Krüppel-like factor 2 programs early exhausted T cell states and restrains antiviral immunity [ATAC-seq]

A key challenge in improving T cell-mediated immunotherapies is defining the factors that regulate functional versus exhaustion T cell fates. Through multi-round in vivo CRISPR screens in chronic LCMV Clone 13 infection and transcription factor (TF) benchmarking, we identified KLF2 as a top TF driving CX3CR1⁺ effector-like exhausted cell (Texeff-like) differentiation. Overexpression of KLF2 converted CX3CR1⁻ cells into Texeff-like cells by direct engagement of key loci. Conversely, loss of KLF2 increased inhibitory receptor expression and redirected cells toward terminal exhaustion. However, early after infection, KLF2 deficiency yielded increased CD8+ T cell accumulation and improved viral control. This effect was, in part, mediated by TOX and improved T cell localization with dendritic cells. Additional deletion of PD-1 further enhanced viral control, but induced severe immunopathology. Collectively, these findings identify KLF2 as a central regulator of the Texeff-like program and underscore exhaustion features as checkpoints balancing antiviral immunity and immunopathology.