Genome-wide CRISPR screening reveals genetic modifiers of mutant EGFR dependence in human NSCLC

  1. Hao Zeng  Is a corresponding author
  2. Johnny Castillo-Cabrera
  3. Mika Manser
  4. Bo Lu
  5. Zinger Yang
  6. Vaik Strande
  7. Damien Begue
  8. Raffaella Zamponi
  9. Shumei Qiu
  10. Frederic Sigoillot
  11. Qiong Wang
  12. Alicia Lindeman
  13. John S Reece-Hoyes
  14. Carsten Russ
  15. Debora Bonenfant
  16. Xiaomo Jiang
  17. Youzhen Wang
  18. Feng Cong  Is a corresponding author
  1. Novartis Institutes for BioMedical Research, United States
  2. Novartis Institutes for BioMedical Research, Switzerland

Abstract

EGFR-mutant NSCLCs frequently respond to EGFR tyrosine kinase inhibitors (TKIs). However, the responses are not durable, and the magnitude of tumor regression is variable, suggesting the existence of genetic modifiers of EGFR dependency. Here, we applied a genome-wide CRISPR-Cas9 screening to identify genetic determinants of EGFR TKI sensitivity and uncovered putative candidates. We show that knockout of RIC8A, essential for G-alpha protein activation, enhanced EGFR TKI-induced cell death. Mechanistically, we demonstrate that RIC8A is a positive regulator of YAP signaling, activation of which rescued the EGFR TKI sensitizing phenotype resulting from RIC8A knockout. We also show that knockout of ARIH2, or other components in the Cullin-5 E3 complex, conferred resistance to EGFR inhibition, in part by promoting nascent protein synthesis through METAP2. Together, these data uncover a spectrum of previously unidentified regulators of EGFR TKI sensitivity in EGFR-mutant human NSCLC, providing insights into the heterogeneity of EGFR TKI treatment responses.

Data availability

The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD014198. CRISPR-Cas9 screen data were summarized in Supplementary File 1 and Supplementary File 2.

The following data sets were generated

Article and author information

Author details

  1. Hao Zeng

    Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, United States
    For correspondence
    hao-1.zeng@novartis.com
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4967-9555
  2. Johnny Castillo-Cabrera

    Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Mika Manser

    Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Bo Lu

    Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Zinger Yang

    Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8543-4841
  6. Vaik Strande

    Analytical Sciences and Imaging, Novartis Institutes for BioMedical Research, Basel, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  7. Damien Begue

    Analytical Sciences and Imaging, Novartis Institutes for BioMedical Research, Basel, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  8. Raffaella Zamponi

    Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Shumei Qiu

    Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  10. Frederic Sigoillot

    Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  11. Qiong Wang

    Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  12. Alicia Lindeman

    Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  13. John S Reece-Hoyes

    Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  14. Carsten Russ

    Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  15. Debora Bonenfant

    Analytical Sciences and Imaging, Novartis Institutes for BioMedical Research, Basel, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  16. Xiaomo Jiang

    Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  17. Youzhen Wang

    Oncology Disease Area, Novartis Institutes for BioMedical Research, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  18. Feng Cong

    Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research, Cambridge, United States
    For correspondence
    feng.cong@novartis.com
    Competing interests
    The authors declare that no competing interests exist.

Funding

No external funding was received for this work.

Ethics

Animal experimentation: All animal work was performed in accordance with Novartis Animal Care and Use Committee (ACUC) regulations and guidelines (reference number 120137). All animals were allowed to acclimate in the Novartis animal facility with access to food and water ad libitum for 3 days prior to manipulation. All cell lines were confirmed as mycoplasma- and rodent pathogens-negative (IMPACT VIII PCR Profile, IDEXX) before implantation.

Reviewing Editor

  1. William C. Hahn, Dana-Farber Cancer Institue, United States

Publication history

  1. Received: July 16, 2019
  2. Accepted: November 4, 2019
  3. Accepted Manuscript published: November 19, 2019 (version 1)
  4. Version of Record published: December 23, 2019 (version 2)

Copyright

© 2019, Zeng 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. Hao Zeng
  2. Johnny Castillo-Cabrera
  3. Mika Manser
  4. Bo Lu
  5. Zinger Yang
  6. Vaik Strande
  7. Damien Begue
  8. Raffaella Zamponi
  9. Shumei Qiu
  10. Frederic Sigoillot
  11. Qiong Wang
  12. Alicia Lindeman
  13. John S Reece-Hoyes
  14. Carsten Russ
  15. Debora Bonenfant
  16. Xiaomo Jiang
  17. Youzhen Wang
  18. Feng Cong
(2019)
Genome-wide CRISPR screening reveals genetic modifiers of mutant EGFR dependence in human NSCLC
eLife 8:e50223.
https://doi.org/10.7554/eLife.50223

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