Kroon, E. | bioRxiv Science

bioRxiv2022

Productive and latent HIV infections originate in resting CD4+ T cells

Productively and latently HIV-infected cells are the source of virus that respectively establishes and sustains systemic infections and the reservoir in which HIV persists and rebounds when anti-retroviral therapy (ART) is interrupted. While infected activated CD4+ T cells are thought to be the principal source of HIV production, and reversion of activated infected cells to a resting state as the major pathway to establishment of the latently infected cell reservoir, we now show that in the earliest stages of detectable HIV infection in the lymphoid tissue reservoir, infection of resting CD4+ T cells establishes the first populations of both productively and latently infected cells. We further show that the early infection of resting T cells reflects their predominance in lymphoid tissues and the expression of pTEFb in vivo in resting T cells to support their infection. The immediate establishment of productively and latently infected cell populations enable HIV to propagate and persist, and generates reservoirs from which infection can rebound despite instituting ART at the earliest stage of detectable infection.

immunology↗

bioRxiv2022

HIV rapidly targets a diverse pool of CD4+ T cells to establish productive and latent infections

Upon infection, HIV disseminates throughout the human body within 1-2 weeks. However, its early cellular targets remain poorly characterized. We analyzed productively and latently infected cells in blood and lymphoid tissue from individuals in acute infection. The phenotype of productively infected cells rapidly evolved with time and differed between blood and lymph nodes. The TCR repertoire of productively infected cells was heavily biased, with preferential infection of previously expanded/disseminated cells, but composed almost exclusively of unique clonotypes, indicating that they were the product of independent infection events. Latent genetically intact proviruses were already archived early in infection. Hence, productive infection is initially established in a pool of phenotypically and clonotypically distinct T cells in blood and lymph nodes and latently infected cells are generated simultaneously. One-Sentence SummaryHIV initially infects phenotypically and clonotypically distinct T cells and establishes a latent reservoir concomitantly.

microbiology↗

bioRxiv2020

Dendritic cells focus CTL responses toward highly conserved and topologically important HIV epitopes

During early HIV Infection, immunodominant T cell responses to highly variable epitopes lead to the selection and expansion of immune escape variants. As a potential therapeutic strategy, we assessed a specialized type 1-polarized monocyte-derived DC dendritic cell (MDC1)-based approach to selectively elicit functional CD8+ cytotoxic T lymphocyte (CTL) responses against highly conserved and topologically important HIV epitopes. Cells were obtained from 10 HIV-infected individuals in the Thailand RV254/SEARH010 cohort who initiated suppressive anti-retroviral therapy (ART) during Fiebig stages I to IV of early infection. Autologous MDC1 were generated for use as peptide antigen presenting cells to induce ex vivo CTL responses against HIV Gag, Pol, Env and Nef. Ultra-conserved (Epigraph) or topologically important (Network) antigens were respectively identified using the Epigraph tool and a structure-based network analysis approach, and each compared to overlapping peptides spanning the entire Gag proteome. MDC1 loaded with either overlapping Gag, Epigraph, or Network 14-21mer peptide pools were consistently capable of activating and expanding HIV-specific T cells to epitopes identified at the 9-13mer peptide level. Some CTL responses occurred outside of known or expected HLA associations, providing evidence of new HLA-associated CTL epitopes. Comparative analyses of peptide pools demonstrated more sequence conservation among the Epigraph antigens, but statistically higher magnitude of CTL responses to Network and Gag peptide groups. Importantly, when select Gag antigens used to initiate the cultures were part of the Network peptide pool, CTL responses directed against these topologically important epitopes were enhanced as compared to when they were included within the complete pool of overlapping Gag peptides. Our study supports that MDC1 can be used to effectively focus CTL responses toward potentially fitness-constrained regions of HIV as a therapeutic strategy to prevent HIV immune escape and control viral replication. Author summaryA major hurdle in the development of a successful HIV immunotherapy is the capacity of the virus to evade the immune response by efficiently establishing epitope variants in response to selective pressure. While effective at suppressing viremia, current regimens of antiretroviral therapy (ART) are not curative. Therefore, achieving immune control of HIV upon cessation of ART as a functional cure, similar to that observed in elite controllers (EC), has been a major therapeutic goal. Such immune control is realized through the actions of antigen-specific cytotoxic T cell lymphocytes (CTL) capable of specifically targeting sequence-conserved epitopes in HIV. In this study, a specialized, antigen presenting, dendritic cell (DC)-based vaccine strategy was used to elicit HIV specific CTL responses in vitro against carefully selected, ultra-conserved and topologically important epitopes. This DC-based approach yielded broad responses against peptide epitopes of both known and unknown HLA-associations, the latter of which implies the uncovering of potentially novel epitopes. Importantly, we demonstrate that CTL responses can be re-directed or focused toward potentially more fitness-constrained regions of the virus, thus highlighting the potential for DC-based therapies to induce immune responses that circumvent the issue of viral escape.

immunology↗