Stage II

The majority of lung cancer patients present with advanced disease that is largely incurable. Efforts to improve the early detection of this disease are critical to decrease lung cancer-related mortality. Low-dose computed tomography (CT) screening in high risk patients has demonstrated reduction in lung cancer related mortality through diagnosis of earlier stage disease at the cost of high false-positive rates and the frequent need for invasive diagnostic testing when indeterminate lung nodules are identified. Detecting tumor specific somatic mutations and/or epigenetic signatures in circulating tumor DNA (ctDNA) represents an attractive non-invasive method for identifying early stage lung cancer. However, to realize this promise for lung cancer screening, where ctDNA from small tumors is miniscule, the development of sensitive, specific, and economical ctDNA based assays is critical. 
The bacterial innate immune system consisting of clustered regularly interspaced short palindromic repeats (CRISPR) and their associated endonucleases (CRISPR-Cas) are specifically adapted to recognize foreign nucleic acids. The recent identification and diagnostic adaptation of certain classes of CRISPR-Cas systems, such as CRISPR-Cas12a and -Cas13a, offer unique platforms on which to develop sensitive, specific, and economical assays for the detection of ctDNA. The goal of the current project is to develop CRISPR-Cas12a and -Cas13a based ctDNA assays that can sensitively detect somatic cancer mutations and aberrant promoter hypermethylation often found in lung cancer patients and to validate these assays in plasma samples of patients with early stage NSCLC and in discriminating between benign and malignant nodules identified by low-dose CT screening studies. 

Statement of the Problem: Cancer develops in a sequenced manner. Patches of lung cells gain the ability to multiply faster than their neighboring normal cells by acquiring mutations. These patches of cells are called “premalignant lesions" (PMLs). Some of these lesions may eventually become cancer. Knowledge about how some PMLs may develop into lung cancer is central to developing tools for Cancer Interception—interrupting the cancer development process and blocking progression to advanced metastatic disease. However, we lack effective lung cancer interception approaches due to our incomplete understanding of the earliest molecular events associated with the development of lung cancer, as well as the challenge in developing personalized tools for early detection and prevention.

Proposed Solution: The Dream Team will use a holistic approach to understand the genetics, immunology, radiological (imaging) profile, and treatment response of patients who show evidence of abnormal lung tissue that puts them at high risk to develop lung cancer. The Team has access to unique groups of patient populations (adenocarcinoma—ADC and squamous cell carcinoma—SCC) with signs of lung cancer risk, and has assembled a collection of blood and tissue specimens from these individuals. The main objective of the Team is to understand how lung cancer develops and test methods that will block the development of cancer. Their three-pronged approach to solve this problem will include:

• Creation of a molecular pre-cancer genome atlas (PCGA) of the lung with the goal of identifying which types of precancerous lung tissue require aggressive treatment and which treatments will block the development of these abnormal lesions to invasive lung cancer.
• Development of two diagnostic tools that can be directly applied in the clinic for simple, yet accurate, detection of early lung cancer: 1) the use of nasal swabs, blood tests, and imaging to confirm whether lung abnormalities found on chest imaging are lung cancer or benign lung disease. 2) blood tests that can identify patients at the earliest stages of lung cancer recurrence, thus enabling their timely and effective intervention with therapies such as those that boost the immune system.
• Development of tests to identify which individuals are most likely to benefit from a number of treatment strategies to intercept lung cancer, including emerging immunotherapies.

Statement of the Problem: Currently, low dose CT (LDCT) screening for lung cancer is recommended for high-risk individuals, defined as current or former smokers (quit within the past 15 years) with a 30-or-more pack-year smoking history, 55 to 74 years of age, and with no evidence of lung cancer. However, uptake of LDCT screening has been impeded by high rates of false-positive results, which in turn add significant physical and emotional stress to patients as well as additional healthcare costs. Since LDCT is now commonly available, lung nodules detected in LDCT scans are plentiful, but imprecise guidelines for care make it a challenge to ensure quality follow-up and expedited diagnoses for those with lung cancer. Furthermore, screening is not available for those who don’t meet the screening criteria (younger age or low smoking history) when they are the exact population among whom lung cancer rates are rising.

Proposed Solution: Leveraging expertise of academic research centers (Massachusetts General Hospital, Broad Institute, and Stanford University) and a non-profit managed-care consortium (Kaiser Permanente), the Dream Team will develop a test called the Lung Cancer Interception Assay (LCIA) to complement LDCT screening.

The proposal is novel in that it will develop complex computational algorithms to combine high-sensitivity/high-accuracy blood-based molecular biomarkers with image-based biomarkers to create the  LCIA assay. At the end of the award period, a streamlined product, the LCIA, will be ready to use in population-level definitive trials for the early detection of lung cancer.

Inadequate biopsy yield is a significant limitation to early lung cancer diagnosis and is a two-pronged problem: (1) Early-stage lung cancers are not adequately targeted during biopsy due to their small size and (2) even if a nodule is adequately targeted, often there is insufficient tumor in the biopsy to make a definitive diagnosis and/or accomplish all diagnostic testing for patient care. Optical coherence tomography (OCT) is a high-resolution imaging modality that provides virtual visualization of tissue volumes orders of magnitude larger than biopsy without tissue removal. Dr. Hariri’s group has developed OCT catheters compatible with standard bronchoscopes and demonstrated that OCT can identify lung nodules and assess pathologic features of lung cancer with high sensitivity/specificity. This project’s aims are to dramatically improve diagnostic capability in lung cancer using large volume OCT to provide (1) virtual intra-procedural evaluation in real-time (VIPER) of biopsy site location and 2) large volume virtual optical biopsy for subsequent pathology diagnosis as a complement to tissue biopsy. In Aim 1, they will assess if in vivo OCT VIPER biopsy assessment increases tumor yield on bronchoscopic biopsy in a powered, blinded clinical study. In Aim 2, they will use the data obtained in Aim 1 to determine the diagnostic accuracy of large volume OCT optical biopsy with tissue biopsy as compared to tissue biopsy alone. This project will result in clinical translation of a powerful, robust new optical bronchoscopy tool that could reduce unnecessary diagnostic procedures, eliminate delayed diagnoses, provide earlier intervention, and improve patient morbidity/mortality.

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.