CD4 help is required for the generation of a transcriptionally distinct cytolytic CD8 T cell subset that arises during chronic viral infection

CD4 help is crucial to sustain the function of exhausted CD8 T cells, yet the detailed mechanisms by which CD4 help regulates CD8 T cell differentiation and function during chronic viral infection remain elusive. Here, using single cell RNA-sequencing (scRNA-seq) we show that CD8 T cells responding to chronic viral infection are more heterogeneous than previously appreciated, with three transcriptionally distinct subsets dominating the late phase of the antiviral response. Importantly, our findings uncover the formation of a previously unrecognized CD8 T cell subset that exhibits potent cytolytic function. This subset is characterized by high expression of killer cell lectin-like receptors Klre1 and Klra9, the chemokine receptor CX3CR1, and the transcription factors T-bet and Zeb2. Notably, our data further demonstrate that the formation of this cytotoxic subset is critically dependent on CD4 help and that exploitation of this developmental pathway may be used therapeutically to enhance the killer function of CD8 T cells infiltrated into the tumor. These findings uncover novel cellular and molecular mechanisms of how CD4 help regulates CD8 T cell differentiation during persistent infection and have implications towards optimizing the generation of protective CD8 T cells in immunotherapy. Two samples (day 8 and day 30) prepared using 10x Genomics Chromium platform