Persistence of a transcriptional chronic scar on HCV-specific CD8+ T cells after DAA-mediated antigen removal

T-cell exhaustion, a functional impairment of virus-specific CD8+ T cells, is a hallmark of chronic HCV infection. Previously, we have reported that exhausted HCV-specific CD8+ T cells are comprised of terminally exhausted CD127-PD1hi and memory-like CD127+PD1+ subsets. Of note, memory-like HCV-specific CD8+ T cells are present during HCV infection and after DAA-mediated cure. Until now it is unclear to what extend memory-like HCV-specific CD8+ T cells resemble conventional memory or exhausted T cells. Additionally, the impact of DAA-mediated viral clearance and the accompanied loss of viral antigen recognition on the phenotype of memory-like HCV-specific CD8+ T cells is currently also unknown.

In order to define the fate of memory-like HCV-specific CD8+ T cells in chronic versus cured HCV infection, we conducted low-input RNAseq analyses of CD127/PD1-based HCV-specific CD8+ T-cell subsets obtained during and after chronic HCV infection targeting conserved and escaped epitopes (n = 5) and after spontaneous resolution of acute HCV infection (n = 3). Furthermore, we performed single cell RNAseq analyses of HCV-specific T cells from six chronically HCV-infected patients including longitudinal analyses after successful DAA therapy (n = 2).

Importantly, although memory-like HCV-specific CD8+ T cells exhibit some transcriptional characteristics of memory T cells, an exhausted signature is dominant even after DAA-mediated viral clearance. This suggests an imprinted exhausted T-cell fate. Thus, memory-like HCV-specific CD8+ T cells are clearly distinct from conventional memory T cells. In accordance with this, spatiotemporal analyses propose a progenitor/progeny relationship of memory-like and terminally exhausted HCV-specific CD8+ T cell subsets during chronic HCV infection. Noteworthy, HCV-specific CD8+ T cells targeting escaped epitopes also displayed an exhausted profile despite the lack of terminally exhausted subsets. Interestingly, however, the transcriptional pattern of these cells was unique compared to memory-like HCV-specific CD8+ T cells targeting conserved epitopes suggesting that duration of antigen recognition may have an impact on the transcriptional CD8+ T cell regulation.

In sum, our results show that chronic HCV infection is strictly linked to an "exhausted" T-cell differentiation that is not reverted by removal of viral antigen or loss of antigen recognition. This has potential implications for the control of re-infection and therapeutic vaccines.