Single cell dark matter in the context of HIV and substance use

Project Abstract The use of cannabis for recreational and medicinal purposes is disproportionately high among people living with HIV-1 (PLWH), with nearly half of cannabis-using PLWH estimated to be at risk for cannabis use disorder. A part of the Single Cell Opioid Responses in the Context of HIV (SCORCH) consortium was formed to address scientific questions about cannabinoids, HIV-1 and antiretroviral therapy (ART) exposure at the single-cell and nuclei level. A significant portion of the human genome consists of repetitive sequences, often called “genomic dark matter” or “junk” DNA of which a large fraction are TEs. Once considered non-functional, TEs are now recognized as key genomic regulators. They can act as promoters, enhancers, and regulators of nearby genes, playing crucial roles in genome evolution and gene regulation. Understanding TE expression at the single-cell level is vital for elucidating their roles in lineage development, cell sub-type identification, and gene regulation. In this application, we propose to harness our newly developed bioinformatic pipeline for single-cell/nuclei transposable element locus level analysis (Stellarscope) and have access to already generated single-cell multiome data as well as new data being generated from 1) a non-human primate model (NHP) of HIV-1 with oral cannabinoid exposure (cannabidiol or Δ9-tetrahydrocannabinol (THC)) and ART , 2) postmortem human brain tissues, and 3) an established human brain organoid model adapted for HIV-1 infection. In two specific aims, we will 1) identify neuronal, glial, and neural stem/progenitor cell TE transcriptional and TE epigenetic gene regulatory states involved in SIV, ART, and cannabinoids in neurogenic regions of the NHP model; 2) identify TE expression of cannabinoid and SIV- relevant cell types and neurogenic brain regions in which SIV and cannabinoids interact to induce anti-inflammatory and neuroprotective cell states; validate HIV-1 and cannabinoid-related cell-type and TE transcriptional changes in a human brain organoid model adapted for HIV- 1 infection. Collectively, these studies will determine the role of TEs in dysregulation of neuroinflammation and neuronal transcriptional and epigenetic dysfunction in the context of HIV-1 infection and cannabinoid use.