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Mahmood N, Arakelian A, Szyf M, Rabbani SA. Methyl-CpG binding domain protein 2 (Mbd2) drives breast cancer progression through the modulation of epithelial-to-mesenchymal transition. Exp Mol Med 2024; 56:959-974. [PMID: 38556549 PMCID: PMC11058268 DOI: 10.1038/s12276-024-01205-2] [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: 12/04/2022] [Revised: 12/27/2023] [Accepted: 01/25/2024] [Indexed: 04/02/2024] Open
Abstract
Methyl-CpG-binding domain protein 2 (Mbd2), a reader of DNA methylation, has been implicated in different types of malignancies, including breast cancer. However, the exact role of Mbd2 in various stages of breast cancer growth and progression in vivo has not been determined. To test whether Mbd2 plays a causal role in mammary tumor growth and metastasis, we performed genetic knockout (KO) of Mbd2 in MMTV-PyMT transgenic mice and compared mammary tumor progression kinetics between the wild-type (PyMT-Mbd2+/+) and KO (PyMT-Mbd2-/-) groups. Our results demonstrated that deletion of Mbd2 in PyMT mice impedes primary tumor growth and lung metastasis at the experimental endpoint (postnatal week 20). Transcriptomic and proteomic analyses of primary tumors revealed that Mbd2 deletion abrogates the expression of several key determinants involved in epithelial-to-mesenchymal transition, such as neural cadherin (N-cadherin) and osteopontin. Importantly, loss of the Mbd2 gene impairs the activation of the PI3K/AKT pathway, which is required for PyMT-mediated oncogenic transformation, growth, and survival of breast tumor cells. Taken together, the results of this study provide a rationale for further development of epigenetic therapies targeting Mbd2 to inhibit the progression of breast cancer.
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Affiliation(s)
- Niaz Mahmood
- Department of Medicine, McGill University, Montréal, QC, H4A3J1, Canada
- Department of Biochemistry, McGill University, Montréal, QC, H3A1A3, Canada
| | - Ani Arakelian
- Department of Medicine, McGill University, Montréal, QC, H4A3J1, Canada
| | - Moshe Szyf
- Department of Pharmacology and Therapeutics, McGill University, Montréal, QC, H3G1Y6, Canada
| | - Shafaat A Rabbani
- Department of Medicine, McGill University, Montréal, QC, H4A3J1, Canada.
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2
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Cao L, Zhou Y, Gao L, Yin H, Zhang M, Zhang H, Ju P, Dou K, Ai S. Ascorbic Acid Induced the Improved Oxygen Vacancy Defects of Bi 4O 5Br 2 and Its Application on Photoelectrochemical Detection of DNA Demethylase MBD2 with Improved Detection Sensitivity. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2306365. [PMID: 38009777 DOI: 10.1002/smll.202306365] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/20/2023] [Indexed: 11/29/2023]
Abstract
Oxygen vacancy defects (OVs) are one of the main strategies for nanomaterials modification to improve the photoactivity, but current methods for fabricating OVs are usually complicated and harsh. It is important to develop simple, rapid, safe, and mild methods to fabricate OVs. By studying the effects of different weak reducing agents, the concentration of the reducing agent and the reaction time on fabrication of OVs, it is found that L-ascorbic acid (AA) gently and rapidly induces the increase of OVs in Bi4O5Br2 at room temperature. The increased OVs not only improve the adsorption of visible light, but also enhance the photocurrent response. Based on this, the preparation of OVs in Bi4O5Br2 is employed to the development of a photoelectrochemical biosensor for the detection of DNA demethylase of methyl-CpG binding domain protein 2 (MBD2). The biosensor shows a wide linear range of 0.1-400 ng mL-1 and a detection limit as low as 0.03 ng mL-1 (3σ). In addition, the effect of plasticizers on MBD2 activity is evaluated using this sensor. This work not only provides a novel method to prepare OVs in bismuth rich materials, but also explores a new novel evaluation tool for studying the ecotoxicological effects of contaminants.
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Affiliation(s)
- LuLu Cao
- College of Chemistry and Material Science, Key Laboratory of Low-Carbon and Green Agriculture Chemistry in Universities of Shandong, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Tai'an, 271018, P. R. China
| | - Yunlei Zhou
- College of Chemistry and Material Science, Key Laboratory of Low-Carbon and Green Agriculture Chemistry in Universities of Shandong, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Tai'an, 271018, P. R. China
| | - Lanlan Gao
- College of Chemistry and Material Science, Key Laboratory of Low-Carbon and Green Agriculture Chemistry in Universities of Shandong, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Tai'an, 271018, P. R. China
| | - Huanshun Yin
- College of Chemistry and Material Science, Key Laboratory of Low-Carbon and Green Agriculture Chemistry in Universities of Shandong, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Tai'an, 271018, P. R. China
| | - Miao Zhang
- College of Chemistry and Material Science, Key Laboratory of Low-Carbon and Green Agriculture Chemistry in Universities of Shandong, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Tai'an, 271018, P. R. China
| | - Haowei Zhang
- College of Chemistry and Material Science, Key Laboratory of Low-Carbon and Green Agriculture Chemistry in Universities of Shandong, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Tai'an, 271018, P. R. China
| | - Peng Ju
- Key Laboratory of Marine Eco-Environmental Science and Technology, Marine Bioresource and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266061, P. R. China
| | - Kunpeng Dou
- College of Information Science and Engineering, Ocean University of China, Qingdao, 266061, P. R. China
| | - Shiyun Ai
- College of Chemistry and Material Science, Key Laboratory of Low-Carbon and Green Agriculture Chemistry in Universities of Shandong, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Tai'an, 271018, P. R. China
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3
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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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4
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Cao L, Zhou Y, Gao L, Zheng Y, Cui X, Yin H, Wang S, Zhang M, Zhang H, Ai S. Photoelectrochemical biosensor for DNA demethylase detection based on enzymatically induced double-stranded DNA digestion by endonuclease-exonuclease system and Bi 4O 5Br 2-Au/CdS photoactive material. Talanta 2023; 262:124670. [PMID: 37245429 DOI: 10.1016/j.talanta.2023.124670] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 03/22/2023] [Accepted: 05/12/2023] [Indexed: 05/30/2023]
Abstract
A novel photoelectrochemical (PEC) biosensor for the detection of DNA demethylase MBD2 was developed based on Bi4O5Br2-Au/CdS photosensitive material. Bi4O5Br2 was firstly modified with gold nanoparticles (AuNPs), following with the modification onto the ITO electrode with CdS to realize the strong photocurrent response as a result of AuNPs had good conductibility and the matched energy between CdS and Bi4O5Br2. In the presence of MBD2, double-stranded DNA (dsDNA) on the electrode surface was demethylated, which triggered the digestion activity of endonuclease HpaII to cleave dsDNA and induced the further cleavage of the dsDNA fragment by exonuclease III (Exo III), causing the release of biotin labeled dsDNA and inhibiting the immobilization of streptavidin (SA) onto the electrode surface. As a results, the photocurrent was increased greatly. However, in the absence of MBD2, HpaII digestion activity was inhibited by DNA methylation modification, which further caused the failure in the release of biotin, leading to the successful immobilization of SA onto the electrode to realize a low photocurrent. The sensor had a detection of 0.3-200 ng/mL and a detection limit was 0.09 ng/mL (3σ). The applicability of this PEC strategy was assessed by studying the effect of environmental pollutants on MBD2 activity.
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Affiliation(s)
- LuLu Cao
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China
| | - Yunlei Zhou
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China.
| | - Lanlan Gao
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China
| | - Yulin Zheng
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China
| | - Xiaoting Cui
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China
| | - Huanshun Yin
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China.
| | - Suo Wang
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China
| | - Miao Zhang
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China
| | - Haowei Zhang
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China
| | - Shiyun Ai
- College of Chemistry and Material Science, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Shandong Agricultural University, 271018, Taian, Shandong, People's Republic of China
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5
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Zhang L, Wang S, Wu GR, Yue H, Dong R, Zhang S, Yu Q, Yang P, Zhao J, Zhang H, Yu J, Yuan X, Xiong W, Yang X, Yong T, Wang CY. MBD2 facilitates tumor metastasis by mitigating DDB2 expression. Cell Death Dis 2023; 14:303. [PMID: 37142578 PMCID: PMC10160113 DOI: 10.1038/s41419-023-05804-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 04/04/2023] [Accepted: 04/06/2023] [Indexed: 05/06/2023]
Abstract
Despite past extensive studies, the pathoetiologies underlying tumor metastasis remain poorly understood, which renders its treatment largely unsuccessful. The methyl-CpG-binding domain 2 (MBD2), a "reader" to interpret DNA methylome-encoded information, has been noted to be involved in the development of certain types of tumors, while its exact impact on tumor metastasis remains elusive. Herein we demonstrated that patients with LUAD metastasis were highly correlated with enhanced MBD2 expression. Therefore, knockdown of MBD2 significantly attenuated the migration and invasion of LUAD cells (A549 and H1975 cell lines) coupled with attenuated epithelial-mesenchymal transition (EMT). Moreover, similar results were observed in other types of tumor cells (B16F10). Mechanistically, MBD2 selectively bound to the methylated CpG DNA within the DDB2 promoter, by which MBD2 repressed DDB2 expression to promote tumor metastasis. As a result, administration of MBD2 siRNA-loaded liposomes remarkably suppressed EMT along with attenuated tumor metastasis in the B16F10 tumor-bearing mice. Collectively, our study indicates that MBD2 could be a promising prognostic marker for tumor metastasis, while administration of MBD2 siRNA-loaded liposomes could be a viable therapeutic approach against tumor metastasis in clinical settings.
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Affiliation(s)
- Lei Zhang
- Department of Respiratory and Critical Care Medicine, The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, 430030, Wuhan, China
| | - Siyuan Wang
- Department of Gerontology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Guo-Rao Wu
- Department of Respiratory and Critical Care Medicine, The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, 430030, Wuhan, China
| | - Huihui Yue
- Department of Respiratory and Critical Care Medicine, The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, 430030, Wuhan, China
| | - Ruihan Dong
- Department of Respiratory and Critical Care Medicine, The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, 430030, Wuhan, China
| | - Shu Zhang
- Department of Respiratory and Critical Care Medicine, The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, 430030, Wuhan, China
| | - Qilin Yu
- Department of Respiratory and Critical Care Medicine, The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, 430030, Wuhan, China
| | - Ping Yang
- Department of Respiratory and Critical Care Medicine, The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, 430030, Wuhan, China
| | - Jianping Zhao
- Department of Respiratory and Critical Care Medicine, The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, 430030, Wuhan, China
| | - Huilan Zhang
- Department of Respiratory and Critical Care Medicine, The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, 430030, Wuhan, China
| | - Jun Yu
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, 430030, Wuhan, China
| | - Xianglin Yuan
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Weining Xiong
- Department of Respiratory and Critical Care Medicine, Shanghai Key Laboratory of Tissue Engineering, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, 639 Zhizaoju Lu, 200011, Shanghai, China
| | - Xiangliang Yang
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, 430074, Wuhan, China.
| | - Tuying Yong
- National Engineering Research Center for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, 430074, Wuhan, China.
| | - Cong-Yi Wang
- Department of Respiratory and Critical Care Medicine, The Center for Biomedical Research, NHC Key Laboratory of Respiratory Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, 430030, Wuhan, China.
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6
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Saatci O, Akbulut O, Cetin M, Sikirzhytski V, Uner M, Lengerli D, O'Quinn EC, Romeo MJ, Caliskan B, Banoglu E, Aksoy S, Uner A, Sahin O. Targeting TACC3 represents a novel vulnerability in highly aggressive breast cancers with centrosome amplification. Cell Death Differ 2023; 30:1305-1319. [PMID: 36864125 PMCID: PMC10154422 DOI: 10.1038/s41418-023-01140-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 02/15/2023] [Accepted: 02/20/2023] [Indexed: 03/04/2023] Open
Abstract
Centrosome amplification (CA) is a hallmark of cancer that is strongly associated with highly aggressive disease and worse clinical outcome. Clustering extra centrosomes is a major coping mechanism required for faithful mitosis of cancer cells with CA that would otherwise undergo mitotic catastrophe and cell death. However, its underlying molecular mechanisms have not been fully described. Furthermore, little is known about the processes and players triggering aggressiveness of cells with CA beyond mitosis. Here, we identified Transforming Acidic Coiled-Coil Containing Protein 3 (TACC3) to be overexpressed in tumors with CA, and its high expression is associated with dramatically worse clinical outcome. We demonstrated, for the first time, that TACC3 forms distinct functional interactomes regulating different processes in mitosis and interphase to ensure proliferation and survival of cancer cells with CA. Mitotic TACC3 interacts with the Kinesin Family Member C1 (KIFC1) to cluster extra centrosomes for mitotic progression, and inhibition of this interaction leads to mitotic cell death via multipolar spindle formation. Interphase TACC3 interacts with the nucleosome remodeling and deacetylase (NuRD) complex (HDAC2 and MBD2) in nucleus to inhibit the expression of key tumor suppressors (e.g., p21, p16 and APAF1) driving G1/S progression, and its inhibition blocks these interactions and causes p53-independent G1 arrest and apoptosis. Notably, inducing CA by p53 loss/mutation increases the expression of TACC3 and KIFC1 via FOXM1 and renders cancer cells highly sensitive to TACC3 inhibition. Targeting TACC3 by guide RNAs or small molecule inhibitors strongly inhibits growth of organoids and breast cancer cell line- and patient-derived xenografts with CA by induction of multipolar spindles, mitotic and G1 arrest. Altogether, our results show that TACC3 is a multifunctional driver of highly aggressive breast tumors with CA and that targeting TACC3 is a promising approach to tackle this disease.
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Affiliation(s)
- Ozge Saatci
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC, 29208, USA.,Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Ozge Akbulut
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC, 29208, USA
| | - Metin Cetin
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC, 29208, USA.,Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Vitali Sikirzhytski
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC, 29208, USA
| | - Meral Uner
- Department of Pathology, Faculty of Medicine, Hacettepe University, 06100, Ankara, Turkey
| | - Deniz Lengerli
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, 06100, Ankara, Turkey
| | - Elizabeth C O'Quinn
- Translational Science Laboratory, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Martin J Romeo
- Translational Science Laboratory, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Burcu Caliskan
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, 06100, Ankara, Turkey
| | - Erden Banoglu
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Gazi University, 06100, Ankara, Turkey
| | - Sercan Aksoy
- Department of Medical Oncology, Hacettepe University Cancer Institute, 06100, Ankara, Turkey
| | - Aysegul Uner
- Department of Pathology, Faculty of Medicine, Hacettepe University, 06100, Ankara, Turkey
| | - Ozgur Sahin
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, SC, 29208, USA. .,Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, 29425, USA.
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7
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Shao X, Zheng Y, Huang Y, Li G, Zou W, Shi L. Hsa-miR-221-3p promotes proliferation and migration in HER2-positive breast cancer cells by targeting LASS2 and MBD2. Histol Histopathol 2022; 37:1099-1112. [PMID: 35734966 DOI: 10.14670/hh-18-483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Human epidermal growth factor receptor (HER2)-positive breast cancers account for nearly 20% of all breast cancer cases and microRNAs (miRNAs) play crucial roles in disease progression. The study was aimed to explore the role of miR-221-3p in HER2-positive breast cancer. METHODS Differentially expressed miRNAs were identified by high-throughput sequencing. Quantitative real-time PCR was used to evaluate mRNA levels of corresponding genes. CKK8 and transwell assays were performed to evaluate cell viability and migration. The translation binding was assessed by luciferase assay. RESULTS Hsa-miR-221-3p was highly upregulated in HER2-positive breast cancer samples, particularly in patients with advanced or metastatic disease, as compared to healthy controls. miR-221-3p upregulation using mimics promoted cell proliferation and migration in HER2-positive cell lines, whereas miR-221-3p suppression had the opposite effect. Additionally, miR-221-3p mimics reduced the expression levels of LASS2 and MBD2 in HER2-positive breast cancer cells; conversely, miR-221-3p inhibition upregulated LASS2 and MBD2. miR-221-3p inhibited the translation of LASS2 and MBD2 by directly binding to their 3'-untranslated regions. Forced expression of LASS2 and MBD2 significantly attenuated the ability of miR-221-3p mimics to enhance cell growth and migration in HER2-positive but not in HER2-negative breast cancer cells. In HER-2-positive breast cancer patients, the levels of miR-221-3p were negatively correlated with the mRNA levels of LASS2 and MBD2. CONCLUSIONS Upregulation of hsa-miR-221-3 in HER2-positive breast cancer contributes to cancer cell proliferation and migration by directly targeting the tumor suppressors LASS2 and MBD2. Therefore, the hsa-miR-221-3 may serve as a promising and actionable therapeutic target in HER2-positive breast cancer.
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Affiliation(s)
- Xiying Shao
- Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences, Zhejiang, PR China.,Department of Breast Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang, PR China.,Department of Breast Medical Oncology, Zhejiang Cancer Hospital, Zhejiang, PR China
| | - Yabing Zheng
- Department of Breast Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang, PR China.,Department of Breast Medical Oncology, Zhejiang Cancer Hospital, Zhejiang, PR China.,Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences, Zhejiang, PR China.
| | - Yuan Huang
- Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences, Zhejiang, PR China.,Department of Breast Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang, PR China.,Department of Breast Medical Oncology, Zhejiang Cancer Hospital, Zhejiang, PR China
| | - Guangliang Li
- Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences, Zhejiang, PR China.,Department of Breast Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang, PR China.,Department of Breast Medical Oncology, Zhejiang Cancer Hospital, Zhejiang, PR China
| | - Weibin Zou
- Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences, Zhejiang, PR China.,Department of Breast Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang, PR China.,Department of Breast Medical Oncology, Zhejiang Cancer Hospital, Zhejiang, PR China
| | - Lei Shi
- Institute of Cancer and Basic Medicine (ICBM), Chinese Academy of Sciences, Zhejiang, PR China.,Department of Breast Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences, Zhejiang, PR China.,Department of Breast Medical Oncology, Zhejiang Cancer Hospital, Zhejiang, PR China
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8
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Çalışkaner ZO. Computational discovery of novel inhibitory candidates targeting versatile transcriptional repressor MBD2. J Mol Model 2022; 28:296. [PMID: 36066769 DOI: 10.1007/s00894-022-05297-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 08/29/2022] [Indexed: 11/30/2022]
Abstract
Genome methylation is a key epigenetic mechanism in various biological events such as development, cellular differentiation, cancer progression, aging, and iPSC reprogramming. Crosstalk between DNA methylation and gene expression is mediated by MBD2, known as the reader of DNA methylation and suggested as a drug target. Despite its magnitude of significance, a scarcely limited number of small molecules to be used as inhibitors have been detected so far. Therefore, we screened a comprehensive compound library to elicit MBD2 inhibitor candidates. Promising molecules were subjected to computational docking analysis by targeting the methylated DNA-binding domain of human MBD2. We could detect reasonable binding energies and docking residues, presumably located in druggable pockets. Docking results were also validated via MD simulation and per-residue energy decomposition calculation. Drug-likeness of these small molecules was assessed through ADMET prediction to foresee off-target side effects for future studies. All computational approaches notably highlighted two compounds named CID3100583 and 8,8-ethylenebistheophylline. These compounds have become prominent as novel candidates, possibly disrupting MBD2MBD-DNA interaction. Consequently, these compounds have been considered prospective inhibitors with the usage potential in a wide range of applications from cancer treatment to somatic cell reprogramming protocols.
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Affiliation(s)
- Zihni Onur Çalışkaner
- Faculty of Engineering and Natural Sciences, Molecular Biology and Genetics Department, Biruni University, 34010, Istanbul, Turkey.
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9
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Loss of MBD2 attenuates MLL-AF9-driven leukemogenesis by suppressing the leukemic cell cycle via CDKN1C. Oncogenesis 2021; 10:79. [PMID: 34789717 PMCID: PMC8599466 DOI: 10.1038/s41389-021-00366-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 09/19/2021] [Accepted: 10/25/2021] [Indexed: 11/09/2022] Open
Abstract
Acute myeloid leukemia (AML) is a deadly cancer characterized by an expanded self-renewal capacity that is associated with the accumulation of immature myeloid cells. Emerging evidence shows that methyl-CpG-binding domain protein 2 (MBD2), a DNA methylation reader, often participates in the transcriptional silencing of hypermethylated genes in cancer cells. Nevertheless, the role of MBD2 in AML remains unclear. Herein, by using an MLL-AF9 murine model and a human AML cell line, we observed that loss of MBD2 could delay the initiation and progression of leukemia. MBD2 depletion significantly reduced the leukemia burden by decreasing the proportion of leukemic stem cells (LSCs) and inhibiting leukemia cell proliferation in serial transplantation experiments, thereby allowing leukemic blasts to transition to a more mature state reflecting normal myelopoiesis. Both gene expression analyses and bioinformatic studies revealed that MBD2 negatively modulated genes related to myeloid differentiation, and was necessary to sustain the MLL-AF9 oncogene-induced gene program. We further demonstrated that MBD2 could promote LSC cell cycle progression through epigenetic regulation of CDKN1C transcription probably by binding to its promoter region. Taken together, our data suggest that MBD2 promotes AML development and could be a therapeutic target for myeloid malignancies.
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10
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Zhang Y, Nalawansha DA, Herath KE, Andrade R, Pflum MKH. Differential profiles of HDAC1 substrates and associated proteins in breast cancer cells revealed by trapping. Mol Omics 2021; 17:544-553. [PMID: 33885658 DOI: 10.1039/d0mo00047g] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Histone deacetylase (HDAC) proteins, which regulate the acetylation state of proteins, are the targets of multiple clinical drugs for cancer treatment. Due to the heterogeneity of tumors, HDAC proteins play different roles in the progression of various cancer types. For example, MDA-MB-468 and MDA-MB-231 cells are both triple negative breast cancer cells but belong to different subtypes that display different response to HDAC inhibitor drugs. To investigate the role of HDAC proteins in breast cancer, the substrate and associated proteins of HDAC1 in MDA-MB-231, MDA-MB-468, and a normal breast epithelial cell line, MCF10A, were analyzed using substrate trapping mutants and proteomics-based mass spectrometry. All three cell lines demonstrated nonoverlapping substrate protein profiles. While both normal MCF10A and cancerous MDA-MB-468 cell lines contained similar HDAC1 associated proteins, including proteins associated with epigenetic and RNA processing mechanisms, the HDAC1 associated protein profile of MDA-MB-231 cells was devoid of expected epigenetic proteins. The variable associated protein profiles of MDA-MB-231 and MDA-MB-468 suggest that HDAC1 plays distinct roles in breast cancer cell biology, which might affect cancer aggressiveness and HDAC inhibitor sensitivity.
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Affiliation(s)
- Yuchen Zhang
- Department of Chemistry, Wayne State University, Detroit, MI, USA.
| | | | - Kavinda E Herath
- Department of Chemistry, Wayne State University, Detroit, MI, USA.
| | - Rafael Andrade
- Department of Chemistry, Wayne State University, Detroit, MI, USA.
| | - Mary Kay H Pflum
- Department of Chemistry, Wayne State University, Detroit, MI, USA.
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11
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Lou D, Wei X, Xiao P, Huo Q, Hong X, Sun J, Shuai Y, Tao G. Demethylation of the NRF2 Promoter Protects Against Carcinogenesis Induced by Nano-SiO 2. Front Genet 2020; 11:818. [PMID: 32849814 PMCID: PMC7399247 DOI: 10.3389/fgene.2020.00818] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/08/2020] [Indexed: 01/10/2023] Open
Abstract
Nano silicon dioxide (Nano-SiO2) has been widely used in industries such as the field of biomedical engineering. Despite the existing evidence that Nano-SiO2 exposure could induce oxidative stress and inflammatory responses in multiple organ systems, the carcinogenicity of Nano-SiO2 exposure has rarely been investigated. Thus in this study, two types of human bronchial epithelial cell lines (16HBE and BEAS-2B) were selected as in vitro models to investigate the carcinogenicity of Nano-SiO2. Our results revealed that Nano-SiO2 induces a malignant cellular transformation in human bronchial epithelial cells according to the soft agar colony formation assay. The carcinogenesis induced by Nano-SiO2 was also confirmed in nude mice. By using immunofluorescence assay and high-performance capillary electrophoresis (HPCE), we observed a genome-wide DNA hypomethylation induced by Nano-SiO2. Besides the reduced enzyme activity of total DNMTs upon Nano-SiO2 treatment, altered expression of DNMTs and methyl-CpG binding proteins were observed. Besides, we found that the expression of NRF2 was activated by demethylation of CpG islands within the NRF2 promoter region and the overexpression of NRF2 could alleviate the carcinogenesis induced by Nano-SiO2. Taken together, our results suggested that Nano-SiO2 induces malignant cellular transformation with a global DNA hypomethylation, and the demethylation of NRF2 promoter activates the expression of NRF2, which plays an important role in protecting against the carcinogenesis induced by Nano-SiO2.
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Affiliation(s)
- Dan Lou
- Shanghai Municipal Center for Disease Control & Prevention, Shanghai, China.,Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Xiaoyi Wei
- Department of Food Science, Shanghai Business School, Shanghai, China
| | - Ping Xiao
- Shanghai Municipal Center for Disease Control & Prevention, Shanghai, China
| | - Qian Huo
- Shanghai Municipal Center for Disease Control & Prevention, Shanghai, China
| | - Xinyu Hong
- Shanghai Municipal Center for Disease Control & Prevention, Shanghai, China
| | - Jingqiu Sun
- Shanghai Municipal Center for Disease Control & Prevention, Shanghai, China
| | - Yi Shuai
- Syngenta (China) Investment Company Limited, Shanghai, China
| | - Gonghua Tao
- Shanghai Municipal Center for Disease Control & Prevention, Shanghai, China
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12
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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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13
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Kim MY, Na I, Kim JS, Son SH, Choi S, Lee SE, Kim JH, Jang K, Alterovitz G, Chen Y, van der Vaart A, Won HS, Uversky VN, Kim CG. Rational discovery of antimetastatic agents targeting the intrinsically disordered region of MBD2. SCIENCE ADVANCES 2019; 5:eaav9810. [PMID: 31799386 PMCID: PMC6867884 DOI: 10.1126/sciadv.aav9810] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 09/20/2019] [Indexed: 06/10/2023]
Abstract
Although intrinsically disordered protein regions (IDPRs) are commonly engaged in promiscuous protein-protein interactions (PPIs), using them as drug targets is challenging due to their extreme structural flexibility. We report a rational discovery of inhibitors targeting an IDPR of MBD2 that undergoes disorder-to-order transition upon PPI and is critical for the regulation of the Mi-2/NuRD chromatin remodeling complex (CRC). Computational biology was essential for identifying target site, searching for promising leads, and assessing their binding feasibility and off-target probability. Molecular action of selected leads inhibiting the targeted PPI of MBD2 was validated in vitro and in cell, followed by confirming their inhibitory effects on the epithelial-mesenchymal transition of various cancer cells. Identified lead compounds appeared to potently inhibit cancer metastasis in a murine xenograft tumor model. These results constitute a pioneering example of rationally discovered IDPR-targeting agents and suggest Mi-2/NuRD CRC and/or MBD2 as a promising target for treating cancer metastasis.
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Affiliation(s)
- Min Young Kim
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - Insung Na
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Ji Sook Kim
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
- Department of Pathology, Hanyang University College of Medicine, Seoul 04763, Korea
| | - Seung Han Son
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - Sungwoo Choi
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - Seol Eui Lee
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - Ji-Hun Kim
- College of Pharmacy, Chungbuk National University, Cheongju, Chungbuk 28160, Korea
| | - Kiseok Jang
- Department of Pathology, Hanyang University College of Medicine, Seoul 04763, Korea
| | - Gil Alterovitz
- Boston Children's Hospital/Harvard Medical School, Boston, MA 02115, USA
| | - Yu Chen
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | | | - Hyung-Sik Won
- Department of Biotechnology, Konkuk University, Chungju, Chungbuk 27478, Korea
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region 142290, Russia
| | - Chul Geun Kim
- Department of Life Science and Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
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14
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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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15
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Balyimez A, Stephans KL, Abazeed ME, Mian OY. The landscape of early carcinogenesis revealed through the lens of integrative genomics, epigenomics, and transcriptomics. J Thorac Dis 2019; 11:2188-2191. [PMID: 31372248 PMCID: PMC6626785 DOI: 10.21037/jtd.2019.06.07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 05/31/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Aysegul Balyimez
- Department of Translational Hematology and Oncology Research, Lerner Research Institute, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Kevin L. Stephans
- Department of Radiation Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Mohamed E. Abazeed
- Department of Translational Hematology and Oncology Research, Lerner Research Institute, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Radiation Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Omar Y. Mian
- Department of Translational Hematology and Oncology Research, Lerner Research Institute, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Radiation Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
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16
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Figueroa CD, Molina L, Bhoola KD, Ehrenfeld P. Overview of tissue kallikrein and kallikrein-related peptidases in breast cancer. Biol Chem 2019; 399:937-957. [PMID: 29885274 DOI: 10.1515/hsz-2018-0111] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 05/17/2018] [Indexed: 12/11/2022]
Abstract
The kallikrein family comprises tissue kallikrein and 14 kallikrein-related peptidases (KLKs) recognized as a subgroup of secreted trypsin- or chymotrypsin-like serine proteases. KLKs are expressed in many cellular types where they regulate important physiological activities such as semen liquefaction, immune response, neural development, blood pressure, skin desquamation and tooth enamel formation. Tissue kallikrein, the oldest member and kinin-releasing enzyme, and KLK3/PSA, a tumor biomarker for prostate cancer are the most prominent components of the family. Additionally, other KLKs have shown an abnormal expression in neoplasia, particularly in breast cancer. Thus, increased levels of some KLKs may increase extracellular matrix degradation, invasion and metastasis; other KLKs modulate cell growth, survival and angiogenesis. On the contrary, KLKs can also inhibit angiogenesis and produce tumor suppression. However, there is a lack of knowledge on how KLKs are regulated in tumor microenvironment by molecules present at the site, namely cytokines, inflammatory mediators and growth factors. Little is known about the signaling pathways that control expression/secretion of KLKs in breast cancer, and further how activation of PAR receptors may contribute to functional activity in neoplasia. A better understanding of these molecular events will allow us to consider KLKs as relevant therapeutic targets for breast cancer.
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Affiliation(s)
- Carlos D Figueroa
- Laboratory of Cellular Pathology, Institute of Anatomy, Histology and Pathology, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile
| | - Luis Molina
- Department of Science, Universidad San Sebastián, sede De la Patagonia, Puerto Montt, Chile
| | - Kanti D Bhoola
- Laboratory of Cellular Pathology, Institute of Anatomy, Histology and Pathology, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile
| | - Pamela Ehrenfeld
- Laboratory of Cellular Pathology, Institute of Anatomy, Histology and Pathology, Faculty of Medicine, Universidad Austral de Chile, Valdivia, Chile.,Centro de Investigaciones del Sistema Nervioso (CISNe), Valdivia, Chile, e-mail:
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17
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Liu W, Cui Y, Ren W, Irudayaraj J. Epigenetic biomarker screening by FLIM-FRET for combination therapy in ER+ breast cancer. Clin Epigenetics 2019; 11:16. [PMID: 30700309 PMCID: PMC6354376 DOI: 10.1186/s13148-019-0620-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 01/21/2019] [Indexed: 01/13/2023] Open
Abstract
Hormone-dependent gene expression involves dynamic and orchestrated regulation of epigenome leading to a cancerous state. Estrogen receptor (ER)-positive breast cancer rely on chromatin remodeling and association with epigenetic factors in inducing ER-dependent oncogenesis and thus cell over-proliferation. The mechanistic differences between epigenetic regulation and hormone signaling provide an avenue for combination therapy of ER-positive breast cancer. We hypothesized that epigenetic biomarkers within single nucleosome proximity of ER-dependent genes could serve as potential therapeutic targets. We described here a Fluorescence lifetime imaging-based Förster resonance energy transfer (FLIM-FRET) methodology for biomarker screening that could facilitate combination therapy based on our study. We screened 11 epigenetic-related markers which include oxidative forms of DNA methylation, histone modifications, and methyl-binding domain proteins. Among them, we identified H4K12acetylation (H4K12ac) and H3K27 acetylation (H3K27ac) as potential epigenetic therapeutic targets. When histone acetyltransferase inhibitor targeting H4K12ac and H3K27ac was combined with tamoxifen, an enhanced therapeutic outcome was observed against ER-positive breast cancer both in vitro and in vivo. Together, we demonstrate a single molecule approach as an effective screening tool for devising targeted epigenetic therapy.
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Affiliation(s)
- Wenjie Liu
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, 47907, USA
- Bindley Bioscience Center, Purdue University, West Lafayette, 47907, IN, USA
- Present Address: Department of Bioengineering, Cancer Center at Illinois, Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, USA
| | - Yi Cui
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, 47907, USA
- Bindley Bioscience Center, Purdue University, West Lafayette, 47907, IN, USA
- Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Wen Ren
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, 47907, USA
- Bindley Bioscience Center, Purdue University, West Lafayette, 47907, IN, USA
| | - Joseph Irudayaraj
- Department of Agricultural and Biological Engineering, Purdue University, West Lafayette, IN, 47907, USA.
- Bindley Bioscience Center, Purdue University, West Lafayette, 47907, IN, USA.
- Present Address: Department of Bioengineering, Cancer Center at Illinois, Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Champaign, IL, 61801, USA.
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18
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Cheng L, Tang Y, Chen X, Zhao L, Liu S, Ma Y, Wang N, Zhou K, Zhou J, Zhou M. Deletion of MBD2 inhibits proliferation of chronic myeloid leukaemia blast phase cells. Cancer Biol Ther 2018; 19:676-686. [PMID: 29565710 DOI: 10.1080/15384047.2018.1450113] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Aberrant methylation of tumour suppressor genes is associated with the progression to a blast crisis in chronic myeloid leukaemia (CML). Methyl-CpG-binding domain protein 2 (MBD2) has been studied as a "reader" of DNA methylation in many cancers, but its role in CML is unclear. We constructed cell models of a homozygous deletion mutation of MBD2 using gene-editing technology in K562 cells and BV173 cells. Here, we demonstrated that the deletion of MBD2 inhibited cell proliferation capacity in vitro. MBD2 deletion also significantly inhibited K562 cell proliferation in a xenograft tumour model in vivo. Additionally, the JAK2/STAT3 signalling pathway, which is abnormally active in CML, was inhibited by MBD2 deletion, and MBD2 deletion could up-regulate the expression of SHP1. In conclusion, our findings suggest that MBD2 is a candidate therapeutic strategy for the CML blast phase.
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Affiliation(s)
- Ling Cheng
- a Department of Hematology , Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Ying Tang
- a Department of Hematology , Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Xing Chen
- a Department of Hematology , Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Lei Zhao
- a Department of Hematology , Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Songya Liu
- a Department of Hematology , Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Yanna Ma
- a Department of Hematology , Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Na Wang
- a Department of Hematology , Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Kuangguo Zhou
- a Department of Hematology , Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Jianfeng Zhou
- a Department of Hematology , Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Mi Zhou
- a Department of Hematology , Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
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19
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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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20
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Ginder GD, Williams DC. Readers of DNA methylation, the MBD family as potential therapeutic targets. Pharmacol Ther 2017; 184:98-111. [PMID: 29128342 DOI: 10.1016/j.pharmthera.2017.11.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
DNA methylation represents a fundamental epigenetic modification that regulates chromatin architecture and gene transcription. Many diseases, including cancer, show aberrant methylation patterns that contribute to the disease phenotype. DNA methylation inhibitors have been used to block methylation dependent gene silencing to treat hematopoietic neoplasms and to restore expression of developmentally silenced genes. However, these inhibitors disrupt methylation globally and show significant off-target toxicities. As an alternative approach, we have been studying readers of DNA methylation, the 5-methylcytosine binding domain family of proteins, as potential therapeutic targets to restore expression of aberrantly and developmentally methylated and silenced genes. In this review, we discuss the role of DNA methylation in gene regulation and cancer development, the structure and function of the 5-methylcytosine binding domain family of proteins, and the possibility of targeting the complexes these proteins form to treat human disease.
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Affiliation(s)
- Gordon D Ginder
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23298, United States; Department of Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, United States; Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, United States.
| | - David C Williams
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, United States.
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21
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Mathot P, Grandin M, Devailly G, Souaze F, Cahais V, Moran S, Campone M, Herceg Z, Esteller M, Juin P, Mehlen P, Dante R. DNA methylation signal has a major role in the response of human breast cancer cells to the microenvironment. Oncogenesis 2017; 6:e390. [PMID: 29058695 PMCID: PMC5668886 DOI: 10.1038/oncsis.2017.88] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 08/07/2017] [Accepted: 08/22/2017] [Indexed: 02/06/2023] Open
Abstract
Breast cancer-associated fibroblasts (CAFs) have a crucial role in tumor initiation, metastasis and therapeutic resistance by secreting various growth factors, cytokines, protease and extracellular matrix components. Soluble factors secreted by CAFs are involved in many pathways including inflammation, metabolism, proliferation and epigenetic modulation, suggesting that CAF-dependent reprograming of cancer cells affects a large set of genes. This paracrine signaling has an important role in tumor progression, thus deciphering some of these processes could lead to relevant discoveries with subsequent clinical implications. Here, we investigated the mechanisms underlying the changes in gene expression patterns associated with the cross-talk between breast cancer cells and the stroma. From RNAseq data obtained from breast cancer cell lines grown in presence of CAF-secreted factors, we identified 372 upregulated genes, exhibiting an expression level positively correlated with the stromal content of breast cancer specimens. Furthermore, we observed that gene expression changes were not mediated through significant DNA methylation changes. Nevertheless, CAF-secreted factors but also stromal content of the tumors remarkably activated specific genes characterized by a DNA methylation pattern: hypermethylation at transcription start site and shore regions. Experimental approaches (inhibition of DNA methylation, knockdown of methyl-CpG-binding domain protein 2 and chromatin immunoprecipitation assays) indicated that this set of genes was epigenetically controlled. These data elucidate the importance of epigenetics marks in the cancer cell reprogramming induced by stromal cell and indicated that the interpreters of the DNA methylation signal have a major role in the response of the cancer cells to the microenvironment.
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Affiliation(s)
- P Mathot
- Dependence Receptors, Cancer and Development Laboratory, Centre de Recherche en Cancérologie de Lyon (CRCL), Inserm U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, Lyon, France
| | - M Grandin
- Dependence Receptors, Cancer and Development Laboratory, Centre de Recherche en Cancérologie de Lyon (CRCL), Inserm U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, Lyon, France
| | - G Devailly
- Department of Developmental Biology, The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, UK
| | - F Souaze
- Cell survival and tumor escape in breast cancer Laboratory, Center for Cancer Research Nantes-Angers UMR 892 Inserm-6299 CNRS/Université de Nantes, Nantes, France
| | - V Cahais
- Epigenetics Group, IARC, Lyon, France
| | - S Moran
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, Spain
| | - M Campone
- Cell survival and tumor escape in breast cancer Laboratory, Center for Cancer Research Nantes-Angers UMR 892 Inserm-6299 CNRS/Université de Nantes, Nantes, France
| | - Z Herceg
- Epigenetics Group, IARC, Lyon, France
| | - M Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - P Juin
- Cell survival and tumor escape in breast cancer Laboratory, Center for Cancer Research Nantes-Angers UMR 892 Inserm-6299 CNRS/Université de Nantes, Nantes, France
| | - P Mehlen
- Dependence Receptors, Cancer and Development Laboratory, Centre de Recherche en Cancérologie de Lyon (CRCL), Inserm U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, Lyon, France
| | - R Dante
- Dependence Receptors, Cancer and Development Laboratory, Centre de Recherche en Cancérologie de Lyon (CRCL), Inserm U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, Lyon, France
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22
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Gigek CO, Chen ES, Smith MAC. Methyl-CpG-Binding Protein (MBD) Family: Epigenomic Read-Outs Functions and Roles in Tumorigenesis and Psychiatric Diseases. J Cell Biochem 2016. [PMID: 26205787 DOI: 10.1002/jcb.25281] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Epigenetics is the study of the heritable changes on gene expression that are responsible for the regulation of development and that have an impact on several diseases. However, it is of equal importance to understand how epigenetic machinery works. DNA methylation is the most studied epigenetic mark and is generally associated with the regulation of gene expression through the repression of promoter activity and by affecting genome stability. Therefore, the ability of the cell to interpret correct methylation marks and/or the correct interpretation of methylation plays a role in many diseases. The major family of proteins that bind methylated DNA is the methyl-CpG binding domain proteins, or the MBDs. Here, we discuss the structure that makes these proteins a family, the main functions and interactions of all protein family members and their role in human disease such as psychiatric disorders and cancer.
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Affiliation(s)
- Carolina Oliveira Gigek
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo (UNIFESP), Rua Botucatu, 740, Edifício Leitão da Cunha, 1, ° andar, CEP 04023-900, São Paulo, SP, Brazil.,Disciplina de Gastroenterologia Cirúrgica, Departamento de Cirurgia, Universidade Federal de São Paulo (UNIFESP), R. Napoleão de Barros, 715, 2º andar, CEP:04024-002, São Paulo, Brazil
| | - Elizabeth Suchi Chen
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo (UNIFESP), Rua Botucatu, 740, Edifício Leitão da Cunha, 1, ° andar, CEP 04023-900, São Paulo, SP, Brazil
| | - Marilia Arruda Cardoso Smith
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo (UNIFESP), Rua Botucatu, 740, Edifício Leitão da Cunha, 1, ° andar, CEP 04023-900, São Paulo, SP, Brazil
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23
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Methyl-CpG-binding protein MBD2 plays a key role in maintenance and spread of DNA methylation at CpG islands and shores in cancer. Oncogene 2016; 36:1328-1338. [PMID: 27593931 DOI: 10.1038/onc.2016.297] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 07/04/2016] [Accepted: 07/17/2016] [Indexed: 02/07/2023]
Abstract
Cancer is characterised by DNA hypermethylation and gene silencing of CpG island-associated promoters, including tumour-suppressor genes. The methyl-CpG-binding domain (MBD) family of proteins bind to methylated DNA and can aid in the mediation of gene silencing through interaction with histone deacetylases and histone methyltransferases. However, the mechanisms responsible for eliciting CpG island hypermethylation in cancer, and the potential role that MBD proteins play in modulation of the methylome remain unclear. Our previous work demonstrated that MBD2 preferentially binds to the hypermethylated GSTP1 promoter CpG island in prostate cancer cells. Here, we use functional genetic approaches to investigate if MBD2 plays an active role in reshaping the DNA methylation landscape at this locus and genome-wide. First, we show that loss of MBD2 results in inhibition of both maintenance and spread of de novo methylation of a transfected construct containing the GSTP1 promoter CpG island in prostate cancer cells and Mbd2-/- mouse fibroblasts. De novo methylation was rescued by transient expression of Mbd2 in Mbd2-/- cells. Second, we show that MBD2 depletion triggers significant hypomethylation genome-wide in prostate cancer cells with concomitant loss of MBD2 binding at promoter and enhancer regulatory regions. Finally, CpG islands and shores that become hypomethylated after MBD2 depletion in LNCaP cancer cells show significant hypermethylation in clinical prostate cancer samples, highlighting a potential active role of MBD2 in promoting cancer-specific hypermethylation. Importantly, co-immunoprecipiation of MBD2 shows that MBD2 associates with DNA methyltransferase enzymes 1 and 3A. Together our results demonstrate that MBD2 has a critical role in 'rewriting' the cancer methylome at specific regulatory regions.
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24
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Grandin M, Mathot P, Devailly G, Bidet Y, Ghantous A, Favrot C, Gibert B, Gadot N, Puisieux I, Herceg Z, Delcros JG, Bernet A, Mehlen P, Dante R. Inhibition of DNA methylation promotes breast tumor sensitivity to netrin-1 interference. EMBO Mol Med 2016; 8:863-77. [PMID: 27378792 PMCID: PMC4967941 DOI: 10.15252/emmm.201505945] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 05/30/2016] [Accepted: 06/03/2016] [Indexed: 01/08/2023] Open
Abstract
In a number of human cancers, NTN1 upregulation inhibits apoptosis induced by its so-called dependence receptors DCC and UNC5H, thus promoting tumor progression. In other cancers however, the selective inhibition of this dependence receptor death pathway relies on the silencing of pro-apoptotic effector proteins. We show here that a substantial fraction of human breast tumors exhibits simultaneous DNA methylation-dependent loss of expression of NTN1 and of DAPK1, a serine threonine kinase known to transduce the netrin-1 dependence receptor pro-apoptotic pathway. The inhibition of DNA methylation by drugs such as decitabine restores the expression of both NTN1 and DAPK1 in netrin-1-low cancer cells. Furthermore, a combination of decitabine with NTN1 silencing strategies or with an anti-netrin-1 neutralizing antibody potentiates tumor cell death and efficiently blocks tumor growth in different animal models. Thus, combining DNA methylation inhibitors with netrin-1 neutralizing agents may be a valuable strategy for combating cancer.
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Affiliation(s)
- Mélodie Grandin
- Dependence Receptors, Cancer and Development Laboratory - Equipe labellisée 'La Ligue', LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon (CRCL), INSERM U1052-CNRS UMR5286 Université de Lyon Centre Léon Bérard, Lyon, France
| | - Pauline Mathot
- Dependence Receptors, Cancer and Development Laboratory - Equipe labellisée 'La Ligue', LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon (CRCL), INSERM U1052-CNRS UMR5286 Université de Lyon Centre Léon Bérard, Lyon, France
| | - Guillaume Devailly
- Dependence Receptors, Cancer and Development Laboratory - Equipe labellisée 'La Ligue', LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon (CRCL), INSERM U1052-CNRS UMR5286 Université de Lyon Centre Léon Bérard, Lyon, France
| | - Yannick Bidet
- Laboratoire d'Oncologie Moléculaire, Centre Jean Perrin, Clermont-Ferrand, France
| | | | - Clementine Favrot
- Dependence Receptors, Cancer and Development Laboratory - Equipe labellisée 'La Ligue', LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon (CRCL), INSERM U1052-CNRS UMR5286 Université de Lyon Centre Léon Bérard, Lyon, France
| | - Benjamin Gibert
- Dependence Receptors, Cancer and Development Laboratory - Equipe labellisée 'La Ligue', LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon (CRCL), INSERM U1052-CNRS UMR5286 Université de Lyon Centre Léon Bérard, Lyon, France
| | - Nicolas Gadot
- Endocrine Differentiation Laboratory, CRCL Université de Lyon Hospices Civils de Lyon Hôpital Edouard Herriot Anatomie Pathologique, Lyon, France
| | - Isabelle Puisieux
- Targeting of the tumor and its immune environment Laboratory CRCL INSERM U1052 CNRS UMR5286 UCBL CLB, Lyon, France
| | | | - Jean-Guy Delcros
- Dependence Receptors, Cancer and Development Laboratory - Equipe labellisée 'La Ligue', LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon (CRCL), INSERM U1052-CNRS UMR5286 Université de Lyon Centre Léon Bérard, Lyon, France
| | - Agnès Bernet
- Dependence Receptors, Cancer and Development Laboratory - Equipe labellisée 'La Ligue', LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon (CRCL), INSERM U1052-CNRS UMR5286 Université de Lyon Centre Léon Bérard, Lyon, France
| | - Patrick Mehlen
- Dependence Receptors, Cancer and Development Laboratory - Equipe labellisée 'La Ligue', LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon (CRCL), INSERM U1052-CNRS UMR5286 Université de Lyon Centre Léon Bérard, Lyon, France
| | - Robert Dante
- Dependence Receptors, Cancer and Development Laboratory - Equipe labellisée 'La Ligue', LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon (CRCL), INSERM U1052-CNRS UMR5286 Université de Lyon Centre Léon Bérard, Lyon, France
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25
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Liu W, Wang N, Lu M, Du XJ, Xing BC. MBD2 as a novel marker associated with poor survival of patients with hepatocellular carcinoma after hepatic resection. Mol Med Rep 2016; 14:1617-23. [PMID: 27315121 PMCID: PMC4940051 DOI: 10.3892/mmr.2016.5404] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 05/31/2016] [Indexed: 01/17/2023] Open
Abstract
Methyl-CpG binding domain 2 (MBD2) leads to the silencing of methylated genes in cancer cells and was implicated in the activation of prometastatic genes in hepatocellular carcinoma (HCC). The present study aimed to investigate the expression status of MBD2 in HCC and the correlation with surgical outcomes. The correlation between clinical prognostic factors and MBD2 were also evaluated. MBD2 expression was analyzed by western blotting in 20 paired HCC and paratumor liver (PTL) tissues. In addition, immunohistochemistry was performed on the 159 HCC samples following hepatic resection performed between January 2003 and October 2008. The correlation between clinicopathological factors and MBD2 expression was also evaluated by statistical analysis to determine the prognostic value of MBD2 expression in HCC. Postoperative prognostic factors were evaluated using univariate and multivariate analyses. Compared with PTL tissues, MBD2 expression was shown to be upregulated in 10 of the 20 HCC tissues (50%) by western blotting. The immunohistochemistry data indicated significant increase of the MBD2 expression level in 81 cases (50.94%) compared with the PTL tissues (0/159, 0%, P<0.001). The upregulated MBD2 expression in HCC tissues was correlated with BCLC stage B, tumor size >5 cm and microscopic vascular invasion. Multivariate analysis revealed that MBD2 was an independent prognostic factor for overall survival [HR, 2.089; P=0.001] and disease-free survival (HR, 1.601; P=0.022). In conclusion, MBD2 expression was elevated in HCC tissue, which suggesting MBD2 as a candidate prognostic marker of HCC.
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Affiliation(s)
- Wei Liu
- Hepatopancreatobiliary Surgery Department Ⅰ, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Peking University School of Oncology, Beijing Cancer Hospital and Institute, Beijing 100142, P.R. China
| | - Na Wang
- Hepatopancreatobiliary Surgery Department Ⅰ, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Peking University School of Oncology, Beijing Cancer Hospital and Institute, Beijing 100142, P.R. China
| | - Min Lu
- Department of Cell Biology and Cancer Research Center, Peking University Health Science Center, Beijing 100083, P.R. China
| | - Xiao-Juan Du
- Department of Cell Biology and Cancer Research Center, Peking University Health Science Center, Beijing 100083, P.R. China
| | - Bao-Cai Xing
- Hepatopancreatobiliary Surgery Department Ⅰ, Key Laboratory of Carcinogenesis and Translational Research, Ministry of Education, Peking University School of Oncology, Beijing Cancer Hospital and Institute, Beijing 100142, P.R. China
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26
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Wood KH, Zhou Z. Emerging Molecular and Biological Functions of MBD2, a Reader of DNA Methylation. Front Genet 2016; 7:93. [PMID: 27303433 PMCID: PMC4880565 DOI: 10.3389/fgene.2016.00093] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 05/10/2016] [Indexed: 01/25/2023] Open
Abstract
DNA methylation is an epigenetic mark that is essential for many biological processes and is linked to diseases such as cancer. Methylation is usually associated with transcriptional silencing, but new research has challenged this model. Both transcriptional activation and repression have recently been found to be associated with DNA methylation in a context-specific manner. How DNA methylation patterns are interpreted into different functional output remains poorly understood. One mechanism involves the protein ‘readers’ of methylation, which includes the methyl-CpG binding domain (MBD) family of proteins. This review examines the molecular and biological functions of MBD2, which binds to CpG methylation and is an integral part of the nucleosome remodeling and histone deacetylation (NuRD) complex. MBD2 has been linked to immune system function and tumorigenesis, yet little is known about its functions in vivo. Recent studies have found the MBD2 protein is ubiquitously expressed, with relatively high levels in the lung, liver, and colon. Mbd2 null mice surprisingly show relatively mild phenotypes compared to mice with loss of function of other MBD proteins. This evidence has previously been interpreted as functional redundancy between the MBD proteins. Here, we examine and contextualize research that suggests MBD2 has unique properties and functions among the MBD proteins. These functions translate to recently described roles in the development and differentiation of multiple cell lineages, including pluripotent stem cells and various cell types of the immune system, as well as in tumorigenesis. We also consider possible models for the dynamic interactions between MBD2 and NuRD in different tissues in vivo. The functions of MBD2 may have direct therapeutic implications for several areas of human disease, including autoimmune conditions and cancer, in addition to providing insights into the actions of NuRD and chromatin regulation.
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Affiliation(s)
- Kathleen H Wood
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
| | - Zhaolan Zhou
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA, USA
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27
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Sperlazza J, Rahmani M, Beckta J, Aust M, Hawkins E, Wang SZ, Zu Zhu S, Podder S, Dumur C, Archer K, Grant S, Ginder GD. Depletion of the chromatin remodeler CHD4 sensitizes AML blasts to genotoxic agents and reduces tumor formation. Blood 2015; 126:1462-72. [PMID: 26265695 PMCID: PMC4573869 DOI: 10.1182/blood-2015-03-631606] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 07/27/2015] [Indexed: 12/23/2022] Open
Abstract
Chromodomain helicase DNA-binding protein 4 (CHD4) is an ATPase that alters the phasing of nucleosomes on DNA and has recently been implicated in DNA double-stranded break (DSB) repair. Here, we show that depletion of CHD4 in acute myeloid leukemia (AML) blasts induces a global relaxation of chromatin that renders cells more susceptible to DSB formation, while concurrently impeding their repair. Furthermore, CHD4 depletion renders AML blasts more sensitive both in vitro and in vivo to genotoxic agents used in clinical therapy: daunorubicin (DNR) and cytarabine (ara-C). Sensitization to DNR and ara-C is mediated in part by activation of the ataxia-telangiectasia mutated pathway, which is preliminarily activated by a Tip60-dependent mechanism in response to chromatin relaxation and further activated by genotoxic agent-induced DSBs. This sensitization preferentially affects AML cells, as CHD4 depletion in normal CD34(+) hematopoietic progenitors does not increase their susceptibility to DNR or ara-C. Unexpectedly, we found that CHD4 is necessary for maintaining the tumor-forming behavior of AML cells, as CHD4 depletion severely restricted the ability of AML cells to form xenografts in mice and colonies in soft agar. Taken together, these results provide evidence for CHD4 as a novel therapeutic target whose inhibition has the potential to enhance the effectiveness of genotoxic agents used in AML therapy.
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MESH Headings
- Animals
- Antibiotics, Antineoplastic/therapeutic use
- Antimetabolites, Antineoplastic/therapeutic use
- Autoantigens/genetics
- Cell Line, Tumor
- Cytarabine/therapeutic use
- DNA Breaks, Double-Stranded/drug effects
- Daunorubicin/therapeutic use
- Female
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Mi-2 Nucleosome Remodeling and Deacetylase Complex/genetics
- Mice, Inbred NOD
- Mice, SCID
- RNA Interference
- Tumor Cells, Cultured
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Affiliation(s)
- Justin Sperlazza
- Cancer and Molecular Medicine PhD Program, Massey Cancer Center, and
| | | | - Jason Beckta
- Massey Cancer Center, and Department of Biochemistry and Molecular Biology
| | | | | | | | | | | | | | - Kellie Archer
- Massey Cancer Center, and Department of Biostatistics, and
| | - Steven Grant
- Massey Cancer Center, and Department of Internal Medicine, Department of Biochemistry and Molecular Biology
| | - Gordon D Ginder
- Massey Cancer Center, and Department of Internal Medicine, Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA
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28
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Rodger EJ, Chatterjee A, Morison IM. 5-hydroxymethylcytosine: a potential therapeutic target in cancer. Epigenomics 2015; 6:503-14. [PMID: 25431943 DOI: 10.2217/epi.14.39] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The ten-eleven translocation enzymes catalyze the conversion of 5-methylcytosine to 5-hydroxymethylcytosine, a distinct epigenetic mark that has an integral role in active demethylation. Genes that regulate the distribution and amount of 5-hydroxymethylcytosine in the genome could be suitable therapeutic targets to correct abnormal methylation in cancer. Here, we present an overview of the role of the 5-hydroxymethylcytosine pathway in human disease and discuss the emergence of innovative techniques that can map the distribution of 5-hydroxymethylcytosine at high resolution. In the context of current epigenetic therapies and by using recent functional studies, we propose plausible mechanisms to target the 5-hydroxymethylcytosine pathway in cancer. As the study of 5-hydroxymethylcytosine is still in its infancy, we provide future perspectives.
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Affiliation(s)
- Euan J Rodger
- Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
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29
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Devailly G, Grandin M, Perriaud L, Mathot P, Delcros JG, Bidet Y, Morel AP, Bignon JY, Puisieux A, Mehlen P, Dante R. Dynamics of MBD2 deposition across methylated DNA regions during malignant transformation of human mammary epithelial cells. Nucleic Acids Res 2015; 43:5838-54. [PMID: 26007656 PMCID: PMC4499136 DOI: 10.1093/nar/gkv508] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 05/05/2015] [Indexed: 12/26/2022] Open
Abstract
DNA methylation is thought to induce transcriptional silencing through the combination of two mechanisms: the repulsion of transcriptional activators unable to bind their target sites when methylated, and the recruitment of transcriptional repressors with specific affinity for methylated DNA. The Methyl CpG Binding Domain proteins MeCP2, MBD1 and MBD2 belong to the latter category. Here, we present MBD2 ChIPseq data obtained from the endogenous MBD2 in an isogenic cellular model of oncogenic transformation of human mammary cells. In immortalized (HMEC-hTERT) or transformed (HMLER) cells, MBD2 was found in a large proportion of methylated regions and associated with transcriptional silencing. A redistribution of MBD2 on methylated DNA occurred during oncogenic transformation, frequently independently of local DNA methylation changes. Genes downregulated during HMEC-hTERT transformation preferentially gained MBD2 on their promoter. Furthermore, depletion of MBD2 induced an upregulation of MBD2-bound genes methylated at their promoter regions, in HMLER cells. Among the 3,160 genes downregulated in transformed cells, 380 genes were methylated at their promoter regions in both cell lines, specifically associated by MBD2 in HMLER cells, and upregulated upon MBD2 depletion in HMLER. The transcriptional MBD2-dependent downregulation occurring during oncogenic transformation was also observed in two additional models of mammary cell transformation. Thus, the dynamics of MBD2 deposition across methylated DNA regions was associated with the oncogenic transformation of human mammary cells.
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Affiliation(s)
- Guillaume Devailly
- Dependence Receptors, Cancer and Development Laboratory - Equipe labellisée 'La Ligue', LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon (CRCL), INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, 69008 Lyon, France
| | - Mélodie Grandin
- Dependence Receptors, Cancer and Development Laboratory - Equipe labellisée 'La Ligue', LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon (CRCL), INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, 69008 Lyon, France
| | - Laury Perriaud
- Institut Curie and INSERM U612, Centre Universitaire, 91405, Orsay, France
| | - Pauline Mathot
- Dependence Receptors, Cancer and Development Laboratory - Equipe labellisée 'La Ligue', LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon (CRCL), INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, 69008 Lyon, France
| | - Jean-Guy Delcros
- Dependence Receptors, Cancer and Development Laboratory - Equipe labellisée 'La Ligue', LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon (CRCL), INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, 69008 Lyon, France
| | - Yannick Bidet
- Laboratoire d'Oncologie Moléculaire, Centre Jean Perrin, 63011 Clermont-Ferrand, France
| | - Anne-Pierre Morel
- EMT and cancer cell plasticity Laboratory - Equipe labellisée 'La Ligue', LabEx DEVweCAN, CRCL, INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, 69008 Lyon, France
| | - Jean-Yves Bignon
- Laboratoire d'Oncologie Moléculaire, Centre Jean Perrin, 63011 Clermont-Ferrand, France
| | - Alain Puisieux
- EMT and cancer cell plasticity Laboratory - Equipe labellisée 'La Ligue', LabEx DEVweCAN, CRCL, INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, 69008 Lyon, France
| | - Patrick Mehlen
- Dependence Receptors, Cancer and Development Laboratory - Equipe labellisée 'La Ligue', LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon (CRCL), INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, 69008 Lyon, France
| | - Robert Dante
- Dependence Receptors, Cancer and Development Laboratory - Equipe labellisée 'La Ligue', LabEx DEVweCAN, Centre de Recherche en Cancérologie de Lyon (CRCL), INSERM U1052-CNRS UMR5286, Université de Lyon, Centre Léon Bérard, 69008 Lyon, France
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30
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Puto LA, Benner C, Hunter T. The DAXX co-repressor is directly recruited to active regulatory elements genome-wide to regulate autophagy programs in a model of human prostate cancer. Oncoscience 2015; 2:362-72. [PMID: 26097870 PMCID: PMC4468322 DOI: 10.18632/oncoscience.152] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 04/08/2015] [Indexed: 01/09/2023] Open
Abstract
While carcinoma of the prostate is the second most common cause of cancer death in the US, current methods and markers used to predict prostate cancer (PCa) outcome are inadequate. This study was aimed at understanding the genome-wide binding and regulatory role of the DAXX transcriptional repressor, recently implicated in PCa. ChIP-Seq analysis of genome-wide distribution of DAXX in PC3 cells revealed over 59,000 DAXX binding sites, found at regulatory enhancers and promoters. ChIP-Seq analysis of DNA methyltransferase 1 (DNMT1), which is a key epigenetic partner for DAXX repression, revealed that DNMT1 binding was restricted to a small number of DAXX sites. DNMT1 and DAXX bound close to transcriptional activator motifs. DNMT1 sites were found to be dependent on DAXX for recruitment by analyzing DNMT1 ChIP-Seq following DAXX knockdown (K/D), corroborating previous findings that DAXX recruits DNMT1 to repress its target genes. Massively parallel RNA sequencing (RNA-Seq) was used to compare the transcriptomes of WT and DAXX K/D PC3 cells. Genes induced by DAXX K/D included those involved in autophagy, and DAXX ChIP-Seq peaks were found close to the transcription start sites (TSS) of autophagy genes, implying they are more likely to be regulated by DAXX. In conclusion, DAXX binds active regulatory elements and co-localizes with DNMT1 in the prostate cancer genome. Given DAXX's putative regulatory role in autophagy, future studies may consider DAXX as a candidate marker and therapeutic target for prostate cancer.
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Affiliation(s)
- Lorena A Puto
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Christopher Benner
- Integrative Genomics and Bioinformatics Core, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Tony Hunter
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
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31
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Desai MA, Webb HD, Sinanan LM, Scarsdale JN, Walavalkar NM, Ginder GD, Williams DC. An intrinsically disordered region of methyl-CpG binding domain protein 2 (MBD2) recruits the histone deacetylase core of the NuRD complex. Nucleic Acids Res 2015; 43:3100-13. [PMID: 25753662 PMCID: PMC4381075 DOI: 10.1093/nar/gkv168] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 02/13/2015] [Accepted: 02/20/2015] [Indexed: 12/20/2022] Open
Abstract
The MBD2-NuRD (Nucleosome Remodeling and Deacetylase) complex is an epigenetic reader of DNA methylation that regulates genes involved in normal development and neoplastic diseases. To delineate the architecture and functional interactions of the MBD2-NuRD complex, we previously solved the structures of MBD2 bound to methylated DNA and a coiled-coil interaction between MBD2 and p66α that recruits the CHD4 nucleosome remodeling protein to the complex. The work presented here identifies novel structural and functional features of a previously uncharacterized domain of MBD2 (MBD2IDR). Biophysical analyses show that the MBD2IDR is an intrinsically disordered region (IDR). However, despite this inherent disorder, MBD2IDR increases the overall binding affinity of MBD2 for methylated DNA. MBD2IDR also recruits the histone deacetylase core components (RbAp48, HDAC2 and MTA2) of NuRD through a critical contact region requiring two contiguous amino acid residues, Arg(286) and Leu(287). Mutating these residues abrogates interaction of MBD2 with the histone deacetylase core and impairs the ability of MBD2 to repress the methylated tumor suppressor gene PRSS8 in MDA-MB-435 breast cancer cells. These findings expand our knowledge of the multi-dimensional interactions of the MBD2-NuRD complex that govern its function.
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Affiliation(s)
- Megha A Desai
- Department of Human and Molecular Genetics and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Heather D Webb
- Department of Pathology and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Leander M Sinanan
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - J Neel Scarsdale
- Institute of Structural Biology and Drug Design, Center for the Study of Biological Complexity, and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Ninad M Walavalkar
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Gordon D Ginder
- Departments of Internal Medicine, Human and Molecular Genetics, and Microbiology and Immunology and Massey Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - David C Williams
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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32
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Deveci M, Küçüktunç O, Eren K, Bozdağ D, Kaya K, Çatalyürek ÜV. Querying Co-regulated Genes on Diverse Gene Expression Datasets Via Biclustering. Methods Mol Biol 2015; 1375:55-74. [PMID: 26626937 DOI: 10.1007/7651_2015_246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Rapid development and increasing popularity of gene expression microarrays have resulted in a number of studies on the discovery of co-regulated genes. One important way of discovering such co-regulations is the query-based search since gene co-expressions may indicate a shared role in a biological process. Although there exist promising query-driven search methods adapting clustering, they fail to capture many genes that function in the same biological pathway because microarray datasets are fraught with spurious samples or samples of diverse origin, or the pathways might be regulated under only a subset of samples. On the other hand, a class of clustering algorithms known as biclustering algorithms which simultaneously cluster both the items and their features are useful while analyzing gene expression data, or any data in which items are related in only a subset of their samples. This means that genes need not be related in all samples to be clustered together. Because many genes only interact under specific circumstances, biclustering may recover the relationships that traditional clustering algorithms can easily miss. In this chapter, we briefly summarize the literature using biclustering for querying co-regulated genes. Then we present a novel biclustering approach and evaluate its performance by a thorough experimental analysis.
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Affiliation(s)
- Mehmet Deveci
- Computer Science and Engineering, The Ohio State University, Columbus, OH, USA
| | - Onur Küçüktunç
- Computer Science and Engineering, The Ohio State University, Columbus, OH, USA
| | - Kemal Eren
- Computer Science and Engineering, The Ohio State University, Columbus, OH, USA
| | - Doruk Bozdağ
- Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Kamer Kaya
- Computer Science and Engineering, Sabancı University, Istanbul, Turkey
| | - Ümit V Çatalyürek
- Biomedical Informatics, Department of Electrical and Computer Engineering, The Ohio State University, Columbus, OH, USA.
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33
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Huang H, Hu G, Cai J, Xia B, Liu J, Li X, Gao W, Zhang J, Liu Y, Zhuang Z. Role of poly(ADP-ribose) glycohydrolase silencing in DNA hypomethylation induced by benzo(a)pyrene. Biochem Biophys Res Commun 2014; 452:708-14. [PMID: 25195819 DOI: 10.1016/j.bbrc.2014.08.146] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 08/26/2014] [Indexed: 12/31/2022]
Abstract
Benzo(a)pyrene (BaP) is a known carcinogen cytotoxic which can trigger extensive cellular responses. Many evidences suggest that inhibitors of poly(ADP-ribose) glycohydrolase (PARG) are potent anticancer drug candidates. However, the role of PARG in BaP carcinogenesis is less understood. Here we used PARG-deficient human bronchial epithelial cell line (shPARG cell) as an in vitro model, and investigated the role of PARG silencing in DNA methylation pattern changed by BaP. Our study shows, BaP treatment decreased global DNA methylation levels in 16HBE cells in a dose-dependent manner, but no dramatic changes were observed in shPARG cells. Further investigation revealed PARG silencing protected DNA methyltransferases (DNMTs) activity from change by BaP exposure. Interestingly, Dnmt1 is PARylated in PARG-null cells after BaP exposure. The results show a role for PARG silencing in DNA hypomethylation induced by BaP that may provide new clue for cancer therapy.
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Affiliation(s)
- Haiyan Huang
- Key Laboratory of Modern Toxicology of Shenzhen, Shenzhen Center for Disease Control and Prevention, Guangdong, China
| | - Gonghua Hu
- Key Laboratory of Modern Toxicology of Shenzhen, Shenzhen Center for Disease Control and Prevention, Guangdong, China; Department of Preventive Medicine, Gannan Medical College, Jiangxi, China
| | - Jianfeng Cai
- Key Laboratory of Modern Toxicology of Shenzhen, Shenzhen Center for Disease Control and Prevention, Guangdong, China
| | - Bo Xia
- Key Laboratory of Modern Toxicology of Shenzhen, Shenzhen Center for Disease Control and Prevention, Guangdong, China
| | - Jianjun Liu
- Key Laboratory of Modern Toxicology of Shenzhen, Shenzhen Center for Disease Control and Prevention, Guangdong, China
| | - Xuan Li
- Key Laboratory of Modern Toxicology of Shenzhen, Shenzhen Center for Disease Control and Prevention, Guangdong, China
| | - Wei Gao
- Key Laboratory of Modern Toxicology of Shenzhen, Shenzhen Center for Disease Control and Prevention, Guangdong, China
| | - Jianqing Zhang
- Key Laboratory of Modern Toxicology of Shenzhen, Shenzhen Center for Disease Control and Prevention, Guangdong, China
| | - Yinpin Liu
- Key Laboratory of Modern Toxicology of Shenzhen, Shenzhen Center for Disease Control and Prevention, Guangdong, China
| | - Zhixiong Zhuang
- Key Laboratory of Modern Toxicology of Shenzhen, Shenzhen Center for Disease Control and Prevention, Guangdong, China.
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34
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Cheishvili D, Chik F, Li CC, Bhattacharya B, Suderman M, Arakelian A, Hallett M, Rabbani SA, Szyf M. Synergistic effects of combined DNA methyltransferase inhibition and MBD2 depletion on breast cancer cells; MBD2 depletion blocks 5-aza-2'-deoxycytidine-triggered invasiveness. Carcinogenesis 2014; 35:2436-46. [PMID: 25178277 DOI: 10.1093/carcin/bgu181] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
5-Aza-2'-deoxycytidine (5-azaCdR) not only inhibits growth of non-invasive breast cancer cells but also increases their invasiveness through induction of pro-metastatic genes. Methylated DNA binding protein 2 (MBD2) is involved in silencing methylated tumor suppressor genes as well as activation of pro-metastatic genes. In this study, we show that a combination of MBD2 depletion and DNA methyltransferases (DNMT) inhibition in breast cancer cells results in a combined effect in vitro and in vivo, enhancing tumor growth arrest on one hand, while inhibiting invasiveness triggered by 5-azaCdR on the other hand. The combined treatment of MBD2 depletion and 5-azaCdR suppresses and augments distinct gene networks that are induced by DNMT inhibition alone. These data point to a potential new approach in targeting the DNA methylation machinery by combination of MBD2 and DNMT inhibitors.
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Affiliation(s)
- David Cheishvili
- Department of Pharmacology and Therapeutics, McGill University and
| | - Flora Chik
- Department of Pharmacology and Therapeutics, McGill University and
| | - Chen Chen Li
- Department of Pharmacology and Therapeutics, McGill University and
| | - Bishnu Bhattacharya
- Department of Pharmacology and Therapeutics, McGill University and Sackler Program for Epigenetics and Developmental Psychobiology, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec H3G 1Y6, Canada, McGill Centre for Bioinformatics, McGill University, 3649 Promenade Sir William Osler, Montreal, Quebec H3G 0B1, Canada and
| | - Matthew Suderman
- Department of Pharmacology and Therapeutics, McGill University and Sackler Program for Epigenetics and Developmental Psychobiology, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec H3G 1Y6, Canada, McGill Centre for Bioinformatics, McGill University, 3649 Promenade Sir William Osler, Montreal, Quebec H3G 0B1, Canada and
| | - Ani Arakelian
- Department of Medicine, McGill University Health Centre, 687 Pine Avenue West, Room H4.67, Montreal, Quebec H3A 1A1, Canada
| | - Michael Hallett
- McGill Centre for Bioinformatics, McGill University, 3649 Promenade Sir William Osler, Montreal, Quebec H3G 0B1, Canada and
| | - Shafaat A Rabbani
- Department of Medicine, McGill University Health Centre, 687 Pine Avenue West, Room H4.67, Montreal, Quebec H3A 1A1, Canada
| | - Moshe Szyf
- Department of Pharmacology and Therapeutics, McGill University and Sackler Program for Epigenetics and Developmental Psychobiology, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec H3G 1Y6, Canada,
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35
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MBD2 and multiple domains of CHD4 are required for transcriptional repression by Mi-2/NuRD complexes. Mol Cell Biol 2012; 32:5078-88. [PMID: 23071088 DOI: 10.1128/mcb.00819-12] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Mi-2/nucleosome remodeling and deacetylase (NuRD) chromatin remodeling complexes are important regulators of chromatin structure and DNA accessibility. We examined requirements for individual domains of chromodomain helicase DNA-binding protein 4 (CHD4), a core catalytic component of NuRD complexes, as well as the NuRD subunit methyl-binding domain protein 2 (MBD2) and methylated DNA, for NuRD function in the context of tissue-specific transcription. By itself, loss of NuRD activity is not sufficient for transcriptional activation. However, NuRD complexes greatly reduce activation of the B cell-specific mb-1 (Cd79a) gene by the transcription factors EBF1 and Pax5. Using our B cell model system, we determined that the two chromodomains and ATPase/helicase and C-terminal domains (CTD) of CHD4 are all necessary for repression of mb-1 promoters by NuRD. All of these domains except the CTD are required for efficient association of CHD4 with mb-1 promoter chromatin. Loss of MBD2 expression or of DNA methylation impaired association of CHD4 with mb-1 promoter chromatin and enhanced its transcription. We conclude that repressive functions of MBD2-containing NuRD complexes are dependent on cooperative interactions between the major domains of CHD4 with histones and DNA and on binding of methylated DNA by MBD2.
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