential role in tumorigenesis. In this study, we describe the biological properties of CK6, a fully human IgG1 monoclonal antibody against the extracellular region of human c-Kit. CK6 specifically binds c-Kit receptor with high affinity (EC 50 = 0.06 nM) and strongly blocks its interaction with SCF (IC 50 = 0.41 nM) in solid phase assays. Flow cytometry shows CK6 binding to c-Kit on the cell surface of human small cell lung carcinoma (SCLC), melanoma, and leukemia tumor cell lines. Furthermore, exposure to CK6 inhibits SCF stimulation of c-Kit tyrosine kinase activity and downstream signaling pathways such as mitogen-activated protein kinase (MAPK) and protein kinase B (AKT), in addition to reducing tumor cell line growth in vitro. CK6 treatment significantly decreases human xenograft tumor growth in NCI-H526 SCLC (T/C% = 57) and Malme-3M melanoma (T/C% = 58) models in vivo. The combination of CK6 with standard of care chemotherapy agents, cisplatin and etoposide for SCLC or dacarbazine for melanoma, more potently reduces tumor growth (SCLC T/C% = 24, melanoma T/C% = 38) compared with CK6 or chemotherapy alone. In summary, our results demonstrate that CK6 is a c-Kit antagonist antibody with tumor growth neutralizing properties and are highly suggestive of potential therapeutic application in treating human malignancies harboring c-Kit receptor.

The TGFβ-miR200-MIG6 pathway orchestrates the EMT-associated kinase switch that induces resistance to EGFR inhibitors

Although specific mutations in the tyrosine kinase domain of epidermal growth factor receptor (EGFR) identify tumors that are responsive to EGFR tyrosine kinase inhibitors (TKI), these genetic alterations are present in only a minority of patients. Patients with tumors expressing wild-type EGFR lack reliable predictive markers of their clinical response to EGFR TKIs. Although epithelial-mesenchymal transition (EMT) has been inversely correlated with the response of cancers to EGFR-targeted therapy, the precise molecular mechanisms underlying this association have not been defined and no specific EMT-associated biomarker of clinical benefit has been identified. Here, we show that during transforming growth factor β (TGFβ)-mediated EMT, inhibition of the microRNAs 200 (miR200) family results in upregulated expression of the mitogen-inducible gene 6 (MIG6), a negative regulator of EGFR. The MIG6-mediated reduction of EGFR occurs concomitantly with a TGFβ-induced EMT-associated kinase switch of tumor cells to an AKT-activated EGFR-independent state. In a panel of 25 cancer cell lines of different tissue origins, we find that the ratio of the expression levels of MIG6 and miR200c is highly correlated with EMT and resistance to erlotinib. Analyses of primary tumor xenografts of patient-derived lung and pancreatic cancers carrying wild-type EGFR showed that the tumor MIG6(mRNA)/miR200 ratio was inversely correlated with response to erlotinib in vivo. Our data demonstrate that the TGFβ-miR200-MIG6 network orchestrates the EMT-associated kinase switch that induces resistance to EGFR inhibitors, and identify a low ratio of MIG6 to miR200 as a promising predictive biomarker of the response of tumors to EGFR TKIs.

KRAS mutation status is associated with enhanced dependency on folate metabolism pathways in non-small cell lung cancer cells

KRAS gene mutation is linked to poor prognosis and resistance to therapeutics in non-small cell lung cancer (NSCLC). In this study, we have explored the possibility of exploiting inherent differences in KRAS-mutant cell metabolism for treatment. This study identified a greater dependency on folate metabolism pathways in KRAS mutant compared with KRAS wild-type NSCLC cell lines. Microarray gene expression and biologic pathway analysis identified higher expression of folate metabolism- and purine synthesis-related pathways in KRAS-mutant NSCLC cells compared with wild-type counterparts. Moreover, pathway analysis and knockdown studies suggest a role for MYC transcriptional activity in the expression of these pathways in KRAS-mutant NSCLC cells. Furthermore, KRAS knockdown and overexpression studies demonstrated the ability of KRAS to regulate expression of genes that comprise folate metabolism pathways. Proliferation studies demonstrated higher responsiveness to methotrexate, pemetrexed, and other antifolates in KRAS-mutant NSCLC cells. Surprisingly, KRAS gene expression is downregulated in KRAS wild-type and KRAS-mutant cells by antifolates, which may also contribute to higher efficacy of antifolates in KRAS-mutant NSCLC cells. In vivo analysis of multiple tumorgraft models in nude mice identified a KRAS-mutant tumor among the pemetrexed-responsive tumors and also demonstrated an association between expression of the folate pathway gene, methylenetetrahydrofolate dehydrogenase 2 (MTHFD2), and antifolate activity. Collectively, we identify altered regulation of folate metabolism in KRAS-mutant NSCLC cells that may account for higher antifolate activity in this subtype of NSCLC.

Integrated next-generation sequencing and avatar mouse models for personalized cancer treatment

BACKGROUND

Current technology permits an unbiased massive analysis of somatic genetic alterations from tumor DNA as well as the generation of individualized mouse xenografts (Avatar models). This work aimed to evaluate our experience integrating these two strategies to personalize the treatment of patients with cancer.

METHODS

We performed whole-exome sequencing analysis of 25 patients with advanced solid tumors to identify putatively actionable tumor-specific genomic alterations. Avatar models were used as an in vivo platform to test proposed treatment strategies.

RESULTS

Successful exome sequencing analyses have been obtained for 23 patients. Tumor-specific mutations and copy-number variations were identified. All samples profiled contained relevant genomic alterations. Tumor was implanted to create an Avatar model from 14 patients and 10 succeeded. Occasionally, actionable alterations such as mutations in NF1, PI3KA, and DDR2 failed to provide any benefit when a targeted drug was tested in the Avatar and, accordingly, treatment of the patients with these drugs was not effective. To date, 13 patients have received a personalized treatment and 6 achieved durable partial remissions. Prior testing of candidate treatments in Avatar models correlated with clinical response and helped to select empirical treatments in some patients with no actionable mutations.

CONCLUSION

The use of full genomic analysis for cancer care is encouraging but presents important challenges that will need to be solved for broad clinical application. Avatar models are a promising investigational platform for therapeutic decision making. While limitations still exist, this strategy should be further tested.

Abstract C159: A human monoclonal antibody targeting the stem cell factor receptor (c-Kit) blocks tumor cell signaling and inhibits tumor growth

Stem cell factor receptor also known as c-Kit is a receptor tyrosine kinase that mediates cell growth, survival, and differentiation signals in response to its ligand stem cell factor (SCF). Aberrant c-Kit expression and/or activation through mutations or autocrine/paracrine signaling mechanisms occur in various malignancies and promote tumor development. Specific therapeutic targeting of c-Kit in cancer is warranted given its cancer role. In this study, we characterize the biological properties of CK6, a fully human IgG1 monoclonal antibody against the extracellular region of human c-Kit. CK6 specifically binds human c-Kit receptor with high affinity (EC50= 0.06nM) and strongly blocks its interaction with SCF (IC50= 0.41nM) in solid phase assays. Flow cytometry shows CK6 binding to the cell surface of small cell lung carcinoma (SCLC), melanoma, leukemia, and other human c-Kit expressing tumor cell lines. Furthermore, exposure to CK6 inhibits SCF stimulation of c-Kit tyrosine kinase activity and downstream signaling pathways in these tumor cell lines. Reduced levels of phosphorylated c-Kit, mitogen-activated protein kinase (MAPK) and protein kinase B/Akt were observed. Given these findings, we evaluated the antitumor growth efficacy of CK6 in several human xenograft tumor models in vivo. CK6 monotherapy treatment significantly suppressed tumor growth of NCI-H526 SCLC (T/C%= 50) and Malme-3M Melanoma (T/C%= 58) xenograft models. The combination of CK6 with standard of care (SOC) chemotherapy agents, cisplatin and etoposide for SCLC or dacarbazine for melanoma, led to enhanced tumor growth inhibition (SCLC T/C%= 12; melanoma T/C%= 38) compared to CK6 monotherapy or SOC alone. In summary, our results demonstrate that CK6 is a c-Kit antagonist antibody with tumor growth neutralizing properties and are highly suggestive of potential therapeutic application in treating human cancers harboring c-Kit receptor.

Citation Information: Mol Cancer Ther 2013;12(11 Suppl):C159.

Citation Format: Maria Lebron, Laura Brennan, Chris Damoci, Marie Prewett, Marina Starodubtseva, Michael Amatulli, Yiwei Zhang, Douglas Burtrum, Paul Balderes, Kris Persaud, David Surguladze, Nick Loizos, Keren Paz, Helen Kotanides. A human monoclonal antibody targeting the stem cell factor receptor (c-Kit) blocks tumor cell signaling and inhibits tumor growth. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr C159.

Integrated genomics and avatar mouse models for personalized cancer treatment

2511

Background: Every cancer has its unique set of molecular changes and the knowledge of such alterations is enabling an individualized approach to cancer treatment. The great intellectual challenge lies in linking confirmed mutations to protein function. Methods: Using massive parallel sequencing we performed whole exome sequencing analysis of 30 patients (pts) with advanced solid tumors to identify putatively actionable tumor-specific genomic alterations. We used 2 in silico methods (Polyphen and SIFT) to estimate the functional significance of a given confirmed mutation. Avatar models generated by direct engraftment of tumor samples from the patients into immunocompromised mice were used as an in vivo platform to test proposed treatment strategies. Results: Successful exome sequencing analyses has been obtained for 28 pts. Tumor specific mutations (Muts) and copy number variations were identified ranging from 5 to 952 and 0 to 956 respectively. All samples profiled contained relevant genomic alterations. Some of the most relevant actionable alterations were: CHEK1, FGFR2, IGF1R, MET, BRCA1, XPC, NOTCH, CREB3LB, GNA11, SMAD4, NF1, PTPRC, PI3KA, DDR2 and EGFR. An Avatar model was generated for 15 patients. In occasions actionable alterations such as muts in NF1, PTPRC, PI3KA and DDR2 failed to provide any benefit when a targeted drug was tested in the Avatar and accordingly treatment of the pts with these drugs was not effective. So far 13 pts have received a personalized treatment: two, as expected based on the avatar model, did not response; 5 resulted in durable partial remissions. Eight pts are currently on treatment with at least disease stabilization. Bench testing of candidate treatments in Avatar models correlated with clinical response and helped to select empirical treatments in patients with no actionable mutations. Conclusions: The use of full genomic analysis for cancer care is promising but presents important challenges that will need to be solved for broad clinical application. Avatar models are a powerful investigational platform for therapeutic decision making and help to guide cancer treatment in the clinic. While limitations still exist, this strategy should be tested in prospective randomized clinical trials.

Abstract 2205: Integrated next generation sequencing and patient-derived xenografts to personalized cancer treatment

Background: The knowledge of actionable somatic genomic alterations present in human tumors is enabling the new era of personalized cancer treatment. The great intellectual challenge lies in linking confirmed mutations to protein function. Personalized tumor graft models (Avatars) can aid in the process of genomic analyses interpretation to ultimately move from molecular profile to medication. Methods: Using massive parallel sequencing we performed whole exome sequencing analysis of tumor and matched normal blood samples of 23 patients (pts) with advanced solid tumors (7 lung cancer, 7 pancreatic cancer, 1 neuroendocrine tumor, 2 glioblastoma, 1 uveal melanoma, 2 melanomas and 3 colon cancer) to identify putatively actionable tumor-specific genomic alterations. Avatar models generated by direct engraftment of tumor samples from the pts into immunocompromised mice were used as an in vivo platform to test proposed treatment strategies. Results: Successful exome sequencing analyses has been obtained for 21 pts (1 patient died prematurely, 1 sample was insufficient). Tumor specific mutations (Muts) and copy number variations were identified ranging from 5 to 952 and 0 to 36 respectively. All samples profiled contained clinically meaningful genomic alterations. A successful Avatar model was generated for 10 out of 17 pts. Two engraftment failures corresponded to EGFR mutant lung tumors resected while pts were receiving erlotinib, which initially grew but then regressed. Some of the most relevant drugabble alterations were: KRAS, CHEK1, FGFR2, IGF1R, MET, BRCA1, XPC, NOTCH, CREB3LB, GNA11, SMAD4 and EGFR. In occasions druggable alterations such as muts in NF1, PTPRC, PI3KA and DDR2 failed to provide any benefit when a targeted drug was tested in the Avatar and accordingly treatment of the pts with these drugs was not effective. In one case, loss of STK11 lead to testing of mTOR and SRC inhibitors resulting in tumor regression both in the Avatar and in the clinic. At present time 10 pts have received a personalized treatment: 2 pts, as expected based on the Avatar model, did not response; 4 pts resulted in durable partial remissions and 4 pts are currently on treatment with disease stabilization. In one of the EGFR mutant lung pts the genomic analysis revealed traces of an acquired mutation and allowed decision making at an earlier time point, prior to relapse. Overall, there was a remarkable correlation between drug activity in the Avatar and clinical outcome in the pts, in terms of drug resistance and sensitivity. Conclusion: The detection of actionable tumor-specific genomic alterations in the clinical setting is feasible. However predicting treatment response to known oncogenes is complex and requires detailed information of how different genetic backgrounds function. Avatar models are a powerful investigational platform for therapeutic decision making and help to guide cancer treatment in the clinic.

Citation Format: Elena Garralda, Keren Paz, Pedro P. López-Casas, Siân Jones, Amanda Katz, Lisa M. Kann, Fernando López-Rios, Francesca Sarno, Fátima Al-Shahrour, David Vasquez, Elizabeth Bruckheimer, Samuel V. Angiuoli, Luis A. Diaz, Alfonso Valencia, Victor E. Velculescu, David Sidransky, Manuel Hidalgo. Integrated next generation sequencing and patient-derived xenografts to personalized cancer treatment. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2205. doi:10.1158/1538-7445.AM2013-2205

Abstract 2793: Development of an androgen-dependent prostate Champions TumorGraft™ cancer model

Prostate cancer (PCa)is the second most frequently diagnosed cancer and the sixth leading cause of cancer death in males, with the highest incidence rates recorded in developed countries such as those in North America (Jemal et al., 2011). While the five year-survival rate for PCa patients with localized disease is 100%, it is only 30.6% once the cancer metastasizes (Vishnu et al., 2010). One of the biggest challenges for finding a better treatment for metastatic PCa is the lack of predictable and accurate preclinical models that closely recapitulate different stages of the pathogenesis of human PCa. Champions Oncology focuses on the development of Champions TumorGraft™ models derived from the direct implantation of patient tumors into immunocompromised mice. Compared to traditional cell line-based xenograft models, the patient-derived TumorGraft models maintain stable gene-expression patterns and mutational status and correlate to clinical predictability. To overcome the challenge for PCa, Champions Oncology has utilized its TumorGraft technology to establish and characterize a new androgen-dependent prostate cancer TumorGraft model, CTG-0488. This involved the implantation of a primary human prostate tumor in immunocompromised mice in a manner that preserves the biological properties of the original human tumor. In this preliminary work, the characteristics of Champion TumorGraft™ model CTG-0488 are showcased, including tumor histology, mutational status, and chemosensitivity profiles to several standard of care compounds. Overall the development of an androgen-dependent prostate cancer Champions TumorGraft™ model will significantly aid in the development of oncology compounds focused on androgen-dependent prostate cancer.

Citation Format: Tin Oo Khor, Keren Paz, Dhanrajan Tiruchinapalli, David Sidransky, Elizabeth M. Bruckheimer. Development of an androgen-dependent prostate Champions TumorGraft™ cancer model. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2793. doi:10.1158/1538-7445.AM2013-2793

Abstract 1329: Personalizing gastrointestinal cancer treatment by the utilization of TumorGraft™ technology

Malignancies of the lower gastrointestinal (GI) tract share similarities in their symptoms, histology, genetic composition and sites of metastasis, but differ in their incidence rates. While colorectal cancer is common with over 130,000 new cases annually in the US alone, small intestinal adenocarcinoma is relatively rare with only 2500 new cases annually. Nevertheless, the overall clinical benefit of “standard of care” therapeutics is negligible, thereby underlining the need for novel therapeutics, especially personalized approaches. Champions Oncology focuses on personalizing cancer treatment via generating Tumorgraft models from each patient's individual whole tumor. The current study describes the attempt to identify a personalized solution for two patients with metastatic colorectal and duodenal cancers. Using Champions revolutionary Tumorgraft™ technology, personalized ‘trials’ were performed in vivo. Tumor fragments, obtained from the patient's liver metastases, were implanted into immunodeficient mice in a manner that preserves the biological properties of the original tumor and supporting stroma. Once the Tumorgrafts models were established, individual therapeutics and combinations were evaluated to identify treatment regimens likely to be maximally effective in the clinic. Each drug study encompassed 16 different treatment groups, including FDA-approved, as well as investigational agents. Of the different treatment arms in the colorectal model, two demonstrated partial response with tumor growth inhibition values of 152 and 149% for irinotecan/cetuximab/sunitinib and bevacizumab/cetuximab/irinotecan, respectively. While the combination of cetuximab/irinotecan resulted in stable disease in the duodenal model as well, complete responses were observed in all mice treated with eribulin as a single agent. Mutation status analysis of the tumors revealed wild type KRAS. Additional molecular characterization is ongoing to determine other potential signatures of response. The results from the Tumorgraft study were recommended to the patients and their medical oncologists and new lines of treatment were commenced subsequently. The results from these Tumorgraft studies, the molecular profile of the tumors, and correlation with clinical outcome will be presented. Results demonstrate the application of Personalized Tumorgraft models to personalized oncology and their impact on the future of cancer treatment.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1329. doi:1538-7445.AM2012-1329

Abstract 5252: Utilization of TumorGraft technology for personalized breast cancer treatment

Breast cancer is the most common cancer among women with over 280,000 new annual cases and 40,000 deaths in the US alone. While hormonal-dependent breast cancer is correlated with good prognosis, an adequate solution for hormonal-independent tumors remains an unmet medical need, largely due to a significant heterogeneity within tumors and their makeover. Various personalized oncology approaches aim at tailoring the optimal regimen for these patients by better understanding their tumor distinctiveness. Champions Oncology focuses on personalizing cancer treatment through the generation of TumorGraft™ models form the patient's own tumor. The current study is focused on the attempt to identify a personalized solution for a patient with HER2-amplified metastatic breast cancer whose disease progressed on Trastuzimab (Herceptin). Using Champions novel and cutting-edge TumorGraft™ technology, the challenge was confronted empirically by preforming a personalized clinical trial in vivo. Tumor fragments, obtained from both the primary breast tumor and lung metastasis, were implanted in immune-deficient mice in a manner that preserves the biological properties of the original tumor and its supporting stroma. Once the TumorGraft™ models were established, panel of drugs and drug combinations were evaluated to help identify treatment regimens that are likely to be most effective for the patient clinically. The drug study encompassed 7 different treatment groups including FDA-approved, as well as investigational agents. Of the 7 treatment arms, 3 demonstrated a significant anti-tumor response with tumor growth inhibition values of 80, 93 and 97% for Lapatinib+Capecitabine, Gemcitabine+Carboplatin and Ixabepilone+Capecitabine, respectively. Molecular analysis of the tumor revealed a truncated HER2 (p95) and a robust HER2 translocation to the nucleus. Additional molecular characterization is ongoing to determine other potential signatures of response. Results from the TumorGraft™ study were recommended to the patient and her medical oncologist and new lines of treatment were commenced subsequently. Herein, we describe the data from the TumorGraft™ drug study, the molecular exploration and the pathway analysis of the primary and the metastatic tumor and the consequences correlation to the clinical outcome.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5252. doi:1538-7445.AM2012-5252

Estimating preclinical efficacy targets utilizing cetuximab efficacy in KRAS mutant and wild-type colorectal cancer models

BACKGROUND

Clinically relevant targets for developmental drug efficacy in animal models of cancer are critical yet understudied parameters.

MATERIALS AND METHODS

Cetuximab, a chimeric antibody to epidermal growth factor receptor (EGFR), was administered to athymic mice bearing subcutaneous tumors established with 13 human colorectal cancer cell lines of varying biomarker status, defined by DNA sequencing and RT-PCR.

RESULTS

If tumor growth inhibition is taken as a target, as is commonly done, then in contrast to the clinical situation where KRAS mutation strongly predicts for a lack of clinically meaningful benefit in colorectal cancer patients, cetuximab alone and in combination with irinotecan-based chemotherapy were efficacious in a similar proportion of KRAS wild-type and mutant models. It was only when tumor regression was utilized to define relevant efficacy that cetuximab monotherapy was efficacious in KRAS wild-type, but not mutant models. Adding cytotoxic therapy to cetuximab treatment increased tumor regression frequency in both genotypes to the point that once again the response was similar for KRAS wild-type and mutant models.

CONCLUSION

Our data support shifting the threshold for claiming clinically relevant targeted therapy efficacy in subcutaneous xenograft models towards tumor regression, rather than tumor growth inhibition, focusing on the evaluation of tumor cells that are addicted to the pathways being targeted.

Abstract 3641: Breaking through the ceiling: A program to significantly increase efficacy in KRAS and BRAF mutant colorectal cancer xenograft tumors whose growth is arrested by Cetuximab + irinotecan therapy

Cetuximab has significant clinical benefits alone or in combination with irinotecan in metastatic colorectal cancer (mCRC) patients with KRAS wild type tumors, but efficacy in patients with KRAS mutant tumors has thus far been elusive. Mutant BRAF in mCRC tumors may also predict for reduced benefit with EGFR antibodies. Interestingly, in preclinical CRC models, cetuximab, alone or in combination with irinotecan, has significant efficacy in tumor models with mutant KRAS or BRAF. Here we examine if this preclinical efficacy can be significantly increased in a screen for add-on therapies that may provide clinically meaningful efficacy in mCRC patients requiring an EGFR antibody.

HT-29 (BRAF mutant-V600E) and HCT-116 (KRAS mutant-G38D) cell lines were utilized as models of CRC. We screened 14 compounds that could potentially add to the effects of cetuximab+irinotecan (C+I) treatment, including inhibitors of inflammation, enzymes, receptor tyrosine kinases, HSP90, cyclins, mTOR, an ATP mimetic, activators of apoptosis and PPARγ.

Of the compounds evaluated only 17-AAG (HSP90 inhibitor), everolimus(mTOR inhibitor) and DC101 (antibody targeting murine VEGFR2) significantly broke the ceiling of tumor stasis established with C+I treatment alone in both models. 17-AAG+C+I resulted in T/C% values of 14 and 32% in HCT-116 and HT-29, respectively, compared to 25 and 62% in the C+I treatment group. Follow up studies showed this benefit to be due to an additive interaction between 17-AAG and irinotecan, which was also associated with significant weight loss. Everolimus+C+I treatment resulted in a T/C% of 15 and 22% in HCT-116 and HT-29, respectively, compared to 22 and 35% in the C+I treatment group. The benefits of everolimus+C+I on the other hand required all three agents. The combination of DC101+C+I was significantly more efficacious than C+I in both models, with a T/C% of 11 and 33% in HCT-116 and HT-29, respectively, compared to 19 and 53% in C+I treatment group. In contrast to these three therapies, all other compounds evaluated did not improve the antitumor effects of C+I alone.

Results demonstrate a ceiling effect in CRC models with KRAS or BRAF gene mutations that may be associated with the limited clinical benefits observed with cetuximab in patients. The fact that this ceiling can be broken with everolimus in a manner that requires cetuximab, supports the potential utility of cetuximab in these patients in a combination approach.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3641. doi:10.1158/1538-7445.AM2011-3641

Abstract 1187: The role of PI3K as a biomarker

The phosphatidylinositol 3-kinase (PI3K) signaling pathway has been implicated in tumorigenesis. Evidence over the past years suggests a pivotal role for the catalytic subunit, PIK3CA, in human cancers. Receptor tyrosine kinases (RTKs) on the cell surface are key regulators of PI3K activity, and RTK antagonists have demonstrated significant anticancer effects in animal models and in patients. However, among tumor harboring activating mutations of PIK3CA, the therapeutic value of RTK antagonists may be compromised. The mutation status of PIK3CA may, therefore, serve as a potential biomarker for both prognosis and response to RTK inhibitors.

Somatic mutations of the pik3ca gene occur primarily in three hot spots, E542K, E545K (exon 9) and H1047R (exon 20). These mutations are detected in a broad spectrum of cancer indications including breast, colorectal and lung. This study was designed to explore the nature of PIK3CA mutations among numerous human cancer cell lines, utilizing mostly cells with the capacity to form tumors in mice. Primers corresponding to exon 9 and 20 of human pik3ca gene were designed. Genomic DNA was harvested from over 200 lines, derived from different human cancer indications. The pik3ca locus was sequenced and its WT or mutation status was determined.

Of these cells, 8% presented mutations equally distributed between exon 9 and 20. The frequency of PIK3CA mutations was particularly high among colon cancer lines, with fewer incidences among lung, breast and ovarian cancer lines. Interestingly, 50% of the PIK3CA mutated lines presented a concurrent mutation of either KRAS or BRAF. The capacity of PIK3CA mutation-bearing cell lines to respond to RTK blockers was then evaluated, and the mechanism contributing to such phenomenon was further discussed.

These results stress PI3K diagnosis value and its potential role as a valid biomarker for patient susceptibility.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1187.

Targeted therapy of the insulin-like growth factor-1 receptor in cancer

Recently, significant progress has been made towards understanding the pathogenesis of cancer from the molecular standpoint. To this end, a growing number of approaches are being exploited for the identification and validation of new therapeutic targets suitable for potent and specific intervention. The type 1 insulin-like growth factor receptor (IGF-1R) system has recently become the focus of major attention in the arena of cancer research. The involvement of the receptor and its downstream signaling cascades in the carcinogenesis process makes this system an excellent target for potential cancer therapy. Indeed, advances in the understanding of the molecular mechanisms behind IGF-1R activation have led to the discovery of agents designed selectively for targeting IGF-1R. The potential application of these inhibitors is currently under intense clinical investigation. This review describes the biology of IGF-1R particularly from a cancer perspective. The attempts to develop effective IGF-1R antagonists are discussed comprehensively with special emphasis on antibodies and small tyrosine kinase inhibitors.