Abstract 1016: Evaluation of progression associated neoepitopes and immune contexture in pulmonary premalignancy
Authors: Krysan Kostyantyn , Tran Linh M. , Grimes Brandon S. , Walser Tonya C. , Wallace William D. , Dubinett Steven M. 
Published: July 2017

Abstract
Lung cancer is the leading cause of cancer death in the US and in the world. Over the past 30 years, the five-year survival rate for lung cancer has increased by only 5%. With the widespread implementation of screening programs, detection of premalignant and early stage disease is increasing. A better understanding of genomic alterations and the microenvironment along the spectrum of early disease could lead to identification of progression-associated mutations (PAMs), defined as those shared between premalignant lesions and invasive cancer, and their neoepitopes. Unleashing the immune response against pulmonary premalignancy could transform therapy and outcomes. FFPE tissue blocks from patients with resected lung adenocarcinoma (ADC) were obtained from the UCLA Lung Cancer Tissue Repository. For each patient, the following regions were dissected from distal airways utilizing Laser Capture Microdissection: a) normal airway epithelial cells (1-3 regions), b) premalignant atypical adenomatous hyperplasia (AAH, 2-4 regions), c) adenocarcinoma in situ (AIS, when present) and d) ADC, 1-3 regions followed by whole exome sequencing. Forty-one complete cases have been sequenced to date. Our data suggest that premalignant lesions from the same patient may a) have different mutational profiles and b) bear progression-associated mutations, common with the primary lung tumor. This inter-lesion heterogeneity suggests that a progression-associated mutational landscape could be defined in longitudinal studies of pulmonary premalignancy which will be the focus of future investigations. Next, utilizing the mutational data, we performed in silico neoantigen analysis to identify potential neoepitopes among the genes mutated in premalignant lesions. The neoantigen analysis demonstrated that among the top 11 peptides with high binding avidity for autologous MHC, 9 were derived from PAMs. This suggests that neoepitopes exist in premalignancy that could serve as targets for development of future vaccines. Finally, we performed the quantitative immunohistochemical (IHC) and immunofluorescence (IF) staining for Granzyme B, PD-1, PDL-1, CD4+, CD8+ and FOXP3 to evaluate cell-mediated immunity on the same samples that were utilized for WES. We found both infiltration of T effector cells as well as upregulation of checkpoints in premalignancy and detected a significant inter-lesional heterogeneity. Our studies lay the ground work for identification of neoepitopes that can be targeted before the development of invasive lung cancer, thus shifting the approach to disease interception through immunoprevention and treatment of the very earliest phase of the disease.
Citation Format: Kostyantyn Krysan, Linh M. Tran, Brandon S. Grimes, Tonya C. Walser, William D. Wallace, Steven M. Dubinett. Evaluation of progression associated neoepitopes and immune contexture in pulmonary premalignancy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1016. doi:10.1158/1538-7445.AM2017-1016