title: The NuRD complex cooperates with DNMTs to maintain silencing of key colorectal tumor suppressor genes.
abstract: Many tumor suppressor genes (TSGs) are silenced through synergistic layers of epigenetic regulation including abnormal DNA hypermethylation of promoter CpG islands, repressive chromatin modifications and enhanced nucleosome deposition over transcription start sites. The protein complexes responsible for silencing of many of such TSGs remain to be identified. Our previous work demonstrated that multiple silenced TSGs in colorectal cancer cells can be partially reactivated by DNA demethylation in cells disrupted for the DNA methyltransferases 1 and 3B (DNMT1 and 3B) or by DNMT inhibitors (DNMTi). Herein, we used proteomic and functional genetic approaches to identify additional proteins that cooperate with DNMTs in silencing these key silenced TSGs in colon cancer cells. We discovered that DNMTs and the core components of the NuRD (Mi-2/nucleosome remodeling and deacetylase) nucleosome remodeling complex, chromo domain helicase DNA-binding protein 4 (CHD4) and histone deacetylase 1 (HDAC1) occupy the promoters of several of these hypermethylated TSGs and physically and functionally interact to maintain their silencing. Consistent with this, we find an inverse relationship between expression of HDAC1 and 2 and these TSGs in a large panel of primary colorectal tumors. We demonstrate that DNMTs and NuRD cooperate to maintain the silencing of several negative regulators of the WNT and other signaling pathways. We find that depletion of CHD4 is synergistic with DNMT inhibition in reducing the viability of colon cancer cells in correlation with reactivation of TSGs, suggesting that their combined inhibition may be beneficial for the treatment of colon cancer. Since CHD4 has ATPase activity, our data identify CHD4 as a potentially novel drug target in cancer.
authors.affiliation: Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, MD, USA.
authors.forename: Y
authors.initials: Y
authors.lastname: Cai
authors.affiliation: Division of Molecular Carcinogenesis, Center for Biomedical Genetics and Cancer Genomics Centre, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
authors.forename: E-J
authors.initials: EJ
authors.lastname: Geutjes
authors.affiliation: Division of Molecular Carcinogenesis, Center for Biomedical Genetics and Cancer Genomics Centre, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
authors.forename: K
authors.initials: K
authors.lastname: de Lint
authors.affiliation: Department of Research and Development, Agendia NV, Amsterdam, The Netherlands.
authors.forename: P
authors.initials: P
authors.lastname: Roepman
authors.affiliation: Division of Molecular Carcinogenesis, Center for Biomedical Genetics and Cancer Genomics Centre, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
authors.forename: L
authors.initials: L
authors.lastname: Bruurs
authors.affiliation: Division of Systems Biology, Center of Excellence for Proteomics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA.
authors.forename: L-R
authors.initials: LR
authors.lastname: Yu
authors.affiliation: Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, MD, USA.
authors.forename: W
authors.initials: W
authors.lastname: Wang
authors.affiliation: Division of Molecular Carcinogenesis, Center for Biomedical Genetics and Cancer Genomics Centre, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
authors.forename: J
authors.initials: J
authors.lastname: van Blijswijk
authors.affiliation: Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, MD, USA.
authors.forename: H
authors.initials: H
authors.lastname: Mohammad
authors.affiliation: Central Microarray and Deep Sequencing Core Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
authors.forename: I
authors.initials: I
authors.lastname: de Rink
authors.affiliation: Division of Molecular Carcinogenesis, Center for Biomedical Genetics and Cancer Genomics Centre, The Netherlands Cancer Institute, Amsterdam, The Netherlands.
authors.forename: R
authors.initials: R
authors.lastname: Bernards
authors.affiliation: Department of Oncology and The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, MD, USA.
authors.forename: S B
authors.initials: SB
authors.lastname: Baylin
mesh_terms: D017209:Apoptosis; D001324:Autoantigens / Q000235:genetics / Q000378:metabolism*; D001374:Azacitidine / Q000031:analogs & derivatives / Q000494:pharmacology; D015179:Colorectal Neoplasms; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000037:antagonists & inhibitors / Q000378:metabolism*; D000077209:Decitabine; D044127:Epigenesis, Genetic; D015870:Gene Expression; D015972:Gene Expression Regulation, Neoplastic; D055785:Gene Knockdown Techniques; D016147:Genes, Tumor Suppressor; D045325:HCT116 Cells; D056284:Histone Deacetylase 1 / Q000235:genetics / Q000378:metabolism*; D056464:Histone Deacetylase 2 / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D056245:Mi-2 Nucleosome Remodeling and Deacetylase Complex / Q000235:genetics / Q000378:metabolism*; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D051153:Wnt Proteins / Q000378:metabolism
chemical_list: D001324:Autoantigens; C115323:CHD4 protein, human; D051153:Wnt Proteins; D000077209:Decitabine; D004248:DNA (Cytosine-5-)-Methyltransferases; C110550:HDAC1 protein, human; C533423:HDAC2 protein, human; D056284:Histone Deacetylase 1; D056464:Histone Deacetylase 2; D056245:Mi-2 Nucleosome Remodeling and Deacetylase Complex; D001374:Azacitidine