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

Motokazu Uchigashima (), Risa Iguchi, Kazuma Fujii, Kaito Shiku, Pratik Kumar, Xinyi Liu, Mari Isogai, Chiaki Hoshino, Manabu Abe, Motohiro Nozumi, Yosuke Okamura, Michihiro Igarashi, Kenji Sakimura, Ryoma Bise, Luke D. Lavis and Takayasu Mikuni ()
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Motokazu Uchigashima: Niigata University
Risa Iguchi: Niigata University
Kazuma Fujii: Kyushu University
Kaito Shiku: Kyushu University
Pratik Kumar: Howard Hughes Medical Institute
Xinyi Liu: Niigata University
Mari Isogai: Niigata University
Chiaki Hoshino: Niigata University
Manabu Abe: Niigata University
Motohiro Nozumi: Niigata University
Yosuke Okamura: Tokai University
Michihiro Igarashi: Niigata University
Kenji Sakimura: Niigata University
Ryoma Bise: Kyushu University
Luke D. Lavis: Howard Hughes Medical Institute
Takayasu Mikuni: Niigata University

Nature Communications, 2025, vol. 16, issue 1, 1-23

Abstract: 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 synapses within 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 semi-automatic analytical pipeline. The combined platform enables whole-cell mapping of total, cell-surface, intracellular, pre-existing, nascent or nascent-and-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.

Date: 2025
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DOI: 10.1038/s41467-025-65813-w

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