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  • Project No: #OxKEN-2023/5
  • Intake: OxKEN 2023



project overview

Celiac disease is common, increasing in prevalence, and leads to significant morbidity and impaired quality of life for patients. Treatment with a gluten-free diet is burdensome, and there is a significant unmet need for improved diagnostics and therapeutics. Celiac disease also serves as an important model for inflammatory diseases – one where the triggering antigen is clearly defined and the tissue pathology (in disease and resolution) readily available for sampling.

Whilst the role of the gluten-specific CD4+ T cell in the immunopathology of celiac disease is well-studied, the cytotoxic CD8+ and γδ+ T cell populations that accumulate in the mucosa during inflammation are less well understood. In particular, the involvement of γδ T cells, which are hugely increased in number in the epithelium in coeliac disease, remain an enigma. Such cells are likely important in a range of inflammatory diseases but Celiac disease offers an important opportunity to study their role in tissue.

Recent evidence indicates that the T cell receptor (TCR) repertoire of this population is perturbed in coeliac disease, suggestive of an antigen-driven role of γδ T cells in celiac disease. However, these antigens remain unknown, as does the functional role of these intriguing cells in the gut in coeliac disease and elsewhere. This project aims to use novel molecular biology approaches and in vitro assays to answer these questions.

Project aims:
1. Characterize the phenotype and transcriptional state of circulating and intestinal γδ T cell populations in health and celiac disease, using single cell RNA sequencing and flow cytometry as well as new spatial (in situ) methods.
2. Explore the functional responses of T cell clones derived from disease-associated intestinal γδ T cells.
3. Identify putative TCR ligands for disease-associated γδ T cells in vitro using intestinal-derived T cell clones.

Unpublished data from our lab shows that CD8+ and γδ+ T cells in the gut in coeliac disease show skewed TCR repertoires, with candidate disease-associated TCR sequences identified. These populations also differ in their transcriptional profile, suggesting that these two cell types play different roles in the disease process. Funding is secured for sequencing and in vitro work to examine these populations in coeliac disease. In addition, we are analysing a recent, large-scale single-cell RNA sequencing project, which will provide further insights into the interactions between these CD8+ and γδ+ T cells and the epithelial cells in coeliac disease, in particular about potential ligands and antigens. These interactions can be addressed using newer spatial methods including high content staining approaches and spatial transcriptomics.

The lab is based in the Translational Gastroenterology Unit, a world-class translational immunology facility at the JR Hospital. The unit works closely with the clinical department, with opportunities to experience specialist clinics and gastrointestinal endoscopy. The close-knit lab group is a supportive training environment, with extensive experience of training clinician-scientists in DPhil research.


Gastrointestinal immunology, coeliac disease, γδ T cells, Intra-epithelial lymphocytes, transcriptomics


Human tissue processing, conventional and spectral flow cytometry, FACS sorting, bulk and single-cell RNA sequencing, cell culture, PCR, biostatistics, specialist coeliac disease and gastro-immunology clinics, gastrointestinal endoscopy, research and clinical journal clubs, presentations at national and international meetings.


  1. Provine, N.M., Binder, B., FitzPatrick, M.E.B., Schuch, A., Garner, L.C., Williamson, K.D., van Wilgenburg, B., Thimme, R., Klenerman, P., Hofmann, M., 2018. Unique and Common Features of Innate-Like Human Vδ2+ γδT Cells and Mucosal-Associated Invariant T Cells. Front. Immunol. 9, 120–32. doi:10.3389/fimmu.2018.00756
  2. FitzPatrick, M.E.B., Provine, N.M., Garner, L.C., Powell, K., Amini, A., Irwin, S., Ferry, H., Ambrose, T., Friend, P., Vrakas, G., Reddy, S., Soilleux, E., Klenerman, P., Allan, P.J., 2019. Human intestinal tissue-resident memory CD8+ T cells comprise transcriptionally and functionally distinct subsets. Cell Reports (In Press).


Michael FitzPatrick Email –

Paul Klenerman Email –