OP028 Single cell RNA sequencing of t-cells in Crohn’s disease identifies tissue specific drug targets
E. Festen1*, R. Weersma1, W.T. Uniken Venema1, M.D. Voskuil1, D. Graham2
1University Medical Center Groningen, Gastroenterology and Hepatology, Groningen, The Netherlands, 2The Broad Institute of MIT and Harvard, Cambridge, USA
Crohn’s disease (CD) is a chronic inflammatory disease, predominantly affecting the terminal ileum.1 Genome-wide association studies have identified ~200 CD risk loci.2 These loci are enriched for genes involved in T cell signalling, highlighting their importance in CD pathology.3 To get true insight in the underlying pathomechanisms, it is crucial to study these T cells in their disease-relevant context: the intestinal mucosa.4 We performed single cell RNA sequencing (scRNA-seq) of paired mucosal and blood T cell samples from CD patients, aiming to increase our insight in CD pathomechanisms and to identify novel drug targets.
We performed scRNA-seq of 5292 CD3+ T cells isolated from peripheral blood (PBL) and from ileal biopsies of CD patients. Biopsies were dissociated and separated into T cells from epithelium (IEL) and lamina propria (LPL). ScRNA-seq was performed with an adapted SmartSeq2 protocol, using 3′-end library generation, and unique molecular identifiers.
Unsupervised clustering of our scRNA-seq data identified five distinct T-cell types. The distribution of cell types differs between IEL, LPL and PBL: cytotoxic T cells (CTL) dominate the IEL, the blood T cell reservoir is mainly composed of quiescent T cells, and T-helper 17 (Th17) cells are the largest population in the LPL. Th17 cells and CTLs show the highest proportion of differentially expressed CD risk genes: such as
We have conducted a unique disease- and tissue-specific transcriptomic characterisation of T cells in CD. We have profiled five distinct T-cell types using scRNAseq data. We show that CD risk genes are significantly overexpressed in ileal mucosal Th17 and CTLs, and provide promising targets for future therapies in CD patients.