Antisense transcript derived HIV-1 cryptic epitopes are recognized by T cells during chronic infection.

Abstract

Alternative reading frames (ARF) of HIV, both sense and antisense directions, have shown to produce polypeptides of unknown functions. Although the roles of these polypeptides are unclear, they can still potentially act as HIV derived antigens, eliciting host T cell responses. These ARF derived epitopes, known as cryptic epitopes (CE), occur commonly in HIV, SIV, and other retroviruses through ribosomal frame-shifting, internal ribosomal entry sites, and alternative start codon initiation. We hypothesize that T cell responses to CE are capable of driving viral escape mutations at a population level. In order to identify CE of HIV capable of driving viral escape, sequence changes in gag, pol, and nef of HIV were identified during acute infection in a cohort of Zambian serodiscordant couples. HLA-I associated polymorphisms in ARF can thus be identified, predicting potentially immunogenic CE. Several CE were identified as a result (N=66), in which the majority appears to have been derived from antisense ARF. These CE were used to stimulate cryopreserved PBMC samples from HIV-1 patients in the chronic stage of infection. We found 8/32 patients responded to at least one predicted CE as shown by IFNγ ELISpot. Interestingly, all 10 immunogenic CEs found in this study were derived from a single antisense reading frame in the pol coding region. Furthermore, these CE were not only capable of eliciting CD8, but also CD4 responses. When examining alternative start codons in each reading frame, we found an enrichment of CUG in the antisense frame containing the immunogenic CE. Together, our results show HIV antisense CE can be targeted by T cells and may therefore have implications for T-cell vaccines.