Transcriptome-Wide Association Study for Inflammatory Bowel Disease Reveals Novel Candidate Susceptibility Genes in Specific Colon Subsites and Tissue Categories. (21st July 2021)

• Record Type: Journal Article
• Authors: Díez-Obrero, Virginia; Moratalla-Navarro, Ferran; Ibáñez-Sanz, Gemma; Guardiola, Jordi; Rodríguez-Moranta, Francisco; Obón-Santacana, Mireia; Díez-Villanueva, Anna; Dampier, Christopher Heaton; Devall, Matthew; Carreras-Torres, Robert; Casey, Graham; Moreno, Victor
• Is Part Of: Journal of Crohn's and colitis. Volume 16:Number 2(2022)
• Page Start: 275
• Page End: 285
• Publication Date: 2021-07-21
• Subjects: Transcriptome-wide association study -- genetic susceptibility -- gene expression; Inflammatory bowel diseases -- Periodicals; 616.344005
• DOI: 10.1093/ecco-jcc/jjab131
• Languages: English
• ISSNs: 1873-9946

Abstract

Abstract: Background and Aims: Genome-wide association studies [GWAS] for inflammatory bowel disease [IBD] have identified 240 risk variants. However, the benefit of understanding the genetic architecture of IBD remains to be exploited. Transcriptome-wide association studies [TWAS] associate gene expression with genetic susceptibility to disease, providing functional insight into risk loci. In this study, we integrate relevant datasets for IBD and perform a TWAS to nominate novel genes implicated in IBD genetic susceptibility. Methods: We applied elastic net regression to generate gene expression prediction models for the University of Barcelona and University of Virginia RNA sequencing project [BarcUVa-Seq] and correlated expression and disease association research [CEDAR] datasets. Together with Genotype-Tissue Expression project [GTEx] data, and GWAS results from about 60 000 individuals, we employed Summary-PrediXcan and Summary-MultiXcan for single and joint analyses of TWAS results, respectively. Results: BarcUVa-Seq TWAS revealed 39 novel genes whose expression in the colon is associated with IBD genetic susceptibility. They included expression markers for specific colon cell types. TWAS meta-analysis including all tissues/cell types provided 186 novel candidate susceptibility genes. Additionally, we identified 78 novel susceptibility genes whose expression is associated with IBD exclusively in immune ( N = 19), epithelial ( N = 25), mesenchymal ( N = 22) and neural ( N = 12) tissue categories. Associated genes were involved in relevant molecular pathways, including pathways related to known IBD therapeutics, such as tumour necrosis factor signalling. Conclusion: These findings provide insight into tissue-specific molecular processes underlying IBD genetic susceptibility. Associated genes could be candidate targets for new therapeutics and should be prioritized in functional studies. Graphical Abstract: