IER5, a DNA damage response gene, is required for Notch-mediated induction of squamous cell differentiation

  1. Li Pan
  2. Madeleine E Lemieux
  3. Tom Thomas
  4. Julia M Rogers
  5. Colin H Lipper
  6. Winston Lee
  7. Carl Johnson
  8. Lynette M Sholl
  9. Andrew P South
  10. Jarrod A Marto
  11. Guillaume O Adelmant
  12. Stephen C Blacklow
  13. Jon C Aster  Is a corresponding author
  1. Brigham and Women's Hospital, United States
  2. Bioinfo, Canada
  3. Harvard Medical School, United States
  4. Thomas Jefferson University, United States
  5. Dana-Farber Cancer Institute, United States
  6. Dana Farber Cancer Institute, United States
  7. Harvard, United States

Abstract

Notch signaling regulates squamous cell proliferation and differentiation and is frequently disrupted in squamous cell carcinomas, in which Notch is tumor suppressive. Here, we show that conditional activation of Notch in squamous cells activates a context-specific gene expression program through lineage-specific regulatory elements. Among direct Notch target genes are multiple DNA damage response genes, including IER5, which we show is required for Notch-induced differentiation of squamous carcinoma cells and TERT-immortalized keratinocytes. IER5 is epistatic to PPP2R2A, a gene that encodes the PP2A B55a subunit, which we show interacts with IER5 in cells and in purified systems. Thus, Notch and DNA-damage response pathways converge in squamous cells on common genes that promote differentiation, which may serve to eliminate damaged cells from the proliferative pool. We further propose that crosstalk involving Notch and PP2A enables tuning and integration of Notch signaling with other pathways that regulate squamous differentiation.

Data availability

Sequencing data have been deposited in GEO under accession codes GSE156488 and GSE156624

The following data sets were generated

Article and author information

Author details

  1. Li Pan

    Department of Pathology, Brigham and Women's Hospital, Boston, United States
    Competing interests
    No competing interests declared.
  2. Madeleine E Lemieux

    Bioinfo, Ontario, Canada
    Competing interests
    No competing interests declared.
  3. Tom Thomas

    Department of Pathology, Brigham and Women's Hospital, Boston, United States
    Competing interests
    No competing interests declared.
  4. Julia M Rogers

    Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
    Competing interests
    No competing interests declared.
  5. Colin H Lipper

    Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
    Competing interests
    No competing interests declared.
  6. Winston Lee

    Department of Pathology, Brigham and Women's Hospital, Boston, United States
    Competing interests
    No competing interests declared.
  7. Carl Johnson

    Department of Pathology, Brigham and Women's Hospital, Boston, United States
    Competing interests
    No competing interests declared.
  8. Lynette M Sholl

    Department of Pathology, Brigham and Women's Hospital, Boston, United States
    Competing interests
    No competing interests declared.
  9. Andrew P South

    Dermatology and Cutaneous Biology, Thomas Jefferson University, Philadelphia, United States
    Competing interests
    No competing interests declared.
  10. Jarrod A Marto

    The Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, United States
    Competing interests
    No competing interests declared.
  11. Guillaume O Adelmant

    Oncologic Pathology, Dana Farber Cancer Institute, Boston, United States
    Competing interests
    No competing interests declared.
  12. Stephen C Blacklow

    Department of Biological Chemistry and Molecular Pharmacology, Harvard, Boston, United States
    Competing interests
    Stephen C Blacklow, SCB is on the SAB for Erasca, Inc., receives sponsored research funding from Novartis and Erasca, Inc, and is a consultant for IFM therapeutics and Ayala Pharmaceuticals..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6904-1981
  13. Jon C Aster

    Department of Pathology, Brigham and Women's Hospital, Boston, United States
    For correspondence
    jaster@rics.bwh.harvard.edu
    Competing interests
    Jon C Aster, JCA is a consultant for Ayala Pharmaceuticals and for Cellestia, Inc. There is no conflict of interest with the work described in this manuscript..
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1957-9070

Funding

Ludwig Institute for Cancer Research (None)

  • Jon C Aster

National Institutes of Health (R35 CA220340)

  • Stephen C Blacklow

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

Reviewing Editor

  1. Apurva Sarin, Institute for Stem Cell Science and Regenerative Medicine, India

Version history

  1. Received: April 20, 2020
  2. Accepted: September 15, 2020
  3. Accepted Manuscript published: September 16, 2020 (version 1)
  4. Version of Record published: October 1, 2020 (version 2)

Copyright

© 2020, Pan 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

  • 1,973
    views
  • 213
    downloads
  • 13
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

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. Li Pan
  2. Madeleine E Lemieux
  3. Tom Thomas
  4. Julia M Rogers
  5. Colin H Lipper
  6. Winston Lee
  7. Carl Johnson
  8. Lynette M Sholl
  9. Andrew P South
  10. Jarrod A Marto
  11. Guillaume O Adelmant
  12. Stephen C Blacklow
  13. Jon C Aster
(2020)
IER5, a DNA damage response gene, is required for Notch-mediated induction of squamous cell differentiation
eLife 9:e58081.
https://doi.org/10.7554/eLife.58081

Share this article

https://doi.org/10.7554/eLife.58081

Further reading

    1. Cancer Biology
    Célia Guérin, David Tulasne
    Review Article

    Tyrosine kinase inhibitors (TKI) directed against MET have been recently approved to treat advanced non-small cell lung cancer (NSCLC) harbouring activating MET mutations. This success is the consequence of a long characterization of MET mutations in cancers, which we propose to outline in this review. MET, a receptor tyrosine kinase (RTK), displays in a broad panel of cancers many deregulations liable to promote tumour progression. The first MET mutation was discovered in 1997, in hereditary papillary renal cancer (HPRC), providing the first direct link between MET mutations and cancer development. As in other RTKs, these mutations are located in the kinase domain, leading in most cases to ligand-independent MET activation. In 2014, novel MET mutations were identified in several advanced cancers, including lung cancers. These mutations alter splice sites of exon 14, causing in-frame exon 14 skipping and deletion of a regulatory domain. Because these mutations are not located in the kinase domain, they are original and their mode of action has yet to be fully elucidated. Less than five years after the discovery of such mutations, the efficacy of a MET TKI was evidenced in NSCLC patients displaying MET exon 14 skipping. Yet its use led to a resistance mechanism involving acquisition of novel and already characterized MET mutations. Furthermore, novel somatic MET mutations are constantly being discovered. The challenge is no longer to identify them but to characterize them in order to predict their transforming activity and their sensitivity or resistance to MET TKIs, in order to adapt treatment.

    1. Cancer Biology
    2. Genetics and Genomics
    Kevin Nuno, Armon Azizi ... Ravindra Majeti
    Research Article

    Relapse of acute myeloid leukemia (AML) is highly aggressive and often treatment refractory. We analyzed previously published AML relapse cohorts and found that 40% of relapses occur without changes in driver mutations, suggesting that non-genetic mechanisms drive relapse in a large proportion of cases. We therefore characterized epigenetic patterns of AML relapse using 26 matched diagnosis-relapse samples with ATAC-seq. This analysis identified a relapse-specific chromatin accessibility signature for mutationally stable AML, suggesting that AML undergoes epigenetic evolution at relapse independent of mutational changes. Analysis of leukemia stem cell (LSC) chromatin changes at relapse indicated that this leukemic compartment underwent significantly less epigenetic evolution than non-LSCs, while epigenetic changes in non-LSCs reflected overall evolution of the bulk leukemia. Finally, we used single-cell ATAC-seq paired with mitochondrial sequencing (mtscATAC) to map clones from diagnosis into relapse along with their epigenetic features. We found that distinct mitochondrially-defined clones exhibit more similar chromatin accessibility at relapse relative to diagnosis, demonstrating convergent epigenetic evolution in relapsed AML. These results demonstrate that epigenetic evolution is a feature of relapsed AML and that convergent epigenetic evolution can occur following treatment with induction chemotherapy.