In situ cell-type-specific cell-surface proteomic profiling in mice

Cell-surface proteins (CSPs) mediate intercellular communication throughout the lives of multicellular organisms. However, there are no generalizable methods for quantitative CSP profiling in specific cell types in vertebrate tissues. Here, we present in situ cell-surface proteome extraction by extracellular labeling (iPEEL), a proximity labeling method in mice that enables spatiotemporally precise labeling of cell-surface proteomes in a cell-type-specific environment in native tissues for discovery proteomics. Applying iPEEL to developing and mature cerebellar Purkinje cells revealed differential enrichment in CSPs with post-translational protein processing and synaptic functions in the developing and mature cell-surface proteomes, respectively. A proteome-instructed in vivo loss-of-function screen identified a critical, multifaceted role for Armh4 in Purkinje cell dendrite morphogenesis. Armh4 overexpression also disrupts dendrite morphogenesis; this effect requires its conserved cytoplasmic domain and is augmented by disrupting its endocytosis. Our results highlight the utility of CSP profiling in native mammalian tissues for identifying regulators of cell-surface signaling.

Automated summary

A new method called iPEEL was developed to identify cell-surface proteomes in specific cell types in their native tissues. By applying iPEEL to studying developing and mature cerebellar Purkinje cells, researchers discovered differential enrichment in cell-surface proteomes with post-translational protein processing and synaptic functions in these cells. They also identified the critical role of Armh4 in Purkinje cell dendrite morphogenesis through in vivo loss-of-function screening. Disrupting Armh4's endocytosis augmented its effect on dendrite morphogenesis. This study highlights the importance of CSP profiling in native mammalian tissues for understanding cell-surface signaling regulations.