Single-cell discovery of mTOR-associated microglial clusters in human mTORopathies

Microglia play a critical role in shaping neuronal circuits during brain development, making them key regulators of normal cortical development and brain function. While microglial heterogeneity has been extensively characterized in neurodegenerative disorders, it remains poorly understood in developmental brain disorders. Tuberous sclerosis complex (TSC) and focal cortical dysplasia (FCD) type II are mechanistic target of rapamycin (mTOR)opathies characterized by malformations of cortical development, drug-resistant epilepsy, and comorbidities, including autism spectrum disorder (ASD). This study aimed to characterize the microglial landscape and cell–cell communication networks in mTORopathies. Using single-cell RNA sequencing, we identified three mTOR-associated microglial populations: lipid-associated disease-associated microglia (DAM)-like, pro-inflammatory, and interferon-responsive DAM-like microglia. The presence of these populations was subsequently validated in cortical tissue. While core transcriptional identities were largely preserved among microglial populations shared between control and mTORopathy samples, cell–cell communication analysis revealed disease-specific alterations, particularly involving inhibitory neuronal circuits, suggesting functional reprogramming. Disease ontology analysis further linked the mTOR-associated microglial populations to both neurodevelopmental and neurodegenerative disorders, indicating the existence of shared microglial activation states across these conditions. Together, these findings reveal distinct microglial states and altered intercellular communication in mTORopathies, providing new insights into microglial dysfunction