RNA-Seq Quantification of the Complete Transcriptome of Genes Expressed in the Small Airway Epithelium of Nonsmokers and Smokers

Morphological changes in the small airway epithelium are the first histopathological manifestations of smoking-induced lung disease. Gene expression profiling using microarrays has permitted the identification of changes in the small airway epithelium of chronic cigarette smokers who have normal pulmonary function. The availability of high throughput, massively parallel RNA sequencing (RNA-Seq) of the entire transcriptome opens the possibility of a higher sensitivity and more detailed characterization of the response of the small airway epithelium to smoking. Epithelial cells were obtained by fiberoptic bronchoscopy and brushing of healthy smokers (n=6) and n=5 healthy nonsmokers, all with normal lung function and chest x-rays. RNA was extracted and used for massively parallel sequencing of PolyA selected transcripts using the Illumina Genome Snalyzer II. Genes were identified with significantly different RNA-Seq expression levels between nonsmokers and smokers.