Cell–cell communication dysregulation in tuberous sclerosis complex cortical tubers and focal cortical dysplasia

Malformations of cortical development are manifestations of mTORopathies, including tubers in context of Tuberous Sclerosis Complex (TSC) cortical tubers and Focal Cortical Dysplasia (FCD), and are associated with epilepsy, often accompanied by comorbidities such as autism spectrum disorder (ASD). This study aims to investigate the cell-type-specific transcriptional alterations and disrupted intercellular communication networks in mTORopathies, focusing on their implications for cortical network dysfunction. Using single-cell RNA sequencing, we identified 33 transcriptionally distinct cell clusters across control and pathological samples, including neuronal, glial, and endothelial populations. Our analysis revealed disease-specific changes, such as the loss of certain glutamatergic and microglial clusters in cortical tubers (TSC), MTOR_FCD and DEPDC5_FCD, and the presence of a unique endothelial cluster in pathological samples. Pathway enrichment analysis highlighted the critical role of synaptic signaling, axonogenesis, and neuroimmune regulation in these disorders. Additionally, cell-cell communication network analysis demonstrated disrupted interactions between neuron-astrocyte, astrocyte-OPC, and microglia-neuron across mTORopathies. We found that the neurexins-neuroligins (NRXN-NLGN) signaling pathway, crucial for synapse formation and stability, was altered in both glutamatergic and GABAergic neurons, reflecting dysregulated synaptic plasticity and impaired neuron-glia communication. These findings provide novel insights into the molecular underpinnings of mTORopathies and suggest potential therapeutic targets to restore cellular communication and synaptic function in these disorders.