NuRD subunit CHD4 regulates super-enhancer accessibility in Rhabdomyosarcoma and represents a general tumor dependency

  1. Joana G Marques
  2. Berkley E Gryder
  3. Blaz Pavlovic
  4. Yeonjoo Chung
  5. Quy A Ngo
  6. Fabian Frommelt
  7. Matthias Gstaiger
  8. Young Song
  9. Katharina Benischke
  10. Dominik Laubscher
  11. Marco Wachtel
  12. Javed Khan
  13. Beat W Schäfer  Is a corresponding author
  1. University Children's Hospital, Switzerland
  2. Center for Cancer Research, National Institutes of Health, United States
  3. ETH Zurich, Switzerland
  4. Institute of Molecular Systems Biology, Switzerland

Abstract

The NuRD complex subunit CHD4 is essential for fusion-positive rhabdomyosarcoma (FP-RMS) survival, but the mechanisms underlying this dependency are not understood. Here, a NuRD-specific CRISPR screen demonstrates that FP-RMS is particularly sensitive to CHD4 amongst the NuRD members. Mechanistically, NuRD complex containing CHD4 localizes to super-enhancers where CHD4 generates a chromatin architecture permissive for the binding of the tumor driver and fusion protein PAX3-FOXO1, allowing downstream transcription of its oncogenic program. Moreover, CHD4 depletion removes HDAC2 from the chromatin, leading to an increase and spread of histone acetylation, and prevents the positioning of RNA Polymerase 2 at promoters impeding transcription initiation. Strikingly, analysis of genome-wide cancer dependency databases identifies CHD4 as a general cancer vulnerability. Our findings describe CHD4, a classically defined repressor, as positive regulator of transcription and super-enhancer accessibility as well as establish this remodeler as an unexpected broad tumor susceptibility and promising drug target for cancer therapy.

Data availability

The proteomics dataset supporting the conclusions of this article is available in the ProteomeXchange Consortium via the PRIDE (Perez-Riverol et al., 2019) repository with the dataset identifier PXD015231 (reviewer account: username - reviewer88401@ebi.ac.uk, password - mErsCglm). High-throughput ChIP-seq and DNase data are available through Gene Expression Omnibus (GEO) Superseries with the accession number GSE140115. ChIP-seq data for H3K27ac, H3K27me3, H3K36me3, H3K4me1, H3K4me2, 587 H3K4me3, BRD4, CTCF, RAD21, HDAC2, and RNA Polymerase 2 as well as DNase I hypersensitivity data obtained for wildtype RH4 cells were previously published (Gryder et al., 2019b, 2017) and are available on the same data repository with the gene accession numbers GSE83728 and GSE116344. The RNA-seq data is available in the European Nucleotide Archive (ENA) with the accession number PRJEB34220 (reviewer account: username - Webin-53797, password - kispiCHD42019).

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Joana G Marques

    Oncology, University Children's Hospital, Zurich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  2. Berkley E Gryder

    Oncogenomics Section, Center for Cancer Research, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Gaithersburg, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Blaz Pavlovic

    Oncology, University Children's Hospital, Zurich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  4. Yeonjoo Chung

    Oncology, University Children's Hospital, Zurich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  5. Quy A Ngo

    Oncology, University Children's Hospital, Zurich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  6. Fabian Frommelt

    Institute of Molecular Systems Biology, ETH Zurich, Zürich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3666-8005
  7. Matthias Gstaiger

    Department of Biology, Institute of Molecular Systems Biology, Zurich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  8. Young Song

    Genetics Branch, Center for Cancer Research, National Institutes of Health, Bethesda, United States
    Competing interests
    The authors declare that no competing interests exist.
  9. Katharina Benischke

    Oncology, University Children's Hospital, Zurich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  10. Dominik Laubscher

    Oncology, University Children's Hospital, Zurich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  11. Marco Wachtel

    Oncology, University Children's Hospital, Zurich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  12. Javed Khan

    Pediatric Oncology Branch, Oncogenomics Section, Center for Cancer Research, National Institutes of Health, Bethesda, United States
    Competing interests
    The authors declare that no competing interests exist.
  13. Beat W Schäfer

    Oncology, University Children's Hospital, Zurich, Switzerland
    For correspondence
    beat.schaefer@kispi.uzh.ch
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5988-2915

Funding

Swiss National Science Foundation (310030_156923 and 31003A_175558)

  • Beat W Schäfer

Cancer League Switzerland (KLS-3868-02-2016)

  • Beat W Schäfer

Childhood Cancer Research Foundation Switzerland

  • Beat W Schäfer

Innovative Medicines Initiative ULTRA-DD (115766)

  • Fabian Frommelt
  • Matthias Gstaiger

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

Copyright

This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

Metrics

  • 6,034
    views
  • 669
    downloads
  • 45
    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. Joana G Marques
  2. Berkley E Gryder
  3. Blaz Pavlovic
  4. Yeonjoo Chung
  5. Quy A Ngo
  6. Fabian Frommelt
  7. Matthias Gstaiger
  8. Young Song
  9. Katharina Benischke
  10. Dominik Laubscher
  11. Marco Wachtel
  12. Javed Khan
  13. Beat W Schäfer
(2020)
NuRD subunit CHD4 regulates super-enhancer accessibility in Rhabdomyosarcoma and represents a general tumor dependency
eLife 9:e54993.
https://doi.org/10.7554/eLife.54993

Share this article

https://doi.org/10.7554/eLife.54993

Further reading

    1. Cancer Biology
    2. Genetics and Genomics
    Hirokazu Kimura, Kamel Lahouel ... Nicholas Jason Roberts
    Research Article

    Interpretation of variants identified during genetic testing is a significant clinical challenge. In this study, we developed a high-throughput CDKN2A functional assay and characterized all possible human CDKN2A missense variants. We found that 17.7% of all missense variants were functionally deleterious. We also used our functional classifications to assess the performance of in silico models that predict the effect of variants, including recently reported models based on machine learning. Notably, we found that all in silico models performed similarly when compared to our functional classifications with accuracies of 39.5–85.4%. Furthermore, while we found that functionally deleterious variants were enriched within ankyrin repeats, we did not identify any residues where all missense variants were functionally deleterious. Our functional classifications are a resource to aid the interpretation of CDKN2A variants and have important implications for the application of variant interpretation guidelines, particularly the use of in silico models for clinical variant interpretation.

    1. Cancer Biology
    2. Developmental Biology
    Sara Jaber, Eliana Eldawra ... Franck Toledo
    Research Article

    Missense ‘hotspot’ mutations localized in six p53 codons account for 20% of TP53 mutations in human cancers. Hotspot p53 mutants have lost the tumor suppressive functions of the wildtype protein, but whether and how they may gain additional functions promoting tumorigenesis remain controversial. Here, we generated Trp53Y217C, a mouse model of the human hotspot mutant TP53Y220C. DNA damage responses were lost in Trp53Y217C/Y217C (Trp53YC/YC) cells, and Trp53YC/YC fibroblasts exhibited increased chromosome instability compared to Trp53-/- cells. Furthermore, Trp53YC/YC male mice died earlier than Trp53-/- males, with more aggressive thymic lymphomas. This correlated with an increased expression of inflammation-related genes in Trp53YC/YC thymic cells compared to Trp53-/- cells. Surprisingly, we recovered only one Trp53YC/YC female for 22 Trp53YC/YC males at weaning, a skewed distribution explained by a high frequency of Trp53YC/YC female embryos with exencephaly and the death of most Trp53YC/YC female neonates. Strikingly, however, when we treated pregnant females with the anti-inflammatory drug supformin (LCC-12), we observed a fivefold increase in the proportion of viable Trp53YC/YC weaned females in their progeny. Together, these data suggest that the p53Y217C mutation not only abrogates wildtype p53 functions but also promotes inflammation, with oncogenic effects in males and teratogenic effects in females.