Evidence map›Paper›PMID 30190427›Full record

ArticleProceedings of the National Academy of Sciences of the United States of America2018

Photoaffinity-engineered protein scaffold for systematically exploring native phosphotyrosine signaling complexes in tumor samples.

Bizhu Chu, An He, Yeteng Tian, Wan He, Peizhong Chen, Jintao Hu, Ruilian Xu, Wenbin Zhou, Mingjie Zhang, Pengyuan Yang and 5 more

Open access · bronzeAbstract readValidation Study
PubMed Full text at PMC Publisher
In one paragraph

Article in Proceedings of the National Academy of Sciences of the United States of America, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.

0numbers the graph read from it
0cells of the map it votes in
11citing papers in PubMed
1.4field-weighted citation impact, top 17% of its field
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

11 citing papers in PubMed, 23 citations in OpenAlex.

  1. Review
  2. Article
  3. Article
  4. Review
  5. Article
  6. Review
  7. Article
  8. Functional and Clinical Proteomic Exploration of Pancreatic Cancer.Molecular & cellular proteomics : MCP · 2023
    Review
  9. Article
  10. [Advances in high-throughput proteomic analysis].Se pu = Chinese journal of chromatography · 2021
    Review
  11. Article
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

15 authors at 6 institutions in 4 countries.

Bizhu ChuDepartment of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China.
An HeDepartment of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China.
Yeteng TianDepartment of Biology, Southern University of Science and Technology, Shenzhen 518055, China.
Wan HeDepartment of Oncology, The Second Clinical Medical College, Shenzhen People's Hospital, Jinan University, Shenzhen 518020, China.
Peizhong ChenDepartment of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China.
Jintao HuDepartment of Pathology, The Second Clinical Medical College, Shenzhen People's Hospital, Jinan University, Shenzhen 518020, China.
Ruilian XuDepartment of Oncology, The Second Clinical Medical College, Shenzhen People's Hospital, Jinan University, Shenzhen 518020, China.
Wenbin ZhouDepartment of Oncology, The Second Clinical Medical College, Shenzhen People's Hospital, Jinan University, Shenzhen 518020, China.
Mingjie ZhangDivision of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.
Pengyuan YangDepartment of Chemistry, Fudan University, Shanghai 200433, China.
Shawn S C LiDepartment of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada.
Ying SunDepartment of Biology, Southern University of Science and Technology, Shenzhen 518055, China; tian.rj@sustc.edu.cn lipf@sustc.edu.cn suny@sustc.edu.cn.
Pengfei LiDepartment of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China; tian.rj@sustc.edu.cn lipf@sustc.edu.cn suny@sustc.edu.cn.
Tony HunterMolecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037.
Ruijun TianDepartment of Chemistry, Southern University of Science and Technology, Shenzhen 518055, China; tian.rj@sustc.edu.cn lipf@sustc.edu.cn suny@sustc.edu.cn.
Southern University of Science and Technology · CNJinan University · CNFudan University · CNHong Kong University of Science and Technology · HKSalk Institute for Biological Studies · USWestern University · CA

Funding

Viral Vector Core (VVC)P30CA014195 · NCI · SALK INSTITUTE FOR BIOLOGICAL STUDIES · PI Ye Zheng · 1985 to 2026
$82.8M
NCI NIH HHS P30 CA014195
6 · The paper itself

Abstract

Phosphotyrosine (pTyr)-regulated protein complexes play critical roles in cancer signaling. The systematic characterization of these protein complexes in tumor samples remains a challenge due to their limited access and the transient nature of pTyr-mediated interactions. We developed a hybrid chemical proteomics approach, termed Photo-pTyr-scaffold, by engineering Src homology 2 (SH2) domains, which specifically bind pTyr proteins, with both trifunctional chemical probes and genetic mutations to overcome these challenges. Dynamic SH2 domain-scaffolding protein complexes were efficiently cross-linked under mild UV light, captured by biotin tag, and identified by mass spectrometry. This approach was successfully used to profile native pTyr protein complexes from breast cancer tissue samples on a proteome scale with high selectivity, achieving about 100 times higher sensitivity for detecting pTyr signaling proteins than that afforded by traditional immunohistochemical methods. Among more than 1,000 identified pTyr proteins, receptor tyrosine kinase PDGFRB expressed on cancer-associated fibroblasts was validated as an important intercellular signaling regulator with poor expression correlation to ERBB2, and blockade of PDGFRB signaling could efficiently suppress tumor growth. The Photo-pTyr-scaffold approach may become a generic tool for readily profiling dynamic pTyr signaling complexes in clinically relevant samples.

Indexed as

AnimalsBenzimidazolesBiomarkers, TumorBreast NeoplasmsCancer-Associated FibroblastsCell Line, TumorErb-b2 Receptor Tyrosine KinasesFemaleHumansMammary Tumor Virus, MouseMass SpectrometryMice, TransgenicPhosphorylationPhosphotyrosinePiperidinesProtein BindingBenzimidazolesBiomarkers, TumorcrenolanibERBB2 protein, humanErb-b2 Receptor Tyrosine KinasesPDGFRB protein, humanPhosphotyrosinePiperidinesReceptor, Platelet-Derived Growth Factor betacancerphosphotyrosine signalingprotein complexprotein labelingproteomics

Identifiers

PMID30190427
PMCPMC6156637
OpenAlexW2891785578

What OpenQuestion holds

Textmetadata
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.