Tu1907 Gene-Smoking Interactions in Inflammatory Bowel Disease

Abstract

Background: Genome-wide association studies (GWAS) have been pivotal to increasing our understanding of intestinal disease. However, the mode by which genetic variation results in phenotypic change remains largely unknown, with many associated polymorphisms likely to modulate gene expression. Analyses of expression quantitative trait loci (eQTL) to date indicate that as many as 50% of these are tissue specific. Here we report a comprehensive eQTL scan of intestinal tissue. Methods: Patients who had undergone ileal pouch anal anastomosis and closure of ileostomy at least one year prior to recruitment were prospectively enrolled at Mount Sinai Hospital in Toronto. Ileal tissue biopsies predominantly normal on endoscopy and histology from the afferent limb of these individuals were obtained and preserved in RNAlater. Total RNA was extracted with the QIAGEN miRNeasy Kit and mRNA analysis was performed on Affymetrix Human Gene 1.0 ST arrays. DNA was obtained from whole-blood samples from the same individuals and genotyped using the Illumina Human OmniExpress platform. Preliminary cis-eQTL analysis (±50Kb around each gene) was carried out on 169 subjects encompassing the expression levels of 19,047 unique autosomal genes listed in the NCBI database and 565,802 dbSNPs (Call Rate ≥ 95%; MAF ≥ 5%; HardyWeinberg χ2 ≤ 6.635). The Kruskal-Wallis test was used to compare expression values across different genotypes and Bonferroni correction for multiple testing was applied at an alpha level of 5%. Results: The presence of 3,074 statistically significant cis-eQTLs associated with 575 genes was detected with this analysis. eQTLs associated with the same expression trait were in high linkage disequilibrium. 230 (40%) of these 575 genes have been reported as quantitative traits in liver tissue by a prior study using similar methodology. After false discovery rate correction for multiple testing, our analysis confirmed previously published cis-eQTLs that are also IBD associated SNPs: rs2298428/UBE2L3, rs1050152/SLC22A4 and rs2631372/SLC22A5. Conversely, the majority of significant cis-eQTLs are novel and possibly tissue specific. These pertain to many aspects of cellular function from division to antigen processing and presentation. Conclusion: eQTL analysis of intestinal tissue substantiates reports in the literature that some eQTLs remain stable across cell types while many others are specific to the sampled location. Our findings not only confirm, but also significantly expand the number of known genotypes associated with expression and could help elucidate the mechanisms of intestinal disease.