Title: Bioinformatic Delineation of the T cell receptor signature of hepatitis B virus control
Funder: Medical Research Foundation

Abstract: Deaths associated with viral hepatitis have increased globally over the last two decades, with hepatitis-B virus (HBV) now causing >700,000 deaths/year. Antivirals can suppress HBV replication but cure will require HBV-specific T cells that can home to the liver to mediate clearance from infected hepatocytes. HBV-specific T cells observed during the chronic phase of infection are archetypal exhausted T cells and their rejuvenation may not be possible due to severe dysfunction and epigenetic reprogramming. An alternative strategy, that has shown promise in pre-clinical models and in patients with HBV-antigen expressing hepatocellular carcinomas, is the adoptive transfer of functional T cells that have been redirected to target HBV by T cell receptor (TCR) gene therapy. The TCR not only defines the specificity of a T cell, but also dictates how the T cell responds to antigen, due to TCR determinants, such as the TCR’s affinity for its cognate MHC-peptide complex. Previously, HBV-reactive TCRs have been identified from peripheral T cells of healthy donors, without selecting T cells on their function, phenotype, or capacity to persist in the liver, the site of viral control. To build on the promise of first generation TCR therapy for HBV, I will use integrated multidimensional single cell analysis to select TCRs associated with HBV control for next generation TCR therapies. I will isolate T cells from the liver of donors that naturally controlled infection and integrate analysis of the surface phenotype, transcriptome, and TCR clonotype to optimally select T cells from which HBV-reactive TCRs will be isolated. After collating a library of HBV-reactive TCRs I will clone their Va/Vb segments into vectors, confirm their fine specificity, and assess the in vitro cytolytic and non-cytolytic antiviral capacity of T cells transfected with these TCRs in HBV culture models. This approach will allow us to investigate the relationship between TCR diversity and transcriptome of HBV-reactive clones in the setting of viral control (resolvers) or chronic viral infection. I will mine the data to investigate whether there are correlates of protection associated with TCR clonal diversity, surface phenotype, transcriptomic signature, or combinations of these T cell parameters. This work is possible due to advances in single cell technologies (RNA sequencing, cell sorting) and our unique access to large numbers of intrahepatic T cells from patients that control HBV infection. Through the work outlined here we will gain a better understanding of the disease mechanism underlying viral hepatitis, by identifying correlates of protection. Ultimately it may allow us to modify the progression of disease by treating HBV infected patients with TCR gene therapy. I will address the important question of whether optimal HBV-reactive TCRs can be isolated from liver resident T cells of patients who controlled HBV infection, and I will fill gaps in our knowledge of T cell clonal diversity and transcriptome in the setting of chronic and controlled HBV infection. My findings will also have broader relevance for T cell biology by elucidating to what extend the TCR determines or predicts T cell functionality in the setting of tissue-residency.


Research activity codes: 2.1 BIOLOGICAL AND ENDOGENOUS FACTORS
Health categories: INFECTION