Single-cell synaptome mapping of endogenous protein subpopulations in mammalian brain
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.
Authors
- Masamichi Isogai (ORCID: https://orcid.org/0000-0002-3095-6439)
- Motokazu Uchigashima (ORCID: https://orcid.org/0000-0002-0878-2233)
- Chiaki Hoshino
- Luke D. Lavis (ORCID: https://orcid.org/0000-0002-0789-6343)
- Pratik Kumar (ORCID: https://orcid.org/0000-0002-9516-0212)
- Kenji Sakimura (ORCID: https://orcid.org/0000-0002-8091-8879)
- Motohiro Nozumi (ORCID: https://orcid.org/0000-0001-5972-2719)
- Yosuke Okamura (ORCID: https://orcid.org/0000-0002-8811-9377)
- Ryoma Bise (ORCID: https://orcid.org/0000-0002-2214-6719)
- Risa Iguchi (ORCID: https://orcid.org/0000-0002-4839-0808)
- Manabu Abe (ORCID: https://orcid.org/0000-0001-8534-2138)
- Takayasu Mikuni (ORCID: https://orcid.org/0000-0002-9769-9369)
- Michihiro Igarashi (ORCID: https://orcid.org/0000-0003-1474-3385)
- Kaito Shiku (ORCID: https://orcid.org/0009-0000-9675-9502)
- Xin-Yi Liu (ORCID: https://orcid.org/0000-0003-2722-4795)
- Kenichi Fujii
Institutions
- Tokai University (JP)
- Howard Hughes Medical Institute (US)
- Kyushu University (JP)
- Janelia Research Campus (US)
- International University of Japan (JP)
- Niigata University (JP)
- The University of Tokyo (JP)
Publication Details
- Journal
- Nature Communications
- Published
- 2025-11-11
- DOI
- https://doi.org/10.1038/s41467-025-65813-w
- Citations
- 2
- Primary Topic
- Biotin and Related Studies
- Type
- article
- Field-Weighted Citation Impact
- 2.30
Funders
- Howard Hughes Medical Institute
- Japan Agency for Medical Research and Development
- Brain Science Foundation
- Kowa Company
- Kowa Life Science Foundation
- Toray Science Foundation
- Japan Society for the Promotion of Science
- Japan Science and Technology Agency