View Abstract

A7081 - Single Cell RNA Sequencing Reveals Bronchial Cell Types that Contribute to Smoking and Lung Cancer Associated Gene Expression Differences
Author Block: G. E. Duclos1, X. Shi1, J. D. Campbell1, Y. Gesthalter1, P. Autissier2, Y. M. Dumas1, R. Terrano1, G. Liu1, M. Lenburg1, A. Spira1, J. Beane1; 1Computational Biomedicine, Boston University School of Medicine, Boston, MA, United States, 2Flow Cytometry Core Facility, Boston University School of Medicine, Boston, MA, United States.
RATIONALE: We have previously shown that bronchial gene expression reflects a physiologic response to cigarette smoke and can serve as a diagnostic biomarker for lung cancer. The potential changes in cell type distribution or cell type-specific gene expression differences that might contribute to these changes are unknown. In this study, we use single cell RNA sequencing (scRNA-Seq) to profile the transcriptomes of single cells procured from the airways of healthy non-smokers (n=6) and smokers (n=6) as well as patients undergoing bronchoscopy for suspicion of lung cancer (n=12) in order to determine the cell type specificity of smoking- and lung cancer-associated bronchial gene expression.
METHODS: We obtained bronchial brushings from healthy smokers (n=6) and non-smokers (n=6) as well as individuals undergoing diagnostic workup for suspect lung cancer (n=5 with lung cancer, n=7 with benign disease). FACS was used to isolate single epithelial and white blood cells from non-smokers and smokers, whereas it was used for unbiased isolation of all live cells from individuals with and without lung cancer. Single cell RNA libraries were prepared using the CEL-Seq protocol (3,420 cells total) and topic modeling was used to characterize molecular subclasses of cells.
RESULTS: We used scRNA-Seq to identify transcriptomically distinct subclasses of basal, ciliated, club, and goblet epithelial cells, as well as T cells and monocytes. We found that many genes previously reported to be up-regulated in the airways of smokers can be attributed to a ciliated cell-specific xenobiotic response and an increase in the number of goblet cells, whereas genes previously reported to be down-regulated in the airways of smokers can be attributed to a loss of club cells. We also found that genes previously reported to be up-regulated in the airways of lung cancer patients predominantly localize to subpopulations of epithelial cells, whereas genes previously reported to be down-regulated in the airways of lung cancer patients predominantly localize to white blood cells (T cells, monocytes).
CONCLUSION: Smoking- and lung cancer-associated bronchial gene expression differences are predominantly the consequence of cell type-specific changes in the airways of smokers and lung cancer patients. Findings from this study may provide insights into the cellular and molecular underpinnings of biomarkers for smoking and lung cancer measured within the airway “field of injury” that will ultimately allow us to improve upon their sensitivity and specificity.