Human-Specific Regulation of CHD2 Controls the Tempo of Cortical Development through Lysosomal Homeostasis

Abstract

The mechanisms linking evolutionary changes in gene regulation to brain development and neurodevelopmental disease susceptibility remain poorly understood. Here, we identify a human-specific variant in an enhancer region that reduces expression of the chromatin remodeler CHD2. We investigate the variant’s functional consequences using genome editing, cross-primate induced pluripotent stem cell models, cortical organoids, single-cell transcriptomics, patient-derived cells, and neuronal network analyses. We demonstrate that CHD2 dosage bidirectionally regulates lysosomal function and autophagosome flux to set the tempo of neuronal maturation. Higher CHD2 expression, as found in ancestralized and non-human primate models, enhances lysosomal degradative capacity and accelerates dendritic and synaptic maturation. Conversely, CHD2 haploinsufficiency yields reciprocal defects and disrupts broader neurodevelopmental transcriptional programs. Restoring lysosomal function genetically or pharmacologically rescues neuronal maturation in CHD2-haploinsufficient neurons, establishing lysosomal dysfunction as a causal and therapeutically tractable mechanism. These findings reveal that CHD2 and lysosomal homeostasis constitute a critical molecular axis regulating the pace of cortical development across evolution and disease.