A gene expression analysis of CD8 resident T cells in uveitis and related conditions

Abstract

Experimental Autoimmune Uveitis (EAU) is a mouse model for non-infectious human uveitis, exhibiting similar clinical characteristics such as leukocyte infiltration into the retina and tissue destruction. EAU can be induced with retinal peptides and progresses through different stages of the disease, including the prodromal phase, primary peak, and secondary regulation. Tissue-resident memory (Trm) CD8 T cells have been identified in EAU; however, their role in the pathogenesis remains unclear. The purpose of this thesis was to analyse the gene expression of retinal CD8 T cells in EAU and compare their transcriptomic profile to those of Trm CD8 T cells in similar inflammatory conditions.

The data presented were generated using a leukocyte transfer model to induce EAU. Retinal CD8 T cells were prepared for mRNA isolation and cDNA library preparation for sequencing on the Illumina platform. Gene expression repositories were queried to identify microarray datasets of Trm CD8 T cells. The bioinformatics workflow was implemented in R/RStudio using Bioconductor packages available for gene expression analysis. Protein-protein interaction networks were constructed using gene-to-protein mapping in Cytoscape.

Trm CD8 T cells from gut, lung, and skin in a LCMV model regulate genes associated with integrins (Itgae, Itga1), chemokine receptors (Ccr5, Cxcr6), retention markers (Cdh1, Rgs1, Rgs2), transcription factors (Bhlhe40, Crem, Csrnp1, Dennd4a, Fosl12, Jun, Junb, Litaf, Nfil3, Nr4a1, Nr4a2, Nr4a3, Rbpj, and Skil), and activation markers (Cish, Fasl, Gzma, Gzmb, Gzmk, Ifng, and Tnf). Brain Trm CD8 T cells exhibited a similar transcriptomic profile. In EAU, retinal CD8 T cells at day 13, 36, and 46, expressed a distinct gene expression signature. However, by day 36 and 46, the retinal CD8 T cells showed a transcriptomic profile similar to bona fide Trm cells from other conditions.

Date of Award	17 Jun 2025
Original language	English
Awarding Institution	University of Bristol
Supervisor	Lindsay B Nicholson (Supervisor)