Single-cell transcriptomics revealed molecular vulnerability in a human midbrain-like organoid model of Parkinson’s disease

The human midbrain-like organoid (hMLO) is a key model system for investigating pathological features of Parkinson's disease (PD), yet how its molecular landscape relates to cellular vulnerability in PD remains unclear. We performed in-depth single-cell characterization of our previously established hMLO model up to 150 days in vitro . Our hMLOs exhibited physiological cell types and broad topographical patterning, consistent with features of the human fetal midbrain. We further identified four distinct dopamine-producing neurons (DaN) subtypes whose molecular profiles span a key transcriptomic axis in the selective vulnerability of DaNs in PD. Knockout of PARK7 , a highly penetrant PD-causing gene, in hMLOs induced cell type-dependent molecular perturbations in mitochondrial activity and synapse biology, and recapitulated PD pathophysiology, including α-synuclein aggregation, Lewy Body-like inclusions, and DaN degeneration with extended culture. This study highlights the utility of our hMLO model in manifesting pathological features and cell type-specific vulnerability, enabling mechanistic studies into PD pathophysiology.