Recruitment of stem-like T cells and resistance to exhaustion support CD4 T cell responses in autoimmunity (scRNA-Seq).

Recent findings suggest that undifferentiated, stem-like, antigen specific T cells serve as an important long-term reservoir for autoimmune CD8 T cell responses. However, it is still unclear whether CD4 T cells exhibit a similar differentiation trajectory culminating in terminal differentiation, acquisition of an exhausted phenotype, and loss of stemness and function. We analyzed islet infiltrating T cells in 8- and 16-week old NOD mice by scRNAseq and flow cytometry and found that while CD4 T cells in autoimmune diabetes share many features of exhaustion with CD8 T cells, expression patterns of inhibitory receptors are distinct in autoimmune T cells compared to T cells in chronic LCMV infection. We performed scRNAseq on T cells isolated from pancreatic islets of 8-week-old and 16-week-old NOD females to compare their transcriptome profile.