A stage-resolved neuron-glia transcriptional atlas reveals a glial inflammatory pivot in epilepsy

Epileptogenesis transforms a healthy brain into an epileptic network, yet the temporal and cell-type-specific molecular events driving this transition remain poorly defined. Neuron-glia interactions are essential in this process, but no study has systematically charted their transcriptional dynamics from the acute insult to chronic epilepsy.

Using the intracortical kainic acid mouse model that recapitulates key hallmarks of mesial temporal lobe epilepsy with hippocampal sclerosis in humans, we performed Fluorescent Activated Nuclear Sorting of NeuN⁺ (neuronal) and NeuN⁻ (glia) nuclei followed by RNA sequencing at 1 h, 24 h, and 3 months after status epilepticus. Differential expression and integrative GO/KEGG analyses resolved stage-specific molecular programs across cell types.

The majority of genes differentially expressed in neurons and glia were exclusive to the respective time point investigated. We also identify a sequential reorganization of cellular gene expression changes during epileptogenesis. The acute phase is dominated by a shared stress response and DNA-repair programs in both neurons and glia. At 24 h, glia undergoes a marked transcriptional pivot involving necroptosis-associated, TNFR1/IFN-linked, and COX-2/chemokine pathways, while neurons display immune- and plasticity-related signatures. By 3 months, transcriptional activity is largely confined to glia and enriched for inflammatory, angiogenic, and gliogenic processes, consistent with long-term neurovascular remodeling. Only a few transcripts, including Parp3 (neurons) and Tlr1 (glia), are dysregulated across all stages.

These findings reveal an orderly transition from an acute protective-leaning program to a early latent glial inflammatory/regulated-death state, culminating in chronic gliopathy. Our work provides, to our knowledge, the first cell-type-resolved temporal atlas of epileptogenesis and identifies the early latent phase as a mechanistically tractable window for antiepileptogenic intervention.