A Cell-Free Antigen Processing System Reveals Factors Critical for HIV-1 Epitope Dominance and Informs Vaccine Design

Abstract

Distinct CD4+T cell epitopes have been associated with spontaneous control of HIV-1 replication, but analysis of antigen-dependent factors that influence epitope selection is lacking. To examine these factors, we used a cell-free antigen processing system that incorporates soluble HLA-DR (DR1), HLA-DM (DM), and cathepsins along with full-length protein antigens for epitope identification by LC-MS/MS. HIV-1 Gag, Pol, Env, Vif, Nef, Tat, and Rev were examined using this system. We identified 35 novel epitopes, including glycopeptides. Epitopes from smaller HIV-1 proteins with crystal structures mapped to regions of low protein stability and higher solvent accessibility. HIV-1 antigens associated with limited CD4+T cell responses were processed efficiently, while some protective epitopes were inefficiently processed. 66% of epitopes obtained from cell-free processing induced memory CD4+T cell responses in HIV-1+ donors, including 10 of 19 novel epitopes. Thus, an in vitro processing system can identify novel HIV-1 epitopes and reveal factors influencing epitope dominance.