Analysis of FOXP3+ Regulatory T Cells That Display Apparent Viral Antigen Specificity during Chronic Hepatitis C Virus Infection

We reported previously that a proportion of natural CD25+ cells isolated from the PBMC of HCV patients can further upregulate CD25 expression in response to HCV peptide stimulation in vitro, and proposed that virus-specific regulatory T cells (Treg) were primed and expanded during the disease. Here we describe epigenetic analysis of the FOXP3 locus in HCV-responsive natural CD25+ cells and show that these cells are not activated conventional T cells expressing FOXP3, but hard-wired Treg with a stable FOXP3 phenotype and function. Of ∼46,000 genes analyzed in genome wide transcription profiling, about 1% were differentially expressed between HCV-responsive Treg, HCV-non-responsive natural CD25+ cells and conventional T cells. Expression profiles, including cell death, activation, proliferation and transcriptional regulation, suggest a survival advantage of HCV-responsive Treg over the other cell populations. Since no Treg-specific activation marker is known, we tested 97 NS3-derived peptides for their ability to elicit CD25 response (assuming it is a surrogate marker), accompanied by high resolution HLA typing of the patients. Some reactive peptides overlapped with previously described effector T cell epitopes. Our data offers new insights into HCV immune evasion and tolerance, and highlights the non-self specific nature of Treg during infection.
Author Summary Hepatitis C virus persistently infects ∼3% of the world population, leading to life threatening liver diseases and liver failure. It is not well understood why the human immune system often fails to clear the virus, although it is likely multi-factorial. It is accepted that effector T cells are critical for clearing infections, but their function can be suppressed by the somewhat elusive regulatory T cells. Our hypothesis, supported by new data, is that a proportion of the regulatory T cells are specifically stimulated by the virus and that these cells are a stable cell population. We find evidence that these suppressive cells have a distinct set of genes activated and importantly might have a survival advantage over effector T cells, which helps to explain why natural regulatory T cells may influence the outcome of HCV infection. We propose that the new information provides a better explanation of chronic HCV infection and will let us focus on the key experiments to test the hypothesis and to design better treatments.