Exploring airway-wide physiological response to cigarette smoke using exon-level expression profiling

Although cigarette smoking is the major cause of lung cancer and chronic obstructive pulmonary disease (COPD), only 10-20% of smokers develop these diseases. Previous studies have shown that physiological responses to smoking can be detected via bronchial epithelium gene-expression profiling, and that heterogeneity in this gene-expression response to smoking is associated with lung cancer. However, the invasiveness of bronchoscopy prevents it from being used in large-scale studies as a screening tool for assessing smoking-related lung cancer risk in asymptomatic individuals. A potential alternative is to profile smoking-induced patterns in oral or nasal mucosa: tissues that are also directly exposed to tobacco smoke In this dissertation, we first examined exon-level gene expression profiles in matched bronchial and nasal epithelial cells obtained from healthy current and never smokers. We found that the majority of the gene-expression consequences of smoking are common to both nasal and bronchial epithelium, and a small number of genes show site-specific effects of smoking. In addition, given that exon-level expression arrays measure individual exons across the whole genome, we identified a hundred alternative splicing events in paired nasal and bronchial epithelium of never smokers. Validated genes include SFRS1, an arginine/serine-rich conserved and essential splicing factor, and several putative targets of SFRS1 (including SFRS1 itself), suggesting that alternative splicing may contribute to site-specific gene-expression responses to smoking in bronchus and nose. To discover smoking related non-invasive biomarkers, we also studied the gene expression from paired oral and nasal mucosa of healthy never, current, and former smokers. We detected a group of genes whose expression changes are reversible and irreversible upon smoking cessation, thus enabling us to develop a non-invasive gene-expression biomarker of past smoking exposure, and identified gene expression changes correlated with cumulative smoke exposure. Taken together, our findings suggest that gene expression profiles in oral or nasal epithelial cells may serve as a non-invasive surrogate to measure airway-wide physiological responses to cigarette smoke and/or other inhaled exposures in large-scale epidemiological studies, and may ultimately serve as early biomarkers/screening tools for smoking-related lung diseases.