Evidence map›Paper›PMID 39024454›Full record

ArticleScience (New York, N.Y.)2024

Multiscale photocatalytic proximity labeling reveals cell surface neighbors on and between cells.

Zhi Lin, Kaitlin Schaefer, Irene Lui, Zi Yao, Andrea Fossati, Danielle L Swaney, Ajikarunia Palar, Andrej Sali, James A Wells

Abstract read
In one paragraph

Article in Science (New York, N.Y.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.

0numbers the graph read from it
0cells of the map it votes in
79citing 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

79 citing papers in PubMed.

  1. Review
  2. Article
  3. Review
  4. Review
  5. Article
  6. Lighting up lipid droplets.Nature chemical biology · 2026
    Article
  7. Chemical Biology 2025: Highlights From the Ch/Bi145 Course at Caltech.Chembiochem : a European journal of chemical biology · 2026
    Review
  8. Article
  9. Review
  10. Review
  11. Review
  12. AbioRxiv : the preprint server for biology · 2026
    Article
  13. Article
  14. Article
  15. Article
  16. HNature chemical biology · 2026
    Article
  17. Article
  18. Article
  19. Article
  20. Article

19 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

9 authors.

Zhi LinDepartment of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.ORCID 0000-0001-6662-7330
Kaitlin SchaeferDepartment of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.ORCID 0000-0003-4825-1389
Irene LuiDepartment of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.ORCID 0000-0002-6171-5443
Zi YaoDepartment of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.
Andrea FossatiDepartment of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.ORCID 0000-0001-5170-4903
Danielle L SwaneyDepartment of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.ORCID 0000-0001-6119-6084
Ajikarunia PalarDepartment of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.ORCID 0000-0001-9357-6970
Andrej SaliDepartment of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.ORCID 0000-0003-0435-6197
James A WellsDepartment of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA.ORCID 0000-0001-8267-5519

Funding

Translational InformaticsP30CA082103 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Alan Ashworth · 1999 to 2026
$209.7M
RESEARCH PROJECT 2U19AI135990 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI ANDREJ SALI · 2018 to 2026
$21.4M
TR&D Project 4. The Imaging Stage: Multiscale Spatiotemporal Modeling of Macromolecular Systems in Cellular NeighborhoodsP41GM109824 · NIGMS · ROCKEFELLER UNIVERSITY · PI ROUT, MICHAEL P · 2014 to 2023
$18.8M
Surfaceomic technologies and antibodies to probe cell surface proteomes and their interactomes at unprecedented small scale and high-resolutionR35GM122451 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI JAMES A WELLS · 2017 to 2026
$5.3M
IMP: Software for Hybrid Determination of Macromolecular Assembly StructuresR01GM083960 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI SALI, ANDREJ · 2008 to 2024
$5.2M
New protein engineering-based tools and technologies for characterizing cell surface proteolysis in cancer cells for novel neo-epitope biomarkers and drug targetsR01CA248323 · NCI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI JAMES A WELLS · 2020 to 2026
$2.6M
Molecular Biophysics Training GrantT32GM149436 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Aashish Manglik · 2023 to 2026
$1.6M
Mapping tumor specific immunopeptidome for antibody-based targeted therapyF32GM149084 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI YAO, ZI · 2023 to 2024
$143k
NCI NIH HHS P30 CA082103NCI NIH HHS R01 CA248323NIAID NIH HHS U19 AI135990NIGMS NIH HHS F32 GM149084NIGMS NIH HHS P41 GM109824NIGMS NIH HHS R01 GM083960NIGMS NIH HHS R35 GM122451
6 · The paper itself

Abstract

Proximity labeling proteomics (PLP) strategies are powerful approaches to yield snapshots of protein neighborhoods. Here, we describe a multiscale PLP method with adjustable resolution that uses a commercially available photocatalyst, Eosin Y, which upon visible light illumination activates different photo-probes with a range of labeling radii. We applied this platform to profile neighborhoods of the oncogenic epidermal growth factor receptor and orthogonally validated more than 20 neighbors using immunoassays and AlphaFold-Multimer prediction. We further profiled the protein neighborhoods of cell-cell synapses induced by bispecific T cell engagers and chimeric antigen receptor T cells. This integrated multiscale PLP platform maps local and distal protein networks on and between cell surfaces, which will aid in the systematic construction of the cell surface interactome, revealing horizontal signaling partners and reveal new immunotherapeutic opportunities.

Indexed as

Eosine Yellowish-(YS)Fluorescent DyesProteomicsStaining and LabelingCatalysisCell MembraneErbB ReceptorsHumansLightPhotochemical ProcessesProtein Interaction MapsReceptors, Chimeric AntigenT-LymphocytesEGFR protein, humanEosine Yellowish-(YS)ErbB ReceptorsFluorescent DyesReceptors, Chimeric Antigen

Identifiers

PMID39024454
PMCPMC12517702

What Socratic holds

Textmetadata
LicenceTDM
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 Socratic graph.