Insights into CD4 T Cell-Mediated Immunity to Influenza Viruses

Thesis (Ph.D.)--University of Rochester. School of Medicine & Dentistry. Dept. of Microbiology and Immunology, 2018.Influenza A viruses continue to pose a threat to human health worldwide and virusspecific CD4 T cells are key to protective immunity. The goal of the experiments within this thesis was to provide novel insight into elements within CD4 T cell responses that influence CD4 T cell specificity and function. Using a combination of novel reporter viruses, intravascular labeling in vivo, multi-parameter flow cytometry, and cytokine ELISpot procedures in two mammalian models, this work examined various stages of the developing immune response and the relationship between antigen acquisition, CD4 T cell fate choice, trafficking and compartmentalization within the inflamed lung, antigen specificity, and cytokine functionality. We found that pandemic 2009 H1N1 virus infection resulted in a broad pattern of viral antigen acquisition in the lung. Complex subpopulations of MHC class II-positive cells from both the hematopoietic and non-hematopoietic lineages were identified, with dynamic shifts over time. Our results demonstrated that antigen access occurs by uptake of exogenous antigen as well as infection. Finally, our results confirmed that many different cell types displayed peptide:MHC class II complexes in situ and possessed the capacity to stimulate influenza-specific CD4 T cells. These results correlated with differences in infection status, cell lineage, and MHC class II expression. These data suggest that there are many different types of antigen presenting cells in the lung that may impose additional checkpoints of CD4 T cell functionality and regulation. At the peak of the immune response, we found that lung CD4 T cells compartmentalized to vasculature and tissue. Antigen-experienced CD4 T cells were enriched in the tissue and expressed higher levels of molecules involved in trafficking to sites of pulmonary infection, damage, and repair. Surprisingly, we found similar representation in the fine specificity, immunodominance hierarchy, and polyfunctional potential of effector CD4 T cells in the two compartments. These results suggest that imprinting of CD4 effector programs in the priming lymph node plays a strong deterministic influence on CD4 function and fate. Also, we provide evidence of cellular intermediates in CD4 T cell trafficking in the lung. Finally, this thesis includes the first description of the CD4 and CD8 T cell repertoires in response to infection, a key step needed to advance the ferret model forward for future transmission and vaccine studies. Mechanistic studies of infection and vaccination in domestic ferrets may reveal novel links between antigen specificity and effector function, cellular correlates of protection, and the merits, consequences, and cellular heterogeneity of complex immunological memory