Effector differentiation and therapeutic reinvigoration of CD8+ T cells in chronic infection depend on KLF2-directed lymph node homing

In this study, we examine the heterogeneity and molecular regulation of CD8 T cells in chronic infection across lymph nodes and spleen. We find that lymph nodes, not the spleen, support the stemness and polyfunctionality of CD8 T cells and their response to PD-1 blocking therapy. We discover that the transcription factor KLF2 is specifically expressed in and required for stem-like precursor and effector-like T cells. Finally, we show that migratory dendritic cell in the lymph nodes support the differentiation and function of CD8 T cells. LCMV-specific P14 transgenic CD8 T cells were transferred into C57B6 mice before infection with chronic LCMV Docile. At day 21 post infection, P14 cells were sorted from the spleens and LNs of these mice and scRNAseq performed. At day 21 post infection, P14 cells were sorted from the spleens and LNs of these mice and scRNAseq performed. To ensure sufficient representation of stem-like cells, we also enriched for Ly108+TIM3- cells. In some experiments KLF2-deficient and control P14 cells were generated using CRISPR/Cas9 technology, subjected to an infection experiment and RNAseq performed as above. Finally, sorted MHC2+/CD11c+ antigen presenting cells from spleen and LN of LCMV Docile infected mice and performed scRNAseq.