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Myers G, Sun Y, Wang Y, Benmhammed H, Cui S. Roles of Nuclear Orphan Receptors TR2 and TR4 during Hematopoiesis. Genes (Basel) 2024; 15:563. [PMID: 38790192 PMCID: PMC11121135 DOI: 10.3390/genes15050563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/24/2024] [Accepted: 04/26/2024] [Indexed: 05/26/2024] Open
Abstract
TR2 and TR4 (NR2C1 and NR2C2, respectively) are evolutionarily conserved nuclear orphan receptors capable of binding direct repeat sequences in a stage-specific manner. Like other nuclear receptors, TR2 and TR4 possess important roles in transcriptional activation or repression with developmental stage and tissue specificity. TR2 and TR4 bind DNA and possess the ability to complex with available cofactors mediating developmental stage-specific actions in primitive and definitive erythrocytes. In erythropoiesis, TR2 and TR4 are required for erythroid development, maturation, and key erythroid transcription factor regulation. TR2 and TR4 recruit and interact with transcriptional corepressors or coactivators to elicit developmental stage-specific gene regulation during hematopoiesis.
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Affiliation(s)
- Greggory Myers
- Departments of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48105, USA; (G.M.); (Y.W.)
| | - Yanan Sun
- Section of Hematology-Medical Oncology, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston Medical Center, Boston, MA 02118, USA; (Y.S.); (H.B.)
| | - Yu Wang
- Departments of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48105, USA; (G.M.); (Y.W.)
| | - Hajar Benmhammed
- Section of Hematology-Medical Oncology, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston Medical Center, Boston, MA 02118, USA; (Y.S.); (H.B.)
| | - Shuaiying Cui
- Section of Hematology-Medical Oncology, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston Medical Center, Boston, MA 02118, USA; (Y.S.); (H.B.)
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2
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Graca Marques J, Pavlovic B, Ngo QA, Pedot G, Roemmele M, Volken L, Kisele S, Perbet R, Wachtel M, Schäfer BW. The Chromatin Remodeler CHD4 Sustains Ewing Sarcoma Cell Survival by Controlling Global Chromatin Architecture. Cancer Res 2024; 84:241-257. [PMID: 37963210 DOI: 10.1158/0008-5472.can-22-3950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 08/30/2023] [Accepted: 11/07/2023] [Indexed: 11/16/2023]
Abstract
Ewing sarcoma is an aggressive cancer with a defective response to DNA damage leading to an enhanced sensitivity to genotoxic agents. Mechanistically, Ewing sarcoma is driven by the fusion transcription factor EWS-FLI1, which reprograms the tumor cell epigenome. The nucleosome remodeling and deacetylase (NuRD) complex is an important regulator of chromatin function, controlling both gene expression and DNA damage repair, and has been associated with EWS-FLI1 activity. Here, a NuRD-focused CRISPR/Cas9 inactivation screen identified the helicase CHD4 as essential for Ewing sarcoma cell proliferation. CHD4 silencing induced tumor cell death by apoptosis and abolished colony formation. Although CHD4 and NuRD colocalized with EWS-FLI1 at enhancers and super-enhancers, CHD4 promoted Ewing sarcoma cell survival not by modulating EWS-FLI1 activity and its oncogenic gene expression program but by regulating chromatin structure. CHD4 depletion led to a global increase in DNA accessibility and induction of spontaneous DNA damage, resulting in an increased susceptibility to DNA-damaging agents. CHD4 loss delayed tumor growth in vivo, increased overall survival, and combination with PARP inhibition by olaparib treatment further suppressed tumor growth. Collectively, these findings highlight the NuRD subunit CHD4 as a therapeutic target in Ewing sarcoma that can potentiate the antitumor activity of genotoxic agents. SIGNIFICANCE CRISPR/Cas9 screening in Ewing sarcoma identifies a dependency on CHD4, which is crucial for the maintenance of chromatin architecture to suppress DNA damage and a promising therapeutic target for DNA damage repair-deficient malignancies.
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Affiliation(s)
- Joana Graca Marques
- Department of Oncology and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Blaz Pavlovic
- Department of Oncology and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Quy A Ngo
- Department of Oncology and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Gloria Pedot
- Department of Oncology and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Michaela Roemmele
- Department of Oncology and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Larissa Volken
- Department of Oncology and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Samanta Kisele
- Department of Oncology and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Romain Perbet
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts
| | - Marco Wachtel
- Department of Oncology and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
| | - Beat W Schäfer
- Department of Oncology and Children's Research Center, University Children's Hospital Zurich, Zurich, Switzerland
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3
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Kim SH, Haynes KA. Reader-Effectors as Actuators of Epigenome Editing. Methods Mol Biol 2024; 2842:103-127. [PMID: 39012592 DOI: 10.1007/978-1-0716-4051-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Epigenome editing applications are gaining broader use for targeted transcriptional control as more enzymes with diverse chromatin-modifying functions are being incorporated into fusion proteins. Development of these fusion proteins, called epigenome editors, has outpaced the study of proteins that interact with edited chromatin. One type of protein that acts downstream of chromatin editing is the reader-effector, which bridges epigenetic marks with biological effects like gene regulation. As the name suggests, a reader-effector protein is generally composed of a reader domain and an effector domain. Reader domains directly bind epigenetic marks, while effector domains often recruit protein complexes that mediate transcription, chromatin remodeling, and DNA repair. In this chapter, we discuss the role of reader-effectors in driving the outputs of epigenome editing and highlight instances where abnormal and context-specific reader-effectors might impair the effects of epigenome editing. Lastly, we discuss how engineered reader-effectors may complement the epigenome editing toolbox to achieve robust and reliable gene regulation.
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Affiliation(s)
- Seong Hu Kim
- Wallace H. Coulter Department of Biomedical Engineering, Emory University School of Medicine, Atlanta, GA, USA
| | - Karmella A Haynes
- Wallace H. Coulter Department of Biomedical Engineering, Emory University School of Medicine, Atlanta, GA, USA.
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4
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Buljan M, Banaei-Esfahani A, Blattmann P, Meier-Abt F, Shao W, Vitek O, Tang H, Aebersold R. A computational framework for the inference of protein complex remodeling from whole-proteome measurements. Nat Methods 2023; 20:1523-1529. [PMID: 37749212 PMCID: PMC10555833 DOI: 10.1038/s41592-023-02011-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 08/16/2023] [Indexed: 09/27/2023]
Abstract
Protein complexes are responsible for the enactment of most cellular functions. For the protein complex to form and function, its subunits often need to be present at defined quantitative ratios. Typically, global changes in protein complex composition are assessed with experimental approaches that tend to be time consuming. Here, we have developed a computational algorithm for the detection of altered protein complexes based on the systematic assessment of subunit ratios from quantitative proteomic measurements. We applied it to measurements from breast cancer cell lines and patient biopsies and were able to identify strong remodeling of HDAC2 epigenetic complexes in more aggressive forms of cancer. The presented algorithm is available as an R package and enables the inference of changes in protein complex states by extracting functionally relevant information from bottom-up proteomic datasets.
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Affiliation(s)
- Marija Buljan
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
- EMPA, Swiss Federal Laboratories for Materials Science and Technology, St Gallen, Switzerland.
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.
| | - Amir Banaei-Esfahani
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Peter Blattmann
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Idorsia Pharmaceuticals, Allschwil, Switzerland
| | - Fabienne Meier-Abt
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Department of Medical Oncology and Hematology, University and University Hospital Zurich, Zurich, Switzerland
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Wenguang Shao
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- State Key Laboratory of Microbial Metabolism, School of Life Science & Biotechnology, and Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Olga Vitek
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
- Faculty of Science, University of Zurich, Zurich, Switzerland.
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5
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Leighton GO, Shang S, Hageman S, Ginder GD, Williams DC. Analysis of the complex between MBD2 and the histone deacetylase core of NuRD reveals key interactions critical for gene silencing. Proc Natl Acad Sci U S A 2023; 120:e2307287120. [PMID: 37552759 PMCID: PMC10433457 DOI: 10.1073/pnas.2307287120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 07/14/2023] [Indexed: 08/10/2023] Open
Abstract
The nucleosome remodeling and deacetylase (NuRD) complex modifies nucleosome positioning and chromatin compaction to regulate gene expression. The methyl-CpG-binding domain proteins 2 and 3 (MBD2 and MBD3) play a critical role in complex formation; however, the molecular details of how they interact with other NuRD components have yet to be fully elucidated. We previously showed that an intrinsically disordered region (IDR) of MBD2 is necessary and sufficient to bind to the histone deacetylase core of NuRD. Building on that work, we have measured the inherent structural propensity of the MBD2-IDR using solvent and site-specific paramagnetic relaxation enhancement measurements. We then used the AlphaFold2 machine learning software to generate a model of the complex between MBD2 and the histone deacetylase core of NuRD. This model is remarkably consistent with our previous studies, including the current paramagnetic relaxation enhancement data. The latter suggests that the free MBD2-IDR samples conformations similar to the bound structure. We tested this model of the complex extensively by mutating key contact residues and measuring binding using an intracellular bioluminescent resonance energy transfer assay. Furthermore, we identified protein contacts that, when mutated, disrupted gene silencing by NuRD in a cell model of fetal hemoglobin regulation. Hence, this work provides insights into the formation of NuRD and highlights critical binding pockets that may be targeted to block gene silencing for therapy. Importantly, we show that AlphaFold2 can generate a credible model of a large complex that involves an IDR that folds upon binding.
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Affiliation(s)
- Gage O. Leighton
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC27599
| | - Shengzhe Shang
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA23298
| | - Sean Hageman
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC27599
| | - Gordon D. Ginder
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA23298
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA23298
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA23298
- Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA23298
| | - David C. Williams
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC27599
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Ma J, Wen X, Xu Z, Xia P, Jin Y, Lin J, Qian J. Abnormal regulation of miR-29b-ID1 signaling is involved in the process of decitabine resistance in leukemia cells. Cell Cycle 2023; 22:1215-1231. [PMID: 37032592 PMCID: PMC10193880 DOI: 10.1080/15384101.2023.2200312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/06/2023] [Accepted: 02/27/2023] [Indexed: 04/11/2023] Open
Abstract
Decitabine (DAC) is an inhibitor of DNA methyltransferase used to treat leukemia, but primary or secondary resistance to DAC may develop during therapy. The mechanisms related to DAC resistance remain poorly understood. In this study, we find that miR-29b expression was decreased in various leukemia cell lines and AML patients and was associated with poor prognosis. In DAC-sensitive cells, miR-29b inhibited cell growth, promoted apoptosis, and increased the sensitivity to DAC. Similarly, it exerted anti-leukemic effects in DAC-resistant cells. When the miR-29b promoter in DAC-resistant cells was demethylated, its expression was not up-regulated. Furthermore, the expression of ID1, one of the target genes of miR-29b, was down-regulated in miR-29b transfected leukemic cells. ID1 promoted cell growth, inhibited cell apoptosis, and decreased DAC sensitivity in leukemic cells in vitro and in vivo. ID1 was down-regulated in DAC-sensitive cells treated with DAC, while it was up-regulated in DAC-resistant cells. Interestingly, the ID1 promoter region was completely unmethylated in both DAC-resistant cells and sensitive cells before DAC treatment. The growth inhibition, increased DAC sensitivity, and apoptosis induced by miR-29b can be eliminated by increasing ID1 expression. These results suggested that DAC regulates ID1 expression by acting on miR-29b. Abnormal ID1 expression of ID1 that is methylation independent and induced by miR-29b may be involved in the process of leukemia cells acquiring DAC resistance.
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Affiliation(s)
- Jichun Ma
- Department of central lab, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
- Zhenjiang Clinical Research Center of Hematology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
- The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xiangmei Wen
- Department of central lab, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
- Zhenjiang Clinical Research Center of Hematology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
- The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Zijun Xu
- Department of central lab, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
- Zhenjiang Clinical Research Center of Hematology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
- The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Peihui Xia
- Department of central lab, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
- Zhenjiang Clinical Research Center of Hematology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
- The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Ye Jin
- Zhenjiang Clinical Research Center of Hematology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
- The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
- Department of Hematology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Jiang Lin
- Department of central lab, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
- Zhenjiang Clinical Research Center of Hematology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
- The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Jun Qian
- Zhenjiang Clinical Research Center of Hematology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
- The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
- Department of Hematology, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
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7
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Strathmann EA, Hölker I, Tschernoster N, Hosseinibarkooie S, Come J, Martinat C, Altmüller J, Wirth B. Epigenetic regulation of plastin 3 expression by the macrosatellite DXZ4 and the transcriptional regulator CHD4. Am J Hum Genet 2023; 110:442-459. [PMID: 36812914 PMCID: PMC10027515 DOI: 10.1016/j.ajhg.2023.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 02/03/2023] [Indexed: 02/23/2023] Open
Abstract
Dysregulated Plastin 3 (PLS3) levels associate with a wide range of skeletal and neuromuscular disorders and the most common types of solid and hematopoietic cancer. Most importantly, PLS3 overexpression protects against spinal muscular atrophy. Despite its crucial role in F-actin dynamics in healthy cells and its involvement in many diseases, the mechanisms that regulate PLS3 expression are unknown. Interestingly, PLS3 is an X-linked gene and all asymptomatic SMN1-deleted individuals in SMA-discordant families who exhibit PLS3 upregulation are female, suggesting that PLS3 may escape X chromosome inactivation. To elucidate mechanisms contributing to PLS3 regulation, we performed a multi-omics analysis in two SMA-discordant families using lymphoblastoid cell lines and iPSC-derived spinal motor neurons originated from fibroblasts. We show that PLS3 tissue-specifically escapes X-inactivation. PLS3 is located ∼500 kb proximal to the DXZ4 macrosatellite, which is essential for X chromosome inactivation. By applying molecular combing in a total of 25 lymphoblastoid cell lines (asymptomatic individuals, individuals with SMA, control subjects) with variable PLS3 expression, we found a significant correlation between the copy number of DXZ4 monomers and PLS3 levels. Additionally, we identified chromodomain helicase DNA binding protein 4 (CHD4) as an epigenetic transcriptional regulator of PLS3 and validated co-regulation of the two genes by siRNA-mediated knock-down and overexpression of CHD4. We show that CHD4 binds the PLS3 promoter by performing chromatin immunoprecipitation and that CHD4/NuRD activates the transcription of PLS3 by dual-luciferase promoter assays. Thus, we provide evidence for a multilevel epigenetic regulation of PLS3 that may help to understand the protective or disease-associated PLS3 dysregulation.
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Affiliation(s)
- Eike A Strathmann
- Institute of Human Genetics, University Hospital of Cologne, University Cologne, Kerpener Str. 34, 50931 Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Institute for Genetics, University of Cologne, 50674 Cologne, Germany
| | - Irmgard Hölker
- Institute of Human Genetics, University Hospital of Cologne, University Cologne, Kerpener Str. 34, 50931 Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Institute for Genetics, University of Cologne, 50674 Cologne, Germany
| | - Nikolai Tschernoster
- Institute of Human Genetics, University Hospital of Cologne, University Cologne, Kerpener Str. 34, 50931 Cologne, Germany; Cologne Center for Genomics and West German Genome Center, University of Cologne, 50931 Cologne, Germany
| | - Seyyedmohsen Hosseinibarkooie
- Institute of Human Genetics, University Hospital of Cologne, University Cologne, Kerpener Str. 34, 50931 Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Institute for Genetics, University of Cologne, 50674 Cologne, Germany
| | - Julien Come
- INSERM/ UEVE UMR 861, Université Paris Saclay, I-STEM, 91100 Corbeil-Essonnes, France
| | - Cecile Martinat
- INSERM/ UEVE UMR 861, Université Paris Saclay, I-STEM, 91100 Corbeil-Essonnes, France
| | - Janine Altmüller
- Cologne Center for Genomics and West German Genome Center, University of Cologne, 50931 Cologne, Germany
| | - Brunhilde Wirth
- Institute of Human Genetics, University Hospital of Cologne, University Cologne, Kerpener Str. 34, 50931 Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, 50931 Cologne, Germany; Institute for Genetics, University of Cologne, 50674 Cologne, Germany; Center for Rare Diseases, University Hospital of Cologne, 50931 Cologne, Germany.
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8
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Li H, Gigi L, Zhao D. CHD1, a multifaceted epigenetic remodeler in prostate cancer. Front Oncol 2023; 13:1123362. [PMID: 36776288 PMCID: PMC9909554 DOI: 10.3389/fonc.2023.1123362] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 01/11/2023] [Indexed: 01/27/2023] Open
Abstract
Chromatin remodeling proteins contribute to DNA replication, transcription, repair, and recombination. The chromodomain helicase DNA-binding (CHD) family of remodelers plays crucial roles in embryonic development, hematopoiesis, and neurogenesis. As the founding member, CHD1 is capable of assembling nucleosomes, remodeling chromatin structure, and regulating gene transcription. Dysregulation of CHD1 at genetic, epigenetic, and post-translational levels is common in malignancies and other human diseases. Through interacting with different genetic alterations, CHD1 possesses the capabilities to exert oncogenic or tumor-suppressive functions in context-dependent manners. In this Review, we summarize the biochemical properties and dysregulation of CHD1 in cancer cells, and then discuss CHD1's roles in different contexts of prostate cancer, with an emphasis on its crosstalk with diverse signaling pathways. Furthermore, we highlight the potential therapeutic strategies for cancers with dysregulated CHD1. At last, we discuss current research gaps in understanding CHD1's biological functions and molecular basis during disease progression, as well as the modeling systems for biology study and therapeutic development.
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Affiliation(s)
- Haoyan Li
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Loraine Gigi
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Texas A&M School of Public Health, Texas A&M University, College Station, TX, United States
| | - Di Zhao
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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9
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Wang J, Zhong F, Li J, Yue H, Li W, Lu X. The epigenetic factor CHD4 contributes to metastasis by regulating the EZH2/β-catenin axis and acts as a therapeutic target in ovarian cancer. J Transl Med 2023; 21:38. [PMID: 36681835 PMCID: PMC9862813 DOI: 10.1186/s12967-022-03854-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 12/26/2022] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The overall survival rate of patients with advanced ovarian cancer (OC) has remained static for several decades. Advanced ovarian cancer is known for its poor prognosis due to extensive metastasis. Epigenetic alterations contribute to tumour progression and therefore are of interest for potential therapeutic strategies. METHODS Following our previous study, we identified that CHD4, a chromatin remodelling factor, plays a strong role in ovarian cancer cell metastasis. We investigated the clinical significance of CHD4 through TCGA and GEO database analyses and explored the effect of CHD4 expression modulation and romidepsin treatment on the biological behaviour of ovarian cancer through CCK-8 and transwell assays. Bioluminescence imaging of tumours in xenografted mice was applied to determine the therapeutic effect of romidepsin. GSEA and western blotting were used to screen the regulatory mechanism of CHD4. RESULTS In ovarian cancer patient specimens, high CHD4 expression was associated with a poor prognosis. Loss of function of CHD4 in ovarian cancer cells induced suppression of migration and invasion. Mechanistically, CHD4 knockdown suppressed the expression of EZH2 and the nuclear accumulation of β-catenin. CHD4 also suppressed the metastasis of ovarian cancer cells and prevented disease progression in a mouse model. To inhibit the functions of CHD4 that are mediated by histone deacetylase, we evaluated the effect of the HDAC1/2 selective inhibitor romidepsin. Our findings indicated that treatment with romidepsin suppressed the progression of metastases in vitro and in vivo. CONCLUSIONS Collectively, our results uncovered an oncogenic function of CHD4 in ovarian cancer and provide a rationale for clinical trials of romidepsin in ovarian cancer patients.
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Affiliation(s)
- Jieyu Wang
- Department of Gynecology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200090, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-Related Disease, Fudan University, Shanghai, 200090, China
| | - Fangfang Zhong
- Department of Pathology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200090, China
| | - Jun Li
- Department of Gynecology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200090, China
| | - Huiran Yue
- Department of Gynecology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200090, China
| | - Wenzhi Li
- Department of Gynecology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200090, China
- Shanghai Key Laboratory of Female Reproductive Endocrine-Related Disease, Fudan University, Shanghai, 200090, China
| | - Xin Lu
- Department of Gynecology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200090, China.
- Shanghai Key Laboratory of Female Reproductive Endocrine-Related Disease, Fudan University, Shanghai, 200090, China.
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10
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Chang SJ, Bin PJ, Luo CW, Chai CY. CHD4 plays a critical role in arsenite-induced oxidative damage in human urothelial carcinoma. Pathol Res Pract 2022; 240:154173. [DOI: 10.1016/j.prp.2022.154173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 09/26/2022] [Accepted: 10/14/2022] [Indexed: 11/15/2022]
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11
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Zhao D, Zhang M, Huang S, Liu Q, Zhu S, Li Y, Jiang W, Kiss DL, Cao Q, Zhang L, Chen K. CHD6 promotes broad nucleosome eviction for transcriptional activation in prostate cancer cells. Nucleic Acids Res 2022; 50:12186-12201. [PMID: 36408932 PMCID: PMC9757051 DOI: 10.1093/nar/gkac1090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 11/19/2022] [Indexed: 11/22/2022] Open
Abstract
Despite being a member of the chromodomain helicase DNA-binding protein family, little is known about the exact role of CHD6 in chromatin remodeling or cancer disease. Here we show that CHD6 binds to chromatin to promote broad nucleosome eviction for transcriptional activation of many cancer pathways. By integrating multiple patient cohorts for bioinformatics analysis of over a thousand prostate cancer datasets, we found CHD6 expression elevated in prostate cancer and associated with poor prognosis. Further comprehensive experiments demonstrated that CHD6 regulates oncogenicity of prostate cancer cells and tumor development in a murine xenograft model. ChIP-Seq for CHD6, along with MNase-Seq and RNA-Seq, revealed that CHD6 binds on chromatin to evict nucleosomes from promoters and gene bodies for transcriptional activation of oncogenic pathways. These results demonstrated a key function of CHD6 in evicting nucleosomes from chromatin for transcriptional activation of prostate cancer pathways.
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Affiliation(s)
- Dongyu Zhao
- Department of Biomedical Informatics, MOE Key Lab of Cardiovascular Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Prostate Cancer Program, Dana-Farber and Harvard Cancer Center, Harvard University, Boston, MA 02115, USA
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Min Zhang
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Shaodong Huang
- Department of Biomedical Informatics, MOE Key Lab of Cardiovascular Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Qi Liu
- Department of Urology, and Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Sen Zhu
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Yanqiang Li
- Prostate Cancer Program, Dana-Farber and Harvard Cancer Center, Harvard University, Boston, MA 02115, USA
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Weihua Jiang
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Daniel L Kiss
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Qi Cao
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Urology, and Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Lili Zhang
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Kaifu Chen
- Prostate Cancer Program, Dana-Farber and Harvard Cancer Center, Harvard University, Boston, MA 02115, USA
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
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12
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Vattem C, Pakala SB. Metastasis-associated protein 1: A potential driver and regulator of the hallmarks of cancer. J Biosci 2022. [DOI: 10.1007/s12038-022-00263-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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13
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Chatterjee B, Ghosh K, Swain A, Nalla KK, Ravula H, Pan A, Kanade SR. The phytochemical brazilin suppress DNMT1 expression by recruiting p53 to its promoter resulting in the epigenetic restoration of p21 in MCF7cells. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2022; 95:153885. [PMID: 34920321 DOI: 10.1016/j.phymed.2021.153885] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 11/23/2021] [Accepted: 12/05/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Cancer is an outcome of uncontrolled cell division eventually associated with dysregulated epigenetic mechanisms, including DNA methylation. DNA methyltransferase 1 is ubiquitously expressed in the proliferating cells and is essential for the maintenance of DNA methylation. It causes the abnormal silencing of tumor suppressor genes in human cancer which is necessary for proliferation, cell cycle progression, and survival. DNMT1 is involved in tumorigenesis of several cancers, its upregulation potentially upscale the promoter level inactivation of transcription of a tumor inhibitory gene by introducing repressive methylation marks on the CpG islands. This epigenetic perturbation caused by DNMT is targeted for cancer therapeutics. PURPOSE To demonstrate the proliferative inhibitory potential of brazilin in human breast cancer cell line (MCF-7) with concurrent mitigation of DNMT1 functional expression and to understand its effect on downstream targets like cell cycle inhibitor p21. STUDY DESIGN/ METHODS The impact of brazilin on the growth and proliferation of the MCF-7 cells was determined using the XTT assay. The global DNA 5-methyl cytosine methylation pattern was analyzed upon brazilin treatment. The gene and protein expression of DNMTs were determined with quantitative RTPCR and western blots respectively. The potential binding sites of transcription factors in the human DNMT1 promoter were predicted using the MatInspector tool on the Genomatix software. The chromatin immunoprecipitation (ChIP) assay was performed to demonstrate the transcription factors occupancy at the promoter. Methylation of promoter CpG islands was determined by the methylation-specific PCR (MSP) upon brazilin treatment. The molecular docking of the human DNMT1 with brazilin (ligand) was performed using the Schrödinger suite. RESULTS The heterotetracyclic compound brazilin, present in the wood of Caesalpinia sappan, inhibited the proliferation of the human breast cancer cell line (MCF-7) and reduced the DNMT1 expression with a decrease in global DNA methylation. Brazilin, by activating p38 MAPK and elevating p53 levels within the exposed cells. The elevated level of p53 enriched the occupancy at binding sites within 200 bp upstream to the transcription start site in the DNMT1 promoter, resulting in reduced DNMT1 gene expression. Furthermore, the brazilin restored the p21 levels in the exposed cells as the CpGs in the p21 promoter (-128 bp/+17 bp) were significantly demethylated as observed in the methylation-specific PCR (MSP). CONCLUSION Highly potential anti-proliferative molecule brazilin can modulate the DNMT1 functional expression and restore the cell cycle inhibitor p21expression. We propose that brazilin can be used in therapeutic interventions to restore the deregulated epigenetic mechanisms in cancer.
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Affiliation(s)
- Biji Chatterjee
- Department of Biochemistry and Molecular Biology, School of Biological Sciences, Central University of Kerala, Kasargod-671316, Kerala, India
| | - Krishna Ghosh
- Department of Biochemistry and Molecular Biology, School of Biological Sciences, Central University of Kerala, Kasargod-671316, Kerala, India
| | - Aishwarya Swain
- Centre for Bioinformatics, Pondicherry University, Puducherry-605014, India
| | - Kiran Kumar Nalla
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Central University P.O., Hyderabad-500046, Telangana, India
| | - Haritha Ravula
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Central University P.O., Hyderabad-500046, Telangana, India
| | - Archana Pan
- Centre for Bioinformatics, Pondicherry University, Puducherry-605014, India
| | - Santosh R Kanade
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Central University P.O., Hyderabad-500046, Telangana, India.
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14
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Jurkowska RZ, Jeltsch A. Enzymology of Mammalian DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:69-110. [DOI: 10.1007/978-3-031-11454-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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15
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Abstract
Chromatin is highly dynamic, undergoing continuous global changes in its structure and type of histone and DNA modifications governed by processes such as transcription, repair, replication, and recombination. Members of the chromodomain helicase DNA-binding (CHD) family of enzymes are ATP-dependent chromatin remodelers that are intimately involved in the regulation of chromatin dynamics, altering nucleosomal structure and DNA accessibility. Genetic studies in yeast, fruit flies, zebrafish, and mice underscore essential roles of CHD enzymes in regulating cellular fate and identity, as well as proper embryonic development. With the advent of next-generation sequencing, evidence is emerging that these enzymes are subjected to frequent DNA copy number alterations or mutations and show aberrant expression in malignancies and other human diseases. As such, they might prove to be valuable biomarkers or targets for therapeutic intervention.
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Affiliation(s)
- Andrej Alendar
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
| | - Anton Berns
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
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16
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Wang H, Feng Y, Sun J, Zhang W, Han Z, Yu S, Gu Y, Cheng X, Lin Z, Na M. Methyl-CpG-Binding Domain Protein 3 Promotes Seizures by Recruiting Methyltransferase DNMT1 to Enhance TREM2 Methylation. Neurochem Res 2021; 46:2451-2462. [PMID: 34173118 DOI: 10.1007/s11064-021-03371-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 10/21/2022]
Abstract
Epilepsy represents a hazardous neurological disorder, underpinned by a pathophysiological process that is yet to be fully understood. Here, we aimed to elucidate the effect of methyl-CpG-binding domain protein 3 (MBD3) on hippocampal neuronal damage in epileptic mice by targeting the phosphatidylinositol 3-kinase/protein kinase B (PI3K/Akt) pathway. The expression of MBD3 was determined by Western blot in a hippocampal neuronal culture (HNC) epileptic model established using the low Mg2+ECF culture method. The interaction between MBD3 and DNA methyltransferase 1 (DNMT1) was determined via co-immunoprecipitation and mass spectrometry analysis. Bisulfite modification and sequencing was performed to evaluate the degree of methylation of triggering receptor expressed on myeloid cells 2 (TREM2). The viability and apoptosis of hippocampal neurons were detected by CCK-8 and TUNEL assays, respectively. Finally, the effect of MBD3 was verified in vivo. MBD3 was highly expressed in the HNC model of epilepsy, with its interaction with DNMT1 found to promote the hypermethylation of TREM2 at site cg25748868. Additionally, decreased TREM2 and inhibited PI3K/Akt pathway was observed in the HNC epileptic model. Simultaneous inhibition of MBD3 and DNMT1 decreased the methylation level at cg25748868, up-regulated TREM2 expression, and activated the PI3K/Akt pathway, thereby arresting neuronal damage. Inhibition of MBD3 reduced the level of epileptic seizures, down-regulated cg25748868 methylation, activated TREM2-mediated signaling pathways, and alleviated hippocampal neuronal damage in the acute seizure mouse models. The present study unveiled that MBD3 and DNMT1 synergistically enhanced hypermethylation of cg25748868 in TREM2, and promoted the onset of epilepsy via inhibition of the PI3K/Akt pathway.
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Affiliation(s)
- Haiyang Wang
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, No. 23, Youzheng Street, Nangang District, Harbin, 150001, Heilongjiang Province, People's Republic of China
| | - Yumeng Feng
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, No. 23, Youzheng Street, Nangang District, Harbin, 150001, Heilongjiang Province, People's Republic of China
| | - Jiaying Sun
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, No. 23, Youzheng Street, Nangang District, Harbin, 150001, Heilongjiang Province, People's Republic of China
| | - Wang Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, No. 23, Youzheng Street, Nangang District, Harbin, 150001, Heilongjiang Province, People's Republic of China
| | - Zhibin Han
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, No. 23, Youzheng Street, Nangang District, Harbin, 150001, Heilongjiang Province, People's Republic of China
| | - Shengkun Yu
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, No. 23, Youzheng Street, Nangang District, Harbin, 150001, Heilongjiang Province, People's Republic of China
| | - Yifei Gu
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, No. 23, Youzheng Street, Nangang District, Harbin, 150001, Heilongjiang Province, People's Republic of China
| | - Xingbo Cheng
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, No. 23, Youzheng Street, Nangang District, Harbin, 150001, Heilongjiang Province, People's Republic of China
| | - Zhiguo Lin
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, No. 23, Youzheng Street, Nangang District, Harbin, 150001, Heilongjiang Province, People's Republic of China
| | - Meng Na
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, No. 23, Youzheng Street, Nangang District, Harbin, 150001, Heilongjiang Province, People's Republic of China.
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17
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Chang CL, Huang CR, Chang SJ, Wu CC, Chen HH, Luo CW, Yip HK. CHD4 as an important mediator in regulating the malignant behaviors of colorectal cancer. Int J Biol Sci 2021; 17:1660-1670. [PMID: 33994851 PMCID: PMC8120460 DOI: 10.7150/ijbs.56976] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/28/2021] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer (CRC) has ranked first in terms of incidence in Taiwan. Surgical resection combined with chemo-, radio-, or targeted-therapies are the main treatments for CRC patients in current clinical practice. However, many CRC patients still respond poorly to these treatments, leading to tumor recurrence and an unacceptably high incidence of metastasis and death. Therefore, appropriate diagnosis, treatment, and drug selection are pressing issues in clinical practice. The Mi-2/nucleosome remodeling and deacetylase complex is an important epigenetic regulator of chromatin structure and gene expression. An important component of this complex is chromodomain-helicase-DNA-binding protein 4 (CHD4), which is involved in DNA repair after injury. Recent studies have indicated that CHD4 has oncogenic functions that inhibit multiple tumor suppressor genes through epigenetic regulation. However, the role of CHD4 in CRC has not yet been well investigated. In this study, we compared CHD4 expression in CRC patients from The Cancer Genome Atlas database. We found higher levels of CHD4 expression in CRC patients. In a series of in vitro experiments, we found that CHD4 affected cell motility and drug sensitivity in CRC cells. In animal models, the depletion of CHD4 affected CRC tumor growth, and the combination of a histone deacetylase 1 (HDAC1) inhibitor and platinum drugs inhibited CHD4 expression and increased the cytotoxicity of platinum drugs. Moreover, CHD4 expression was also a prognostic biomarker in CRC patients. Based on the above results, we believe that CHD4 expression is a viable biomarker for predicting metastasis CRC patients, and it has the potential to become a target for drug development.
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Affiliation(s)
- Chia-Lo Chang
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chi-Ruei Huang
- Center for Shockwave Medicine and Tissue Engineering, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan.,Division of Cardiology, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Shu-Jyuan Chang
- Department of Pathology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Department of Pathology, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chun-Chieh Wu
- Department of Pathology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Hong-Hwa Chen
- Division of Colorectal Surgery, Department of Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chi-Wen Luo
- Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Division of Breast Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Hon-Kan Yip
- Center for Shockwave Medicine and Tissue Engineering, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan.,Division of Cardiology, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan.,Institute for Translational Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital Kaohsiung, Taiwan.,Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan.,Department of Nursing, Asia University Taichung, Taiwan.,Division of Cardiology, Department of Internal Medicine, Xiamen Chang Gung Hospital, Xiamen, Fujian, China
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18
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Lüdtke TH, Wojahn I, Kleppa MJ, Schierstaedt J, Christoffels VM, Künzler P, Kispert A. Combined genomic and proteomic approaches reveal DNA binding sites and interaction partners of TBX2 in the developing lung. Respir Res 2021; 22:85. [PMID: 33731112 PMCID: PMC7968368 DOI: 10.1186/s12931-021-01679-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/07/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Tbx2 encodes a transcriptional repressor implicated in the development of numerous organs in mouse. During lung development TBX2 maintains the proliferation of mesenchymal progenitors, and hence, epithelial proliferation and branching morphogenesis. The pro-proliferative function was traced to direct repression of the cell-cycle inhibitor genes Cdkn1a and Cdkn1b, as well as of genes encoding WNT antagonists, Frzb and Shisa3, to increase pro-proliferative WNT signaling. Despite these important molecular insights, we still lack knowledge of the DNA occupancy of TBX2 in the genome, and of the protein interaction partners involved in transcriptional repression of target genes. METHODS We used chromatin immunoprecipitation (ChIP)-sequencing and expression analyses to identify genomic DNA-binding sites and transcription units directly regulated by TBX2 in the developing lung. Moreover, we purified TBX2 containing protein complexes from embryonic lung tissue and identified potential interaction partners by subsequent liquid chromatography/mass spectrometry. The interaction with candidate proteins was validated by immunofluorescence, proximity ligation and individual co-immunoprecipitation analyses. RESULTS We identified Il33 and Ccn4 as additional direct target genes of TBX2 in the pulmonary mesenchyme. Analyzing TBX2 occupancy data unveiled the enrichment of five consensus sequences, three of which match T-box binding elements. The remaining two correspond to a high mobility group (HMG)-box and a homeobox consensus sequence motif. We found and validated binding of TBX2 to the HMG-box transcription factor HMGB2 and the homeobox transcription factor PBX1, to the heterochromatin protein CBX3, and to various members of the nucleosome remodeling and deacetylase (NuRD) chromatin remodeling complex including HDAC1, HDAC2 and CHD4. CONCLUSION Our data suggest that TBX2 interacts with homeobox and HMG-box transcription factors as well as with the NuRD chromatin remodeling complex to repress transcription of anti-proliferative genes in the pulmonary mesenchyme.
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Affiliation(s)
- Timo H Lüdtke
- Institut Für Molekularbiologie, Medizinische Hochschule Hannover, Hannover, Germany
| | - Irina Wojahn
- Institut Für Molekularbiologie, Medizinische Hochschule Hannover, Hannover, Germany
| | - Marc-Jens Kleppa
- Institut Für Molekularbiologie, Medizinische Hochschule Hannover, Hannover, Germany
| | - Jasper Schierstaedt
- Institut Für Molekularbiologie, Medizinische Hochschule Hannover, Hannover, Germany
- Plant-Microbe Systems, Leibniz Institute of Vegetable and Ornamental Crops, Großbeeren, Germany
| | - Vincent M Christoffels
- Department of Anatomy, Embryology and Physiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Patrick Künzler
- Institut Für Pflanzengenetik, Leibniz Universität Hannover, Hannover, Germany
| | - Andreas Kispert
- Institut Für Molekularbiologie, Medizinische Hochschule Hannover, Hannover, Germany.
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19
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Sharma A, Liu H, Herwig-Carl MC, Chand Dakal T, Schmidt-Wolf IGH. Epigenetic Regulatory Enzymes: mutation Prevalence and Coexistence in Cancers. Cancer Invest 2021; 39:257-273. [PMID: 33411587 DOI: 10.1080/07357907.2021.1872593] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Epigenetic regulation is an important layer of transcriptional control with the particularity to affect the broad spectrum of genome. Over the years, largely due to the substantial number of recurrent mutations, there have been hundreds of novel driver genes characterized in various cancers. Additionally, the relative contribution of two dysregulated epigenomic entities (DNA methylation and histone modifications) that gradually drive the cancer phenotype remains in the research focus. However, a complex scenario arises when the disease phenotype does not harbor any relevant mutation or an abnormal transcription level. Although the cancer landscape involves the contribution of multiple genetic and non-genetic factors, herein, we discuss specifically the mutation spectrum of epigenetically-related enzymes in cancer. In addition, we address the coexistence of these two epigenetic entities in malignant human diseases, especially cancer. We suggest that the study of epigenetically-related somatic mutations in the early cellular differentiation stage of embryonic development might help to understand their later-staged footprints in the cancer genome. Furthermore, understanding the co-occurrence and/or inverse association of different disease types and redefining the general definition of "healthy" controls could provide insights into the genome reorganization.
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Affiliation(s)
- Amit Sharma
- Department of Integrated Oncology, CIO Bonn, University Hospital Bonn, Bonn, Germany.,Department of Neurology, University Hospital Bonn, Bonn, Germany
| | - Hongde Liu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing, China
| | | | - Tikam Chand Dakal
- Department of Biotechnology, Mohanlal Sukhadia University, Rajasthan, India
| | - Ingo G H Schmidt-Wolf
- Department of Integrated Oncology, CIO Bonn, University Hospital Bonn, Bonn, Germany
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20
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CHD4 Predicts Aggressiveness in PTC Patients and Promotes Cancer Stemness and EMT in PTC Cells. Int J Mol Sci 2021; 22:ijms22020504. [PMID: 33419089 PMCID: PMC7825451 DOI: 10.3390/ijms22020504] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/31/2020] [Accepted: 01/01/2021] [Indexed: 12/31/2022] Open
Abstract
Chromodomain-helicase-DNA-binding protein 4 (CHD4), a core subunit of the nucleosome remodeling and deacetylation (NuRD) complex is highly expressed in several cancers. However, its role in the pathogenesis and progression of papillary thyroid carcinoma (PTC) has not been investigated. We investigated the prognostic significance of CHD4 in a large cohort of Middle Eastern PTC patients and explored the functional role of CHD4 in regulating cancer stemness and EMT in PTC cells. CHD4 overexpression was observed in 45.3% (650/1436) of PTCs, and was associated with aggressive clinico-pathological parameters and worse outcome. Functional analysis using PTC cell lines showed that forced expression of CHD4 promoted cell proliferation, spheroid growth, migration, invasion and progression of epithelial to mesenchymal transition (EMT) in PTC cells whereas its knockdown reversed the effect. Methylation of E-cadherin was associated with loss of expression in CHD4 expressing cells, while CHD4 depletion reactivated E-cadherin expression. Most importantly, knockdown of mesenchymal transcriptional factors, Snail1 or Zeb1, attenuated the spheroid growth in CHD4 expressing PTC cells, showing a potential link between EMT activation and stemness maintenance in PTC. These findings suggest that CHD4 might be a promising therapeutic target in the treatment of patients with an aggressive subtype of PTC.
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21
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He L, Chang H, Qi Y, Zhang B, Shao Q. ceRNA Networks: The Backbone Role in Neoadjuvant Chemoradiotherapy Resistance/Sensitivity of Locally Advanced Rectal Cancer. Technol Cancer Res Treat 2021; 20:15330338211062313. [PMID: 34908512 PMCID: PMC8689620 DOI: 10.1177/15330338211062313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/21/2021] [Accepted: 11/02/2021] [Indexed: 11/30/2022] Open
Abstract
Approximately 40% of rectal cancers during initial diagnosis are identified as locally advanced rectal cancers (LARCs), for which the standardized treatment scenario is total mesorectal excision following neoadjuvant chemoradiotherapy (nCRT). nCRT can lead to discernible reductions in local relapse rate and distant metastasis rate in LARC patients, in whom previously inoperable tumors may potentially be surgically removed. However, only 4% to 20% cases can attain pathological complete response, and the remaining patients who are unresponsive to nCRT have to suffer from the side effects plus toxicities and may encounter poor survival outcomes due to the late surgical intervention. As such, employing potential biomarkers to differentiate responders from nonresponders before nCRT implementation appears to be the overarching goal. Well-defined competing endogenous RNA (ceRNA) networks include long noncoding RNA (lncRNA)-microRNA (miRNA)-mRNA and circRNA-miRNA-mRNA networks. As ceRNAs, lncRNAs, and circRNAs sponge miRNAs to indirectly suppress miRNAs downstream of oncogenic mRNAs or tumor-suppressive mRNAs. The abnormal expression of mRNAs regulates the nCRT-induced DNA damage repair process through pluralistic carcinogenic signaling pathways, thereby bringing about alterations in the nCRT resistance/sensitivity of tumors. Moreover, many molecular mechanisms relevant to cell proliferation, metastasis, or apoptosis of cancers (eg, epithelial-mesenchymal transition and caspase-9-caspase-3 pathway) are influenced by ceRNA networks. Herein, we reviewed a large group of abnormally expressed mRNAs and noncoding RNAs that are associated with nCRT resistance/sensitivity in LARC patients and ultimately pinpointed the backbone role of ceRNA networks in the molecular mechanisms of nCRT resistance/sensitivity.
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Affiliation(s)
- Lin He
- Department of Radiotherapy, Tangdu Hospital, Air Force Military Medical University, Xi’an, Shaanxi Province, China
- Cancer Centre, Faculty of Health Sciences, University of Macau, Macau, SAR, China
| | - Hao Chang
- Department of Radiotherapy, Tangdu Hospital, Air Force Military Medical University, Xi’an, Shaanxi Province, China
| | - Yuhong Qi
- Department of Radiotherapy, Tangdu Hospital, Air Force Military Medical University, Xi’an, Shaanxi Province, China
| | - Bing Zhang
- Department of Radiotherapy, Tangdu Hospital, Air Force Military Medical University, Xi’an, Shaanxi Province, China
| | - Qiuju Shao
- Department of Radiotherapy, Tangdu Hospital, Air Force Military Medical University, Xi’an, Shaanxi Province, China
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22
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Klutstein M. Cause and effect in epigenetics - where lies the truth, and how can experiments reveal it?: Epigenetic self-reinforcing loops obscure causation in cancer and aging. Bioessays 2020; 43:e2000262. [PMID: 33236359 DOI: 10.1002/bies.202000262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 12/19/2022]
Abstract
Epigenetic changes are implicated in aging and cancer. Sometimes, it is clear whether the causing agent of the condition is a genetic factor or epigenetic. In other cases, the causative factor is unclear, and could be either genetic or epigenetic. Is there a general role for epigenetic changes in cancer and aging? Here, I present the paradigm of causative roles executed by epigenetic changes. I discuss cases with clear roles of the epigenome in cancer and aging, and other cases showing involvement of other factors. I also present the possibility that sometimes causality is difficult to assign because of the presence of self-reinforcing loops in epigenetic regulation. Such loops hinder the identification of the causative factor. I provide an experimental framework by which the role of the epigenome can be examined in a better setting and where the presence of such loops could be investigated in more detail.
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Affiliation(s)
- Michael Klutstein
- Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Ein Kerem, Jerusalem, Israel
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23
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Rashid F, Ahmad S, Irudayaraj JMK. Effect of Perfluorooctanoic Acid on the Epigenetic and Tight Junction Genes of the Mouse Intestine. TOXICS 2020; 8:toxics8030064. [PMID: 32872178 PMCID: PMC7560341 DOI: 10.3390/toxics8030064] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/13/2022]
Abstract
Perfluorooctanoic acid (PFOA) has been implicated in various toxicities including neurotoxicity, genotoxicity, nephrotoxicity, epigenetic toxicity, immunotoxicity, reproductive toxicity, and hepatotoxicity. However, information on the accumulation of PFOA in the intestine and its toxic effects on intestinal epigenetics and tight junction (TJ) genes is sparse. CD1 mice were dosed with PFOA (1, 5, 10, or 20 mg/kg/day) for 10 days, and its accumulation and induced alterations in the expression of epigenetic and tight junction genes in the small intestine and colon were evaluated using LC-MS and qPCR techniques. PFOA reduced the expression levels of DNA methyltransferases (Dnmt1, Dnmt3a, Dnmt3b) primarily in the small intestine whereas, in the colon, a decrease was observed only at high concentrations. Moreover, ten-eleven translocation genes (Tet2 and Tet3) expression was dysregulated in the small intestine, whereas in the colon Tets remained unaffected. The tight junction genes Claudins (Cldn), Occludin (Ocln), and Tight Junction Protein (Tjp) were also heavily altered in the small intestine. TJs responded differently across the gut, in proportion to PFOA dosing. Our study reveals that PFOA triggers DNA methylation changes and alters the expression of genes essential for maintaining the physical barrier of intestine, with more profound effects in the small intestine compared to the colon.
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Affiliation(s)
- Faizan Rashid
- Biomedical Research Center in Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, IL 61801, USA; (F.R.); (S.A.)
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Saeed Ahmad
- Biomedical Research Center in Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, IL 61801, USA; (F.R.); (S.A.)
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Joseph Maria Kumar Irudayaraj
- Biomedical Research Center in Mills Breast Cancer Institute, Carle Foundation Hospital, Urbana, IL 61801, USA; (F.R.); (S.A.)
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Correspondence: ; Tel.: +1-765-404-0499
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24
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Saravanaraman P, Selvam M, Ashok C, Srijyothi L, Baluchamy S. De novo methyltransferases: Potential players in diseases and new directions for targeted therapy. Biochimie 2020; 176:85-102. [PMID: 32659446 DOI: 10.1016/j.biochi.2020.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 06/06/2020] [Accepted: 07/07/2020] [Indexed: 12/16/2022]
Abstract
Epigenetic modifications govern gene expression by guiding the human genome on 'what to express and what not to'. DNA methyltransferases (DNMTs) establish methylation patterns on DNA, particularly in CpG islands, and such patterns play a major role in gene silencing. DNMTs are a family of proteins/enzymes (DNMT1, 2, 3A, 3B, and 3L), among which, DNMT1 (maintenance methyltransferase) and DNMT3 (de novo methyltransferases) that direct mammalian development and genome imprinting are highly investigated. In recent decades, many studies revealed a strong association of DNA methylation patterns with gene expression in various clinical conditions. Differential expression of DNMT3 family proteins and their splice variants result in changes in methylation patterns and such alterations have been associated with the initiation and progression of various diseases, especially cancer. This review will discuss the aberrant modifications generated by DNMT3 proteins under various clinical conditions, suggesting a potential signature for de novo methyltransferases in targeted disease therapy. Further, this review discusses the possibility of using 'CpG island methylation signatures' as promising biomarkers and emphasizes 'targeted hypomethylation' by disrupting the interaction of specific DNMT-protein complexes as the future of cancer therapeutics.
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Affiliation(s)
- Ponne Saravanaraman
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India
| | - Murugan Selvam
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India
| | - Cheemala Ashok
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India
| | - Loudu Srijyothi
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India
| | - Sudhakar Baluchamy
- Department of Biotechnology, Pondicherry Central University, Pondicherry, 605014, India.
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25
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Gong W, Ni M, Chen Z, Zheng Z. Expression and clinical significance of methyl-CpG binding domain protein 2 in high-grade serous ovarian cancer. Oncol Lett 2020; 20:2749-2756. [PMID: 32782591 PMCID: PMC7400232 DOI: 10.3892/ol.2020.11836] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 06/08/2020] [Indexed: 12/12/2022] Open
Abstract
Platinum resistance is an important cause of clinical recurrence and mortality of patients with high-grade serous ovarian cancer (HGSOC). Methyl-CpG binding domain protein 2 (MBD2) serves an important role in tumor progression; however, its role in HGSOC remains unclear. The aim of the present study was to investigate the expression of MBD2 in HGSOC and its role in drug resistance and prognosis of HGSOC. MBD2 expression was analyzed by immunohistochemical staining and western blotting. The associations between MBD2 expression and clinical pathological features, platinum resistance and patient prognosis were analyzed using a χ2 test, Kaplan-Meier analysis and Cox regression analysis. Positive MBD2 expression was detected in 73 (63.5%) of the HGSOC tissue samples, whereas it was undetectable in all 16 normal tissue samples (100%) analyzed, indicating a significantly higher expression level in tumor tissues compared with normal tissues (P<0.001). Additionally, MBD2 expression was significantly higher in platinum-resistant cases compared with that in platinum-sensitive cases (P<0.05). In addition, high expression of MBD2 was negatively associated with relapse-free survival (P<0.05). In conclusion, MBD2 was demonstrated to be a potential drug target and a biomarker for poor prognosis in HGSOC.
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Affiliation(s)
- Wangang Gong
- College of Life Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, P.R. China.,Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China.,Zhejiang Cancer Research Institute, Cancer Hospital of The University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, P.R. China.,Zhejiang Cancer Research Institute, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China
| | - Maowei Ni
- Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China.,Zhejiang Cancer Research Institute, Cancer Hospital of The University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, P.R. China.,Zhejiang Cancer Research Institute, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China
| | - Zhongbo Chen
- Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China.,Zhejiang Cancer Research Institute, Cancer Hospital of The University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, P.R. China.,Zhejiang Cancer Research Institute, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China
| | - Zhiguo Zheng
- Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China.,Zhejiang Cancer Research Institute, Cancer Hospital of The University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, P.R. China.,Zhejiang Cancer Research Institute, Zhejiang Cancer Hospital, Hangzhou, Zhejiang 310022, P.R. China
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26
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Salvati A, Gigantino V, Nassa G, Mirici Cappa V, Ventola GM, Cracas DGC, Mastrocinque R, Rizzo F, Tarallo R, Weisz A, Giurato G. Global View of Candidate Therapeutic Target Genes in Hormone-Responsive Breast Cancer. Int J Mol Sci 2020; 21:ijms21114068. [PMID: 32517194 PMCID: PMC7312026 DOI: 10.3390/ijms21114068] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 05/29/2020] [Accepted: 06/03/2020] [Indexed: 12/17/2022] Open
Abstract
Breast cancer (BC) is a heterogeneous disease characterized by different biopathological features, differential response to therapy and substantial variability in long-term-survival. BC heterogeneity recapitulates genetic and epigenetic alterations affecting transformed cell behavior. The estrogen receptor alpha positive (ERα+) is the most common BC subtype, generally associated with a better prognosis and improved long-term survival, when compared to ERα-tumors. This is mainly due to the efficacy of endocrine therapy, that interfering with estrogen biosynthesis and actions blocks ER-mediated cell proliferation and tumor spread. Acquired resistance to endocrine therapy, however, represents a great challenge in the clinical management of ERα+ BC, causing tumor growth and recurrence irrespective of estrogen blockade. Improving overall survival in such cases requires new and effective anticancer drugs, allowing adjuvant treatments able to overcome resistance to first-line endocrine therapy. To date, several studies focus on the application of loss-of-function genome-wide screenings to identify key (hub) “fitness” genes essential for BC progression and representing candidate drug targets to overcome lack of response, or acquired resistance, to current therapies. Here, we review the biological significance of essential genes and relative functional pathways affected in ERα+ BC, most of which are strictly interconnected with each other and represent potential effective targets for novel molecular therapies.
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Affiliation(s)
- Annamaria Salvati
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, 84081 Baronissi (SA), Italy; (A.S.); (V.G.); (G.N.); (V.M.C.); (F.R.); (R.T.)
| | - Valerio Gigantino
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, 84081 Baronissi (SA), Italy; (A.S.); (V.G.); (G.N.); (V.M.C.); (F.R.); (R.T.)
| | - Giovanni Nassa
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, 84081 Baronissi (SA), Italy; (A.S.); (V.G.); (G.N.); (V.M.C.); (F.R.); (R.T.)
| | - Valeria Mirici Cappa
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, 84081 Baronissi (SA), Italy; (A.S.); (V.G.); (G.N.); (V.M.C.); (F.R.); (R.T.)
| | | | | | | | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, 84081 Baronissi (SA), Italy; (A.S.); (V.G.); (G.N.); (V.M.C.); (F.R.); (R.T.)
| | - Roberta Tarallo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, 84081 Baronissi (SA), Italy; (A.S.); (V.G.); (G.N.); (V.M.C.); (F.R.); (R.T.)
| | - Alessandro Weisz
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, 84081 Baronissi (SA), Italy; (A.S.); (V.G.); (G.N.); (V.M.C.); (F.R.); (R.T.)
- CRGS—Genome Research Center for Health, University of Salerno Campus of Medicine, 84081 Baronissi (SA), Italy
- Correspondence: (A.W.); (G.G.); Tel.: +39-089-965043 (A.W.); +39-089-968286 (G.G.)
| | - Giorgio Giurato
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, 84081 Baronissi (SA), Italy; (A.S.); (V.G.); (G.N.); (V.M.C.); (F.R.); (R.T.)
- Correspondence: (A.W.); (G.G.); Tel.: +39-089-965043 (A.W.); +39-089-968286 (G.G.)
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27
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Kovács T, Szabó-Meleg E, Ábrahám IM. Estradiol-Induced Epigenetically Mediated Mechanisms and Regulation of Gene Expression. Int J Mol Sci 2020; 21:ijms21093177. [PMID: 32365920 PMCID: PMC7246826 DOI: 10.3390/ijms21093177] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 04/22/2020] [Accepted: 04/28/2020] [Indexed: 12/20/2022] Open
Abstract
Gonadal hormone 17β-estradiol (E2) and its receptors are key regulators of gene transcription by binding to estrogen responsive elements in the genome. Besides the classical genomic action, E2 regulates gene transcription via the modification of epigenetic marks on DNA and histone proteins. Depending on the reaction partner, liganded estrogen receptor (ER) promotes DNA methylation at the promoter or enhancer regions. In addition, ERs are important regulators of passive and active DNA demethylation. Furthermore, ERs cooperating with different histone modifying enzymes and chromatin remodeling complexes alter gene transcription. In this review, we survey the basic mechanisms and interactions between estrogen receptors and DNA methylation, demethylation and histone modification processes as well as chromatin remodeling complexes. The particular relevance of these mechanisms to physiological processes in memory formation, embryonic development, spermatogenesis and aging as well as in pathophysiological changes in carcinogenesis is also discussed.
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Affiliation(s)
- Tamás Kovács
- Molecular Neuroendocrinology Research Group, Institute of Physiology, Medical School, Centre for Neuroscience, Szentágothai Research Center, University of Pécs, H-7624 Pécs, Hungary;
| | - Edina Szabó-Meleg
- Department of Biophysics, Medical School, University of Pécs, H-7624 Pécs, Hungary;
| | - István M. Ábrahám
- Molecular Neuroendocrinology Research Group, Institute of Physiology, Medical School, Centre for Neuroscience, Szentágothai Research Center, University of Pécs, H-7624 Pécs, Hungary;
- Correspondence:
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28
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Cellular thermal shift analysis for interrogation of CRISPR-assisted proteomic changes. Biotechniques 2020; 68:180-184. [DOI: 10.2144/btn-2019-0100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
CRISPR–Cas9 has proven to be a versatile tool for the discovery of essential genetic elements involved in various disease states. CRISPR-assisted dense mutagenesis focused on therapeutically challenging protein complexes allows us to systematically perturb protein-coding sequences in situ and correlate them with functional readouts. Such perturbations can mimic targeting by therapeutics and serve as a foundation for the discovery of highly specific modulators. However, translation of such genomics data has been challenging due to the missing link for proteomics under the physiological state of the cell. We present a method based on cellular thermal shift assays to easily interrogate proteomic shifts generated by CRISPR-assisted dense mutagenesis, as well as a case focused on NuRD epigenetic complex.
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29
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Masoodi T, Siraj AK, Siraj S, Azam S, Qadri Z, Albalawy WN, Parvathareddy SK, Al-Sobhi SS, Al-Dayel F, Alkuraya FS, Al-Kuraya KS. Whole-Exome Sequencing of Matched Primary and Metastatic Papillary Thyroid Cancer. Thyroid 2020; 30:42-56. [PMID: 31668133 PMCID: PMC6983753 DOI: 10.1089/thy.2019.0052] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Background: Distant metastasis is a rare occurrence in thyroid cancer, and it can be associated with poor prognosis. The genomic repertoires of various solid malignancies have previously been reported but remain underexplored in metastatic papillary thyroid cancer (PTC). Furthermore, whether distant metastases harbor distinct genetic alterations beyond those observed in primary tumors is unknown. Methods: We performed whole-exome sequencing on 14 matched distant metastases, primary PTC tumors, and normal tissues. Point mutations, copy number alterations, cancer cell fractions, and mutational signatures were defined using the state-of-the-art bioinformatics methods. All likely deleterious variants were validated by orthogonal methods. Results: Genomic differences were observed between primary and distant metastatic deposits, with a median of 62% (range 21-92%) of somatic mutations detected in metastatic tissues, but absent from the corresponding primary tumor sample. Mutations in known driver genes including BRAF, NRAS, and HRAS were shared and preferentially clonal in both sites. However, likely deleterious variants affecting DNA methylation and transcriptional repression signaling genes including SIN3A, RBBP1, and CHD4 were found to be restricted in the metastatic lesions. Moreover, a mutational signature shift was observed between the mutations that are specific or enriched in the metastatic and primary lesions. Conclusions: Primary PTC and distant metastases differ in their range of somatic alterations. Genomic analysis of distant metastases provides an opportunity to identify potentially clinically informative alterations not detected in primary tumors, which might influence decisions for personalized therapy in PTC patients with distant metastasis.
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Affiliation(s)
- Tariq Masoodi
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Abdul K. Siraj
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Sarah Siraj
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Saud Azam
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Zeeshan Qadri
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Wafaa N. Albalawy
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | | | - Saif S. Al-Sobhi
- Department of Surgery, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Fouad Al-Dayel
- Department of Pathology, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Fowzan S. Alkuraya
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
- Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Fowzan S. Alkuraya, MD, Department of Genetics, King Faisal Specialist Hospital and Research Centre, MBC-03, PO Box 3354, Riyadh 11211, Saudi Arabia
| | - Khawla S. Al-Kuraya
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
- Address correspondence to: Khawla S. Al-Kuraya, MD, Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Center, MBC#98-16, PO Box 3354, Riyadh 11211, Saudi Arabia
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30
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Brumbaugh J, Di Stefano B, Hochedlinger K. Reprogramming: identifying the mechanisms that safeguard cell identity. Development 2019; 146:146/23/dev182170. [PMID: 31792064 DOI: 10.1242/dev.182170] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Development and homeostasis rely upon concerted regulatory pathways to establish the specialized cell types needed for tissue function. Once a cell type is specified, the processes that restrict and maintain cell fate are equally important in ensuring tissue integrity. Over the past decade, several approaches to experimentally reprogram cell fate have emerged. Importantly, efforts to improve and understand these approaches have uncovered novel molecular determinants that reinforce lineage commitment and help resist cell fate changes. In this Review, we summarize recent studies that have provided insights into the various chromatin factors, post-transcriptional processes and features of genomic organization that safeguard cell identity in the context of reprogramming to pluripotency. We also highlight how these factors function in other experimental, physiological and pathological cell fate transitions, including direct lineage conversion, pluripotency-to-totipotency reversion and cancer.
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Affiliation(s)
- Justin Brumbaugh
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Bruno Di Stefano
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA.,Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA.,Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA.,Department of Genetics, Harvard Medical School, Boston, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.,Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA
| | - Konrad Hochedlinger
- Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA .,Center for Regenerative Medicine, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA.,Cancer Center, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA.,Department of Genetics, Harvard Medical School, Boston, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.,Harvard Stem Cell Institute, 1350 Massachusetts Avenue, Cambridge, MA 02138, USA
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31
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Identification of CHD4-β1 integrin axis as a prognostic marker in triple-negative breast cancer using next-generation sequencing and bioinformatics. Life Sci 2019; 238:116963. [DOI: 10.1016/j.lfs.2019.116963] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 10/07/2019] [Accepted: 10/12/2019] [Indexed: 01/07/2023]
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32
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Hasan N, Ahuja N. The Emerging Roles of ATP-Dependent Chromatin Remodeling Complexes in Pancreatic Cancer. Cancers (Basel) 2019; 11:E1859. [PMID: 31769422 PMCID: PMC6966483 DOI: 10.3390/cancers11121859] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 02/08/2023] Open
Abstract
Pancreatic cancer is an aggressive cancer with low survival rates. Genetic and epigenetic dysregulation has been associated with the initiation and progression of pancreatic tumors. Multiple studies have pointed to the involvement of aberrant chromatin modifications in driving tumor behavior. ATP-dependent chromatin remodeling complexes regulate chromatin structure and have critical roles in stem cell maintenance, development, and cancer. Frequent mutations and chromosomal aberrations in the genes associated with subunits of the ATP-dependent chromatin remodeling complexes have been detected in different cancer types. In this review, we summarize the current literature on the genomic alterations and mechanistic studies of the ATP-dependent chromatin remodeling complexes in pancreatic cancer. Our review is focused on the four main subfamilies: SWItch/sucrose non-fermentable (SWI/SNF), imitation SWI (ISWI), chromodomain-helicase DNA-binding protein (CHD), and INOsitol-requiring mutant 80 (INO80). Finally, we discuss potential novel treatment options that use small molecules to target these complexes.
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Affiliation(s)
| | - Nita Ahuja
- Department of Surgery, Yale University School of Medicine, New Haven, CT 06520, USA;
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33
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Bowler EH, Smith-Vidal A, Lester A, Bell J, Wang Z, Bell CG, Wang Y, Divecha N, Skipp PJ, Ewing RM. Deep proteomic analysis of Dnmt1 mutant/hypomorphic colorectal cancer cells reveals dysregulation of epithelial-mesenchymal transition and subcellular re-localization of Beta-Catenin. Epigenetics 2019; 15:107-121. [PMID: 31448663 PMCID: PMC6961695 DOI: 10.1080/15592294.2019.1656154] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
DNA methyltransferase I plays the central role in maintenance of CpG DNA methylation patterns across the genome and alteration of CpG methylation patterns is a frequent and significant occurrence across many cancers. Cancer cells carrying hypomorphic alleles of Dnmt1 have become important tools for understanding Dnmt1 function and CpG methylation. In this study, we analyse colorectal cancer cells with a homozygous deletion of exons 3 to 5 of Dnmt1, resulting in reduced Dnmt1 activity. Although this cell model has been widely used to study the epigenome, the effects of the Dnmt1 hypomorph on cell signalling pathways and the wider proteome are largely unknown. In this study, we perform the first quantitative proteomic analysis of this important cell model and identify multiple signalling pathways and processes that are significantly dysregulated in the hypomorph cells. In Dnmt1 hypomorph cells, we observed a clear and unexpected signature of increased Epithelial-to-Mesenchymal transition (EMT) markers as well as reduced expression and sub-cellular re-localization of Beta-Catenin. Expression of wild-type Dnmt1 in hypomorph cells or knock-down of wild-type Dnmt1 did not recapitulate or rescue the observed protein profiles in Dnmt1 hypomorph cells suggesting that hypomorphic Dnmt1 causes changes not solely attributable to Dnmt1 protein levels. In summary, we present the first comprehensive proteomic analysis of the widely studied Dnmt1 hypomorph colorectal cancer cells and identify redistribution of Dnmt1 and its interaction partner Beta-Catenin.
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Affiliation(s)
- Emily H Bowler
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Alex Smith-Vidal
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Alex Lester
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Joseph Bell
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Zhenghe Wang
- School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Christopher G Bell
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Yihua Wang
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Nullin Divecha
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Paul J Skipp
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Rob M Ewing
- School of Biological Sciences, University of Southampton, Southampton, UK
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34
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Wang HC, Chou CL, Yang CC, Huang WL, Hsu YC, Luo CW, Chen TJ, Li CF, Pan MR. Over-Expression of CHD4 Is an Independent Biomarker of Poor Prognosis in Patients with Rectal Cancers Receiving Concurrent Chemoradiotherapy. Int J Mol Sci 2019; 20:ijms20174087. [PMID: 31438571 PMCID: PMC6747537 DOI: 10.3390/ijms20174087] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/19/2019] [Accepted: 08/19/2019] [Indexed: 12/18/2022] Open
Abstract
Neoadjuvant concurrent chemoradiotherapy (CCRT), followed by radical proctectomy, is the standard treatment for locally advanced rectal cancer. However, a poor response and therapeutic resistance continue to occur despite this treatment. In this study, we analyzed the microarray datasets (GSE68204) of rectal cancer from the Gene Expression Omnibus database, and identified CHD4 as one of the most significantly up-regulated genes among all subunits of the nucleosome remodeling and histone deacetylation (NuRD) complex, in non-responders to CCRT, among locally advanced rectal cancer (LARC) patients. We confirmed the predictive and prognostic significance of CHD4 expression in CCRT treatment, and its correlation with other clinicopathological features, such as tumor regression grade (TRG), therapeutic response, and patient survival. This was carried out by immunohistochemical studies on endoscopic biopsy tissues from 172 rectal cancer patients, receiving neoadjuvant concurrent chemoradiotherapy (CCRT). A high expression of CHD4 was significantly associated with pre-treatment tumor status (p < 0.001) and lymph node metastasis (p < 0.001), post-treatment tumor status (p < 0.001), and lymph node metastasis (p < 0.001), vascular invasion (p = 0.042), and tumor regression grade (p = 0.001). A high expression of CHD4 could also predict poor disease-specific survival and metastasis-free survival (log-rank test, p = 0.0373 and p < 0.0001, respectively). In multivariate Cox proportional-hazards regression analysis, CHD4 overexpression was an independent factor of poor prognosis for metastasis-free survival (HR, 4.575; 95% CI, 1.717–12.192; p = 0.002). By in vitro studies, based on cell line models, we also demonstrated that, the overexpression of CHD4 induced radio-resistance in microsatellite instability-high (MSI-H) colorectal cells (CRCs). On the contrary, the knockdown of CHD4 enhanced radiosensitivity in microsatellite stable (MSS) CRCs. Altogether, we have identified CHD4 as an important regulator of radio-resistance in both MSI-H and MSS CRC cell lines.
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Affiliation(s)
- Hui-Ching Wang
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Division of Hematology and Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Chia-Lin Chou
- Division of Colon & Rectal Surgery, Department of Surgery, Chi Mei Medical Center, Tainan 710, Taiwan
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan
| | - Ching-Chieh Yang
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan
- Department of Radiation Oncology, Chi-Mei Medical Center, Tainan 710, Taiwan
- Department of Pharmacy, Chia-Nan University of Pharmacy and Science, Tainan 71745, Taiwan
| | - Wei-Lun Huang
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Radiation Oncology, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan
| | - Yin-Chou Hsu
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Emergency Medicine, E-Da Hospital, I-Shou University, Kaohsiung 824, Taiwan
| | - Chi-Wen Luo
- Division of Breast Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
| | - Tzu-Ju Chen
- Institute of Biomedical Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan
- Department of Pathology, Chi Mei Medical Center, Tainan 710, Taiwan
- Department of Optometry, Chung Hwa University of Medical Technology, Tainan 717, Taiwan
| | - Chien-Feng Li
- Department of Pathology, Chi Mei Medical Center, Tainan 710, Taiwan
- Department of Medical Research, Chi Mei Medical Center, Tainan 710, Taiwan
- National Institute of Cancer Research, National Health Research Institute, Tainan 704, Taiwan
| | - Mei-Ren Pan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
- Drug Development and Value Creation Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan.
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Smith R, Sellou H, Chapuis C, Huet S, Timinszky G. CHD3 and CHD4 recruitment and chromatin remodeling activity at DNA breaks is promoted by early poly(ADP-ribose)-dependent chromatin relaxation. Nucleic Acids Res 2019; 46:6087-6098. [PMID: 29733391 PMCID: PMC6158744 DOI: 10.1093/nar/gky334] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 04/23/2018] [Indexed: 12/12/2022] Open
Abstract
One of the first events to occur upon DNA damage is the local opening of the compact chromatin architecture, facilitating access of repair proteins to DNA lesions. This early relaxation is triggered by poly(ADP-ribosyl)ation by PARP1 in addition to ATP-dependent chromatin remodeling. CHD4 recruits to DNA breaks in a PAR-dependent manner, although it lacks any recognizable PAR-binding domain, and has the ability to relax chromatin structure. However, its role in chromatin relaxation at the site of DNA damage has not been explored. Using a live cell fluorescence three-hybrid assay, we demonstrate that the recruitment of CHD4 to DNA damage, while being poly(ADP-ribosyl)ation-dependent, is not through binding poly(ADP-ribose). Additionally, we show that CHD3 is recruited to DNA breaks in the same manner as CHD4 and that both CHD3 and CHD4 play active roles in chromatin remodeling at DNA breaks. Together, our findings reveal a two-step mechanism for DNA damage induced chromatin relaxation in which PARP1 and the PAR-binding remodeler activities of Alc1/CHD1L induce an initial chromatin relaxation phase that promotes the subsequent recruitment of CHD3 and CHD4 via binding to DNA for further chromatin remodeling at DNA breaks.
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Affiliation(s)
- Rebecca Smith
- Biomedical Center Munich, Physiological Chemistry, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany.,Univ Rennes, CNRS, Structure fédérative de recherche Biosit, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F- 35000 Rennes, France
| | - Hafida Sellou
- Univ Rennes, CNRS, Structure fédérative de recherche Biosit, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F- 35000 Rennes, France
| | - Catherine Chapuis
- Univ Rennes, CNRS, Structure fédérative de recherche Biosit, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F- 35000 Rennes, France
| | - Sébastien Huet
- Univ Rennes, CNRS, Structure fédérative de recherche Biosit, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F- 35000 Rennes, France
| | - Gyula Timinszky
- Biomedical Center Munich, Physiological Chemistry, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany.,MTA SZBK Lendület DNA damage and nuclear dynamics research group, Biological Research Center of the Hungarian Academy of Sciences, 6276 Szeged, Hungary
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36
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Klanert G, Fernandez DJ, Weinguny M, Eisenhut P, Bühler E, Melcher M, Titus SA, Diendorfer AB, Gludovacz E, Jadhav V, Xiao S, Stern B, Lal M, Shiloach J, Borth N. A cross-species whole genome siRNA screen in suspension-cultured Chinese hamster ovary cells identifies novel engineering targets. Sci Rep 2019; 9:8689. [PMID: 31213643 PMCID: PMC6582146 DOI: 10.1038/s41598-019-45159-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 05/29/2019] [Indexed: 12/16/2022] Open
Abstract
High-throughput siRNA screens were only recently applied to cell factories to identify novel engineering targets which are able to boost cells towards desired phenotypes. While siRNA libraries exist for model organisms such as mice, no CHO-specific library is publicly available, hindering the application of this technique to CHO cells. The optimization of these cells is of special interest, as they are the main host for the production of therapeutic proteins. Here, we performed a cross-species approach by applying a mouse whole-genome siRNA library to CHO cells, optimized the protocol for suspension cultured cells, as this is the industrial practice for CHO cells, and developed an in silico method to identify functioning siRNAs, which also revealed the limitations of using cross-species libraries. With this method, we were able to identify several genes that, upon knockdown, enhanced the total productivity in the primary screen. A second screen validated two of these genes, Rad21 and Chd4, whose knockdown was tested in additional CHO cell lines, confirming the induced high productivity phenotype, but also demonstrating the cell line/clone specificity of engineering effects.
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Affiliation(s)
- Gerald Klanert
- Austrian Centre of Industrial Biotechnology, Graz, Austria
- University of Natural Resources and Life Sciences, Vienna, Austria
| | | | - Marcus Weinguny
- Austrian Centre of Industrial Biotechnology, Graz, Austria
- University of Natural Resources and Life Sciences, Vienna, Austria
| | - Peter Eisenhut
- Austrian Centre of Industrial Biotechnology, Graz, Austria
- University of Natural Resources and Life Sciences, Vienna, Austria
| | - Eugen Bühler
- Division of Preclinical Innovation, NCATS, NIH, Rockville, MD, USA
| | - Michael Melcher
- Austrian Centre of Industrial Biotechnology, Graz, Austria
- University of Natural Resources and Life Sciences, Vienna, Austria
| | - Steven A Titus
- Division of Preclinical Innovation, NCATS, NIH, Rockville, MD, USA
| | | | - Elisabeth Gludovacz
- University of Natural Resources and Life Sciences, Vienna, Austria
- Medical University of Vienna, Vienna, Austria
| | - Vaibhav Jadhav
- Austrian Centre of Industrial Biotechnology, Graz, Austria
| | - Su Xiao
- Biotechnology Core Laboratory, NIDDK, NIH, Bethesda, MD, USA
| | - Beate Stern
- Department of Biomedicine, University of Bergen, Bergen, Norway
- UniTargetingResearch AS, Bergen, Norway
| | - Madhu Lal
- Division of Preclinical Innovation, NCATS, NIH, Rockville, MD, USA.
| | - Joseph Shiloach
- Biotechnology Core Laboratory, NIDDK, NIH, Bethesda, MD, USA.
| | - Nicole Borth
- Austrian Centre of Industrial Biotechnology, Graz, Austria.
- University of Natural Resources and Life Sciences, Vienna, Austria.
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Mahmood N, Rabbani SA. DNA Methylation Readers and Cancer: Mechanistic and Therapeutic Applications. Front Oncol 2019; 9:489. [PMID: 31245293 PMCID: PMC6579900 DOI: 10.3389/fonc.2019.00489] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 05/23/2019] [Indexed: 12/14/2022] Open
Abstract
DNA methylation is a major epigenetic process that regulates chromatin structure which causes transcriptional activation or repression of genes in a context-dependent manner. In general, DNA methylation takes place when methyl groups are added to the appropriate bases on the genome by the action of "writer" molecules known as DNA methyltransferases. How these methylation marks are read and interpreted into different functionalities represents one of the main mechanisms through which the genes are switched "ON" or "OFF" and typically involves different types of "reader" proteins that can recognize and bind to the methylated regions. A tightly balanced regulation exists between the "writers" and "readers" in order to mediate normal cellular functions. However, alterations in normal methylation pattern is a typical hallmark of cancer which alters the way methylation marks are written, read and interpreted in different disease states. This unique characteristic of DNA methylation "readers" has identified them as attractive therapeutic targets. In this review, we describe the current state of knowledge on the different classes of DNA methylation "readers" identified thus far along with their normal biological functions, describe how they are dysregulated in cancer, and discuss the various anti-cancer therapies that are currently being developed and evaluated for targeting these proteins.
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Affiliation(s)
- Niaz Mahmood
- Department of Medicine, McGill University Health Centre, Montréal, QC, Canada
| | - Shafaat A Rabbani
- Department of Medicine, McGill University Health Centre, Montréal, QC, Canada
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Vymetalkova V, Vodicka P, Vodenkova S, Alonso S, Schneider-Stock R. DNA methylation and chromatin modifiers in colorectal cancer. Mol Aspects Med 2019; 69:73-92. [PMID: 31028771 DOI: 10.1016/j.mam.2019.04.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/11/2019] [Accepted: 04/15/2019] [Indexed: 12/15/2022]
Abstract
Colorectal carcinogenesis is a multistep process involving the accumulation of genetic alterations over time that ultimately leads to disease progression and metastasis. Binding of transcription factors to gene promoter regions alone cannot explain the complex regulation pattern of gene expression during this process. It is the chromatin structure that allows for a high grade of regulatory flexibility for gene expression. Posttranslational modifications on histone proteins such as acetylation, methylation, or phosphorylation determine the accessibility of transcription factors to DNA. DNA methylation, a chemical modification of DNA that modulates chromatin structure and gene transcription acts in concert with these chromatin conformation alterations. Another epigenetic mechanism regulating gene expression is represented by small non-coding RNAs. Only very recently epigenetic alterations have been included in molecular subtype classification of colorectal cancer (CRC). In this chapter, we will provide examples of the different epigenetic players, focus on their role for epithelial-mesenchymal transition and metastatic processes and discuss their prognostic value in CRC.
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Affiliation(s)
- Veronika Vymetalkova
- Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic; Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Albertov 4, 128 00, Prague, Czech Republic; Biomedical Centre, Faculty of Medicine in Pilsen, Charles University in Prague, 323 00, Pilsen, Czech Republic
| | - Pavel Vodicka
- Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic; Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Albertov 4, 128 00, Prague, Czech Republic; Biomedical Centre, Faculty of Medicine in Pilsen, Charles University in Prague, 323 00, Pilsen, Czech Republic
| | - Sona Vodenkova
- Institute of Experimental Medicine of the Czech Academy of Sciences, Videnska 1083, 142 00 Prague, Czech Republic; Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University, Albertov 4, 128 00, Prague, Czech Republic
| | - Sergio Alonso
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute, (IGTP-PMPPC), Campus Can Ruti, 08916, Badalona, Barcelona, Spain
| | - Regine Schneider-Stock
- Experimental Tumorpathology, Institute of Pathology, University Hospital of Friedrich-Alexander-University Erlangen-Nürnberg, Universitätsstrasse 22, 91054, Erlangen, Germany.
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D'Alesio C, Bellese G, Gagliani MC, Lechiara A, Dameri M, Grasselli E, Lanfrancone L, Cortese K, Castagnola P. The chromodomain helicase CHD4 regulates ERBB2 signaling pathway and autophagy in ERBB2 + breast cancer cells. Biol Open 2019; 8:bio.038323. [PMID: 30967373 PMCID: PMC6504000 DOI: 10.1242/bio.038323] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The chromodomain helicase DNA-binding 4 (CHD4), a member of the nucleosome remodeling and deacetylases (NuRD) complex, has been identified as an oncogene that modulates proliferation and migration of breast cancers (BC). ERBB2 is an oncogenic driver in 20–30% of BC in which its overexpression leads to increased chemoresistance. Here we investigated whether CHD4 depletion affects the ERBB2 cascade and autophagy, which represents a mechanism of resistance against Trastuzumab (Tz), a therapeutic anti-ERBB2 antibody. We show that CHD4 depletion in two ERBB2+ BC cell lines strongly inhibits cell proliferation, induces p27KIP1 upregulation, Tyr1248 ERBB2 phosphorylation, ERK1/2 and AKT dephosphorylation, and downregulation of both ERBB2 and PI3K levels. Moreover, CHD4 silencing impairs late stages of autophagy, resulting in increased levels of LC3 II and SQSTM1/p62, lysosomal enlargement and accumulation of autolysosomes (ALs). Importantly, we show that CHD4 depletion and concomitant treatment with Tz prevent cell proliferation in vitro. Our results suggest that CHD4 plays a critical role in modulating cell proliferation, ERBB2 signaling cascade and autophagy and provide new insights on CHD4 as a potential target for the treatment of ERBB2+ BC. Summary: Inhibition of CHD4 expression impairs cell proliferation and survival through downregulation of ERBB2 signaling and block of autophagy. Therefore, CHD4 should be considered a potential target in ERBB2+ breast cancers.
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Affiliation(s)
- Carolina D'Alesio
- DIMES, Department of Experimental Medicine, Human Anatomy, Università di Genova, Via Antonio de Toni 14, 16132, Genova, Italy.,DIMI, Department of Internal Medicine, Pharmacology, Università di Genova, Viale Benedetto XV, 16132, Genova, Italy
| | - Grazia Bellese
- DIMES, Department of Experimental Medicine, Human Anatomy, Università di Genova, Via Antonio de Toni 14, 16132, Genova, Italy
| | - Maria Cristina Gagliani
- DIMES, Department of Experimental Medicine, Human Anatomy, Università di Genova, Via Antonio de Toni 14, 16132, Genova, Italy
| | - Anastasia Lechiara
- DIMES, Department of Experimental Medicine, Human Anatomy, Università di Genova, Via Antonio de Toni 14, 16132, Genova, Italy
| | - Martina Dameri
- DIMES, Department of Experimental Medicine, Human Anatomy, Università di Genova, Via Antonio de Toni 14, 16132, Genova, Italy
| | - Elena Grasselli
- DISTAV, Department of Earth, Environment and Life science, Università di Genova, Corso Europa 26, 16132, Genova, Italy
| | - Luisa Lanfrancone
- Department of Experimental Oncology, European Institute of Oncology, Via Adamello 16, 20139, Milano, Italy
| | - Katia Cortese
- DIMES, Department of Experimental Medicine, Human Anatomy, Università di Genova, Via Antonio de Toni 14, 16132, Genova, Italy
| | - Patrizio Castagnola
- IRCCS Ospedale Policlinico San Martino, Largo Rosanna Benzi 10, 16132, Genova, Italy
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40
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The DNA Methylation Machinery. Clin Epigenetics 2019. [DOI: 10.1007/978-981-13-8958-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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41
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Chong SJF, Lai JXH, Eu JQ, Bellot GL, Pervaiz S. Reactive Oxygen Species and Oncoprotein Signaling-A Dangerous Liaison. Antioxid Redox Signal 2018; 29:1553-1588. [PMID: 29186971 DOI: 10.1089/ars.2017.7441] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
SIGNIFICANCE There is evidence to implicate reactive oxygen species (ROS) in tumorigenesis and its progression. This has been associated with the interplay between ROS and oncoproteins, resulting in enhanced cellular proliferation and survival. Recent Advances: To date, studies have investigated specific contributions of the crosstalk between ROS and signaling networks in cancer initiation and progression. These investigations have challenged the established dogma of ROS as agents of cell death by demonstrating a secondary function that fuels cell proliferation and survival. Studies have thus identified (onco)proteins (Bcl-2, STAT3/5, RAS, Rac1, and Myc) in manipulating ROS level as well as exploiting an altered redox environment to create a milieu conducive for cancer formation and progression. CRITICAL ISSUES Despite these advances, drug resistance and its association with an altered redox metabolism continue to pose a challenge at the mechanistic and clinical levels. Therefore, identifying specific signatures, altered protein expressions, and modifications as well as protein-protein interplay/function could not only enhance our understanding of the redox networks during cancer initiation and progression but will also provide novel targets for designing specific therapeutic strategies. FUTURE DIRECTIONS Not only a heightened realization is required to unravel various gene/protein networks associated with cancer formation and progression, particularly from the redox standpoint, but there is also a need for developing more sensitive tools for assessing cancer redox metabolism in clinical settings. This review attempts to summarize our current knowledge of the crosstalk between oncoproteins and ROS in promoting cancer cell survival and proliferation and treatment strategies employed against these oncoproteins. Antioxid. Redox Signal.
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Affiliation(s)
- Stephen Jun Fei Chong
- 1 Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore , Singapore, Singapore
| | - Jolin Xiao Hui Lai
- 1 Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore , Singapore, Singapore
| | - Jie Qing Eu
- 2 Cancer Science Institute , Singapore, Singapore
| | - Gregory Lucien Bellot
- 1 Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore , Singapore, Singapore .,3 Department of Hand and Reconstructive Microsurgery, National University Health System , Singapore, Singapore
| | - Shazib Pervaiz
- 1 Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore , Singapore, Singapore .,4 NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore , Singapore, Singapore .,5 National University Cancer Institute, National University Health System , Singapore, Singapore .,6 School of Biomedical Sciences, Curtin University , Perth, Australia
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42
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Sondka Z, Bamford S, Cole CG, Ward SA, Dunham I, Forbes SA. The COSMIC Cancer Gene Census: describing genetic dysfunction across all human cancers. Nat Rev Cancer 2018; 18:696-705. [PMID: 30293088 PMCID: PMC6450507 DOI: 10.1038/s41568-018-0060-1] [Citation(s) in RCA: 844] [Impact Index Per Article: 140.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The Catalogue of Somatic Mutations in Cancer (COSMIC) Cancer Gene Census (CGC) is an expert-curated description of the genes driving human cancer that is used as a standard in cancer genetics across basic research, medical reporting and pharmaceutical development. After a major expansion and complete re-evaluation, the 2018 CGC describes in detail the effect of 719 cancer-driving genes. The recent expansion includes functional and mechanistic descriptions of how each gene contributes to disease generation in terms of the key cancer hallmarks and the impact of mutations on gene and protein function. These functional characteristics depict the extraordinary complexity of cancer biology and suggest multiple cancer-related functions for many genes, which are often highly tissue-dependent or tumour stage-dependent. The 2018 CGC encompasses a second tier, describing an expanding list of genes (currently 145) from more recent cancer studies that show supportive but less detailed indications of a role in cancer.
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Affiliation(s)
- Zbyslaw Sondka
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, UK.
| | - Sally Bamford
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Charlotte G Cole
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Sari A Ward
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ian Dunham
- Open Targets, Wellcome Genome Campus, Hinxton, Cambridge, UK
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Simon A Forbes
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
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43
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Högström J, Heino S, Kallio P, Lähde M, Leppänen VM, Balboa D, Wiener Z, Alitalo K. Transcription Factor PROX1 Suppresses Notch Pathway Activation via the Nucleosome Remodeling and Deacetylase Complex in Colorectal Cancer Stem-like Cells. Cancer Res 2018; 78:5820-5832. [PMID: 30154153 DOI: 10.1158/0008-5472.can-18-0451] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 06/25/2018] [Accepted: 08/20/2018] [Indexed: 11/16/2022]
Abstract
The homeobox transcription factor PROX1 is induced by high Wnt/β-catenin activity in intestinal adenomas and colorectal cancer, where it promotes tumor progression. Here we report that in LGR5+ colorectal cancer cells, PROX1 suppresses the Notch pathway, which is essential for cell fate in intestinal stem cells. Pharmacologic inhibition of Notch in ex vivo 3D organoid cultures from transgenic mouse intestinal adenoma models increased Prox1 expression and the number of PROX1-positive cells. Notch inhibition led to increased proliferation of the PROX1-positive colorectal cancer cells, but did not affect their ability to give rise to PROX1-negative secretory cells. Conversely, PROX1 deletion increased Notch target gene expression and NOTCH1 promoter activity, indicating reciprocal regulation between PROX1 and the Notch pathway in colorectal cancer. PROX1 interacted with the nucleosome remodeling and deacetylase (NuRD) complex to suppress the Notch pathway. Thus, our data suggests that PROX1 and Notch suppress each other and that PROX1-mediated suppression of Notch mediates its stem cell function in colorectal cancer.Significance: These findings address the role of the PROX1 homeobox factor as a downstream effector of Wnt/β-catenin singling in colorectal cancer stem cells and show that PROX1 inhibits the Notch pathway and helps to enforce the stem cell phenotype and inhibit differentiation. Cancer Res; 78(20); 5820-32. ©2018 AACR.
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Affiliation(s)
- Jenny Högström
- Translational Cancer Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Sarika Heino
- Translational Cancer Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Pauliina Kallio
- Translational Cancer Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Marianne Lähde
- Translational Cancer Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Veli-Matti Leppänen
- Translational Cancer Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Diego Balboa
- Molecular Neurology Program and Biomedicum Stem Cell Center, University of Helsinki, Helsinki, Finland
| | - Zoltán Wiener
- Translational Cancer Biology Research Program, University of Helsinki, Helsinki, Finland
| | - Kari Alitalo
- Translational Cancer Biology Research Program, University of Helsinki, Helsinki, Finland.
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44
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Dutta B, Park JE, Qing ITY, Kon OL, Sze SK. Soy-Derived Phytochemical Genistein Modifies Chromatome Topology to Restrict Cancer Cell Proliferation. Proteomics 2018; 18:e1700474. [PMID: 29963755 DOI: 10.1002/pmic.201700474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 06/22/2018] [Indexed: 12/18/2022]
Abstract
Epidemiological data indicate that human cancer risk is significantly reduced by the consumption of soy-based foods containing the "phytoestrogen" genistein, which can signal via host cell estrogen receptors. While additional chemoprotective effects of genistein induced by epigenetic factors have also been reported, the key molecules and mechanisms involved are poorly defined. We therefore investigated genistein effects on chromatin-bound proteins in the estrogen receptor-deficient cell line MDA-MB-231 which is insensitive to phytoestrogen signaling. After exposure to low-dose genistein for >1 month, MDA-MB-231 cells exhibited stable epigenetic alterations that are analyzed via partial MNase digestion and TMT-based quantitative proteomics. 3177 chromatin-bound proteins are identified with high confidence, including 882 molecules that displayed altered binding topology after cell conditioning with genistein. Prolonged phytochemical exposure conferred heritable changes in the binding topology of key epigenetic regulators including ATRX, SUV39H1/H2, and HP1BP3 that are preserved in untreated progeny, resulting in sustained downregulation of proliferation genes and reduced cell growth. These data indicate that soy derivative genistein exerts complex estrogen receptor-independent effects on the epigenome likely to influence tumorigenesis by restricting cell growth.
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Affiliation(s)
- Bamaprasad Dutta
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Jung Eun Park
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Ivan Toh Yi Qing
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Oi Lian Kon
- Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, 169610, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
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Covalent Modifications of Histone H3K9 Promote Binding of CHD3. Cell Rep 2018; 21:455-466. [PMID: 29020631 DOI: 10.1016/j.celrep.2017.09.054] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/12/2017] [Accepted: 09/15/2017] [Indexed: 12/15/2022] Open
Abstract
Chromatin remodeling is required for genome function and is facilitated by ATP-dependent complexes, such as nucleosome remodeling and deacetylase (NuRD). Among its core components is the chromodomain helicase DNA binding protein 3 (CHD3) whose functional significance is not well established. Here, we show that CHD3 co-localizes with the other NuRD subunits, including HDAC1, near the H3K9ac-enriched promoters of the NuRD target genes. The tandem PHD fingers of CHD3 bind histone H3 tails and posttranslational modifications that increase hydrophobicity of H3K9-methylation or acetylation (H3K9me3 or H3K9ac)-enhance this interaction. Binding of CHD3 PHDs promotes H3K9Cme3-nucleosome unwrapping in vitro and perturbs the pericentric heterochromatin structure in vivo. Methylation or acetylation of H3K9 uniquely alleviates the intra-nucleosomal interaction of histone H3 tails, increasing H3K9 accessibility. Collectively, our data suggest that the targeting of covalently modified H3K9 by CHD3 might be essential in diverse functions of NuRD.
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Wachtel M, Schäfer BW. PAX3-FOXO1: Zooming in on an “undruggable” target. Semin Cancer Biol 2018; 50:115-123. [DOI: 10.1016/j.semcancer.2017.11.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 10/31/2017] [Accepted: 11/13/2017] [Indexed: 12/17/2022]
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Wang XQ, Bai HM, Li ST, Sun H, Min LZ, Tao BB, Zhong J, Li B. Knockdown of HDAC1 expression suppresses invasion and induces apoptosis in glioma cells. Oncotarget 2018. [PMID: 28624794 PMCID: PMC5564623 DOI: 10.18632/oncotarget.18227] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Glioma is the most common malignant tumor of the central nervous system, with a low survival rate of five years worldwide. Although high expression and prognostic value of histone deacetylase 1 (HDAC1) have been recently reported in various types of human tumors, the molecular mechanism underlying the biological function of HDAC1 in glioma is still unclear. We found that HDAC1 was elevated in glioma tissues and cell lines. HDAC1 expression was closely related with pathological grade and overall survival of patients with gliomas. Downregulation of HDAC1 inhibited cell proliferation, prevented invasion of glioma cell lines, and induced cell apoptosis. The expression of apoptosis and metastasis related molecules were detected by RT-PCR and Western blot, respectively, in U251 and T98G cells with HDAC1 knockdown. We found that HDAC1 knockdown upregulated expression of BIM, BAX, cleaved CASPASE3 and E-CADHERIN, and decreased expression of TWIST1, SNAIL and MMP9 in U251 and T98G cells with HDAC1 knockdown. In vivo data showed that knockdown of HDAC1 inhibited tumor growth in nude mice. In summary, HDAC1 may therefore be considered an unfavorable progression indicator for glioma patients, and may also serve as a potential therapeutic target.
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Affiliation(s)
- Xiao-Qiang Wang
- Department of Neurosurgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Hong-Min Bai
- Department of Neurosurgery, Guangzhou General Hospital of Guangzhou Military Command, Guangzhou 510010, China
| | - Shi-Ting Li
- Department of Neurosurgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Hui Sun
- Department of Neurosurgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Ling-Zhao Min
- Department of Neurosurgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Bang-Bao Tao
- Department of Neurosurgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Jun Zhong
- Department of Neurosurgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Bin Li
- Department of Neurosurgery, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
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Seelan RS, Mukhopadhyay P, Pisano MM, Greene RM. Effects of 5-Aza-2'-deoxycytidine (decitabine) on gene expression. Drug Metab Rev 2018; 50:193-207. [PMID: 29455551 DOI: 10.1080/03602532.2018.1437446] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
5-Aza-2'-deoxycytidine (AzaD), also known as Decitabine, is a deoxycytidine analog that is typically used to activate methylated and silenced genes by promoter demethylation. However, a survey of the scientific literature indicates that promoter demethylation may not be the only (or, indeed, the major) mechanism by which AzaD affects gene expression. Regulation of gene expression by AzaD can occur in several ways, including some that are independent of DNA demethylation. Results from several studies indicate that the effect of AzaD on gene expression is highly context-dependent and can differ for the same gene under different environmental settings. This may, in part, be due to the nature of the silencing mechanism(s) involved - DNA methylation, repressive histone modifications, or a combination of both. The varied effects of AzaD on such context-dependent regulation of gene expression may underlie some of the diverse responses exhibited by patients undergoing AzaD therapy. In this review, we describe the salient properties of AzaD with particular emphasis on its diverse effects on gene expression, aspects that have barely been discussed in most reviews of this interesting drug.
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Affiliation(s)
- Ratnam S Seelan
- a Department of Surgical and Hospital Dentistry, Division of Craniofacial Development and Anomalies , ULSD, University of Louisville , Louisville , KY , USA
| | - Partha Mukhopadhyay
- a Department of Surgical and Hospital Dentistry, Division of Craniofacial Development and Anomalies , ULSD, University of Louisville , Louisville , KY , USA
| | - M Michele Pisano
- a Department of Surgical and Hospital Dentistry, Division of Craniofacial Development and Anomalies , ULSD, University of Louisville , Louisville , KY , USA
| | - Robert M Greene
- a Department of Surgical and Hospital Dentistry, Division of Craniofacial Development and Anomalies , ULSD, University of Louisville , Louisville , KY , USA
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Zhou M, Zhou K, Cheng L, Chen X, Wang J, Wang XM, Zhang Y, Yu Q, Zhang S, Wang D, Huang L, Huang M, Ma D, Cheng T, Wang CY, Yuan W, Zhou J. MBD2 Ablation Impairs Lymphopoiesis and Impedes Progression and Maintenance of T-ALL. Cancer Res 2018; 78:1632-1642. [PMID: 29330145 DOI: 10.1158/0008-5472.can-17-1434] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 11/23/2017] [Accepted: 01/09/2018] [Indexed: 11/16/2022]
Abstract
Aberrant DNA methylation patterns in leukemia might be exploited for therapeutic targeting. In this study, we employed a genetically deficient mouse model to explore the role of the methylated DNA binding protein MBD2 in normal and malignant hematopoiesis. MBD2 ablation led to diminished lymphocytes. Functional defects of the lymphoid compartment were also observed after in vivo reconstitution of MBD2-deficient hematopoietic stem cells (HSC). In an established model of Notch1-driven T-cell acute lymphoblastic leukemia (T-ALL), MBD2 ablation impeded malignant progression and maintenance by attenuating the Wnt signaling pathway. In clinical specimens of human T-ALL, Wnt signaling pathway signatures were significantly enhanced and positively correlated with the expression and function of MBD2. Furthermore, a number of typical Wnt signaling inhibitory genes were abnormally hypermethylated in primary human T-ALL. Abnormal activation of Wnt signaling in T-ALL was switched off by MBD2 deletion, partially by reactivating epigenetically silenced Wnt signaling inhibitors. Taken together, our results define essential roles for MBD2 in lymphopoiesis and T-ALL and suggest MBD2 as a candidate therapeutic target in T-ALL.Significance: This study highlights a methylated DNA binding protein as a candidate therapeutic target to improve the treatment of T-cell acute lymphoblastic leukemias, as a new starting point for developing epigenetic therapy in this and other lymphoid malignancies. Cancer Res; 78(7); 1632-42. ©2018 AACR.
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Affiliation(s)
- Mi Zhou
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Kuangguo Zhou
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ling Cheng
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xing Chen
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jue Wang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiao-Min Wang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Yingchi Zhang
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Qilin Yu
- The Center for Biomedical Research, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shu Zhang
- The Center for Biomedical Research, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Di Wang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Liang Huang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Mei Huang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ding Ma
- Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Cong-Yi Wang
- The Center for Biomedical Research, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Weiping Yuan
- State Key Laboratory of Experimental Hematology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China.
| | - Jianfeng Zhou
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China. .,Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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50
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Luo CW, Wu CC, Chang SJ, Chang TM, Chen TY, Chai CY, Chang CL, Hou MF, Pan MR. CHD4-mediated loss of E-cadherin determines metastatic ability in triple-negative breast cancer cells. Exp Cell Res 2018; 363:65-72. [PMID: 29305962 DOI: 10.1016/j.yexcr.2017.12.032] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 12/25/2017] [Accepted: 12/31/2017] [Indexed: 12/21/2022]
Abstract
Triple-negative breast cancer (TNBC) is a subtype of cancer with aggressive behaviors (high recurrence and metastasis rate) and poor prognosis. Therefore, studying the determining factors that lead to malignant TNBCs is necessary to develop personalized therapy and improve survival rates. In this study, we first analyzed levels of chromodomain helicase DNA binding protein 4 (CHD4) in 60 TNBC patients by immunohistochemical staining. We then clarified the role of CHD4 in TNBC and non-TNBC cell lines. Our clinical data indicated that higher CHD4 expression is positively correlated with metastatic stage, tumor recurrence, and survival status. Consistent with the clinical analytical data, our in vitro data also indicated that high level of CHD4 is positively correlated with malignant behaviors in TNBC cells, such as cell motility and mortality. For further analyses, we found that E-cadherin, N-cadherin and fibronetin are involved in CHD4-mediated epithelial-mesenchymal transition (EMT). Silencing of CHD4 also increased drug sensitivity to cisplatin and PARP1 inhibitor, especially in TNBC cells. Altogether, our findings showed that CHD4 is not only a potential prognostic biomarker for TNBC patient survival, but is also a powerful candidate in the development of new anti-cancer agents in TNBC.
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Affiliation(s)
- Chi-Wen Luo
- Department of Pathology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan; Division of Cardiology, Chang Gung Memorial Hospital-Kaohsiung Medical Center, Kaohsiung, Taiwan
| | - Chun-Chieh Wu
- Department of Pathology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Shu-Jyuan Chang
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Tsung-Ming Chang
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | - Tzu-Yi Chen
- Graduate Institute of Clinical Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chee-Yin Chai
- Department of Pathology, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan; Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Department of Pathology, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chia-Lo Chang
- Division of Colon and Rectal Surgery, Department of Surgery, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine Kaohsiung, Taiwan
| | - Ming-Feng Hou
- Graduate Institute of Clinical Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Department of Surgery, Kaohsiung Municipal Hsiao Kang Hospital, Kaohsiung, Taiwan; Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.
| | - Mei-Ren Pan
- Graduate Institute of Clinical Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan; Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.
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