Background
The persistent HIV latent reservoir is a major impediment to the eradication of HIV infection for people living with HIV (PLWH). CD8+ T cell-based approaches to control viral rebound have in part been unsuccessful due to the emergence of epitope escape mutations. Our laboratory identified a subset of epitopes, known as highly networked CD8+ T cell epitopes, that are constrained from mutation and are preferentially targeted by individuals who spontaneously control HIV. In this study, we assessed whether highly networked epitopes represent a set of mutationally constrained targets in the latent HIV reservoir for durable HIV suppression.
Methods
To determine mutational frequencies of highly networked and non-networked epitopes in the latent reservoir, we performed proviral and near full-length individual proviral (FLIP) sequencing on genomic DNA obtained from sorted latently infected CD4+ T cells derived from 22 PLWH on suppressive ART. Participants also maintained undetectable viral loads at the time of sample collection. Mutational sequence analysis of viral epitopes was performed using an established computational pipeline to quantify the quantity and quality of viral mutations. We subsequently investigated the extent to which CTLs can cross-recognize wild type (WT) and mutant (mt) networked and non-networked epitopes using cross-reactivity assays.
Results
Sequences analyses revealed that highly networked epitopes overall had a markedly reduced frequency of mutations than non-networked epitopes in integrated proviruses (P<0.0001), and when the analysis was limited to epitopes restricted by individual HLA class I haplotypes (P<0.0002). Moreover, non-networked epitopes exhibited a marked enrichment for either multiple mutations (>1) or non-conservative mutations. In addition, T cell responses to highly networked epitopes demonstrated preserved recognition of mutated epitopes from proviral sequences, whereas mutated non-networked epitopes had significantly reduced recognition.
Conclusions
These data demonstrate that highly networked epitopes have markedly fewer overall and non-conservative mutations in the latent reservoir from ART-suppressed PLWH. CD8+ T cells recognize mutants of high networked epitopes better than mutants of non-networked epitopes. These findings therefore suggest that highly networked epitopes represent a set of mutationally constrained targets for therapeutic T cell vaccine development that may enable durable viral suppression following ART cessation.