The impact of proviral epigenetics on HIV-1 rebound

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Abstract Despite the successful development of antiretroviral therapies (ART), the long-awaited cure for HIV has still not been discovered. The virus integrates into DNA of tissues throughout the body and becomes latent after institution of ART. Persons receiving ART cannot discontinue their medications, as in most cases the virus will simply rebound upon ART cessation. One approach to finding a cure is to eliminate the reservoir by bringing the virus out of latency so that infected cells might be killed by ART or the host immune system. Epigenetic mechanisms are believed to play an important role in retroviral persistence and latency, yet little is known about the epigenetic markers associated with the HIV reservoir. Recent studies have found a role for repressive histone methylation in the epigenetic control of HIV latency in primary cells expanded in vitro, but there are no studies in clinical samples without in vitro manipulation. The objective of this proposal is to establish patterns of two repressive epigenetic modifications associated with HIV proviruses and their surrounding integration sites in peripheral blood, and to determine how the presence of these modifications affects chromatin accessibility of the HIV provirus and its subsequent impact on viral rebound following ART interruption. Using longitudinal peripheral blood samples from seven ART Treatment Interruption (ATI) cohorts from the AIDS Clinical Trials Group, we will examine cytosine methylation, H3K27me3, and open chromatin across each provirus and its surrounding integration sites from people with HIV pre- and post- ATI. Using these data, we will examine the combinatorial effects of repressive epigenetic marks upon chromatin accessibility of the provirus and its surrounding genomic environment, and then further evaluate how these epigenetic marks impact rebound post-ATI. The results of the proposed studies will provide crucial information about the epigenetic regulation of HIV suppression during ART and its effect upon viral rebound during ATI. This will yield putative targets to eliminate HIV from the reservoir.