Abstract 393: NOTCH1 inactivating mutation mediates sensitivity to PI3K/mTOR inhibitors in head and neck squamous cell carcinoma

Recently published whole exome sequencing studies in head and neck squamous cell carcinoma (HNSCC) tumors revealed that few had therapeutically targetable alterations using current strategies. This finding defines translational gap between genomics and HNSCC treatment. One potential targetable alteration is PIK3CA mutations. However, clinical trials testing PI3K/mTOR pathway inhibitors have had limited success and these inhibitors only lead to cell cycle arrest in PIK3CA mutant HNSCC cell lines. Thus, there is a critical need to identify therapeutic vulnerabilities for common mutation groups, including tumor suppressors, in HNSCC. One of these molecular subgroups is NOTCH1 which is the second most frequently mutated gene in HNSCC, with a 10-15% prevalence of inactivating mutations. Although there are several studies underscoring the importance of NOTCH1 as a tumor suppressor in HNSCC, none has identified a therapy that targets NOTCH1 mutant (mut) HNSCC. Our objective was to identify predictive biomarkers of sensitivity to PI3K/mTOR inhibitors by integrating drug and multiple-omics data.

Cell viability with six PI3K/mTOR inhibitors in 68 HNSCC lines was measured by the CellTiter Glo assay. The peak plasma concentration of each drug was used as the cut-off to determine sensitivity. We observed a striking correlation between NOTCH1mut and sensitivity to PI3K/mTOR pathway inhibitors. When fisher's exact test was performed, NOTCH1mut lines were more sensitive to GSK2126458 (P<0.027), BYL719 (P<0.004) and PQR309 (P<0.014) than NOTCH1 wild type cell lines. NOTCH1 was also identified as an upstream regulator in sensitive cell lines by Ingenuity® Pathway Analysis. Basal NOTCH1 protein expression was higher in HNSCC lines resistant to PI3K/mTOR inhibition using unsupervised hierarchical clustering of Reverse Phase Protein Array data.

NOTCH1mut lines underwent more apoptosis after GSK2126458 treatment compared to NOTCH1wt lines (PCI15B- 48.1 fold; P<0.05, HN31- 46.9 fold; P<0.05). There was also increased accumulation of cells in G1 after GSK2126458 treatment in NOTCH1mut lines (PCI15B-1.3 fold, P<0.05; HN31- 1.4 fold, P<0.05). To check if inhibition of NOTCH1 pathway inhibition sensitizes NOTCH1wt lines to PI3K/mTOR inhibition, resistant NOTCH1wt lines were treated with Gamma secretase inhibitors and GSK2126458. The combination led to significantly decreased cell viability (DAPT- 1.5 fold and YO010227- 1.7 fold). The combination studies will be further expanded to 38 NOTCH1wt lines. On-going studies include assessment of drug sensitivity in vivo, mechanistic studies and the effect of genetic manipulation of NOTCH1 signaling on sensitivity to PI3K/mTOR inhibitors.

Our data suggests that loss of active NOTCH1 signaling confers sensitivity to PI3K/mTOR inhibition. If the combination of NOTCH1 and PI3K/mTOR inhibition leads to apoptosis, this combination could be translated into the clinic.

Citation Format: Faye M. Johnson, Vaishnavi Sambandam, Li Shen, Ming Zhang, Rishi Saigal, Pan Tong, Tuhina Mazumdar, Lauren A. Byers, Curtis Pickering, Jeffrey N. Myers, Jing Wang, Mitchell Frederick. NOTCH1 inactivating mutation mediates sensitivity to PI3K/mTOR inhibitors in head and neck squamous cell carcinoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 393.

Abstract 3793: Cell-based, high-throughput screen for small molecule inducers of cell death in HPV-associated head and neck cancers

High-risk human papillomavirus (HPV) is an oncogenic virus associated with 90% of cervical cancers, over 60% of oropharyngeal carcinoma cases and over 90% of anogenital cancers. Although HPV-positive cancers are molecularly, clinically and epidemiologically distinct from HPV-negative cancers, there are no specific or targeted therapies for HPV-positive cancers. In order to identify small molecule inhibitors that target HPV-positive cancers, we performed a high throughput drug screen on 24 cervical cancer and head and neck squamous cell carcinoma (HNSCC) cell lines (12 HPV-positive and 12 HPV-negative) to determine if these cell lines display differential sensitivity based on HPV status. HPV-positive cell lines with doubling times of less than 72 hours were selected for the screen. Unsupervised clustering of HNSCC cell lines based on protein expression levels obtained from reverse phase protein array (RPPA) was used to select matched HPV-negative cell lines by Spearman's rank-order correlation. Cytotoxic chemotherapeutics and agents targeting a broad range of processes including cell cycle control and DNA damage response were obtained from commercial vendors and academic collaborators. Drug sensitivity was measured by using nuclear staining to monitor cell death and proliferation after 72h of treatment. The screen of 1062 unique compounds at 6 different concentrations (0-3μM) in 24 cell lines represents 25,448 cell line – drug interactions. To ensure the robustness and reproducibility of the screen, the Z-factor and standard deviation for biological replicates were calculated. A Z-factor greater 0.5 was considered acceptable and the mean standard deviation across all drugs for each cell line was 0.06. Drug sensitivity was determined by calculating IC50 and area under the curve (AUC) values. Overall, HPV-positive HNSCC cell lines showed greater sensitivity to 13 drugs from different classes. Particularly, HPV-positive HNSCC cells were more sensitive to p38 MAPK and B-Raf inhibitors including LY2228820 (p < 0.01), regorafenib (p < 0.01), sorafenib (p < 0.05) and SB590885 (p < 0.05). On the other hand, HPV-negative HNSCC lines showed increased sensitivity to 30 drugs among these, palbociclib (p < 0.01), a CDK 4/6 inhibitor, and ryuvidine (p <0.05) which is reported to inhibit CDK 4. We are currently in the process of performing mechanistic studies and identifying genomic characteristics that influence sensitivity to B-Raf and p38 MAPK inhibitors in HPV-associated cancers using the genomic analyses and drug sensitivity data. Given the difference in clinical outcomes based on HPV status, any validated chemical-genomic interactions we discover will provide strong support for HPV-based treatment plans that may improve efficacy, allow for dose de-escalation and prevent permanent toxicity in patients.

Citation Format: Nene N. Kalu, Tuhina Mazumdar, Pan Tong, Li Shen, Jing Wang, Lauren Averett Byers, Faye M. Johnson. Cell-based, high-throughput screen for small molecule inducers of cell death in HPV-associated head and neck cancers. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3793.

Abstract 4757: Identification of biomarkers that predict response of head and neck squamous cell carcinoma to mitotic inhibitors

Objectives: It is urgent to explore novel biomarkers and therapeutic targets for that are relevant to head and neck squamous cell carcinoma (HNSCC), which is the 6th most common cancer worldwide. Based on a prior drug screen, we identified 3 mitotic inhibitors (AZD7762, AZD1775, volasertib) as effective therapies for HNSCC. Our objective with this study is to identify mechanisms of response and potential biomarkers of response and

Methods: Cell viability assays were performed by the CellTiter-Glo Luminescent method in a panel of 68 fingerprinted HNSCC cell lines using the 3 drugs at concentrations of 0.018 to 9.613 μM. Cell cycle, apoptosis and altered pathway protein expression after cells treated by the polo-like kinase 1 (PLK1) inhibitor volasertib were investigated by FACS, TUNEL and western blots respectively. An orthotopic mouse model of HNSCC was used to confirm the antitumor effects of PLK1 inhibition in vivo. To determine the mechanisms of drug sensitivity, we analyzed the correlation between gene expression, protein expression, gene mutation and drug sensitivity using modified two-sample t-tests were performed. The beta-uniform mixture (BUM) model was used to control false discovery rate (FDR). For correlations between drug sensitivity and gene mutations, we performed Fisher's exact test.

Results: Using the IC80 values with the peak plasma concentration of each drug as the cut-off to determine sensitivity, 34, 44 and 20 HNSCC cell lines were sensitive AZD1775 (Wee inhibitor), AZD7762 (CHK1/2 inhibitor) and volasertib (PLK1 inhibitor) respectively. HNSCC harboring AJUBA mutations were more sensitive to these 3 inhibitors and those with RAS mutations more resistant. PLK1 inhibition led to G2/M arrest, but only sensitive cell lines underwent substantial apoptosis following PLK1 inhibition. Decreases of the levels of phosphorylated TCTP were observed following treatment with volasertib confirming PLK1 inhibition. There was a significant decrease of tumor volumes and prolongation of survival in the mice bearing orthotopic HNSCC tumors treated with volasertib in vivo.

Conclusions: PLK1 inhibition was an effective therapy in vitro and in vivo models of HNSCC. We identified the AJUBA and RAS mutations as potential candidate biomarkers of response to these mitotic inhibitors in HNSCC. This study identified the therapeutic potential of PLK1 as a novel therapeutic target for HNSCC.

Citation Format: Ming Zhang, Shaohua Peng, Tuhina Mazumdar, Vaishnavi Sambandam, Li Shen, Pan Tong, Lerong Li, Lauren Byers, Curtis Pickering, Mitchell Frederick, Jeffrey N. Myers, Jing Wang, Faye M. Johnson. Identification of biomarkers that predict response of head and neck squamous cell carcinoma to mitotic inhibitors. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4757.

Abstract 4665: The combination of polo-like kinase 1 inhibition and erlotinib overcomes T790M-mediated drug resistance in vitro and in vivo in non-small cell lung cancer

Introduction: Activation of epidermal growth factor receptor (EGFR) leads to the development and progression of human epithelial cancers, including non-small cell lung cancer (NSCLC). EGFR tyrosine kinase inhibitors (EGFR-TKI) are effective therapy for NSCLC with activating EGFR mutations. However, acquired resistance to EGFR-TKIs is unavoidable and occurs through various molecular mechanisms including the development of T790M secondary EGFR mutations, MET amplification, epithelial-mesenchymal transition (EMT) and other mechanisms. One of potential strategy to overcome EGFR-TKIs is through inhibition of polo-like kinase 1 (PLK1). PLK1 is one of the key regulators of mitotic progression and a DNA damage recovery checkpoint. PLK1 inhibitors are at various stages of clinical development. Our previous studies showed that mesenchymal NSCLC cell lines are more sensitive to PLK1 inhibitor than epithelial ones. This study examines the efficacy of PLK1 inhibition in NSCLC cell lines with acquired resistance to the EGFR-TKI erlotinib.

Methods: Erlotinib resistant cell lines were developed in EGFR mutant, erlotinib sensitive cell lines PC9, HCC4006 and HCC827 by chronic exposure to stepwise increased concentrations of erlotinib. The effects of the PLK1 inhibitor volasertib alone or combined with erlotinib on proliferation, apoptosis, cell cycle, EGFR-dependent signaling, DNA damage and DNA damage response signaling were evaluated using CellTiter-Glo assay, TUNEL assay, BrDU incorporation assay, comet assay, western blot and immunofluorescence. Sensitivity of volasertib alone or in combination with erlotinib was also detected in the human tumor xenograft model. The combination index (CI) was calculated by Calcusyn software.

Results: Acquired erlotinib resistant NSCLC cell lines with endogenous EGFR mutations (PC9, HCC4006 and HCC827) showed diverse resistance mechanisms: T790M EGFR mutation, MET amplification and EMT. Four of the 6 ER clones that underwent EMT became more sensitive to volasertib. Volasertib and erlotinib demonstrated synergistic effects only in cells bearing T790M EGFR mutations where we observed more pronounced G2M arrest and increased apoptosis. Volasertib alone or in combination showed enhanced DNA damage, activation of CHK1/ATR and CHK2/ATM pathways and an increase in γH2AX foci but only a modest effect on canonical signaling downstream of EGFR. The combination treatment exhibited a pronounced reduction in the size of tumor compared to single agent treatment in subcutaneous xenograft model generated with T790M mutant EGFR TKI-resistant PC9 cell line.

Conclusions: These data demonstrate that PLK1 inhibition alone induces apoptosis and DNA damage in EGFR-TKI resistant cell lines with EMT. The combination of volasertib and erlotinib overcomes T790M-mediated drug resistance in vitro and in vivo.

Citation Format: Ratnakar Singh, Yuehong Wang, Liguang Wang, Monique Nilsson, Ruchitha Goonatilake, Pan Tong, Lerong Li, Uma Giri, Jing Wang, John V. Heymach, Faye M. Johnson. The combination of polo-like kinase 1 inhibition and erlotinib overcomes T790M-mediated drug resistance in vitro and in vivo in non-small cell lung cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4665.

Phase I Study of LY2606368, a Checkpoint Kinase 1 Inhibitor, in Patients With Advanced Cancer

PURPOSE

The primary objective was to determine safety, toxicity, and a recommended phase II dose regimen of LY2606368, an inhibitor of checkpoint kinase 1, as monotherapy.

PATIENTS AND METHODS

This phase I, nonrandomized, open-label, dose-escalation trial used a 3 + 3 dose-escalation scheme and included patients with advanced solid tumors. Intravenous LY2606368 was dose escalated from 10 to 50 mg/m(2) on schedule 1 (days 1 to 3 every 14 days) or from 40 to 130 mg/m(2) on schedule 2 (day 1 every 14 days). Safety measures and pharmacokinetics were assessed, and pharmacodynamics were measured in blood, hair follicles, and circulating tumor cells.

RESULTS

Forty-five patients were treated; seven experienced dose-limiting toxicities (all hematologic). The maximum-tolerated doses (MTDs) were 40 mg/m(2) (schedule 1) and 105 mg/m(2) (schedule 2). The most common related grade 3 or 4 treatment-emergent adverse events were neutropenia, leukopenia, anemia, thrombocytopenia, and fatigue. Grade 4 neutropenia occurred in 73.3% of patients and was transient (typically < 5 days). Febrile neutropenia incidence was low (7%). The LY2606368 exposure over the first 72 hours (area under the curve from 0 to 72 hours) at the MTD for each schedule coincided with the exposure in mouse xenografts that resulted in maximal tumor responses. Minor intra- and intercycle accumulation of LY2606368 was observed at the MTDs for both schedules. Two patients (4.4%) had a partial response; one had squamous cell carcinoma (SCC) of the anus and one had SCC of the head and neck. Fifteen patients (33.3%) had a best overall response of stable disease (range, 1.2 to 6.7 months), six of whom had SCC.

CONCLUSION

An LY2606368 dose of 105 mg/m(2) once every 14 days is being evaluated as the recommended phase II dose in dose-expansion cohorts for patients with SCC.

Epithelial-Mesenchymal Transition Predicts Polo-Like Kinase 1 Inhibitor-Mediated Apoptosis in Non-Small Cell Lung Cancer

PURPOSE

To identify new therapeutic targets for non-small cell lung cancer (NSCLC), we systematically searched two cancer cell line databases for sensitivity data on a broad range of drugs. We identified polo-like kinase 1 (PLK1) as the most promising target for further investigation based on a subset of sensitive NSCLC cell lines and inhibitors that were in advanced clinical development.

EXPERIMENTAL DESIGN

To identify potential biomarkers of response of NSCLC to PLK1 inhibition and mechanisms of PLK1 inhibitor-induced apoptosis, integrated analysis of gene and protein expression, gene mutations, and drug sensitivity was performed using three PLK1 inhibitors (volasertib, BI2536, and GSK461364) with a large panel of NSCLC cell lines.

RESULTS

The NSCLC cell lines had different sensitivities to PLK1 inhibition, with a minority demonstrating sensitivity to all three inhibitors. PLK1 inhibition led to G2-M arrest, but only treatment-sensitive cell lines underwent substantial apoptosis following PLK1 inhibition. NSCLC lines with high epithelial-mesenchymal transition (EMT) gene signature scores (mesenchymal cell lines) were more sensitive to PLK1 inhibition than epithelial lines (P< 0.02). Likewise, proteomic profiling demonstrated that E-cadherin expression was higher in the resistant cell lines than in the sensitive ones (P< 0.01). Induction of an epithelial phenotype by expression of the miRNA miR-200 increased cellular resistance to PLK1 inhibition. Also, KRAS mutation and alterations in the tight-junction, ErbB, and Rho signaling pathways correlated with drug response of NSCLC.

CONCLUSIONS

In this first reported large-scale integrated analysis of PLK1 inhibitor sensitivity, we demonstrated that EMT leads to PLK1 inhibition sensitivity of NSCLC cells. Our findings have important clinical implications for mesenchymal NSCLC, a significant subtype of the disease that is associated with resistance to currently approved targeted therapies.

Radiation therapy (with or without neck surgery) for phenotypic human papillomavirus-associated oropharyngeal cancer

BACKGROUND

Favorable outcomes for human papillomavirus-associated oropharyngeal cancer have led to interest in identifying a subgroup of patients with the lowest risk of disease recurrence after therapy. De-intensification of therapy for this group may result in survival outcomes that are similar to those associated with current therapy but with less toxicity. To advance this effort, this study analyzed the outcomes of oropharyngeal cancer patients treated with or without systemic therapy.

METHODS

This was a retrospective study of patients with oropharyngeal cancer treated between 1985 and 2012. The criteria for inclusion were ≤10 pack-years of cigarette smoking and stage III/IVA cancer limited to T1-3, N1-N2b, and T3N0 disease. A survival analysis was performed with the primary endpoint of progression-free survival (PFS).

RESULTS

The cohort included 857 patients. Systemic therapy was given to 439 patients (51%). The median survival was 80 months. The 2-year PFS rate was 91%. When the analysis was limited to 324 patients irradiated without systemic therapy, the 2- and 5-year PFS rates were 90% and 85%, respectively. Furthermore, for these 324 patients, the 5-year PFS rates for T1, T2, and T3 disease were 90%, 83%, and 70%, respectively. The 5-year PFS rate for patients treated with systemic therapy for T3 disease was 77% (P = .07).

CONCLUSIONS

According to the low-risk definition currently established in cooperative trials, the patients had a 2-year PFS rate approximating 90%. When patients who were treated with radiation alone were evaluated, no compromise was observed in this high rate of PFS, which is higher than the 2-year PFS thresholds used in current cooperative trials. Cancer 2016;122:1702-7. © 2016 American Cancer Society.

Abstract 1826: Characterization of HPV-positive head and neck cancer cell lines as preclinical models for targeted therapy

Background:Head and neck squamous cell carcinoma (HNSCC) is the 6th most frequently diagnosed non-skin cancer in the world. Risk factors associated with HNSCC include smoking, alcohol use and human papillomavirus (HPV) infection. With the decline in tobacco use, there has been an increase in the incidence of HPV-associated head and neck cancers. Our increased understanding of the mutational landscape demonstrates that HPV-positive and HPV-negative HNSCC are molecularly distinct. Additionally, patients with HPV-positive tumors respond better to therapy and have better prognosis overall. However, there are no targeted therapies for HPV+ HNSCC. Human cell lines can serve as preclinical models for studying cancer progression and identifying possible therapeutic targets. Our aim was to determine if HNSCC tumors and cell lines derived from head and neck tumors display similar proteomic profiles. Methods: Reverse phase protein array (RPPA) analysis was performed on 66 HNSCC cell lines. The HPV-status of these cell lines was determined by quantitative and reverse transcriptase polymerase chain reaction (PCR). Results: Real-time PCR analysis confirmed that 9 of the 66 cell lines were HPV-positive. Differential expression of 156 proteins was analyzed and proteomic pathway scores were determined by t-test in HPV-positive and HPV-negative HNSCC cell lines. We identified significant proteomic differences between HPV-positive and negative HNSCC cell lines. As observed in HPV-positive head and neck tumors, the clinical biomarker p16 was overexpressed in HPV-positive cell lines (p-value &lt;0.0001). Furthermore, the expression of other cell cycle proteins p21 (p-value &lt;0.0001) is lower in HPV-positive cell lines while cyclin E1 (p-value &lt;0.03) and pRb (p-value &lt;0.0001) are higher in HPV-positive cell lines. Similar to RPPA profiles of HNSCC tumors, HPV-positive cell lines show less epithelial to mesenchymal transition as indicated by lower levels of fibronectin and N-cadherin. When compared to HNSCC tumors, we also observed dysregulated expression of receptor tyrosine kinases such as epidermal growth factor receptor (EGFR). In comparison to HNSCC tumors, cell lines share similar trends in proteomic profiles. Conclusion: Our findings suggest that HNSCC cell lines are suitable preclinical models for the discovery of pathways activated in HPV-positive HNSCC and identification of possible targets for new therapeutic strategies.

Citation Format: Nene N. Kalu, Tuhina Mazumdar, Lixia Diao, Patrick Kwok Shing Ng, Jing Wang, Jeffery Myers, Faye M. Johnson, Lauren Averett Byers. Characterization of HPV-positive head and neck cancer cell lines as preclinical models for targeted therapy. [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 1826. doi:10.1158/1538-7445.AM2015-1826

Abstract 2427: The difference of drug sensitivity between HPV-positive and HPV-negative head and neck squamous cell carcinoma cell lines

Objectives: Infection with the human papillomavirus (HPV) is an important risk factor for development of head and neck squamous cell carcinoma (HNSCC). Strikingly, HPV-positive HNSCCs carry a more favorable prognosis and are a biologically distinct subgroup when compared with their HPV-negative counterparts. We aimed to discover novel therapeutic targets by conducting a high-throughput drug screening platform in vitro with both FDA approved and investigational drugs. Based on our prior proteomic analysis we tested inhibitors of pathways activated in HPV+ HNSCC tumors.

Methods: Cell viability assays were performed by the Cell Titer Glo method in a panel of 66 fingerprinted HNSCC cell lines using 13 drugs at concentrations of 0.011 to 9.613 μM. This panel includes 9 HPV+ lines and 57 HPV- lines (5 oropharynx, 15 oral cavity, and 37 others). The IC50 values were calculated. Western Blot assay was used to confirm that the drugs inhibited their targets.

Results: We observed a wide range of sensitivities to all 13 drugs with the exception of BKM120 which was effective in all tested lines (Table 1). In contrast, nearly all cell lines were resistant to BMN673, ruxolitinib, LEE011, and selicilib. The HPV+ cell lines were more sensitive to MEK162 (p&lt;0.05) and resistant to Bosutinib (p&lt;0.01) when compared to the HPV- HNSCC cell lines or oropharynx and oral cavity cell lines (Table 2). Western blotting confirmed target inhibition for the targeted therapies.

Conclusions: For most agents tested, HNSCC cell lines displayed similar drug sensitivity regardless of the tumor site. However, HPV+ lines were more sensitive to MEK162 and more resistant to Bosutinib. Future analysis will include comparing drug sensitivity to mutation, gene and protein expression in these lines. Taken together, the results may provide a rationale for the clinical evaluation of MEK inhibitors as a molecular targeted approach for the treatment of HPV+ HNSCC.

Table 1. IC50 values in 66 HNSCC cell lines

DrugDrug's targetMedian IC50 (μM)Range of IC50(μM)Cmax (μM)ErlotinibEGFR5.970.12- &gt;9.614LEE011CDK4/69.610.01- &gt;9.61NABKM120PI3K0.640.01- &gt;1.434MEK162MEK9.610.01- &gt;9.611BosutinibSrc2.320.19- &gt;9.610.8SeliciclibCDK2/59.610.01- &gt;9.619.02VolasertibPLK1.120.01- &gt;9.611.2AZD7762CHK1/20.120.02- &gt;3.02NADocetaxelChemotherapy9.610.01- &gt;9.610.08CisplatinChemotherapy8.620.01- &gt;9.617.33RuxolitinibJAK9.610.01- &gt;9.611.48AZD1775Wee10.250.03- &gt;7.521.65BMN673PARP9.610.20- &gt;9.610.07

Citation Format: Ming Zhang, Tuhina Mazumdar, Shaohua Peng, Pan Tong, Vaishnavi Sambandam, Lauren A. Byers, Jeffrey N. Myers, Jing Wang, Faye M. Johnson. The difference of drug sensitivity between HPV-positive and HPV-negative head and neck squamous cell carcinoma cell lines. [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 2427. doi:10.1158/1538-7445.AM2015-2427

Abstract 417: Integrative drug sensitivity analysis of PI3K /mTOR pathway inhibitors in Head and Neck Squamous Cell Carcinoma (HNSCC)

Background: HNSCC is the sixth most common cancer worldwide. To date, Cetuximab is the only approved targeted therapy for HNSCC treatment. Thus,there is an immediate need to discover effective targets. Two pharmacogenomic HTS studies, Cancer Genome Project (CGP) and Cancer Cell Line Encyclopedia (CCLE) provide a large repository of drug sensitivity data. The PI3K/mTOR pathway is one of the frequently activated signaling cascades in HNSCC. However, it is unclear which class of PI3K/mTOR inhibitors is most promising and which biomarkers may be used to predict sensitivity. The rationale for this study is to identify novel biomarkers to targets such as PI3K/mTOR pathway by data mining these public databases. The potential biomarkers will be characterized in vitro in 68 HNSCC cell lines.Methods:The landscape of drug sensitivity profiles in 23 HNSCC cell lines (CGP) was analyzed by boxplot illustrations. Drugs that induce growth inhibition at low doses (median≤10 μM) were considered “effective”. Chemotherapy drugs, drugs with missing values and unknown targets were excluded from analyses. Hierarchical clustering of cell lines was performed based on drug sensitivity using GOWER distance metric and Ward's linkage after normalization. Clustering of 140 drugs based on their sensitivity profiles was also done. In vitro, drug response to PI3K pathway inhibitors in 28 HNSCC cell lines was assessed by ATP based cell viability assay (CellTiter-Glo). Results: In the CGP datasets, we identified a set of effective drugs with median IC75&lt;10 μM. These include drugs targeting HDAC, HSP, BCL2 and CHK1/2, and PI3K/mTOR pathway. When hierarchical clustering of drugs based on drug sensitivity was performed, 3 clusters were classified. Predictably, chemotherapy agents clustered together. Selective drugs that were effective in a subset of cell lines were also identified. To identify cell lines that were uniformly sensitive to inhibitors targeting the PI3K/mTOR pathway, diverse classes of inhibitors targeting PI3K pathway were selected and drug sensitivity was analyzed across 28 HNSCC cell lines. Notably, all cell lines were sensitive to the pan Class I PI3K inhibitor, BKM120 (IC75 &lt;Cmax: 1.68 μM). We identified seven lines that were resistant and twelve lines that were sensitive to different PI3K/mTOR inhibitors. To identify novel biomarkers of sensitivity, we will use Reverse Phase Protein Array (RPPA), exome sequencing and gene expression data on cells that are uniformly sensitive and resistant to PI3K pathway inhibition. Conclusion: HNSCC cell lines were sensitive to a broad range of targeted therapies in in vitro screens including several inhibitors of the PI3K/mTOR pathway. We independently confirmed sensitivity to similar inhibitors and identified lines that were universally sensitive and resistant to this class of drug for biomarker development.

Citation Format: Vaishnavi Sambandam, Li Shen, Ming Zhang, Rishi Saigal, Lauren A. Byers, Curtis Pickering, Jeffrey N. Myers, Jing Wang, Faye M. Johnson. Integrative drug sensitivity analysis of PI3K /mTOR pathway inhibitors in Head and Neck Squamous Cell Carcinoma (HNSCC). [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 417. doi:10.1158/1538-7445.AM2015-417

Wee-1 Kinase Inhibition Sensitizes High-Risk HPV+ HNSCC to Apoptosis Accompanied by Downregulation of MCl-1 and XIAP Antiapoptotic Proteins

PURPOSE

Although the majority of patients with HPV(+) oropharyngeal cancers have a favorable prognosis, there are some patients with tumors that are resistant to aggressive chemoradiotherapy with unusual patterns of locoregional and systemic recurrences. Therefore, more effective therapies are needed. In this study, we investigated the chemosensitizing efficacy of the selective Wee-1 kinase inhibitor, AZD-1775, in HPV(+) head and neck squamous cell carcinoma (HNSCC).

EXPERIMENTAL DESIGN

Clonogenic survival assays and an orthotopic mouse model of HPV(+) oral cancer were used to examine the in vitro and in vivo sensitivity of HPV(+) HNSCC cell lines to AZD-1775 in combination with cisplatin, respectively. Cell-cycle analysis, DNA damage (γH2AX), homologous recombination (HR), and apoptosis were examined to dissect molecular mechanisms.

RESULTS

We found that AZD-1775 displays single-agent activity and enhances the response of HPV(+) HNSCC cells to cisplatin both in vitro and in vivo. The sensitivity of the HPV(+) HNSCC cells to AZD-1775 alone or in combination with cisplatin was associated with G2 checkpoint abrogation, persistent DNA damage, and apoptosis induction. This finding of AZD-1775 increasing the sensitivity of HPV(+) HNSCC cells to cisplatin through apoptosis was not seen previously in the HPV(-) HNSCC cancer cells and is accompanied by a decreased expression of the antiapoptotic proteins, MCl-1and XIAP, which appear to be cleaved following AZD-1775 treatment.

CONCLUSIONS

AZD-1775 selectively sensitizes HPV(+) HNSCC cells and orthotopic oral xenografts to cisplatin through apoptosis and support the clinical investigation of AZD-1775 in combination with cisplatin particularly in patients with advanced and recurrent metastatic HPV(+) HNSCC tumors.

Phase I study of intermittent oral dosing of the insulin-like growth factor-1 and insulin receptors inhibitor OSI-906 in patients with advanced solid tumors

PURPOSE

We determined the maximum tolerated dose (MTD), safety, pharmacokinetics, pharmacodynamics, and preliminary activity of OSI-906, a potent, oral, dual inhibitor of insulin-like growth factor-1 receptor (IGF1R) and insulin receptor (IR), in patients with advanced solid tumors.

EXPERIMENTAL DESIGN

This was a multicenter, open-label, dose escalation phase I study evaluating three intermittent dosing schedules of once-daily OSI-906 [schedule (S) 1, days 1-3 every 14 days; S2, days 1-5 every 14 days; S3, days 1-7 every 14 days]. A fed-fasting expansion cohort was included in the study.

RESULTS

Seventy-nine patients were enrolled: 62 in S1, 4 in S2, and 13 in S3. S2 was discontinued. Dose-limiting toxicity comprised grade 3-4 hyperglycemia, vomiting, fatigue, and prolonged QTc interval. The MTD and recommended phase II dose of OSI-906 was 600 mg for both S1 and S3 schedules. Other common adverse events were grade 1-2 nausea, vomiting, fatigue, and diarrhea. The pharmacokinetics of OSI-906 was dose linear, and the terminal half-life ranged between 2 and 6 hours. High-fat meals had a moderate effect on the pharmacokinetics of OSI-906. At the MTD, inhibition of IGF1R and IR was observed in peripheral blood mononuclear cells. An increase in plasma IGF1 concentrations, an indirect measure of IGF1R signaling inhibition, was seen at doses ≥ 450 mg. Two patients with adrenocortical carcinoma achieved partial responses.

CONCLUSION

The MTD of 600 mg was well tolerated and associated with preliminary antitumor activity. These data support further evaluation of OSI-906 in solid tumors.

drexplorer: A tool to explore dose-response relationships and drug-drug interactions

MOTIVATION

Nonlinear dose-response models are primary tools for estimating the potency [e.g. half-maximum inhibitory concentration (IC) known as IC50] of anti-cancer drugs. We present drexplorer software, which enables biologists to evaluate replicate reproducibility, detect outlier data points, fit different models, select the best model, estimate IC values at different percentiles and assess drug-drug interactions. drexplorer serves as a computation engine within the R environment and a graphical interface for users who do not have programming backgrounds.

Gene mutations in primary tumors and corresponding patient-derived xenografts derived from non-small cell lung cancer

Molecular annotated patient-derived xenograft (PDX) models are useful for the preclinical investigation of anticancer drugs and individualized anticancer therapy. We established 23 PDXs from 88 surgical specimens of lung cancer patients and determined gene mutations in these PDXs and their paired primary tumors by ultradeep exome sequencing on 202 cancer-related genes. The numbers of primary tumors with deleterious mutations in TP53, KRAS, PI3KCA, ALK, STK11, and EGFR were 43.5%, 21.7%, 17.4%, 17.4%, 13.0%, and 8.7%, respectively. Other genes with deleterious mutations in ≥3 (13.0%) primary tumors were MLL3, SETD2, ATM, ARID1A, CRIPAK, HGF, BAI3, EP300, KDR, PDGRRA and RUNX1. Of 315 mutations detected in the primary tumors, 293 (93%) were also detected in their corresponding PDXs, indicating that PDXs have the capacity to recapitulate the mutations in primary tumors. Nevertheless, a substantial number of mutations had higher allele frequencies in the PDXs than in the primary tumors, or were not detectable in the primary tumor, suggesting the possibility of tumor cell enrichment in PDXs or heterogeneity in the primary tumors. The molecularly annotated PDXs generated from this study could be useful for future translational studies.

Abstract 903: Evaluation of predictive biomarkers and resistance mechanisms of PI3K pathway inhibition in head and neck squamous cell carcinoma

Head and neck Squamous cell carcinoma (HNSCC) is a lethal, disabling and disfiguring cancer with no biomarker-directed therapeutic options. We are in a desperate need for novel targeted therapies. PI3K/AKT/mTOR is one of the most often altered pathways in HNSCC. This pathway is important for cancer cell signaling and several pharmacological inhibitors are already in clinical trials for other cancer types. Our lab previously found that HNSCC cell lines with PIK3CA mutations were more sensitive to pathway inhibitors compared to other PI3K pathway alterations such as PIK3CA amplification or PTEN loss and that activation of ERK is one mechanism responsible for PI3K inhibitor resistance. In this report we extended our study to further investigate the predictive biomarkers, biological effects of PI3K inhibition, the potential pathways of resistance and the use of rational drug combination in a diverse panel of HNSCC cell lines. We tested 64 HNSCC cell lines with the PI3K inhibitor GDC0941 and correlated drug sensitivity with basal PI3K pathway activation, PI3K copy number or PIK3CA mutation. We confirmed that cell lines with PIK3CA mutations were more sensitive to GDC0941 (P= 6.35X 10 -13) and those with amplification were not. We tested another four PI3K pathway inhibitors, including one PI3K inhibitor GSK1059615, one dual PI3K/mTOR inhibitor GDC0980, one AKT inhibitor GDC690693 and one mTOR inhibitor AZD8055 in a panel of 18 cell lines and found that the trend of drug sensitivity was similar (P &lt; 0.05) in two PI3K inhibitors and one dual inhibitor where as AKT and mTOR inhibitors had a distinct trend. We evaluated the basal activation of PI3K/AKT/mTOR pathway using reverse phase protein array (RPPA) with two proteomic scores: PI3K/AKT and TSC/mTOR. Neither score predicted sensitivity to GDC0941. We also analyzed the PI3K/AKT and TSC/mTOR scores in 200 HNSCC tumors from the TCGA . In the same way PIK3CA amplification did not correlate with the scores whereas the PI3K/AKT score was higher in the PIK3CA mutants (P &lt; 0.039) compared to WT PIK3CA. The RPPA did identify several biomarkers, including VEGFR2, pCRAF and PCNA, whose expression correlated with GDC0941 sensitivity. Treatment with GDC0941 caused cell cycle arrest in sensitive cell lines, but not in resistant cell lines. To identify potential resistance pathways following GDC0941 treatment in resistant lines, we tested 39 phosphoproteins using phosphoscan analysis and found that EGFR, IGF-1R, RET, FGFR3, and M-CSFR were activated in resistant cell lines after incubation with GDC0941. Combination therapy with GDC0941 and the EGFR inhibitor erlotinib was synergistic in resistant cell lines. Our data will be useful to conduct biomarker-based clinical trials in HNSCC in the near future.

Citation Format: Tuhina Mazumdar, Lauren A. Byers, Patrick Ng, Gordon B. Mills, Shaohua Peng, Lixia Diao, Youhong Fan, Katherine Stemke-Hale, John V. Heymach, Jeffrey N. Myers, Bonnie S. Glisson, Faye M. Johnson. Evaluation of predictive biomarkers and resistance mechanisms of PI3K pathway inhibition in head and neck squamous cell carcinoma. [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 903. doi:10.1158/1538-7445.AM2014-903

A comprehensive evaluation of biomarkers predictive of response to PI3K inhibitors and of resistance mechanisms in head and neck squamous cell carcinoma

The PI3K/AKT/mTOR pathway is frequently activated in head and neck squamous cell carcinoma (HNSCC), but pathway inhibition has variable efficacy. Identification of predictive biomarkers and mechanisms of resistance would allow selection of patients most likely to respond and novel therapeutic combinations. The purpose of this study was to extend recent discoveries regarding the PI3K/AKT/mTOR pathway in HNSCC by more broadly examining potential biomarkers of response, by examining pathway inhibitors with a diverse range of targets, and by defining mechanisms of resistance and potential combination therapies. We used reverse-phase protein arrays (RPPA) to simultaneously evaluate expression of 195 proteins; SNP array to estimate gene copy number; and mass array to identify mutations. We examined altered signaling at baseline and after pathway inhibition. Likewise, we examined the activation of the PI3K/AKT/mTOR pathway in HNSCC tumors by RPPA. Cell lines with PIK3CA mutations were sensitive to pathway inhibitors, whereas amplification status did not predict sensitivity. While we identified a set of individual candidate biomarkers of response to pathway inhibitors, proteomic pathway scores did not correlate with amplification or mutation and did not predict response. Several receptor tyrosine kinases, including EGFR and ERK, were activated following PI3K inhibition in resistant cells; dual pathway inhibition of PI3K and EGFR or MEK demonstrated synergy. Combined MEK and PI3K inhibition was markedly synergistic in HRAS-mutant cell lines. Our findings indicate that clinical trials of single-agent PI3K/AKT/mTOR pathway inhibitors in selected populations and of PI3K/EGFR or PI3K/MEK inhibitor combinations are warranted; we plan to conduct such trials.

A phase I/II study combining erlotinib and dasatinib for non-small cell lung cancer

BACKGROUND

EGFR and Src are frequently activated in non-small cell lung cancer (NSCLC). In preclinical models, combining EGFR and Src inhibition has additive synergistic effects. We conducted a phase I/II trial of the combination of Src inhibitor dasatinib with EGFR inhibitor erlotinib to determine the maximum tolerated dose (MTD), pharmacokinetic drug interactions, biomarkers, and efficacy in NSCLC.

METHODS

The phase I 3+3 dose-escalation study enrolled patients with solid tumors to determine the MTD. The phase II trial enrolled patients with advanced NSCLC who had undergone no previous treatments to determine progression-free survival (PFS) and response. Pharmacokinetic and tissue biomarker analyses were performed.

RESULTS

MTD was 150 mg of erlotinib and 70 mg of dasatinib daily based on 12 patients treated in the phase I portion. No responses were observed in phase I. The 35 NSCLC patients treated in phase II had an overall disease control rate of 59% at 6 weeks. Five patients (15%) had partial responses; all had activating EGFR mutations. Median PFS was 3.3 months. Epithelial-mesenchymal transition markers did not correlate with outcomes.

CONCLUSION

The combination of erlotinib and dasatinib is safe and feasible in NSCLC. The results of this study do not support use of this combination in molecularly unselected NSCLC.