Pathological variants in HPDL cause collapse of the neuro-glial unit during human cortical maturation

Biallelic variants in HPDL cause a severe neurological disorder in childhood, but the mechanisms linking early developmental abnormalities to later cortical degeneration remain unclear. Here, using long-term iPSC-derived human cortical cultures derived from four patients, we investigated the late consequences of HPDL deficiency through quantitative immunofluorescence and bulk RNA-seq. We found that HPDL-deficient cortical cultures undergo progressive synaptic impairment, with marked loss of PSD95-positive postsynaptic puncta despite largely preserved general neuronal maturation markers. This phenotype is accompanied by a profound reduction in astrocytes and oligodendrocytes, together with increased neuronal apoptosis and transcriptional dysregulation of genes linked to extracellular matrix organization, cellular stress, and neurodegeneration. Unexpectedly, late-stage mutant cultures also show reactivation of early developmental programs, including aberrant expression of NEUROD4 and other proneural regulators, suggesting instability of cell identity during cortical maturation. Together, these findings support a model in which HPDL deficiency first perturbs cortical developmental timing and later drives collapse of the neuro-glial unit, linking premature neurogenesis to synaptic failure, glial loss, and progressive neurodegeneration.