View Abstract

A5941 - Immune Alterations in the Airway Transcriptome of Lung Cancer Patients
Author Block: J. Lel1, E. Billatos1, E. Moses1, C. S. Stevenson2, M. Lorenzi3, G. Liu1, J. D. Campbell1, Y. Koga1, J. Zhang1, F. Duan4, H. Marques4, A. Maoz1, M. E. Lenburg1, A. Spira1, J. Beane1, DECAMP Consortium; 1Boston University School of Medicine, Boston, MA, United States, 2Janssen Pharmaceuticals, London, United Kingdom, 3Janssen Pharmaceuticals, Spring House, PA, United States, 4Brown University, Providence, RI, United States.
Rationale
Gene expression in the airway reflects the complex milieu of environmental exposure, disease state, and disease vulnerability within which lung cancer develops. We previously developed and validated a gene expression-based biomarker in brushings from the main stem bronchus, to aid the diagnostic work-up of patients undergoing bronchoscopy for suspicion of lung cancer. Here we profile endobronchial biopsies of the central airway to be able to identify lung cancer-associated gene expression changes in a wider range of cell types, including immune cells.
Methods
Endobronchial biopsies from normal-appearing regions of the central airway were collected and snap frozen from ever smokers (age >45, pack-years > 20) undergoing diagnostic work up for indeterminate pulmonary nodules (7-30 mm in diameter) at military and VA hospitals within the DECAMP consortium. Total RNA sequencing of the bronchial biopsy was performed on 38 samples (20 malignant, 18 benign). High quality sequencing data were used for all analyses. Differential gene expression associated with cancer status was identified using EdgeR while adjusted for smoking, COPD and RNA quality. Functional enrichment of differentially expressed genes was explored with the EnrichR tool, and gene set enrichment analysis (GSEA) was used to compare our data set to known lung cancer signatures. CIBERSORT was used to infer immune cell content. Each biopsy was scored for a pre-malignant lesion gene expression signature associated with histologic severity using GSVA.
Results
We identified 22 genes differentially expressed with lung cancer status (3 genes up-regulated with cancer and 19 genes down-regulated). The down-regulated genes were strongly associated with immune-related pathways, including cytokine interactions, inflammatory response, neutrophil degranulation and the complement pathway. Additionally, neutrophils and monocytes were predicted to be decreased in the airway of cancer subjects. We found a strong correlation between two previously published lung cancer-associated gene sets and the up- and down-regulated genes in the bronchial biopsies of subjects with lung cancer. We compared the top differentially expressed genes associated with pre-malignant squamous lesions, and found that the down-regulated genes were strongly correlated with genes down-regulated in subjects with squamous cell carcinoma in our cohort.
Conclusions
We found gene expression alterations within the central airway wall of ever smokers with lung cancer as compared to subjects with benign nodules. Down-regulated genes in cancer subjects are strongly associated with functions of the immune response and a decrease in airway leukocyte content, implying an airway-wide immunosuppressive microenvironment among smokers who develop lung cancer.