Microglia and macrophages alterations in the CNS during acute SIV infection: a single-cell analysis in rhesus macaques
Authors: Xu Xiaoke , Niu Meng , Lamberty Benjamin G. , Emanuel Katy , Trease Andrew J. , Tabassum Mehnaz , Lifson Jeffrey D. , Fox Howard S. 
Published: April 2024

ABSTRACTHuman Immunodeficiency Virus (HIV) is widely acknowledged for its profound impact on the immune system. Although HIV primarily affects peripheral CD4 T cells, its influence on the central nervous system (CNS) cannot be overlooked. Within the brain, microglia and CNS-associated macrophages (CAMs) serve as the primary targets for HIV, as well as for the simian immunodeficiency virus (SIV) in nonhuman primates. This infection can lead to neurological effects and the establishment of a viral reservoir. Given the gaps in our understanding of how these cells respondin vivoto acute CNS infection, we conducted single-cell RNA sequencing (scRNA-seq) on myeloid cells from the brains of three rhesus macaques 12-days after SIV infection, along with three uninfected controls. Our analysis revealed six distinct microglial clusters including homeostatic microglia, preactivated microglia, and activated microglia expressing high levels of inflammatory and disease-related molecules. In response to acute SIV infection, the population of homeostatic and preactivated microglia decreased, while the activated and disease-related microglia increased. All microglial clusters exhibited upregulation of MHC class I molecules and interferon-related genes, indicating their crucial roles in defending against SIV during the acute phase. All microglia clusters also upregulated genes linked to cellular senescence. Additionally, we identified two distinct CAM populations: CD14lowCD16hiand CD14hiCD16lowCAMs. Interestingly, during acute SIV infection, the dominant CAM population changed to one with an inflammatory phenotype. Notably, specific upregulated genes within one microglia and one macrophage cluster were associated with neurodegenerative pathways, suggesting potential links to neurocognitive disorders. This research sheds light on the intricate interactions between viral infection, innate immune responses, and the CNS, providing valuable insights for future investigations.AUTHOR SUMMARYHIV’s entry into the central nervous system (CNS) can lead to neurological dysfunction, including HIV-associated neurocognitive disorders (HAND), and the establishment of a viral reservoir. While microglia and CNS-associated macrophages (CAMs) are the primary targets of HIV in the CNS, their responses during acute HIV infection remain poorly defined. To address this, we employed the scRNA-seq technique to study microglial and CAM populations in rhesus macaques during acute SIV infection. By identifying signature genes associated with different phenotypes and mapping them to various biological and pathological pathways, we discovered two myeloid cell clusters strongly linked to neurodegenerative disorders. Additionally, other clusters were associated with inflammatory pathways, suggesting varying degrees of activation among different myeloid cell populations in the brain, possibly mediated by distinct signaling pathways. All microglia clusters developed signs of the cellular senescence pathway. These findings shed light on the immunological and pathological effects of different myeloid phenotypes in the brain during acute SIV infection, providing valuable insights for future therapeutic strategies targeting this critical stage and aiming to eliminate the viral reservoir.