Research Findings

2025.11.11

Single-cell synaptome mapping of endogenous protein subpopulations in mammalian brain

▶Nat Commun 16, 9705 (2025). https://doi.org/10.1038/s41467-025-65813-w

Motokazu Uchigashima1,2, Risa Iguchi1, Kazuma Fujii3, Kaito Shiku3, Pratik Kumar4, Xinyi Liu1, Mari Isogai1, Chiaki Hoshino1, Manabu Abe5, Motohiro Nozumi6, Yosuke Okamura7,8, Michihiro Igarashi6, Kenji Sakimura5, Ryoma Bise3, Luke D. Lavis4 & Takayasu Mikuni1

  1. Department of Cellular Neuropathology, Brain Research Institute, Niigata University
  2. International Research Center for Neurointelligence (WPIIRCN), The University of Tokyo
  3. Department of Advanced Information Technology, Faculty of Information Science and Electrical Engineering, Kyushu University
  4. Janelia Research Campus, Howard Hughes Medical Institute, USA
  5. Department of Animal Model Development, Brain Research Institute, Niigata University
  6. Department of Neurochemistry and Molecular Cell Biology, School of Medicine, and Graduate School of Medical and Dental Sciences, Niigata University
  7. Department of Applied Chemistry, School of Engineering, Tokai University
  8. Micro/Nano Technology Center, Tokai University

Abstract

Different spatial or temporal protein populations, such as cell-surface/intracellular or pre-existing/nascent subpopulations, determine the basal and activity-induced functions of individual synapseswithin a neuron in vivo.Here, we developed a simple and generalizable platform to image different spatial and temporal subpopulations of endogenous proteins at thousands of synapses in single neurons in the mammalian brain. The platform is based on the development, improvement and integration of CRISPR-Cas9-mediated protein labeling methods, chemical tag labeling techniques, and a semiautomatic analytical pipeline. The combined platform enables whole-cell mapping of total, cell-surface, intracellular, pre-existing, nascent or nascentand-surface populations of endogenous proteins, such as receptor, scaffold and signaling proteins, at thousands of synapses in individual neurons in living or fixed mouse brain. Our single-cell "synaptome" mapping of endogenous protein subpopulations comprehensively visualizes the spatial representation of synapse diversity in protein localization, trafficking and turnover, providing valuable insights into single-cell organization and computations in the brain.

*Reprinted under a CC BY NC ND 4.0 license.

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