Evidence map›Paper›PMID 39105364›Full record

ArticleJournal of materials chemistry. B2024

Proximity labeling expansion microscopy (PL-ExM) evaluates interactome labeling techniques.

Sohyeon Park, Xiaorong Wang, Yajin Mo, Sicheng Zhang, Xiangpeng Li, Katie C Fong, Clinton Yu, Arthur A Tran, Lorenzo Scipioni, Zhipeng Dai and 3 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of materials chemistry. B, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Review
  2. Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

13 authors.

Sohyeon ParkCenter for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA. xiaoyu.shi@uci.edu.
Xiaorong WangPhysiology and Biophysics, University of California, Irvine, Irvine, CA 92697, USA.
Yajin MoCenter for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA. xiaoyu.shi@uci.edu.
Sicheng ZhangDepartment of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA.ORCID http://orcid.org/0000-0003-2451-8587
Xiangpeng LiDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA.ORCID http://orcid.org/0000-0002-4230-5676
Katie C FongDepartment of Developmental and Cell Biology, University of California, Irvine, Irvine, CA 92697, USA.
Clinton YuPhysiology and Biophysics, University of California, Irvine, Irvine, CA 92697, USA.
Arthur A TranCardiovascular Research Institute, School of Medicine, University of California, San Francisco, San Francisco 94143, USA.
Lorenzo ScipioniLaboratory for Fluorescence Dynamics, University of California, Irvine, Irvine, CA 92697, USA.
Zhipeng DaiDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA.
Xiao HuangSchool of Biomedical Engineering, Science and Health Systems, Drexel University, Philadelphia, PA 19104, USA.
Lan HuangPhysiology and Biophysics, University of California, Irvine, Irvine, CA 92697, USA.
Xiaoyu ShiCenter for Complex Biological Systems, University of California, Irvine, Irvine, CA 92697, USA. xiaoyu.shi@uci.edu.ORCID http://orcid.org/0000-0002-9634-2659

Funding

Univ.of Calif., Irvine Cancer Center Support GrantP30CA062203 · NCI · UNIVERSITY OF CALIFORNIA-IRVINE · PI Melanie Funes · 1994 to 2026
$57.9M
Supplement: Advancing Proteomics Technologies to Decipher the Ubiquitin-Proteasome SystemR35GM145249 · NIGMS · UNIVERSITY OF CALIFORNIA-IRVINE · PI Lan Huang · 2022 to 2026
$3.2M
Gel-based Optical-isolation Single-Cell 3D Spatial MultiomicsDP2GM150017 · NIGMS · UNIVERSITY OF CALIFORNIA-IRVINE · PI SHI, XIAOYU · 2022 to 2025
$2.6M
Elucidating How Primary Cilia Regulate Hedgehog Signaling by Super-Resolution MicroscopyR00GM126136 · NIGMS · UNIVERSITY OF CALIFORNIA-IRVINE · PI SHI, XIAOYU · 2020 to 2022
$746k
NCI NIH HHS P30 CA062203NIGMS NIH HHS DP2 GM150017NIGMS NIH HHS R00 GM126136NIGMS NIH HHS R35 GM145249
6 · The paper itself

Abstract

Understanding protein-protein interactions (PPIs) through proximity labeling has revolutionized our comprehension of cellular mechanisms and pathology. Various proximity labeling techniques, such as HRP, APEX, BioID, TurboID, and μMap, have been widely used to biotinylate PPIs or organelles for proteomic profiling. However, the variability in labeling precision and efficiency of these techniques often results in limited reproducibility in proteomic detection. We address this persistent challenge by introducing proximity labeling expansion microscopy (PL-ExM), a super-resolution imaging technique that combines expansion microscopy with proximity labeling techniques. PL-ExM enabled up to 17 nm resolution with microscopes widely available, providing visual comparison of the labeling precision, efficiency, and false positives of different proximity labeling methods. Our mass spectrometry proteomic results confirmed that PL-ExM imaging is reliable in guiding the selection of proximity labeling techniques and interpreting the proteomic results with new spatial information.

Indexed as

ProteomicsHumansMicroscopyProtein Interaction MappingProteinsStaining and LabelingProteins

Identifiers

PMID39105364
PMCPMC11426358

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.