Abstract

The Fbw7 ubiquitin ligase targets many proteins for proteasomal degradation, which include oncogenic transcription factors (TFs) (e.g., c-Myc, c-Jun, Notch). Fbw7 is a tumor suppressor and tumors often contain mutations in FBXW7, the gene that encodes Fbw7. The complexity of its substrate network has obscured the mechanisms of Fbw7-associated tumorigenesis, yet this understanding is needed for developing therapies. We used an integrated approach employing RNA-Seq and high-resolution mapping (CUT&RUN) of histone modifications and TF occupancy (c-Jun and c-Myc) to examine the combinatorial effects of mis-regulated Fbw7 substrates in colorectal cancer cells with engineered tumor-associated FBXW7 null or missense mutations. Both Fbw7 mutations caused widespread transcriptional changes associated with active chromatin and altered TF occupancy: some were common to both Fbw7 mutant cell lines, whereas others were mutation specific. We identified loci where both Jun and Myc were co-regulated by Fbw7, suggesting that substrates may have synergistic effects. One co-regulated gene was CIITA, the master regulator of MHC Class II gene expression. Fbw7 loss increased MHC Class II expression and Fbw7 mutations were correlated with increased CIITA expression in TCGA colorectal tumors and cell lines, which may have immunotherapeutic implications for Fbw7-associated cancers. Analogous studies in neural stem cells in which FBXW7 had been acutely deleted closely mirrored the results in colorectal cancer cells. Gene set enrichment analyses revealed Fbw7-asssociated pathways that were conserved across both cell types that may reflect fundamental Fbw7 functions. These analyses provide a framework for understanding normal and neoplastic context specific Fbw7 functions.

Data availability

- RNA-Seq and CUT&RUN sequencing data have been deposited in GEO under accession code GSE184041. Secure access token: cdmhkumwvtovbqn- All data generated or analyzed during the study are included in the manuscript and supporting files. Supplement figures are included as a separate PDF. Source Data files have been provided for Figures 1, 2, 3, 5 and 6. List of source data with a brief description can be found at the end of the manuscript.- Computational tools used in the study are mentioned in the Materials and Methods section. Code used are available at https://github.com/hnthirima.

The following data sets were generated

Article and author information

Author details

  1. Heshani Nayanga Thirmanne

    Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States
    Competing interests
    No competing interests declared.
  2. Feinan Wu

    Genomics and Bioinformatics Resource, Fred Hutchinson Cancer Research Center, Seattle, United States
    Competing interests
    No competing interests declared.
  3. Derek H Janssens

    Basic Science Division, Fred Hutchinson Cancer Research Center, Seattle, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1079-9525
  4. Jherek Swanger

    Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States
    Competing interests
    No competing interests declared.
  5. Ahmed Diab

    Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States
    Competing interests
    No competing interests declared.
  6. Heather Feldman

    Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, United States
    Competing interests
    No competing interests declared.
  7. Robert A Amezquita

    Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, United States
    Competing interests
    No competing interests declared.
  8. Raphael Gottardo

    Vaccine and Infectious Disease Division, University of Washington, Seattle, United States
    Competing interests
    No competing interests declared.
  9. Patrick J Paddison

    Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, United States
    Competing interests
    No competing interests declared.
  10. Steven Henikoff

    Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States
    For correspondence
    steveh@fhcrc.org
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7621-8685
  11. Bruce E Clurman

    Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, United States
    For correspondence
    bclurman@fredhutch.org
    Competing interests
    Bruce E Clurman, is an equity holder and paid consultant for Coho Therapeutics, a start up biotechnology company focused on molecular glues. There is no funding or relationship to this paper. He also has a sponsored research agreement from Coho Therapeutics to fund work that is unrelated to this manuscript..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5835-9361

Funding

National Cancer Institute (T32 CA080416)

  • Heshani Nayanga Thirmanne

National Cancer Institute (R01 CA215647)

  • Bruce E Clurman

National Cancer Institute (P30 CA015704)

  • Bruce E Clurman

National Institutes of Health (R01 HG010492)

  • Steven Henikoff

National Institutes of Health (R01NS119650)

  • Patrick J Paddison

National Cancer Institute (R01 CA190957)

  • Patrick J Paddison

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

Reviewing Editor

  1. Wade Harper, Harvard Medical School, United States

Version history

  1. Received: September 30, 2021
  2. Preprint posted: October 21, 2021 (view preprint)
  3. Accepted: February 16, 2022
  4. Accepted Manuscript published: February 28, 2022 (version 1)
  5. Version of Record published: March 16, 2022 (version 2)
  6. Version of Record updated: March 30, 2022 (version 3)

Copyright

© 2022, Thirmanne 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. Heshani Nayanga Thirmanne
  2. Feinan Wu
  3. Derek H Janssens
  4. Jherek Swanger
  5. Ahmed Diab
  6. Heather Feldman
  7. Robert A Amezquita
  8. Raphael Gottardo
  9. Patrick J Paddison
  10. Steven Henikoff
  11. Bruce E Clurman
(2022)
Global and context-specific transcriptional consequences of oncogenic Fbw7 mutations
eLife 11:e74338.
https://doi.org/10.7554/eLife.74338

Share this article

https://doi.org/10.7554/eLife.74338

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