The T cell response to HCV infection is characterized by a range of functional defects collectively termed exhaustion, however the mechanisms that specify this defective state, and the potential for recovery of T cell exhaustion are not known. In this project we will define the global epigenetic state of T cell exhaustion in order to understand the mechanisms that regulate HCV-specific T cell function and the potential for reversibility of exhaustion following elimination of the virus. To achieve this goal, we have optimized assays to generate global histone modification maps from only a few thousand cells, allowing us to study directly the epigenetic state of antigen-specific cells from humans.
AIM 1 : Define the chromatin landscape of CDS T cells specific for chronic vs. acute infection. Our hypothesis is that T cell exhaustion is associated with specific alterations of the profile of chromatin modification in CDS T cells. We will undertake comparative epigenetic analysis of CDS T cells specific for HCV, CMV and influenza virus to determine if chronic infection is associated with global and gene-specific differences in chromatin state. We will identify and experimentally validate candidate regulators of the exhausted CDS T cells We will also use the mouse model of chronic LCMV infection to study the epigenetic state of exhausted CDS T cells over time, validating our findings in humans.
AIM 2. Determine whether the epigenetic state of HCV-specific CDS T cells is altered by cure of infection. Our hypothesis is that cure of HCV with direct acting antiviral (DAA) therapy will be associated with a partial remodeling of the epigenetic landscape of exhaustion. We will compare the epigenetic state of HCV-specific CDS T cells in the same individual before and after DAA therapy. We will use the chronic LCMV model to test whether increasing duration of infection and exposure to Type 1 interferons "cements" the epigenetic and functional state of exhausted CDS T cells. Our proposal is significant because it will determine whether the differentiation state of exhausted CDS T cells is regulated at the epigenetic level. It will identify and validate novel TFs that are differentially active in exhausted CDS T cells. It will determine whether the epigenetic state of exhausted CD8T cells can change following cure of chronic infection.
HCV is associated with profound defects in the function of virus-specific T cells but the mechanisms that regulate exhausted T cells, and the potential for reversibility with antiviral therapy are not fully understood. This project will map the epigenetic regulatory landscape of CDS T cells responding to chronic viral infection and test if this landscape is altered by cure of infection.
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