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.