Spatially resolved single-cell atlas reveals cortical glial reactivity associated with regions of neuronal growth programs in both hemispheres after stroke

Recovery after focal motor cortex stroke relies on structural remodeling of neuronal circuits in the perilesional cortex (PLC) and contralesional cortex (CLC). Although transcriptomic studies have identified distinct reactive glial states after stroke, how their spatial organization relates to processes of tissue degeneration and neuronal circuit remodeling remains poorly understood. We used a custom 347-gene Xenium spatial transcriptomics panel to profile approximately 650,000 cells across both hemispheres of male and female mice 7 days after photothrombotic stroke. We identified injury-associated myeloid populations concentrated within the infarct and reactive astrocytes enriched in the glial scar. Distinct reactive populations also extended into spared cortex, including an interferon-associated myeloid population and a reactive astrocyte population that was present in both PLC and CLC. Spatial mapping further revealed elevated neuronal growth-associated gene expression in both regions, particularly among layer 5 extratelencephalic projection neurons, which include corticospinal neurons. Intriguingly, reactive glial populations were enriched in regions exhibiting elevated neuronal growth-associated gene expression, including areas of the CLC containing axons and presynaptic terminals originating from the PLC. Together, these findings reveal a striking spatial association between reactive glial populations and neurons exhibiting elevated growth-associated gene expression and support glial-neuronal interactions as potential targets for promoting circuit remodeling and functional recovery after stroke.