Dissecting the transcriptome of Parkin (PRKN)-linked Parkinson’s disease using 2D and 3D hiPSC-neuronal models

Mutations in the Parkin (PRKN) gene are the most common known cause of autosomal recessive early-onset Parkinson’s disease (PD), and Parkin dysfunction represents a risk factor for idiopathic PD. Parkin is an E3 ubiquitin ligase, involved in protein quality control and the removal of damaged mitochondria. Here, we generate human induced pluripotent stem cell (hiPSC)-derived midbrain dopaminergic neurons using both a 2D differentiation protocol and our recently developed 3D method based on the microencapsulation of hiPSCs in small alginate/fibronectin beads. The transcriptional signature of cells from PD patients carrying PRKN mutations is evaluated at the neuronal stage and during the differentiation process. Analyses of mutation-specific gene sets and associated pathways reveal multiple biological processes implicated in PRKN-pathology, including synaptic and metabolic function, inflammation, and intracellular trafficking, reflecting a layered disease development. These data map the contribution of Parkin in early PD pathogenesis and progression before overt neurodegeneration.