MA04.06 Lung Epithelium Whole Transcriptome Signatures That Reflect Incident Lung Cancer Case-Control Status

Abstract

Focusing early detection and prevention efforts on those at high risk for lung cancer is central to leveraging such strategies. Notably, that risk persists even after removal of a lung cancer, as reflected in lung recurrences, which are common, and usually occur remote from the surgical removal site. This implies risk for future incident lung cancer is represented in the biology of broad areas of lung epithelium, before, during, and after diagnosis. Given that somatic mutations in the bronchial tree are known to persist for decades, there is a suggestion that smoking transforms the entire epithelium at several somatic and gene regulatory levels. We hypothesize that the normal lung epithelium contains expression and epigenetic epithelial signatures that are representative of donor case-control status, that is poised for carcinogenesis. As a first step, in order to identify differentially expressed genes (DEGs) associated with aging, smoking and cancer case-control status, we analyzed RNA-seq transcriptome data of laser capture microdissected (LCM) bronchial and alveolar epithelium separately, in paired tissue sets of 40- and 74 respective individuals, summarized here. Read count was the main normalization variable. We also measured differentially methylated sites (DME) by whole genome bisulfite genome sequencing (WGBSeq), covering >60% of the genome/methylome [as of this deadline, these methylome data are not yet fully analyzed]. Mean subject age for 77 total subjects was 65 (+/-9.9), 19% current-, 76% former, 5% never smokers. For each cell type, we modeled gene expression level as a result of aging, gender, smoking and case-control status. We put all four clinical variables age, gender, smoking status, case-control status) along with cell type (alveolar/bronchial) into the model, to avoid potential confounding effects. We discovered 175 DEGs discriminating case-control status (FDR p<0.05) in alveolar and bronchial cells combined, and 420 case-control DEGs with bronchial cells alone. Bronchial cells displayed 31 DEGs discriminating current versus former smokers (FDR-adjusted P<0.05). Gene ontology (David) clusters for case-control discrimination in these “normal” bronchial epithelia included energetics pathways (GO 0042776/0006754; ATP biosynthesis) as well as transcriptional and translational regulation pathways; KEGG clusters also included oxidative phosphorylation pathways (hsa00190), among others. There is a donor case-control discriminant expression signature for human lung bronchial captured cells, emphasizing bioenergetically-deranged metabolic pathways, among others. If confirmed in larger studies that measure deranged metabolites directly, metabolomics biomarkers representing bioenergetics and other pathways may serve to define those individuals whose epithelia is tilted toward carcinogenesis, and therefore are at increased risk for lung cancer.