Chemotherapy

Targeted therapies such as erlotinib or gefitinib for EGFR-mutated lung cancer and crizotinib for ALK-translocated lung cancer can yield remarkable responses and significant clinical benefit. Other mutations in genes such as K-RAS, BRAF, and PI3K, among others, are also being actively investigated as targets of new drugs in clinical trials. However, a substantial number of patients (~40%) have no mutations when tested with a panel of known oncogenic mutations. The aim of this research proposal is to identify novel somatic genomic alterations in lung cancer, using an existing tumor bank of lung cancer cases with known clinical and tumor genetic information. We will focus on those lung cancers that are known to be wildtype on SNaPshot and ALK FISH (fluorescence in situ hybridization) (i.e., negative for over 50 tested oncogenic mutations), and perform both deep sequencing of exomes and a comprehensive search for translocations involving kinases. We believe that this effort will identify novel tumor genomic changes that can be targets for therapy.

There is recent evidence that metformin, a drug commonly used to treat diabetes, has anticancer effects and can significantly improve the rate of pathological response in breast cancers treated with chemotherapy. We propose to review clinical records of lung cancer patients treated over the past 25 years at Johns Hopkins to determine whether metformin treatment is associated with improved clinical response to chemotherapy for lung cancer. Because our preliminary laboratory work suggests that lung cancer cells with mutations of the LKB1 gene are particularly sensitive to metformin, we will secondarily determine whether mutations of the LKB1 gene (which is mutated in up to 40% of lung adenocarcinomas) are associated with a higher frequency of response to chemotherapy among these patients treated with metformin. In a second specific aim, we will conduct studies using xenografts of human lung cancers in the laboratory to further examine possible links between LKB1 mutations and response to metformin, with or without paclitaxel. Establishing such a link could lead to improved chemotherapy (using metformin in combination with conventional chemotherapy drugs) and to development of a biomarker that can identify patients with cancers who might have improved response to chemotherapy with metformin.

The most effective curative modality we have for lung cancer is still surgery, but, even with optimum surgery, many patients relapse and die of their lung cancer, and this fraction is improved only slightly by adjuvant chemotherapy, which is nonetheless toxic for everybody. Thus, we need to identify prognostic biomarkers (to define which patients are likely to relapse after surgery) and predictive biomarkers (to define who will benefit from adjuvant therapy, and what specific type of adjuvant therapy should be used on each particular patient). In this proposal, collaborators from two different lung cancer SPOREs in three different universities will use two sets of high information-content analyses of protein and RNA expression already acquired on a cohort of early-stage lung cancer patients who did not receive adjuvant chemotherapy and in a panel of cell lines rigorously characterized for sensitivity to platinum doublets, and will add to that data funded by this proposal on a new cohort of patients treated with adjuvant chemotherapy to generate our classifier. This classifier will then be reduced to a small number of RNA or protein assays and tested in a larger set of resected patients with and without adjuvant chemotherapy.

Small cell lung cancer (SCLC) is a common, aggressive, and exceptionally lethal malignancy that is usually metastatic at the time of diagnosis. Newly diagnosed SCLC is remarkably sensitive to chemotherapy, with response rates of over 60% to cisplatin and etoposide even in patients with extensive-stage disease. These chemotherapy responses are often both rapid and deep, but are never curative: extensive-stage disease recurs universally, in most cases within a few months after completion of first-line therapy. Recurrent SCLC is remarkably refractory to treatment. The median overall survival of patients with extensive-stage SCLC is about nine months from the time of initial diagnosis, and the 5-year survival is less than 1%. Defining the basis of acquired chemotherapy resistance in SCLC could have clear and important ramifications for clinical management of this disease. Targeting the key determinants of acquired chemoresistance could be integrated into first-line treatment, and/or could drive rational targeted therapeutic studies for recurrent disease. We now have in hand multiple technical approaches that could comprehensively define the genomic and epigenetic changes that drive acquired resistance in SCLC. In this award application, we propose two parallel approaches to analyzing acquired resistance in SCLC: analysis of primary samples and patient-derived xenografts before and after acquired resistance.

Background & Significance: Phase I studies with the anti-programmed death-1 antibody (anti-PD-1), nivolumab, in advanced non-small-cell lung cancer (NSCLC) have demonstrated remarkably durable responses in heavily pretreated patients that lasted a median 17 months. However, in these studies very few patients have had tumors available for immune analysis, and basic data on immune measures pre- and post-treatment are not available. This study will move the treatment paradigm forward by assessing the safety and feasibility of preoperative anti-PD-1 in NSCLC and providing detailed information on the effect of PD-1 modulation on the lung tumor immune microenvironment.

Methods: Patients with newly diagnosed stage IB-IIIA NSCLC will receive two doses of nivolumab 3mg/kg IV on day-28 and day-14 prior to planned surgery on day 0. Serial blood samples for immune markers will be obtained. The primary endpoint of this study is the safety and feasibility of preoperative nivolumab in resectable NSCLC. For the exploratory immune analyses, initial tumor biopsy, post-treatment resection specimen, and serial peripheral blood samples will be evaluated for expression of immune markers with the primary comparison being intra-patient, pre- and post-treatment.

Experimental Approach & Statistical Analysis Plan: As this is the first time that nivolumab has been administered pre-operatively in NSCLC, the study will commence with a run-in phase where six patients will be monitored continuously for adverse events through eight weeks following surgery. Overall, the study will continue without pause to a 12-patient expansion phase if none or one of the six patients experiences DLT in the run-in. Detailed statistical plans for the safety and feasibility endpoints and exploratory immune endpoints are described in the main body of this application.

Small cell lung cancer (SCLC) is an aggressive form of lung cancer with dismal survival rates. New strategies are urgently needed to improve clinical outcomes for SCLC patients. Recently, we identified high expression of the DNA-repair protein poly (ADP-ribose) polymerase 1 (PARP-1) in SCLC cell lines and tumors through a large-scale, proteomic profiling project. In vitro data from our group has shown that PARP inhibitors have single-agent activity in SCLC and potentiate the activity of chemotherapies that work by inducing DNA damage. Based on these results, we are conducting an investigator-initiated, Phase II clinical trial of the oral alkylating agent temozolomide (TMZ) with or without the PARP inhibitor ABT-888 for patients with relapsed SCLC. We hypothesize that PARP1’s action as an E2F1 co-activator contributes to the overexpression of multiple E2F1-regulated DNA repair proteins, resulting in resistance to chemotherapy. Thus, targeting PARP1 will decrease expression of E2F1-regulated DNA repair proteins, as well as directly inhibit PARP-mediated DNA repair, resulting in decreased cell viability and improved clinical outcomes in patients treated with TMZ and the PARP inhibitor. In the studies proposed here, we will test in vitro and in vivo sensitivity of SCLC to ABT-888 and TMZ, alone and in combination, and develop predictive biomarkers of response that will be tested in our Phase II clinical trial. The ultimate goal of this laboratory and clinical research is to develop PARP inhibitors as a novel therapy for SCLC.

Cancer therapy needs to be better personalized to individual patients, each of whom carries a unique spectrum of mutations, inherited and/or acquired. One of the best cases for this is lung cancer, where molecular subgrouping patients and targeting their mutations has shown promise. While many groups have searched fervently for additional tumor-acquired mutations that are associated with drug sensitivity and resistance, few have emerged since the discovery of the initial mutations, such as EGFR. In contrast, we have applied our expertise in microRNAs (miRNAs), their biologic function and interaction with oncogenes, and as a result have discovered a new class of inherited, germ-line mutations that appear to have strong potential as companion diagnostics. These mutations are in a relatively unexplored region of the genome, the 3’ untranslated regions (UTRs), once thought to be junk DNA. The first such discovered biomarker, the “KRAS-variant,” is an inherited 3’UTR mutation in KRAS, which affects microRNA (miRNA) binding and KRAS pathway expression, as well as tumor biology. The KRAS-variant was first shown to be a genetic marker for an increased risk of developing non-small cell lung cancer (NSCLC). In addition, our data indicate that this variant represents an inherited form of an activated KRAS allele, one of the most important human oncogenes. Several groups have found that the KRAS-variant acts as a biomarker of poor outcomes across multiple cancers, including head and neck cancer, ovarian cancer, and colon cancer. We as well as others have shown that this biomarker is predictive of response to specific cancer treatments, and is not just prognostic of aggressive tumor biology. For example, the KRAS-variant predicts resistance to cisplatin in ovarian and head and neck cancer, resistance to cetuximab in combination with irinotecan chemotherapy, but sensitivity to cetuximab when delivered alone. Furthermore, our preliminary data in this proposal indicate that the KRAS-variant is a powerful companion diagnostic predicting poor response to specific agents, and excellent response to others. These findings, combined with evidence that this allele of KRAS can be targeted using siRNA and miRNA strategies that we have pioneered, leads us to believe that this KRAS-3’UTR mutation is a powerful companion diagnostic in lung cancer, and ultimately may be a critical new target for cancer therapy.

Whole genome pooled retroviral shRNA screens were performed in NSCLC cell lines A549 and NCI-H460. Out of nearly 18,000 genes, the top hit whose knockdown most reproducibly showed cytoxicity was PSMA1, a core subunit of the 20S proteasome. The combination of radiotherapy and PSMA1 knockdown significantly enhanced tumor control in a mouse xenograft model. We observed that proteasome inhibition results in increases in nuclear 1κBa, which in turn decreases NF-κB binding to the promoters of Fanconi Anemia/Homologous Recombination (HR) genes including FANCD2 and BRCA1. This reduces the expression and subsequent availability of these DNA repair proteins for recruitment to double strand breaks (DSBs) induced by radiation. These mechanistic studies provided the basis for the proposed hypothesis-driven translational research.

The central hypothesis is that high levels of HR-mediated repair of radiation-induced DNA DSBs are associated with poor tumor control, which may be improved with proteasome inhibitors. First, CT-guided fractionated radiotherapy ± bortezomib will be tested in diverse genetically engineered mouse models of NSCLC to identify mutations and other biomarkers associated with responses to radiation and/or proteasome inhibitors. Immunofluorescence and immunohistochemistry against proteins, identified in prior mechanistic studies, as well as gene expression profiling (GEP), will be performed. Then, the biomarkers will be examined in archived specimens from patients treated with radiotherapy, to assess associations with outcomes. DASL will be used to perform GEP studies using formalin-fixed, paraffin-embedded specimens. The goal will be to identify pathway-based expression signatures that predict poor outcomes with radiotherapy and improved outcomes with addition of proteasome inhibitors.

Platinum-based concurrent chemoradiation (CRT) remains the standard treatment for patients with locally advanced, stage III non-small cell lung cancer (NSCLC). Outcomes for this large subgroup remain dismal, and no progress has been made in this area in the last three decades. Novel treatment options and predictive biomarkers to improve upon the outcome and reduce the toxicity of our current treatment paradigms are sorely needed. Our overall hypothesis is that the identification of acquired resistance pathways and synergistic targets for platinum-radiation therapy will lead to improved treatments and patient selection. We will pursue in vitro and in vivo xenograft studies to assess the synergistic role of PARP inhibition and ERCC1 modulation in the setting of CRT and will correlate these findings with a biomarker study using human tumor specimens. We will further validate YAP as a promising actionable target and will assess the interactions of concurrent chemoradiation with YAP blockade based on our preliminary data of synergy. Then, we will pursue an unbiased, functional shRNA genetic screen to identify further essential treatment resistance pathways, and carefully selected targets will be validated through a series of biochemical and functional assessment steps. The predictive value of biomarkers will be tested in retrospective cohorts of patients treated with cisplatin-radiation for locally advanced non-small cell lung cancer enrolled in our lung cancer database. Last, our unique tissue bank of pre- and post-neoadjuvant treatment specimens will be used for the identification of novel resistance markers based on modulation of expression upon neoadjuvant therapy, and functional validation of resistance biomarkers and novel treatment candidates will be pursued. These studies should provide the foundation for biomarker-driven translational and clinical studies in this area of major unmet clinical need.