Immunodominance of flavivirus CD4 T cell responses

Flaviviruses comprise a number of important human pathogens such as such Yellow fever (YF), dengue, West Nile, Japanese encephalitis, Zika and tick-borne encephalitis (TBE) viruses, which pose an increasing threat to public health worldwide. They are transmitted to their vertebrate hosts by mosquitoes or ticks and have the potential to emerge in new geographical areas, as recently most dramatically exemplified by Zika virus outbreaks in Oceania and the Americas. Neutralizing antibodies directed against viral surface protein E are critical components of the immune response and contribute to long-term protection against flaviviruses. These antibodies are synthesized by B cells with the help of T cells, which recognize peptides derived from a protein antigen, internalized and processed by the B cell. For flaviviruses, such T helper cell epitopes can not only be derived from E but also from the two other proteins of the virion (C-capsid and prM/M-membrane). It is a hallmark of T helper cell responses that they are focused on a few peptides. The mechanisms that lead to this immunodominance, however, are still largely unknown, but in addition to host-specific factors, the three-dimensional structure of virus proteins may be critical for epitope selection. A major aim of the proposed project is therefore to identify the epitopes of T helper cells in the flavivirus structural proteins in the context of human infections with Zika, WN and the live YF vaccine virus. Since these flaviviruses have a conserved protein structure despite highly different amino acid sequences, a comparison of the location of the epitopes in the three-dimensional structure of these proteins will allow to draw conclusions with respect to protein structural factors that contribute to the epitope dominance. The influence of structural features will also be investigated in the second part of this project, through in vitro T cell activation assays in the TBE virus system. The use of structurally defined antigen preparations in these in vitro approaches will allow us to investigate aspects of immunodominance that cannot be addressed in infected humans. The expected results will reveal new insights in the fine-specificities and immunodominance of human T cell responses that will be relevant to technologies of rational vaccine design.

Immunodominance of flavivirus CD4 T cell responses CD4 T cells are critical components of the immune response after infection and vaccination and contribute to the generation of neutralizing antibodies and long-lived immunity against viruses. The induction of such helper T cell responses requires that CD4 T cells recognize peptides derived from a protein antigen, internalized and processed by B cells. It is a hallmark of helper T cell responses that they are focused on a few peptides. The mechanisms that lead to this immunodominance, however, are still largely unknown, but in addition to host-specific factors, the three-dimensional structure of virus proteins may be critical for epitope selection. The knowledge of factors that influence epitope dominance at a structural level is therefore important for a more complete understanding of the mechanisms of protective immunity. Flaviviruses provide an excellent opportunity to address these issues with medically important RNA viruses because their proteins are structurally conserved but highly diverse at the amino acid level. The comparative analysis of CD4 T cell responses in humans after infection with distantly related flaviviruses, such as yellow fever, West-Nile, and Zika viruses, sharing only about 40% identical amino acids of their envelope E proteins, therefore allowed us to study the contribution of structural factors to the selection and dominance of CD4 T cell epitopes. In this project, we gained novel insights into the specific protein sites yielding immunodominant T cell epitopes, by investigating CD4 T cell responses in large cohorts of patients with Yellow fever, West Nile, or Zika virus infections. We obtained data on structurally conserved immunodominant protein regions and identified several epitopes in the viral capsid and envelope proteins that are critically involved in the T-cell response during natural infection or vaccination. Furthermore, we could show that our findings extend beyond yellow fever, West Nile, and Zika viruses and that the identified epitope regions are also relevant targets for other medically important flaviviruses, such as Japanese encephalitis, Dengue, and tick-borne encephalitis viruses. The findings provide new insights into the molecular mechanisms that control flavivirus T cell responses with important implications for protective immunity and rational vaccine design.