Green, A. A.; Vashist, T. D.; Jakhmola, S.; Chen, X.; Baidwan, G.; Buchanan, J.; Tiwari, S. K.; Griffin, E.; Howell, A.; Lee, Y.; Moore, D. J.; Gianella, S.; Smith, D. M.; Zhu, Q.; Walss-Bass, C.; Wang, A.; Mukamel, E. A.; Gaulton, K. J.; Rana, T. M.

Opioid use disorder (OUD), which frequently co-occurs with HIV infection, causes long-term neurological disease, yet the epigenetic and transcriptomic effects of OUD and HIV on specific cell types and regions of the brain are poorly understood. To assess the cell-type specific impacts of OUD and HIV across the human brain, we measured single cell transcriptomes and epigenomes of 580,353 cells in the prefrontal cortex, amygdala and cerebellum of 44 donors. We cataloged over 750k candidate cis-regulatory elements (cCREs) and identified gene regulatory networks (GRNs) of transcription factor activity across 35 neuronal and non-neuronal cell types. We identified specific neuronal and glial populations whose cCREs were significantly enriched for genetic risk of addiction-related traits. In OUD donors, we found evidence for reduced metabolic function in neurons in the PFC and cerebellum as well as increased gene expression related to voltage-gated calcium channel activity in the cerebellum. Using a cerebellar organoid model, fentanyl treatment reduced metabolic activity while increasing neuronal activity. Across brain regions, HIV activated immune-related pathways in glial populations, while comorbid OUD and HIV exacerbated metabolic changes in cortical glial cells. Cerebellum-specific Bergmann glia, in addition to forebrain microglia and astrocytes, showed expansion of reactive state identity in HIV. These results highlight shared and specific changes to immune, synaptic, and metabolic processes in OUD and HIV across brain regions and reveal that cerebellar cell types are distinctly affected by opioid abuse.