Human brain slice culture model of STXBP1 encephalopathy reveals disruption of neuronal network activity and changes...

STXBP1 haploinsufficiency, a major genetic cause of developmental and epileptic encephalopathies, exhibits variability in clinical severity and remains poorly understood mechanistically. Although STXBP1 encodes a core presynaptic protein essential for SNARE-mediated neurotransmitter release, evidence from rodent models and patient-derived neurons indicates that its deficiency produces far broader molecular and cellular disruptions across multiple neurodevelopmental processes. Understanding how these widespread perturbations contribute to STXBP1 encephalopathy requires integrative approaches that extend beyond single-phenotype assays. Here, we used foetal human organotypic cortical cultures that preserve tissue architecture including the transient subplate, a critical hub in early cortical network development. Human cultures (15-18 post-conception weeks) retaining intact subplate, cortical plate, and progenitor zone organisation, were subjected to shRNA-mediated STXBP1 knockdown. We combined live calcium imaging, targeted transcriptomics, protein expression validation, and neurite-growth assays to assess functional and structural outcomes. STXBP1 knockdown disrupted spontaneous subplate neuronal network activity observed by calcium imaging at 14 days in vitro, reducing signal amplitude and synchronicity, indicating impaired early circuit function. Transcriptomic profiling revealed dysregulation of gene expression involved in synaptogenesis, ion transport, and extracellular matrix organisation. Protein-level analyses confirmed alterations in key synaptic components. At the cellular level, neurons exhibited shortened neurites and accumulation of the axon-guidance receptor EPHA4 at growth cones, suggesting defects in early connectivity. These findings expand the mechanistic framework of STXBP1 encephalopathy beyond synaptic dysfunction to encompass coordinated molecular, structural and network-level pathology during a critical window of cortical development, highlighting convergent pathways that may inform early therapeutic strategies.