Evolution of the HIV-1 integration site landscape and inducible reservoir in early-treated people

TL;DR

This study shows that HIV persists in infected cells even with early treatment, and the virus becomes enriched in inactive parts of the genome over time.

Contribution

The study reveals post-integration selection mechanisms and detects the inducible reservoir in early-treated individuals for the first time.

Findings

Clonal expansion contributes to reservoir persistence even in early-treated individuals.

Proviruses in heterochromatin regions become enriched after five years on ART.

A new method detects the inducible reservoir in individuals with small reservoir sizes.

Abstract

Persistence of the HIV-1 reservoir is the major barrier to a cure. Little is known about the dynamics of the proviral integration site landscape and inducibility of the viral reservoir in early-treated individuals. Here, we perform a longitudinal analysis of the viral reservoir in individuals who started treatment during acute infection and compare these findings to chronically-treated individuals. Even in early-treated individuals, clonal expansion contributes to reservoir persistence. Integration site analysis reveals similar distributions after one year of antiretroviral therapy (ART), irrespective of treatment initiation timing. Notably, proviruses integrated in heterochromatin regions are already detected in early-treated individuals after one year on ART and are progressively enriched after five years on ART, suggesting post-integration selection mechanisms. Using a lipid nanoparticle containing Tat mRNA (Tat-LNP) in combination with phorbol myristate acetate (PMA), we detect for the first time the inducible reservoir in individuals treated during acute infection with small reservoir sizes. Furthermore, we show that, in both the acute and chronic cohorts, the inducible reservoir shifts towards a more differentiated T cell compartment over time. Collectively, these findings indicate that clonal expansion and integration site selection contribute to reservoir persistence early after ART initiation in individuals treated shortly after seroconversion.

Despite ART, HIV persists in a small pool of infected cells. This reservoir is the main barrier to curing HIV. We studied how this reservoir changes over time in people who started treatment very early after infection and compared them to people who started later. We found that, even with early treatment, the infected cells persist and expand over time. After 5 years on ART, in people who started treatment early, HIV becomes enriched in regions of the genome that are less transcriptionally active, suggesting that selective pressures shape which infected cells persist. We also applied a new combination of latency reversal agents, allowing us for the first time to detect the inducible reservoir even in people with very small reservoir sizes. Finally, we observed that the inducible reservoir shifts towards more differentiated types of immune cells over time on ART. Together, our findings provide new insights into how HIV persists despite early treatment.

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