Characterization of candidate genes in inflammatory bowel disease–associated risk loci
Joanna M. Peloquin, Gautam Goel, Lingjia Kong, Hailiang Huang, Talin Haritunians, R. Balfour Sartor, Mark J. Daly, Rodney D. Newberry, Dermot P. McGovern, Vijay Yajnik, Sergio A. Lira, Ramnik J. Xavier
Joanna M. Peloquin, Gautam Goel, Lingjia Kong, Hailiang Huang, Talin Haritunians, R. Balfour Sartor, Mark J. Daly, Rodney D. Newberry, Dermot P. McGovern, Vijay Yajnik, Sergio A. Lira, Ramnik J. Xavier
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Research Article Gastroenterology Inflammation

Characterization of candidate genes in inflammatory bowel disease–associated risk loci

Abstract

GWAS have linked SNPs to risk of inflammatory bowel disease (IBD), but a systematic characterization of disease-associated genes has been lacking. Prior studies utilized microarrays that did not capture many genes encoded within risk loci or defined expression quantitative trait loci (eQTLs) using peripheral blood, which is not the target tissue in IBD. To address these gaps, we sought to characterize the expression of IBD-associated risk genes in disease-relevant tissues and in the setting of active IBD. Terminal ileal (TI) and colonic mucosal tissues were obtained from patients with Crohn’s disease or ulcerative colitis and from healthy controls. We developed a NanoString code set to profile 678 genes within IBD risk loci. A subset of patients and controls were genotyped for IBD-associated risk SNPs. Analyses included differential expression and variance analysis, weighted gene coexpression network analysis, and eQTL analysis. We identified 116 genes that discriminate between healthy TI and colon samples and uncovered patterns in variance of gene expression that highlight heterogeneity of disease. We identified 107 coexpressed gene pairs for which transcriptional regulation is either conserved or reversed in an inflammation-independent or -dependent manner. We demonstrate that on average approximately 60% of disease-associated genes are differentially expressed in inflamed tissue. Last, we identified eQTLs with either genotype-only effects on expression or an interaction effect between genotype and inflammation. Our data reinforce tissue specificity of expression in disease-associated candidate genes, highlight genes and gene pairs that are regulated in disease-relevant tissue and inflammation, and provide a foundation to advance the understanding of IBD pathogenesis.

Authors

Joanna M. Peloquin, Gautam Goel, Lingjia Kong, Hailiang Huang, Talin Haritunians, R. Balfour Sartor, Mark J. Daly, Rodney D. Newberry, Dermot P. McGovern, Vijay Yajnik, Sergio A. Lira, Ramnik J. Xavier

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Figure 2

Characterization of mucosal gene expression of inflammatory bowel disease risk genes in healthy terminal ileum and colon tissues.

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Characterization of mucosal gene expression of inflammatory bowel diseas...
(A) In healthy controls, a unique set of genes is differentially expressed in the terminal ileum (TI) versus colon, but not between ascending and descending colon, suggesting tissue specificity between TI and colon, but not specific expression in the ascending or descending colon. The heat map is colored in a row-normalized fashion, i.e., red indicates the highest value for that specific gene, and blue indicates the lowest value for the same gene. Statistical significance of genes between TI samples (n = 13) and colon samples (n = 24) was estimated by computing the signal-to-noise ratio statistic. Genes with FDR-adjusted P values of ≤0.05 and signal-to-noise ratios >0.9 (absolute value) were selected as significant. The top 25 upregulated and downregulated significant genes are shown. (B and C) Using a publicly available microarray data set (GSE16879) for gene expression from 6 healthy TI and colon samples, the differential signature of 116 genes between healthy colon and TI was tested for significance as independent validation. Colon-specific upregulated genes were enriched and upregulated in the colon samples (FDR q = 0.008; gene set enrichment analysis [GSEA] P = 0.0045, hypergeometric test), whereas the TI-specific upregulated genes were enriched in the downregulated genes from the colon samples (FDR q = 0.005; GSEA P = 0.0013, hypergeometric test). The GSEA-based enrichment score (ES) reflects the degree to which a gene set is overrepresented at the top or bottom of a ranked list of genes. GSEA calculates the ES by going down the ranked list of genes, increasing a running-sum statistic when a gene is in the gene set and decreasing it when it is not. The magnitude of the increment depends on the correlation of the gene with the phenotype. The ES is the maximum deviation from 0 encountered in going down the list. A positive ES indicates gene set enrichment at the top of the ranked list; a negative ES indicates gene set enrichment at the bottom of the ranked list.