Initial reports documented a reversal of T cell exhaustion post-DAA treatment, characterized by enhanced proliferation of HCV-specific CD8+ T cells [
79], diminished PD-1 expression [80-82], and a transition toward a TCF-1+CD127+ memory-like T cell phenotype [
83]. However, one study found that only partial restoration of immune responses could be obtained in HCV patients treated with DAA, with increased proliferation of HCV-specific CD4 and CD8 T-cells, accompanied by an impaired ability to secrete IFNγ and IL2 [
84]. Also, a recent study highlighted the importance of early DAA treatment commencement, during the acute phase of HCV infection, which led to a reduction of immune exhaustion and to stronger HCV-specific T-cell responses after treatment, thus reducing the risk of possible reinfection [
85].
A previous study also revealed that recovery from exhaustion is related to the duration of T cell stimulation, with prolonged antigenic stimulation being associated with an irreversible state of exhaustion [
86]. The authors showed that antigen removal by successful DAA treatment induced phenotypic changes in exhausted T cells, which seem differentiated toward a memory like profile. However, these changes did not translate into a functional recovery, since the level of transcriptional regulators typical of exhausted cells, such as TOX, a key driver of T cell exhaustion, did not normalize after cure [
86]. Failure of normalization of transcriptional regulators of T cell exhaustion represents an immunological scar which, intriguingly, is not detectable in T cells exposed to antigen for a limited time [
86]. In line with this, another study used single-cell transcriptomics to demonstrate that, despite terminally exhausted HCV specific CD8 T cells decreased after DAA, a signature of exhaustion persisted after cure [
87]. Epigenetic studies analyzing the chromatin accessibility explained the reasons behind this apparently irreversible state of exhaustion. For instance, Yates
et al discovered a similar epigenetic profile in response to chronic stimulation in antigen-specific exhausted CD8 T cells in multiple human viral infections, including HCV, and showed that this epigenetic state of exhaustion signature persists for over a year after DAA-induced virus eradication [
88]. Epigenetic scars included super-enhancer elements near exhaustion-associated key transcription factors TOX and HIF1A [
88]. In agreement with the above, other studies showed that checkpoint-blockade immunotherapy did not fundamentally reverse exhaustion-associated epigenetic changes, supporting the epigenetic irreversibility of exhausted T cells [
89,
90]. Therefore, HCV infection leaves an epigenetic signature on the host chromatin that is not fully reversed following DAA-induced virus eradication, resulting in a state of exhaustion in HCV-specific CD8 T cells that does not offer protection from subsequent viral reinfection, as demonstrated in a non-human model [
91]. Interestingly, among the epigenetic changes, DNA methylation status has been associated with aging. Specifically, it has been shown that the gain or loss of CpG methylation over time is a valid method to estimate biological age [
92]. Analysis of the DNA-methylation status in PBMCs to calculate the epigenetic age acceleration [EAA] in chronic HCV infection showed that HCV infection induces an acceleration of epigenetic age which was only partially reverted by DAA treatment during a long-term follow-up. Moreover, individuals who developed HCC post-eradication showed the most pronounced epigenetic aging acceleration without signs of reversal [
93].
Interestingly, the severity of T cell exhaustion was shown to be associated with the metabolism of HCV specific T cells, identifying enolase as a metabolic regulator of severely exhausted T cells. Thus, in chronic HCV infection, severely exhausted CD8 T cells exhibited mitochondrial impairment linked to elevated liver inflammation, and reduced enolase activity [
94]. Notably, DAA therapy partially improved mitochondrial polarization in HCV-specific CD8+ T cells [
94]. These findings are akin to those of others who also observed improved mitochondrial polarization in HCV-specific CD8+ T cells following viral eradication [
5]. In contrast, others did not observe a mitochondrial functional recovery in HCV-specific CD8+ T cell metabolism [
95].