Single Cell RNA Sequencing Atlas of Canine Duodenal Mucosa in Chronic Inflammatory Enteropathy and Health

Abstract: Background – Canine chronic inflammatory enteropathy (CIE) is a complex disorder that currently requires intestinal biopsy histopathology for diagnosis. However, results of this diagnostic fail to elucidate disease-related molecular processes. Cutting edge molecular tools, such as single cell RNA sequencing (scRNA-seq), enable unprecedented investigation of disease pathogenesis, with the potential to shed light on the cellular and transcriptomic changes driving CIE.
Hypothesis/Objectives – To use scRNA-seq to define canine duodenal cellular constituents and investigate how CIE alters transcriptional programs.
Animals – Three healthy research colony Beagles and 3 client-owned CIE dogs with chronic diarrhea.
Methods – Descriptive case-control study. For each dog, 15 mucosal pinch biopsies were collected from the duodenum via upper GI endoscopy. Biopsies were digested in preparation for scRNA-seq. Samples from all 6 dogs were integrated into one dataset, then unsupervised clustering was completed. CIE associated changes were identified by comparing relative abundances of individual cell subsets and transcriptomic profiles.
Results – Transcriptional profiling of 40,000 cells from the 6 dogs’ duodenal biopsies highlighted the presence of 35 unique cell populations, with approximately 50% of cells being immune and the remainder epithelial or stromal. Evaluation of integrated dataset revealed substantial intra-dog variability. Despite this, analysis suggested CIE has an impact on the transcriptional programs of both immune and non-immune cells.
Conclusions and clinical importance – We present a high-resolution dataset demonstrating the cellular heterogeneity in canine duodenal mucosa in health and CIE, offering a new vantage point to understand intestinal pathobiology.