Evidence map›Paper›PMID 41219189›Full record

ArticleNature communications2025

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 and 6 more

Abstract read
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

16 authors.

Motokazu UchigashimaDepartment of Cellular Neuropathology, Brain Research Institute, Niigata University, Niigata, Japan. uchigashima@bri.niigata-u.ac.jp.ORCID http://orcid.org/0000-0002-0878-2233
Risa IguchiDepartment of Cellular Neuropathology, Brain Research Institute, Niigata University, Niigata, Japan.ORCID http://orcid.org/0000-0002-4839-0808
Kazuma FujiiDepartment of Advanced Information Technology, Faculty of Information Science and Electrical Engineering, Kyushu University, Fukuoka, Japan.
Kaito ShikuDepartment of Advanced Information Technology, Faculty of Information Science and Electrical Engineering, Kyushu University, Fukuoka, Japan.ORCID http://orcid.org/0009-0000-9675-9502
Pratik KumarJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.ORCID http://orcid.org/0000-0002-9516-0212
Xinyi LiuDepartment of Cellular Neuropathology, Brain Research Institute, Niigata University, Niigata, Japan.
Mari IsogaiDepartment of Cellular Neuropathology, Brain Research Institute, Niigata University, Niigata, Japan.
Chiaki HoshinoDepartment of Cellular Neuropathology, Brain Research Institute, Niigata University, Niigata, Japan.
Manabu AbeDepartment of Animal Model Development, Brain Research Institute, Niigata University, Niigata, Japan.ORCID http://orcid.org/0000-0001-8534-2138
Motohiro NozumiDepartment of Neurochemistry and Molecular Cell Biology, School of Medicine, and Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan.ORCID http://orcid.org/0000-0001-5972-2719
Yosuke OkamuraDepartment of Applied Chemistry, School of Engineering, Tokai University, Hiratsuka, Kanagawa, Japan.
Michihiro IgarashiDepartment of Neurochemistry and Molecular Cell Biology, School of Medicine, and Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan.ORCID http://orcid.org/0000-0003-1474-3385
Kenji SakimuraDepartment of Animal Model Development, Brain Research Institute, Niigata University, Niigata, Japan.
Ryoma BiseDepartment of Advanced Information Technology, Faculty of Information Science and Electrical Engineering, Kyushu University, Fukuoka, Japan.
Luke D LavisJanelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.ORCID http://orcid.org/0000-0002-0789-6343
Takayasu MikuniDepartment of Cellular Neuropathology, Brain Research Institute, Niigata University, Niigata, Japan. tmikuni@bri.niigata-u.ac.jp.ORCID http://orcid.org/0000-0002-9769-9369

Funding

Human Frontier Science Program (HFSP) CDA00043/2019-CJapan Agency for Medical Research and Development (AMED) JP19dm0207080, JP21wm0525014, and JP24wm0625117Kowa Life Science Foundation N/AMEXT | Japan Science and Technology Agency (JST) JPMJFR231MMEXT | Japan Society for the Promotion of Science (JSPS) JP20K21461, JP20H03349, JP20H05918, JP23K18160, and JP24K02130MEXT | JST | Precursory Research for Embryonic Science and Technology (PRESTO) JPMJPR16F9Uehara Memorial Foundation N/A
6 · The paper itself

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.

Indexed as

BrainNeuronsSingle-Cell AnalysisSynapsesAnimalsCRISPR-Cas SystemsMiceMice, Inbred C57BL

Identifiers

PMID41219189
PMCPMC12606364

What OpenQuestion holds

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LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.