Characterization of the mechanism by which the RB/E2F pathway controls expression of the cancer genomic DNA deaminase APOBEC3B

  1. Pieter A Roelofs
  2. Chai Yeen Goh
  3. Boon Haow Chua
  4. Matthew C Jarvis
  5. Teneale A Stewart
  6. Jennifer L McCann
  7. Rebecca M McDougle
  8. Michael A Carpenter
  9. John WM Martens
  10. Paul N Span
  11. Dennis Kappei
  12. Reuben S Harris  Is a corresponding author
  1. University of Minnesota, United States
  2. National University of Singapore, Singapore
  3. Howard Hughes Medical Institute, University of Minnesota, United States
  4. Erasmus MC Cancer Institute, Erasmus University Medical Center, Netherlands
  5. Radboud University Medical Center, Netherlands [NL]

Abstract

APOBEC3B (A3B)-catalyzed DNA cytosine deamination contributes to the overall mutational landscape in breast cancer. Molecular mechanisms responsible for A3B upregulation in cancer are poorly understood. Here, we show that a single E2F cis-element mediates repression in normal cells and that expression is activated by its mutational disruption in a reporter construct or the endogenous A3B gene. The same E2F site is required for A3B induction by polyomavirus T antigen indicating a shared molecular mechanism. Proteomic and biochemical experiments demonstrate binding of wildtype but not mutant E2F promoters by repressive PRC1.6/E2F6 and DREAM/E2F4 complexes. Knockdown and overexpression studies confirm involvement of these repressive complexes in regulating A3B expression. Altogether, these studies demonstrate that A3B expression is suppressed in normal cells by repressive E2F complexes and that viral or mutational disruption of this regulatory network triggers overexpression in breast cancer and provides fuel for tumor evolution.

Data availability

Raw mass spectrometry data will be accessible through the ProteomeXchange Consortium via the PRIDE (Vizcaino et al., 2016) partner repository with the dataset identifier PXD020473. Additional data generated or analysed during this study are included in the manuscript and supporting files.

Article and author information

Author details

  1. Pieter A Roelofs

    Biochemistry, University of Minnesota, Minneapolis, United States
    Competing interests
    No competing interests declared.
  2. Chai Yeen Goh

    Translational Medicine, National University of Singapore, Singapore, Singapore
    Competing interests
    No competing interests declared.
  3. Boon Haow Chua

    Translational Medicine, National University of Singapore, Singapore, Singapore
    Competing interests
    No competing interests declared.
  4. Matthew C Jarvis

    Microbiology and Immunology, University of Minnesota, Minneapolis, United States
    Competing interests
    No competing interests declared.
  5. Teneale A Stewart

    Biochemistry, University of Minnesota, Minneapolis, United States
    Competing interests
    No competing interests declared.
  6. Jennifer L McCann

    Microbiology and Immunology, University of Minnesota, Minneapolis, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0458-1335
  7. Rebecca M McDougle

    Biochemistry, University of Minnesota, Minneapolis, United States
    Competing interests
    No competing interests declared.
  8. Michael A Carpenter

    Biochemistry, Howard Hughes Medical Institute, University of Minnesota, Minneapolis, United States
    Competing interests
    No competing interests declared.
  9. John WM Martens

    Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, Netherlands
    Competing interests
    No competing interests declared.
  10. Paul N Span

    Radboud University Medical Center, Nijmegen, Netherlands [NL]
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1930-6638
  11. Dennis Kappei

    Translational Medicine, National University of Singapore, Singapore, Singapore
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3582-2253
  12. Reuben S Harris

    Biochemistry, Howard Hughes Medical Institute, University of Minnesota, Minneapolis, United States
    For correspondence
    rsh@umn.edu
    Competing interests
    Reuben S Harris, RSH is a co-founder, shareholder, and consultant of ApoGen Biotechnologies Inc..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9034-9112

Funding

National Cancer Institute (P01-CA234228)

  • Reuben S Harris

KWF Kankerbestrijding (KWF10270)

  • John WM Martens
  • Paul N Span
  • Reuben S Harris

National Research Foundation Singapore (NMRC/OFYIRG/055/2017)

  • Dennis Kappei

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

Reviewing Editor

  1. Maureen E Murphy, The Wistar Institute, United States

Version history

  1. Received: May 5, 2020
  2. Accepted: September 25, 2020
  3. Accepted Manuscript published: September 28, 2020 (version 1)
  4. Version of Record published: October 13, 2020 (version 2)

Copyright

© 2020, Roelofs 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. Pieter A Roelofs
  2. Chai Yeen Goh
  3. Boon Haow Chua
  4. Matthew C Jarvis
  5. Teneale A Stewart
  6. Jennifer L McCann
  7. Rebecca M McDougle
  8. Michael A Carpenter
  9. John WM Martens
  10. Paul N Span
  11. Dennis Kappei
  12. Reuben S Harris
(2020)
Characterization of the mechanism by which the RB/E2F pathway controls expression of the cancer genomic DNA deaminase APOBEC3B
eLife 9:e61287.
https://doi.org/10.7554/eLife.61287

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https://doi.org/10.7554/eLife.61287

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