CXCR4 and CXCR6 dually limit T cell entry into the polyomavirus-infected brain.

T cell responses are vital for controlling viral infection in the central nervous system (CNS), but must be tightly regulated to limit tissue-damaging inflammation. Using mouse polyomavirus (MuPyV) CNS infection, an in vivo model for JCPyV-induced Progressive Multifocal Leukoencephalopathy (PML), we investigated sites of early infection, immune responses, and recruitment of T cells to the brain. Multiplexed error-robust fluorescence in situ hybridization (MERFISH) single-cell spatial transcriptomics was applied to assess the regionality of virus infection and brain-resident cell and infiltrating leukocyte responses. MERFISH, immunofluorescence microscopy, quantitative PCR, and flow cytometry demonstrate that the ependyma is the predominant region of MuPyV CNS infection and localization of T cells, and implicated CXCR4 and CXCR6 in T cell migration to the ependyma and subventricular zone. Using CXCR6 knockout mice and a specific CXCR4 small molecule antagonist, we found that the combined impairment of CXCR6 and CXCR4 signaling resulted in elevated infiltration of T cells in the MuPyV-infected brain. This work demonstrates that CXCR4 and CXCR6 act in a nonredundant fashion to restrict T cell accumulation to the polyomavirus-infected ependyma, with important implications for ongoing efforts to use JCPyV-specific T cell adoptive immunotherapy for PML. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12974-025-03496-2.