Abstract 4156: Inter-individual variation in allele specific expression of catalase (CAT) in normal bronchial epithelial cells and association of putative cis-regulatory CAT SNP rs12807961 with lung cancer risk
Authors: Jiyoun Yeo, Xaiolu Zhang, Erin L. Crawford, James C. Willey
Journal: Cancer Research (2014)

Abstract Background: Catalase (CAT) is a key antioxidant gene expressed at high levels in most human tissues, including normal bronchial epithelial cells (NBEC). NBEC CAT expression is more disperse (more high and low extreme values) among subjects with cancer compared to controls. CAT shares this property with 14 other antioxidant and DNA repair genes comprised by the Lung Cancer Risk Test (LCRT) reported from this laboratory. We hypothesize that inter-individual variation in CAT regulation in NBEC is in part due to inter-individual variation at one or more cis-regulatory single nucleotide polymorphisms (SNPs). If so, this should manifest as inter-individual variation in allele-specific CAT expression in NBEC. Through funding in part from RC2 CA148572 and HL108016 we collected NBEC samples from over 500 subjects at risk for lung cancer. In this pilot study, we assessed allele-specific and total expression of multiple genes in NBEC samples from 85 subjects and assessed the genotype at putative cis-regulatory CAT SNP rs12807961 in gDNA from 95 subjects. Methods: RNA extracted from normal bronchial airway brush specimens of 85 subjects (26 cancer cases and 59 non-cancer controls) was reverse transcribed. Using next generation sequencing (NGS), allele-specific expression (ASE) was measured as allelic imbalance in each cDNA at three marker SNPs in the CAT coding region (rs1049982, rs769217, and rs704724) and one putative regulatory SNP (rs12807961) that was 4364 bases upstream of transcription start site, using gDNA as control. Specifically, each cDNA and matched peripheral blood cell gDNA sample was subjected to targeted competitive template multiplex PCR amplicon library generation followed by NGS (Blomquist et al, PLOS one, 2013) on Illumina Hiseq platform. The genotype at putative cis-regulatory SNP rs12807961 was assessed in gDNA from 95 subjects including those assessed for ASE (a total of 31 cancer cases and 64 non-cancer controls) using a TaqMan® SNP Genotyping Assay. Results: Among heterozygotes, there was significant inter-individual variation in cDNA allelic imbalance at rs1049982 (p&amp;lt;0.001, n=40) and rs769217 (p&amp;lt;0.001, n=28) as measured by F-test using matched gDNA controls. In this cohort there was insufficient number of heterozygotes at rs704724 (n=2) to assess ASE. Among all 95 subjects assessed for rs12807961 genotype, nine were homozygous minor allele at the rs12807961 CAT SNP. Of these, 7/31 cancer cases and 2/64 non-cancer controls were homozygous minor allele. This difference was significant by two-tailed Fisher exact test (P&amp;lt;0.05) following Bonferroni adjustment for multiple testing. Conclusions: These data support the hypothesis that cis-regulatory DNA variants contribute to inter-individual variation in CAT regulation in NBEC and that this is associated with lung cancer risk. Citation Format: Jiyoun Yeo, Xaiolu Zhang, Erin L. Crawford, James C. Willey. Inter-individual variation in allele specific expression of catalase (CAT) in normal bronchial epithelial cells and association of putative cis-regulatory CAT SNP rs12807961 with lung cancer risk. [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 4156. doi:10.1158/1538-7445.AM2014-4156