Host-Dependent Mechanisms that Guide the Longitudinal Dynamic of Sites of SIV Integration

Project Summary HIV integrates into the host genome and enters a state of latency, enabling infected cells to escape immune recognition and clearance. Eliminating the latent reservoir will require an understanding of the early host mechanisms that regulate latency establishment and mechanisms that reinforce latency during ART suppression. This can be achieved by investigating three major questions: provirus integration preferences, the “where.” The host mechanisms that regulate proviral integration, the “how.” The effect of integration on the host transcriptional and epigenetics programs. There is growing evidence of the host's early factors, including the levels of metabolites of host and commensal bacteria origin, specific cytokines, or frequencies of activated innate and adaptive immune cells in modulating key host immune mechanisms that could promote disease progression and increase susceptibility to infection as a result of heightened levels of immune homeostasis and effector function perturbation. However, our knowledge of the host early mechanisms that regulate SIV integration and the impact of integration on the overall host immune system is poorly understood. In this proposal, I will leverage existing samples collected from SIV-infected ART-suppressed rhesus macaques at baseline (pre-infection), before ART initiation, and during ART suppression to generate an ATLAS of SIV integration sites. In these animals, we observed a significant dynamic range of integrated SIV DNA before ART initiation, suggesting that host factors could be responsible for the heterogeneity of the replication-competent SIV reservoir. To delineate the impact of the host factors on the SIV integration, we will use single-cell assays that capture host gene expression and chromatin accessibility, as well as plasma levels of cytokines and metabolites of the host and commensal bacteria to characterize the mechanisms triggered early in infection by host factors that regulate SIV integration and determine how SIV integration impacts the host transcriptome and epigenome. The outcome of this study could uncover intricate mechanisms by which the host's immune system influences SIV integration and how integration, in turn, shapes the host gene expression and immune functions. These insights can pave the way for innovative therapeutic strategies to prevent viral integration or reverse host immune dysfunction, ultimately offering new possibilities for HIV cure research.