T cell-mediated SIV dissemination into the CNS: a single-cell transcriptomic analysis

Background CNS infection by HIV-1 contributes to neuroinflammation, cognitive impairments, and the establishment of viral reservoirs. Although HIV-1 is known to enter the brain early in infection via "Trojan horse" leukocytes, including infected monocytes and CD4⁺T cells, the specific cellular phenotypes facilitating this process during acute infection remain incompletely characterized. Objective This study aims to characterize the roles of brain lymphocytes during acute infection and primary CD4+ T cell phenotypes seeding the SIV to the CNS. Methods scRNA-seq was performed on brain and blood cells of three acutely SIV-infected rhesus macaques. The transcriptomic data were analyzed using bioinformatics approaches and validated through in vitro co-culture assays and re-analysis of a publicly available scRNA-seq dataset. Results We found a distinct cell cluster in the brain co-expressing myeloid and lymphoid genes, suggesting brain myeloid cells may engulf CD4+ T cells entering from the blood. This finding was confirmed in by coculture studies of macrophages and T cells, and identified specific chemokines could distinguish such cells. Acute infection induced an increase in proliferating CD4+ cytotoxic-like T cells, which had high expression of viral entry receptors and adhesion molecules, indicating their role in CNS infection. Additionally, transcriptomic analysis revealed upregulation of cytotoxic genes, MHC class II molecules, ISG15, and USP18 in brain lymphocytes, indicating a robust immune response to acute infection. Conclusion Our findings suggest that CD4⁺cytotoxic-like T cells represent a key lymphocyte subset responsible for initiating SIV entry into the brain and triggering neuroinflammatory processes. Furthermore, interactions between infiltrating lymphocytes and brain-resident myeloid cells may facilitate viral propagation within the CNS.