RNAseq analysis of mouse tumor-infiltrating CD8 T cells WT or KO for AhR

Cancer immuno-surveillance and response to checkpoint blockade therapy can be affected by multiple environmental factors, including nutrition. However, the direct effects of individual nutrients on anti-tumoral immune responses remain poorly understood. Here we addressed the impact of dietary ligands of Aryl Hydrocarbon receptor (AhR), a transcription factor activated by indoles and tryptophan catabolites generated through food digestion and microbiota metabolism. We show that T cells are the direct cellular targets of dietary AhR ligands. Transcriptomic analysis showed that tonic activation of AhR promotes anti-PD1-mediated reinvigoration of progenitor exhausted CD8 T cells by controlling their metabolic fitness, and licences the functional program of effector CD8 T cells. For RNA-seq analysis of T cells, samples were prepared by pooling tumors from 4 individual mice in each group. Cells were sorted on a FACSAria instrument. Effector CD8 T cells were gated as live CD11b- CD3+ CD4- CD8+ PD1- CD62L- and 'progenitor exhausted' CD8 T cells were gated as live CD11b- CD3+ CD4- CD8+ PD1+ CD62L- Slamf6+.