Multifactorial heterogeneity of virus-specific T cells and association with the progression of human chronic hepatitis B infection

Abstract

Associations between chronic antigen stimulation, T cell dysfunction and the expression of various inhibitory receptors are well characterized in several mouse and human systems. However, during chronic hepatitis B virus (CHB) infection T cell responses are blunted with low frequencies of virus-specific T cells observed making these parameters difficult to study. Here, using mass cytometry and a highly multiplexed combinatorial pMHC tetramer strategy that allows for the detection of rare antigen-specific T cells, we simultaneously probed 484 unique HLA-A*1101-restricted epitopes spanning the entire hepatitis B virus (HBV) genome on T cells from patients at various stages of CHB. Numerous HBV-specific T cell populations were detected, validated and profiled. T cells specific for two of epitopes (HBVpol387 and HBVcore169) displayed differing and complex heterogeneities that were associated with the disease progression, and the expression of inhibitory receptors on these cells were not linearly related with their extent of T cell dysfunction. For HBVcore169-specific CD8+ T cells, we found that cellular markers associated with long-term memory, poly-functionality, as well as the presence of several previously unidentified public TCR clones correlated with viral control. Using high-dimensional trajectory analysis of these cellular phenotypes, a pseudo-time metric was constructed that fit with the status of viral infection in corresponding patients. This was validated in a longitudinal cohort of patients undergoing anti-viral therapy. Our study uncovers complex relationships of inhibitory receptors between the profiles of antigen-specific T cells and the status of CHB with implications for new strategies of therapeutic intervention.