Time resolved phosphoproteomics reveals scaffolding and catalysis-responsive patterns of SHP2-dependent signaling

  1. Vidyasiri Vemulapalli
  2. Lily A Chylek
  3. Alison Erickson
  4. Anamarija Pfeiffer
  5. Khal-Hentz Gabriel
  6. Jonathan LaRochelle
  7. Kartik Subramanian
  8. Ruili Cao
  9. Kimberley Stegmaier
  10. Morvarid Mohseni
  11. Matthew J LaMarche
  12. Michael G Acker
  13. Peter K Sorger
  14. Steven P Gygi
  15. Stephen C Blacklow  Is a corresponding author
  1. Harvard Medical School, United States
  2. Novo Nordisk Foundation and University of Copenhagen, Denmark
  3. Broad Institute of Harvard and MIT, United States
  4. Novartis Institutes for Biomedical Research, United States

Abstract

SHP2 is a protein tyrosine phosphatase that normally potentiates intracellular signaling by growth factors, antigen receptors, and some cytokines, yet is frequently mutated in human cancer. Here, we examine the role of SHP2 in the responses of breast cancer cells to EGF by monitoring phosphoproteome dynamics when SHP2 is allosterically inhibited by SHP099. The dynamics of phosphotyrosine abundance at more than 400 tyrosine residues reveal six distinct response signatures following SHP099 treatment and washout. Remarkably, in addition to newly identified substrate sites on proteins such as occludin, ARHGAP35, and PLCγ2, another class of sites shows reduced phosphotyrosine abundance upon SHP2 inhibition. Sites of decreased phospho-abundance are enriched on proteins with two nearby phosphotyrosine residues, which can be directly protected from dephosphorylation by the paired SH2 domains of SHP2 itself. These findings highlight the distinct roles of the scaffolding and catalytic activities of SHP2 in effecting a transmembrane signaling response.

Data availability

Quantitative proteomics data have been deposited in the mass spectrometry interactive virtual environment (MassIVE) database with the accession code MSV000083702. All other data generated in this study are in the manuscript and supporting files.

The following data sets were generated

Article and author information

Author details

  1. Vidyasiri Vemulapalli

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
    Competing interests
    No competing interests declared.
  2. Lily A Chylek

    Systems Biology, Harvard Medical School, Boston, United States
    Competing interests
    No competing interests declared.
  3. Alison Erickson

    Cell Biology, Harvard Medical School, Boston, United States
    Competing interests
    No competing interests declared.
  4. Anamarija Pfeiffer

    Center for Protein Research, Novo Nordisk Foundation and University of Copenhagen, Copenhagen, Denmark
    Competing interests
    No competing interests declared.
  5. Khal-Hentz Gabriel

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
    Competing interests
    No competing interests declared.
  6. Jonathan LaRochelle

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
    Competing interests
    No competing interests declared.
  7. Kartik Subramanian

    Department of Systems Biology, Harvard Medical School, Boston, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6900-8882
  8. Ruili Cao

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
    Competing interests
    No competing interests declared.
  9. Kimberley Stegmaier

    Broad Institute of Harvard and MIT, Cambridge, United States
    Competing interests
    No competing interests declared.
  10. Morvarid Mohseni

    Oncology, Novartis Institutes for Biomedical Research, Cambridge, United States
    Competing interests
    Morvarid Mohseni, Novartis employee while this work was performed..
  11. Matthew J LaMarche

    Global Discovery Chemistry, Novartis Institutes for Biomedical Research, Cambridge, United States
    Competing interests
    Matthew J LaMarche, Novartis employee while this work was performed..
  12. Michael G Acker

    Oncology, Novartis Institutes for Biomedical Research, Cambridge, United States
    Competing interests
    Michael G Acker, Novartis employee while this work was performed..
  13. Peter K Sorger

    HMS LINCS Center, Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3364-1838
  14. Steven P Gygi

    Department of Cell Biology, Harvard Medical School, Boston, United States
    Competing interests
    No competing interests declared.
  15. Stephen C Blacklow

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
    For correspondence
    stephen_blacklow@hms.harvard.edu
    Competing interests
    Stephen C Blacklow, SCB receives research funding for this project from Novartis, is a member of the SAB of Erasca, Inc., is an advisor to MPM Capital, and is a consultant on unrelated projects for IFM, Scorpion Therapeutics, and Ayala Therapeutics..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6904-1981

Funding

Novartis Institutes for BioMedical Research

  • Vidyasiri Vemulapalli
  • Khal-Hentz Gabriel
  • Jonathan LaRochelle
  • Kimberley Stegmaier
  • Stephen C Blacklow

National Cancer Institute (R35 CA220340)

  • Stephen C Blacklow

National Heart, Lung, and Blood Institute (U54-HL127365)

  • Lily A Chylek
  • Peter K Sorger

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Jonathan A Cooper, Fred Hutchinson Cancer Research Centre, United States

Version history

  1. Received: October 23, 2020
  2. Accepted: March 21, 2021
  3. Accepted Manuscript published: March 23, 2021 (version 1)
  4. Version of Record published: April 6, 2021 (version 2)

Copyright

© 2021, Vemulapalli et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Vidyasiri Vemulapalli
  2. Lily A Chylek
  3. Alison Erickson
  4. Anamarija Pfeiffer
  5. Khal-Hentz Gabriel
  6. Jonathan LaRochelle
  7. Kartik Subramanian
  8. Ruili Cao
  9. Kimberley Stegmaier
  10. Morvarid Mohseni
  11. Matthew J LaMarche
  12. Michael G Acker
  13. Peter K Sorger
  14. Steven P Gygi
  15. Stephen C Blacklow
(2021)
Time resolved phosphoproteomics reveals scaffolding and catalysis-responsive patterns of SHP2-dependent signaling
eLife 10:e64251.
https://doi.org/10.7554/eLife.64251

Share this article

https://doi.org/10.7554/eLife.64251

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