HIV-associated neurocognitive disorders (HAND) persist in the era of combination antiretroviral therapy (cART). Proof of HIV latency in human CNS is currently lacking, despite continued high prevalence of HIV- associated neurologic disease and increasing recognition of CNS viral escape in people stably suppressed with cART. One of the major issues regarding CNS HIV in need for study is HIV integration. With other words, whether CNS HIV integration has biologically significant impact, contributing to pathogenesis? Issues of CNS functional deficit are further complicated by the co-registered epidemic of opiate and other substance use disorders (SUD) in people living with HIV/AIDS (PLWHA), as SUD also have profound impact on CNS function, and potentially on HIV latency. Nowhere in the CNS is this more evident than in the neuroanatomic overlap of HIV and SUD in striatonigral dopaminergic circuitry and frontostriatal projections, sites of predilection for functional and neurobiologic disease as well as for increased burden of HIV infection. Accordingly, directly utilizing brain tissues in these regions, from neurologically well-characterized HIV-infected individuals with and without SUD, the goal of this application will be: (i) to replicate for brain some of the emerging genomic mechanisms recently discovered in peripheral cells, linking HIV host genome integration and virus latency to nuclear topography and open chromatin; (ii) to explore whether HIV signatures in transcriptomes and epigenomes in dopaminergic circuitry is associated with prospectively monitored neurological status in the years before death and exposure to drug of abuse; (iii) explore HIV expression and integration in potential reservoir cells of the brain, including microglia and astrocytes derived from HIV+ brain at autopsy and (iv) explore the impact of substance history on HIV integration and activity in primary microglial cultures derived from HIV- brains at autopsy and (vi) expose primary microglia in culture to drugs of abuse and HIV. The innovative experiments proposed here are expected to offer novel insights into epigenomic landscapes in specific brain cells and explore potential links between neurogenomic status of the infected brain and neurological and cognitive symptoms and substance abuse. While recognizing the high-risk aspects, these analyses will nevertheless have predictable, high gain benefits in understanding the complex neurobiology underlying HIV-associated CNS disease in PLWHA and SUD.