ABSTRACT: The primary immune cells in the brain, microglia and CNS-associated macrophages (CAMs), are key targets for HIV in humans and SIV in nonhuman primates. Infection with these viruses can lead to neurological dysfunction collectively referred to as HAND. While antiretroviral therapy (ART) has proven effective in managing HAND, particularly the severe form known as HIV-associated dementia (HAD), its efficacy in preventing milder forms remains limited, leaving HAND a prevalent complication among PWH. Substance abuse, notably with opioids such as morphine and its synthetic product heroin, as well as pharmaceutical opioids, is relatively common in people with HIV (PWH) and the progression of HIV and its associated complications is exacerbated in opioid-using PWH. This study investigates the individual and combined effects of ART-treated SIV infection and morphine use on brain myeloid cells in rhesus macaques. Using single nucleus multiomic sequencing (integrating gene expression and chromatin accessibility), we examined the phenotypic, transcriptomic, and epigenomic changes in microglia and CAMs. Our findings confirm that ART significantly restores homeostasis in brain myeloid cells during SIV infection in macaques, paralleling its effects in HIV-infected humans. However, integration of data from ART-suppressed PWH with our macaque data suggested that there were more activation/inflammatory phenotypes of brain myeloid cells in PWH compared to ART-suppressed SIV-infected macaques. Additionally, we found that morphine exhibits immunosuppressive effects on brain myeloid cells, characterized by reduced antiviral phenotypes, downregulation of immune activation genes, including MHC class II and interferon-inducible proteins, and lack of the enrichment of the transcription factors in the AP-1 and ETS families activity. Gene co-expression network analysis further confirmed that the brain myeloid cell activation is associated with ART-treated infection, with no or negative correlation with morphine use. However, morphine exposures might indirectly affect the brain myeloid cells’ activation and functions, probably through endocrine receptors. These findings provide a deeper understanding of the effects of SIV infection on brain myeloid cells within the context of ART-treated SIV infection and opioid abuse, a critical consideration for PWH. Insights gained from this study could inform clinical approaches and therapeutic development for this vulnerable population.
