Single Cell RNA Sequencing Unveils Distinct Cellular Dynamics in Celiac Disease Duodenal Biopsies

Celiac disease (CeD) is the most common autoimmune disorder in the U.S., affecting at least 1% of the population. The ingestion of gluten-containing proteins triggers an adaptive immune response, causing intestinal damage and leading to both gastrointestinal and systemic symptoms. Despite a strong genetic predisposition, the mechanistic understanding of CeD remains limited. The lack of approved therapy, other than dietary avoidance of gluten which is difficult and often unsuccessful, underscores the need to identify new mechanisms that can provide insights for developing therapeutics. To gain an unbiased view of the transcriptional landscape of the duodenum, we compared duodenal biopsies showing active CeD to normal controls using single-cell RNA sequencing. We analyzed fresh research biopsies from 4 patients with active CeD, confirmed by diagnostic biopsies from the same endoscopy, as well as 2 healthy control biopsies without specific pathological changes. Our analysis captured every major intestinal mucosal cell type including all subsets of immune cells, epithelial cells and stromal cells. Among these, enterocytes and activated T cells exhibited the most significant differences between CeD biopsies and controls. In CeD biopsies, CD8+TCR αβ and TCR γδ T cells were the primary producers of IFNG, a feature that was largely absent in the control biopsies. Moreover, enterocytes that express villous defining marker APOA4+ showed elevated levels of IFNGR1, suggesting an increased responsiveness to IFNγ produced by CeD T cells. We assessed effects of IFNγ on potential target molecules expressed on enterocytes that could activate and trigger killing by CTL. Bioinformatic ligand receptor analyses showed frequent interactions between intraepithelial CTLs and enterocyte HLA-E or HLA-B, suggesting that IFNγ production by the CTLs likely promotes further CTL recruitment and antigen-dependent killing of the villous epithelium.