Deciphering the protein dynamics and molecular determinants of iPSC-derived neurons

Abstract

Neuronal development is a multistep process with different regulatory programs that shapes neurons to form dendrites, axons and synapses. To date, knowledge on neuronal development is largely based on murine data and largely restricted to the genomic and transcriptomic level. Advances in stem cell differentiation now enable the study of human neuronal development, and here we provide a mass spectrometry-based quantitative proteomic signature, at high temporal resolution, of human stem cellderived neurons. To reveal proteomic changes during neuronal development we make use of two differentiation approaches, either by expression of neurogenin-2 (Ngn2) leading to glutamatergic induced neurons (iN) or via small molecule manipulations, leading to patterned motor neurons. Our analysis revealed key proteins that show significant expression changes (FDR <0.001) during neuronal differentiation. We overlay our proteomics data with available transcriptomic data during neuronal differentiation and show distinct, datatype-specific, signatures. Overall, we provide a rich resource of information on proteins associated with human neuronal development, and moreover, highlight several signaling pathways involved, such as Wnt and Notch. 2 KEYWORDS iPSC; human; neuron differentiation; quantitative mass spectrometry; TMT-10plex

Emerging proteomic approaches to identify the underlying pathophysiology of neurodevelopmental and neurodegenerative disorders

“…The same methodology can be used to track the changes in the proteomic profile of other differentiation protocols. Varderidou et al used two iPSC to neuron differentiation protocols, expression of NGN2 to generate excitatory neurons and small molecules to generate motor neurons [135]. Interestingly, they compared both the proteome and transcriptome during neuronal differentiation and found that both methods have different signatures, highlighting significant differences between the RNA and protein levels within human engineered neurons.…”