Single-cell transcriptomics of human iPSC differentiation dynamics reveal a core molecular network of Parkinson\u2019s disease

Gabriela Novak,Kamil Grzyb,Michela Bernini,Alexander Skupin,Steven Finkbeiner,Dimitrios Kyriakis,Sophie Rodius,Gunnar Dittmar

doi:10.1038/s42003-021-02973-7

Abstract

Parkinson’s disease (PD) is the second-most prevalent neurodegenerative disorder, characterized by the loss of dopaminergic neurons (mDA) in the midbrain. The underlying mechanisms are only partly understood and there is no treatment to reverse PD progression. Here, we investigated the disease mechanism using mDA neurons differentiated from human induced pluripotent stem cells (hiPSCs) carrying the ILE368ASN mutation within the PINK1 gene, which is strongly associated with PD. Single-cell RNA sequencing (RNAseq) and gene expression analysis of a PINK1-ILE368ASN and a control cell line identified genes differentially expressed during mDA neuron differentiation. Network analysis revealed that these genes form a core network, members of which interact with all known 19 protein-coding Parkinson’s disease-associated genes. This core network encompasses key PD-associated pathways, including ubiquitination, mitochondrial function, protein processing, RNA metabolism, and vesicular transport. Proteomics analysis showed a consistent alteration in proteins of dopamine metabolism, indicating a defect of dopaminergic metabolism in PINK1-ILE368ASN neurons. Our findings suggest the existence of a network onto which pathways associated with PD pathology converge, and offers an inclusive interpretation of the phenotypic heterogeneity of PD.

Highlights

Parkinson’s disease (PD) is the second-most prevalent neurodegenerative disorder, characterized by the loss of dopaminergic neurons in the midbrain
PD is characterized by the death of the midbrain dopaminergic neurons found in the substantia nigra region of the brain, which are selectively sensitive to Parkinson’s disease-associated neuronal cell death[4,5,6,7]
The aim of this study was to identify genes that were differentially expressed as a result of a mutation in the PINK1 gene, using midbrain dopaminergic (mDA) neurons differentiated from patient-derived induced pluripotent stem cells (iPSCs), a model relevant to PD

Summary

Introduction

Parkinson’s disease (PD) is the second-most prevalent neurodegenerative disorder, characterized by the loss of dopaminergic neurons (mDA) in the midbrain. PD is characterized by the death of the midbrain dopaminergic (mDA) neurons found in the substantia nigra region of the brain, which are selectively sensitive to Parkinson’s disease-associated neuronal cell death[4,5,6,7] This results in the development of motor deficits, including bradykinesia, rigidity, and tremor, but many patients develop non-motor symptoms, such as depression or dementia[8]. Despite the small fraction of cases they explain, these mutations provide an important window into the underlying molecular mechanisms of PD because they identify pathways which, when disrupted, are able to cause the disease Many of these mutations converge on mitochondrial homeostasis, repair, and mitophagy. The development of cellular reprogramming allows nowadays for the conversion of somatic cells into induced pluripotent stem cells (iPSCs), which can subsequently be differentiated into neurons

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