KEAP1 loss modulates sensitivity to kinase targeted therapy in lung cancer

  1. Elsa Beyer Krall
  2. Belinda Wang
  3. Diana M Munoz
  4. Nina Ilic
  5. Srivatsan Raghavan
  6. Matthew J Niederst
  7. Kristine Yu
  8. David A Ruddy
  9. Andrew J Aguirre
  10. Jong Wook Kim
  11. Amanda J Redig
  12. Justin F Gainor
  13. Juliet A Williams
  14. John M Asara
  15. John G Doench
  16. Pasi A Janne
  17. Alice T Shaw
  18. Robert E McDonald III
  19. Jeffrey A Engelman
  20. Frank Stegmeier
  21. Michael R Schlabach
  22. William C Hahn  Is a corresponding author
  1. KSQ Therapeutics, United States
  2. Dana-Farber Cancer Institute, United States
  3. Novartis Institute for Biomedical Research, United States
  4. Massachusetts General Hospital, United States
  5. Beth Israel Deaconess Medical Center, United States
  6. Broad Institute of Harvard and MIT, United States

Abstract

Inhibitors that target the receptor tyrosine kinase (RTK)/Ras/mitogen-activated protein kinase (MAPK) pathway have led to clinical responses in lung and other cancers, but some patients fail to respond and in those that do resistance inevitably occurs1-4. To understand intrinsic and acquired resistance to inhibition of MAPK signaling, we performed CRISPR-Cas9 gene deletion screens in the setting of BRAF, MEK, EGFR, and ALK inhibition. Loss of KEAP1, a negative regulator of NFE2L2/NRF2, modulated the response to BRAF, MEK, EGFR, and ALK inhibition in BRAF-, NRAS-, KRAS-, EGFR-, and ALK-mutant lung cancer cells. Treatment with inhibitors targeting the RTK/MAPK pathway increased reactive oxygen species (ROS) in cells with intact KEAP1, and loss of KEAP1 abrogated this increase. In addition, loss of KEAP1 altered cell metabolism to allow cells to proliferate in the absence of MAPK signaling. These observations suggest that alterations in the KEAP1/NRF2 pathway may promote survival in the presence of multiple inhibitors targeting the RTK/Ras/MAPK pathway.

Article and author information

Author details

  1. Elsa Beyer Krall

    KSQ Therapeutics, Cambridge, United States
    Competing interests
    No competing interests declared.
  2. Belinda Wang

    Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
    Competing interests
    No competing interests declared.
  3. Diana M Munoz

    Oncology Disease Area, Novartis Institute for Biomedical Research, Cambridge, United States
    Competing interests
    No competing interests declared.
  4. Nina Ilic

    Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
    Competing interests
    No competing interests declared.
  5. Srivatsan Raghavan

    Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
    Competing interests
    No competing interests declared.
  6. Matthew J Niederst

    Oncology Disease Area, Novartis Institute for Biomedical Research, Cambridge, United States
    Competing interests
    No competing interests declared.
  7. Kristine Yu

    Oncology Disease Area, Novartis Institute for Biomedical Research, Cambridge, United States
    Competing interests
    No competing interests declared.
  8. David A Ruddy

    Oncology Disease Area, Novartis Institute for Biomedical Research, Cambridge, United States
    Competing interests
    No competing interests declared.
  9. Andrew J Aguirre

    Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
    Competing interests
    No competing interests declared.
  10. Jong Wook Kim

    Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
    Competing interests
    No competing interests declared.
  11. Amanda J Redig

    Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
    Competing interests
    No competing interests declared.
  12. Justin F Gainor

    Department of Medicine, Massachusetts General Hospital, Boston, United States
    Competing interests
    No competing interests declared.
  13. Juliet A Williams

    Oncology Disease Area, Novartis Institute for Biomedical Research, Cambridge, United States
    Competing interests
    No competing interests declared.
  14. John M Asara

    Department of Medicine, Beth Israel Deaconess Medical Center, Boston, United States
    Competing interests
    No competing interests declared.
  15. John G Doench

    Broad Institute of Harvard and MIT, Cambridge, United States
    Competing interests
    No competing interests declared.
  16. Pasi A Janne

    Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
    Competing interests
    No competing interests declared.
  17. Alice T Shaw

    Department of Medicine, Massachusetts General Hospital, Boston, United States
    Competing interests
    No competing interests declared.
  18. Robert E McDonald III

    Oncology Disease Area, Novartis Institute for Biomedical Research, Cambridge, United States
    Competing interests
    No competing interests declared.
  19. Jeffrey A Engelman

    Oncology Disease Area, Novartis Institute for Biomedical Research, Cambridge, United States
    Competing interests
    No competing interests declared.
  20. Frank Stegmeier

    KSQ Therapeutics, Cambridge, United States
    Competing interests
    No competing interests declared.
  21. Michael R Schlabach

    KSQ Therapeutics, Cambridge, United States
    Competing interests
    No competing interests declared.
  22. William C Hahn

    Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, United States
    For correspondence
    william_hahn@dfci.harvard.edu
    Competing interests
    William C Hahn, A consultant and receives research support from Novartis.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2840-9791

Funding

National Cancer Institute (R01 CA130998)

  • William C Hahn

Dana-Farber Cancer Institute Hale Center for Pancreatic Cancer

  • Andrew J Aguirre

Perry S. Levy Endowed Fellowship

  • Andrew J Aguirre

Harvard Catalyst and Harvard Clinical and Translational Science Center (UL1 TR001102)

  • Andrew J Aguirre

National Cancer Institute (U01 CA176058)

  • William C Hahn

National Cancer Institute (U01 CA199253)

  • William C Hahn

Hope Funds for Cancer Research (Postdoctoral Fellowship HFCR-11-03-03)

  • Elsa Beyer Krall

National Institutes of Health (Postdoctoral Fellowship F32 CA189306)

  • Elsa Beyer Krall

Susan G. Komen Foundation (Postdoctoral Fellowship PDF12230602)

  • Nina Ilic

Terri Brodeur Breast Cancer Foundation (Postdoctoral Fellowship)

  • Nina Ilic

Pancreatic Cancer Action Network (Samuel Stroum Fellowship)

  • Andrew J Aguirre

American Society of Clinical Oncology (Young Investigator Award)

  • Andrew J Aguirre

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

Ethics

Animal experimentation: Mice were maintained and handled in accordance with the Novartis Institutes for Biomedical Research (NIBR) Animal Care and Use Committee protocols and regulations.

Reviewing Editor

  1. Martin McMahon, University of Utah Medical Schoo, United States

Publication history

  1. Received: June 21, 2016
  2. Accepted: January 31, 2017
  3. Accepted Manuscript published: February 1, 2017 (version 1)
  4. Version of Record published: February 13, 2017 (version 2)
  5. Version of Record updated: October 31, 2017 (version 3)

Copyright

© 2017, Krall 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. Elsa Beyer Krall
  2. Belinda Wang
  3. Diana M Munoz
  4. Nina Ilic
  5. Srivatsan Raghavan
  6. Matthew J Niederst
  7. Kristine Yu
  8. David A Ruddy
  9. Andrew J Aguirre
  10. Jong Wook Kim
  11. Amanda J Redig
  12. Justin F Gainor
  13. Juliet A Williams
  14. John M Asara
  15. John G Doench
  16. Pasi A Janne
  17. Alice T Shaw
  18. Robert E McDonald III
  19. Jeffrey A Engelman
  20. Frank Stegmeier
  21. Michael R Schlabach
  22. William C Hahn
(2017)
KEAP1 loss modulates sensitivity to kinase targeted therapy in lung cancer
eLife 6:e18970.
https://doi.org/10.7554/eLife.18970

Further reading

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    The transformation of normal to malignant cells is accompanied by substantial changes in gene expression programs through diverse mechanisms. Here, we examined the changes in the landscape of transcription start sites and alternative promoter (AP) usage and their impact on the translatome in TCL1-driven chronic lymphocytic leukemia (CLL). Our findings revealed a marked elevation of APs in CLL B cells from Eµ-Tcl1 transgenic mice, which are particularly enriched with intra-genic promoters that generate N-terminally truncated or modified proteins. Intra-genic promoter activation is mediated by (1) loss of function of ‘closed chromatin’ epigenetic regulators due to the generation of inactive N-terminally modified isoforms or reduced expression; (2) upregulation of transcription factors, including c-Myc, targeting the intra-genic promoters and their associated enhancers. Exogenous expression of Tcl1 in MEFs is sufficient to induce intra-genic promoters of epigenetic regulators and promote c-Myc expression. We further found a dramatic translation downregulation of transcripts bearing CNY cap-proximal trinucleotides, reminiscent of cells undergoing metabolic stress. These findings uncovered the role of Tcl1 oncogenic function in altering promoter usage and mRNA translation in leukemogenesis.