1
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Ma X, Xu S, Zhou Y, Zhang Q, Yang H, Wan B, Yang Y, Miao Z, Xu X. Targeting Nr2e3 to Modulate Tet2 Expression: Therapeutic Potential for Depression Treatment. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2400726. [PMID: 38881534 DOI: 10.1002/advs.202400726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 06/01/2024] [Indexed: 06/18/2024]
Abstract
Epigenetic mechanisms such as DNA methylation and hydroxymethylation play a significant role in depression. This research has shown that Ten-eleven translocation 2 (Tet2) deficiency prompts depression-like behaviors, but Tet2's transcriptional regulation remains unclear. In the study, bioinformatics is used to identify nuclear receptor subfamily 2 group E member 3 (Nr2e3) as a potential Tet2 regulator. Nr2e3 is found to enhance Tet2's transcriptional activity by binding to its promoter region. Nr2e3 knockdown in mouse hippocampus leads to reduced Tet2 expression, depression-like behaviors, decreased hydroxymethylation of synaptic genes, and downregulation of synaptic proteins like postsynaptic density 95 KDa (PSD95) and N-methy-d-aspartate receptor 1 (NMDAR1). Fewer dendritic spines are also observed. Nr2e3 thus appears to play an antidepressant role under stress. In search of potential treatments, small molecule compounds to increase Nr2e3 expression are screened. Azacyclonal (AZA) is found to enhance the Nr2e3/Tet2 pathway and exhibited antidepressant effects in stressed mice, increasing PSD95 and NMDAR1 expression and dendritic spine density. This study illuminates Tet2's upstream regulatory mechanism, providing a new target for identifying early depression biomarkers and developing treatments.
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Affiliation(s)
- Xiaohua Ma
- Department of Neurology, the First Affiliated Hospital of Soochow University, Suzhou, 215000, China
- Institute of Neuroscience, Soochow University, Suzhou, 215123, China
| | - Shiyao Xu
- Institute of Neuroscience, Soochow University, Suzhou, 215123, China
| | - Yaohui Zhou
- Institute of Neuroscience, Soochow University, Suzhou, 215123, China
| | - Qian Zhang
- Institute of Neuroscience, Soochow University, Suzhou, 215123, China
| | - Hao Yang
- Department of Fetology, the First Affiliated Hospital of Soochow University, Suzhou, 215006, China
| | - Bo Wan
- Institute of Neuroscience, Soochow University, Suzhou, 215123, China
| | - Yong Yang
- Department of Psychiatry, the Affiliated Guangji Hospital of Soochow University, Suzhou, Jiangsu, 215000, China
| | - Zhigang Miao
- Institute of Neuroscience, Soochow University, Suzhou, 215123, China
| | - Xingshun Xu
- Department of Neurology, the First Affiliated Hospital of Soochow University, Suzhou, 215000, China
- Institute of Neuroscience, Soochow University, Suzhou, 215123, China
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Soochow University, Suzhou, Jiangsu, 215123, China
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Younesian S, Mohammadi MH, Younesian O, Momeny M, Ghaffari SH, Bashash D. DNA methylation in human diseases. Heliyon 2024; 10:e32366. [PMID: 38933971 PMCID: PMC11200359 DOI: 10.1016/j.heliyon.2024.e32366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Aberrant epigenetic modifications, particularly DNA methylation, play a critical role in the pathogenesis and progression of human diseases. The current review aims to reveal the role of aberrant DNA methylation in the pathogenesis and progression of diseases and to discuss the original data obtained from international research laboratories on this topic. In the review, we mainly summarize the studies exploring the role of aberrant DNA methylation as diagnostic and prognostic biomarkers in a broad range of human diseases, including monogenic epigenetics, autoimmunity, metabolic disorders, hematologic neoplasms, and solid tumors. The last section provides a general overview of the possibility of the DNA methylation machinery from the perspective of pharmaceutic approaches. In conclusion, the study of DNA methylation machinery is a phenomenal intersection that each of its ways can reveal the mysteries of various diseases, introduce new diagnostic and prognostic biomarkers, and propose a new patient-tailored therapeutic approach for diseases.
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Affiliation(s)
- Samareh Younesian
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, 1971653313 Iran
| | - Mohammad Hossein Mohammadi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, 1971653313 Iran
| | - Ommolbanin Younesian
- School of Medicine, Tonekabon Branch, Islamic Azad University, Tonekabon, 46841-61167 Iran
| | - Majid Momeny
- The Brown Foundation Institute of Molecular Medicine, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, 77030 TX, USA
| | - Seyed H. Ghaffari
- Hematology, Oncology and Stem Cell Transplantation Research Center, Shariati Hospital, Tehran University of Medical Sciences, Tehran, 1411713135 Iran
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, 1971653313 Iran
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3
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Caldwell BA, Li L. Epigenetic regulation of innate immune dynamics during inflammation. J Leukoc Biol 2024; 115:589-606. [PMID: 38301269 PMCID: PMC10980576 DOI: 10.1093/jleuko/qiae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 02/03/2024] Open
Abstract
Innate immune cells play essential roles in modulating both immune defense and inflammation by expressing a diverse array of cytokines and inflammatory mediators, phagocytizing pathogens to promote immune clearance, and assisting with the adaptive immune processes through antigen presentation. Rudimentary innate immune "memory" states such as training, tolerance, and exhaustion develop based on the nature, strength, and duration of immune challenge, thereby enabling dynamic transcriptional reprogramming to alter present and future cell behavior. Underlying transcriptional reprogramming are broad changes to the epigenome, or chromatin alterations above the level of DNA sequence. These changes include direct modification of DNA through cytosine methylation as well as indirect modifications through alterations to histones that comprise the protein core of nucleosomes. In this review, we will discuss recent advances in our understanding of how these epigenetic changes influence the dynamic behavior of the innate immune system during both acute and chronic inflammation, as well as how stable changes to the epigenome result in long-term alterations of innate cell behavior related to pathophysiology.
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Affiliation(s)
- Blake A. Caldwell
- Department of Biological Sciences, Virginia Tech, 970 Washington St. SW, Blacksburg, VA 24061-0910, USA
| | - Liwu Li
- Department of Biological Sciences, Virginia Tech, 970 Washington St. SW, Blacksburg, VA 24061-0910, USA
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4
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Basak J, Piotrzkowska D, Kucharska-Lusina A, Majsterek I. Association between the Cytosine Hydroxymethylation and the Expression of microRNA in Multiple Sclerosis in Polish Population. Int J Mol Sci 2023; 24:13923. [PMID: 37762229 PMCID: PMC10531266 DOI: 10.3390/ijms241813923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Multiple sclerosis is a chronic demyelinating disorder with an unclear etiology. A key role is thought to be played by Th17 cells and microRNAs associated with Th17, such as miR-155, miR-326 and miR-223. The present study compared the methylation and hydroxymethylation levels of CpG sites within promoters of these microRNA between MS patients and controls using PBMCs and analyzed their relationship with microRNA expression. Significant intergroup differences were found between the levels of 5-hmC within the CpG-1 miR-155 promoter and CpG within the miR-326 promoter; in addition, miR-155-5p and miR-223-3p expression was elevated in MS patients. Correlation analysis showed a positive relationship between the level of 5-hmC of CpG-2 in the miR-223 promoter and miR-223-3p level. As it is possible to pharmacologically modulate the level of epigenetic modifications, our findings cast light on the etiology of MS and support the development of more effective therapies.
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Affiliation(s)
| | | | | | - Ireneusz Majsterek
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, Mazowiecka 5, 92-215 Lodz, Poland (A.K.-L.)
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Reyes-Mata MP, Mireles-Ramírez MA, Griñán-Ferré C, Pallàs M, Pavón L, Guerrero-García JDJ, Ortuño-Sahagún D. Global DNA Methylation and Hydroxymethylation Levels in PBMCs Are Altered in RRMS Patients Treated with IFN-β and GA-A Preliminary Study. Int J Mol Sci 2023; 24:ijms24109074. [PMID: 37240421 DOI: 10.3390/ijms24109074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 04/15/2023] [Accepted: 05/11/2023] [Indexed: 05/28/2023] Open
Abstract
Multiple sclerosis (MS) is a chronic disease affecting the central nervous system (CNS) due to an autoimmune attack on axonal myelin sheaths. Epigenetics is an open research topic on MS, which has been investigated in search of biomarkers and treatment targets for this heterogeneous disease. In this study, we quantified global levels of epigenetic marks using an ELISA-like approach in Peripheral Blood Mononuclear Cells (PBMCs) from 52 patients with MS, treated with Interferon beta (IFN-β) and Glatiramer Acetate (GA) or untreated, and 30 healthy controls. We performed media comparisons and correlation analyses of these epigenetic markers with clinical variables in subgroups of patients and controls. We observed that DNA methylation (5-mC) decreased in treated patients compared with untreated and healthy controls. Moreover, 5-mC and hydroxymethylation (5-hmC) correlated with clinical variables. In contrast, histone H3 and H4 acetylation did not correlate with the disease variables considered. Globally quantified epigenetic DNA marks 5-mC and 5-hmC correlate with disease and were altered with treatment. However, to date, no biomarker has been identified that can predict the potential response to therapy before treatment initiation.
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Affiliation(s)
- María Paulina Reyes-Mata
- Laboratorio de Neuroinmunobiología Molecular, Instituto de Investigación en Ciencias Biomédicas (IICB), Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara, Guadalajara 44340, Mexico
| | - Mario Alberto Mireles-Ramírez
- Unidad Médica de Alta Especialidad (UMAE), Hospital de Especialidades (HE), Centro Médico Nacional de Occidente (CMNO), IMSS, Guadalajara 44340, Mexico
| | - Christian Griñán-Ferré
- Pharmacology Section, Department of Pharmacology, Toxicology and Therapeutic Chemistry, Faculty of Pharmacy and Food Sciences, Institute of Neuroscience, Universitat de Barcelona, 08028 Barcelona, Spain
- CiberNed, Network Center for Neurodegenerative Diseases, National Spanish Health Institute Carlos III, 28220 Madrid, Spain
| | - Mercè Pallàs
- Pharmacology Section, Department of Pharmacology, Toxicology and Therapeutic Chemistry, Faculty of Pharmacy and Food Sciences, Institute of Neuroscience, Universitat de Barcelona, 08028 Barcelona, Spain
- CiberNed, Network Center for Neurodegenerative Diseases, National Spanish Health Institute Carlos III, 28220 Madrid, Spain
| | - Lenin Pavón
- Laboratorio de Psicoinmunología, Instituto Nacional de Psiquiatría Ramón de la Fuente Muñiz, Mexico City 14370, Mexico
| | - José de Jesús Guerrero-García
- Banco de Sangre Central, Unidad Médica de Alta Especialidad (UMAE), Hospital de Especialidades (HE), Centro Médico Nacional de Occidente (CMNO), IMSS, Guadalajara 44340, Mexico
- Departamento de Farmacobiología, Centro Universitario de Ciencias Exactas e Ingenierías (CUCEI), Universidad de Guadalajara, Guadalajara 44340, Mexico
| | - Daniel Ortuño-Sahagún
- Laboratorio de Neuroinmunobiología Molecular, Instituto de Investigación en Ciencias Biomédicas (IICB), Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara, Guadalajara 44340, Mexico
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6
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Gerecke C, Egea Rodrigues C, Homann T, Kleuser B. The Role of Ten-Eleven Translocation Proteins in Inflammation. Front Immunol 2022; 13:861351. [PMID: 35386689 PMCID: PMC8977485 DOI: 10.3389/fimmu.2022.861351] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/28/2022] [Indexed: 12/11/2022] Open
Abstract
Ten-eleven translocation proteins (TET1-3) are dioxygenases that oxidize 5-methyldeoxycytosine, thus taking part in passive and active demethylation. TETs have shown to be involved in immune cell development, affecting from self-renewal of stem cells and lineage commitment to terminal differentiation. In fact, dysfunction of TET proteins have been vastly associated with both myeloid and lymphoid leukemias. Recently, there has been accumulating evidence suggesting that TETs regulate immune cell function during innate and adaptive immune responses, thereby modulating inflammation. In this work, we pursue to review the current and recent evidence on the mechanistic aspects by which TETs regulate immune cell maturation and function. We will also discuss the complex interplay of TET expression and activity by several factors to modulate a multitude of inflammatory processes. Thus, modulating TET enzymes could be a novel pharmacological approach to target inflammation-related diseases and myeloid and lymphoid leukemias, when their activity is dysregulated.
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Affiliation(s)
- Christian Gerecke
- Department of Pharmacology and Toxicology, Institute of Pharmacy, Freie Universität Berlin, Germany
| | - Caue Egea Rodrigues
- Department of Pharmacology and Toxicology, Institute of Pharmacy, Freie Universität Berlin, Germany
| | - Thomas Homann
- Department of Pharmacology and Toxicology, Institute of Pharmacy, Freie Universität Berlin, Germany
| | - Burkhard Kleuser
- Department of Pharmacology and Toxicology, Institute of Pharmacy, Freie Universität Berlin, Germany
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7
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Li J, Li L, Sun X, Deng T, Huang G, Li X, Xie Z, Zhou Z. Role of Tet2 in Regulating Adaptive and Innate Immunity. Front Cell Dev Biol 2021; 9:665897. [PMID: 34222235 PMCID: PMC8247589 DOI: 10.3389/fcell.2021.665897] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/25/2021] [Indexed: 12/16/2022] Open
Abstract
Accumulated evidence indicates that epigenetic modifications play central roles in gene expression regulation and participate in developing many autoimmune and autoinflammatory diseases. Mechanistically, epigenetic modifications act as a bridge between environmental and cellular factors and susceptibility genes. DNA methylation is a critical epigenetic modification that is regulated by ten-eleven translocation (TET) enzymes. Accumulating evidence has revealed that TET family proteins function as gene regulators and antitumor drug targets mainly because of their ability to oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). Recently, the effect of Tet2, an essential TET protein, on the development of autoimmune diseases has been explored. In this review, we summarize the current understanding of Tet2 in immune response regulation, clarify the mechanisms of Tet2 in B and T cell differentiation and function, and discuss the opposing effects of Tet2 on inflammatory gene expression in the immune system to provide new potential therapeutic targets for related diseases.
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Affiliation(s)
- Jiaqi Li
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Lifang Li
- Department of Ultrasound, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Xiaoxiao Sun
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Tuo Deng
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Gan Huang
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Xia Li
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhiguo Xie
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhiguang Zhou
- National Clinical Research Center for Metabolic Diseases, Key Laboratory of Diabetes Immunology (Central South University), Ministry of Education, Department of Metabolism and Endocrinology, The Second Xiangya Hospital of Central South University, Changsha, China
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8
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Kiselev IS, Kulakova OG, Boyko AN, Favorova OO. DNA Methylation As an Epigenetic Mechanism in the Development of Multiple Sclerosis. Acta Naturae 2021; 13:45-57. [PMID: 34377555 PMCID: PMC8327151 DOI: 10.32607/actanaturae.11043] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 09/24/2020] [Indexed: 12/13/2022] Open
Abstract
The epigenetic mechanisms of gene expression regulation are a group of the key cellular and molecular pathways that lead to inherited alterations in genes' activity without changing their coding sequence. DNA methylation at the C5 position of cytosine in CpG dinucleotides is amongst the central epigenetic mechanisms. Currently, the number of studies that are devoted to the identification of methylation patterns specific to multiple sclerosis (MS), a severe chronic autoimmune disease of the central nervous system, is on a rapid rise. However, the issue of the contribution of DNA methylation to the development of the different clinical phenotypes of this highly heterogeneous disease has only begun to attract the attention of researchers. This review summarizes the data on the molecular mechanisms underlying DNA methylation and the MS risk factors that can affect the DNA methylation profile and, thereby, modulate the expression of the genes involved in the disease's pathogenesis. The focus of our attention is centered on the analysis of the published data on the differential methylation of DNA from various biological samples of MS patients obtained using both the candidate gene approach and high-throughput methods.
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Affiliation(s)
- I. S. Kiselev
- Pirogov Russian National Research Medical University, Moscow, 117997 Russia
| | - O. G. Kulakova
- Pirogov Russian National Research Medical University, Moscow, 117997 Russia
| | - A. N. Boyko
- Pirogov Russian National Research Medical University, Moscow, 117997 Russia
| | - O. O. Favorova
- Pirogov Russian National Research Medical University, Moscow, 117997 Russia
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9
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Baulina N, Kiselev I, Favorova O. Imprinted Genes and Multiple Sclerosis: What Do We Know? Int J Mol Sci 2021; 22:1346. [PMID: 33572862 PMCID: PMC7866243 DOI: 10.3390/ijms22031346] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/23/2021] [Accepted: 01/26/2021] [Indexed: 02/06/2023] Open
Abstract
Multiple sclerosis (MS) is a chronic autoimmune neurodegenerative disease of the central nervous system that arises from interplay between non-genetic and genetic risk factors. The epigenetics functions as a link between these factors, affecting gene expression in response to external influence, and therefore should be extensively studied to improve the knowledge of MS molecular mechanisms. Among others, the epigenetic mechanisms underlie the establishment of parent-of-origin effects that appear as phenotypic differences depending on whether the allele was inherited from the mother or father. The most well described manifestation of parent-of-origin effects is genomic imprinting that causes monoallelic gene expression. It becomes more obvious that disturbances in imprinted genes at the least affecting their expression do occur in MS and may be involved in its pathogenesis. In this review we will focus on the potential role of imprinted genes in MS pathogenesis.
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Affiliation(s)
- Natalia Baulina
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (I.K.); (O.F.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Ivan Kiselev
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (I.K.); (O.F.)
| | - Olga Favorova
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia; (I.K.); (O.F.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
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10
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Ghaderian S, Shomali N, Behravesh S, Danbaran GR, Hemmatzadeh M, Aslani S, Jadidi-Niaragh F, Hosseinzadeh R, Torkamandi S, Mohammadi H. The emerging role of lncRNAs in multiple sclerosis. J Neuroimmunol 2020; 347:577347. [PMID: 32745803 DOI: 10.1016/j.jneuroim.2020.577347] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 07/05/2020] [Accepted: 07/23/2020] [Indexed: 12/12/2022]
Abstract
Multiple sclerosis (MS) is the most common inflammatory demyelinating disease of the central nervous system (CNS) with various clinical manifestations. The characteristic of MS is that myelin is attacked by the body's immune system and increases the electrical capacity of axons, and is the primary pathophysiological mechanism of the transmission block. Studies have shown that epigenetic factors participate in the development of MS. LncRNAs are highly abundant and heterogeneous linear RNA transcripts with lengths exceeding 200 nucleotides and no protein-coding potential. Currently, pieces of evidence have demonstrated that lncRNAs have fundamental actions in multiple cellular pathways, including immune system regulation, epithelial-mesenchymal transition (EMT), cancer cell growth and metastasis, cellular homeostasis, and embryo development. It has been demonstrated that epigenetic mechanisms have an abundant role in the pathogenesis of MS in which the role of lncRNAs as epigenetic regulatory molecules in molecular processes has been proven. In this paper, we have focused on the correlation between MS and lncRNAs, the role of lncRNA in the pathogenesis of the disease, and the diagnostic and prognostic potential of lncRNA in MS.
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Affiliation(s)
- Samin Ghaderian
- Student Research Committee, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Navid Shomali
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Immunology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Soheil Behravesh
- Student Research Committee, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | | | - Maryam Hemmatzadeh
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Immunology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Saeed Aslani
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Farhad Jadidi-Niaragh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ramin Hosseinzadeh
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Shahram Torkamandi
- Department of Medical Genetics and Immunology, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran.
| | - Hamed Mohammadi
- Non-Communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran; Department of Immunology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran.
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11
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Wei H, Yin X, Tang H, Gao Y, Liu B, Wu Q, Tian Q, Hao Y, Bi H, Guo D. Hypomethylation of Notch1 DNA is associated with the occurrence of uveitis. Clin Exp Immunol 2020; 201:317-327. [PMID: 32479651 DOI: 10.1111/cei.13471] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 04/24/2020] [Accepted: 05/20/2020] [Indexed: 11/28/2022] Open
Abstract
Uveitis is a serious intra-ocular inflammatory disease that can lead to visual impairment even blindness worldwide. Notch signaling can regulate the differentiation of naive CD4+ T cells, influencing the development of uveitis. DNA methylation is closely related to the autoimmune diseases. In this study, we measured the Notch1 DNA methylation level, determined the Notch1 and related DNA methylases mRNA expression and evaluated the ratio of T helper type 17 regulatory T cell (Th17/Treg ) in peripheral blood mononuclear cells (PBMCs) from uveitis patients and normal control subjects; we also tested the levels of relevant inflammatory cytokines in serum from the participants. Results indicated that compared with those in normal control individuals, the expression of ten-eleven translocation 2 (TET2) and Notch1 mRNA is elevated in uveitis patients, whereas the methylation level in Notch1 DNA promotor region [-842 ~ -646 base pairs (bp)] is down-regulated, and is unrelated to anatomical location. Moreover, the Th17/Treg ratio is up-regulated in PBMCs from uveitis patients, accompanied by the elevated levels of proinflammatory cytokines [e.g. interleukin (IL)-2, IL-6, IL-17 and interferon (IFN)-γ] in serum from uveitis patients. These findings suggest that the over-expression of TET2 DNA demethylase may lead to hypomethylation of Notch1, activate the Notch1 signaling, induce naive CD4+ T cells to differentiate theTh17 subset and thus disturb the balance of the Th17/Treg ratio in uveitis patients. Overall, hypomethylation of Notch1 DNA is closely associated with the occurrence of uveitis. Our study preliminarily reveals the underlying mechanism for the occurrence of uveitis related to the hypomethylation of Notch1 DNA, providing a novel therapeutic strategy against uveitis in clinical practice.
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Affiliation(s)
- H Wei
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - X Yin
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - H Tang
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Y Gao
- Shandong Provincial Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Therapy of Ocular Diseases, Shandong, Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Therapy of Ocular Diseases in Universities, Shandong, Eye Institute of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - B Liu
- Department of Blood Transfusion, Linyi People's Hospital, Linyi, China
| | - Q Wu
- Affiliated Eye Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Q Tian
- Affiliated Eye Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Y Hao
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - H Bi
- Shandong Provincial Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Therapy of Ocular Diseases, Shandong, Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Therapy of Ocular Diseases in Universities, Shandong, Eye Institute of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - D Guo
- Shandong Provincial Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Therapy of Ocular Diseases, Shandong, Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Therapy of Ocular Diseases in Universities, Shandong, Eye Institute of Shandong University of Traditional Chinese Medicine, Jinan, China
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12
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Celarain N, Tomas-Roig J. Aberrant DNA methylation profile exacerbates inflammation and neurodegeneration in multiple sclerosis patients. J Neuroinflammation 2020; 17:21. [PMID: 31937331 PMCID: PMC6961290 DOI: 10.1186/s12974-019-1667-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 11/27/2019] [Indexed: 12/12/2022] Open
Abstract
Multiple sclerosis (MS) is an autoimmune and demyelinating disease of the central nervous system characterised by incoordination, sensory loss, weakness, changes in bladder capacity and bowel function, fatigue and cognitive impairment, creating a significant socioeconomic burden. The pathogenesis of MS involves both genetic susceptibility and exposure to distinct environmental risk factors. The gene x environment interaction is regulated by epigenetic mechanisms. Epigenetics refers to a complex system that modifies gene expression without altering the DNA sequence. The most studied epigenetic mechanism is DNA methylation. This epigenetic mark participates in distinct MS pathophysiological processes, including blood-brain barrier breakdown, inflammatory response, demyelination, remyelination failure and neurodegeneration. In this study, we also accurately summarised a list of environmental factors involved in the MS pathogenesis and its clinical course. A literature search was conducted using MEDLINE through PubMED and Scopus. In conclusion, an exhaustive study of DNA methylation might contribute towards new pharmacological interventions in MS by use of epigenetic drugs.
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Affiliation(s)
- Naiara Celarain
- Girona Neuroimmunology and Multiple Sclerosis Unit (UNIEM), Dr. Josep Trueta University Hospital and Girona Biomedical Research Institute (IDIBGI), Girona, Spain.
| | - Jordi Tomas-Roig
- Girona Neuroimmunology and Multiple Sclerosis Unit (UNIEM), Dr. Josep Trueta University Hospital and Girona Biomedical Research Institute (IDIBGI), Girona, Spain.
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13
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Identifying the culprits in neurological autoimmune diseases. J Transl Autoimmun 2019; 2:100015. [PMID: 32743503 PMCID: PMC7388404 DOI: 10.1016/j.jtauto.2019.100015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/27/2019] [Accepted: 09/03/2019] [Indexed: 12/16/2022] Open
Abstract
The target organ of neurological autoimmune diseases (NADs) is the central or peripheral nervous system. Multiple sclerosis (MS) is the most common NAD, whereas Guillain-Barré syndrome (GBS), myasthenia gravis (MG), and neuromyelitis optica (NMO) are less common NADs, but the incidence of these diseases has increased exponentially in the last few years. The identification of a specific culprit in NADs is challenging since a myriad of triggering factors interplay with each other to cause an autoimmune response. Among the factors that have been associated with NADs are genetic susceptibility, epigenetic mechanisms, and environmental factors such as infection, microbiota, vitamins, etc. This review focuses on the most studied culprits as well as the mechanisms used by these to trigger NADs. Neurological autoimmune diseases are caused by a complex interaction between genes, environmental factors, and epigenetic deregulation. Infectious agents can cause an autoimmune reaction to myelin epitopes through molecular mimicry and/or bystander activation. Gut microbiota dysbiosis contributes to neurological autoimmune diseases. Smoking increases the risk of NADs through inflammatory signaling pathways, oxidative stress, and Th17 differentiation. Deficiency in vitamin D favors NAD development through direct damage to the central and peripheral nervous system.
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14
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DNA methylation and hydroxymethylation are associated with the degree of coronary atherosclerosis in elderly patients with coronary heart disease. Life Sci 2019; 224:241-248. [DOI: 10.1016/j.lfs.2019.03.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/08/2019] [Accepted: 03/09/2019] [Indexed: 01/24/2023]
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15
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Tang Y, Luo M, Pan K, Ahmad T, Zhou T, Miao Z, Zhou H, Sun H, Xu X, Namaka M, Wang Y. DNA hydroxymethylation changes in response to spinal cord damage in a multiple sclerosis mouse model. Epigenomics 2018; 11:323-335. [PMID: 30426768 DOI: 10.2217/epi-2018-0162] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
AIM Roles of DNA 5-hydroxymethylcytosine (5hmC) in myelin repair were investigated in an experimental autoimmune encephalomyelitis (EAE) mouse model via its regulation on BDNF. METHODS DNA 5hmC level and its limiting enzymes were detected in EAE mice. RESULTS Global 5hmC modification, Tet1 and Tet2 significantly decreased in the spinal cord tissues of EAE mice. BDNF protein and mRNA decreased and were highly associated with BDNF 5hmC. Vitamin C, a Tet co-factor, increased global DNA 5hmC and reduced the neurological deficits at least by increasing BDNF 5hmC modification and protein levels. CONCLUSION Tet protein-mediated 5hmC modifications represent a critical target involved in EAE-induced myelin damage. Targeting epigenetic modification may be a therapeutic strategy for multiple sclerosis.
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Affiliation(s)
- Yan Tang
- Department of Neurology, The Second Affiliated Hospital of Soochow University, Suzhou City, PR China.,Faculty of Health Sciences, College of Pharmacy, University of Manitoba, Manitoba, Winnipeg R3E 3P4, Canada.,Institute of Neuroscience, Soochow University, Suzhou City, PR China
| | - Man Luo
- Department of Neurology, The Second Affiliated Hospital of Soochow University, Suzhou City, PR China
| | - Kailing Pan
- Institute of Neuroscience, Soochow University, Suzhou City, PR China
| | - Tina Ahmad
- Faculty of Health Sciences, College of Pharmacy, University of Manitoba, Manitoba, Winnipeg R3E 3P4, Canada
| | - Ting Zhou
- Faculty of Health Sciences, College of Pharmacy, University of Manitoba, Manitoba, Winnipeg R3E 3P4, Canada
| | - Zhigang Miao
- Institute of Neuroscience, Soochow University, Suzhou City, PR China
| | - Hang Zhou
- Institute of Neuroscience, Soochow University, Suzhou City, PR China
| | - Hao Sun
- Department of Orthopedics, Clinical Medical College, Yangzhou University, Yangzhou City, PR China
| | - Xingshun Xu
- Department of Neurology, The Second Affiliated Hospital of Soochow University, Suzhou City, PR China.,Institute of Neuroscience, Soochow University, Suzhou City, PR China
| | - Michael Namaka
- Faculty of Health Sciences, College of Pharmacy, University of Manitoba, Manitoba, Winnipeg R3E 3P4, Canada
| | - Yongxiang Wang
- Department of Orthopedics, Clinical Medical College, Yangzhou University, Yangzhou City, PR China.,Department of Orthopedics, Northern Jiangsu People's Hospital, Yangzhou City, PR China
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16
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Marycz K, Kornicka K, Irwin‐Houston JM, Weiss C. Combination of resveratrol and 5-azacytydine improves osteogenesis of metabolic syndrome mesenchymal stem cells. J Cell Mol Med 2018; 22:4771-4793. [PMID: 29999247 PMCID: PMC6156237 DOI: 10.1111/jcmm.13731] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 05/24/2018] [Indexed: 12/13/2022] Open
Abstract
Endocrine disorders have become more and more frequently diagnosed in humans and animals. In horses, equine metabolic syndrome (EMS) is characterized by insulin resistance, hyperleptinemia, hyperinsulinemia, inflammation and usually by pathological obesity. Due to an increased inflammatory response in the adipose tissue, cytophysiological properties of adipose derived stem cells (ASC) have been impaired, which strongly limits their therapeutic potential. Excessive accumulation of reactive oxygen species, mitochondria deterioration and accelerated ageing of those cells affect their multipotency and restrict the effectiveness of the differentiation process. In the present study, we have treated ASC isolated from EMS individuals with a combination of 5-azacytydine (AZA) and resveratrol (RES) in order to reverse their aged phenotype and enhance osteogenic differentiation. Using SEM and confocal microscope, cell morphology, matrix mineralization and mitochondrial dynamics were assessed. Furthermore, we investigated the expression of osteogenic-related genes with RT-PCR. We also investigated the role of autophagy during differentiation and silenced PARKIN expression with siRNA. Obtained results indicated that AZA/RES significantly enhanced early osteogenesis of ASC derived from EMS animals. Increased matrix mineralization, RUNX-2, collagen type I and osteopontin levels were noted. Furthermore, we proved that AZA/RES exerts its beneficial effects by modulating autophagy and mitochondrial dynamics through PARKIN and RUNX-2 activity.
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Affiliation(s)
- Krzysztof Marycz
- Department of Experimental BiologyWroclaw University of Environmental and Life SciencesWroclawPoland
- Wroclaw Research Centre EIT+WrocławPoland
| | - Katarzyna Kornicka
- Department of Experimental BiologyWroclaw University of Environmental and Life SciencesWroclawPoland
| | | | - Christine Weiss
- PferdePraxis Dr. Med. Vet. Daniel WeissFreienbachSwitzerland
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17
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Ma Y, De Jager PL. Designing an epigenomic study. Mult Scler 2018; 24:604-609. [PMID: 29692225 DOI: 10.1177/1352458517750770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Yiyi Ma
- Center for Translational and Computational Neuro-immunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA/Cell Circuits Program, Broad Institute, Cambridge, MA, USA
| | - Philip L De Jager
- Center for Translational and Computational Neuro-immunology, Department of Neurology, Columbia University Medical Center, New York, NY, USA/Cell Circuits Program, Broad Institute, Cambridge, MA, USA
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18
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Kader F, Ghai M, Maharaj L. The effects of DNA methylation on human psychology. Behav Brain Res 2017; 346:47-65. [PMID: 29237550 DOI: 10.1016/j.bbr.2017.12.004] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 11/01/2017] [Accepted: 12/05/2017] [Indexed: 01/05/2023]
Abstract
DNA methylation is a fundamental epigenetic modification in the human genome; pivotal in development, genomic imprinting, X inactivation, chromosome stability, gene expression and methylation aberrations are involved in an array of human diseases. Methylation at promoters is associated with transcriptional repression, whereas gene body methylation is generally associated with gene expression. Extrinsic factors such as age, diets and lifestyle affect DNA methylation which consequently alters gene expression. Stress, anxiety, depression, life satisfaction, emotion among numerous other psychological factors also modify DNA methylation patterns. This correlation is frequently investigated in four candidate genes; NR3C1, SLC6A4, BDNF and OXTR, since regulation of these genes directly impact responses to social situations, stress, threats, behaviour and neural functions. Such studies underpin the hypothesis that DNA methylation is involved in deviant human behaviour, psychological and psychiatric conditions. These candidate genes may be targeted in future to assess the correlation between methylation, social experiences and long-term behavioural phenotypes in humans; and may potentially serve as biomarkers for therapeutic intervention.
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Affiliation(s)
- Farzeen Kader
- School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000 South Africa.
| | - Meenu Ghai
- School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000 South Africa.
| | - Leah Maharaj
- School of Life Sciences, University of KwaZulu-Natal, Westville Campus, Durban 4000 South Africa.
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19
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Valentini E, Zampieri M, Malavolta M, Bacalini MG, Calabrese R, Guastafierro T, Reale A, Franceschi C, Hervonen A, Koller B, Bernhardt J, Slagboom PE, Toussaint O, Sikora E, Gonos ES, Breusing N, Grune T, Jansen E, Dollé MET, Moreno-Villanueva M, Sindlinger T, Bürkle A, Ciccarone F, Caiafa P. Analysis of the machinery and intermediates of the 5hmC-mediated DNA demethylation pathway in aging on samples from the MARK-AGE Study. Aging (Albany NY) 2017; 8:1896-1922. [PMID: 27587280 PMCID: PMC5076444 DOI: 10.18632/aging.101022] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 08/15/2016] [Indexed: 12/22/2022]
Abstract
Gradual changes in the DNA methylation landscape occur throughout aging virtually in all human tissues. A widespread reduction of 5-methylcytosine (5mC), associated with highly reproducible site-specific hypermethylation, characterizes the genome in aging. Therefore, an equilibrium seems to exist between general and directional deregulating events concerning DNA methylation controllers, which may underpin the age-related epigenetic changes. In this context, 5mC-hydroxylases (TET enzymes) are new potential players. In fact, TETs catalyze the stepwise oxidation of 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), driving the DNA demethylation process based on thymine DNA glycosylase (TDG)-mediated DNA repair pathway. The present paper reports the expression of DNA hydroxymethylation components, the levels of 5hmC and of its derivatives in peripheral blood mononuclear cells of age-stratified donors recruited in several European countries in the context of the EU Project 'MARK-AGE'. The results provide evidence for an age-related decline of TET1, TET3 and TDG gene expression along with a decrease of 5hmC and an accumulation of 5caC. These associations were independent of confounding variables, including recruitment center, gender and leukocyte composition. The observed impairment of 5hmC-mediated DNA demethylation pathway in blood cells may lead to aberrant transcriptional programs in the elderly.
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Affiliation(s)
- Elisabetta Valentini
- Department of Cellular Biotechnologies and Hematology, Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome 00161, Italy.,Pasteur Institute-Fondazione Cenci Bolognetti, Rome 00161, Italy
| | - Michele Zampieri
- Department of Cellular Biotechnologies and Hematology, Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome 00161, Italy.,Pasteur Institute-Fondazione Cenci Bolognetti, Rome 00161, Italy
| | - Marco Malavolta
- National Institute of Health and Science on Aging (INRCA), Nutrition and Ageing Centre, Scientific and Technological Research Area, 60100 Ancona, Italy
| | - Maria Giulia Bacalini
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna 40126, Italy.,CIG-Interdepartmental Center "L. Galvani", Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Roberta Calabrese
- Department of Cellular Biotechnologies and Hematology, Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome 00161, Italy.,Pasteur Institute-Fondazione Cenci Bolognetti, Rome 00161, Italy
| | - Tiziana Guastafierro
- Department of Cellular Biotechnologies and Hematology, Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome 00161, Italy.,Pasteur Institute-Fondazione Cenci Bolognetti, Rome 00161, Italy
| | - Anna Reale
- Department of Cellular Biotechnologies and Hematology, Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome 00161, Italy
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna 40126, Italy.,CIG-Interdepartmental Center "L. Galvani", Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Antti Hervonen
- The School of Medicine, The University of Tampere, 33014 Tampere, Finland
| | - Bernhard Koller
- Department for Internal Medicine, University Teaching Hospital Hall in Tirol, Tirol, Austria
| | | | - P Eline Slagboom
- Department of Molecular Epidemiology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Olivier Toussaint
- University of Namur, Research Unit on Cellular Biology, Namur B-5000, Belgium
| | - Ewa Sikora
- Laboratory of the Molecular Bases of Ageing, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093 Warsaw, Poland
| | - Efstathios S Gonos
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, Athens, Greece
| | - Nicolle Breusing
- Institute of Nutritional Medicine (180c), University of Hohenheim, 70599 Stuttgart, Gemany
| | - Tilman Grune
- German Institute of Human Nutrition Potsdam-Rehbruecke (DIfE), 14558 Nuthetal, Germany
| | - Eugène Jansen
- Centre for Health Protection, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands
| | - Martijn E T Dollé
- Centre for Health Protection, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands
| | - María Moreno-Villanueva
- Molecular Toxicology Group, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Thilo Sindlinger
- Molecular Toxicology Group, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Alexander Bürkle
- Molecular Toxicology Group, Department of Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Fabio Ciccarone
- Department of Biology, University of Rome "Tor Vergata", 00133 Rome, Italy.,Shared senior authorship
| | - Paola Caiafa
- Department of Cellular Biotechnologies and Hematology, Faculty of Pharmacy and Medicine, Sapienza University of Rome, Rome 00161, Italy.,Pasteur Institute-Fondazione Cenci Bolognetti, Rome 00161, Italy.,Shared senior authorship
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20
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Pinto-Medel MJ, Oliver-Martos B, Urbaneja-Romero P, Hurtado-Guerrero I, Ortega-Pinazo J, Serrano-Castro P, Fernández Ó, Leyva L. Global methylation correlates with clinical status in multiple sclerosis patients in the first year of IFNbeta treatment. Sci Rep 2017; 7:8727. [PMID: 28821874 PMCID: PMC5562733 DOI: 10.1038/s41598-017-09301-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/25/2017] [Indexed: 02/08/2023] Open
Abstract
The alteration of DNA methylation patterns are a key component of disease onset and/or progression. Our objective was to evaluate the differences in Long Interspersed Nuclear Element-1 (LINE-1) methylation levels, as a surrogate marker of global DNA methylation, between multiple sclerosis (MS) patients and healthy controls. In addition, we assessed the association of LINE-1 methylation with clinical disease activity in patients treated with IFNbeta (IFNβ). We found that individuals with high levels of LINE-1 methylation showed 6-fold increased risk of suffering MS. Additionally, treated MS patients who bear high LINE-1 methylation levels had an 11-fold increased risk of clinical activity. Moreover, a negative correlation between treatment duration and percentage of LINE-1 methylation, that was statistically significant exclusively in the group of patients without clinical activity, was observed. Our data suggest that in MS patients, a slight global DNA hypermethylation occurs that may be related to the pathophysiology of the disease. In addition, global DNA methylation levels could play a role as a biomarker for the differential clinical response to IFNβ.
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Affiliation(s)
- María Jesús Pinto-Medel
- UGC Neurociencias, Laboratorio de Investigación. Instituto de Investigación Biomedica de Málaga (IBIMA), Hospital Regional Universitario de Málaga, Universidad de Málaga (UMA), Málaga, Spain.
| | - Begoña Oliver-Martos
- UGC Neurociencias, Laboratorio de Investigación. Instituto de Investigación Biomedica de Málaga (IBIMA), Hospital Regional Universitario de Málaga, Universidad de Málaga (UMA), Málaga, Spain
| | - Patricia Urbaneja-Romero
- UGC Neurociencias, Servicio de Neurología, Fundación Pública Andaluza para la Investigación de Málaga en Biomedicina y Salud (FIMABIS), Málaga, Spain
| | - Isaac Hurtado-Guerrero
- UGC Neurociencias, Laboratorio de Investigación. Instituto de Investigación Biomedica de Málaga (IBIMA), Hospital Regional Universitario de Málaga, Universidad de Málaga (UMA), Málaga, Spain
| | - Jesús Ortega-Pinazo
- UGC Neurociencias, Laboratorio de Investigación. Instituto de Investigación Biomedica de Málaga (IBIMA), Hospital Regional Universitario de Málaga, Universidad de Málaga (UMA), Málaga, Spain
| | - Pedro Serrano-Castro
- UGC Neurociencias, Servicio de Neurología, Hospital Regional Universitario de Málaga, Málaga, Spain
| | - Óscar Fernández
- UGC Neurociencias, Laboratorio de Investigación. Instituto de Investigación Biomedica de Málaga (IBIMA), Hospital Regional Universitario de Málaga, Universidad de Málaga (UMA), Málaga, Spain
| | - Laura Leyva
- UGC Neurociencias, Laboratorio de Investigación. Instituto de Investigación Biomedica de Málaga (IBIMA), Hospital Regional Universitario de Málaga, Universidad de Málaga (UMA), Málaga, Spain
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21
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Zheleznyakova GY, Piket E, Marabita F, Pahlevan Kakhki M, Ewing E, Ruhrmann S, Needhamsen M, Jagodic M, Kular L. Epigenetic research in multiple sclerosis: progress, challenges, and opportunities. Physiol Genomics 2017; 49:447-461. [PMID: 28754822 DOI: 10.1152/physiolgenomics.00060.2017] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/24/2017] [Indexed: 01/02/2023] Open
Abstract
Multiple sclerosis (MS) is a chronic inflammatory and demyelinating disease of the central nervous system. MS likely results from a complex interplay between predisposing causal gene variants (the strongest influence coming from HLA class II locus) and environmental risk factors such as smoking, infectious mononucleosis, and lack of sun exposure/vitamin D. However, little is known about the mechanisms underlying MS development and progression. Moreover, the clinical heterogeneity and variable response to treatment represent additional challenges to a comprehensive understanding and efficient treatment of disease. Epigenetic processes, such as DNA methylation and histone posttranslational modifications, integrate influences from the genes and the environment to regulate gene expression accordingly. Studying epigenetic modifications, which are stable and reversible, may provide an alternative approach to better understand and manage disease. We here aim to review findings from epigenetic studies in MS and further discuss the challenges and clinical opportunities arising from epigenetic research, many of which apply to other diseases with similar complex etiology. A growing body of evidence supports a role of epigenetic processes in the mechanisms underlying immune pathogenesis and nervous system dysfunction in MS. However, disparities between studies shed light on the need to consider possible confounders and methodological limitations for a better interpretation of the data. Nevertheless, translational use of epigenetics might offer new opportunities in epigenetic-based diagnostics and therapeutic tools for a personalized care of MS patients.
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Affiliation(s)
- Galina Y Zheleznyakova
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Eliane Piket
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Francesco Marabita
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Majid Pahlevan Kakhki
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Ewoud Ewing
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Sabrina Ruhrmann
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Maria Needhamsen
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
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22
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Barazeghi E, Gill AJ, Sidhu S, Norlén O, Dina R, Palazzo FF, Hellman P, Stålberg P, Westin G. A role for TET2 in parathyroid carcinoma. Endocr Relat Cancer 2017. [PMID: 28642344 DOI: 10.1530/erc-17-0009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Primary hyperparathyroidism (pHPT) is rarely caused by parathyroid carcinoma (PC, <1-5% of pHPT cases). The TET proteins oxidize the epigenetic mark 5-methylcytosine to 5-hydroxymethylcytosine (5hmC) and inactivation by mutation or epigenetic deregulation of TET1 and TET2 play important roles in various cancers. Recently, we found that 5hmC was severely reduced in all of the analyzed PCs and with deranged expression of TET1 for the majority of PCs. Here, we have examined the expression of the TET2 protein in 15 5hmC-negative PCs from patients who had local invasion or metastases. Cell growth and cell migratory roles for TET2 as well as epigenetic deregulated expression were addressed. Immunohistochemistry revealed very low/undetectable expression of TET2 in all PCs and verified for two PCs that were available for western blotting analysis. Knockdown of TET2 in the parathyroid cell line sHPT-1 resulted in increased cell growth and increased cell migration. DNA sequencing of TET2 in PCs revealed two common variants and no obvious inactivating mutations. Quantitative bisulfite pyrosequencing analysis of the TET2 promoter CpG island revealed higher CpG methylation level in the PCs compared to that in normal tissues and treatment of a PC primary cell culture with the DNA methylation inhibitor 5-aza-2'-deoxycytidine caused increased expression of the methylated TET2 gene. Hence, the data suggest that deregulated expression of TET2 by DNA hypermethylation may contribute to the aberrantly low level of 5hmC in PCs and further that TET2 plays a cell growth and cell migratory regulatory role and may constitute a parathyroid tumor suppressor gene.
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Affiliation(s)
- Elham Barazeghi
- Department of Surgical SciencesEndocrine Unit, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Anthony J Gill
- Cancer Diagnosis and Pathology Research GroupKolling Institute of Medical Research, St Leonards, New South Wales, Australia
| | - Stan Sidhu
- Department of SurgeryRoyal North Shore Hospital, St Leonards, New South Wales, Australia
- University of SydneySydney, New South Wales, Australia
| | - Olov Norlén
- Department of Surgical SciencesEndocrine Unit, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
- Department of SurgeryRoyal North Shore Hospital, St Leonards, New South Wales, Australia
- University of SydneySydney, New South Wales, Australia
| | - Roberto Dina
- Department of HistopathologyHammersmith Hospital, Imperial College, London, UK
| | - F Fausto Palazzo
- Department of Endocrine SurgeryHammersmith Hospital, Imperial College, London, UK
| | - Per Hellman
- Department of Surgical SciencesEndocrine Unit, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Peter Stålberg
- Department of Surgical SciencesEndocrine Unit, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Gunnar Westin
- Department of Surgical SciencesEndocrine Unit, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
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23
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Hodjat M, Rahmani S, Khan F, Niaz K, Navaei–Nigjeh M, Mohammadi Nejad S, Abdollahi M. Environmental toxicants, incidence of degenerative diseases, and therapies from the epigenetic point of view. Arch Toxicol 2017; 91:2577-2597. [DOI: 10.1007/s00204-017-1979-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 05/04/2017] [Indexed: 01/12/2023]
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24
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Emerging Role for Methylation in Multiple Sclerosis: Beyond DNA. Trends Mol Med 2017; 23:546-562. [PMID: 28478950 DOI: 10.1016/j.molmed.2017.04.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 03/29/2017] [Accepted: 04/10/2017] [Indexed: 12/29/2022]
Abstract
Multiple Sclerosis (MS) is a chronic inflammatory disease of the central nervous system. The inflammatory and neurodegenerative pathways driving MS are modulated by DNA, lysine, and arginine methylation, as evidenced by studies made possible by novel tools for methylation detection or loss of function. We present evidence that MS is associated with genetic variants and metabolic changes that impact on methylation. Further, we comprehensively review current understanding of how methylation can impact on central nervous system (CNS) resilience and neuroregenerative potential, as well as inflammatory versus regulatory T helper (Th) cell balance. These findings are discussed in the context of therapeutic relevance for MS, with broad implications in other neurologic and immune-mediated diseases.
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Peedicayil J. Epigenetic Drugs for Multiple Sclerosis. Curr Neuropharmacol 2016; 14:3-9. [PMID: 26813117 PMCID: PMC4787283 DOI: 10.2174/1570159x13666150211001600] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 01/19/2015] [Accepted: 02/09/2015] [Indexed: 01/01/2023] Open
Abstract
There is increasing evidence that abnormalities in epigenetic mechanisms of gene expression contribute to the development of multiple sclerosis (MS). Advances in epigenetics have given rise to a new class of drugs, epigenetic drugs. Although many classes of epigenetic drugs are being investigated, at present most attention is being paid to two classes of epigenetic drugs: drugs that inhibit DNA methyltransferase (DNMTi) and drugs that inhibit histone deacetylase (HDACi). This paper discusses the potential use of epigenetic drugs in the treatment of MS, focusing on DNMTi and HDACi. Preclinical drug trials of DNMTi and HDACi for the treatment of MS are showing promising results. Epigenetic drugs could improve the clinical management of patients with MS.
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Affiliation(s)
- Jacob Peedicayil
- Department of Pharmacology and Clinical Pharmacology Christian Medical College Vellore India.
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Sokratous M, Dardiotis E, Tsouris Z, Bellou E, Michalopoulou A, Siokas V, Arseniou S, Stamati T, Tsivgoulis G, Bogdanos D, Hadjigeorgiou GM. Deciphering the role of DNA methylation in multiple sclerosis: emerging issues. AUTOIMMUNITY HIGHLIGHTS 2016; 7:12. [PMID: 27605361 PMCID: PMC5014764 DOI: 10.1007/s13317-016-0084-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 08/24/2016] [Indexed: 11/29/2022]
Abstract
Multiple sclerosis (MS) is an autoimmune inflammatory and neurodegenerative disease of the central nervous system that involves several not yet fully elucidated pathophysiologic mechanisms. There is increasing evidence that epigenetic modifications at level of DNA bases, histones, and micro-RNAs may confer risk for MS. DNA methylation seems to have a prominent role in the epigenetics of MS, as aberrant methylation in the promoter regions across genome may underlie several processes involved in the initiation and development of MS. In the present review, we discuss current understanding regarding the role of DNA methylation in MS, possible therapeutic implications and future emerging issues.
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Affiliation(s)
- Maria Sokratous
- Department of Neurology, Laboratory of Neurogenetics, University of Thessaly, University Hospital of Larissa, Larissa, Greece
| | - Efthimios Dardiotis
- Department of Neurology, Laboratory of Neurogenetics, University of Thessaly, University Hospital of Larissa, Larissa, Greece
| | - Zisis Tsouris
- Department of Neurology, Laboratory of Neurogenetics, University of Thessaly, University Hospital of Larissa, Larissa, Greece
| | - Eleni Bellou
- Department of Neurology, Laboratory of Neurogenetics, University of Thessaly, University Hospital of Larissa, Larissa, Greece
| | - Amalia Michalopoulou
- Department of Neurology, Laboratory of Neurogenetics, University of Thessaly, University Hospital of Larissa, Larissa, Greece
| | - Vasileios Siokas
- Department of Neurology, Laboratory of Neurogenetics, University of Thessaly, University Hospital of Larissa, Larissa, Greece
| | - Stylianos Arseniou
- Department of Neurology, Laboratory of Neurogenetics, University of Thessaly, University Hospital of Larissa, Larissa, Greece
| | - Tzeni Stamati
- Department of Neurology, Laboratory of Neurogenetics, University of Thessaly, University Hospital of Larissa, Larissa, Greece
| | - Georgios Tsivgoulis
- Second Department of Neurology, University of Athens, School of Medicine, "Attikon" University Hospital, Athens, Greece
| | - Dimitrios Bogdanos
- Department of Rheumatology and Clinical Immunology, Faculty of Medicine, School of Health Sciences, University General Hospital of Larissa, University of Thessaly Viopolis, 40500, Larissa, Greece.,Cellular Immunotherapy and Molecular Immunodiagnostics, Biomedical Section, Center for Research and Technology-Hellas (CERTH)-Institute for Research and Technology-Thessaly (IRETETH), 41222, Larissa, Greece
| | - Georgios M Hadjigeorgiou
- Department of Neurology, Laboratory of Neurogenetics, University of Thessaly, University Hospital of Larissa, Larissa, Greece.
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Ciccarone F, Valentini E, Zampieri M, Caiafa P. 5mC-hydroxylase activity is influenced by the PARylation of TET1 enzyme. Oncotarget 2016; 6:24333-47. [PMID: 26136340 PMCID: PMC4695189 DOI: 10.18632/oncotarget.4476] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/30/2015] [Indexed: 12/15/2022] Open
Abstract
5-hydroxymethylcytosine is a new epigenetic modification deriving from the oxidation of 5-methylcytosine by the TET hydroxylase enzymes. DNA hydroxymethylation drives DNA demethylation events and is involved in the control of gene expression. Deregulation of TET enzymes causes developmental defects and is associated with pathological conditions such as cancer. Little information thus far is available on the regulation of TET activity by post-translational modifications. Here we show that TET1 protein is able to interact with PARP-1/ARTD1 enzyme and is target of both noncovalent and covalent PARylation. In particular, we have demonstrated that the noncovalent binding of ADP-ribose polymers with TET1 catalytic domain decreases TET1 hydroxylase activity while the covalent PARylation stimulates TET1 enzyme. In addition, TET1 activates PARP-1/ARTD1 independently of DNA breaks. Collectively, our results highlight a complex interplay between PARylation and TET1 which may be helpful in coordinating the multiple biological roles played by 5-hydroxymethylcytosine and TET proteins.
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Affiliation(s)
- Fabio Ciccarone
- Department of Cellular Biotechnologies and Hematology, "Sapienza" University of Rome and Pasteur Institute-Fondazione Cenci Bolognetti, Rome, Italy
| | - Elisabetta Valentini
- Department of Cellular Biotechnologies and Hematology, "Sapienza" University of Rome and Pasteur Institute-Fondazione Cenci Bolognetti, Rome, Italy
| | - Michele Zampieri
- Department of Cellular Biotechnologies and Hematology, "Sapienza" University of Rome and Pasteur Institute-Fondazione Cenci Bolognetti, Rome, Italy
| | - Paola Caiafa
- Department of Cellular Biotechnologies and Hematology, "Sapienza" University of Rome and Pasteur Institute-Fondazione Cenci Bolognetti, Rome, Italy
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Ciccarone F, Malavolta M, Calabrese R, Guastafierro T, Bacalini MG, Reale A, Franceschi C, Capri M, Hervonen A, Hurme M, Grubeck‐Loebenstein B, Koller B, Bernhardt J, Schӧn C, Slagboom PE, Toussaint O, Sikora E, Gonos ES, Breusing N, Grune T, Jansen E, Dollé M, Moreno‐Villanueva M, Sindlinger T, Bürkle A, Zampieri M, Caiafa P. Age-dependent expression of DNMT1 and DNMT3B in PBMCs from a large European population enrolled in the MARK-AGE study. Aging Cell 2016; 15:755-65. [PMID: 27169697 PMCID: PMC4933658 DOI: 10.1111/acel.12485] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2016] [Indexed: 01/31/2023] Open
Abstract
Aging is associated with alterations in the content and patterns of DNA methylation virtually throughout the entire human lifespan. Reasons for these variations are not well understood. However, several lines of evidence suggest that the epigenetic instability in aging may be traced back to the alteration of the expression of DNA methyltransferases. Here, the association of the expression of DNA methyltransferases DNMT1 and DNMT3B with age has been analysed in the context of the MARK-AGE study, a large-scale cross-sectional study of the European general population. Using peripheral blood mononuclear cells, we assessed the variation of DNMT1 and DNMT3B gene expression in more than two thousand age-stratified women and men (35-75 years) recruited across eight European countries. Significant age-related changes were detected for both transcripts. The level of DNMT1 gradually dropped with aging but this was only observed up to the age of 64 years. By contrast, the expression of DNMT3B decreased linearly with increasing age and this association was particularly evident in females. We next attempted to trace the age-related changes of both transcripts to the influence of different variables that have an impact on changes of their expression in the population, including demographics, dietary and health habits, and clinical parameters. Our results indicate that age affects the expression of DNMT1 and DNMT3B as an almost independent variable in respect of all other variables evaluated.
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Affiliation(s)
- Fabio Ciccarone
- Faculty of Pharmacy and MedicineDepartment of Cellular Biotechnologies and HematologySapienza University of RomeRome00161Italy
- Pasteur Institute‐Fondazione Cenci BolognettiRome00161Italy
- Present address: Department of BiologyUniversity of Rome ‘Tor Vergata’Via della Ricerca Scientifica 100133RomeItaly
| | - Marco Malavolta
- National Institute of Health and Science on Aging (INRCA)Nutrition and Ageing CentreScientific and Technological Research Area60100AnconaItaly
| | - Roberta Calabrese
- Faculty of Pharmacy and MedicineDepartment of Cellular Biotechnologies and HematologySapienza University of RomeRome00161Italy
- Pasteur Institute‐Fondazione Cenci BolognettiRome00161Italy
| | - Tiziana Guastafierro
- Faculty of Pharmacy and MedicineDepartment of Cellular Biotechnologies and HematologySapienza University of RomeRome00161Italy
- Pasteur Institute‐Fondazione Cenci BolognettiRome00161Italy
| | - Maria Giulia Bacalini
- Department of Experimental, Diagnostic and Specialty MedicineAlma Mater Studiorum‐University of BolognaBologna40126Italy
- CIG‐Interdepartmental Center ‘L. Galvani’Alma Mater StudiorumUniversity of Bologna40126BolognaItaly
| | - Anna Reale
- Faculty of Pharmacy and MedicineDepartment of Cellular Biotechnologies and HematologySapienza University of RomeRome00161Italy
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty MedicineAlma Mater Studiorum‐University of BolognaBologna40126Italy
- CIG‐Interdepartmental Center ‘L. Galvani’Alma Mater StudiorumUniversity of Bologna40126BolognaItaly
| | - Miriam Capri
- Department of Experimental, Diagnostic and Specialty MedicineAlma Mater Studiorum‐University of BolognaBologna40126Italy
- CIG‐Interdepartmental Center ‘L. Galvani’Alma Mater StudiorumUniversity of Bologna40126BolognaItaly
| | - Antti Hervonen
- The School of MedicineThe University of Tampere33014TampereFinland
| | - Mikko Hurme
- The School of MedicineThe University of Tampere33014TampereFinland
| | | | - Bernhard Koller
- Department for Internal MedicineUniversity Teaching Hospital Hall in TirolMilserstr. 106060Hall in TirolAustria
| | | | | | - P. Eline Slagboom
- Department of Molecular EpidemiologyLeiden University Medical CentreLeidenThe Netherlands
| | - Olivier Toussaint
- Research Unit on Cellular BiologyUniversity of NamurRue de Bruxelles, 61NamurB‐5000Belgium
| | - Ewa Sikora
- Laboratory of the Molecular Bases of AgeingNencki Institute of Experimental BiologyPolish Academy of Sciences3 Pasteur Street02‐093WarsawPoland
| | - Efstathios S. Gonos
- National Hellenic Research FoundationInstitute of BiologyMedicinal Chemistry and BiotechnologyAthensGreece
| | - Nicolle Breusing
- Institute of Nutritional Medicine (180c)University of HohenheimFruwirthstraße 1270599StuttgartGermany
| | - Tilman Grune
- German Institute of Human Nutrition Potsdam‐Rehbruecke (DIfE)Arthur‐Scheunert‐Allee 114‐11614558NuthetalGermany
| | - Eugène Jansen
- Centre for Health ProtectionNational Institute for Public Health and the EnvironmentPO Box 13720BA BilthovenThe Netherlands
| | - Martijn Dollé
- Centre for Health ProtectionNational Institute for Public Health and the EnvironmentPO Box 13720BA BilthovenThe Netherlands
| | | | - Thilo Sindlinger
- Molecular Toxicology GroupDepartment of BiologyUniversity of Konstanz78457KonstanzGermany
| | - Alexander Bürkle
- Molecular Toxicology GroupDepartment of BiologyUniversity of Konstanz78457KonstanzGermany
| | - Michele Zampieri
- Faculty of Pharmacy and MedicineDepartment of Cellular Biotechnologies and HematologySapienza University of RomeRome00161Italy
- Pasteur Institute‐Fondazione Cenci BolognettiRome00161Italy
| | - Paola Caiafa
- Faculty of Pharmacy and MedicineDepartment of Cellular Biotechnologies and HematologySapienza University of RomeRome00161Italy
- Pasteur Institute‐Fondazione Cenci BolognettiRome00161Italy
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Hack LM, Dick AL, Provençal N. Epigenetic mechanisms involved in the effects of stress exposure: focus on 5-hydroxymethylcytosine. ENVIRONMENTAL EPIGENETICS 2016; 2:dvw016. [PMID: 29492296 PMCID: PMC5804530 DOI: 10.1093/eep/dvw016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 06/03/2016] [Accepted: 06/11/2016] [Indexed: 05/31/2023]
Abstract
5-hydroxymethylcytosine (5hmC) is a recently re-discovered transient intermediate in the active demethylation pathway that also appears to play an independent role in modulating gene function. Epigenetic marks, particularly 5-methylcytosine, have been widely studied in relation to stress-related disorders given the long-lasting effect that stress has on these marks. 5hmC is a good candidate for involvement in the etiology of these disorders given its elevated concentration in mammalian neurons, its dynamic regulation during development of the central nervous system, and its high variability among individuals. Although we are unaware of any studies published to date examining 5 hmC profiles in human subjects who have developed a psychiatric disorder after a life stressor, there is emerging evidence from the animal literature that 5hmC profiles are altered in the context of fear-conditioning paradigms and stress exposure, suggesting a possible role for 5hmC in the biological underpinnings of stress-related disorders. In this review, the authors examine the available approaches for profiling 5hmC and describe their advantages and disadvantages as well as discuss the studies published thus far investigating 5hmC in the context of fear-related learning and stress exposure in animals. The authors also highlight the global versus locus-specific regulation of 5hmC in these studies. Finally, the limitations of the current studies and their implications are discussed.
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Affiliation(s)
- Laura M. Hack
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University Medical School, Atlanta, GA, USA
| | - Alec L.W. Dick
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Nadine Provençal
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
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Aslani S, Jafari N, Javan MR, Karami J, Ahmadi M, Jafarnejad M. Epigenetic Modifications and Therapy in Multiple Sclerosis. Neuromolecular Med 2016; 19:11-23. [PMID: 27382982 DOI: 10.1007/s12017-016-8422-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 06/30/2016] [Indexed: 01/03/2023]
Abstract
Breakthroughs in genetic studies, like whole human genome sequencing and genome-wide association studies (GWAS), have richened our knowledge of etiopathology of autoimmune diseases (AID) through discovery of genetic patterns. Nonetheless, the precise etiology of autoimmune diseases remains largely unknown. The lack of complete concordance of autoimmune disease in identical twins suggests that non-genetic factors also play a major role in determining disease susceptibility. Although there is no certain definition, epigenetics has been known as heritable alterations in gene function without changes in the nucleotide sequence. DNA methylation, histone modifications, and microRNA-associated gene expression suppression are the central mechanisms for epigenetic regulations. Multiple sclerosis (MS) is a disorder of the central nervous system (CNS), characterized by both inflammatory and neurodegenerative features. Although studies on epigenetic alterations in MS only began in the past decade, a mounting number of surveys suggest that epigenetic changes may be involved in the initiation and development of MS, probably through bridging the effects of environmental risk factors to genetics. Arming with clear understanding of epigenetic dysregulations underpins development of epigenetic therapies. Identifying agents inhibiting the enzymes controlling epigenetic modifications, particularly DNA methyltransferases and histone deacetylases, will be promising therapeutic tool toward MS. In the article underway, it is aimed to go through the recent progresses, attempting to disclose how epigenetics associates with the pathogenesis of MS and how can be used as therapeutic approach.
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Affiliation(s)
- Saeed Aslani
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Naser Jafari
- Markey Cancer Center, University of Kentucky, 741 South Limestone St. Biomedical Biological Research Building (BBSRB), 378D, Lexington, KY, 40506, USA.
| | - Mohammad Reza Javan
- Department of Immunology, Faculty of Medicine, Zabol University of Medical Sciences, Zabol, Iran
| | - Jafar Karami
- Department of Immunology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Majid Ahmadi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mahmoud Jafarnejad
- Department of Pharmacology, School of Medicine, Ardabil University of Medical Science, Ardabil, Iran
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DNA Methylation: a New Player in Multiple Sclerosis. Mol Neurobiol 2016; 54:4049-4059. [PMID: 27314687 DOI: 10.1007/s12035-016-9966-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 06/08/2016] [Indexed: 12/11/2022]
Abstract
Multiple sclerosis (MS) is a neurological and chronic inflammatory disease that is mediated by demyelination and axonal degeneration in the central nervous system (CNS). Studies have shown that immune system components such as CD4+, CD8+, CD44+ T cells, B lymphatic cells, and inflammatory cytokines play a critical role in inflammatory processes and myelin damage associated with MS. Nevertheless, the pathogenesis of MS remains poorly defined. DNA methylation, a significant epigenetic modification, is reported to be extensively involved in MS pathogenesis through the regulation of gene expression. This review focuses on DNA methylation involved in MS pathogenesis. Evidence showed the hypermethylation of human leukocyte antigen-DRB1 (HLA-DRB1) in CD4+ T cells, the genome-wide DNA methylation in CD8+ T cells, the hypermethylation of interleukin-4 (IL-4)/forkhead winged helix transcription factor 3 (Foxp3), and the demethylation of interferon-γ (IFN-γ)/IL-17a in CD44+ encephalitogenic T cells. Studies also showed the hypermethylation of SH2-containing protein tyrosine phosphatase-1 (SHP-1) in peripheral blood mononuclear cells (PBMCs) and methylated changes of genes regulating oligodendrocyte and neuronal function in normal-appearing white matter. Clarifying the mechanism of aberrant methylation on MS may explain part of the pathology and will lead to the development of a new therapeutic target for the treatment of MS in the future.
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Hohos NM, Lee K, Ji L, Yu M, Kandasamy MM, Phillips BG, Baile CA, He C, Schmitz RJ, Meagher RB. DNA cytosine hydroxymethylation levels are distinct among non-overlapping classes of peripheral blood leukocytes. J Immunol Methods 2016; 436:1-15. [PMID: 27164004 PMCID: PMC5131182 DOI: 10.1016/j.jim.2016.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 04/19/2016] [Accepted: 05/02/2016] [Indexed: 12/22/2022]
Abstract
BACKGROUND Peripheral blood leukocytes are the most commonly used surrogates to study epigenome-induced risk and epigenomic response to disease-related stress. We considered the hypothesis that the various classes of peripheral leukocytes differentially regulate the synthesis of 5-methylcytosine (5mCG) and its removal via Ten-Eleven Translocation (TET) dioxygenase catalyzed hydroxymethylation to 5-hydroxymethylcytosine (5hmCG), reflecting their responsiveness to environment. Although it is known that reductions in TET1 and/or TET2 activity lead to the over-proliferation of various leukocyte precursors in bone marrow and in development of chronic myelomonocytic leukemia and myeloproliferative neoplasms, the role of 5mCG hydroxymethylation in peripheral blood is less well studied. RESULTS We developed simplified protocols to rapidly and reiteratively isolate non-overlapping leukocyte populations from a single small sample of fresh or frozen whole blood. Among peripheral leukocyte types we found extreme variation in the levels of transcripts encoding proteins involved in cytosine methylation (DNMT1, 3A, 3B), the turnover of 5mC by demethylation (TET1, 2, 3), and DNA repair (GADD45A, B, G) and in the global and gene-region-specific levels of DNA 5hmCG (CD4+ T cells≫CD14+ monocytes>CD16+ neutrophils>CD19+ B cells>CD56+ NK cells>Siglec8+ eosinophils>CD8+ T cells). CONCLUSIONS Our data taken together suggest a potential hierarchy of responsiveness among classes of leukocytes with CD4+, CD8+ T cells and CD14+ monocytes being the most distinctly poised for a rapid methylome response to physiological stress and disease.
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Affiliation(s)
- Natalie M Hohos
- Department of Foods and Nutrition, University of Georgia, Athens, GA, USA.
| | - Kevin Lee
- Department of Genetics, University of Georgia, Athens, GA, USA.
| | - Lexiang Ji
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA.
| | - Miao Yu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
| | | | - Bradley G Phillips
- Clinical and Administrative Pharmacy, University of Georgia, Athens, GA, USA.
| | - Clifton A Baile
- Department of Foods and Nutrition, University of Georgia, Athens, GA, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
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Zhang F, Gao C, Ma XF, Peng XL, Zhang RX, Kong DX, Simard AR, Hao JW. Expression Profile of Long Noncoding RNAs in Peripheral Blood Mononuclear Cells from Multiple Sclerosis Patients. CNS Neurosci Ther 2016; 22:298-305. [PMID: 26842313 PMCID: PMC5067595 DOI: 10.1111/cns.12498] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 11/25/2015] [Accepted: 11/26/2015] [Indexed: 12/25/2022] Open
Abstract
AIMS Long noncoding RNAs (lncRNAs) play a key role in regulating immunological functions. Their impact on the chronic inflammatory disease multiple sclerosis (MS), however, remains unknown. We investigated the expression of lncRNAs in peripheral blood mononuclear cells (PBMCs) of patients with MS and attempt to explain their possible role in the process of MS. METHODS For this study, we recruited 26 patients with MS according to the revised McDonald criteria. Then, we randomly chose 6 patients for microarray analysis. Microarray assays identified outstanding differences in lncRNA expression, which were verified through real-time PCR. LncRNA functions were annotated for target genes using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, and regulatory relationships between lncRNAs and target genes were analyzed using the "cis" and "trans" model. RESULTS There were 2353 upregulated lncRNAs, 389 downregulated lncRNAs, 1037 upregulated mRNAs, and 279 downregulated mRNAs in patients with MS compared to healthy control subjects (fold change >2.0). Real-time PCR results of six aberrant lncRNAs were consistent with the microarray data. The coexpression network comprised 864 lncRNAs and 628 mRNAs. Among differentially expressed lncRNAs, 10 lncRNAs were predicted to have 10 cis-regulated target genes, and 33 lncRNAs might regulate their trans target genes. CONCLUSIONS We identified a subset of dysregulated lncRNAs and mRNAs. The differentially expressed lncRNAs may be important in the process of MS. However, the specific molecular mechanisms and biological functions of these lncRNAs in the pathogenesis of MS need further study.
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Affiliation(s)
- Fang Zhang
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Chao Gao
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Xiao-Feng Ma
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China
| | - Xiao-Lin Peng
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Rong-Xin Zhang
- Laboratory of Immunology and Inflammation, Department of Immunology and Research Center of Basic Medical Sciences, Tianjin Key Laboratory of Cellular and Molecular Immunology, Tianjin Medical University, Tianjin, China
| | - De-Xin Kong
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Alain R Simard
- Département de Chimie et Biochimie, Université de Moncton, Moncton, NB, Canada
| | - Jun-Wei Hao
- Department of Neurology, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, China
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DNA methylation perspectives in the pathogenesis of autoimmune diseases. Clin Immunol 2016; 164:21-7. [PMID: 26821302 DOI: 10.1016/j.clim.2016.01.011] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 01/23/2016] [Accepted: 01/23/2016] [Indexed: 12/19/2022]
Abstract
DNA methylation is now widely recognized as being critical to maintain the function of immune cells. Recent studies suggest that aberrant DNA methylation levels not only can result in immune cells autoreactivity in vitro, but also are related to autoimmunity in vivo. Environmental factors and genetic polymorphisms cause abnormal methylation, which affects the expression of certain immune-related genes, being becoming hot spot of explaining the mechanism of autoimmune diseases. This paper reviews the importance of abnormal methylation during the development of common autoimmune diseases, such as systemic lupus erythematosus, rheumatoid arthritis, multiple sclerosis and type 1 diabetes, aiming at a better understanding of the pathogenesis of autoimmune diseases and providing new ideas for the treatment of these diseases.
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Expression of DNA methylation genes in secondary progressive multiple sclerosis. J Neuroimmunol 2015; 290:66-9. [PMID: 26711572 DOI: 10.1016/j.jneuroim.2015.11.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 11/13/2015] [Accepted: 11/23/2015] [Indexed: 12/20/2022]
Abstract
Multiple sclerosis (MS) is an immunoinflammatory disease of the central nervous system that seems to be influenced by DNA methylation. We sought to explore the expression pattern of genes involved in the control of DNA methylation in Secondary Progressive (SP) MS patients' PBMCs. We have found that SP MS is characterized by a significant upregulation of two genes belonging to the MBD family genes, MBD2 and MBD4, and by a downregulation of TDG and TET3.
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Epigenetic dynamics in immunity and autoimmunity. Int J Biochem Cell Biol 2015; 67:65-74. [DOI: 10.1016/j.biocel.2015.05.022] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 05/21/2015] [Accepted: 05/22/2015] [Indexed: 02/01/2023]
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TET proteins in cancer: Current 'state of the art'. Crit Rev Oncol Hematol 2015; 96:425-36. [PMID: 26276226 DOI: 10.1016/j.critrevonc.2015.07.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Revised: 05/26/2015] [Accepted: 07/16/2015] [Indexed: 12/31/2022] Open
Abstract
Aberrations in DNA methylation patterns are observed from the early stages of carcinogenesis. However, the mechanisms that drive these changes remain elusive. The recent characterization of ten-eleven translocation (TET) enzymes as a source of newly modified cytosines (5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine) has shed new light on the DNA demethylation process. These cytosines are intermediates of an active DNA demethylation process and are epigenetic markers per se. In this review, we discuss the mechanism and function of TET proteins in biological processes as well as current knowledge regarding their expression and regulation in cancer.
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Intracellular Protein Shuttling: A Mechanism Relevant for Myelin Repair in Multiple Sclerosis? Int J Mol Sci 2015; 16:15057-85. [PMID: 26151843 PMCID: PMC4519887 DOI: 10.3390/ijms160715057] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 06/23/2015] [Accepted: 06/25/2015] [Indexed: 12/15/2022] Open
Abstract
A prominent feature of demyelinating diseases such as multiple sclerosis (MS) is the degeneration and loss of previously established functional myelin sheaths, which results in impaired signal propagation and axonal damage. However, at least in early disease stages, partial replacement of lost oligodendrocytes and thus remyelination occur as a result of resident oligodendroglial precursor cell (OPC) activation. These cells represent a widespread cell population within the adult central nervous system (CNS) that can differentiate into functional myelinating glial cells to restore axonal functions. Nevertheless, the spontaneous remyelination capacity in the adult CNS is inefficient because OPCs often fail to generate new oligodendrocytes due to the lack of stimulatory cues and the presence of inhibitory factors. Recent studies have provided evidence that regulated intracellular protein shuttling is functionally involved in oligodendroglial differentiation and remyelination activities. In this review we shed light on the role of the subcellular localization of differentiation-associated factors within oligodendroglial cells and show that regulation of intracellular localization of regulatory factors represents a crucial process to modulate oligodendroglial maturation and myelin repair in the CNS.
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Epigenetic control of autoimmune diseases: From bench to bedside. Clin Immunol 2015; 157:1-15. [DOI: 10.1016/j.clim.2014.12.013] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 11/17/2014] [Accepted: 12/18/2014] [Indexed: 01/10/2023]
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Zampieri M, Ciccarone F, Calabrese R, Franceschi C, Bürkle A, Caiafa P. Reconfiguration of DNA methylation in aging. Mech Ageing Dev 2015; 151:60-70. [PMID: 25708826 DOI: 10.1016/j.mad.2015.02.002] [Citation(s) in RCA: 182] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 01/20/2015] [Accepted: 02/19/2015] [Indexed: 12/12/2022]
Abstract
A complex interplay between multiple biological effects shapes the aging process. The advent of genome-wide quantitative approaches in the epigenetic field has highlighted the effective impact of epigenetic deregulation, particularly of DNA methylation, on aging. Age-associated alterations in DNA methylation are commonly grouped in the phenomenon known as "epigenetic drift" which is characterized by gradual extensive demethylation of genome and hypermethylation of a number of promoter-associated CpG islands. Surprisingly, specific DNA regions show directional epigenetic changes in aged individuals suggesting the importance of these events for the aging process. However, the epigenetic information obtained until now in aging needs a re-consideration due to the recent discovery of 5-hydroxymethylcytosine, a new DNA epigenetic mark present on genome. A recapitulation of the factors involved in the regulation of DNA methylation and the changes occurring in aging will be described in this review also considering the data available on 5 hmC.
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Affiliation(s)
- Michele Zampieri
- Department of Cellular Biotechnologies and Hematology, "Sapienza" University of Rome, Rome 00161, Italy; Pasteur Institute-Fondazione Cenci Bolognetti, Rome 00161, Italy
| | - Fabio Ciccarone
- Department of Cellular Biotechnologies and Hematology, "Sapienza" University of Rome, Rome 00161, Italy; Pasteur Institute-Fondazione Cenci Bolognetti, Rome 00161, Italy
| | - Roberta Calabrese
- Department of Cellular Biotechnologies and Hematology, "Sapienza" University of Rome, Rome 00161, Italy; Pasteur Institute-Fondazione Cenci Bolognetti, Rome 00161, Italy
| | - Claudio Franceschi
- Department of Experimental Pathology, Alma Mater Studiorum, University of Bologna, Bologna 40126, Italy
| | - Alexander Bürkle
- Molecular Toxicology Group, Department of Biology, University of Konstanz, Konstanz D-78457, Germany
| | - Paola Caiafa
- Department of Cellular Biotechnologies and Hematology, "Sapienza" University of Rome, Rome 00161, Italy; Pasteur Institute-Fondazione Cenci Bolognetti, Rome 00161, Italy.
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Rawłuszko-Wieczorek AA, Siera A, Horbacka K, Horst N, Krokowicz P, Jagodziński PP. Clinical significance of DNA methylation mRNA levels of TET family members in colorectal cancer. J Cancer Res Clin Oncol 2015; 141:1379-92. [PMID: 25557833 PMCID: PMC4469774 DOI: 10.1007/s00432-014-1901-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 12/18/2014] [Indexed: 12/13/2022]
Abstract
Purpose
Ten eleven translocation (TET) enzyme activity is essential for active DNA demethylation in biological processes, and their altered expression has been observed in various malignancies. Therefore, we investigated DNA methylation and mRNA levels of all TETs in colorectal cancer (CRC) patients. Methods TET mRNA levels were evaluated using quantitative RT-PCR in primary cancerous and histopathologically unchanged colorectal tissues from patients who underwent radical surgical colon resection (n = 113). DNA methylation levels of the TET CpG island were assessed using bisulfite DNA sequencing and high-resolution melting analysis. Results We found reduced transcript levels of TET1, TET2 and TET3 in cancerous tissue compared with their histopathologically unchanged counterparts (p = 0.000011; p = 0.000001; p = 0.00031, respectively). Importantly, multivariate Cox regression analysis revealed favorable overall survival (OS) and disease-free survival (DFS) outcomes for patients with high TET2 mRNA levels in histopathologically unchanged tissue (HROS = 0.091, 95 % CI 0.011–0.77, p = 0.028; HRDFS = 0.21, 95 % CI 0.04–1.06, p = 0.059). Moreover, we found no DNA methylation in the TET2 and TET3 promoter regions in cancerous and histopathologically unchanged tissue. In contrast, we reported TET1 DNA hypermethylation in a small fraction of patients (n = 12/113). Conclusion To best of our knowledge, our study is the first to investigate TET mRNA levels in a cohort of CRC patients and correlate them with patients’ prognosis. Present study provides the evidence that TET2 mRNA expression may be an independent prognostic factor for disease recurrence and outcome. Additionally, our findings initially indicate the importance of DNA methylation in regulating TET1 expression. Electronic supplementary material The online version of this article (doi:10.1007/s00432-014-1901-2) contains supplementary material, which is available to authorized users.
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MacDonald IA, Hathaway NA. Epigenetic roots of immunologic disease and new methods for examining chromatin regulatory pathways. Immunol Cell Biol 2014; 93:261-70. [PMID: 25533290 DOI: 10.1038/icb.2014.105] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 10/31/2014] [Indexed: 12/19/2022]
Abstract
The ability to accurately quantitate and experimentally examine epigenetic modifications across the human genome has exploded in the past decade. This has given rise to a wealth of new information concerning the contributions of epigenetic regulatory networks to the pathogenesis of human disease. In particular, immunological disorders have strong developmental roots in chromatin regulatory pathways. In this review, we focus on the epigenetic signatures and new discoveries revealing the epigenetic compositions of specific immunological cancers and autoimmune diseases. We also comment on the conserved epigenetic roots among diverse immunological disorders and suggest inhibition strategies that may be relevant for future treatment. Finally, we highlight emerging experimental tools with the capability to examine the mechanisms of chromatin regulatory enzymes with a high level of temporal control. The knowledge of genetic and epigenetic defects in immunological disease combined with new experimental approaches will elucidate the contribution of individual enzymes in complex epigenetic regulatory networks. This could lead to new diagnostic and therapeutic approaches for some very diverse and difficult to treat human diseases.
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Affiliation(s)
- Ian A MacDonald
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Chapel Hill, NC, USA
| | - Nathaniel A Hathaway
- 1] Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Chapel Hill, NC, USA [2] Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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