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Proteome dynamics in iPSC-derived human dopaminergic neurons – part 2: protein turnover dynamics using SILAC

ABSTRACT: Dopaminergic neurons participate in fundamental physiological processes and are the cell type primarily affected in Parkinson’s disease (PD). Their analysis is challenging due to the intricate nature of their function, their involvement in diverse neurological processes, their heterogeneity and localization in deep brain regions. Consequently, most of the research on the protein dynamics of dopaminergic neurons has been performed in animal cells ex vivo. Here we use iPSC-derived, human mid-brain specific dopaminergic neurons to study general features of their proteome biology. We use dynamic SILAC to measure the half-life of more than 4,300 proteins. We report uniform turnover rates of conserved protein complexes and identify several outliers in the mitochondrial outer membrane and mitophagy pathway. Our study provides a workflow and resource for future applications of quantitative proteomics in iPSC-derived human neurons.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: Claudia Cavarischia Rega

LAB HEAD: Boris Macek

PROVIDER: PXD051015 | Pride | 2024-09-12

REPOSITORIES: Pride

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Proteome dynamics in iPSC-derived human dopaminergic neurons – part 3: dynamic SILAC to study local synthesis and trafficking of proteins

Project description:Dopaminergic neurons participate in fundamental physiological processes and are the cell type primarily affected in Parkinson’s disease (PD). Their analysis is challenging due to the intricate nature of their function, their involvement in diverse neurological processes, their heterogeneity and localization in deep brain regions. Consequently, most of the research on the protein dynamics of dopaminergic neurons has been performed in animal cells ex vivo. Here we use iPSC-derived, human mid-brain specific dopaminergic neurons to study general features of their proteome biology. We use differential dynamic SILAC labeling in combination with microfluidic devices to analyze local protein synthesis and transport between axons and soma. We report 105 potentially novel axonal markers and detect translocation of 269 proteins between axons and the soma in the time frame of our analysis (120 hours). Importantly, we provide evidence for local synthesis of 154 proteins in the axon and their retrograde transport to the soma. Our study provides a workflow and resource for future applications of quantitative proteomics in iPSC-derived human neurons

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