CD8+ T cells during acute viral respiratory infection are uniquely differentiated and regulated by multiple inhibitory receptors

Acute viral infection typically generates functional effector CD8+ T cells that aid in pathogen clearance. However, during acute viral lower respiratory infection (LRI), lung CD8+ T cells are functionally impaired and do not optimally control viral replication, while spleen CD8+ T cells specific for the same viral epitopes remain fully functional. To better understand the mechanisms governing lung CD8+ T cell impairment, we used flow cytometry to sort anti-viral CD8+ T cells during viral LRI. Lung and spleen cells were stained with MHC-class I tetramers representing the immunodominant anti-viral CD8+ T cell epitope. We then sorted to high purity: naïve CD8+ T cells, spleen epitope-specific CD8+ T cells, lung epitope-specific CD8+ cells and secondary infection lung epitope-specific CD8+ T cells. We then performed a genome wide transcriptional analysis of these cells to characterize the gene expression profile of lung CD8+ T cell impairment. Epitope-specific lung and spleen CD8+ T cells were obtained using flow cytometric sorting of MHC-class I tetramer stained CD8+ T cells at day 7 after human metapneumovirus (HMPV) infection. Tetramers were specific for the immunodominant M195 epitope (derived from the M protein of HMPV) in B6-Kb0Db0;B7.2 transgenic (B7tg) mice. Naïve CD44-CD62L+ CD8+ T cells were also obtained from the spleen. In a separate group, mice were primed with M195 peptide-pulsed LPS-matured bone marrow-derived dendritic cells, challenged with HMPV two weeks later, and secondary M195-specific CD8+ T cells were obtained at day 7 post-challenge.