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Abstract

Parkinson’s disease (PD) is a common debilitating neurodegenerative disorder, characterized by a progressive loss of dopaminergic (DA) neurons. Mutations, gene dosage increase, and single nucleotide polymorphisms in the α-synuclein-encoding gene SNCA either cause or increase the risk for PD. However, neither the function of α-synuclein in health and disease, nor its role throughout development is fully understood. Here, we introduce DeePhys, a new tool that allows for data-driven functional phenotyping of neuronal cell lines by combining electrophysiological features inferred from high-density microelectrode array (HD-MEA) recordings with a robust machine learning workflow. We apply DeePhys to human induced pluripotent stem cell (iPSC)-derived DA neuron-astrocyte co-cultures harboring the prominent SNCA mutation A53T and an isogenic control line. Moreover, we demonstrate how DeePhys can facilitate the assessment of cellular and network-level electrophysiological features to build functional phenotypes and to evaluate potential treatment interventions. We find that electrophysiological features across all scales proved to be highly specific for the A53T phenotype, enabled to predict the genotype and age of individual cultures with high accuracy, and revealed a mutant-like phenotype after downregulation of α-synuclein.