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

Post-stroke recovery relies on structural remodeling of neuronal circuits in both the spared ipsilesional and contralesional cortices. RNA sequencing studies have identified distinct states of glial reactivity after stroke, but how these states are spatially organized at the single-cell level in relation to neuronal responses remains unknown. Consequently, it remains unclear which reactive states are lesion-restricted versus remote regions, such as the contralesional cortex, and how remote glial responses relate to the neuronal growth programs that support circuit repair. To address this, we used imaging-based subcellular spatial transcriptomics to profile ~650,000 cells across both hemispheres in male and female mice 7 days after cortical ischemic stroke, a critical timepoint for neuroplasticity. Reactive glial states differed significantly in their spatial organization from the lesion: scar-forming astrocytes and infiltrating pro-inflammatory myeloid cells were confined to the perilesional rim, whereas a reactive microglial state and a reactive astrocyte state extended into remote gray and white matter of the contralesional hemisphere. Mapping neuronal growth-associated gene expression across the entire cortex, we found substantial activation in both the perilesional and homotopic contralesional cortex, and these same regions showed significantly increased proportions of reactive microglia and astrocytes. Together, these findings identify spatially organized neuronal growth and glial activation states in both hemispheres after stroke and nominate regions for investigating spatial relationships between complex cell types and functional recovery.