Single Cell Transcriptomics of Refractory Epilepsy (RE) patients in Colombia.

The human neocortex is composed of dozens to hundreds of distinct cell types, whose gene expression patterns maintain the balanced electric signaling during all the life. Although the brain has shown a high adaptive capacity to tolerate disruptions, some alterations in these genetic programs can contribute to the pathogenesis of various neurological disorders, including epilepsy, autism spectrum disorder, Alzheimer’s disease, and Parkinson’s disease. Genetic factors are especially implicated in a specific form known as refractory or drug-resistant epilepsy (DRE), which is diagnosed when two or more antiepileptic treatment regimens fail to control seizures. In this study, we investigated the cellular and molecular landscape of DRE using brain tissue from five pediatric Colombian patients. Six samples collected during surgical resection were analyzed using single-cell RNA sequencing (scRNA-seq) and long-read genome sequencing (PacBio HiFi). We identified differentially expressed genes (DEGs) across distinct cell types, integrating transcriptomic data with single nucleotide polymorphisms (SNPs), insertions, deletions, and structural variants. Functional enrichment analysis revealed glial-driven dysregulation of synaptic signaling, impaired glial–neuronal communication, and altered expression of transporters and calcium signaling genes. Notably, aberrant activation of taste receptors in neurons was associated with neuroinflammatory processes. These findings suggest that DRE arises from complex, cell-type-specific disruptions that compromise network stability and seizure control.