Single-Cell Approaches Define the Murine Leptomeninges: Cortical Brain Interface as a Distinct Cellular Neighborhood Composed of Neural and Non-neural Cell Types

The interface barrier between the brain surface and the adjacent meninges is important for regulating exchanges of fluid, protein, and immune cells between the CNS and periphery. However, the cell types that form this important interface are not yet fully defined. To address this limitation, we used single-cell RNA sequencing (scRNA-seq) and single-cell spatial transcriptomics together with morphological lineage tracing and immunostaining to describe the cell types forming the interface barrier of the adult murine cortex. We show that the cortical interface is composed of three major cell types, leptomeningeal cells, border astrocytes, and tissue-resident macrophages. On the nonparenchymal side, the interface is composed of transcriptionally distinct PDGFRα-positive leptomeningeal cells that are intermingled with macrophages. This leptomeningeal layer is lined by a population of transcriptionally distinct border astrocytes. The interface neighborhood is rich in growth factor mRNAs, including many leptomeningeal ligands predicted to act on both the border astrocytes and macrophages. On the CNS side of the interface is the relatively cell-sparse cortical layer 1 containing interneurons, microglia, parenchymal astrocytes, oligodendrocyte precursor cells, and oligodendrocytes. Except for the border astrocytes, layer 1 cells are not closely associated with the interface, suggesting that secreted ligands may be the major way the brain interface communicates with the underlying cortical parenchyma. Thus, our data provide a molecular/cellular resource describing the brain interface cell types and their interactions, thereby enabling future studies investigating how this distinct cellular compartment regulates CNS:periphery interactions.