Abstract 3154: Sequencing of the small RNA transcriptome in cytologically normal bronchial airway epithelium of smokers with and without lung cancer

Abstract

Abstract Introduction: Based on the concept that cigarette smoke creates a molecular field of injury in epithelial cells throughout the respiratory tract, we have previously shown that mRNA expression differences in cytologically normal airway epithelial cells in patients with and without lung cancer can serve as a clinically-relevant lung cancer biomarker. MicroRNAs are short, non-coding RNAs that can each regulate the expression of hundreds of target genes and can be reliably detected in clinical samples with variable quality. The goal of this study is to generate a microRNA biomarker in the airway epithelium of smokers for the diagnosis of lung cancer. Methods: Cytologically-normal bronchial airway epithelial cells were collected via brushings of the mainstem bronchus of smokers undergoing fiberoptic bronchoscopy for suspicion of lung cancer (n=128). Subjects were followed after their bronchoscopy until a final diagnosis of lung cancer (n=75) or an alternate benign diagnosis (n=53) was made. The small RNA transcriptome (<40 nucleotides) was sequenced using the Illumina HiSeq 2000 with multiplexing (8 samples/lane). Reads were aligned to hg19 using Bowtie allowing up to 3 mismatches and 10 locations to the genome. Linear models were used to associate expression profiles with disease-related phenotypes while controlling for differences in the total number of reads and other clinical covariates. Results: An average of 10.6 million reads was sequenced per sample with 77% of these reads having at least one alignment to the human genome. In addition, 75% of the aligned reads mapped to known microRNA precursors. 508 novel microRNA precursors were predicted using the miRDeep algorithm. 362 mature microRNAs were considered consistently expressed (Median Absolute Deviation > 20). 98 of these microRNAs were differentially expressed between current and former smokers and 56 microRNAs differentially expressed in the airway epithelium of smokers with and without lung cancer (p<0.05; 18 expected by chance at this threshold). Conclusions: We have sequenced the small RNA transcriptome in the cytologically-normal proximal airway epithelium of smokers and have identified microRNA expression profiles associated with smoking status and/or a final diagnosis of lung cancer. In the future, a microRNA biomarker will be developed on these samples using procedures outlined in the MicroArray Quality Control (MAQC)-II project and tested on an independent cohort in order to confirm their ability to serve as an early diagnostic tool for lung cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3154. doi:1538-7445.AM2012-3154