Abstract 2534: Single-cell RNA sequencing reveals lung cancer-associated alterations in bronchial cell subpopulations in the mainstem bronchus
Authors: Shi Xingyi , Duclos Grant , Campbell Joshua , Gesthalter Yaron , Autissier Patrick , Dumas Yves M. , Terrano Robert , Liu Gang , Lenburg Marc E. , Spira Avrum , Beane Jennifer 
Published: August 2018

Abstract
RATIONALE: We have previously shown that gene expression alterations in the mainstem bronchus epithelium reflects a physiologic response to cigarette smoke and can serve as a diagnostic biomarker for lung cancer. Furthermore, we have shown that single cell RNA sequencing (scRNA-Seq) can be used to detect smoking-associated gene expression alterations within specific airway epithelial and immune cell types. In this study, we use scRNA-Seq to profile the transcriptomes of single cells procured from the airways of patients with or without lung cancer in order to detect cancer-associated alterations within specific cell types.
METHODS: We obtained bronchial brushings in the mainstem bronchus from ever smokers undergoing diagnostic bronchoscopy for suspect lung cancer. Patients were followed post-procedure until a final lung cancer diagnosis (n=5; 3 adenocaricinomas, 1 squamous cell carcinoma and 1 large cell carcinoma) or benign disease (n=7) was made. Single cells were isolated using FACS (n=190/donor) and RNA library preparation was performed using the CEL-Seq protocol followed by RNA-seq (75nt paired-end) on an Illumina Hiseq 2500. Latent Dirichlet allocation was used to identify transcriptomically distinct cellular subpopulations specific to the airways of patients with and without lung cancer.
RESULTS: We detected distinct subpopulations of bronchial cells expressing known markers of basal (KRT5), ciliated (FOXJ1), club (SCGB1A1), and goblet (MUC5AC) epithelial cells. Cell type distributions differed between cancer status and within cancer sub-types. Specifically, patients with cancer had an increase in FOXJ1+ cells. Many of the genes in the previously reported diagnostic biomarker such as ATP12A and NKX3-1 are expressed in specific cell types.
CONCLUSION: The scRNA-Seq data of the normal appearing airways of subjects with and without lung cancer suggests that the epithelial and immune cell types present and their relative proportions change with cancer status. Additionally, previously described lung cancer biomarker genes are expressed in a cell type specific manner indicating that future biomarker improvements may be made by examining subpopulations of cells. Analysis of a greater number of samples is needed to make robust conclusions regarding the changes associated with smoking, cancer, and cancer subtype in this sample population.
Citation Format: Xingyi Shi, Grant Duclos, Joshua Campbell, Yaron Gesthalter, Patrick Autissier, Yves M. Dumas, Robert Terrano, Gang Liu, Marc E. Lenburg, Avrum Spira, Jennifer Beane. Single-cell RNA sequencing reveals lung cancer-associated alterations in bronchial cell subpopulations in the mainstem bronchus [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2534.