Investigating hepatitis B virus-specific CD8 T cells and their role in viral clearance during chronic infection

Hepatitis B virus (HBV) infection poses a global health challenge, with more than 250 million people suffering from chronic infection and no curative treatment available. CD8 T cells are considered necessary mediators of viral clearance of HBV infection. However, there is a lack of information about the HBV epitope landscape across different HLA types, which has been a limitation for the study of HBV-specific CD8 T cells.

The overall goal of this study was to expand the existing repertoire of HBV-derived epitopes and apply them to investigate the role of HBV-specific CD8 T cells in resolving chronic HBV infection. To do this, we utilized DNA barcode-labelled pMHC multimers to identify CD8 T cell recognition of more than 2100 distinct HBV peptides spanning the entire proteome of 8 different HBV genotypes and restricted by 12 different HLA types. With this technique, we identified 169 distinct HBV epitopes, most of which were novel. Furthermore, we were able to map these epitopes to specific regions of all the HBV proteins, indicating these areas are immunodominant. There was no observed difference in the number of epitopes being recognized between patients with acute and chronic HBV infection. Additionally, we demonstrated both HBV-specific CD8 T cell activation in chronic patients and cross-recognition of some of these epitopes.

We also investigated how CD8 T cell recognition towards HBV is associated with the clinical outcomes of HBV. Discontinuation of nucleos(t)ide analogue (NUC) therapy in virally suppressed chronic HBV patients has been associated with higher chances of achieving a functional cure of HBV. Treatment stop has been proposed to induce the anti-HBV immune response, and therefore we investigated the link between CD8 T cell recognition of HBV and clinical outcomes in a longitudinal study. We discovered an association between CD8 T cell recognition of two HLA-A*11:01 epitopes and the ability to reduce the level of HBsAg following treatment discontinuation. This association was only observed after treatment had ended, suggesting a response triggered by NUC discontinuation. Furthermore, our phenotype analysis showed that patients with a greater level of HBsAg reduction after ending treatment had a higher frequency of both activated and exhausted HBV-specific and total CD8 T cells. This difference was present already during treatment and could serve as a predictive marker for safe NUC discontinuation.

Lastly, we evaluated the efficacy of a DNA vaccine aiming to induce T cell responses towards HBV using DNA barcodes. Besides inducing functional CD4 T cell responses towards core epitopes, the vaccine induced mainly low-frequency CD8 T cell responses targeting polymerase epitopes, suggesting limited CD8 T cell contribution.

In summary, the results presented in this thesis provide insights into the HBV-specific CD8 T cell repertoire. The findings highlight the potential of HBV-specific CD8 T cells as predictive markers for treatment outcomes in chronic HBV infection and lays the foundation for future studies in the development of immune-based therapies for chronic HBV infection.