Single cell RNA sequencing to uncover intestinal cell-type specific cis-eQTL driving inherited predisposition to IBD

IBD is characterized by a chronic idiopathic inflammation of the gastrointestinal (GI) tract and consist of two main forms: ulcerative colitis and Crohn’s disease. The importance of genetic susceptibility has been well established through Genome Wide Association Studies (GWAS), which have identified over 200 risk loci for IBD. However, the « true causative » genes in these loci have been identified for only few on the basis of independently associated coding variants. Fine-mapping studies suggested that most risk variants cause “cis”-eQTL in disease relevant cell types, but recent post-GWAS studies could not find matching cis-eQTLs for the majority of risk loci (137/200). This indicates that the relevant cell types were either not present amongst the analyzed cell populations or under-represented.
In this study, we performed cis-eQTL analysis with single cell RNA-seq of human gut biopsies to uncover the truly relevant cell types with higher resolution and unbiased approach. Biopsies were collected from three GI locations (ileum, transverse colon, rectum) from the same individuals. Cell suspensions were prepared, tagged by location and cell fraction using TotalseqB hashtag antibodies for multiplexing and processed to the 10X Genomics Chromium. Data were analyzed using Cellranger and Seurat to identify the cell clusters and marker genes. In total, 50 individuals’ biopsies data were integrated. Simultaneously, genotype was analyzed with Infinium OmniExpress-24v1 chip from 1 ml blood and imputed. Both scRNA-seq data and imputed genotypes were input to qtltools v1.3.1 for cis-eQTL anlaysis. Analysis are actually ongoing and will certainly generate new set of cell-based eQTL and determine whether some of these drive inherited predisposition to IBD by comparing the corresponding expression association patterns with disease association patterns using methods developed in our laboratory.