Newly recruited intraepithelial Ly6A+CCR9+CD4+ T cells protect against enteric viral infection

The intestinal epithelium comprises the body's largest surface exposed to viruses. Additionally, the gut epithelium hosts a large population of intraepithelial T lymphocytes, or IELs, although their role in resistance against viral infections remain elusive. By fate-mapping T cells recruited to the murine intestine, we observed accumulation of newly recruited CD4+ T cells after infection with murine norovirus CR6 and adenovirus type-2 (AdV), but not reovirus. CR6 and AdV-recruited intraepithelial CD4+ T cells co-express Ly6A and CCR9, exhibit T helper 1 and cytotoxic profiles and confer protection against AdV in vivo and in an organoid model in an IFN-g-dependent manner. Ablation of the T cell receptor (TCR) or the transcription factor ThPOK in CD4+ T cells prior to AdV infection prevented viral control, while TCR ablation during infection did not impact viral clearance. These results uncover a protective role for intraepithelial Ly6A+CCR9+CD4+ T cells against enteric adenovirus. Overall design: RNAseq analysis of recently recruited small intestinal intraepithelial CD4+CD62L-Tomato+ T cells 10 days post murine Adenovirus-2 infected or PBS treated mice.