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

S Andrew Shuster1, Jiefu Li2, URee Chon1

  • 1Department of Biology and Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Neurosciences Program, Stanford University, CA 94305, USA.

Neuron
|October 11, 2022
PubMed
Summary

We developed in situ cell-surface proteome extraction by extracellular labeling (iPEEL) for cell-type-specific profiling of cell-surface proteins in mouse tissues. This method identified Armh4

Keywords:
Purkinje cellcell-surface proteincell-surface proteomecell-surface signalingdendrite morphogenesisdiscovery proteomicsproximity labeling

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Area of Science:

  • Proteomics
  • Cell Biology
  • Neuroscience

Background:

  • Cell-surface proteins (CSPs) are crucial for intercellular communication in multicellular organisms.
  • Existing methods lack generalizability for quantitative CSP profiling in specific cell types within vertebrate tissues.
  • Understanding cell-surface proteomes is vital for deciphering cell signaling and function.

Purpose of the Study:

  • To develop a generalizable method for quantitative cell-surface proteome profiling in native tissues.
  • To investigate cell-type-specific cell-surface proteomes in developing and mature cerebellar Purkinje cells.
  • To identify novel regulators of Purkinje cell dendrite morphogenesis.

Main Methods:

  • Developed in situ cell-surface proteome extraction by extracellular labeling (iPEEL), a proximity labeling technique.
  • Applied iPEEL to mouse cerebellar Purkinje cells at different developmental stages.
  • Conducted a proteome-instructed in vivo loss-of-function screen to identify functional CSPs.

Main Results:

  • iPEEL enabled spatiotemporally precise labeling of cell-surface proteomes in a cell-type-specific manner within native tissues.
  • Differential enrichment of CSPs involved in post-translational modification (developing) and synaptic functions (mature) was observed in Purkinje cells.
  • Identified Armorphan 4 (Armh4) as a critical regulator of Purkinje cell dendrite morphogenesis, with its cytoplasmic domain and endocytosis being key.

Conclusions:

  • iPEEL is a powerful tool for discovery proteomics of cell-surface proteins in native mammalian tissues.
  • CSP profiling in situ can reveal dynamic changes in cell-surface composition during development.
  • Armh4 plays a multifaceted role in regulating neuronal development, highlighting the importance of cell-surface signaling.