Autoimmune CD4 T cell exhaustion is counteracted by peripheral circulating T cell population with stem-like potential

Stem-like antigen specific T cells serve as a reservoir for autoimmune CD8 T cell responses. However, it is unclear whether CD4 T cells depend on a similar population to counteract depletion through terminal differentiation and exhaustion. Single cell RNAseq and flow cytometric analysis of NOD islet-infiltrating T cells revealed the heterogeneity of CD4 cells, with subpopulations displaying features of exhaustion. Blockade of T cell entry with FTY720 reduced T cell numbers in the tissue, and protected NOD mice from diabetes. Moreover, islet CD4 T cells progressively lose TCF1 expression overtime. Transfer experiments and T cell tracking in photoconvertible NOD.KikGR mice showed peripheral circulating T cells with stem-like TCF1+ phenotype as an important source for autoimmune T cells. We observed that islet infiltrating CD62L+ naïve-like T cells include low affinity antigen specific cells, show activation of TCR regulated genes, and exhibit epigenetic signature distinct from lymph node bona fide naïve T cells. Similarly, BDC2.5 islet antigen specific T cells circulating in peripheral non-draining lymphoid organs exhibit phenotypic and epigenetic signature of pre-primed, but largely undifferentiated T cells. Collectively, our data indicates that autoimmune CD4 T cell persistence is sustained through continuous recruitment of new T cells from circulating non-differentiated stem-like compartment.