NuRD subunit CHD4 regulates super-enhancer accessibility in Rhabdomyosarcoma and represents a general tumor dependency
- University Children's Hospital, Switzerland
- Center for Cancer Research, National Institutes of Health, United States
- ETH Zurich, Switzerland
- 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).
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Selective Disruption of Core Regulatory Transcription [ChIP-seq]Gene Expression Omnibus GSE116344.
Article and author information
Author details
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.
Reviewing Editor
- Xiaobing Shi, Van Andel Institute, United States
Version history
- Received: January 8, 2020
- Accepted: August 2, 2020
- Accepted Manuscript published: August 3, 2020 (version 1)
- Version of Record published: August 19, 2020 (version 2)
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.
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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
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Enhancers are critical for regulating tissue-specific gene expression, and genetic variants within enhancer regions have been suggested to contribute to various cancer-related processes, including therapeutic resistance. However, the precise mechanisms remain elusive. Using a well-defined drug-gene pair, we identified an enhancer region for dihydropyrimidine dehydrogenase (DPD, DPYD gene) expression that is relevant to the metabolism of the anti-cancer drug 5-fluorouracil (5-FU). Using reporter systems, CRISPR genome-edited cell models, and human liver specimens, we demonstrated in vitro and vivo that genotype status for the common germline variant (rs4294451; 27% global minor allele frequency) located within this novel enhancer controls DPYD transcription and alters resistance to 5-FU. The variant genotype increases recruitment of the transcription factor CEBPB to the enhancer and alters the level of direct interactions between the enhancer and DPYD promoter. Our data provide insight into the regulatory mechanisms controlling sensitivity and resistance to 5-FU.
