Single-nucleus transcriptomic analysis reveals subfield-specific cell-to-cell synaptic reorganisation of the mouse hippocampus in focal temporal lobe epilepsy

Here, we generated a single-nucleus RNA-seq dataset from ipsilateral hippocampi collected two weeks after status epilepticus in the mouse intra-amygdala kainic acid model, including kainic acid-treated and PBS-treated control mice. A total of 34,737 nuclei were sequenced using the 10x Genomics platform, representing the major hippocampal cell populations.

Differential expression analysis revealed cell subtype- and subfield-specific transcriptional changes, with prominent dysregulation in dentate gyrus neurons and astrocytes, including altered synaptic, inflammatory, and cholesterol-related pathways. Cell-cell communication analysis also suggested remodelling of hippocampal signalling across cell populations. This dataset provides a cell type-resolved resource for investigating molecular changes associated with chronic epilepsy in this model.