Mechanisms controlling HIV latency and pathogenesis in microglia

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PROJECT SUMMARY The life expectancy of people with HIV (PWH) has improved significantly in the past decades with the introduction of antiretroviral therapies (ART). Nevertheless, the risk for developing comorbidities including HIV-associated neurocognitive impairment even in “well-controlled” PWH is significantly increased. One obstacle to the eradication of HIV and treatment of HIV-associated neurocognitive impairment is the lack of knowledge about the epigenetic mechanisms of HIV in microglia. Specifically, little is known about the extent of HIV integration into the host’s genome, specifically that of microglia, in PWH under ART; the viral and epigenetic gene regulatory mechanisms regulating HIV latency and neuropathogenesis; and whether the integrated HIV provirus is intact or defective, potentially inducing a chronic immune response in the brain. To address these knowledge gaps, we will use archived human post-mortem specimens obtained from the National NeuroAIDS Tissue Consortium (NNTC) as well as microglia-like cells generated from human induced pluripotent stem cells (iPSC-MG). We will use single cell multi-omics (RNA/ATAC-Seq) approaches to specifically obtain the transcriptomic and epigenomic landscapes of the viral and host genomes using single cell technologies. To decipher the epigenetic landscape including the potentially altered histone modification landscape of microglia and HIV, we will perform in addition ChIP-seq. Our proposed investigations are strongly supported by compelling preliminary data providing a gene expression and chromatin accessibility atlas of human microglia isolated from three PWH. In addition, we propose a novel approach to identify viral integration sites in microglia from human post-mortem samples and iPSC-MG using state-of-the-art Long-read sequencing and artificial intelligence technologies technology. We will use our established iPSC-MG HIV model system to further test the effect of ART on the epigenetic landscape, including histone modification and transcription factor binding, to understand the mechanisms regulating HIV latency and neuropathogenesis. In Aim 1, we will identify microglia gene expression signatures and their underlying gene regulatory mechanisms in HIV infection. For Aim 2, we will establish Long-read sequencing to decipher HIV-integration sites. In Aim 3, we will use iPSC-MG to identify the viral epigenetic landscape in microglia in the presence and absence of ART.