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Lax E, Do Carmo S, Enuka Y, Sapozhnikov DM, Welikovitch LA, Mahmood N, Rabbani SA, Wang L, Britt JP, Hancock WW, Yarden Y, Szyf M. Methyl-CpG binding domain 2 (Mbd2) is an epigenetic regulator of autism-risk genes and cognition. Transl Psychiatry 2023; 13:259. [PMID: 37443311 PMCID: PMC10344909 DOI: 10.1038/s41398-023-02561-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 06/29/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
The Methyl-CpG-Binding Domain Protein family has been implicated in neurodevelopmental disorders. The Methyl-CpG-binding domain 2 (Mbd2) binds methylated DNA and was shown to play an important role in cancer and immunity. Some evidence linked this protein to neurodevelopment. However, its exact role in neurodevelopment and brain function is mostly unknown. Here we show that Mbd2-deficiency in mice (Mbd2-/-) results in deficits in cognitive, social and emotional functions. Mbd2 binds regulatory DNA regions of neuronal genes in the hippocampus and loss of Mbd2 alters the expression of hundreds of genes with a robust down-regulation of neuronal gene pathways. Further, a genome-wide DNA methylation analysis found an altered DNA methylation pattern in regulatory DNA regions of neuronal genes in Mbd2-/- mice. Differentially expressed genes significantly overlap with gene-expression changes observed in brains of Autism Spectrum Disorder (ASD) individuals. Notably, downregulated genes are significantly enriched for human ortholog ASD risk genes. Observed hippocampal morphological abnormalities were similar to those found in individuals with ASD and ASD rodent models. Hippocampal Mbd2 knockdown partially recapitulates the behavioral phenotypes observed in Mbd2-/- mice. These findings suggest that Mbd2 is a novel epigenetic regulator of genes that are associated with ASD in humans. Mbd2 loss causes behavioral alterations that resemble those found in ASD individuals.
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Affiliation(s)
- Elad Lax
- Department of Molecular Biology, Ariel University, Ariel, Israel.
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada.
| | - Sonia Do Carmo
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Yehoshua Enuka
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Daniel M Sapozhnikov
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Lindsay A Welikovitch
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA, 02129, USA
- Harvard Medical School, Boston, MA, 02115, USA
| | - Niaz Mahmood
- Department of Medicine, McGill University Health Center, Montreal, QC, Canada
- Department of Biochemistry, McGill University, Montreal, QC, Canada
| | - Shafaat A Rabbani
- Department of Medicine, McGill University Health Center, Montreal, QC, Canada
| | - Liqing Wang
- Division of Transplant Immunology, Department of Pathology and Laboratory Medicine, and Biesecker Center for Pediatric Liver Diseases, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jonathan P Britt
- Department of Psychology, McGill University, Montreal, QC, Canada
| | - Wayne W Hancock
- Division of Transplant Immunology, Department of Pathology and Laboratory Medicine, and Biesecker Center for Pediatric Liver Diseases, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yosef Yarden
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Moshe Szyf
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
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2
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Sahu RK, Verma VV, Kumar A, Tandon S, Chandra Das B, Hedau ST. In silico prediction and interaction of resveratrol on methyl-CpG binding proteins by molecular docking and MD simulations study. RSC Adv 2022; 12:11493-11504. [PMID: 35425086 PMCID: PMC9006347 DOI: 10.1039/d2ra00432a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 03/31/2022] [Indexed: 11/26/2022] Open
Abstract
Resveratrol enhances the BRCA1 gene expression and the MBD family of proteins bind to the promoter region of the BRCA1 gene. However, the molecular interaction is not yet reported. Here we have analyzed the binding affinity of resveratrol with MBD proteins. Our results suggest that resveratrol binds to the MBD proteins with higher binding affinity toward MeCP2 protein (ΔG = −6.5) by sharing four hydrogen bonds as predicted by molecular docking studies. Further, the molecular dynamics simulations outcomes showed that the backbones of all three protein–ligand complexes are stabilized after the period of 75 ns, constantly fluctuating around the deviations of 0.4 Å, 0.5 Å and 0.7 Å for MBD1, MBD2 and MeCP2, respectively. The inter-molecular hydrogen bonding trajectory analysis for protein–ligand complexes also support the strong binding between MeCP2–resveratrol complex. Further, binding free energy calculations showed binding energy of −94.764 kJ mol−1, −53.826 kJ mol−1 and −36.735 kJ mol−1 for MeCP2–resveratrol, MBD2–resveratrol and MBD1–resveratrol complexes, respectively, which also supported our docking results. Our study also highlighted that the MBD family of proteins forms a binding interaction with other signaling proteins that are involved in various cancer initiation pathways. Resveratrol enhances the BRCA1 gene expression and the MBD family of proteins bind to the promoter region of the BRCA1 gene.![]()
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Affiliation(s)
- Ram Krishna Sahu
- Division of Molecular Oncology, National Institute of Cancer Prevention and Research, ICMR, I – 7, Sector – 39, Noida – 201 301, Utter Pradesh, India
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Noida – 201301, Utter Pradesh, India
| | - Ved Vrat Verma
- Information System for Research Management Division, ICMR, Aruna Asif Ali Marg, New Delhi – 110029, India
| | - Amit Kumar
- Information System for Research Management Division, ICMR, Aruna Asif Ali Marg, New Delhi – 110029, India
| | - Simran Tandon
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Noida – 201301, Utter Pradesh, India
| | - Bhudev Chandra Das
- Amity Institute of Molecular Medicine & Stem Cell Research, Amity University, Noida – 201301, Utter Pradesh, India
| | - Suresh T. Hedau
- Division of Molecular Oncology, National Institute of Cancer Prevention and Research, ICMR, I – 7, Sector – 39, Noida – 201 301, Utter Pradesh, India
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3
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Abumustafa W, Zamer BA, Khalil BA, Hamad M, Maghazachi AA, Muhammad JS. Protein arginine N-methyltransferase 5 in colorectal carcinoma: Insights into mechanisms of pathogenesis and therapeutic strategies. Biomed Pharmacother 2021; 145:112368. [PMID: 34794114 DOI: 10.1016/j.biopha.2021.112368] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 10/20/2021] [Accepted: 10/20/2021] [Indexed: 12/14/2022] Open
Abstract
Protein arginine N-methyltransferase 5 (PRMT5) enzyme is one of the eight canonical PRMTs, classified as a type II PRMT, induces arginine monomethylation and symmetric dimethylation. PRMT5 is known to be overexpressed in multiple cancer types, including colorectal cancer (CRC), where its overexpression is associated with poor survival. Recent studies have shown that upregulation of PRMT5 induces tumor growth and metastasis in CRC. Moreover, various novel PRMT5 inhibitors tested on CRC cell lines showed promising anticancer effects. Also, it was suggested that PRMT5 could be a valid biomarker for CRC diagnosis and prognosis. Hence, a deeper understanding of PRMT5-mediated CRC carcinogenesis could provide new avenues towards developing a targeted therapy. In this study, we started with in silico analysis correlating PRMT5 expression in CRC patients as a prelude to further our investigation of its role in CRC. We then carried out a comprehensive review of the scientific literature that dealt with the role(s) of PRMT5 in CRC pathogenesis, diagnosis, and prognosis. Also, we have summarized key findings from in vitro research using various therapeutic agents and strategies directly targeting PRMT5 or disrupting its function. In conclusion, PRMT5 seems to play a significant role in the pathogenesis of CRC; therefore, its prognostic and therapeutic potential merits further investigation.
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Affiliation(s)
- Wafaa Abumustafa
- Department of Basic Medical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates; Research Institute of Medical & Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Batoul Abi Zamer
- Department of Basic Medical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates; Research Institute of Medical & Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Bariaa A Khalil
- Research Institute of Medical & Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Mawieh Hamad
- Research Institute of Medical & Health Sciences, University of Sharjah, Sharjah, United Arab Emirates; Department of Medical Laboratory Sciences, College of Health Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Azzam A Maghazachi
- Research Institute of Medical & Health Sciences, University of Sharjah, Sharjah, United Arab Emirates; Department of Clinical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Jibran Sualeh Muhammad
- Department of Basic Medical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates; Research Institute of Medical & Health Sciences, University of Sharjah, Sharjah, United Arab Emirates.
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4
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Su X, Wang S, Zhang H, Yang G, Bai Y, Liu P, Meng L, Jiang X, Xin Y. Sulforaphane prevents angiotensin II-induced cardiomyopathy by activation of Nrf2 through epigenetic modification. J Cell Mol Med 2021; 25:4408-4419. [PMID: 33793066 PMCID: PMC8093985 DOI: 10.1111/jcmm.16504] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 03/03/2021] [Accepted: 03/12/2021] [Indexed: 02/06/2023] Open
Abstract
Nuclear factor erythroid 2-related factor (Nrf2) is an important regulator of cellular antioxidant defence. We previously showed that SFN prevented Ang II-induced cardiac damage via activation of Nrf2. However, the underlying mechanism of SFN's persistent cardiac protection remains unclear. This study aimed to explore the potential of SFN in activating cardiac Nrf2 through epigenetic mechanisms. Wild-type mice were injected subcutaneously with Ang II, with or without SFN. Administration of chronic Ang II-induced cardiac inflammatory factor expression, oxidative damage, fibrosis and cardiac remodelling and dysfunction, all of which were effectively improved by SFN treatment, coupled with an up-regulation of Nrf2 and downstream genes. Bisulfite genome sequencing and chromatin immunoprecipitation (ChIP) were performed to detect the methylation level of the first 15 CpGs and histone H3 acetylation (Ac-H3) status in the Nrf2 promoter region, respectively. The results showed that SFN reduced Ang II-induced CpG hypermethylation and promoted Ac-H3 accumulation in the Nrf2 promoter region, accompanied by the inhibition of global DNMT and HDAC activity, and a decreased protein expression of key DNMT and HDAC enzymes. Taken together, SFN exerts its cardioprotective effect through epigenetic modification of Nrf2, which may partially contribute to long-term activation of cardiac Nrf2.
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Affiliation(s)
- Xuling Su
- Department of Radiation Oncology, The First Hospital of Jilin University, Changchun, China.,Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun, China
| | - Shudong Wang
- The Center of Cardiovascular Diseases, The First Hospital of Jilin University, Changchun, China
| | - Haiying Zhang
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun, China
| | - Ge Yang
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun, China
| | - Yang Bai
- The Center of Cardiac Surgery, The First Hospital of Jilin University, Changchun, China
| | - Pinyi Liu
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun, China
| | - Lingbin Meng
- Department of Hematology and Medical Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | - Xin Jiang
- Department of Radiation Oncology, The First Hospital of Jilin University, Changchun, China
| | - Ying Xin
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun, China
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5
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Loss of MBD2 affects early T cell development by inhibiting the WNT signaling pathway. Exp Cell Res 2020; 398:112400. [PMID: 33271126 DOI: 10.1016/j.yexcr.2020.112400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 11/21/2020] [Accepted: 11/22/2020] [Indexed: 12/30/2022]
Abstract
DNA methylation alters the expression of certain genes without any alteration to the DNA sequence and is a dynamic process during normal hematopoietic differentiation. As an epigenetic regulator, methyl-CpG-binding domain protein 2 (MBD2) is an important member of the MBD protein family and is acknowledged as a "reader" of DNA methylation. We used a mouse model to study the effects of MBD2 on the early development of T cells. Here, we found that MBD2 deficiency led to retardation of T cell differentiation at the DN3 stage. Meanwhile, decreased proliferative capacity and increased apoptosis were detected in Mbd2-/- DN thymocytes. Furthermore, we found the WNT pathway was significantly down-regulated in Mbd2-/- DN thymocytes: DKK1 (Dickkopf-1) expression was significantly increased, while TCF7 (transcription factor 7) and c-MYC were down-regulated. Thus, these findings established that MBD2 acted as a dominant regulator to imprint DN T cell development via the WNT pathway.
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6
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Li L, Li N, Liu N, Huo F, Zheng J. MBD2 Correlates with a Poor Prognosis and Tumor Progression in Renal Cell Carcinoma. Onco Targets Ther 2020; 13:10001-10012. [PMID: 33116585 PMCID: PMC7548338 DOI: 10.2147/ott.s256226] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 08/27/2020] [Indexed: 01/21/2023] Open
Abstract
Purpose DNA methylation plays an important role in regulating gene expression. Methyl-CpG-binding domain (MBD) proteins recognize and bind to methylated DNA, which mediate gene silencing by the interaction with deacetylases and histone methyltransferases. MBD2 has been reported in various human cancers; however, its clinical implication and potential regulatory role in renal cell carcinoma (RCC) have not been elaborated. Materials and Methods In the study, we estimated the expression and prognostic value of MBD2 in RCC cell lines and tissues by Western blotting and immunohistochemistry. The associations of MBD2 expression and pathological characters and survival in RCC patients were performed using χ2 and Kaplan-Meier survival analysis, respectively. Univariate and multivariable Cox regression analyses suggested the independent predictors in RCC prognosis. The functional role of MBD2 in RCC progression was assessed by in vitro cell experiments. In addition, we identified the MBD2-mediated alterations of protein-related proliferation and EMT markers in RCC cells after MBD2 overexpression and knockdown. Results We found that the protein levels of MBD2 were upregulated in RCC cells and tissues. High MBD2 expression was related to TNM stage and predicted poorer survival in RCC. Enforced expression of MBD2 significantly promoted the proliferation, cycle progress, invasion and migration of RCC cells in vitro. However, downregulating MBD2 remarkably weakened the above cell functions. Mechanistically, the promotive effect of MBD2 overexpression may be regulated by its effects onp21, p53 and Cyclin D1 expression and EMT process. Conclusion These results indicated that MBD2confers an oncogenic function in the malignant progression of RCC. MBD2 could be served as a meaningful prognostic biomarker and a latent therapeutic target in RCC patients.
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Affiliation(s)
- Liantao Li
- Cancer Institute, Xuzhou Medical University, Xuzhou 221000, People's Republic of China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221000, People's Republic of China.,Department of Radiation Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221000, People's Republic of China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou 221000, People's Republic of China
| | - Na Li
- Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221000, People's Republic of China.,Department of Radiation Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221000, People's Republic of China
| | - Nianli Liu
- Cancer Institute, Xuzhou Medical University, Xuzhou 221000, People's Republic of China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou 221000, People's Republic of China
| | - Fuchun Huo
- Department of Pathology, Xuzhou Medical University, Xuzhou 221000, People's Republic of China
| | - Junnian Zheng
- Cancer Institute, Xuzhou Medical University, Xuzhou 221000, People's Republic of China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou 221000, People's Republic of China
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7
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Xu L, Sun WJ, Jia AJ, Qiu LL, Xiao B, Mu L, Li JM, Zhang XF, Wei Y, Peng C, Zhang DS, Xiang XD. MBD2 regulates differentiation and function of Th17 cells in neutrophils- dominant asthma via HIF-1α. JOURNAL OF INFLAMMATION-LONDON 2018; 15:15. [PMID: 30150897 PMCID: PMC6102869 DOI: 10.1186/s12950-018-0191-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 08/07/2018] [Indexed: 01/18/2023]
Abstract
Background T helper 17 (Th17) cells have proven to be crucial in the pathogenesis of neutrophils-dominant asthma. Hypoxia inducible factor-1α (HIF-1α) is involved in allergic responses in asthma. Our previous studies indicated that Methtyl-CpG binding domain protein 2 (MBD2) expression was increased in asthma patients. The aim of the present study is to understand how MBD2 interacts with HIF-1α to regulate Th17 cell differentiation and IL-17 expression in neutrophils-dominant asthma. Methods A neutrophils-dominant asthma mouse model was established using female C57BL/6 mice to investigate Th17 cell differentiation and MBD2 and HIF-1α expression regulation using flow cytometry, western blot or qRT-PCR. MBD2 and HIF-1α genes were silenced or overexpressed through lentiviral transduction to explore the roles of MBD2 in Th17 cell differentiation and IL-17 release in neutrophils-dominant asthma. Results A neutrophilic inflammatory asthma phenotype model was established successfully. This was characterized by airway hyperresponsiveness (AHR), increased BALF neutrophil granulocytes, activated Th17 cell differentiation, and high IL-17 levels. MBD2 and HIF-1α expression were significantly increased in the lung and spleen cells of mice with neutrophils-dominant asthma. Through overexpression or silencing of MBD2 and HIF-1α genes, we have concluded that MBD2 and HIF-1α regulate Th17 cell differentiation and IL-17 secretion. Moreover, MBD2 was also found to regulate HIF-1α expression. Conclusions Our findings have uncovered new roles for MBD2 and HIF-1α, and provide novel insights into the epigenetic regulation of neutrophils-dominant asthma. Electronic supplementary material The online version of this article (10.1186/s12950-018-0191-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Li Xu
- 1Department of the Second Thoracic Medicine, The Affiliated Cancer Hospital of Xiangya School of Medicine and Hunan Cancer Hospital, Central South University, 283 Tongzipo Road, Changsha, 410006 Hunan China
| | - Wen J Sun
- 2Department of Respiratory Medicine, Hunan Centre for Evidence-based Medicine, Research Unit of Respiratory Diseases, The Second Xiangya Hospital, Central South University, 139 Middle Renmin Road, Changsha, 410011 Hunan China
| | - Ai J Jia
- 2Department of Respiratory Medicine, Hunan Centre for Evidence-based Medicine, Research Unit of Respiratory Diseases, The Second Xiangya Hospital, Central South University, 139 Middle Renmin Road, Changsha, 410011 Hunan China
| | - Lu L Qiu
- 2Department of Respiratory Medicine, Hunan Centre for Evidence-based Medicine, Research Unit of Respiratory Diseases, The Second Xiangya Hospital, Central South University, 139 Middle Renmin Road, Changsha, 410011 Hunan China
| | - Bing Xiao
- 3Department of Emergency, The Second Xiangya Hospital, Central South University, 139 Middle Renmin Road, Changsha, Hunan 410011 People's Republic of China
| | - Lin Mu
- 2Department of Respiratory Medicine, Hunan Centre for Evidence-based Medicine, Research Unit of Respiratory Diseases, The Second Xiangya Hospital, Central South University, 139 Middle Renmin Road, Changsha, 410011 Hunan China.,4Department of Respiratory Medicine, Peace Hospital, Changzhi Medical College, Changzhi, 046000 Shanxi China
| | - Jian M Li
- 2Department of Respiratory Medicine, Hunan Centre for Evidence-based Medicine, Research Unit of Respiratory Diseases, The Second Xiangya Hospital, Central South University, 139 Middle Renmin Road, Changsha, 410011 Hunan China.,5Department of Respiratory Medicine, Hunan Provincial People's Hospital, 61 West Jiefang Road, Changsha, 410005 Hunan China
| | - Xiu F Zhang
- 2Department of Respiratory Medicine, Hunan Centre for Evidence-based Medicine, Research Unit of Respiratory Diseases, The Second Xiangya Hospital, Central South University, 139 Middle Renmin Road, Changsha, 410011 Hunan China.,6Department of Respiratory Medicine, The Second Hospital, University of South China, 30 Jiefang Road, Hengyang, 421001 Hunan China
| | - Yan Wei
- Department of Respiratory, The First Hospital of Guangyuan City, 490 Juguo Road, Guangyuan, 628000 Sichuan China
| | - Cong Peng
- 8Dermatology and Venereology Department, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008 Hunan China
| | - Dong S Zhang
- 3Department of Emergency, The Second Xiangya Hospital, Central South University, 139 Middle Renmin Road, Changsha, Hunan 410011 People's Republic of China
| | - Xu D Xiang
- 3Department of Emergency, The Second Xiangya Hospital, Central South University, 139 Middle Renmin Road, Changsha, Hunan 410011 People's Republic of China
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8
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Chromatin dynamics at the core of kidney fibrosis. Matrix Biol 2018; 68-69:194-229. [DOI: 10.1016/j.matbio.2018.02.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 02/16/2018] [Accepted: 02/17/2018] [Indexed: 02/06/2023]
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9
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Cheng L, Tang Y, Chen X, Zhao L, Liu S, Ma Y, Wang N, Zhou K, Zhou J, Zhou M. Deletion of MBD2 inhibits proliferation of chronic myeloid leukaemia blast phase cells. Cancer Biol Ther 2018; 19:676-686. [PMID: 29565710 DOI: 10.1080/15384047.2018.1450113] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Aberrant methylation of tumour suppressor genes is associated with the progression to a blast crisis in chronic myeloid leukaemia (CML). Methyl-CpG-binding domain protein 2 (MBD2) has been studied as a "reader" of DNA methylation in many cancers, but its role in CML is unclear. We constructed cell models of a homozygous deletion mutation of MBD2 using gene-editing technology in K562 cells and BV173 cells. Here, we demonstrated that the deletion of MBD2 inhibited cell proliferation capacity in vitro. MBD2 deletion also significantly inhibited K562 cell proliferation in a xenograft tumour model in vivo. Additionally, the JAK2/STAT3 signalling pathway, which is abnormally active in CML, was inhibited by MBD2 deletion, and MBD2 deletion could up-regulate the expression of SHP1. In conclusion, our findings suggest that MBD2 is a candidate therapeutic strategy for the CML blast phase.
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Affiliation(s)
- Ling Cheng
- a Department of Hematology , Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Ying Tang
- a Department of Hematology , Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Xing Chen
- a Department of Hematology , Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Lei Zhao
- a Department of Hematology , Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Songya Liu
- a Department of Hematology , Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Yanna Ma
- a Department of Hematology , Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Na Wang
- a Department of Hematology , Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Kuangguo Zhou
- a Department of Hematology , Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Jianfeng Zhou
- a Department of Hematology , Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Mi Zhou
- a Department of Hematology , Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
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10
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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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11
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Klungland A, Robertson AB. Oxidized C5-methyl cytosine bases in DNA: 5-Hydroxymethylcytosine; 5-formylcytosine; and 5-carboxycytosine. Free Radic Biol Med 2017; 107:62-68. [PMID: 27890639 DOI: 10.1016/j.freeradbiomed.2016.11.038] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 11/17/2016] [Accepted: 11/23/2016] [Indexed: 01/31/2023]
Abstract
Recent reports suggest that the Tet enzyme family catalytically oxidize 5-methylcytosine in mammalian cells. The oxidation of 5-methylcytosine can result in three chemically distinct species - 5-hydroxymethylcytsine, 5-formylcytosine, and 5-carboxycytosine. While the base excision repair machinery processes 5-formylcytosine and 5-carboxycytosine rapidly, 5-hydroxymethylcytosine is stable under physiological conditions. As a stable modification 5-hydroxymethylcytosine has a broad range of functions, from stem cell pluriopotency to tumorigenesis. The subsequent oxidation products, 5-formylcytosine and 5-carboxycytosine, are suggested to be involved in an active DNA demethylation pathway. This review provides an overview of the biochemistry and biology of 5-methylcytosine oxidation products.
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Affiliation(s)
- Arne Klungland
- Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, Norway; Institute of Basic Medical Sciences, University of Oslo, PO Box 1018 Blindern, N-0315 Oslo, Norway
| | - Adam B Robertson
- Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, Norway.
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12
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Zhang L, Zhu H, Li Y, Dai X, Zhou B, Li Q, Zuo X, Luo H. The role of IFI35 in lupus nephritis and related mechanisms. Mod Rheumatol 2017; 27:1010-1018. [PMID: 28064541 DOI: 10.1080/14397595.2016.1270387] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
OBJECTIVES It's reported that multiple genes in the IFN-γ/STAT1 pathway were hypomethylated and associated with the pathogenesis of lupus nephritis (LN). Our previous study using microarray analysis suggested that interferon induced 35-kDa protein (IFI35) was hypomethylated and increased in LN. However, the role of IFI35 in LN and related mechanism remains to be elucidate. METHODS The expressions of IFNγR, STAT1, IFI35 and MBD2 in the human kidneys tissues was detected by real-time PCR and Western blot. The protein levels of IFI35 in the human kidney tissues were detected by immunohistochemistry. The methylation status of IFNγR, STAT1 and IFI35 were detected by methylation specific PCR. Cell proliferation assay was evaluated using cell counting kit 8; pcDNA-IFI35 (pcDNA-MBD2) or IFI35 RNAi (MBD2 RNAi) was used to upregulated or downregulated the expression of the IFI35 and MBD2. RESULTS The expressions of IFNγR, STAT1 and IFI35 in the LN kidneys were significantly higher than controls. IFI35 was expressed in mesangial cells, and positively correlated with the proliferation of mesangial cells. IFNγR, STAT1and IFI35 was hypomethylated and MBD2 was increased in LN kidneys. In vitro data confirmed those findings: after stimulating with the serum from LN patients, the proliferation of human renal mesangial cells (HRMCs) was increased. The expressions of the three members of IFNγ signal pathway were hypomethylated and upregulated. However, this effect was reversed by MBD2 knockdown. IFI35 promoted the proliferation of HRMCs and was regulated by MBD2. CONCLUSION Our results demonstrated that IFI35 enhances the proliferation of mesangial cells and was regulated by MBD2 in LN.
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Affiliation(s)
- Lihua Zhang
- a Department of Rheumatology , Xiangya Hospital, Central South University , Changsha , Hunan , People's Republic of China
| | - Honglin Zhu
- a Department of Rheumatology , Xiangya Hospital, Central South University , Changsha , Hunan , People's Republic of China
| | - Yisha Li
- a Department of Rheumatology , Xiangya Hospital, Central South University , Changsha , Hunan , People's Republic of China
| | - Xiaodan Dai
- a Department of Rheumatology , Xiangya Hospital, Central South University , Changsha , Hunan , People's Republic of China
| | - Bin Zhou
- a Department of Rheumatology , Xiangya Hospital, Central South University , Changsha , Hunan , People's Republic of China
| | - Quanzhen Li
- b Department of Immunology and Internal Medicine , University of Texas Southwestern Medical Center , Dallas , TX , USA
| | - Xiaoxia Zuo
- a Department of Rheumatology , Xiangya Hospital, Central South University , Changsha , Hunan , People's Republic of China
| | - Hui Luo
- a Department of Rheumatology , Xiangya Hospital, Central South University , Changsha , Hunan , People's Republic of China
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13
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Gigek CO, Chen ES, Smith MAC. Methyl-CpG-Binding Protein (MBD) Family: Epigenomic Read-Outs Functions and Roles in Tumorigenesis and Psychiatric Diseases. J Cell Biochem 2016. [PMID: 26205787 DOI: 10.1002/jcb.25281] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Epigenetics is the study of the heritable changes on gene expression that are responsible for the regulation of development and that have an impact on several diseases. However, it is of equal importance to understand how epigenetic machinery works. DNA methylation is the most studied epigenetic mark and is generally associated with the regulation of gene expression through the repression of promoter activity and by affecting genome stability. Therefore, the ability of the cell to interpret correct methylation marks and/or the correct interpretation of methylation plays a role in many diseases. The major family of proteins that bind methylated DNA is the methyl-CpG binding domain proteins, or the MBDs. Here, we discuss the structure that makes these proteins a family, the main functions and interactions of all protein family members and their role in human disease such as psychiatric disorders and cancer.
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Affiliation(s)
- Carolina Oliveira Gigek
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo (UNIFESP), Rua Botucatu, 740, Edifício Leitão da Cunha, 1, ° andar, CEP 04023-900, São Paulo, SP, Brazil.,Disciplina de Gastroenterologia Cirúrgica, Departamento de Cirurgia, Universidade Federal de São Paulo (UNIFESP), R. Napoleão de Barros, 715, 2º andar, CEP:04024-002, São Paulo, Brazil
| | - Elizabeth Suchi Chen
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo (UNIFESP), Rua Botucatu, 740, Edifício Leitão da Cunha, 1, ° andar, CEP 04023-900, São Paulo, SP, Brazil
| | - Marilia Arruda Cardoso Smith
- Disciplina de Genética, Departamento de Morfologia e Genética, Universidade Federal de São Paulo (UNIFESP), Rua Botucatu, 740, Edifício Leitão da Cunha, 1, ° andar, CEP 04023-900, São Paulo, SP, Brazil
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14
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Methyl-CpG-binding protein MBD2 plays a key role in maintenance and spread of DNA methylation at CpG islands and shores in cancer. Oncogene 2016; 36:1328-1338. [PMID: 27593931 DOI: 10.1038/onc.2016.297] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 07/04/2016] [Accepted: 07/17/2016] [Indexed: 02/07/2023]
Abstract
Cancer is characterised by DNA hypermethylation and gene silencing of CpG island-associated promoters, including tumour-suppressor genes. The methyl-CpG-binding domain (MBD) family of proteins bind to methylated DNA and can aid in the mediation of gene silencing through interaction with histone deacetylases and histone methyltransferases. However, the mechanisms responsible for eliciting CpG island hypermethylation in cancer, and the potential role that MBD proteins play in modulation of the methylome remain unclear. Our previous work demonstrated that MBD2 preferentially binds to the hypermethylated GSTP1 promoter CpG island in prostate cancer cells. Here, we use functional genetic approaches to investigate if MBD2 plays an active role in reshaping the DNA methylation landscape at this locus and genome-wide. First, we show that loss of MBD2 results in inhibition of both maintenance and spread of de novo methylation of a transfected construct containing the GSTP1 promoter CpG island in prostate cancer cells and Mbd2-/- mouse fibroblasts. De novo methylation was rescued by transient expression of Mbd2 in Mbd2-/- cells. Second, we show that MBD2 depletion triggers significant hypomethylation genome-wide in prostate cancer cells with concomitant loss of MBD2 binding at promoter and enhancer regulatory regions. Finally, CpG islands and shores that become hypomethylated after MBD2 depletion in LNCaP cancer cells show significant hypermethylation in clinical prostate cancer samples, highlighting a potential active role of MBD2 in promoting cancer-specific hypermethylation. Importantly, co-immunoprecipiation of MBD2 shows that MBD2 associates with DNA methyltransferase enzymes 1 and 3A. Together our results demonstrate that MBD2 has a critical role in 'rewriting' the cancer methylome at specific regulatory regions.
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15
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Walkiewicz KW, Girault JA, Arold ST. How to awaken your nanomachines: Site-specific activation of focal adhesion kinases through ligand interactions. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2015; 119:60-71. [PMID: 26093249 DOI: 10.1016/j.pbiomolbio.2015.06.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Revised: 06/07/2015] [Accepted: 06/14/2015] [Indexed: 01/12/2023]
Abstract
The focal adhesion kinase (FAK) and the related protein-tyrosine kinase 2-beta (Pyk2) are highly versatile multidomain scaffolds central to cell adhesion, migration, and survival. Due to their key role in cancer metastasis, understanding and inhibiting their functions are important for the development of targeted therapy. Because FAK and Pyk2 are involved in many different cellular functions, designing drugs with partial and function-specific inhibitory effects would be desirable. Here, we summarise recent progress in understanding the structural mechanism of how the tug-of-war between intramolecular and intermolecular interactions allows these protein 'nanomachines' to become activated in a site-specific manner.
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Affiliation(s)
- Katarzyna W Walkiewicz
- King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Sciences and Engineering, Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
| | - Jean-Antoine Girault
- Inserm, UMR-S 839, F-75005 Paris, France; Université Pierre & Marie Curie (UPMC), Sorbonne Universités, F-75005 Paris, France; Institut du Fer à Moulin, F-75005 Paris, France
| | - Stefan T Arold
- King Abdullah University of Science and Technology (KAUST), Division of Biological and Environmental Sciences and Engineering, Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia.
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16
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A dominant role for the methyl-CpG-binding protein Mbd2 in controlling Th2 induction by dendritic cells. Nat Commun 2015; 6:6920. [PMID: 25908537 PMCID: PMC4413429 DOI: 10.1038/ncomms7920] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Accepted: 03/13/2015] [Indexed: 12/16/2022] Open
Abstract
Dendritic cells (DCs) direct CD4(+) T-cell differentiation into diverse helper (Th) subsets that are required for protection against varied infections. However, the mechanisms used by DCs to promote Th2 responses, which are important both for immunity to helminth infection and in allergic disease, are currently poorly understood. We demonstrate a key role for the protein methyl-CpG-binding domain-2 (Mbd2), which links DNA methylation to repressive chromatin structure, in regulating expression of a range of genes that are associated with optimal DC activation and function. In the absence of Mbd2, DCs display reduced phenotypic activation and a markedly impaired capacity to initiate Th2 immunity against helminths or allergens. These data identify an epigenetic mechanism that is central to the activation of CD4(+) T-cell responses by DCs, particularly in Th2 settings, and reveal methyl-CpG-binding proteins and the genes under their control as possible therapeutic targets for type-2 inflammation.
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17
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Yang Y, Li D, Yang Y, Jiang G. An integrated analysis of the effects of microRNA and mRNA on esophageal squamous cell carcinoma. Mol Med Rep 2015; 12:945-52. [PMID: 25823933 PMCID: PMC4438920 DOI: 10.3892/mmr.2015.3557] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 03/16/2015] [Indexed: 01/29/2023] Open
Abstract
Esophageal squamous cell cancer (ESCC) is an aggressive type of cancer with poor prognosis and leading to decreased quality of life. The identification of patients at increased risk of esophageal squamous cell cancer may improve current understanding of the role of micro (mi)RNA in tumorigenesis, since the miRNA pattern of these patients may be associated with tumorigenesis. In the present study, the miRNA and mRNA expression profiles of ESCC tissue samples and adjacent normal control tissue samples were obtained from two dependent GEO series. Bioinformatics analyses, including the use of the Gene Oncology and Kyoto Encyclopedia of Genes and Genomes databases, were used to identify genes and pathways, which were specifically associated with miRNA-associated ESCC oncology. A total of 17 miRNAs and 1,670 probes were differentially expressed in the two groups, and the differentially expressed miRNA and target interactions were analyzed. The mRNA of miRNA target genes were found to be involve 49 GO terms and 14 pathways. Of the genes differentially expressed between the two groups, miRNA-181a, miRNA-202, miRNA-155, FNDC3B, BNC2 and MBD2 were the most significantly altered and may be important in the regulatory network. In the present study, a novel pattern of differential miRNA-target expression was constructed, which with further investigation, may provide novel targets for diagnosing and understanding the mechanism of ESCC.
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Affiliation(s)
- Yong Yang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital Affiliated Tongji University, Shanghai 200433, P.R. China
| | - Dianbo Li
- Department of Thoracic Surgery, Linyi Tumor Hospital, Linyi, Shandong 276001, P.R. China
| | - Yang Yang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital Affiliated Tongji University, Shanghai 200433, P.R. China
| | - Gening Jiang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital Affiliated Tongji University, Shanghai 200433, P.R. China
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18
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Cao Y, Guo WT, Tian S, He X, Wang XW, Liu X, Gu KL, Ma X, Huang D, Hu L, Cai Y, Zhang H, Wang Y, Gao P. miR-290/371-Mbd2-Myc circuit regulates glycolytic metabolism to promote pluripotency. EMBO J 2015; 34:609-23. [PMID: 25603933 DOI: 10.15252/embj.201490441] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Enhanced glycolysis is a main feature of pluripotent stem cells (PSCs) and is proposed to be important for the maintenance and induction of pluripotency. The molecular mechanism underlying enhanced glycolysis in PSCs is not clear. Using Dgcr8-/- mouse embryonic stem cells (ESCs) that lack mature miRNAs, we found that miR-290 cluster of miRNAs stimulates glycolysis by upregulating glycolytic enzymes Pkm2 and Ldha, which are also essential for the induction of pluripotency during reprogramming. Mechanistically, we identified Mbd2, a reader for methylated CpGs, as the target of miR-290 cluster that represses glycolysis and reprogramming. Furthermore, we discovered Myc as a key target of Mbd2 that controls metabolic switch in ESCs. Importantly, we demonstrated that miR-371 cluster, a human homolog of miR-290 cluster, stimulates glycolysis to promote the reprogramming of human fibroblasts. Hence, we identified a previously unappreciated mechanism by which miR-290/371 miRNAs orchestrate epigenetic, transcriptional and metabolic networks to promote pluripotency in PSCs and during reprogramming.
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Affiliation(s)
- Yang Cao
- The CAS Key Laboratory of Innate Immunity and Chronic Disease, Innovation Center for Cell Biology, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Wen-Ting Guo
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Shengya Tian
- The CAS Key Laboratory of Innate Immunity and Chronic Disease, Innovation Center for Cell Biology, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Xiaoping He
- The CAS Key Laboratory of Innate Immunity and Chronic Disease, Innovation Center for Cell Biology, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Xi-Wen Wang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Xiaomeng Liu
- Biodynamic Optical Imaging Center, College of Life Sciences, Peking University, Beijing, China
| | - Kai-Li Gu
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Xiaoyu Ma
- The CAS Key Laboratory of Innate Immunity and Chronic Disease, Innovation Center for Cell Biology, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - De Huang
- The CAS Key Laboratory of Innate Immunity and Chronic Disease, Innovation Center for Cell Biology, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Lan Hu
- The CAS Key Laboratory of Innate Immunity and Chronic Disease, Innovation Center for Cell Biology, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yongping Cai
- Department of Pathology, School of Medicine, Anhui Medical University, Hefei, China
| | - Huafeng Zhang
- The CAS Key Laboratory of Innate Immunity and Chronic Disease, Innovation Center for Cell Biology, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Yangming Wang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Ping Gao
- The CAS Key Laboratory of Innate Immunity and Chronic Disease, Innovation Center for Cell Biology, School of Life Sciences, University of Science and Technology of China, Hefei, China
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Tenga MJ, Lazar IM. Proteomic snapshot of breast cancer cell cycle: G1/S transition point. Proteomics 2013; 13:48-60. [PMID: 23152136 DOI: 10.1002/pmic.201200188] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2012] [Revised: 09/22/2012] [Accepted: 10/25/2012] [Indexed: 01/16/2023]
Abstract
The biological processes that unfold during the G1-phase of the cell cycle are dependent on extracellular mitogenic factors that signal the cell to enter a state of quiescence, or commit to a cell-cycle round by passing the restriction point (R-point) and enter the S-phase. Unlike normal cells, cancer cells evolved the ability to evade the R-point and continue through the cell cycle even in the presence of extensive DNA damage or absence of mitogenic signals. The purpose of this study was to perform a quantitative proteomic evaluation of the biological processes that are responsible for driving MCF-7 breast cancer cells into division even when molecular checkpoints such as the G1/S R-point are in place. Nuclear and cytoplasmic fractions of the G1 and S cell-cycle phases were analyzed by LC-MS/MS to result in the confident identification of more than 2700 proteins. Statistical evaluation of the normalized data resulted in the selection of proteins that displayed twofold or more change in spectral counts in each cell state. Pathway mapping, functional annotation clustering, and protein interaction network analysis revealed that the top-scoring clusters that could play a role in overriding the G1/S transition point included DNA damage response, chromatin remodeling, transcription/translation regulation, and signaling proteins.
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Affiliation(s)
- Milagros J Tenga
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 246021, USA
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20
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Mirza S, Sharma G, Parshad R, Gupta SD, Pandya P, Ralhan R. Expression of DNA methyltransferases in breast cancer patients and to analyze the effect of natural compounds on DNA methyltransferases and associated proteins. J Breast Cancer 2013; 16:23-31. [PMID: 23593078 PMCID: PMC3625766 DOI: 10.4048/jbc.2013.16.1.23] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 02/27/2013] [Indexed: 02/08/2023] Open
Abstract
Purpose The DNA methylation mediated by specific DNA methyltransferases (DNMTs), results in the epigenetic silencing of multiple genes which are implicated in human breast cancer. We hypothesized that the natural compounds modulate the expression of DNMTs and their associated proteins in the breast cancer cell lines and affect the methylation mediated gene silencing. Methods The DNMTs transcript expression was analyzed by reverse transcription-polymerase chain reaction (RT-PCR) in the tumors and the adjacent normal breast tissues of the patients with invasive ductal breast carcinoma. We tested the hypothesis that the natural compounds, viz., epigallocatechin gallate (EGCG), genistein, withaferin A, curcumin, resveratrol, and guggulsterone, have demethylation potential. To investigate this hypothesis, we analyzed the DNMTs expression at the transcript levels, followed by the analysis of DNMT1 and its associated proteins (HDAC1, MeCP2, and MBD2). Results The increased DNMTs transcripts expression, viz., DNMT1, DNMT3a, and DNMT3b, in the breast cancer tissues suggest involvement of the DNMTs in the breast carcinogenesis. Quantitative RT-PCR analysis revealed that the treatment with natural compounds, viz., EGCG, genistein, withaferin A, curcumin, resveratrol, and guggulsterone, resulted in a significant decrease in the transcript levels of all the DNMTs investigated. Importantly, these natural compounds decreased the protein levels of DNMT1, HDAC1, and MeCP2. Conclusion Our results demonstrate that the natural compounds, EGCG, genistein, withaferin A, curcumin, resveratrol, and guggulsterone, have the potential to reverse the epigenetic changes. Moreover, their lack of toxicity makes these natural compounds promising candidates for the chemoprevention of the breast cancer. In-depth future mechanistic studies aimed to elucidate how these compounds affect the gene transcription are warranted.
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Affiliation(s)
- Sameer Mirza
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
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Kasap E, Boyacioglu SÖ, Korkmaz M, Yuksel ES, Unsal B, Kahraman E, Ozütemiz O, Yuceyar H. Aurora kinase A (AURKA) and never in mitosis gene A-related kinase 6 (NEK6) genes are upregulated in erosive esophagitis and esophageal adenocarcinoma. Exp Ther Med 2012; 4:33-42. [PMID: 23060919 DOI: 10.3892/etm.2012.561] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 04/19/2012] [Indexed: 02/07/2023] Open
Abstract
Gastroesophageal reflux disease is a risk factor for esophageal adenocarcinoma yet studies that have investigated the relationship between erosive esophagitis and esophageal adenocarcinoma have usually focused on symptom-related evidence or polymorphisms. There are no epigenetic gene expression studies on this topic. In this study, we aimed to evaluate the relationship between erosive esophagitis and esophageal adenocarcinoma to identify whether there is a genetic predisposition for esophageal adenocarcinoma. The Human Epigenetic Chromatin Modification Enzyme RT(2) Profiler(™) PCR array (PAHS-085A) was used to detect the expression of 84 key genes encoding enzymes. This was carried out prospectively for samples from 60 patients (20 patients as a control group, 20 patients with erosive esophagitis and 20 patients with esophageal adenocarcinoma). AURKA, AURKB, NEK6 were expressed at significantly higher levels in esophageal adenocarcinoma compared to the control group. MBD2 was expressed at significantly lower levels in the esophageal adenocarcinoma group compared to the control group. AURKA, AURKC, HDAC9 and NEK6 were expressed at significantly higher levels in erosive esophagitis compared to the control group. There was no difference in upregulated gene expression between the erosive esophagitis and esophageal adenocarcinoma. MBD2 was significantly downregulated in esophageal adenocarcinoma compared to erosive esophagitis. NEK6 and AURKA were significantly upregulated in esophageal adenocarcinoma and erosive esophagitis compared to the control group. This is a novel study on the genetic predisposition for erosive esophagitis and esophageal adenocarcinoma. AURKA and NEK6 are two promising genetic markers for erosive esophagitis and esophageal adenocarcinoma.
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Ping SY, Shen KH, Yu DS. Epigenetic regulation of vascular endothelial growth factor a dynamic expression in transitional cell carcinoma. Mol Carcinog 2012; 52:568-79. [PMID: 22392726 DOI: 10.1002/mc.21892] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2011] [Revised: 01/30/2012] [Accepted: 02/06/2012] [Indexed: 11/11/2022]
Abstract
Vascular endothelial growth factor A (VEGF-A) is a key mediator in the neovascularization of cancers. We have found that VEGF-A was expressed at significantly higher levels in high-grade transitional cell carcinoma (TCC) cells than low-grade TCC cells in our previous study. In the present study, promoter methylation pattern was assessed and quantified by bisulfite genomic sequencing (BGS) and specific VEGF-A CpG sites in low-grade, but not in high-grade, TCC cells were observed. Reporter assays indicated that hypermethylation of nine CpG sites can inhibit the transcriptional activity of the VEGF-A gene. Subsequent chromatin immunoprecipitation (ChIP) assay revealed down-regulation of transcription activity of VEGF-A with increasing binding of methyl-CpG-binding protein 2 (MBD2) and trimethyl-histone H3 (Lys9) proteins to these CpG sites in low-grade TCC cells during hypermethylation. Furthermore, treatment of low-grade TCC cells with DNA methyltransferase inhibitor and histone deacetylase inhibitor can restore the expression of VEGF-A and promote the invasive ability of low-grade TCC cells. Hypermethylation with lower expression levels of VEGF-A in low-grade TCC tumors than high-grade TCC tumors was also confirmed in clinical specimens by reverse transcriptase-PCR and pyrosequencing analyses. Our findings are the first results indicating that VEGF-A expression is suppressed in low-grade TCC tumors by promoter hypermethylation. This offers a new perspective on the role of VEGF-A in TCC tumor behavior.
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Affiliation(s)
- Szu-Yuan Ping
- Graduate Institute of Life Science, National Defense Medical Center, Taipei, Taiwan, Republic of China
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Zaina S, Lund G. Epigenetic memory, MBD2 and the endothelium. Curr Opin Lipidol 2012; 23:78-9. [PMID: 22241329 DOI: 10.1097/mol.0b013e32834f429d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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A two-stage association study identifies methyl-CpG-binding domain protein 2 gene polymorphisms as candidates for breast cancer susceptibility. Eur J Hum Genet 2012; 20:682-9. [PMID: 22258532 PMCID: PMC3355265 DOI: 10.1038/ejhg.2011.273] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Genome-wide association studies for breast cancer have identified over 40 single-nucleotide polymorphisms (SNPs), a subset of which remains statistically significant after genome-wide correction. Improved strategies for mining of genome-wide association data have been suggested to address heritable component of genetic risk in breast cancer. In this study, we attempted a two-stage association design using markers from a genome-wide study (stage 1, Affymetrix Human SNP 6.0 array, cases=302, controls=321). We restricted our analysis to DNA repair/modifications/metabolism pathway related gene polymorphisms for their obvious role in carcinogenesis in general and for their known protein–protein interactions vis-à-vis, potential epistatic effects. We selected 22 SNPs based on linkage disequilibrium patterns and high statistical significance. Genotyping assays in an independent replication study of 1178 cases and 1314 controls were attempted using Sequenom iPLEX Gold platform (stage 2). Six SNPs (rs8094493, rs4041245, rs7614, rs13250873, rs1556459 and rs2297381) showed consistent and statistically significant associations with breast cancer risk in both stages, with allelic odds ratios (and P-values) of 0.85 (0.0021), 0.86 (0.0026), 0.86 (0.0041), 1.17 (0.0043), 1.20 (0.0103) and 1.13 (0.0154), respectively, in combined analysis (N=3115). Of these, three polymorphisms were located in methyl-CpG-binding domain protein 2 gene regions and were in strong linkage disequilibrium. The remaining three SNPs were in proximity to RAD21 homolog (S. pombe), O-6-methylguanine-DNA methyltransferase and RNA polymerase II-associated protein 1. The identified markers may be relevant to breast cancer susceptibility in populations if these findings are confirmed in independent cohorts.
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Characterization of type II and III restriction-modification systems from Bacillus cereus strains ATCC 10987 and ATCC 14579. J Bacteriol 2011; 194:49-60. [PMID: 22037402 DOI: 10.1128/jb.06248-11] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The genomes of two Bacillus cereus strains (ATCC 10987 and ATCC 14579) have been sequenced. Here, we report the specificities of type II/III restriction (R) and modification (M) enzymes. Found in the ATCC 10987 strain, BceSI is a restriction endonuclease (REase) with the recognition and cut site CGAAG 24-25/27-28. BceSII is an isoschizomer of AvaII (G/GWCC). BceSIII cleaves at ACGGC 12/14. The BceSIII C terminus resembles the catalytic domains of AlwI, MlyI, and Nt.BstNBI. BceSIV is composed of two subunits and cleaves on both sides of GCWGC. BceSIV activity is strongly stimulated by the addition of cofactor ATP or GTP. The large subunit (R1) of BceSIV contains conserved motifs of NTPases and DNA helicases. The R1 subunit has no endonuclease activity by itself; it strongly stimulates REase activity when in complex with the R2 subunit. BceSIV was demonstrated to hydrolyze GTP and ATP in vitro. BceSIV is similar to CglI (GCSGC), and homologs of R1 are found in 11 sequenced bacterial genomes, where they are paired with specificity subunits. In addition, homologs of the BceSIV R1-R2 fusion are found in many sequenced microbial genomes. An orphan methylase, M.BceSV, was found to modify GCNGC, GGCC, CCGG, GGNNCC, and GCGC sites. A ParB-methylase fusion protein appears to nick DNA nonspecifically. The ATCC 14579 genome encodes an active enzyme Bce14579I (GCWGC). BceSIV and Bce14579I belong to the phospholipase D (PLD) family of endonucleases that are widely distributed among Bacteria and Archaea. A survey of type II and III restriction-modification (R-M) system genes is presented from sequenced B. cereus, Bacillus anthracis, and Bacillus thuringiensis strains.
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Shu L, Khor TO, Lee JH, Boyanapalli SSS, Huang Y, Wu TY, Saw CLL, Cheung KL, Kong ANT. Epigenetic CpG demethylation of the promoter and reactivation of the expression of Neurog1 by curcumin in prostate LNCaP cells. AAPS JOURNAL 2011; 13:606-14. [PMID: 21938566 DOI: 10.1208/s12248-011-9300-y] [Citation(s) in RCA: 121] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Accepted: 09/08/2011] [Indexed: 12/21/2022]
Abstract
Curcumin (CUR), a major bioactive polyphenolic component from turmeric curry, Curcuma longa, has been shown to be a potent anti-cancer phytochemical with well-established anti-inflammatory and anti-oxidative stress effects. Chromatin remodeling-related epigenetic regulation has emerged as an important mechanism of carcinogenesis, chemoprevention, and chemotherapy. CUR has been found to inhibit histone acetyltransferase activity, and it was also postulated to be a potential DNA methyltransferase (DNMT) and histone deacetylase (HDAC) inhibitor. In this study, we show that when human prostate LNCaP cells were treated with CUR, it led to demethylation of the first 14 CpG sites of the CpG island of the Neurog1 gene and restored the expression of this cancer-related CpG-methylation epigenome marker gene. At the protein level, CUR treatment had limited effects on the expression of epigenetic modifying proteins MBD2, MeCP2, DNMT1, and DNMT3a. Using ChIP assay, CUR decreased MeCP2 binding to the promoter of Neurog1 dramatically. CUR treatment showed different effects on the protein expression of HDACs, increasing the expression of HDAC1, 4, 5, and 8 but decreasing HDAC3. However, the total HDAC activity was decreased upon CUR treatment. Further analysis of the tri-methylation of histone 3 at lysine 27 (H3K27me3) showed that CUR decreased the enrichment of H3K27me3 at the Neurog1 promoter region as well as at the global level. Taken together, our present study provides evidence on the CpG demethylation ability of CUR on Neurog1 while activating its expression, suggesting a potential epigenetic modifying role for this phytochemical compound in human prostate cancer cells.
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Affiliation(s)
- Limin Shu
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, 08854, USA
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Badran AH, Furman JL, Ma AS, Comi TJ, Porter JR, Ghosh I. Evaluating the global CpG methylation status of native DNA utilizing a bipartite split-luciferase sensor. Anal Chem 2011; 83:7151-7. [PMID: 21797230 DOI: 10.1021/ac2015239] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Epigenetic modifications play an essential role in the regulation of gene expression and ultimately cell fate. Methylation of cytosine at CpG dinucleotides (mCpG) is an important epigenetic mark that has been correlated with cancer when present at promoter sites of tumor suppressor genes. To develop a rapid methodology for the direct assessment of global levels of DNA methylation, we first interrogated the methyl-CpG binding domains (MBDs), the Kaiso family of Cys(2)-His(2) zinc fingers, and an SET- and RING-associated domain using a split-luciferase reassembly methodology. We identified MBD1 as the most selective domain for the discrimination between mCpG and CpG sites with over 90-fold selectivity. Utilizing a bipartite strategy, we constructed a purely methylation-dependent bipartite sensor for the direct detection of global levels of DNA methylation by attaching MBD1 domains to each of the split-luciferase halves. This new sensor was validated for the direct determination of genomic DNA methylation levels in in vitro studies without any intervening chemical or enzymatic processing of DNA. Finally, we demonstrated that this bipartite sensor can be utilized for monitoring dose-dependent changes in global levels of methylation in DNA from HeLa cells challenged with 5-aza-2'-deoxycytidine, a DNA methyltransferase inhibitor.
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Affiliation(s)
- Ahmed H Badran
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
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Mian OY, Wang SZ, Zhu SZ, Gnanapragasam MN, Graham L, Bear HD, Ginder GD. Methyl-binding domain protein 2-dependent proliferation and survival of breast cancer cells. Mol Cancer Res 2011; 9:1152-62. [PMID: 21693597 DOI: 10.1158/1541-7786.mcr-11-0252] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Methyl cytosine binding domain protein 2 (MBD2) has been shown to bind to and mediate repression of methylated tumor suppressor genes in cancer cells, where repatterning of CpG methylation and associated gene silencing is common. We have investigated the role of MBD2 in breast cancer cell growth and tumor suppressor gene expression. We show that stable short hairpin RNA (shRNA)-mediated knockdown of MBD2 leads to growth suppression of cultured human mammary epithelial cancer lines, SK-BR-3, MDA-MB-231, and MDA-MB-435. The peak antiproliferative occurs only after sustained, stable MBD2 knockdown. Once established, the growth inhibition persists over time and leads to a markedly decreased propensity for aggressive breast cancer cell lines to form in vivo xenograft tumors in Bagg Albino (BALB)/C nu/nu mice. The growth effects of MBD2 knockdown are accompanied by derepression of tumor suppressor genes, including DAPK1 and KLK10. Chromatin immunoprecipitation assays and bisulfite sequencing show MBD2 binding directly to the hyper methylated and CpG-rich promoters of both DAPK1 and KLK10. Remarkably, the promoter CpG island-associated methylation of these genes remained stable despite robust transcriptional activation in MBD2 knockdown cells. Expression of a shRNA-resistant MBD2 protein resulted in restoration of growth and resilencing of the MBD2-dependent tumor suppressor genes. Our data suggest that uncoupling CpG methylation from repressive chromatin remodeling and histone modifications by removing MBD2 is sufficient to initiate and maintain tumor suppressor gene transcription and suppress neoplastic cell growth. These results show a role for MBD2 in cancer progression and provide support for the prospect of targeting MBD2 therapeutically in aggressive breast cancers.
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Affiliation(s)
- Omar Y Mian
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, USA
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Umezu T, Ohyashiki K, Ohyashiki JH. Detection method for quantifying global DNA methylation by fluorescence correlation spectroscopy. Anal Biochem 2011; 415:145-50. [PMID: 21600184 DOI: 10.1016/j.ab.2011.04.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 04/16/2011] [Accepted: 04/21/2011] [Indexed: 12/27/2022]
Abstract
A method for quantifying global DNA methylation using fluorescence correlation spectroscopy (FCS) has been established. The single-molecule methylation assay (SMMA) is based on two methodologies. One methodology, FCS, estimates the translational diffusion coefficient of molecules in solution, whereas the other methodology uses the high affinity of methyl-CpG-binding domain protein 2 (MBD2) to bind specifically to methylated DNA. We studied the specific binding rates of fluorescence-labeled MBD2 and methylated DNA from biological samples using the automated FCS system. Using a standard curve with methylated control DNA, we developed the SMMA index to assess the global DNA methylation level of the biological samples. A marked decrease in the SMMA index was observed when human leukemia cell lines (U937 and K562) were cultured with DNA demethylating agents. Our findings clearly indicate the applicability of SMMA as a simple and rapid tool for quantifying global DNA methylation. SMMA may prove useful for genome-wide comparative methylation analyses of malignancies and as an indicator of the demethylation effects of epigenetic drugs.
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Affiliation(s)
- Tomohiro Umezu
- Department of Molecular Science, Tokyo Medical University, Tokyo 160-0023, Japan.
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Chromatin mechanisms regulating gene expression in health and disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011; 711:12-25. [PMID: 21627039 DOI: 10.1007/978-1-4419-8216-2_2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
It is now well established that the interplay of sequence-specific DNA binding proteins with chromatin components and the subsequent expression of differential genetic programs is the major determinant of developmental decisions. The last years have seen an explosion of basic research that has significantly enhanced our understanding of the basic principles of gene expression control. While many questions are still open, we are now at the stage where we can exploit this knowledge to address questions of how deregulated gene expression and aberrant chromatin programming contributes to disease processes. This chapter will give a basic introduction into the principles of epigenetics and the determinants of chromatin structure and will discuss the molecular mechanisms of aberrant gene regulation in blood cell diseases, such as inflammation and leukemia.
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Prospects for epigenetic compounds in the treatment of autoimmune disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011; 711:150-61. [PMID: 21627048 DOI: 10.1007/978-1-4419-8216-2_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
There is growing evidence for a role for epigenetic mechanisms in the development of autoimmune diseases. In most cases ofautoimmune disease the precise epigenetic mechanism involved remains to be resolved, however DNA hypomethylation accompanied by hypoacetylation ofhistone H3/H4 is commonly observed. Due to the reversible nature of epigenetic marks their maintenance enzymes such as DNA methyltransferases (DNMTs), histone deacetylases (HDACs) and histone lysine methyltransferases (HKMT) are attractive drug targets. Small molecule inhibitors of histone modification and DNA methylation maintenance are increasingly becoming available and will be useful chemical biological tools to dissect epigenetic mechanisms in these diseases. However, although epigenetic therapies used in cancer treatment are a promising starting point for the exploration of autoimmune disease treatment, there is a requirement for more specific and less toxic agents for these chronic diseases or for use as chemopreventative agents.
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Lan J, Hua S, He X, Zhang Y. DNA methyltransferases and methyl-binding proteins of mammals. Acta Biochim Biophys Sin (Shanghai) 2010; 42:243-52. [PMID: 20383462 DOI: 10.1093/abbs/gmq015] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In mammals, DNA methylation, characterized by the transfer of the methyl group from S-adenosylmethionines to a base (mainly referred to cytosine), acts as a major epigenetic modification. In parallel to DNA sequences arrangement, modification of methylation to DNA sequences has far-reaching influence on biological functions and activities, for it involves controlling gene transcription, regulating chromatin structure, sustaining genome stability and integrity, maintaining parental imprinting and X-chromosome inactivation, suppressing homologous recombination as well as limiting transposable elements, during which DNA methyltransferases (DNMTs) and methyl-binding proteins play important roles. Their aberrance can give rise to dysregulation of gene expression, cell maltransformation and so on. Hence, it is necessary to gain a good understanding of these two important kinds of proteins, which will help to better investigate the epigenetic mechanisms and manipulate the modifications according to our will based on its reversibility. Here we briefly review our current understanding of DNMTs and methyl-binding proteins in mammals.
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Affiliation(s)
- Jie Lan
- Institution of biotechnology, Northwest Sci-Tech University of Agriculture and Forestry, Yangling, China.
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Yu S, Khor TO, Cheung KL, Li W, Wu TY, Huang Y, Foster BA, Kan YW, Kong AN. Nrf2 expression is regulated by epigenetic mechanisms in prostate cancer of TRAMP mice. PLoS One 2010; 5:e8579. [PMID: 20062804 PMCID: PMC2799519 DOI: 10.1371/journal.pone.0008579] [Citation(s) in RCA: 170] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2009] [Accepted: 12/06/2009] [Indexed: 12/17/2022] Open
Abstract
Nuclear factor-erythroid 2 p45-related factor 2 (Nrf2) is a transcription factor which regulates the expression of many cytoprotective genes. In the present study, we found that the expression of Nrf2 was suppressed in prostate tumor of the Transgenic Adenocarcinoma of Mouse Prostate (TRAMP) mice. Similarly, the expression of Nrf2 and the induction of NQO1 were also substantially suppressed in tumorigenic TRAMP C1 cells but not in non-tumorigenic TRAMP C3 cells. Examination of the promoter region of the mouse Nrf2 gene identified a CpG island, which was methylated at specific CpG sites in prostate TRAMP tumor and in TRAMP C1 cells but not in normal prostate or TRAMP C3 cells, as shown by bisulfite genomic sequencing. Reporter assays indicated that methylation of these CpG sites dramatically inhibited the transcriptional activity of the Nrf2 promoter. Chromatin immunopreceipitation (ChIP) assays revealed increased binding of the methyl-CpG-binding protein 2 (MBD2) and trimethyl-histone H3 (Lys9) proteins to these CpG sites in the TRAMP C1 cells as compared to TRAMP C3 cells. In contrast, the binding of RNA Pol II and acetylated histone H3 to the Nrf2 promoter was decreased. Furthermore, treatment of TRAMP C1 cells with DNA methyltransferase (DNMT) inhibitor 5-aza-2′-deoxycytidine (5-aza) and histone deacetylase (HDAC) inhibitor trichostatin A (TSA) restored the expression of Nrf2 as well as the induction of NQO1 in TRAMP C1 cells. Taken together, these results indicate that the expression of Nrf2 is suppressed epigenetically by promoter methylation associated with MBD2 and histone modifications in the prostate tumor of TRAMP mice. Our present findings reveal a novel mechanism by which Nrf2 expression is suppressed in TRAMP prostate tumor, shed new light on the role of Nrf2 in carcinogenesis and provide potential new directions for the detection and prevention of prostate cancer.
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Affiliation(s)
- Siwang Yu
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey, United States of America
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Mingmalairak S, Tohda M, Murakami Y, Matsumoto K. Possible Involvement of Signal Transducers and Activators of Transcription 3 System on Depression in the Model Mice Brain. Biol Pharm Bull 2010; 33:636-40. [DOI: 10.1248/bpb.33.636] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Salin Mingmalairak
- Division of Medicinal Pharmacology, Institute of Natural Medicine, University of Toyama
| | - Michihisa Tohda
- Division of Medicinal Pharmacology, Institute of Natural Medicine, University of Toyama
| | - Yukihisa Murakami
- Division of Medicinal Pharmacology, Institute of Natural Medicine, University of Toyama
| | - Kinzo Matsumoto
- Division of Medicinal Pharmacology, Institute of Natural Medicine, University of Toyama
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Stapnes C, Gjertsen BT, Reikvam H, Bruserud Ø. Targeted therapy in acute myeloid leukaemia: current status and future directions. Expert Opin Investig Drugs 2009; 18:433-55. [DOI: 10.1517/14728220902787628] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Camilla Stapnes
- Haukeland University Hospital, Department of Medicine, Section for Haematology, N-5021 Bergen, Norway ;
| | - Bjørn Tore Gjertsen
- Haukeland University Hospital, Department of Medicine, Section for Haematology, N-5021 Bergen, Norway ;
| | - Håkon Reikvam
- Haukeland University Hospital, Department of Medicine, Section for Haematology, N-5021 Bergen, Norway ;
| | - Øystein Bruserud
- Haukeland University Hospital, Department of Medicine, Section for Haematology, N-5021 Bergen, Norway ;
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Zeng L, Yap KL, Ivanov AV, Wang X, Mujtaba S, Plotnikova O, Rauscher FJ, Zhou MM. Structural insights into human KAP1 PHD finger-bromodomain and its role in gene silencing. Nat Struct Mol Biol 2008; 15:626-33. [PMID: 18488044 DOI: 10.1038/nsmb.1416] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2008] [Accepted: 03/14/2008] [Indexed: 12/30/2022]
Abstract
The tandem PHD finger-bromodomain, found in many chromatin-associated proteins, has an important role in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). Here we report the three-dimensional solution structure of the tandem PHD finger-bromodomain of KAP1. The structure reveals a distinct scaffold unifying the two protein modules, in which the first helix, alpha(Z), of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD finger on the other. A comprehensive mutation-based structure-function analysis correlating transcriptional repression, ubiquitin-conjugating enzyme 9 (UBC9) binding and SUMOylation shows that the PHD finger and the bromodomain of KAP1 cooperate as one functional unit to facilitate lysine SUMOylation, which is required for KAP1 co-repressor activity in gene silencing. These results demonstrate a previously unknown unified function for the tandem PHD finger-bromodomain as an intramolecular small ubiquitin-like modifier (SUMO) E3 ligase for transcriptional silencing.
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Affiliation(s)
- Lei Zeng
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York University, 1425 Madison Avenue, New York, New York 10029, USA
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Abstract
Histone lysine acetylation is central to epigenetic control of gene transcription. The bromodomain, found in chromatin-associated proteins and histone acetyltranferases, functions as the sole protein module known to bind acetyl-lysine motifs. Recent structural and functional analyses of bromodomains' recognition of lysine-acetylated peptides derived from major acetylation sites in histones and cellular proteins provide new insights into differences in ligand binding selectivity as well as unifying features of histone recognition by the bromodomains. These new findings highlight the functional importance of bromodomain/acetyl-lysine binding as a pivotal mechanism for regulating protein-protein interactions in histone-directed chromatin remodeling and gene transcription. These new studies also support the notion that functional diversity of a conserved bromodomain structural fold is achieved by evolutionary changes of structurally flexible amino-acid sequences in the ligand binding site such as the ZA and BC loops.
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Affiliation(s)
- S Mujtaba
- Department of Structural and Chemical Biology, Mount Sinai School of Medicine, New York, NY 10029, USA
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Gutierrez A, Sommer RJ. Functional diversification of the nematode mbd2/3 gene between Pristionchus pacificus and Caenorhabditis elegans. BMC Genet 2007; 8:57. [PMID: 17725827 PMCID: PMC2000911 DOI: 10.1186/1471-2156-8-57] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2007] [Accepted: 08/28/2007] [Indexed: 01/10/2023] Open
Abstract
Background Several members of the Methyl-Binding Domain protein family link DNA methylation with chromatin remodeling complexes in vertebrates. Amongst the four classes of MBD proteins, MBD2/3 is the most highly conserved and widespread in metazoans. We have previously reported that an mbd2/3 like gene (mbd-2) is encoded in the genomes of the nematodes Pristionchus pacificus, Caenorhabditis elegans and Caenorhabditis briggsae. RNAi knock-down of mbd-2 in the two Caenorhabditis species results in varying percentages of lethality. Results Here, we report that a general feature of nematode MBD2/3 proteins seems to be the lack of a bona fide methyl-binding domain. We isolated a null allele of mbd-2 in P. pacificus and show that Ppa-mbd-2 mutants are viable, fertile and display a fully penetrant egg laying defect. This egg laying defect is partially rescued by treatment with acetylcholine or nicotine suggesting a specific function of this protein in vulval neurons. Using Yeast-two-hybrid screens, Ppa-MBD-2 was found to associate with microtubule interacting and vesicle transfer proteins. Conclusion These results imply that MBD2/3 proteins in nematodes are more variable than their relatives in insects and vertebrates both in structure and function. Moreover, nematode MBD2/3 proteins assume functions independent of DNA methylation ranging from the indispensable to the non-essential.
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Affiliation(s)
- Arturo Gutierrez
- Max-Planck Institute for Developmental Biology, Department for Evolutionary Biology, Spemannstrasse 37, D-72076 Tübingen, Germany
| | - Ralf J Sommer
- Max-Planck Institute for Developmental Biology, Department for Evolutionary Biology, Spemannstrasse 37, D-72076 Tübingen, Germany
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Miremadi A, Oestergaard MZ, Pharoah PDP, Caldas C. Cancer genetics of epigenetic genes. Hum Mol Genet 2007; 16 Spec No 1:R28-49. [PMID: 17613546 DOI: 10.1093/hmg/ddm021] [Citation(s) in RCA: 194] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The cancer epigenome is characterised by specific DNA methylation and chromatin modification patterns. The proteins that mediate these changes are encoded by the epigenetics genes here defined as: DNA methyltransferases (DNMT), methyl-CpG-binding domain (MBD) proteins, histone acetyltransferases (HAT), histone deacetylases (HDAC), histone methyltransferases (HMT) and histone demethylases. We review the evidence that these genes can be targeted by mutations and expression changes in human cancers.
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Affiliation(s)
- Ahmad Miremadi
- Cancer Genomics Program, Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, UK
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Shukeir N, Pakneshan P, Chen G, Szyf M, Rabbani SA. Alteration of the methylation status of tumor-promoting genes decreases prostate cancer cell invasiveness and tumorigenesis in vitro and in vivo. Cancer Res 2006; 66:9202-10. [PMID: 16982764 DOI: 10.1158/0008-5472.can-06-1954] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We tested the hypothesis that cell invasiveness and tumorigenesis are driven by hypomethylation of genes involved in tumor progression. Highly invasive human prostate cancer cells PC-3 were treated with either the methyl donor S-adenosylmethionine (SAM) or methyl DNA-binding domain protein 2 antisense oligonucleotide (MBD2-AS). Both treatments resulted in a dose- and time-dependent inhibition of key genes, such as urokinase-type plasminogen activator (uPA), matrix metalloproteinase-2 (MMP-2), and vascular endothelial growth factor expression to decrease tumor cell invasion in vitro. No change in the levels of expression of genes already known to be methylated in late-stage prostate cancer cells, such as glutathione S-transferase P1 and androgen receptor, was seen. Inoculation of PC-3 cells pretreated with SAM and MBD2-AS into the flank of male BALB/c nu/nu mice resulted in the development of tumors of significantly smaller volume compared with animals inoculated with PC-3 cells treated with vehicle alone or MBD2 scrambled oligonucleotide. Immunohistochemical analysis of tumors showed the ability of SAM and MBD2-AS to significantly decrease tumoral uPA and MMP-2 expression along with levels of angiogenesis and survival pathway signaling molecules. Bisulfite sequencing analysis of tumoral genomic DNA showed that inhibition of both uPA and MMP-2 expression was due to methylation of their 5' regulatory region. These studies support the hypothesis that DNA hypomethylation controls the activation of multiple tumor-promoting genes and provide valuable insight into developing novel therapeutic strategies against this common disease, which target the demethylation machinery.
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Affiliation(s)
- Nicholas Shukeir
- Department of Medicine, McGill University, Montreal, Quebec, Canada
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Tan CP, Nakielny S. Control of the DNA methylation system component MBD2 by protein arginine methylation. Mol Cell Biol 2006; 26:7224-35. [PMID: 16980624 PMCID: PMC1592890 DOI: 10.1128/mcb.00473-06] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
DNA methylation is vital for proper chromatin structure and function in mammalian cells. Genetic removal of the enzymes that catalyze DNA methylation results in defective imprinting, transposon silencing, X chromosome dosage compensation, and genome stability. This epigenetic modification is interpreted by methyl-DNA binding domain (MBD) proteins. MBD proteins respond to methylated DNA by recruiting histone deacetylases (HDAC) and other transcription repression factors to the chromatin. The MBD2 protein is dispensable for animal viability, but it is implicated in the genesis of colon tumors. Here we report that the MBD2 protein is controlled by arginine methylation. We identify the protein arginine methyltransferase enzymes that catalyze this modification and show that arginine methylation inhibits the function of MBD2. Arginine methylation of MBD2 reduces MBD2-methyl-DNA complex formation, reduces MBD2-HDAC repression complex formation, and impairs the transcription repression function of MBD2 in cells. Our report provides a molecular description of a potential regulatory mechanism for an MBD protein family member. It is the first to demonstrate that protein arginine methyltransferases participate in the DNA methylation system of chromatin control.
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Affiliation(s)
- Choon Ping Tan
- Cancer Research UK, London Research Institute, Lincoln's Inn Fields Laboratories, London WC2A 3PX, United Kingdom
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Stein RA. Insights into a new gene involved in cobalamin metabolism. Clin Genet 2006. [DOI: 10.1111/j.1399-0004.2006.0623b.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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