Stage II

Despite focused research in conventional therapies, the 5-year survival rate of lung cancer patients remains only 15%. Due to the lack of reliable early diagnostic techniques, most patients are diagnosed with advanced-stage disease and therefore have a poor prognosis. There are more than 100 million current and former smokers in the US who have elevated risk for lung cancer and may benefit from a non-invasive test for early detection. Patients at risk may have subclinical disease for years prior to diagnosis. Therefore the clinical challenge is to develop lung cancer detection methods that are effective during this window of opportunity to increase the rate of early detection and thereby spur early treatment and improve lung cancer patient outcomes. During tumorigenesis, the developing tumor forms a complex cellular microenvironment that produces many soluble mediators, such as proteins and miRNAs, which are important for tumor initiation and growth and thus can serve as lung cancer biomarkers. Because the pulmonary vascular bed comprises approximately 50% of the body’s total vasculature, the peripheral blood is expected to reflect even small variations in lung cancer biomarkers.

Over the past decade, our laboratory has gathered substantial data supporting the analysis of soluble mediators of lung carcinogenesis including inflammatory cytokines, growth and angiogenic factors, and miRNA. Additionally, a considerable literature has developed describing the contribution of these factors to lung carcinogenesis. Based on these findings, in our preliminary studies we have developed a plasma protein-based biomarker panel that accurately distinguished between lung cancer patients and at-risk control subjects. Our predictive model provided 97% sensitivity, 77% specificity, and an area under the ROC of .93 for stage 1 vs. high-risk controls. Because recent studies demonstrated that circulating miRNA can serve as robust and specific diagnostic biomarkers, we developed a panel of 17 miRNAs relevant to lung carcinogenesis. In our preliminary studies utilizing this miRNA panel, we were able to detect miRNAs that are differentially expressed in the plasma of lung cancer patients as compared to high-risk controls. We hypothesize that the proteins and miRNA profiles will each contribute unique information and thus, an integrated panel of protein and miRNA markers may provide higher sensitivity for early lung cancer detection than either platform alone.

Specific aims for the current proposal include: 1) to identify protein profiles in plasma associated with early-stage lung cancer, 2) to identify plasma miRNA profiles associated with early stage lung cancer, and 3) to integrate miRNA and cytokine biomarkers established in Aims 1 and 2 to improve early-stage lung cancer detection. The first and second aims address the clinical problems of patients at risk for lung cancer who present with a suspicious pulmonary nodule of indeterminate significance that has be further evaluated.

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.

Lung cancer is the leading cause of death for men and women in the United States. Screening methods for the early detection of lung cancer must be developed to circumvent the phenomenon that sees the majority of patients being diagnosed with advanced, and thus incurable, lung cancer. While computerized tomography was demonstrated to reduce mortality by 20% in a high-risk smoker patient cohort, further examination of this method, complementary screening methods, and tools to screen less at-risk populations are needed to make the detection of early-stage lung cancer most beneficial. Using the expertise of our multidisciplinary clinical lung cancer team (Drs. Kelly, Gandara, Cooke, Yoneda, and Murin) with leaders in metabolomics and lipid biology (Dr. Fiehn) and glycomics (Drs. Miyamoto and Lebrilla), we aim to identify mass spectroscopy-detectible biomarkers of early lung cancer. The advent of “omics” technologies will allow us to expand the current pool of DNA and protein biomarkers and facilitate our vision of a systems-biology screening and/or diagnostic tool based on “biomarker panels.” Our approach begins with a discovery phase that will identify biomarkers in tumor and blood with the aim of finding blood-based biomarkers that most closely reflect tumor biology. Next we will proceed to the testing phase to determine the performance of these biomarkers in four independent cohorts (two lung cancer cohorts, healthy controls, and benign nodules). Biomarkers that meet our pre-specified criteria will require further evaluation that is beyond the scope of this proposal.

The overarching concept guiding our work is that combinations of biomarkers and imaging characteristics will be most robust in predicting which patients with lung nodules should receive an aggressive diagnostic and/or therapeutic approach and which patients should be monitored for nodule stability over time. Our objectives are to improve two biomarker tests that already have shown significant promise-- sputum chromosomal aneusomy by fluorescence in situ hybridization (CA-FISH) and the analysis of multiple serum analytes by a highly multiplexed aptamer-based assay developed by SomaLogic, Inc.-- and then to compare test performance with predictive models based on nodule and patient characteristics. These objectives are based on two separate hypotheses: 1. The current CA-FISH assay panel can be further improved by the development of two sub-panels, one for detection of squamous cell carcinoma of the lung (SCC) and the second for the detection of adenocarcinoma of the lung (AC). 2. The current aptamer-based analysis can be further improved by developing separate assays specifically designed for the detection of AC, SCC, K-ras, and EGFR-mutated lung tumors. The assays will then be applied to sputum and blood specimens from the Pittsburgh SPORE Pittsburgh Lung Screening Study (PLuSS) and Colorado SPORE Lung Nodule cohorts, in concert with analysis of the CT characteristics of the corresponding lung nodules, including size, volume, density, location, or airway involvement, to compare test performances and to assess whether combining tests would be valuable.

Evaluating suspicious pulmonary nodules in the setting of a lung cancer diagnostic work-up is a common clinical management challenge. High resolution multi-detector computed tomography visualizes many noncalcified lesions that could represent either potentially lethal cancers or benign processes. Although the vast majority of these nodules are benign, non-neoplastic lesions, a subset will be malignant and in these cases, patients could benefit from immediate treatment. A non-invasive test that maintains a high sensitivity and specificity across the spectrum of clinical presentations of pulmonary nodules would be of tremendous clinical benefit by reducing the number unnecessary invasive procedures and minimizing the time between detection and definitive treatment. The overall goal for the proposed studies is to develop a convenient and low-cost serum test that will, either alone or in combination with clinical features, accurately classify indeterminate nodules and direct proper clinical management. Our approach to develop such a test will be to profile and identify which proteins detected in the serum at the time of the detection of these nodules were immunogenic and induced the production of circulating autoantibodies. Differences in the autoantibody profile between the malignant and non-malignant groups will then be further evaluated against additional clinical specimens from both our institution and two pre-specified collaborator institutions to identify the optimal test for this urgent clinical need. Once completed, we anticipate this test will aid clinicians in deciding the optimal treatment for patients found to have suspicious nodules and improve the current standard of care.

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.

Screening smokers with CT can detect lung cancer at relatively early stages, and thus reduce mortality. However, CT screening for lung cancer has a poor specificity, often resulting in unnecessary treatments to smokers who have benign diseases. The objective of this proposal is to develop genomic- and non-coding RNA (ncRNA)-based biomarkers in sputum that can complement CT for lung cancer early detection in smokers.  Proposed aim 1 is to define sputum ncRNA signatures of early-stage lung cancer using next-generation sequencing (NGS). Proposed aim 2 is to optimize a panel of sputum ncRNA biomarkers with CT for the early detection of lung cancer. Proposed aim 3 is to integrate our previously identified genomic biomarkers and the newly optimized panel of ncRNA biomarkers with CT for the early detection of lung cancer in independent case-control series. Future use of the biomarkers in clinical practice for screening smokers for lung cancer will increase CT’s specificity, and hence reduce harmful and unnecessary treatments to many smokers who have benign diseases. Integrating the biomarkers with CT could assist making decisions for the management of abnormal findings in the lungs and enabling effective treatments to be immediately initiated for lung cancer. The study will translate the strengths of novel ncRNA profiling data developed from NGS into clinical settings by using a simple and cost-effective approach, and thus bridge the gap between basic research and patient care.