Spatiotemporal transcriptomic mapping reveals region-specific glial activation and astrocyte subtype shifts in epileptogenesis beyond the hippocampus

Temporal lobe epilepsy (TLE) is a prevalent neurological disorder often initiated by status epilepticus (SE), followed by a latent phase that culminates in chronic epilepsy. The molecular and cellular mechanisms driving this transformation remain incompletely understood. Here, we applied Visium-based spatial transcriptomics to coronal brain sections from lithium-pilocarpine–induced SE rats and controls (n = 16) to map transcriptional dynamics across epileptogenesis. Spatial clustering accurately defined anatomically relevant regions and canonical markers in controls. Comparative analyses revealed extensive SE-associated transcriptional alterations spanning latent and chronic phases across all examined regions. Notably, spatial profiling demonstrated that microglial activation and reactive astrogliosis extended well beyond the hippocampus, encompassing white matter tracts and multiple thalamic nuclei during the latent phase. Cell-type deconvolution further identified pronounced regional shifts in astrocyte functional subtypes within these reactive zones. These findings uncover the spatial heterogeneity of epileptogenic processes, highlighting previously underappreciated thalamic and white matter involvement. The identification of region-specific glial responses and astrocyte subtype transitions provides new mechanistic insights into epileptogenesis and underscores the need for region- and cell-type–targeted strategies to inform therapeutic interventions in TLE.