Tye-Din, J. A. | bioRxiv Science

bioRxiv2026

Single-cell multi-omics maps clonal IEL expansion and epithelial remodelling in refractory coeliac disease

Background Refractory coeliac disease type 1 (RCD1) lacks defining molecular markers, and the immune and epithelial mechanisms sustaining intestinal injury remain poorly understood. Objective To define the clonal immune and epithelial states that distinguish RCD1 from active coeliac disease (ACD) and determine their spatial organisation in the duodenal mucosa. Design We integrated single-cell RNA sequencing, CITE-seq surface proteomics and paired T-cell receptor sequencing of duodenal immune and epithelial compartments from Healthy controls (n = 6), ACD (n = 7), RCD1 (n = 9) and RCD2 (n = 2), with spatial transcriptomics in a subset of biopsies. Results RCD1 showed widespread TCR{beta} and TCR{gamma}{delta} clonal expansion across multiple IEL states, extending beyond previously defined mutation-bearing aberrant clones. Distinct IEL populations converged on a shared programme of adaptive persistence, innate-like signalling, metabolic fitness and cytoskeletal remodelling; GZMK expression marked both clonally expanded and non-clonal disease-associated states. In parallel, RCD1 epithelium showed loss of mature absorptive cell states and expansion of stress-associated, immune-interacting and regenerative programmes. Transit-amplifying cells acquired differentiation and tissue-remodelling signatures, while enteroendocrine cells expanded and developed a sensory-neurosecretory programme involving TRPA1, TRPV1, vesicle trafficking and NEUROD1 regulon activity. Spatial transcriptomics localised regenerative and enteroendocrine-associated epithelial programmes adjacent to immune-visible epithelial regions and KLRK1/GZMK-expressing IEL-rich niches in refractory tissue. Conclusion RCD1 represents a distinct mucosal state characterised by coordinated clonal IEL adaptation and epithelial remodelling, rather than simple amplification of ACD, providing a cellular framework for persistent tissue injury and disease stratification.

immunology↗

bioRxiv2025

Functional immune profiling reveals CD4+ T cell dysregulation associated with celiac disease

T cells integrate signals from antigen and co-stimulatory receptors to calibrate the strength and quality of their responses. This signal integration is influenced by genetic background, which can modulate thresholds for immune tolerance and strength of responses to threat. Celiac disease (CeD) is an autoimmune disorder driven by well-defined genetic risk and characterised by immune dysregulation in response to dietary gluten. However, whether sensitivity or response differences in naive T cell programming contributes to disease susceptibility is not known. To investigate such variation, we developed a sensitive quantitative platform, the momentum assay, which combines standardised, T cell activation with subsequent stimulus withdrawal, enabling measurement of T cell proliferation and survival over time. This assay is integrated with the Cyton2 mathematical model to infer underlying cellular timer programs from population-level dynamics. We applied this method to assess whether naive T cells from individuals with celiac disease (CeD) exhibited altered responses compared to healthy donors (HDs). We found that CD4+ but not CD8+ T cells from CeD patients showed a hypo-proliferative response following stimulation, associated with impaired secretion of the proliferative and pro-survival cytokine IL-2. Moreover, surface expression of early activation marker, CD69 remained elevated for longer on CD4+ T cells from CeD donors after stimulus withdrawal, suggesting prolonged activation and subtle alterations in regulatory feedback mechanisms. These findings reveal previously unrecognised quantitative alterations in naive T cell programming in CeD and underscore the utility of model-based analytical frameworks for detecting subtle functional perturbations in complex immune-mediated diseases.

immunology↗