CXCR3 regulates stem and proliferative CD8+ T cells during chronic infection by promoting interactions with DCs in splenic bridging channels

Production of armed effector CD8+ T cells during persistent infection requires a stable pool of stem-like cells that can give rise to short-lived effector T cells via a proliferative intermediate population. In chronic infection models marked by T cell exhaustion, this process can be transiently induced by check-point blockade, but it occurs spontaneously and continuously in the spleens of mice chronically infected with the protozoan intracellular parasite, Toxoplasma gondii, providing a unique opportunity to examine the steps in the differentiation process. Using this model, we observed distinct locations and gene expression patterns for stem-like memory cells, proliferative intermediate cells, and terminally differentiated effector cells, implying a link between differentiation and discrete anatomical niches in the spleen. Loss of the chemokine receptor CXCR3 on parasite-specific T cells did not impair their white pulp to red pulp migration but reduced their interactions with CXCR3 ligand-producing type 2 conventional DCs in the bridging channels and impaired their transition from memory to intermediate states, leading to a build up of memory T cells localized to the red pulp. These results demonstrate a critical role for CXCR3 during chronic infection by increasing T cell exposure to differentiation-inducing signals during red pulp migration, providing a dynamic and flexible mechanism for modulating effector differentiation in response to environmental signals. RNA-seq was performed on GRA6-specific CD8+ T cell subsets isolated from four mice chronically infected with T. gondii (biological replicates). T cells were isolated using FACS sorting on infected splenocytes and divided into three functionally distinct subsets using CXCR3 and KLRG1 staining: Memory cells (TMEM: CXCR3+ KLRG1-), Intermediate cells (TINT: CXCR3+ KLRG1+), and Effector cells (TEFF: CXCR3- KLRG1+). One TMEM sample and one TINT sample were removed from the analysis due to low RNA quality, resulting in 10 samples in total.