Characterization of DNA repair in genomic and transcriptomic evolution of early lung carcinogenesis

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Project Summary/Abstract Lung cancer remains the leading cause of cancer-related mortality in the United States and is particularly problematic in U.S. veterans, who are at an increased risk for lung cancer resulting in approximately 5,500 excess veteran deaths per year. This is largely due to the late stage at which lung cancer is diagnosed. However, resection of pre-malignant and stage I non-small cell lung cancers (NSCLC) results in cure in most patients. Current recommendations include screening high-risk patients for lung cancer by low dose computed tomography (CT) of the chest due to a 20% relative risk reduction in mortality. However, debate exists on the patient population most likely to benefit from this intervention. Pre-malignant lesions such as atypical adenomatous hyperplasia and early lung adenocarcinomas, identified as nodules on chest CT, are often indistinguishable from benign nodules, which can lead to aggressive diagnostic and therapeutic interventions, and possibly harm, in patients with benign nodules or delayed diagnosis in those with NSCLC. Better diagnostic and therapeutic targets are needed to detect and treat pre-malignant and early non-small cell lung cancers when cure is likely. A better understanding of the mechanisms underlying transition from pre-malignant to frankly malignant non-small cell lung cancers is essential for more accurate and timely diagnosis and ultimately improved survival. Genomic instability is a hallmark of cancer, and altered DNA repair pathways have been associated with increased risk of lung cancers. The DNA repair protein, Xeroderma Pigmentosum Group C (XPC) gene expression is decreased by chronic cigarette smoke in mice, and low XPC is identified early and often in human lung adenocarcinomas. Our laboratory has discovered a critical role of XPC in protection against development of cigarette smoke and carcinogen-induced lung adenocarcinoma development. We recently found that XPC protects against histologic progression of mouse NTCU-induced lung squamous cell carcinomas. Our preliminary data suggests progression of carcinogen-induced lung cancers in XPC deficient mice is associated with increasing copy genomic complexity with higher histologic grade. Based on these findings, we hypothesize that decreased DNA repair by XPC leads to pre-malignant lesions with characteristic mutational and epigenetic signatures that predict progression to lung cancer. We propose to study this in three aims, using human samples of pre-malignant and early NSCLC specimens complemented by our well-established, XPC-deficient urethane lung adenocarcinoma progression model. In Aim 1, we will identify the impact of XPC in transition from pre-malignant to early and late adenocarcinoma pathologic grades by performing single cell sequencing on specimens isolated from urethane-treated XPC deficient mice, and confirm orthologous changes in humans using archived genomic data (NCBI Gene Expression Omnibus) and mechanistic in vitro studies. In Aim 2, we will determine the mechanistic impact of immune evasion on lung carcinogenesis using PD-L1 inhibitor, atezolizumab, in our mouse lung adenocarcinoma progression model, and define characteristic immunogenotypic characteristics of atezolizumab-resistant lung adenocarcinomas. Finally, in Aim 3, we will determine the impact of DNA repair on critical genomic and epigenetic changes in pre-malignant and early human lung squamous cell carcinomas. DNA repair capacity, determined by host cell reactivation assay, will be compared to bronchial epithelial cell dysplasia regression or persistence, and clonal genomic and transcriptomic differences studied in dysplastic samples which progressed/persisted vs regressed. Studying the mechanisms and genomic instability in early NSCLC development may allow for earlier recognition and novel therapeutic targets in early non-small cell lung cancer.