Single-cell profiling of cortical tubers in tuberous sclerosis complex shows molecular structure preservation and massive reorganization of metabolism

Tuberous sclerosis complex (TSC) is a multisystemic genetic disorder associated with loss-of-function mutations in the TSC1 or TSC2 gene, which lead mTOR pathway hyperactivation and epileptogenesis. Cortical tubers are the hallmark of TSC and represent disorganized cortical structure underlying the generation of focal seizures. Here, we report single-nucleus RNA sequencing in resected cortical tubers vs matched pediatric controls. Strikingly, in spite of severe cortical disorganization, we found that cortical tubers preserve all neuronal subtypes, even the rarest ones. Moreover, we showed that principal neurons largely preserve spatial position based on transcriptional signatures. Principal neurons and layer 1-2 GABAergic neurons that modulate upper cortical circuits exhibited the largest gene expression changes. Interestingly, multiple mTOR pathway gene expression changes in TSC counteracted mTOR hyperactivation. TSC neuronal, but not glial, networks exhibited massive metabolic reorganization with a reduction in mitochondrial respiration and a concomitant switch to fatty acid metabolism. Finally, we show that neuron-specific AMPA receptor signaling might underlie epileptogenesis in TSC and could represent a potential candidate for therapeutic targeting.