Single-cell transcriptomics revealed molecular vulnerability in a human midbrain-like organoid model of Parkinson's Disease [scRNA-Seq]

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 an in-depth single-cell characterization of our previously established hMLO model up to 150 days in vitro. Our hMLOs exhibited various physiological cell types and broad topographical patterning that resemble that of human fetal midbrain. We further identified four distinct dopamine-producing neuron (DaN) subtypes whose molecular profiles span a key transcriptomic axis in the selective vulnerability of DaNs in PD. Deletion of PARK7, a highly penetrant PD-causing gene, from hMLOs induced cell type-dependent molecular perturbations in mitochondrial activity and synapse biology, and recapitulated PD pathophysiology including a-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. Overall design: We characterized our previously established human pluripotent stem cell-derived three-dimensional organoid model of the human midbrain (hMLO) with single-cell and spatial resolution. We also investigated the effect of a PD-causing mutation, namely loss-of-function of the DJ-1 protein, with batch-matched WT and isogenic DJ-1 KO hESC-derived hMLOs. These scRNAseq experiments were performed across the period of day 65-153.