Human forebrain assembloids modeling a neurodevelopmental disorder reveals neural circuit deficits via DNA damage

Cortical circuit dysfunction is strongly linked to neurodevelopmental disorders (NDDs). The mechanisms by which disruptions in early cortical development lead to defects in mature human neural circuit function are not well understood. Here, using human forebrain assembloids from individuals with the 15q13.3 microdeletion syndrome, we identified dysregulation of early gene networks in cortical neurons that results in migration deficits, reduced synaptic connections and decreased activity in inhibitory neuron subpopulations. These early inhibitory defects resulted in hyperactive networks and synaptic hyperconnectivity in maturing forebrain assembloids. Using unbiased spatial transcriptomics, we revealed regional transcriptional and cell-cell signaling disturbances, including elevated DNA damage in inhibitory neurons linked to Fanconi anemia-associated nuclease 1 (FAN1), a DNA repair enzyme. Collectively, our findings establish a human brain assembloid framework that reveals how early DNA damage–related mechanisms and cell type–specific vulnerabilities contribute to neural circuit dysfunction, providing mechanistic insight into the neurodevelopmental and neuropsychiatric features of the 15q13.3 microdeletion.