The Influence of CD4 T Cell Specificity on Differentiation of the Repertoire and Shaping the Adaptive Immune Response to Influenza Infection

Thesis (Ph.D.)--University of Rochester. School of Medicine & Dentistry. Dept. of Microbiology and Immunology, 2016.We have sought to understand the role that epitope specificity in the CD4 T cell repertoire has on the functional outcome of both the CD4 T cell response and ultimately the B cell response to influenza infection. Protection against influenza infection, provided by immune memory elicited from either infection or vaccination, is primarily mediated by neutralizing antibody. The humoral response is in turn dependent on the follicular helper T cell (Tfh) response for the provision of cognate T cell help in the germinal center reaction. Accordingly, we envision several scenarios where T cell specificity may be affecting the immune response, including the selection of which B cells receive help, and which CD4 T cells become Tfh. To this end, this thesis work has taken a twopronged approach to elucidate the effects of specificity in shaping the adaptive immune response. First, we employed a strategy of peptide priming to establish memory CD4 T cells so that we could directly query the effects of T cell specificity on the primary B cell response to influenza infection. We discovered that only T cells of matched protein specificity were capable of helping antigen-specific B cells. Nucleoprotein-specific CD4 T cell memory was uniquely positioned to provide help to NP-specific B cells, but were unable to boost the HA-specific B cell response, indicating that T cell help was both limiting and selective for the primary B cell response. The opposite was true of HA specific CD4 cells. This work underscored the importance of CD4 T cell memory in shaping novel B cell responses to infection. To understand the role of specificity in selecting CD4 T cells into a pathway of Tfh differentiation, we studied the repertoire of Tfh and NonTfh cells generated after influenza infection. Surprisingly, we delineated distinct epitopes in two different influenza proteins that were more proficient at driving a Tfh-biased effector response. For many epitopes, these preferences persisted in responses to both protein vaccination, and in the context of heterologous protein vaccination using constructs containing influenza epitopes. We were able to demonstrate that T cell specificity was sufficient to drive a particular differentiation bias towards either Tfh or NonTfh despite the overlying cytokine and costimulatory milieu provided by infection or vaccination. We have demonstrated the importance of CD4 T cell specificity both in shaping the effector repertoire of responding CD4 T cells, and in selecting the specificity of the B cell response to infection. This work contributes to our understanding of how the effector CD4 T cell repertoire is developed, and how CD4 T cell memory can influence future responses to infection or vaccination. The implications for human vaccine design are several-fold, including the following. These results delineate a potential approach for optimizing the CD4 T cell effector repertoire for antibody responses, a strategy for focusing the B cell response to infection by tailoring CD4 T cell memory. Finally, these results suggest key parameters that should be quantified in predicting neutralizing vaccine responses in human subjects