The CUL5 ubiquitin ligase complex mediates resistance to CDK9 and MCL1 inhibitors in lung cancer cells

  1. Shaheen Kabir
  2. Justin Cidado
  3. Courtney Andersen
  4. Cortni Dick
  5. Pei-Chun Lin
  6. Therese Mitros
  7. Hong Ma
  8. Seung Hyun Baik
  9. Matthew A Belmonte
  10. Lisa Drew
  11. Jacob E Corn  Is a corresponding author
  1. University of California, Berkeley, United States
  2. AstraZeneca, United States

Abstract

Overexpression of anti-apoptotic proteins MCL1 and Bcl-xL are frequently observed in many cancers. Inhibitors targeting MCL1 are in clinical development, however numerous cancer models are intrinsically resistant to this approach. To discover mechanisms underlying resistance to MCL1 inhibition, we performed multiple flow-cytometry based genome-wide CRISPR screens interrogating two drugs that directly (MCL1i) or indirectly (CDK9i) target MCL1. Remarkably, both screens identified three components (CUL5, RNF7 and UBE2F) of a cullin-RING ubiquitin ligase complex (CRL5) that resensitized cells to MCL1 inhibition. We find that levels of the BH3-only pro-apoptotic proteins Bim and Noxa are proteasomally regulated by the CRL5 complex. Accumulation of Noxa caused by depletion of CRL5 components was responsible for re-sensitization to CDK9 inhibitor, but not MCL1 inhibitor. Discovery of a novel role of CRL5 in apoptosis and resistance to multiple types of anti-cancer agents suggests the potential to improve combination treatments.

Data availability

Sequencing data is being deposited into SRA under accession code: SUB5033643

The following data sets were generated

Article and author information

Author details

  1. Shaheen Kabir

    Innovative Genomics Institute, University of California, Berkeley, Berkeley, United States
    Competing interests
    No competing interests declared.
  2. Justin Cidado

    IMED Oncology, AstraZeneca, Waltham, United States
    Competing interests
    Justin Cidado, employed by AstraZeneca, from whom funded research support was received..
  3. Courtney Andersen

    IMED Oncology, AstraZeneca, Waltham, United States
    Competing interests
    Courtney Andersen, employed by AstraZeneca, from whom funded research support was received..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-2064-2273
  4. Cortni Dick

    IMED Oncology, AstraZeneca, Waltham, United States
    Competing interests
    Cortni Dick, employed by AstraZeneca, from whom funded research support was received..
  5. Pei-Chun Lin

    Innovative Genomics Institute, University of California, Berkeley, Berkeley, United States
    Competing interests
    No competing interests declared.
  6. Therese Mitros

    Innovative Genomics Institute, University of California, Berkeley, Berkeley, United States
    Competing interests
    No competing interests declared.
  7. Hong Ma

    Innovative Genomics Institute, University of California, Berkeley, Berkeley, United States
    Competing interests
    No competing interests declared.
  8. Seung Hyun Baik

    Innovative Genomics Institute, University of California, Berkeley, Berkeley, United States
    Competing interests
    No competing interests declared.
  9. Matthew A Belmonte

    IMED Oncology, AstraZeneca, Waltham, United States
    Competing interests
    Matthew A Belmonte, employed by AstraZeneca, from whom funded research support was received..
  10. Lisa Drew

    IMED Oncology, AstraZeneca, Waltham, United States
    Competing interests
    Lisa Drew, employed by AstraZeneca, from whom funded research support was received..
  11. Jacob E Corn

    Innovative Genomics Institute, University of California, Berkeley, Berkeley, United States
    For correspondence
    jacob.corn@biol.ethz.ch
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7798-5309

Funding

AstraZeneca

  • Shaheen Kabir
  • Justin Cidado
  • Courtney Andersen
  • Cortni Dick
  • Pei-Chun Lin
  • Hong Ma
  • Matthew A Belmonte
  • Lisa Drew
  • Jacob E Corn

National Institutes of Health (DP2 HL141006)

  • Jacob E Corn

Li Ka Shing Foundation

  • Jacob E Corn

Heritage Medical Research Institute

  • Jacob E Corn

California Institute for Regenerative Medicine (DISC1-08776)

  • Shaheen Kabir
  • Seung Hyun Baik
  • Jacob E Corn

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

Reviewing Editor

  1. Michael R Green, Howard Hughes Medical Institute, University of Massachusetts Medical School, United States

Publication history

  1. Received: December 15, 2018
  2. Accepted: July 5, 2019
  3. Accepted Manuscript published: July 11, 2019 (version 1)
  4. Version of Record published: August 20, 2019 (version 2)
  5. Version of Record updated: October 7, 2019 (version 3)

Copyright

© 2019, Kabir 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.

Metrics

  • 3,921
    Page views
  • 710
    Downloads
  • 13
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Shaheen Kabir
  2. Justin Cidado
  3. Courtney Andersen
  4. Cortni Dick
  5. Pei-Chun Lin
  6. Therese Mitros
  7. Hong Ma
  8. Seung Hyun Baik
  9. Matthew A Belmonte
  10. Lisa Drew
  11. Jacob E Corn
(2019)
The CUL5 ubiquitin ligase complex mediates resistance to CDK9 and MCL1 inhibitors in lung cancer cells
eLife 8:e44288.
https://doi.org/10.7554/eLife.44288

Further reading

    1. Cancer Biology
    2. Computational and Systems Biology
    Jonathan Rodriguez, Abdon Iniguez ... Richard A Van Etten
    Research Article Updated

    Chronic myeloid leukemia (CML) is a blood cancer characterized by dysregulated production of maturing myeloid cells driven by the product of the Philadelphia chromosome, the BCR-ABL1 tyrosine kinase. Tyrosine kinase inhibitors (TKIs) have proved effective in treating CML, but there is still a cohort of patients who do not respond to TKI therapy even in the absence of mutations in the BCR-ABL1 kinase domain that mediate drug resistance. To discover novel strategies to improve TKI therapy in CML, we developed a nonlinear mathematical model of CML hematopoiesis that incorporates feedback control and lineage branching. Cell–cell interactions were constrained using an automated model selection method together with previous observations and new in vivo data from a chimeric BCR-ABL1 transgenic mouse model of CML. The resulting quantitative model captures the dynamics of normal and CML cells at various stages of the disease and exhibits variable responses to TKI treatment, consistent with those of CML patients. The model predicts that an increase in the proportion of CML stem cells in the bone marrow would decrease the tendency of the disease to respond to TKI therapy, in concordance with clinical data and confirmed experimentally in mice. The model further suggests that, under our assumed similarities between normal and leukemic cells, a key predictor of refractory response to TKI treatment is an increased maximum probability of self-renewal of normal hematopoietic stem cells. We use these insights to develop a clinical prognostic criterion to predict the efficacy of TKI treatment and design strategies to improve treatment response. The model predicts that stimulating the differentiation of leukemic stem cells while applying TKI therapy can significantly improve treatment outcomes.

    1. Cancer Biology
    2. Cell Biology
    Katarzyna Bogucka-Janczi, Gregory Harms ... Krishnaraj Rajalingam
    Research Advance Updated

    The actin cytoskeleton is tightly controlled by RhoGTPases, actin binding-proteins and nucleation-promoting factors to perform fundamental cellular functions. We have previously shown that ERK3, an atypical MAPK, controls IL-8 production and chemotaxis (Bogueka et al., 2020). Here, we show in human cells that ERK3 directly acts as a guanine nucleotide exchange factor for CDC42 and phosphorylates the ARP3 subunit of the ARP2/3 complex at S418 to promote filopodia formation and actin polymerization, respectively. Consistently, depletion of ERK3 prevented both basal and EGF-dependent RAC1 and CDC42 activation, maintenance of F-actin content, filopodia formation, and epithelial cell migration. Further, ERK3 protein bound directly to the purified ARP2/3 complex and augmented polymerization of actin in vitro. ERK3 kinase activity was required for the formation of actin-rich protrusions in mammalian cells. These findings unveil a fundamentally unique pathway employed by cells to control actin-dependent cellular functions.