Single-cell proteomic maps of human induced pluripotent stem cells and their differentiation into motor neurons

The majority of single cell-studies use RNA to identify the cell state. However, many RNAs are transient and decrease in response to elevated protein to control homeostasis. Thus, final cell states are largely defined by their unique and dynamic protein composition not RNA. Here a single-cell proteomics approach was used to identify the proteomic profile of human induced pluripotent stem cells (iPSCs) before and during their in vitro differentiation to motor neurons. By measuring up to 1000 proteins in each cell, novel clusters of growing iPSCs could be characterized along with a new proteomic pathway that defines motor neuron development. Interestingly, there was a dynamic and cell type-specific discordance between the protein levels and their corresponding messenger RNAs. This lays the foundation for drawing new single-cell proteomic maps of developing human tissues. IN BRIEFIn this article, we report the first single-cell proteomic maps of induced pluripotent stem cells (iPSCs) and their differentiation into motor neurons (MNs). By identifying proteomes of individual cells, we resolve iPSC and MN states, their proteomic, metabolomic and organellar heterogeneity. We show considerable, stage-specific discordance between the transcriptome and the proteome in differentiated neurons.