Chronic TFE3 activation in TFE3-associated neurodevelopmental disorder drives metabolic rigidity, lysosomal failure, and cell-extracellular matrix destabilization

The transcription factor TFE3 coordinates cellular adaptation to stress. While its acute activation is cytoprotective, chronic TFE3 dysregulation is linked to diverse pathologies. Here, we characterize the cellular landscape of TFE3-NDD, a recently described neurodevelopmental disorder caused by mutations that disrupt the TFE3-Rag GTPase interface, leading to constitutive TFE3 nuclear localization. Using patient-derived fibroblasts, we show that TFE3-NDD is primarily a metabolic and homeostatic disorder. Mutant cells undergo a profound rewiring toward oxidative phosphorylation (OXPHOS), resulting in metabolic rigidity and a vulnerability to energy failure. Despite a massive expansion of the lysosomal compartment, we observe a paradoxical qualitative failure characterized by impaired acidification, defective protease maturation, increased lysosomal exocytosis, and aberrant cathepsin K secretion. This secretory phenotype is coupled with a destabilized cell-extracellular matrix interface, marked by impaired migration, defective coordination between actomyosin tension and focal adhesion maturation, and a loss of synaptic stabilizers. Notably, TFE3-NDD shares a signature of high OXPHOS and ferroptosis resistance with TFE3-dependent cancers, such as translocation renal cell carcinoma. Our findings reveal how the chronic hyperactivation of a protective stress-response factor collapses cellular homeostasis, providing a mechanistic framework for the tissue malformations and neurodevelopmental deficits that define TFE3-NDD.