Single cell RNA sequencing of TCF-1+ precursor cells reacting to LCMV gp33 vs np396 multimers sorted 30 days after infection with LCMV Armstrong [scRNA-Seq + TCR 10x]

T-cell exhaustion limits effector T-cell function in chronic infection and tumors. The development of these hypofunctional T-cells and of their precursors was considered to require stimulatory conditions met only upon persisting exposure to antigen and inflammation. In sharp contrast, we found similar T-cell populations in the early phase of acute infections. At that stage early developing TCF1+ precursor population shows an unexpected diversity, which includes precursors of normal memory T-cells but also cells with a phenotype, gene-expression, and epigenetic profile that resembles precursors of exhausted T-cells found in chronic infections. We demonstrate that high ligand affinity promotes, and PD-1 signaling restricts the development of these precursors. While these exhausted precursors are initially frequently found, they decline without being completely lost in infections the immune system resolves. We therefore concluded that precursor T-cells with at least two distinct phenotypes are preemptively generated irrespectively of the outcome of the infection. In this experiment, the transcriptome and TCR-sequences of endogenous gp33 or np396 specific CD8 T-cells were analyzed on day 30 post infection to assess the role of TCR-affinity and antigen-specificity in the formation of the different CD8 T-cell precursors. Tcf7-reporter mice were infected with 2x10e5 PFU of LCMV Armstrong intra-peritoneally. On day 30 pi the spleens of the animals were harvested and reporter-positive cells reacting to gp33 or np396 multimers were isolated, sorted and subjected to the 10x library pipeline.