Single-nucleus transcriptomics-based drug screening platform for focal cortical dysplasia

Focal cortical dysplasias (FCDs) are a major cause of drug-resistant epilepsy, yet their molecular and pathological complexity has limited the development of effective antiseizure medications. Here, we performed single-nucleus RNA sequencing on 49 human neocortical specimens spanning FCDI-III. We identified prominent transcriptional alterations in non-neuronal populations, particularly astrocytes and vascular cells, with signatures suggestive of endothelial and smooth muscle cell dysfunction. In contrast, neuronal populations exhibited additional subtype-specific heterogeneity. Notably, vascular-associated signatures were consistently observed across FCD subtypes, suggesting a convergent feature of diseased cortex. To systematically explore candidate interventions, we integrated cell-type-resolved transcriptional signatures with the Connectivity Map to prioritize compounds from ~40,000 perturbagens. This analysis yielded 20 candidates, among which four compounds (Betamethasone, Lodamin, Valproxam, and Licochalcone A) reduced seizure-like activity in vivo, as assessed by behavioral assays and local field potential recordings. These effects were further evaluated in an mTOR-driven FCD model. Collectively, our findings establish a transcriptome-guided framework for linking multicellular disease signatures to candidate therapeutic strategies in refractory epilepsy.