Single Cell Analysis of Epigenetic Mechanisms that Regulate HIV-1 CNS Latency and Neuropathogenesis

Current antiretroviral therapies (ART) are successful in suppressing HIV-1 replication in most individuals. However, cessation of ART results in emergence of HIV-1 from a latent viral reservoir, thereby requiring a lifetime ART regime. The best-described HIV-1 reservoir is that of CD4+ T lymphocytes in circulating blood and lymphoid tissues that contain a transcriptionally silent but replication-competent virus. The brain is also an important viral reservoir site, but it is poorly characterized due to the challenges in obtaining specimens for analyses. Despite its effectiveness, multiple toxicities are associated with ART, especially the high prevalence of HIV-associated neurocognitive deficits. The research described in this application will use human autopsy specimens to investigate two key issues regarding HIV-1 infection of the brain: 1) epigenetic mechanisms that regulate active and latent HIV-1 infection in the brain; 2) mechanisms underlying neuropathogenesis and neurocognitive deficits in HIV-1-infected individuals on suppressive ART. Brain specimens from prefrontal cortex and hippocampus from HIV-1 infected individuals treated with ART death will be obtained from the National NeuroAIDS Consortium. Matched HIV-1-negative control specimens will be obtained from the UTHealth Brain Collection. Single cell RNA sequencing technology will be utilized to identify long noncoding RNAs (lncRNAs), mRNAs, and microRNAs (miRNAs) that are dysregulated in HIV-1-infected individuals. Validation experiments will be performed in HIV-1-infected microglia cells to identify dysregulated lncRNAs and miRNAs that contribute to HIV-1 replication, latency, and neuropathogenesis. Completion of the proposed work is likely to identify therapeutic approaches to treat HIV-1 infection of the brain.