High-Resolution Molecular Profiling of Epileptic Brain Activity via Explanted Depth Electrodes [RNA-seq]

Understanding neurological disorders necessitates systems-level approaches that integrate multimodal data, but progress has been hindered by limited sample availability, and the absence of combined electrophysiological and molecular data from live patients. Here, we demonstrate that stereo electroencephalography (sEEG)—stereologically-implanted electrodes routinely used for monitoring epilepsy—enables the integration of RNA sequencing and epigenome maps with in vivo recordings and brain imaging. Here we report a method MoPEDE (Molecular Profiling of Epileptic Brain Activity via Explanted Depth Electrodes) that enables this by recovering extensive protein-coding transcripts and DNA methylation profiles from explanted depth electrodes containing matched electrophysical and radiological data, hence allowing for high-resolution reconstructions of brain structure and function in patients. Our proof-of-concept study shows that epilepsies of different etiologies have distinct molecular landscapes and identifies transcripts correlating with neurophysiological signals, including immediate early genes, inflammation markers, and axon guidance molecules. Additionally, we identify DNA methylation profiles indicative of transcriptionally permissive or restrictive chromatin states. While gene expression gradients corresponded with the assigned epileptogenicity index, we found outlier molecular fingerprints in some electrodes, potentially indicating seizure spread or generation zones not detected during clinical assessments. These findings validate that RNA profiles and genome-wide epigenetic data from explanted sEEGs offer high-resolution surrogate molecular landscapes of brain activity. This revolutionary approach has the potential to enhance diagnostic decisions and deepen our understanding of epileptogenic processes.