Combination therapy with topotecan, paclitaxel, and bevacizumab improves progression-free survival in recurrent small cell neuroendocrine carcinoma of the cervix

OBJECTIVES

To assess if the combination of topotecan, paclitaxel, and bevacizumab (TPB) was active in recurrent SCCC and to compare the survival of patients with SCCC who received TPB to a group of women with SCCC who did not receive this regimen.

METHODS

We retrospectively analyzed women with recurrent SCCC who received chemotherapy as primary therapy. Women treated with TPB for first recurrence were compared to women treated with non-TPB chemotherapy.

RESULTS

Thirteen patients received TPB, and 21 received non-TPB chemotherapy, most commonly platinum with or without a taxane. Median progression-free survival (PFS) was 7.8months for TPB and 4.0months for non-TPB regimens (hazard ratio [HR] 0.21, 95% CI 0.09-0.54, P=0.001). Median overall survival (OS) was 9.7months for TPB and 9.4months for non-TPB regimens (HR 0.53, 95% CI 0.23-1.22, P=0.13). Eight women (62%) who received TPB versus four (19%) who received non-TPB regimens were on treatment for >6months (P=0.02), and four patients (31%) in the TPB group versus two (10%) in the non-TPB group were on treatment for >12months (P=0.17). In the TPB group, three patients (23%) had complete response, two (15%) had complete response outside the brain with progression in the brain, 3 (23%) had a partial response, 2 (15%) had stable disease, and 3 (23%) had progressive disease.

CONCLUSIONS

These findings indicate that TPB for recurrent SCCC significantly improved PFS over non-TPB regimens, and trends towards improved OS. Furthermore, a significant number of patients had a durable clinical benefit.

The BATTLE-2 Study: A Biomarker-Integrated Targeted Therapy Study in Previously Treated Patients With Advanced Non-Small-Cell Lung Cancer

PURPOSE

By applying the principles of real-time biopsy, biomarker-based, adaptively randomized studies in non-small-cell lung cancer (NSCLC) established by the Biomarker-Integrated Approaches of Targeted Therapy for Lung Cancer Elimination (BATTLE) trial, we conducted BATTLE-2 (BATTLE-2 Program: A Biomarker-Integrated Targeted Therapy Study in Previously Treated Patients With Advanced Non-Small Cell Lung Cancer), an umbrella study to evaluate the effects of targeted therapies focusing on KRAS-mutated cancers.

PATIENTS AND METHODS

Patients with advanced NSCLC (excluding sensitizing EGFR mutations and ALK gene fusions) refractory to more than one prior therapy were randomly assigned, stratified by KRAS status, to four arms: (1) erlotinib, (2) erlotinib plus MK-2206, (3) MK-2206 plus AZD6244, or (4) sorafenib. Tumor gene expression profiling-targeted next-generation sequencing was performed to evaluate predictive and prognostic biomarkers.

RESULTS

Two hundred patients, 27% with KRAS-mutated (KRAS mut+) tumors, were adaptively randomly assigned to erlotinib (n = 22), erlotinib plus MK-2206 (n = 42), MK-2206 plus AZD6244 (n = 75), or sorafenib (n = 61). In all, 186 patients were evaluable, and the primary end point of an 8-week disease control rate (DCR) was 48% (arm 1, 32%; arm 2, 50%; arm 3, 53%; and arm 4, 46%). For KRAS mut+ patients, DCR was 20%, 25%, 62%, and 44% whereas for KRAS wild-type patients, DCR was 36%, 57%, 49%, and 47% for arms 1, 2, 3, and 4, respectively. Median progression-free survival was 2.0 months, not different by KRAS status, 1.8 months for arm 1, and 2.5 months for arms 2 versus arms 3 and 4 in KRAS mut+ patients (P = .04). Median overall survival was 6.5 months, 9.0 and 5.1 months for arms 1 and 2 versus arms 3 and 4 in KRAS wild-type patients (P = .03). Median overall survival was 7.5 months in mesenchymal versus 5 months in epithelial tumors (P = .02).

CONCLUSION

Despite improved progression-free survival on therapy that did not contain erlotinib for KRAS mut+ patients and improved prognosis for mesenchymal tumors, better biomarker-driven treatment strategies are still needed.

AXL Inhibition Suppresses the DNA Damage Response and Sensitizes Cells to PARP Inhibition in Multiple Cancers

Epithelial to mesenchymal transition (EMT) is associated with a wide range of changes in cancer cells, including stemness, chemo- and radio-resistance, and metastasis. The mechanistic role of upstream mediators of EMT has not yet been well characterized. Recently, we showed that non-small cell lung cancers (NSCLC) that have undergone EMT overexpress AXL, a receptor tyrosine kinase. AXL is also overexpressed in a subset of triple-negative breast cancers (TNBC) and head and neck squamous cell carcinomas (HNSCC), and its overexpression has been associated with more aggressive tumor behavior and linked to resistance to chemotherapy, radiotherapy, and targeted therapy. Because the DNA repair pathway is also altered in patient tumor specimens overexpressing AXL, it is hypothesized that modulation of AXL in cells that have undergone EMT will sensitize them to agents targeting the DNA repair pathway. Downregulation or inhibition of AXL directly reversed the EMT phenotype, led to decreased expression of DNA repair genes, and diminished efficiency of homologous recombination (HR) and RAD51 foci formation. As a result, AXL inhibition caused a state of HR deficiency in the cells, making them sensitive to inhibition of the DNA repair protein, PARP1. AXL inhibition synergized with PARP inhibition, leading to apoptotic cell death. AXL expression also associated positively with markers of DNA repair across TNBC, HNSCC, and NSCLC patient cohorts.

IMPLICATIONS

The novel role for AXL in DNA repair, linking it to EMT, suggests that AXL can be an effective therapeutic target in combination with targeted therapy such as PARP inhibitors in several different malignancies. Mol Cancer Res; 15(1); 45-58. ©2016 AACR.

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.

Safety and efficacy of single-agent rovalpituzumab tesirine (SC16LD6.5), a delta-like protein 3 (DLL3)-targeted antibody-drug conjugate (ADC) in recurrent or refractory small cell lung cancer (SCLC)

LBA8505

Background: SCLC remains among the most deadly of malignancies. Rovalpituzumab tesirine is a first-in-class ADC comprised of a humanized monoclonal antibody against DLL3, a dipeptide linker, and a pyrrolobenzodiazepine (PBD) dimer toxin. DLL3 is highly expressed in neuroendocrine tumors, including approximately 80% of SCLC. The emerging results of the SCLC patients (pts) in a first-in-human study (NCT01901653) are reported here. Methods: Pts with progressive SCLC after at least 1 previous systemic therapy were eligible. Efficacy was assessed by the investigator via RECIST v1.1, and toxicity graded per CTCAE v4.03. When available, archived tumor tissue was assessed retrospectively for DLL3 expression by immunohistochemistry. Results: Seventy-four (74) pts were enrolled at dose levels ranging from 0.05 to 0.8 mg/kg at either q3w or q6w. Among evaluable pts treated at doses of 0.2-0.4 mg/kg, 15/61 (25%; 95% CI 15-37%) achieved a best response of PR or CR, and 44/61 (72%; 95% CI 59-83%) achieved clinical benefit (best response of at least SD). Among pts with available archive tissue specimens and ≥ 50% of cells expressing DLL3 (DLL3hi, an intended companion diagnostic cutoff), 12/22 (55%; 95% CI 32-76%) achieved a best response of PR or CR, and 20/22 (91%; 95% CI 71-99%) achieved clinical benefit, with a median overall survival of 8 (range 1-18+) months. In 3rd line DLL3hi pts (n = 10), where no approved therapy currently exists, the ORR and CBR were 70% and 90%, respectively, with at least 4 evaluable pts achieving OS of > 6 (8, 15, 18 and 18) months. Among responders treated at the phase 2 dose of 0.3 mg/kg, the median duration of response was 6 (range 1-8+) months. Among all SCLC pts, the most common grade 3+ toxicities considered study drug-related have included serosal effusions (14%), thrombocytopenia (12%) and skin reactions (8%). Conclusions: With manageable toxicity, rovalpituzumab tesirine demonstrates encouraging single-agent anti-tumor activity and durability in recurrent or refractory SCLC. A single-arm pivotal study in 3rd line DLL3-expressing SCLC has been initiated. Clinical trial information: NCT01901653.

Selecting Reliable mRNA Expression Measurements Across Platforms Improves Downstream Analysis

With increasing use of publicly available gene expression data sets, the quality of the expression data is a critical issue for downstream analysis, gene signature development, and cross-validation of data sets. Thus, identifying reliable expression measurements by leveraging multiple mRNA expression platforms is an important analytical task. In this study, we propose a statistical framework for selecting reliable measurements between platforms by modeling the correlations of mRNA expression levels using a beta-mixture model. The model-based selection provides an effective and objective way to separate good probes from probes with low quality, thereby improving the efficiency and accuracy of the analysis. The proposed method can be used to compare two microarray technologies or microarray and RNA sequencing measurements. We tested the approach in two matched profiling data sets, using microarray gene expression measurements from the same samples profiled on both Affymetrix and Illumina platforms. We also applied the algorithm to mRNA expression data to compare Affymetrix microarray data with RNA sequencing measurements. The algorithm successfully identified probes/genes with reliable measurements. Removing the unreliable measurements resulted in significant improvements for gene signature development and functional annotations.

Small cell lung cancer: will recent progress lead to improved outcomes?

Small cell lung cancer (SCLC) is an aggressive neuroendocrine malignancy with a unique natural history characterized by a short doubling time, high growth fraction, and early development of widespread metastases. Although a chemotherapy- and radiation-sensitive disease, SCLC typically recurs rapidly after primary treatment, with only 6% of patients surviving 5 years from diagnosis. This disease has been notable for the absence of major improvements in its treatment: Nearly four decades after the introduction of a platinum-etoposide doublet, therapeutic options have remained virtually unchanged, with correspondingly little improvement in survival rates. Here, we summarize specific barriers and challenges inherent to SCLC research and care that have limited progress in novel therapeutic development to date. We discuss recent progress in basic and translational research, especially in the development of mouse models, which will provide insights into the patterns of metastasis and resistance in SCLC. Opportunities in clinical research aimed at exploiting SCLC biology are reviewed, with an emphasis on ongoing trials. SCLC has been described as a recalcitrant cancer, for which there is an urgent need for accelerated progress. The NCI convened a panel of laboratory and clinical investigators interested in SCLC with a goal of defining consensus recommendations to accelerate progress in the treatment of SCLC, which we summarize here.

A Patient-Derived, Pan-Cancer EMT Signature Identifies Global Molecular Alterations and Immune Target Enrichment Following Epithelial-to-Mesenchymal Transition

PURPOSE

We previously demonstrated the association between epithelial-to-mesenchymal transition (EMT) and drug response in lung cancer using an EMT signature derived in cancer cell lines. Given the contribution of tumor microenvironments to EMT, we extended our investigation of EMT to patient tumors from 11 cancer types to develop a pan-cancer EMT signature.

EXPERIMENTAL DESIGN

Using the pan-cancer EMT signature, we conducted an integrated, global analysis of genomic and proteomic profiles associated with EMT across 1,934 tumors including breast, lung, colon, ovarian, and bladder cancers. Differences in outcome and in vitro drug response corresponding to expression of the pan-cancer EMT signature were also investigated.

RESULTS

Compared with the lung cancer EMT signature, the patient-derived, pan-cancer EMT signature encompasses a set of core EMT genes that correlate even more strongly with known EMT markers across diverse tumor types and identifies differences in drug sensitivity and global molecular alterations at the DNA, RNA, and protein levels. Among those changes associated with EMT, pathway analysis revealed a strong correlation between EMT and immune activation. Further supervised analysis demonstrated high expression of immune checkpoints and other druggable immune targets, such as PD1, PD-L1, CTLA4, OX40L, and PD-L2, in tumors with the most mesenchymal EMT scores. Elevated PD-L1 protein expression in mesenchymal tumors was confirmed by IHC in an independent lung cancer cohort.

CONCLUSIONS

This new signature provides a novel, patient-based, histology-independent tool for the investigation of EMT and offers insights into potential novel therapeutic targets for mesenchymal tumors, independent of cancer type, including immune checkpoints.

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 <0.0001). Furthermore, the expression of other cell cycle proteins p21 (p-value <0.0001) is lower in HPV-positive cell lines while cyclin E1 (p-value <0.03) and pRb (p-value <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 3579: Identification of biomarkers of AXL-mediated drug resistance in head and neck squamous cell carcinoma

Background:

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

Methods:

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

Results:

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

Conclusions:

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

Citation Format: Kavitha Balaji, Robert Cardnell, Lixia Diao, Pan Tong, Milena Mak, You Hong Fan, Fatemeh Masrorpour, Steven L. Warner, David J. Bearss, Ignacio Wistuba, Gordon B. Mills, John Heymach, Khandan Keyomarsi, Jing Wang, Lauren Averett Byers. Identification of biomarkers of AXL-mediated drug resistance in head and neck squamous cell carcinoma. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3579. doi:10.1158/1538-7445.AM2015-3579

Altering the Course of Small Cell Lung Cancer: Targeting Cancer Stem Cells via LSD1 Inhibition

In this issue of Cancer Cell, Mohammad et al. describe LSD1, a histone demethylase, as a therapeutic target in SCLC with a unique epigenetic signature to predict drug sensitivity. Inhibition of LSD1 reduces cell proliferation and stem cell maintenance while promoting cell differentiation and reducing tumor growth in preclinical models.

Proliferation and maturation of human leukemia cells in liquid culture

Bone marrow from patients with acute myelogenous leukemia (AML), acute myelomonocytic leukemia (AMML), chronic myelogenous leukemia (CML), preleukemia, and from healthy volunteers was cultured using a recently developed liquid diffusion technique. Differential and viable cell counts and 3H-thymidine labeling indices were performed at intervals up to 30 days. Differentiation was assessed morphologically by light and electron microscopy, histochemically, and by functional tests for phagocytosis and the presence of surface receptors for IgG. Colony-stimulating activity (CSA) was assayed against normal human bone marrow by the agar colony technique. In acute leukemia cultures, viable cell counts usually fell within the normal range. However, most AML cells failed to demonstrate significant maturation in vitro, and did not produce detectable CSA. In AMML cultures, maturation was defective but some differentiated macrophages were observed and the cells produced high concentrations of CSA. Preleukemic cultures demonstrated normal growth but maturation was impaired as evidenced by a high percentage of immature cells during the first 7 days. CML cultures showed abnormally high growth capacity resulting in viable cell counts 2-3 times normal. In the chronic phase of CML, maturation was qualitatively normal and the cells produced CSA. With the onset of blast transformation, maturation became abnormal but growth remained high. These studies support a concept of AML as a primary defect in cellular maturation and of CML as a primary abnormality of proliferation. The production of CSA by neoplastic cells relates to the degree of monocyte-macrophage differentiation within the leukemic population. Human preleukemia is characterized by a failure of normal maturation in vitro.

Small cell lung cancer: where do we go from here?

Small cell lung cancer (SCLC) is an aggressive disease that accounts for approximately 14% of all lung cancers. In the United States, approximately 31,000 patients are diagnosed annually with SCLC. Despite numerous clinical trials, including at least 40 phase 3 trials since the 1970s, systemic treatment for patients with SCLC has not changed significantly in the past several decades. Consequently, the 5-year survival rate remains low at <7% overall, and most patients survive for only 1 year or less after diagnosis. Unlike nonsmall cell lung cancer (NSCLC), in which major advances have been made using targeted therapies, there are still no approved targeted drugs for SCLC. Significant barriers to progress in SCLC include 1) a lack of early detection modalities, 2) limited tumor tissue for translational research (eg, molecular profiling of DNA, RNA, and/or protein alterations) because of small diagnostic biopsies and the rare use of surgical resection in standard treatment, and 3) rapid disease progression with poor understanding of the mechanisms contributing to therapeutic resistance. In this report, the authors review the current state of SCLC treatment, recent advances in current understanding of the underlying disease biology, and opportunities to advance translational research and therapeutic approaches for patients with SCLC.