Single-cell transcriptome sequencing reveals the cellular heterogeneity of small intestine tissue in celiac disease

Background: Celiac disease (CeD) is an autoimmune small intestinal disease caused by gluten protein ingestion by genetically susceptible individuals. Genome-wide association studies and transcriptomic data have limited capacity to capture intercellular genetic variations. We aim to construct a single-cell transcriptome spectrum, analyze the immune microenvironment and cellular heterogeneity, discover disease-related specific genes and markers, and explore the pathogenesis of CeD. Methods: We performed single-cell RNA sequencing (scRNA-seq) on three small intestine biopsies from patients with CeD and three healthy Chinese controls. Immunohistochemistry (IHC) and quantitative PCR (qPCR) were used to validate potential diagnostic biomarkers of disease-differential genes. Results: A total of 10 cell subpopulations were annotated, including three types of epithelial and stromal cells and seven types of immune cells. IHC revealed a pronounced overexpression of T cell disease-differential genes, TRAT1, BCL11B, and ETS1 in intraepithelial lymphocytes in the CeD group. Further clinical validation using qPCR confirmed that ETS1 (P = 0.010), TRAT1 (P ＜ 0.001), and BCL11B (P = 0.036) w