Abstract

Background Focal cortical dysplasia (FCD) is a common neurodevelopmental disorder characterised by cortical malformations and is a major cause of drug-resistant epilepsy. FCD type I (FCDI) presents with architectural abnormalities of the neocortex but without cytological abnormalities. Currently, FCDI remains a significant clinical challenge. Methods Epileptogenic cortical tissues from three FCDI patients and three relatively normal neocortical tissues as controls were analysed using single-nucleus RNA sequencing and spatial transcriptomic for multi-omics integration. Results This study constructed a single-cell spatial transcriptomic atlas of the epileptogenic cortex from FCDI patients. Excitatory neurons (ENs) and astrocytes (Ast) exhibited the most prominent alterations in FCDI. Hub genes associated with FCDI were identified in ENs, and a transcription factor (TF)‒hub gene regulatory network was constructed. Notably, CBLN2 high Ex-1 was identified as being potentially involved in processes related to neuronal hyperexcitability and cortical development in FCDI. Western blot and immunofluorescence assays validated the altered expression of selected key genes and TFs at the protein level. Additionally, Ast exhibited increased heterogeneity, impaired differentiation and a higher proportion of immature Ast in FCDI, with predicted TFs regulating this process. Further analysis revealed aberrant signalling pathways and ligand‒receptor interactions between ENs and Ast in FCDI, with spatial co-localisation patterns that may contribute to disease progression. Conclusions This study highlights the specific dysregulation of ENs and Ast, along with aberrant cellular communication, which may play a critical role in the pathogenesis of FCDI. These findings provide novel insights into the molecular mechanisms underlying FCDI and offer potential therapeutic targets for precision treatment and drug development.