Single-cell multi-omics maps clonal IEL expansion and epithelial remodelling in refractory coeliac disease
Year: 2026
Type: preprint
Study design: Observational Study
Abstract: 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 TCRαβ and TCRγδ 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.
Authors: Michael Li, Arman Safavi, Jerome Samir, Raymond Louie, Esmaeil Roohparvar Basmenj, Martina Bonomi, Thiruni Adikari, Brian Gloss, Jun Xing, Katherine Jackson, Andrew Calcino, Dan Suan, Valentina Vaira, Claire Milthorpe, Melinda Hardy, Etienne Masle-Farquhar, Scott Read, Matt Field, Luca Elli, Marco Vincenzo Lenti, Antonio Di Sabatino, Rachele Ciccocioppo, Jason A. Tye-Din, Golo Ahlenstiel, Christopher C. Goodnow, Mandeep Singh, Fabio Luciani
Institutions: UNSW Sydney, Westmead Institute for Medical Research, University of Oxford, Garvan Institute of Medical Research, James Cook University, University of Milan, Walter and Eliza Hall Institute of Medical Research, University of Pavia, Policlinico San Matteo Fondazione, University of Chieti-Pescara, Western Sydney Local Health District, Western Sydney University
Language: English
Subfield: Gastroenterology
Field: Medicine
Domain: Health Sciences
Open Access status: green
Awards: Systems immunology of antigen specific T cells: from single-cell to immune protection, Leveraging gluten challenge in coeliac disease to improve its diagnosis and management, Revealing how tolerance checkpoints fail in human autoimmune diseases and how to target therapy, Pathological and therapeutic antibody production, Harnessing Pathogenic Immune Cells to Develop a New Diagnostic for Non-Responders and Refractory Conditions in Celiac Disease
OpenAlex ID: W7207557035