High-Dimensional Single-Cell Analysis Reveals Coordinated Age-Dependent Neuroinflammatory Microglia-T cell Circuits in the Brain

Ali, M. A.; Siam, M. H. B.; Vardaman, D.; Bolding, C.; Brazell, J. N.; Whatley, A. D.; Risley, C. A.; Tidwell, H.; Hossain, S. N.; Samal, J.; Harms, A. S.; Tyrrell, D. J.

doi:10.64898/2025.12.10.693494

bioRxiv · 10.64898/2025.12.10.693494

High-Dimensional Single-Cell Analysis Reveals Coordinated Age-Dependent Neuroinflammatory Microglia-T cell Circuits in the Brain

Ali, M. A.·Siam, M. H. B.·Vardaman, D.·Bolding, C.·Brazell, J. N.·Whatley, A. D.·Risley, C. A.·Tidwell, H.·Hossain, S. N.·Samal, J.·Harms, A. S.·Tyrrell, D. J.

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Abstract

Aging and cerebrovascular pathology drive neuroinflammation in vascular dementia (VaD) but immune mechanisms underlying this interplay remain unresolved. Leveraging multi-modal high-dimensional imaging, flow cytometry, and split pool ligation transcriptomic sequencing in a mouse model of VaD, we constructed a brain immune cell atlas spanning young and aged mice in health and disease. We profiled microglia, T cells, macrophages, neutrophils, and B cells and integrated transcriptomics, cell-cell communication, multiplex imaging, and comparative analysis with human microglia. We found striking depletion of Ccr7+ naive T cells and expansion of Gzmk+ cytotoxic Cd8+ effector memory T cells in the aging brain. At the same time, microglia shifted toward a pro-inflammatory state with enhanced activity of major histocompatibility class complex I (MHC-I) to T cell receptor and co-stimulation from CD86 to CD28. These shifts suggest enhanced neuroinflammatory polarization within the aged brain and in VaD. These signals were strongest from activated microglia to Gzmk+ Cd8+ TEM cells, indicating that age-related microglial polarization may sustain cytotoxic T cell activation in the aged brain. Our findings suggest pro-inflammatory microglia and Gzmk+ CD8+ TEM cells are central drivers of immune brain aging and highlights a therapeutic potential to disrupt age-related neuroinflammatory cascades in VaD.

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Ali, M. A., Siam, M. H. B., Vardaman, D., Bolding, C., Brazell, J. N., Whatley, A. D., Risley, C. A., Tidwell, H., Hossain, S. N., Samal, J., Harms, A. S., Tyrrell, D. J.. 2025-12-13. High-Dimensional Single-Cell Analysis Reveals Coordinated Age-Dependent Neuroinflammatory Microglia-T cell Circuits in the Brain. https://doi.org/10.64898/2025.12.10.693494

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