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. Overall design: We based our study on the lithium-pilocarpine model of TLE introduced before and selected four time points to conduct a comprehensive study of epileptogenesis: 5, 10, 20 and 40 days after SE induction (D5, D10, D20 and D40). The latent period is supposed to start as soon as SE ends, either by itself or because of drug injection. Nonetheless, acute SE effects seem to appear around D2 in hippocampus and can be observed until D3. Latent period total duration in itself is highly dependent on SE duration, SE arresting method, strain, age and gender. A mean duration for TLE models is estimated to be 15 days. So D10 and D20 were selected to encompass the medium to late latent period. Finally, considering the variability of latent/chronic switch, D40 was chosen to represent the chronic period but without being too far into it.