Abstract 4251: Identification of expression quantitative trait loci at lung cancer and COPD risk genes in normal bronchial epithelial cells
Authors: Crawford Erin L. , Yeo Jiyoun , Zhang Xiaolu , Padda Karan , Arend Taylor , Blomquist Thomas M. , Levin Albert M. , Lu Mei , Willey James C. 
Published: May 2015

Abstract
Background: Lung cancer and chronic obstructive pulmonary disease (COPD) and are leading causes of morbidity and mortality both in the United States and worldwide. Inhalation of cigarette smoke is the primary known and preventable cause but only 10-15% of heavy smokers develop these diseases. This suggests that cigarette smoke exposure interacts with inherited susceptibility factors to determine risk. While some susceptibility genes are known, they account for less than 5% of risk for either disease. There is urgent need to identify heritable susceptibility factors that explain the majority of lung cancer and COPD risk. In this study we focused on discovery of cis-regulatory expression quantitative trait loci (eQTL) responsible for inter-individual variation in the expression of genes that we and/or others have reported to display altered regulation in subjects with lung cancer or COPD. Through funding in part from RC2 CA148572 and HL108016 we collected normal bronchial epithelial cell (NBEC) samples from over 500 subjects with lung cancer or COPD or demographically at risk for lung cancer or COPD. In this pilot study, we assessed allele-specific expression (ASE) and total expression of multiple putative risk genes in NBEC samples from 85 subjects.
Methods: A targeted competitive multiplex next generation sequencing (NGS) method (STAndardized RNA SEQuencing [STARSEQ]; Blomquist et al, PLOS one 2013) was used to quantify a) allele specific expression (ASE) and total expression at 140 single nucleotide polymorphism (SNP) sites among 41 target genes (including eleven of 14 genes comprised by the previously reported lung cancer risk test (Blomquist et al, Can. Res. 2009) in NBEC total RNA from 85 subjects (26 cancer cases and 59 non-cancer controls), and b) allelic representation and putative cis-regulatory single nucleotide polymorphisms (rSNPs) in matched peripheral blood leukocyte genomic (g)DNA from the same subjects. Heterozygosity was determined by gDNA analysis.
Results: Significant (p&lt;0.05) inter-individual variation in ASE measured as allelic imbalance relative to matched gDNA was observed for: CAT, CCND2, ERCC4, ERCC5, KEAP1, MUC5B and TP73. Among these genes, for some the same allele was typically expressed at a higher level among the subjects studied (e.g. ERCC5 rs17655) which suggests a closely proximal cis-regulatory SNP and for others the over expressed allele was random (e.g. CAT rs1049982) which suggests a more distal cis regulatory SNP.
Conclusions: This small study of 85 subjects provides evidence for cis-regulatory eQTL in selected genes with high prior likelihood for contributing to lung cancer and COPD risk. The genes with ASE reported here will be among those included in additional studies in archived NBEC samples from 500 subjects aiming to further optimize current tests for lung cancer and COPD risk and better understand mechanisms of risk.
Citation Format: Erin L. Crawford, Jiyoun Yeo, Xiaolu Zhang, Karan Padda, Taylor Arend, Thomas M. Blomquist, Albert M. Levin, Mei Lu, James C. Willey. Identification of expression quantitative trait loci at lung cancer and COPD risk genes in normal bronchial epithelial cells. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4251. doi:10.1158/1538-7445.AM2014-4251