Elucidating the Potential of Networked CD8+ T Cell Epitopes Towards a Functional HIV Cure

Abstract

The latent HIV-1 reservoir presents a major obstacle to the cure of HIV infection. While CD8+ T cells represent a promising modality for viral suppression and eradication, these efforts have been greatly impeded by the emergence of epitope escape mutations. Recent work from our laboratory identified a subset of epitopes, known as networked epitopes, which are preferentially targeted by spontaneous controllers of HIV and mitigate against CD8+ T cell epitope escape due to their presence at structurally constrained regions of the viral proteome. In this thesis, we investigated whether networked epitopes exhibited reduced mutational frequencies within the latent reservoir of people living with HIV (PLWH) on suppressive antiretroviral therapy and thereby could promote sustained CD8+ T cell recognition and clearance of latently infected cells. To accomplish this, we performed integrated proviral DNA sequencing and near full-length individual proviral (FLIP) sequencing on genomic DNA derived from CD4+ T cells from twenty-two individuals on suppressive antiretroviral therapy (ART), who initiated treatment during chronic infection. Mutations across all optimal, HLA-restricted, and cytotoxic T lymphocytes (CTL)- targeted epitopes were quantified using a computational pipeline designed to assess overall, conservative and non-conservative residue substitutions. From this analysis, we observed that networked epitopes displayed markedly reduced mutational frequencies compared to non- networked epitopes in both integrated proviral DNA (p .0001) and near full-length proviral clones (p.0002) for overall and non-conservative mutations. Moreover, epitope network scores correlated inversely with mutational frequency, suggesting an association between the degree of structural epitope constraint and viral escape. Analyses of endogenous CD8+ T cell responses with PLWH revealed enhanced cross-recognition by T cells for variants of networked epitope, in contrast to the pronounced loss of recognition observed for mutated non-networked epitopes. Correspondingly, CD8+ T cell clones directed toward networked epitopes exhibited superior clearance of reactivated latent CD4+ T cells derived from ART-suppressed individuals. Together, these findings demonstrate that networked HIV epitopes exhibit reduced immune escape, superior preservation of CD8+ T cell recognition, and enhanced clearance of the latent reservoir in comparison to non-networked epitopes. This reveals their potential promise as targets for therapeutic T cell-based interventions aimed at achieving durable reservoir suppression following ART cessation.