Investigation of T cell populations in coeliac disease and intestinal transplantation using functional, transcriptomic, and T cell receptor repertoire analysis approaches

Coeliac disease (CD) is caused by an adaptive immune response to gluten, however the gluten- specific CD4+ T cell response is insufficient to cause tissue damage in isolation. CD8+ intra-epithelial T cells (IELs) mediate epithelial cell damage in CD, which is thought to occur in a TCR-independent manner, while the role of γδ IELs, which are increased in CD, remains enigmatic. I sought to investigate CD8+ and γδ T cell populations in CD.
After optimisation of intestinal tissue dissociation, TCR repertoire sequencing (TCRseq) and single- cell RNA sequencing (scRNAseq) (Chapter 3), I examined intestinal CD8+ and γδ T cells in CD using flow cytometry, bulk and single-cell RNAseq, and TCRseq (Chapter 4). I confirmed previously reported changes in γδ TCR repertoires in CD, and identified perturbations in the CD8+ TCR repertoire, including enrichment of TRBV28-expressing clonotypes in CD. Bulk and scRNAseq approaches identified an activated, cytotoxic, highly regulated, tissue-resident population of CD8+ T cells associated with CD, which were associated with these TRBV28 clonotypes, consistent with a TCR-driven CD8+ T cell process involved in CD pathogenesis.
This work on CD led further research in two directions, examining the wider landscape of human γδ T cells and their relationships to other innate-like T cells, and exploring CD8+ T cell heterogeneity in tissue resident populations in the human gut.
First, I examined transcriptional, phenotypic, and functional heterogeneity in human γδ T cells (Chapter 5). scRNAseq and flow cytometry of circulating γδ T cells revealed a Vδ2+ γδ T cell effector spectrum, from an innate-like, cytokine-responsive CD26bright population to a highly cytotoxic GPR56+ population. CD26bright Vδ2+ T cells were highly similar to MAIT cells, in transcriptional profile, phenotype, and function, in particular in their IFNγ- and IL-26-dominated response to cytokine stimulation. In addition, unexpected heterogeneity within naive non-Vδ2 T cell populations was identified, including a SOX4+ subset that expressed the gut-homing chemokine receptor CCR9.
Second, I used intestinal transplantation as a model to study tissue resident memory (TRM) CD8+ T cells in the small intestine (Chapter 6). scRNAseq identified two transcriptionally distinct subsets of bona fide CD8+ TRM cells in the human gut, differing in their expression of cytotoxic molecules, chemokine receptors, and integrins. Further flow cytometry and functional assays demonstrated that these populations differed in phenotype and function.
In sum, I have explored CD8+ and γδ T cell biology in coeliac disease, health, and intestinal transplantation. The work raises questions about the nature of classification systems of cell types in immunology, and the shared and distinct features of unconventional and innate-like T cells.

Keywords: T cells
celiac disease
TRM cells
transplantation
MAIT cells
tissue residency
intestine
coeliac disease
γδ T cells
gluten
mucosal immunology
tissue resident memory T cells
intestinal transplantation
Advisor: Klenerman, P
Soilleux, E