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Kim SH, Haynes KA. Reader-Effectors as Actuators of Epigenome Editing. Methods Mol Biol 2024; 2842:103-127. [PMID: 39012592 DOI: 10.1007/978-1-0716-4051-7_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Epigenome editing applications are gaining broader use for targeted transcriptional control as more enzymes with diverse chromatin-modifying functions are being incorporated into fusion proteins. Development of these fusion proteins, called epigenome editors, has outpaced the study of proteins that interact with edited chromatin. One type of protein that acts downstream of chromatin editing is the reader-effector, which bridges epigenetic marks with biological effects like gene regulation. As the name suggests, a reader-effector protein is generally composed of a reader domain and an effector domain. Reader domains directly bind epigenetic marks, while effector domains often recruit protein complexes that mediate transcription, chromatin remodeling, and DNA repair. In this chapter, we discuss the role of reader-effectors in driving the outputs of epigenome editing and highlight instances where abnormal and context-specific reader-effectors might impair the effects of epigenome editing. Lastly, we discuss how engineered reader-effectors may complement the epigenome editing toolbox to achieve robust and reliable gene regulation.
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Affiliation(s)
- Seong Hu Kim
- Wallace H. Coulter Department of Biomedical Engineering, Emory University School of Medicine, Atlanta, GA, USA
| | - Karmella A Haynes
- Wallace H. Coulter Department of Biomedical Engineering, Emory University School of Medicine, Atlanta, GA, USA.
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2
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Chen C, Liu X, Chang CY, Wang HY, Wang RF. The Interplay between T Cells and Cancer: The Basis of Immunotherapy. Genes (Basel) 2023; 14:genes14051008. [PMID: 37239368 DOI: 10.3390/genes14051008] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/17/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Over the past decade, immunotherapy has emerged as one of the most promising approaches to cancer treatment. The use of immune checkpoint inhibitors has resulted in impressive and durable clinical responses in the treatment of various cancers. Additionally, immunotherapy utilizing chimeric antigen receptor (CAR)-engineered T cells has produced robust responses in blood cancers, and T cell receptor (TCR)-engineered T cells are showing promising results in the treatment of solid cancers. Despite these noteworthy advancements in cancer immunotherapy, numerous challenges remain. Some patient populations are unresponsive to immune checkpoint inhibitor therapy, and CAR T cell therapy has yet to show efficacy against solid cancers. In this review, we first discuss the significant role that T cells play in the body's defense against cancer. We then delve into the mechanisms behind the current challenges facing immunotherapy, starting with T cell exhaustion due to immune checkpoint upregulation and changes in the transcriptional and epigenetic landscapes of dysfunctional T cells. We then discuss cancer-cell-intrinsic characteristics, including molecular alterations in cancer cells and the immunosuppressive nature of the tumor microenvironment (TME), which collectively facilitate tumor cell proliferation, survival, metastasis, and immune evasion. Finally, we examine recent advancements in cancer immunotherapy, with a specific emphasis on T-cell-based treatments.
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Affiliation(s)
- Christina Chen
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Xin Liu
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Che-Yu Chang
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Helen Y Wang
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Rong-Fu Wang
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Department of Pediatrics, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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Ai K, Li X, Zhang P, Pan J, Li H, He Z, Zhang H, Yi L, Kang Y, Wang Y, Chen J, Li Y, Xiang X, Chai X, Zhang D. Genetic or siRNA inhibition of MBD2 attenuates the UUO- and I/R-induced renal fibrosis via downregulation of EGR1. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 28:77-86. [PMID: 35356685 PMCID: PMC8933641 DOI: 10.1016/j.omtn.2022.02.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 02/25/2022] [Indexed: 12/20/2022]
Abstract
DNA methylation plays a pivotal role in the progression of renal fibrosis. Methyl-CpG–binding domain protein 2 (MBD2), a protein reader of methylation, is involved in the development of acute kidney injury (AKI) caused by vancomycin. However, the role and mechanism of action of MBD2 in renal remain unclear. In this study, MBD2 mediated extracellular matrix (ECM) production induced by TGF-β1 in Boston University mouse proximal tubule (BUMPT) cells,and upregulated the expression EGR1 to promote ECM production in murine embryonic NIH 3T3 fibroblasts. ChIP analysis demonstrated that MBD2 physically interacted with the promoter region of the CpG islands of EGR1 genes and then activated their expression by inducing hypomethylation of the promoter region. In vivo, PT-MBD2-KO attenuated unilateral ureteral obstruction (UUO)-induced renal tubulointerstitial fibrosis via downregulation of EGR1, which was demonstrated by the downregulation of fibronectin (FN), collagen I and IV, α-SMA, and EGR1. Injection of MBD2-siRNA attenuated the UUO- and I/R-induced renal fibrosis. Those molecular changes were verified by biopsies from patients with obstructive nephropathy (OB). These data collectively demonstrated that inhibition of MBD2 reduces renal fibrosis via downregulating EGR1, which could be a target for treatment of fibrotic kidney disease.
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Affiliation(s)
- Kai Ai
- Department of Emergency Medicine, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China.,Emergency Medicine and Difficult Diseases Institute, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China.,Department of Urology, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China
| | - Xiaozhou Li
- Department of Emergency Medicine, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China.,Emergency Medicine and Difficult Diseases Institute, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China
| | - Pan Zhang
- Department of Emergency Medicine, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China.,Emergency Medicine and Difficult Diseases Institute, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China.,Department of Epidemiology and Health Statistics, Xiangya School of Public Health, Central South University, Changsha, Hunan 410011, People's Republic of China
| | - Jian Pan
- Department of Emergency Medicine, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China.,Emergency Medicine and Difficult Diseases Institute, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China
| | - Huiling Li
- Department of Ophthalmology, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China
| | - Zhibiao He
- Department of Emergency Medicine, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China.,Emergency Medicine and Difficult Diseases Institute, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China
| | - Hongliang Zhang
- Department of Emergency Medicine, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China.,Emergency Medicine and Difficult Diseases Institute, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China
| | - Lei Yi
- Department of Urology, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China
| | - Ye Kang
- Department of Urology, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China
| | - Yinhuai Wang
- Department of Urology, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China
| | - Junxiang Chen
- Department of Nephrology, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China
| | - Yijian Li
- Department of Urology, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China
| | - Xudong Xiang
- Department of Emergency Medicine, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China.,Emergency Medicine and Difficult Diseases Institute, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China
| | - Xiangping Chai
- Department of Emergency Medicine, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China.,Emergency Medicine and Difficult Diseases Institute, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China
| | - Dongshan Zhang
- Department of Emergency Medicine, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China.,Emergency Medicine and Difficult Diseases Institute, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, People's Republic of China
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4
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Methyl-CpG-binding domain protein 2 contributes to renal fibrosis through promoting polarized M1 macrophages. Cell Death Dis 2022; 13:125. [PMID: 35136032 PMCID: PMC8826408 DOI: 10.1038/s41419-022-04577-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 12/14/2021] [Accepted: 01/19/2022] [Indexed: 12/20/2022]
Abstract
Recent studies reported that Methyl-CpG–binding domain protein 2 (MBD2) promoted M2 macrophages accumulation to increase bleomycin-induced pulmonary fibrosis. However, the role and mechanism of action of MBD2 in macrophages differentiation and renal fibrosis remain largely unknown. In the current study, MBD2 not only promoted the differentiation of resting M0 macrophages to polarized M2 macrophages, but also induced them to polarized M1 macrophages and the transition of M2 to M1 macrophages. ChIP analysis demonstrated that MBD2 physically interacted with the promoter region of the CpG islands of G0S2 genes, and then activated their expression by inducing hypomethylation of the promoter region. Interestingly, the data demonstrated that the role of G0S2 in macrophages differentiation is consistent with MBD2. Furthermore, Co-culture of activated M1 macrophages and murine embryonic NIH 3T3 fibroblasts indicated that MBD2 mediated the M1-induction of ECM production by embryonic NIH 3T3 fibroblasts via promotion of G0S2. In addition, we also found that inhibition of MBD2 suppressed LPS induced the expression of p53 as well as activation and expression of stat3 in RAW264.7 macrophages. In vivo, MBD2 LysMcre attenuated unilateral ureteral obstruction (UUO) and ischemia/reperfusion (I/R)-induced renal fibrosis via downregulation of G0S2, which was demonstrated by the downregulation of fibronectin (FN), collagen I and IV, α-SMA, G0S2. These data collectively demonstrated that MBD2 in macrophages contributed to UUO and I/R-induced renal fibrosis through the upregulation of G0S2, which could be a target for treatment for chronic kidney disease.
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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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Ikram MF, Farhat SM, Mahboob A, Baig S, Yaqinuddin A, Ahmed T. Expression of DnMTs and MBDs in AlCl 3-Induced Neurotoxicity Mouse Model. Biol Trace Elem Res 2021; 199:3433-3444. [PMID: 33174148 DOI: 10.1007/s12011-020-02474-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/03/2020] [Indexed: 10/23/2022]
Abstract
Alteration in DNA methylation after aluminum exposure has been shown to contribute in pathogenesis of Alzheimer's disease (AD). This study is aimed to determine the effect of Al exposure (42 and 60 days) on learning and memory and the expression of proteins involved in DNA methylation (MBD1, MBD2, MBD3, MeCP2 (methyl CpG binding protein 2), DnMT1 and DnMT3a). Male BALB/c mice were treated with AlCl3 for either 42 days or 60 days. After treatment completion, learning and memory were compared to the control group using novel object recognition test, elevated plus maze test, open field test, and Morris water maze test. The treated animals and their respective controls were sacrificed after cognitive testing and samples from their whole cortex and hippocampus were harvested for gene expression analysis. Mice treated with AlCl3 showed significant cognitive deficit with impaired short-term memory, elevated anxiety, and deterioration in spatial and reference memory. The AlCl3 treatment showed significant reduction in the expression of MBDs in the whole cortex at 60 days of treatment as compared to control. AlCl3-treated animals showed decreased expression of MBDs and DnMT3a in the hippocampus for longer treated animals but strikingly, MBD2 showed significantly increased expression in AlCl3-treated animals at 60 days p ≤ 0.001. In conclusion, this study showed that AlCl3-treated animals showed significant memory and cognitive deficits and it is associated with significant changes in the expression of proteins involved in DNA methylation mechanism. Moreover, different Al exposure duration had slightly different effects.
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Affiliation(s)
- Muhammad Faisal Ikram
- Department of Anatomy, College of Medicine, Alfaisal University, Riyadh, Kingdom of Saudi Arabia
- Medical College, Ziauddin University, Karachi, Pakistan
| | - Syeda Mehpara Farhat
- Neurobiology Laboratory, Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology (NUST), Sector H-12, Islamabad, 44000, Pakistan
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - Aamra Mahboob
- Neurobiology Laboratory, Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology (NUST), Sector H-12, Islamabad, 44000, Pakistan
| | - Saeeda Baig
- Department of Biochemistry, Ziauddin University, Karachi, Pakistan
| | - Ahmed Yaqinuddin
- Department of Anatomy, College of Medicine, Alfaisal University, Riyadh, Kingdom of Saudi Arabia
| | - Touqeer Ahmed
- Neurobiology Laboratory, Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology (NUST), Sector H-12, Islamabad, 44000, Pakistan.
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7
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Prominent Role of Histone Modifications in the Regulation of Tumor Metastasis. Int J Mol Sci 2021; 22:ijms22052778. [PMID: 33803458 PMCID: PMC7967218 DOI: 10.3390/ijms22052778] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 03/08/2021] [Indexed: 12/22/2022] Open
Abstract
Tumor aggressiveness and progression is highly dependent on the process of metastasis, regulated by the coordinated interplay of genetic and epigenetic mechanisms. Metastasis involves several steps of epithelial to mesenchymal transition (EMT), anoikis resistance, intra- and extravasation, and new tissue colonization. EMT is considered as the most critical process allowing cancer cells to switch their epithelial characteristics and acquire mesenchymal properties. Emerging evidence demonstrates that epigenetics mechanisms, DNA methylation, histone modifications, and non-coding RNAs participate in the widespread changes of gene expression that characterize the metastatic phenotype. At the chromatin level, active and repressive histone post-translational modifications (PTM) in association with pleiotropic transcription factors regulate pivotal genes involved in the initiation of the EMT process as well as in intravasation and anoikis resistance, playing a central role in the progression of tumors. Herein, we discuss the main epigenetic mechanisms associated with the different steps of metastatic process, focusing in particular on the prominent role of histone modifications and the modifying enzymes that mediate transcriptional regulation of genes associated with tumor progression. We further discuss the development of novel treatment strategies targeting the reversibility of histone modifications and highlight their importance in the future of cancer therapy.
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8
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Huang X, Zhao Q, Li D, Ren B, Yue L, Shi F, Wang X, Zheng C, Chen X, Zhang C, Zhang W. Association between gene promoter methylation of the one-carbon metabolism pathway and serum folate among patients with hyperhomocysteinemia. Eur J Clin Nutr 2020; 74:1677-1684. [DOI: 10.1038/s41430-020-0657-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 04/29/2020] [Accepted: 04/30/2020] [Indexed: 12/23/2022]
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9
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Li C, Lu W, Yang L, Li Z, Zhou X, Guo R, Wang J, Wu Z, Dong Z, Ning G, Shi Y, Gu Y, Chen P, Hao Z, Han T, Yang M, Wang W, Huang X, Li Y, Gao S, Hu R. MKRN3 regulates the epigenetic switch of mammalian puberty via ubiquitination of MBD3. Natl Sci Rev 2020; 7:671-685. [PMID: 34692086 PMCID: PMC8288866 DOI: 10.1093/nsr/nwaa023] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 01/10/2020] [Accepted: 02/13/2020] [Indexed: 12/30/2022] Open
Abstract
Central precocious puberty (CPP) refers to a human syndrome of early puberty initiation with characteristic increase in hypothalamic production and release of gonadotropin-releasing hormone (GnRH). Previously, loss-of-function mutations in human MKRN3, encoding a putative E3 ubiquitin ligase, were found to contribute to about 30% of cases of familial CPP. MKRN3 was thereby suggested to serve as a ‘brake’ of mammalian puberty onset, but the underlying mechanisms remain as yet unknown. Here, we report that genetic ablation of Mkrn3 did accelerate mouse puberty onset with increased production of hypothalamic GnRH1. MKRN3 interacts with and ubiquitinates MBD3, which epigenetically silences GNRH1 through disrupting the MBD3 binding to the GNRH1 promoter and recruitment of DNA demethylase TET2. Our findings have thus delineated a molecular mechanism through which the MKRN3–MBD3 axis controls the epigenetic switch in the onset of mammalian puberty.
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Affiliation(s)
- Chuanyin Li
- Department of Pediatrics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenli Lu
- Department of Pediatrics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Liguang Yang
- Department of Pediatrics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhengwei Li
- Department of Pediatrics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyi Zhou
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Rong Guo
- Department of Pediatrics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junqi Wang
- Department of Pediatrics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhebao Wu
- Center for Pituitary Tumor, Ruijin Hospital Affiliated to Shanghai Jiao Tong University, Shanghai 200025, China
| | - Zhiya Dong
- Department of Pediatrics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Guang Ning
- Shanghai Institute of Endocrine and Metabolic Diseases, Shanghai Key Laboratory for Endocrine Tumors and E-Institute for Endocrinology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yujiang Shi
- Division of Endocrinology, Diabetes and Hypertension, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Yinmin Gu
- CAS Key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Peng Chen
- Department of Pediatrics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zijian Hao
- Department of Pediatrics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tianting Han
- Department of Pediatrics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meiqiang Yang
- Department of Pediatrics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Wang
- Department of Pediatrics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xuehui Huang
- College of Life Sciences, Shanghai Normal University, Shanghai 200234, China
| | - Yixue Li
- Department of Pediatrics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Shan Gao
- CAS Key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Ronggui Hu
- Department of Pediatrics, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai 200072, China
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10
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Hodges AJ, Hudson NO, Buck-Koehntop BA. Cys 2His 2 Zinc Finger Methyl-CpG Binding Proteins: Getting a Handle on Methylated DNA. J Mol Biol 2019:S0022-2836(19)30567-4. [PMID: 31628952 DOI: 10.1016/j.jmb.2019.09.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/13/2019] [Accepted: 09/16/2019] [Indexed: 12/12/2022]
Abstract
DNA methylation is an essential epigenetic modification involved in the maintenance of genomic stability, preservation of cellular identity, and regulation of the transcriptional landscape needed to maintain cellular function. In an increasing number of disease conditions, DNA methylation patterns are inappropriately distributed in a manner that supports the disease phenotype. Methyl-CpG binding proteins (MBPs) are specialized transcription factors that read and translate methylated DNA signals into recruitment of protein assemblies that can alter local chromatin architecture and transcription. MBPs thus play a key intermediary role in gene regulation for both normal and diseased cells. Here, we highlight established and potential structure-function relationships for the best characterized members of the zinc finger (ZF) family of MBPs in propagating DNA methylation signals into downstream cellular responses. Current and future investigations aimed toward expanding our understanding of ZF MBP cellular roles will provide needed mechanistic insight into normal and disease state functions, as well as afford evaluation for the potential of these proteins as epigenetic-based therapeutic targets.
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Affiliation(s)
- Amelia J Hodges
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT, 84112, USA
| | - Nicholas O Hudson
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT, 84112, USA
| | - Bethany A Buck-Koehntop
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT, 84112, USA.
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11
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Chen R, Hou R, Hong X, Yan S, Zha J. Organophosphate flame retardants (OPFRs) induce genotoxicity in vivo: A survey on apoptosis, DNA methylation, DNA oxidative damage, liver metabolites, and transcriptomics. ENVIRONMENT INTERNATIONAL 2019; 130:104914. [PMID: 31226563 DOI: 10.1016/j.envint.2019.104914] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/07/2019] [Accepted: 06/09/2019] [Indexed: 05/03/2023]
Abstract
BACKGROUND As potential substitutes for polybrominated diphenyl ethers (PBDEs), organophosphate flame retardants (OPFRs) have been frequently detected in the environment. However, the genotoxicity induced by these OPFRs has rarely been described, and the results reported in previous studies are conflicting and inconsistent. OBJECTIVES The present study aimed to determine how OPFRs induced genetic toxicity in vivo. METHODS Using Chinese rare minnow as a model, the toxicity of three OPFRs was screened with RNA-seq. To verify the OPFR-induced genotoxicity, alkaline comet assay, cell apoptosis analysis, HPLC-based DNA methylation assay, 8-OHdG assay, bioconcentration and biotransformation investigation were performed. RESULTS According to transcriptomic data, TDCIPP exposure substantially altered the pathways related to DNA damage, including the cell cycle, DNA replication, Fanconi anemia pathway, p53 signaling pathway, and various DNA repair pathways. Although TBOEP and TPHP did not affect DNA damage, TDCIPP induced DNA damage in a dose-dependent manner. TDCIPP also induced apoptosis, altered the activities of caspase-3 and -9, and increased the 8-OHdG levels, while a significant difference in the levels of DNA methylation induced by OPFRs was not observed. CONCLUSIONS Based on these results, TDCIPP induced DNA oxidative damage, eventually leading to genotoxicity in vivo.
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Affiliation(s)
- Rui Chen
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100085, China
| | - Rui Hou
- School of Environmental Science and Engineering, Guangdong University of Technology, Guangzhou 510006, Guangdong, China
| | - Xiangsheng Hong
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100085, China
| | - Saihong Yan
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, Beijing 100085, China
| | - Jinmiao Zha
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Beijing Key Laboratory of Industrial Wastewater Treatment and Reuse, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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12
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Wu X, Shen J, Xiao Z, Li J, Zhao Y, Zhao Q, Cho CH, Li M. An overview of the multifaceted roles of miRNAs in gastric cancer: Spotlight on novel biomarkers and therapeutic targets. Biochem Pharmacol 2019; 163:425-439. [PMID: 30857828 DOI: 10.1016/j.bcp.2019.03.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/07/2019] [Indexed: 02/07/2023]
Abstract
MicroRNAs (miRNAs) are a group of small non-coding RNAs that have displayed strong association with gastric cancer (GC). Through the repression of target mRNAs, miRNAs regulate many biological pathways that are involved in cell proliferation, apoptosis, migration, invasion, metastasis as well as drug resistance. The detection of miRNAs in tissues and in body fluids emerges as a promising method in the diagnosis and prognosis of GC, due to their unique expression pattern in correlation with GC. Notably, miRNAs are also identified as potential therapeutic targets for GC therapy. The present review is thus to highlight the multifaceted roles of miRNAs in GC and in GC therapies, which would give indications for future research.
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Affiliation(s)
- Xu Wu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, Sichuan, China; South Sichuan Institute of Translational Medicine, Luzhou 646000, Sichuan, China
| | - Jing Shen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, Sichuan, China; South Sichuan Institute of Translational Medicine, Luzhou 646000, Sichuan, China
| | - Zhangang Xiao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, Sichuan, China; South Sichuan Institute of Translational Medicine, Luzhou 646000, Sichuan, China
| | - Jing Li
- Department of Oncology and Hematology, Hospital (T.C.M.) Affiliated to Southwest Medical University, Luzhou 646000, Sichuan, China
| | - Yueshui Zhao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, Sichuan, China; South Sichuan Institute of Translational Medicine, Luzhou 646000, Sichuan, China
| | - Qijie Zhao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, Sichuan, China; South Sichuan Institute of Translational Medicine, Luzhou 646000, Sichuan, China
| | - Chi Hin Cho
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, Sichuan, China; South Sichuan Institute of Translational Medicine, Luzhou 646000, Sichuan, China.
| | - Mingxing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou 646000, Sichuan, China; South Sichuan Institute of Translational Medicine, Luzhou 646000, Sichuan, China.
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13
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Cofre J, Saalfeld K, Abdelhay E. Cancer as an Embryological Phenomenon and Its Developmental Pathways: A Hypothesis regarding the Contribution of the Noncanonical Wnt Pathway. ScientificWorldJournal 2019; 2019:4714781. [PMID: 30940992 PMCID: PMC6421044 DOI: 10.1155/2019/4714781] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 12/18/2018] [Accepted: 01/29/2019] [Indexed: 02/07/2023] Open
Abstract
For gastrulation to occur in human embryos, a mechanism that simultaneously regulates many different processes, such as cell differentiation, proliferation, migration, and invasion, is required to consistently and effectively create a human being during embryonic morphogenesis. The striking similarities in the processes of cancer and gastrulation have prompted speculation regarding the developmental pathways involved in their regulation. One of the fundamental requirements for the developmental pathways in gastrulation and cancer is the ability to respond to environmental stimuli, and it has been proposed that the Kaiso and noncanonical Wnt pathways participate in the mechanisms regulating these developmental pathways. In particular, these pathways might also explain the notable differences in invasive capacity between cancers of endodermal and mesodermal origins and cancers of ectodermal origin. Nevertheless, the available information indicates that cancer is an abnormal state of adult human cells in which developmental pathways are reactivated in inappropriate temporal and spatial contexts.
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Affiliation(s)
- Jaime Cofre
- Laboratório de Embriologia Molecular e Câncer, Universidade Federal de Santa Catarina, Sala 313b, 88040-900 Florianópolis, SC, Brazil
| | - Kay Saalfeld
- Laboratório de Filogenia Animal, Universidade Federal de Santa Catarina, Brazil
| | - Eliana Abdelhay
- Divisão de Laboratórios do CEMO, Instituto Nacional do Câncer, Rio de Janeiro, Brazil
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14
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Gonzalez-Fierro A, Dueñas-González A. Emerging DNA methylation inhibitors for cancer therapy: challenges and prospects. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2019. [DOI: 10.1080/23808993.2019.1571906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
| | - Alfonso Dueñas-González
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México UNAM/Instituto Nacional de Can cerología, México City, Mexico
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15
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Hudson NO, Whitby FG, Buck-Koehntop BA. Structural insights into methylated DNA recognition by the C-terminal zinc fingers of the DNA reader protein ZBTB38. J Biol Chem 2018; 293:19835-19843. [PMID: 30355731 DOI: 10.1074/jbc.ra118.005147] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 10/16/2018] [Indexed: 02/05/2023] Open
Abstract
Methyl-CpG-binding proteins (MBPs) are selective readers of DNA methylation that play an essential role in mediating cellular transcription processes in both normal and diseased cells. This physiological function of MBPs has generated significant interest in understanding the mechanisms by which these proteins read and interpret DNA methylation signals. Zinc finger and BTB domain-containing 38 (ZBTB38) represents one member of the zinc finger (ZF) family of MBPs. We recently demonstrated that the C-terminal ZFs of ZBTB38 exhibit methyl-selective DNA binding within the ((A/G)TmCG(G/A)(mC/T)(G/A)) context both in vitro and within cells. Here we report the crystal structure of the first four C-terminal ZBTB38 ZFs (ZFs 6-9) in complex with the previously identified methylated consensus sequence at 1.75 Å resolution. From the structure, methyl-selective binding is preferentially localized at the 5' mCpG site of the bound DNA, which is facilitated through a series of base-specific interactions from residues within the α-helices of ZF7 and ZF8. ZF6 and ZF9 primarily stabilize ZF7 and ZF8 to facilitate the core base-specific interactions. Further structural and biochemical analyses, including solution NMR spectroscopy and electrophoretic mobility gel shift assays, revealed that the C-terminal ZFs of ZBTB38 utilize an alternative mode of mCpG recognition from the ZF MBPs structurally evaluated to date. Combined, these findings provide insight into the mechanism by which this ZF domain of ZBTB38 selectively recognizes methylated CpG sites and expands our understanding of how ZF-containing proteins can interpret this essential epigenetic mark.
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Affiliation(s)
| | - Frank G Whitby
- Biochemistry, University of Utah, Salt Lake City, Utah 84112
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16
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Hudson NO, Buck-Koehntop BA. Zinc Finger Readers of Methylated DNA. Molecules 2018; 23:E2555. [PMID: 30301273 PMCID: PMC6222495 DOI: 10.3390/molecules23102555] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/03/2018] [Accepted: 10/05/2018] [Indexed: 01/07/2023] Open
Abstract
DNA methylation is a prevalent epigenetic modification involved in regulating a number of essential cellular processes, including genomic accessibility and transcriptional outcomes. As such, aberrant alterations in global DNA methylation patterns have been associated with a growing number of disease conditions. Nevertheless, the full mechanisms by which DNA methylation information is interpreted and translated into genomic responses is not yet fully understood. Methyl-CpG binding proteins (MBPs) function as important mediators of this essential process by selectively reading DNA methylation signals and translating this information into down-stream cellular outcomes. The Cys₂His₂ zinc finger scaffold is one of the most abundant DNA binding motifs found within human transcription factors, yet only a few zinc finger containing proteins capable of conferring selectivity for mCpG over CpG sites have been characterized. This review summarizes our current structural understanding for the mechanisms by which the zinc finger MBPs evaluated to date read this essential epigenetic mark. Further, some of the biological implications for mCpG readout elicited by this family of MBPs are discussed.
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Affiliation(s)
- Nicholas O Hudson
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112-0850, USA.
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17
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Zhang Y, Yang Y, Zhang F, Liao X, Shao Z, Li D. Epigenetic silencing of RNF144A expression in breast cancer cells through promoter hypermethylation and MBD4. Cancer Med 2018; 7:1317-1325. [PMID: 29473320 PMCID: PMC5911569 DOI: 10.1002/cam4.1324] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 12/11/2017] [Accepted: 12/13/2017] [Indexed: 12/27/2022] Open
Abstract
Emerging evidence shows that ring finger protein 144A (RNF144A), a poorly characterized member of the Ring-between-Ring (RBR) family of E3 ubiquitin ligases, is a potential tumor suppressor gene. However, its regulatory mechanism in breast cancer remains undefined. Here, we report that RNF144A promoter contains a putative CpG island and the methylation levels of RNF144A promoter are higher in primary breast tumors than those in normal breast tissues. Consistently, RNF144A promoter methylation levels are associated with its transcriptional silencing in breast cancer cells, and treatment with DNA methylation inhibitor 5-Aza-2-deoxycytidine (AZA) reactivates RNF144A expression in cells with RNF144A promoter hypermethylation. Furthermore, genetic knockdown or pharmacological inhibition of endogenous methyl-CpG-binding domain 4 (MBD4) results in increased RNF144A expression. These findings suggest that RNF144A is epigenetically silenced in breast cancer cells by promoter hypermethylation and MBD4.
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Affiliation(s)
- Ye Zhang
- Shanghai Cancer Center and Institutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Yin‐Long Yang
- Shanghai Cancer Center and Institutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
- Department of OncologyShanghai Cancer CenterShanghai Medical CollegeFudan UniversityShanghai200032China
- Cancer InstituteShanghai Cancer CenterShanghai Medical CollegeFudan UniversityShanghai200032China
- Department of Breast SurgeryShanghai Cancer CenterShanghai Medical CollegeFudan UniversityShanghai200032China
- Key Laboratory of Breast Cancer in ShanghaiShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Fang‐Lin Zhang
- Shanghai Cancer Center and Institutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
- Department of OncologyShanghai Cancer CenterShanghai Medical CollegeFudan UniversityShanghai200032China
- Cancer InstituteShanghai Cancer CenterShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Xiao‐Hong Liao
- Shanghai Cancer Center and Institutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
- Department of OncologyShanghai Cancer CenterShanghai Medical CollegeFudan UniversityShanghai200032China
- Cancer InstituteShanghai Cancer CenterShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Zhi‐Min Shao
- Shanghai Cancer Center and Institutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
- Department of OncologyShanghai Cancer CenterShanghai Medical CollegeFudan UniversityShanghai200032China
- Cancer InstituteShanghai Cancer CenterShanghai Medical CollegeFudan UniversityShanghai200032China
- Department of Breast SurgeryShanghai Cancer CenterShanghai Medical CollegeFudan UniversityShanghai200032China
- Key Laboratory of Breast Cancer in ShanghaiShanghai Medical CollegeFudan UniversityShanghai200032China
| | - Da‐Qiang Li
- Shanghai Cancer Center and Institutes of Biomedical SciencesShanghai Medical CollegeFudan UniversityShanghai200032China
- Department of OncologyShanghai Cancer CenterShanghai Medical CollegeFudan UniversityShanghai200032China
- Cancer InstituteShanghai Cancer CenterShanghai Medical CollegeFudan UniversityShanghai200032China
- Department of Breast SurgeryShanghai Cancer CenterShanghai Medical CollegeFudan UniversityShanghai200032China
- Key Laboratory of Breast Cancer in ShanghaiShanghai Medical CollegeFudan UniversityShanghai200032China
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18
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Zhu F, Wu Q, Ni Z, Lei C, Li T, Shi Y. miR-19a/b and MeCP2 repress reciprocally to regulate multidrug resistance in gastric cancer cells. Int J Mol Med 2018; 42:228-236. [PMID: 29568890 PMCID: PMC5979884 DOI: 10.3892/ijmm.2018.3581] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 02/20/2018] [Indexed: 12/18/2022] Open
Abstract
Despite the improvement in gastric cancer (GC) treatment, multidrug resistance (MDR) is still a significant reason for chemotherapy failure. Our previous studies have demonstrated that miR-19a/b upregulation directly promoted MDR in GC cells. However, the exact regulation and the potential molecule mechanisms have not been fully clarified. In this study, we found that miR-19a/b was directly involved in 5-aza-2'-deoxycytidine (5-Aza-dC) induced MDR of GC cells. Mechanically, demethylation of miR-19a/b repressed methyl CpG binding protein 2 (MeCP2) expression via direct binding at the 3'-untranslated regions, which then alleviated the inhibitory effects of MeCP2 on miR-19a/b expression. Thus, the mutual regulatory network sustains preservation of the expression levels of miR-19a/b. We further demonstrated that miR-19a/b expression was inversely correlated to MeCP2 expression in GC tissues. These data showed an intimate interplay among miR-19a/b methylation, MeCP2 activity, and MDR, revealing a potential therapeutic target for GC.
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Affiliation(s)
- Fei Zhu
- State Key Laboratory of Cancer Biology and Institute of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Qiong Wu
- State Key Laboratory of Cancer Biology and Institute of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Zhen Ni
- State Key Laboratory of Cancer Biology and Institute of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Chao Lei
- State Key Laboratory of Cancer Biology and Institute of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Ting Li
- State Key Laboratory of Cancer Biology and Institute of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
| | - Yongquan Shi
- State Key Laboratory of Cancer Biology and Institute of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, P.R. China
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19
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Cui Y, Li J, Weng L, Wirbisky SE, Freeman JL, Liu J, Liu Q, Yuan X, Irudayaraj J. Regulatory landscape and clinical implication of MBD3 in human malignant glioma. Oncotarget 2018; 7:81698-81714. [PMID: 27835581 PMCID: PMC5340251 DOI: 10.18632/oncotarget.13173] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 10/19/2016] [Indexed: 12/19/2022] Open
Abstract
In this article we inspect the roles and functions of the methyl-CpG-binding domain protein 3 (MBD3) in human malignant glioma, to assess its potential as an epigenetic biomarker for prognosis. The regulatory effects of MBD3 on glioma transcriptome were first profiled by high-throughput microarray. Our results indicate that MBD3 is involved in both transcriptional activation and repression. Furthermore, MBD3 fine-controls a spectrum of proteins critical for cellular metabolism and proliferation, thereby contributing to an exquisite anti-glioma network. Specifically, the expression of MHC class II molecules was found to positively correlate with MBD3, which provides new insight into the immune escape of gliomagenesis. In addition, MBD3 participates in constraining a number of oncogenic non-coding RNAs whose over-activation could drive cells into excessive growth and higher malignancy. Having followed up a pilot cohort, we noted that the survival of malignant glioma patients was proportional to the content of MBD3 and 5-hydroxymethylcytosine (5hmC) in their tumor cells. The progression-free survival (PFS) and overall survival (OS) were relatively poor for patients with lower amount of MBD3 and 5hmC in the tissue biopsies. Taken together, this work enriches our understanding of the mechanistic involvement of MBD3 in malignant glioma.
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Affiliation(s)
- Yi Cui
- Department of Neurosurgery, Xiangya Hospital of Central South University, Changsha, Hunan 410008, China.,Biological Engineering and Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA
| | - Jian Li
- Department of Neurosurgery, Xiangya Hospital of Central South University, Changsha, Hunan 410008, China
| | - Ling Weng
- Department of Neurology, Xiangya Hospital of Central South University, Changsha, Hunan 410008, China
| | - Sara E Wirbisky
- School of Health Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Jennifer L Freeman
- School of Health Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Jingping Liu
- Department of Neurosurgery, Xiangya Hospital of Central South University, Changsha, Hunan 410008, China
| | - Qing Liu
- Department of Neurosurgery, Xiangya Hospital of Central South University, Changsha, Hunan 410008, China.,The Institute of Skull Base Surgery & Neuro-Oncology at Hunan, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Xianrui Yuan
- Department of Neurosurgery, Xiangya Hospital of Central South University, Changsha, Hunan 410008, China.,The Institute of Skull Base Surgery & Neuro-Oncology at Hunan, Xiangya Hospital, Changsha, Hunan 410008, China
| | - Joseph Irudayaraj
- Biological Engineering and Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA
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20
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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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21
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Zhang R, Liu L, Yao Y, Fei F, Wang F, Yang Q, Gui Y, Wang X. High Resolution Imaging of DNA Methylation Dynamics using a Zebrafish Reporter. Sci Rep 2017; 7:5430. [PMID: 28710355 PMCID: PMC5511286 DOI: 10.1038/s41598-017-05648-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 06/01/2017] [Indexed: 12/17/2022] Open
Abstract
As one of the major epigenetic modifications, DNA methylation is constantly regulated during embryonic development, cell lineage commitment, and pathological processes. To facilitate real-time observation of DNA methylation, we generated a transgenic zebrafish reporter of DNA methylation (zebraRDM) via knockin of an mCherry-fused methyl-CpG binding domain (MBD) probe driven by the bactin2 promoter. The probe colocalized with heterochromatin, and its intensity was positively correlated with 5 mC immunostaining at a subcellular resolution in early embryos. Biochemical assays indicated that cells with stronger fluorescence maintained a higher level of DNA methylation, and time-lapse imaging at the blastula stage showed that the level of DNA methylation was transiently strengthened during mitosis. By crossing zebraRDM with other fluorescent transgenic lines, we demonstrate that the reporter can visually distinguish different cell lineages in organs like the heart. Our zebraRDM reporter therefore serves as a convenient and powerful tool for high-resolution investigation of methylation dynamics in live animals.
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Affiliation(s)
- Ranran Zhang
- Cardiovascular Center, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Lian Liu
- Cardiovascular Center, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Yuxiao Yao
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Fei Fei
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Feng Wang
- Cardiovascular Center, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Qian Yang
- Cardiovascular Center, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Yonghao Gui
- Cardiovascular Center, Children's Hospital of Fudan University, Shanghai, 201102, China.
| | - Xu Wang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
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22
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Mossman BT. Cell Signaling and Epigenetic Mechanisms in Mesothelioma. ASBESTOS AND MESOTHELIOMA 2017. [DOI: 10.1007/978-3-319-53560-9_10] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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23
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Methylation of Notch3 modulates chemoresistance via P-glycoprotein. Eur J Pharmacol 2016; 792:7-14. [DOI: 10.1016/j.ejphar.2016.10.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/14/2016] [Accepted: 10/21/2016] [Indexed: 12/12/2022]
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24
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Sun L, Fang J. Epigenetic regulation of epithelial-mesenchymal transition. Cell Mol Life Sci 2016; 73:4493-4515. [PMID: 27392607 PMCID: PMC5459373 DOI: 10.1007/s00018-016-2303-1] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 06/10/2016] [Accepted: 06/30/2016] [Indexed: 12/12/2022]
Abstract
Epithelial-mesenchymal transition (EMT) is an essential process for morphogenesis and organ development which reversibly enables polarized epithelial cells to lose their epithelial characteristics and to acquire mesenchymal properties. It is now evident that the aberrant activation of EMT is also a critical mechanism to endow epithelial cancer cells with migratory and invasive capabilities associated with metastatic competence. This dedifferentiation program is mediated by a small cohort of pleiotropic transcription factors which orchestrate a complex array of epigenetic mechanisms for the wide-spread changes in gene expression. Here, we review major epigenetic mechanisms with an emphasis on histone modifications and discuss their implications in EMT and tumor progression. We also highlight mechanisms underlying transcription regulation concerted by various chromatin-modifying proteins and EMT-inducing transcription factors at different molecular layers. Owing to the reversible nature of epigenetic modifications, a thorough understanding of their functions in EMT will not only provide new insights into our knowledge of cancer progression and metastasis, but also facilitate the development of diagnostic and therapeutic strategies for human malignancy.
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Affiliation(s)
- Lidong Sun
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA
| | - Jia Fang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA.
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Abstract
SUMMARYEpigenetic changes are present in all human cancers and are now known to cooperate with genetic alterations to drive the cancer phenotype. These changes involve DNA methylation, histone modifiers and readers, chromatin remodelers, microRNAs, and other components of chromatin. Cancer genetics and epigenetics are inextricably linked in generating the malignant phenotype; epigenetic changes can cause mutations in genes, and, conversely, mutations are frequently observed in genes that modify the epigenome. Epigenetic therapies, in which the goal is to reverse these changes, are now one standard of care for a preleukemic disorder and form of lymphoma. The application of epigenetic therapies in the treatment of solid tumors is also emerging as a viable therapeutic route.
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Affiliation(s)
- Stephen B Baylin
- Cancer Biology Program, Johns Hopkins University, School of Medicine, Baltimore, Maryland 21287
| | - Peter A Jones
- Van Andel Research Institute, Grand Rapids, Michigan 49503
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MBD3 mediates epigenetic regulation on EPAS1 promoter in cancer. Tumour Biol 2016; 37:13455-13467. [PMID: 27465550 DOI: 10.1007/s13277-016-5237-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 07/15/2016] [Indexed: 10/21/2022] Open
Abstract
Hypoxia-inducible factor 2α (HIF2α) plays critical roles in cancer progression. Although the mechanisms of HIF2α translation and degradation have been well studied, the mechanism for HIF2α regulation at transcriptional level is still not fully understood. Here, we present evidence that DNA methylation in promoter contributes to transcription of EPAS1 coding HIF2α. Methylated CpG binding protein 3 (MBD3) contributes to the intricate regulatory mechanism. We showed that MBD3 bound to the EPAS1 promoter in breast cancer cells and amplified EPAS1 transcription through demethylating CpG located around transcriptional start site in MDA-MB-468 cells. This enabled MDA-MB-468 cells to activate HIF2α-mediated angiogenesis. However, in 7860 cells, the demethylation function of MBD3 on EPAS1 was not observed because of the poor methylated-CpG promoter. Nevertheless, depletion of MBD3 induced by shRNA decreased EPAS1 transcription and therefore decreased HIF2α-mediated cellular response in both MDA-MB-468 and 7860 cancer cells. These results indicated that the endogenous MBD3 was involved in regulating the transcription and therefore the transcriptional activities of HIF2α, suggesting that MBD3 may be a potential therapeutic target of tumor.
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Liu Y, Jin X, Li Y, Ruan Y, Lu Y, Yang M, Lin D, Song P, Guo Y, Zhao S, Dong B, Xie Y, Dang Q, Quan C. DNA methylation of claudin-6 promotes breast cancer cell migration and invasion by recruiting MeCP2 and deacetylating H3Ac and H4Ac. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2016; 35:120. [PMID: 27461117 PMCID: PMC4962420 DOI: 10.1186/s13046-016-0396-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 07/13/2016] [Indexed: 11/30/2022]
Abstract
Background Claudin-6 (CLDN6), a member of claudin transmembrane protein family, has recently been reported to be undetectable or at low levels in human breast cancer cell lines and tissues and plays a role in suppression of migration and invasion in breast cancer cells. In addition, it is reported that CLDN6 expression is regulated by DNA methylation in various human cancers and cell lines. However, it is unclear how DNA methylation regulates CLDN6 expression. Here we show the mechanism by which DNA methylation regulates CLDN6 expression in human breast cancer cell line MCF-7. Methods RT-PCR, Western blot and immunofluorescent staining were utilized to investigate CLDN6 expression in breast cancer tissues and MCF-7 cells. Methylation-Specific PCR (MSP) was applied to determine DNA methylation status in CLDN6 gene promoter region. Wound-healing assay and invasion assay were utilized to test mobility of MCF-7 cells treated with 5-aza-dC (DNA methyltransferase inhibitor). MeCP2 binding, H3Ac and H4Ac in CLDN6 promoter region were analyzed by ChIP assay. Nuclease accessibility assay was performed for analysis of the chromatin conformation of CLDN6 gene. To study the role of CLDN6 in malignant progression, we used RNAi to knockdown CLDN6 expression in MCF-7 cells treated with 5-aza-dC, and examined the mobility of MCF-7 cells by wound-healing assay and invasion assay. Results 5-aza-dC and TSA (histone deacetylase inhibitor) application induced CLDN6 expression in MCF-7 cells respectively and synergistically. 5-aza-dC treatment induced CLDN6 demethylation, inhibited MeCP2 binding to CLDN6 promoter and increased H3Ac and H4Ac in the promoter. In addition, TSA increased H4Ac, not H3Ac in the promoter. The chromatin structure of CLDN6 gene became looser than the control group after treating with 5-aza-dC in MCF-7 cells. 5-aza-dC up-regulated CLDN6 expression and suppressed migration and invasion in MCF-7 cells, whereas CLDN6 silence restored tumor malignance in MCF-7 cells. Conclusions DNA methylation down-regulates CLDN6 expression through MeCP2 binding to the CLDN6 promoter, deacetylating H3 and H4, and altering chromatin structure, consequently promoting migratory and invasive phenotype in MCF-7 cells.
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Affiliation(s)
- Yafang Liu
- The Key Laboratory of Pathology, Ministry of Education, College of Basic Medical Science, Jilin University, 126 Xinmin Street, Changchun, Jilin, 130021, China.,Department of Pathology, the First Affiliated Hospital of Jilin University, 126 Xinmin Street, Changchun, Jilin, 130021, China
| | - Xiangshu Jin
- The Key Laboratory of Pathology, Ministry of Education, College of Basic Medical Science, Jilin University, 126 Xinmin Street, Changchun, Jilin, 130021, China
| | - Yanru Li
- The Key Laboratory of Pathology, Ministry of Education, College of Basic Medical Science, Jilin University, 126 Xinmin Street, Changchun, Jilin, 130021, China
| | - Yang Ruan
- The Key Laboratory of Pathology, Ministry of Education, College of Basic Medical Science, Jilin University, 126 Xinmin Street, Changchun, Jilin, 130021, China
| | - Yan Lu
- The Key Laboratory of Pathology, Ministry of Education, College of Basic Medical Science, Jilin University, 126 Xinmin Street, Changchun, Jilin, 130021, China
| | - Minlan Yang
- The Key Laboratory of Pathology, Ministry of Education, College of Basic Medical Science, Jilin University, 126 Xinmin Street, Changchun, Jilin, 130021, China
| | - Dongjing Lin
- The Key Laboratory of Pathology, Ministry of Education, College of Basic Medical Science, Jilin University, 126 Xinmin Street, Changchun, Jilin, 130021, China
| | - Peiye Song
- The Key Laboratory of Pathology, Ministry of Education, College of Basic Medical Science, Jilin University, 126 Xinmin Street, Changchun, Jilin, 130021, China
| | - Yantong Guo
- The Key Laboratory of Pathology, Ministry of Education, College of Basic Medical Science, Jilin University, 126 Xinmin Street, Changchun, Jilin, 130021, China
| | - Shuai Zhao
- The Key Laboratory of Pathology, Ministry of Education, College of Basic Medical Science, Jilin University, 126 Xinmin Street, Changchun, Jilin, 130021, China
| | - Bing Dong
- The Key Laboratory of Pathology, Ministry of Education, College of Basic Medical Science, Jilin University, 126 Xinmin Street, Changchun, Jilin, 130021, China
| | - Yinping Xie
- The Key Laboratory of Pathology, Ministry of Education, College of Basic Medical Science, Jilin University, 126 Xinmin Street, Changchun, Jilin, 130021, China
| | - Qihua Dang
- The Key Laboratory of Pathology, Ministry of Education, College of Basic Medical Science, Jilin University, 126 Xinmin Street, Changchun, Jilin, 130021, China
| | - Chengshi Quan
- The Key Laboratory of Pathology, Ministry of Education, College of Basic Medical Science, Jilin University, 126 Xinmin Street, Changchun, Jilin, 130021, China.
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Protein palmitoylation activate zygotic gene expression during the maternal-to-zygotic transition. Biochem Biophys Res Commun 2016; 475:194-201. [DOI: 10.1016/j.bbrc.2016.05.074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 05/13/2016] [Indexed: 12/31/2022]
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Yan K, You L, Degerny C, Ghorbani M, Liu X, Chen L, Li L, Miao D, Yang XJ. The Chromatin Regulator BRPF3 Preferentially Activates the HBO1 Acetyltransferase but Is Dispensable for Mouse Development and Survival. J Biol Chem 2015; 291:2647-63. [PMID: 26677226 DOI: 10.1074/jbc.m115.703041] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Indexed: 12/12/2022] Open
Abstract
To interpret epigenetic information, chromatin readers utilize various protein domains for recognition of DNA and histone modifications. Some readers possess multidomains for modification recognition and are thus multivalent. Bromodomain- and plant homeodomain-linked finger-containing protein 3 (BRPF3) is such a chromatin reader, containing two plant homeodomain-linked fingers, one bromodomain and a PWWP domain. However, its molecular and biological functions remain to be investigated. Here, we report that endogenous BRPF3 preferentially forms a tetrameric complex with HBO1 (also known as KAT7) and two other subunits but not with related acetyltransferases such as MOZ, MORF, TIP60, and MOF (also known as KAT6A, KAT6B, KAT5, and KAT8, respectively). We have also characterized a mutant mouse strain with a lacZ reporter inserted at the Brpf3 locus. Systematic analysis of β-galactosidase activity revealed dynamic spatiotemporal expression of Brpf3 during mouse embryogenesis and high expression in the adult brain and testis. Brpf3 disruption, however, resulted in no obvious gross phenotypes. This is in stark contrast to Brpf1 and Brpf2, whose loss causes lethality at E9.5 and E15.5, respectively. In Brpf3-null mice and embryonic fibroblasts, RT-quantitative PCR uncovered no changes in levels of Brpf1 and Brpf2 transcripts, confirming no compensation from them. These results indicate that BRPF3 forms a functional tetrameric complex with HBO1 but is not required for mouse development and survival, thereby distinguishing BRPF3 from its paralogs, BRPF1 and BRPF2.
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Affiliation(s)
- Kezhi Yan
- From the Rosalind and Morris Goodman Cancer Research Center, Departments of Biochemistry and Medicine, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Linya You
- From the Rosalind and Morris Goodman Cancer Research Center, Medicine, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Cindy Degerny
- From the Rosalind and Morris Goodman Cancer Research Center
| | - Mohammad Ghorbani
- From the Rosalind and Morris Goodman Cancer Research Center, Medicine, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Xin Liu
- From the Rosalind and Morris Goodman Cancer Research Center
| | - Lulu Chen
- the State Key Laboratory of Reproductive Medicine, Research Center for Bone and Stem Cells, Department of Human Anatomy, Nanjing Medical University, Nanjing 210029, China, and
| | - Lin Li
- From the Rosalind and Morris Goodman Cancer Research Center, Medicine, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Dengshun Miao
- the State Key Laboratory of Reproductive Medicine, Research Center for Bone and Stem Cells, Department of Human Anatomy, Nanjing Medical University, Nanjing 210029, China, and
| | - Xiang-Jiao Yang
- From the Rosalind and Morris Goodman Cancer Research Center, Departments of Biochemistry and Medicine, McGill University, Montreal, Quebec H3A 1A3, Canada, the McGill University Health Center, Montreal, Quebec H3A 1A3, Canada
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Liang L, Lutz BM, Bekker A, Tao YX. Epigenetic regulation of chronic pain. Epigenomics 2015; 7:235-45. [PMID: 25942533 DOI: 10.2217/epi.14.75] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Chronic pain arising from peripheral inflammation and tissue or nerve injury is a common clinical symptom. Although intensive research on the neurobiological mechanisms of chronic pain has been carried out during previous decades, this disorder is still poorly managed by current drugs such as opioids and nonsteroidal anti-inflammatory drugs. Inflammation, tissue injury and/or nerve injury-induced changes in gene expression in sensory neurons of the dorsal root ganglion, spinal cord dorsal horn and pain-associated brain regions are thought to participate in chronic pain genesis; however, how these changes occur is still elusive. Epigenetic modifications including DNA methylation and covalent histone modifications control gene expression. Recent studies have shown that peripheral noxious stimulation changes DNA methylation and histone modifications and that these changes may be related to the induction of pain hypersensitivity under chronic pain conditions. This review summarizes the current knowledge and progress in epigenetic research in chronic pain and discusses the potential role of epigenetic modifications as therapeutic antinociceptive targets in this disorder.
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Affiliation(s)
- Lingli Liang
- Department of Anesthesiology, New Jersey Medical School, Rutgers, The State University of New Jersey, 185 S. Orange Avenue, MSB F-548, Newark, NJ 07103, USA
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Bellacosa A, Drohat AC. Role of base excision repair in maintaining the genetic and epigenetic integrity of CpG sites. DNA Repair (Amst) 2015; 32:33-42. [PMID: 26021671 DOI: 10.1016/j.dnarep.2015.04.011] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cytosine methylation at CpG dinucleotides is a central component of epigenetic regulation in vertebrates, and the base excision repair (BER) pathway is important for maintaining both the genetic stability and the methylation status of CpG sites. This perspective focuses on two enzymes that are of particular importance for the genetic and epigenetic integrity of CpG sites, methyl binding domain 4 (MBD4) and thymine DNA glycosylase (TDG). We discuss their capacity for countering C to T mutations at CpG sites, by initiating base excision repair of G · T mismatches generated by deamination of 5-methylcytosine (5mC). We also consider their role in active DNA demethylation, including pathways that are initiated by oxidation and/or deamination of 5mC.
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Affiliation(s)
- Alfonso Bellacosa
- Cancer Epigenetics Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA 19111, United States.
| | - Alexander C Drohat
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St., Baltimore, MD 21201, United States.
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Yang L, Cui Y, Shen J, Lin F, Wang X, Long M, Wei J, Zhang H. Antitumor activity of SA12, a novel peptide, on SKBr-3 breast cancer cells via the mitochondrial apoptosis pathway. Drug Des Devel Ther 2015; 9:1319-30. [PMID: 25767377 PMCID: PMC4354433 DOI: 10.2147/dddt.s75780] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Breast cancer is considered to be the most common malignancy in women. Treatment of breast cancer has been focused on molecular targeted therapy, and anticancer peptides are considered to be some of the most promising candidate drugs. In the current study, we used mRNA-peptide display technology to screen antibreast cancer peptides and identified a novel peptide, SA12, which showed significant activity in the inhibition of proliferation and induction of apoptosis in SKBr-3 breast cancer cells. The mechanism by which SA12 peptide triggers apoptosis was further investigated using a pull-down assay, reverse transcription-polymerase chain reaction, and Western blotting analysis. The results demonstrated that this peptide could interact with tumor-associated proteins MECP2 and CDC20B, which further induced apoptosis of tumor cells via the mitochondrial pathway involving the Bcl-2 family and related caspases. We propose that the novel SA12 peptide has the potential to provide a new strategy for the development of targeted therapy in breast cancer.
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Affiliation(s)
- Longfei Yang
- Department of Medical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, People's Republic of China
| | - Ying Cui
- Department of Medical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, People's Republic of China
| | - Jianjun Shen
- Department of Medical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, People's Republic of China
| | - Fang Lin
- Department of Medical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, People's Republic of China
| | - Xi Wang
- Department of Medical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, People's Republic of China
| | - Min Long
- Department of Medical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, People's Republic of China
| | - Junxia Wei
- Department of Medical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, People's Republic of China
| | - Huizhong Zhang
- Department of Medical Laboratory and Research Center, Tangdu Hospital, Fourth Military Medical University, Xi'an, People's Republic of China
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Calcagno DQ, de Arruda Cardoso Smith M, Burbano RR. Cancer type-specific epigenetic changes: gastric cancer. Methods Mol Biol 2015; 1238:79-101. [PMID: 25421656 DOI: 10.1007/978-1-4939-1804-1_5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Gastric cancer (GC) remains a major cause of mortality despite declining rate in the world. Epigenetic alterations contribute significantly to the development and progression of gastric tumors. Epigenetic refers to the number of modifications of the chromatin structure that affect gene expression without altering the primary sequence of DNA, and these changes lead to transcriptional activation or silencing of the gene. Over the years, the study of epigenetic processes has increased, and novel therapeutic approaches have emerged. This chapter summarizes the main epigenomic mechanisms described recently involved in gastric carcinogenesis, focusing on the roles that aberrant DNA methylation, histone modifications (histone acetylation and methylation), and miRNAs (oncogenic and tumor suppressor function of miRNA) play in the onset and progression of gastric tumors. Clinical implications of these epigenetic alterations in GC are also discussed.
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Affiliation(s)
- Danielle Queiroz Calcagno
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Rua dos Mundurucus, 4487, Guamá, CEP 66073-000 Belém, PA, Brazil,
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Abstract
Galectin-3, a member of a β-galactoside-binding protein family, is involved in normal growth development as well as cancer progression and metastasis, but the detailed mechanisms of its functions or its transcriptional regulations are not well understood. Besides, several regulatory elements such as GC box, CRE motif, AP-1 site, and NF-κB sites, the promoter of galectin-3 gene (LGALS3) contains several CpG islands that can be methylated during tumorigenesis of prostate leading to the gene silencing. Here we describe protocols for identification of galectin-3 DNA methylation, suppression of DNA methyltransferases to reactivate galectin-3 expression, and development of methylation-specific polymerase chain reaction (MS-PCR) to assess galectin-3 expression in various biological specimens such as tissue, serum, and urine samples.
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Affiliation(s)
- Hafiz Ahmed
- Department of Biochemistry and Molecular Biology, Institute of Marine and Environmental Technology, Greenebaum Cancer Center, University of Maryland School of Medicine, 701 East Pratt Street, Baltimore, MD, 21202, USA,
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Osorio J, Ji P, Drackley J, Luchini D, Loor J. Smartamine M and MetaSmart supplementation during the peripartal period alter hepatic expression of gene networks in 1-carbon metabolism, inflammation, oxidative stress, and the growth hormone–insulin-like growth factor 1 axis pathways. J Dairy Sci 2014; 97:7451-64. [DOI: 10.3168/jds.2014-8680] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 08/18/2014] [Indexed: 01/09/2023]
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Koh DI, Han D, Ryu H, Choi WI, Jeon BN, Kim MK, Kim Y, Kim JY, Parry L, Clarke AR, Reynolds AB, Hur MW. KAISO, a critical regulator of p53-mediated transcription of CDKN1A and apoptotic genes. Proc Natl Acad Sci U S A 2014; 111:15078-83. [PMID: 25288747 PMCID: PMC4210320 DOI: 10.1073/pnas.1318780111] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
An unresolved issue in genotoxic stress response is identification of induced regulatory proteins and how these activate tumor suppressor p53 to determine appropriate cell responses. Transcription factor KAISO was previously described to repress transcription following binding to methylated DNA. In this study, we show that KAISO is induced by DNA damage in p53-expressing cells and then interacts with the p53-p300 complex to increase acetylation of p53 K320 and K382 residues, although decreasing K381 acetylation. Moreover, the p53 with this particular acetylation pattern shows increased DNA binding and potently induces cell cycle arrest and apoptosis by activating transcription of CDKN1A (cyclin-dependent kinase inhibitor 1) and various apoptotic genes. Analogously, in Kaiso KO mouse embryonic fibroblast cells, p53-to-promoter binding and up-regulation of p21 and apoptosis gene expression is significantly compromised. KAISO may therefore be a critical regulator of p53-mediated cell cycle arrest and apoptosis in response to various genotoxic stresses in mammalian cells.
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Affiliation(s)
- Dong-In Koh
- Brain Korea 21 Plus Project for Medical Sciences, Department of Biochemistry and Molecular Biology, Severance Biomedical Research Institute, Yonsei University School of Medicine, SeoDaeMoon-Ku, Seoul 120-752, Korea
| | - Dohyun Han
- Department of Biomedical Sciences and Biomedical Engineering, Seoul National University College of Medicine, Seoul 110-799, Korea
| | - Hoon Ryu
- VA Boston Healthcare System and Department of Neurology, Boston University School of Medicine, Boston, MA 02130
| | - Won-Il Choi
- Brain Korea 21 Plus Project for Medical Sciences, Department of Biochemistry and Molecular Biology, Severance Biomedical Research Institute, Yonsei University School of Medicine, SeoDaeMoon-Ku, Seoul 120-752, Korea
| | - Bu-Nam Jeon
- Brain Korea 21 Plus Project for Medical Sciences, Department of Biochemistry and Molecular Biology, Severance Biomedical Research Institute, Yonsei University School of Medicine, SeoDaeMoon-Ku, Seoul 120-752, Korea
| | - Min-Kyeong Kim
- Brain Korea 21 Plus Project for Medical Sciences, Department of Biochemistry and Molecular Biology, Severance Biomedical Research Institute, Yonsei University School of Medicine, SeoDaeMoon-Ku, Seoul 120-752, Korea
| | - Youngsoo Kim
- Department of Biomedical Sciences and Biomedical Engineering, Seoul National University College of Medicine, Seoul 110-799, Korea
| | - Jin Young Kim
- Mass Spectrometry Research Center, Korea Basic Science Institute, Ochang-eup, Cheongwon-gun, Chungbuk 363-883, Korea
| | - Lee Parry
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3XQ, United Kingdom; and
| | - Alan R Clarke
- Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3XQ, United Kingdom; and
| | - Albert B Reynolds
- Department of Cell Biology, Vanderbilt University, Nashville, TN 37232-2175
| | - Man-Wook Hur
- Brain Korea 21 Plus Project for Medical Sciences, Department of Biochemistry and Molecular Biology, Severance Biomedical Research Institute, Yonsei University School of Medicine, SeoDaeMoon-Ku, Seoul 120-752, Korea;
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Kar S, Sengupta D, Deb M, Shilpi A, Parbin S, Rath SK, Pradhan N, Rakshit M, Patra SK. Expression profiling of DNA methylation-mediated epigenetic gene-silencing factors in breast cancer. Clin Epigenetics 2014; 6:20. [PMID: 25478034 PMCID: PMC4255691 DOI: 10.1186/1868-7083-6-20] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 09/29/2014] [Indexed: 12/21/2022] Open
Abstract
Background DNA methylation mediates gene silencing primarily by inducing repressive chromatin architecture via a common theme of interaction involving methyl-CpG binding (MBD) proteins, histone modifying enzymes and chromatin remodelling complexes. Hence, targeted inhibition of MBD protein function is now considered a potential therapeutic alternative for thwarting DNA hypermethylation prompted neoplastic progress. We have analyzed the gene and protein expression level of the principal factors responsible for gene silencing, that is, DNMT and MBD proteins in MCF-7 and MDA-MB-231 breast cancer cell lines after treatment with various epigenetic drugs. Results Our study reveals that the epigenetic modulators affect the expression levels at both transcript and protein levels as well as encourage growth arrest and apoptosis in MCF-7 and MDA-MB-231 cells. AZA, TSA, SFN, and SAM inhibit cell growth in MCF-7 and MDA-MB-231 cell lines in a dose-dependent manner, that is, with increasing concentrations of drugs the cell viability gradually decreases. All the epigenetic modulators promote apoptotic cell death, as is evident form increased chromatin condensation which is a distinct characteristic of apoptotic cells. From FACS analysis, it is also clear that these drugs induce G2-M arrest and apoptosis in breast cancer cells. Further, transcript and protein level expression of MBDs and DNMTs is also affected - after treatment with epigenetic drugs; the level of transcripts/mRNA of MBDs and DNMTs has consistently increased in general. The increase in level of gene expression is substantiated at the protein level also where treated cells show higher expression of DNMT1, DNMT3A, DNMT3B, and MBD proteins in comparison to untreated cells. In case of tissue samples, the expression of different DNMTs is tissue stage-specific. DNMT1 exhibits significantly higher expression in the metastatic stage, whereas, DNMT3A and DNMT3B have higher expression in the primary stage in comparison to the metastatic samples. Conclusion The epigenetic modulators AZA, TSA, SFN, and SAM may provide opportunities for cancer prevention by regulating the components of epigenetic gene-silencing machinery especially DNMTs and MBDs.
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Affiliation(s)
- Swayamsiddha Kar
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008, India
| | - Dipta Sengupta
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008, India
| | - Moonmoon Deb
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008, India
| | - Arunima Shilpi
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008, India
| | - Sabnam Parbin
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008, India
| | - Sandip Kumar Rath
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008, India
| | - Nibedita Pradhan
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008, India
| | - Madhumita Rakshit
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008, India
| | - Samir Kumar Patra
- Epigenetics and Cancer Research Laboratory, Biochemistry and Molecular Biology Group, Department of Life Science, National Institute of Technology, Rourkela, Odisha 769008, India
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Uzdensky A, Demyanenko S, Bibov M, Sharifulina S, Kit O, Przhedetski Y, Pozdnyakova V. Expression of proteins involved in epigenetic regulation in human cutaneous melanoma and peritumoral skin. Tumour Biol 2014; 35:8225-33. [PMID: 24850177 DOI: 10.1007/s13277-014-2098-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Accepted: 05/13/2014] [Indexed: 12/21/2022] Open
Abstract
Epigenetic processes play a critical role in melanoma development. However, little is known about proteins responsible for epigenetic transformations in melanoma cells. The processes in the peritumoral skin within the excision margin are almost unstudied. We studied the changes in expression of 112 proteins involved in epigenetic regulation of gene expression in the human cutaneous melanoma and its peritumoral zone using "The Proteomic Antibody Microarrays" (GRAA2, Sigma-Aldrich). Dimethylated histone H3 at lysines 4 and 9 as well as proteins involved in the regulation of transcription (histone deacetylases HDAC-1 and HDAC-11, DNA methyl-binding protein Kaiso), cell cycle control (protein kinases Aurora-В and PKR, chromosome protein CENP-E , and phosphorylated and acetylated histone H3), DNA repair (phosphorylated histone H2AX), and nuclear protein import (importins α3 and α5/7) were over-expressed in the melanoma tissue as compared with normal skin. At the same time, HDAC-10 and proliferating cell nuclear antigen PCNA were downregulated. In the peritumoral skin, at the excision margin (1-2 cm from the melanoma edge), we observed similar changes in expression of these proteins and, additionally, over-expression of arginine methyltransferases PRMT5 and NAD-dependent histone deacetylase SIR2. Histone methyltransferase G9a and metastasis-associated protein 2 were downregulated. Therefore, epigenetic regulation that requires histone modifications and expression of some regulatory proteins is of importance for melanoma development and propagation. The observed changes in the peritumoral skin may indicate the epigenetic pre-tuning in this zone possibly involved in malignant transformation. These results can be potentially useful for melanoma diagnostics and targeted therapy.
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Affiliation(s)
- Anatoly Uzdensky
- Department of Biophysics and Biocybernetics, Southern Federal University, 194/1, Stachky ave., NII NK, Stachky prospect, Rostov-on-Don, 344090, Russia,
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Pontes TB, Chen ES, Gigek CO, Calcagno DQ, Wisnieski F, Leal MF, Demachki S, Assumpção PP, Artigiani R, Lourenço LG, Burbano RR, Arruda Cardoso Smith M. Reduced mRNA expression levels of MBD2 and MBD3 in gastric carcinogenesis. Tumour Biol 2013; 35:3447-53. [DOI: 10.1007/s13277-013-1455-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 11/19/2013] [Indexed: 12/19/2022] Open
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Wang LS, Kuo CT, Stoner K, Yearsley M, Oshima K, Yu J, Huang THM, Rosenberg D, Peiffer D, Stoner G, Huang YW. Dietary black raspberries modulate DNA methylation in dextran sodium sulfate (DSS)-induced ulcerative colitis. Carcinogenesis 2013; 34:2842-50. [PMID: 24067901 PMCID: PMC3845896 DOI: 10.1093/carcin/bgt310] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 08/26/2013] [Accepted: 09/11/2013] [Indexed: 12/14/2022] Open
Abstract
UNLABELLED Ulcerative colitis (UC) is characterized by chronic inflammation of the colon. During inflammation, NF-κB is increased in colonic epithelial cells and in immune cells, leading to increases in proinflammatory cytokines. These events then increase DNA methyltransferases (DNMTs), which silence a subset of tumor suppressor genes by promoter methylation. Negative regulators of the Wnt pathway are frequently methylated in UC, leading to dysregulation of the pathway and, potentially, to colorectal cancer. We determined if black raspberries (BRBs) influence promoter methylation of suppressors in the Wnt pathway in dextran sodium sulfate (DSS)-induced UC. C57BL/6J mice received 1% DSS and were fed either control or 5% BRB diets. Mice were euthanized on days 7, 14 and 28, and their colons, spleen and bone marrow were collected. Berries reduced ulceration at day 28. This was accompanied by decreased staining of macrophages and neutrophils and decreased NF-κB p65 nuclear localization in the colon at all time points. At day 7, BRBs demethylated the promoter of dkk3, leading to its increased messenger RNA (mRNA) expression in colon, spleen and bone marrow. β-Catenin nuclear localization, c-Myc staining as well as protein expression of DNMT3B, histone deacetylases 1 and 2 (HDAC1 and HDAC2) and methyl-binding domain 2 (MBD2) were all decreased in colon; mRNA expression of these four proteins was decreased in bone marrow cells by BRBs. These results suggest that BRBs suppress colonic ulceration by correcting promoter hypermethylation of suppressor genes in the colon, as well as in the spleen and bone marrow that systematically regulate inflammation. SUMMARY Our results suggest that dietary BRBs suppress colonic ulceration by correcting promoter hypermethylation of suppressor genes in the colon, as well as in the spleen and bone marrow that systematically regulate inflammation in DSS-induced UC.
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Affiliation(s)
- Li-Shu Wang
- *To whom correspondence should be addressed. Department of Medicine, Division of Hematology and Oncology, Medical College of Wisconsin, Room C4930, 8701 Watertown Plank Road, TBRC, Milwaukee, WI 53226, USA. Tel: +1 414 955 2827; Fax: +1 414 955 2821;
| | - Chieh-Ti Kuo
- Department of Medicine, Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Comprehensive Cancer Center and
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Molecular Medicine, Cancer Therapy & Research Center, University of Texas Health Science Center, San Antonio, TX 78229-39000, USA
- HealthNet, Inc., Colon Cancer Prevention Program, University of Connecticut Health Center Farmington, CT 06030-3101, USA and
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | | | - Martha Yearsley
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
| | - Kiyoko Oshima
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | | | - Tim H.-M. Huang
- Department of Molecular Medicine, Cancer Therapy & Research Center, University of Texas Health Science Center, San Antonio, TX 78229-39000, USA
| | - Daniel Rosenberg
- HealthNet, Inc., Colon Cancer Prevention Program, University of Connecticut Health Center Farmington, CT 06030-3101, USA and
| | - Dan Peiffer
- Department of Medicine, Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Comprehensive Cancer Center and
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Molecular Medicine, Cancer Therapy & Research Center, University of Texas Health Science Center, San Antonio, TX 78229-39000, USA
- HealthNet, Inc., Colon Cancer Prevention Program, University of Connecticut Health Center Farmington, CT 06030-3101, USA and
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Gary Stoner
- Department of Medicine, Division of Hematology and Oncology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Comprehensive Cancer Center and
- Department of Pathology, The Ohio State University, Columbus, OH 43210, USA
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
- Department of Molecular Medicine, Cancer Therapy & Research Center, University of Texas Health Science Center, San Antonio, TX 78229-39000, USA
- HealthNet, Inc., Colon Cancer Prevention Program, University of Connecticut Health Center Farmington, CT 06030-3101, USA and
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
| | - Yi-Wen Huang
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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Li L, Lorzadeh A, Hirst M. Regulatory variation: an emerging vantage point for cancer biology. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2013; 6:37-59. [DOI: 10.1002/wsbm.1250] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Luolan Li
- Centre for High-Throughput Biology, Department of Microbiology & Immunology; University of British Columbia; Vancouver, British Columbia Canada
| | - Alireza Lorzadeh
- Centre for High-Throughput Biology, Department of Microbiology & Immunology; University of British Columbia; Vancouver, British Columbia Canada
| | - Martin Hirst
- Centre for High-Throughput Biology, Department of Microbiology & Immunology; University of British Columbia; Vancouver, British Columbia Canada
- Canada's Michael Smith Genome Sciences Centre; BC Cancer Agency; Vancouver, British Columbia Canada
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Santini V, Melnick A, Maciejewski JP, Duprez E, Nervi C, Cocco L, Ford KG, Mufti G. Epigenetics in focus: Pathogenesis of myelodysplastic syndromes and the role of hypomethylating agents. Crit Rev Oncol Hematol 2013; 88:231-45. [DOI: 10.1016/j.critrevonc.2013.06.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 05/14/2013] [Accepted: 06/12/2013] [Indexed: 12/22/2022] Open
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Lee MR, Prasain N, Chae HD, Kim YJ, Mantel C, Yoder MC, Broxmeyer HE. Epigenetic regulation of NANOG by miR-302 cluster-MBD2 completes induced pluripotent stem cell reprogramming. Stem Cells 2013; 31:666-81. [PMID: 23255147 DOI: 10.1002/stem.1302] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 11/14/2012] [Accepted: 11/21/2012] [Indexed: 01/10/2023]
Abstract
While most somatic cells undergoing induced pluripotent stem (iPS) cell reprogramming with Yamanaka factors accumulate at stable partially reprogrammed stages, the molecular mechanisms required to achieve full reprogramming are unknown. MicroRNAs (miRNAs) fine-tune mRNA translation and are implicated in reprogramming, but miRNA functional targets critical for complete iPS cell reprogramming remain elusive. We identified methyl-DNA binding domain protein 2 (MBD2) as an epigenetic suppressor, blocking full reprogramming of somatic to iPS cells through direct binding to NANOG promoter elements preventing transcriptional activation. When we overexpressed miR-302 cluster we observed a significant increase in conversion of partial to fully reprogrammed iPS cells by suppressing MBD2 expression, thereby increasing NANOG expression. Thus, expression of exogenous miR-302 cluster (without miR-367) is efficient in attaining a fully reprogrammed iPS state in partially reprogrammed cells by relieving MBD2-mediated inhibition of NANOG expression. Our studies provide a direct molecular mechanism involved in generating complete human iPS cell reprogramming to study disease pathogenesis, drug screening, and for potential cell-based therapies.
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Affiliation(s)
- Man Ryul Lee
- Department of Microbiology and Immunology and Indiana University School of Medicine, Indianapolis, Indiana 46202-5181, USA
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Choi WI, Jeon BN, Yoon JH, Koh DI, Kim MH, Yu MY, Lee KM, Kim Y, Kim K, Hur SS, Lee CE, Kim KS, Hur MW. The proto-oncoprotein FBI-1 interacts with MBD3 to recruit the Mi-2/NuRD-HDAC complex and BCoR and to silence p21WAF/CDKN1A by DNA methylation. Nucleic Acids Res 2013; 41:6403-20. [PMID: 23658227 PMCID: PMC3711425 DOI: 10.1093/nar/gkt359] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The tumour-suppressor gene CDKN1A (encoding p21Waf/Cip1) is thought to be epigenetically repressed in cancer cells. FBI-1 (ZBTB7A) is a proto-oncogenic transcription factor repressing the alternative reading frame and p21WAF/CDKN1A genes of the p53 pathway. FBI-1 interacts directly with MBD3 (methyl-CpG–binding domain protein 3) in the nucleus. We demonstrated that FBI-1 binds both non-methylated and methylated DNA and that MBD3 is recruited to the CDKN1A promoter through its interaction with FBI-1, where it enhances transcriptional repression by FBI-1. FBI-1 also interacts with the co-repressors nuclear receptor corepressor (NCoR), silencing mediator for retinoid and thyroid receptors (SMRT) and BCL-6 corepressor (BCoR) to repress transcription. MBD3 regulates a molecular interaction between the co-repressor and FBI-1. MBD3 decreases the interaction between FBI-1 and NCoR/SMRT but increases the interaction between FBI-1 and BCoR. Because MBD3 is a subunit of the Mi-2 autoantigen (Mi-2)/nucleosome remodelling and histone deacetylase (NuRD)-HDAC complex, FBI-1 recruits the Mi-2/NuRD-HDAC complex via MBD3. BCoR interacts with the Mi-2/NuRD-HDAC complex, DNMTs and HP1. MBD3 and BCoR play a significant role in the recruitment of the Mi-2/NuRD-HDAC complex– and the NuRD complex–associated proteins, DNMTs and HP. By recruiting DNMTs and HP1, Mi-2/NuRD-HDAC complex appears to play key roles in epigenetic repression of CDKN1A by DNA methylation.
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Affiliation(s)
- Won-Il Choi
- Department of Biochemistry and Molecular Biology, BK21 Project for Medical Science, Severance Biomedical Research Institute, Yonsei University School of Medicine, 50 Yonsei-Ro, SeoDaeMoon-Gu, Seoul, 120-752, Korea
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Shankar S, Kumar D, Srivastava RK. Epigenetic modifications by dietary phytochemicals: implications for personalized nutrition. Pharmacol Ther 2013; 138:1-17. [PMID: 23159372 PMCID: PMC4153856 DOI: 10.1016/j.pharmthera.2012.11.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 11/01/2012] [Indexed: 12/20/2022]
Abstract
In the last two decades, the study of epigenetic modification emerged as one of the major areas of cancer treatment targeted by dietary phytochemicals. Recent studies with various types of cancers revealed that the epigenetic modifications are associated with the food source corresponds to dietary phytochemicals. The dietary phytochemicals have been used in Asian countries for thousands of years to cure several diseases including cancer. They have been reported to modulate the several biological processes including histone modification, DNA methylation and non-coding microRNA expression. These events play a vital role in carcinogenesis. Various studies suggest that a number of dietary compounds present in vegetables, spices and other herbal products have epigenetic targets in cancer cells. Dietary phytochemicals have been reported to repair DNA damage by enhancing histone acetylation that helps to restrain cell death, and also alter DNA methylation. These phytochemicals are able to modulate epigenetic modifications and their targets to cure several cancers. Epigenetic aberrations dynamically contribute to cancer pathogenesis. Given the individualized traits of epigenetic biomarkers, the personalized nutrition will help us to prevent various types of cancer. In this review, we will discuss the effect of dietary phytochemicals on genetic and epigenetic modifications and how these modifications help to prevent various types of cancers and improve health outcomes.
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Affiliation(s)
- Sharmila Shankar
- Department of Pathology and Laboratory Medicine, The University of Kansas Medical Center, The University of Kansas Cancer Center, 3901 Rainbow Boulevard, Kansas City, KS, 66160, USA
| | - Dhruv Kumar
- Department of Pharmacology, Toxicology and Therapeutics, and Medicine, The University of Kansas Medical Center, The University of Kansas Cancer Center, 3901 Rainbow Boulevard, Kansas City, KS, 66160, USA
| | - Rakesh K. Srivastava
- Department of Pharmacology, Toxicology and Therapeutics, and Medicine, The University of Kansas Medical Center, The University of Kansas Cancer Center, 3901 Rainbow Boulevard, Kansas City, KS, 66160, USA
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Calcagno DQ, Gigek CO, Chen ES, Burbano RR, Smith MDAC. DNA and histone methylation in gastric carcinogenesis. World J Gastroenterol 2013; 19:1182-92. [PMID: 23482412 PMCID: PMC3587474 DOI: 10.3748/wjg.v19.i8.1182] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 06/13/2012] [Accepted: 06/28/2012] [Indexed: 02/06/2023] Open
Abstract
Epigenetic alterations contribute significantly to the development and progression of gastric cancer, one of the leading causes of cancer death worldwide. Epigenetics refers to the number of modifications of the chromatin structure that affect gene expression without altering the primary sequence of DNA, and these changes lead to transcriptional activation or silencing of the gene. Over the years, the study of epigenetic processes has increased, and novel therapeutic approaches that target DNA methylation and histone modifications have emerged. A greater understanding of epigenetics and the therapeutic potential of manipulating these processes is necessary for gastric cancer treatment. Here, we review recent research on the effects of aberrant DNA and histone methylation on the onset and progression of gastric tumors and the development of compounds that target enzymes that regulate the epigenome.
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Zeisberg EM, Zeisberg M. The role of promoter hypermethylation in fibroblast activation and fibrogenesis. J Pathol 2012; 229:264-73. [DOI: 10.1002/path.4120] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 09/25/2012] [Accepted: 09/27/2012] [Indexed: 01/26/2023]
Affiliation(s)
- Elisabeth M Zeisberg
- Department of Cardiology and Pneumology; Göttingen University Medical Centre, Georg August University; Göttingen Germany
- German Centre for Cardiovascular Research (DZHK); Göttingen Germany
| | - Michael Zeisberg
- Department of Nephrology and Rheumatology; Göttingen University Medical Centre, Georg August University; Göttingen Germany
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Hoshino I, Matsubara H. MicroRNAs in cancer diagnosis and therapy: from bench to bedside. Surg Today 2012; 43:467-78. [PMID: 23129027 DOI: 10.1007/s00595-012-0392-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Accepted: 05/17/2012] [Indexed: 12/12/2022]
Abstract
Epigenetic changes, such as DNA methylation and histone modifications, regulate gene expression. It is speculated that investigating the fundamental epigenetic mechanisms and their gene regulation will promote a better understanding of cancer development. The idea of epigenetic modification has been extended to microRNAs (miRs). MiRs are single-stranded RNA molecules, about 19-25 ribonucleotides in length, which regulate gene expression post-transcriptionally and can act as tumor suppressors or oncogenes. We review the most recent findings related to their mechanisms of action, the modification of miR expression, and their relationship to cancer. We also discuss the potential application of miRs in the clinical setting, such as for biomarkers and therapy.
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Affiliation(s)
- Isamu Hoshino
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Inohana 1-8-1, Chuo-ku, Chiba 260-8670, Japan
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Reddy MA, Park JT, Natarajan R. Epigenetic modifications and diabetic nephropathy. Kidney Res Clin Pract 2012; 31:139-50. [PMID: 26894019 PMCID: PMC4716094 DOI: 10.1016/j.krcp.2012.07.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 06/30/2012] [Accepted: 07/09/2012] [Indexed: 01/15/2023] Open
Abstract
Diabetic nephropathy (DN) is a major complication associated with both type 1 and type 2 diabetes, and a leading cause of end-stage renal disease. Conventional therapeutic strategies are not fully efficacious in the treatment of DN, suggesting an incomplete understanding of the gene regulation mechanisms involved in its pathogenesis. Furthermore, evidence from clinical trials has demonstrated a "metabolic memory" of prior exposure to hyperglycemia that continues to persist despite subsequent glycemic control. This remains a major challenge in the treatment of DN and other vascular complications. Epigenetic mechanisms such as DNA methylation, nucleosomal histone modifications, and noncoding RNAs control gene expression through regulation of chromatin structure and function and post-transcriptional mechanisms without altering the underlying DNA sequence. Emerging evidence indicates that multiple factors involved in the etiology of diabetes can alter epigenetic mechanisms and regulate the susceptibility to diabetes complications. Recent studies have demonstrated the involvement of histone lysine methylation in the regulation of key fibrotic and inflammatory genes related to diabetes complications including DN. Interestingly, histone lysine methylation persisted in vascular cells even after withdrawal from the diabetic milieu, demonstrating a potential role of epigenetic modifications in metabolic memory. Rapid advances in high-throughput technologies in the fields of genomics and epigenomics can lead to the identification of genome-wide alterations in key epigenetic modifications in vascular and renal cells in diabetes. Altogether, these findings can lead to the identification of potential predictive biomarkers and development of novel epigenetic therapies for diabetes and its associated complications.
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Affiliation(s)
| | | | - Rama Natarajan
- Department of Diabetes, Beckman Research Institute of City of Hope, Duarte, California, USA
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Abstract
Chemoresistance of tumors is often reported to be due to overexpression of efflux transporters or genetic alterations of signaling pathways. More recently, there is increasing evidence that epigenetic modification contributes to the phenomenon of drug resistance. Despite alteration of DNA methylation or histone modifications, deregulated miRNA expression patterns of tumor cells have been identified as interfering with drug response. Attempts to modify the expression of selected miRNAs have partly led to intriguing improvements of chemotherapy response. This review focuses on the major epigenetic mechanisms, including the role of miRNA expression contributing to drug resistance and the role of epigenetic drugs to overcome nonresponse arising under conventional chemotherapy.
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Affiliation(s)
- Sierk Haenisch
- Institute of Experimental & Clinical Pharmacology, University Hospital Schleswig-Holstein, Campus Kiel, Arnold-Heller-Street 3, Building 30, D-24105 Kiel, Germany
| | - Ingolf Cascorbi
- Institute of Experimental & Clinical Pharmacology, University Hospital Schleswig-Holstein, Campus Kiel, Arnold-Heller-Street 3, Building 30, D-24105 Kiel, Germany
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