Evidence map›Paper›PMID 36313159›Full record

ArticleACS central science2022

Direct Identification of Proteolytic Cleavages on Living Cells Using a Glycan-Tethered Peptide Ligase.

Kaitlin Schaefer, Irene Lui, James R Byrnes, Emily Kang, Jie Zhou, Amy M Weeks, James A Wells

Abstract read
In one paragraph

Article in ACS central science, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.

0numbers the graph read from it
0cells of the map it votes in
13citing 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

13 citing papers in PubMed.

  1. Article
  2. Review
  3. Article
  4. Article
  5. Article
  6. Article
  7. Review
  8. Article
  9. A general approach for selection of epitope-directed binders to proteins.Proceedings of the National Academy of Sciences of the United States of America · 2024
    Article
  10. Article
  11. Article
  12. Engineered molecular sensors for quantifying cell surface crowding.Proceedings of the National Academy of Sciences of the United States of America · 2023
    Article
  13. 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

7 authors.

Kaitlin SchaeferDepartment of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158, United States.
Irene LuiDepartment of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158, United States.
James R ByrnesDepartment of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158, United States.
Emily KangDepartment of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158, United States.
Jie ZhouDepartment of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158, United States.
Amy M WeeksDepartment of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158, United States.ORCID https://orcid.org/0000-0003-4700-8256
James A WellsDepartment of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158, United States.ORCID https://orcid.org/0000-0001-8267-5519

Funding

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
NCI NIH HHS R01 CA248323
6 · The paper itself

Abstract

Proteolytic cleavage of cell surface proteins triggers critical processes including cell-cell interactions, receptor activation, and shedding of signaling proteins. Consequently, dysregulated extracellular proteases contribute to malignant cell phenotypes including most cancers. To understand these effects, methods are needed that identify proteolyzed membrane proteins within diverse cellular contexts. Herein we report a proteomic approach, called cell surface N-terminomics, to broadly identify precise cleavage sites (neo-N-termini) on the surface of living cells. First, we functionalized the engineered peptide ligase, called stabiligase, with an N-terminal nucleophile that enables covalent attachment to naturally occurring glycans. Upon the addition of a biotinylated peptide ester, glycan-tethered stabiligase efficiently tags extracellular neo-N-termini for proteomic analysis. To demonstrate the versatility of this approach, we identified and characterized 1532 extracellular neo-N-termini across a panel of different cell types including primary immune cells. The vast majority of cleavages were not identified by previous proteomic studies. Lastly, we demonstrated that single oncogenes,

Identifiers

PMID36313159
PMCPMC9615116

What Socratic holds

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LicenceCC BY
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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.