Acquisition of residency programs by T cells entering the human brain

Surveillance by T cells is mandatory for maintaining a healthy state of the central nervous system (CNS), while aberrant accumulation of T cells is linked to neuroinflammatory diseases. To understand the phenotype of T cells recruited into distinct CNS compartments, we studied CD8+ and CD4+ T cells isolated from CNS border compartments (choroid plexus and meninges), intrathecal compartments (cerebrospinal fluid (CSF) and subcortical white matter (WM)), and paired peripheral blood of human brain donors. Flow-cytometric analyses revealed that T cells in all CNS compartments show an effector memory phenotype. Tissue residency-associated integrins (CD49a, CD103), chemokine receptors (CCR2, CCR5), and brain T cell-associated CD20, but not the canonical tissue resident memory T-cell marker CD69, were enriched in T cells from both CNS border compartments compared to blood. While small circulating fractions co-expressed these border-associated markers, the interaction of T cells with brain endothelium resulted in up-regulation of CD49a and CD103, with a further gain of CD20 upon trans-endothelial migration. In contrast to border compartments, intrathecal T cells were additionally characterized by a high expression of CD69. The transcriptomes of intrathecal T cells from CSF and WM were very similar and displayed a tissue residency-associated pattern. Still, WM-derived T cells showed a lower expression of markers associated with migratory potential (CRTAM, RGS1), recent activation (CD25, HLA-DR), and co-stimulation (CD28), which was associated with reduced Eomes expression. This work demonstrates the versatility of T-cell phenotypes across CNS compartments and provides insight into the programs regulating their recruitment and maintenance within the CNS. Overall design: RNAseq profiling of primary isolated CD4 and CD8 T cells from control brain donors from circulation, CSF and white matter