Fanconi anemia pathway protects neuron–glial lineage integrity by resolving differentiation-induced endogenous DNA damage

Fanconi anemia (FA) is a congenital DNA repair disorder classically characterized by bone-marrow failure, yet emerging neurodevelopmental manifestations encompassing both congenital malformations and progressive neurodegeneration in FA patients remain mechanistically unexplained. Here we show that loss of the FA pathway selectively compromises neuroectodermal lineage progression in human cellular models, leading to impaired neuronal morphology, defective expression of neuronal and oligodendroglial markers, mitochondrial dysfunction, and defective electrophysiology. Mechanistically, transcriptional reprogramming during neural differentiation triggers a metabolic surge of endogenous formaldehyde, resulting in the accumulation of DNA-protein crosslinks (DPCs) and subsequent cell apoptosis in FANCL –/– cells. These defects are effectively rescued by restoring either FANCL or the formaldehyde-detoxifying enzyme ADH5. Moreover, conditioned media from FANCL –/– neural culture induces a reactive astrogliosis-like response in recipient cells, supporting a non-cell autonomous pro-inflammatory component. Together, our findings establish the FA pathway as a critical safeguard of neurodevelopment, coordinating both intrinsic lineage maturation and extrinsic paracrine homeostasis.