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Nie F, Jiang J, Ning J. Exploration of the prognostic value of methylation regulators related to m5C in papillary thyroid carcinoma. Medicine (Baltimore) 2024; 103:e38623. [PMID: 38905403 PMCID: PMC11191899 DOI: 10.1097/md.0000000000038623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/28/2024] [Indexed: 06/23/2024] Open
Abstract
The incidence of papillary thyroid carcinoma (PTC) has increased significantly in recent years, and for patients with metastatic and recurrent PTC, the options for treatment currently available are insufficient. To date, the exact molecular mechanism underlying PTC is still not fully understood. 5-Methylcytosine (m5C) RNA methylation is associated with the prognosis of a variety of tumors. However, the molecular mechanisms and biomarkers associated with m5C in the diagnosis, treatment, and prognosis of this disease have not been fully elucidated. Ten m5C regulators with significantly different expression levels were included in this study. Immune infiltration analysis revealed significant negative correlations between most of these regulators and regulatory T cells. TRDMT1, NSUN5, and NSUN6 had high weights and strong correlations in the protein-protein interaction network. Using gene ontology, Kyoto Encyclopedia of Genes and Genomes, and gene set enrichment analysis, 1489 differentially expressed genes were screened from The Cancer Genome Atlas messenger RNA matrix, indicating that these differentially expressed genes were significantly enriched in various pathways and functions related to cancers. Four m5C regulators, NSUN2, NSUN4, NSUN6, and DNMT3B, were screened as prognostic markers by least absolute shrinkage and selection operator regression analysis, and NSUN2 and NSUN6 were identified as risk factors for poor prognosis. We found that the prognostic prediction model constructed using the m5C regulators NSUN2, NSUN4, NSUN6, and DNMT3B showed good prognostic prediction ability and diagnostic ability. This model was applied to predict the survival probability of patients with PTC, the prediction ability of 5-year survival was the best. The multi-factor prognostic prediction model combined with the tumor node metastasis stage and risk score grouping showed better prognostic predictive power.
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Affiliation(s)
- Furong Nie
- Department of Endocrinology, Shenzhen Longhua District Central Hospital, Shenzhen 518110, Guangdong, China
| | - Jiacheng Jiang
- Department of Hepatology, The First Hospital of Hunan University of Chinese Medicine, Changsha 410007, Hunan, China
| | - Jie Ning
- Department of Endocrinology, Shenzhen Longhua District Central Hospital, Shenzhen 518110, Guangdong, China
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2
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Zhao Y, Xing C, Peng H. ALYREF (Aly/REF export factor): A potential biomarker for predicting cancer occurrence and therapeutic efficacy. Life Sci 2024; 338:122372. [PMID: 38135116 DOI: 10.1016/j.lfs.2023.122372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/09/2023] [Accepted: 12/18/2023] [Indexed: 12/24/2023]
Abstract
5-Methylcytosine (m5C) methylation is present in almost all types of RNA as an essential epigenetic modification. It is dynamically modulated by its associated enzymes, including m5C methyltransferases (NSUN, DNMT and TRDMT family members), demethylases (TET family and ALKBH1) and binding proteins (YTHDF2, ALYREF and YBX1). Among them, aberrant expression of the RNA-binding protein ALYREF can facilitate a variety of malignant phenotypes such as maintenance of proliferation, malignant heterogeneity, metastasis, and drug resistance to cell death through different regulatory mechanisms, including pre-mRNA processing, mRNA stability, and nuclear-cytoplasmic shuttling. The induction of these cellular processes by ALYREF results in treatment resistance and poor outcomes for patients. However, there are currently few reports of clinical applications or drug trials related to ALYREF. In addition, the looming observations on the role of ALYREF in the mechanisms of carcinogenesis and disease prognosis have triggered considerable interest, but critical evidence is not available. For example, animal experiments and ALYREF small molecule inhibitor trials. In this review, we, therefore, revisit the literature on ALYREF and highlight its importance as a prognostic biomarker for early prevention and as a therapeutic target.
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Affiliation(s)
- Yan Zhao
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Cheng Xing
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Hongling Peng
- Department of Hematology, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China; Hunan Key Laboratory of Tumor Models and Individualized Medicine, Changsha, Hunan 410011, China; Hunan Engineering Research Center of Cell Immunotherapy for Hematopoietic Malignancies, Changsha, Hunan 410011, China.
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3
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Mashauri HL. Scurvy: A treatable forgotten fatal differential diagnosis and potential etiology of leukemia and aplastic anemia in pediatric population. Health Sci Rep 2023; 6:e1611. [PMID: 37808934 PMCID: PMC10552072 DOI: 10.1002/hsr2.1611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/10/2023] Open
Abstract
Scurvy is a rare nutritional deficiency disease which is less likely to be suspected and it mostly lead to delayed diagnosis. It can present with features which can mislead clinicians to misdiagnose the condition as leukemia or aplastic anemia. This can subject patients to the wrong management which leads to poor outcome and increased preventable morbidity and mortality. Vitamin C deficiency is still prevalent among pediatric population even in the modern days and should no longer be considered as historical condition. Chromosomal fragility has been greatly accounted for the development of leukemia and aplastic anemia secondary to various triggers. The role of vitamin C toward DNA stability, prevention, and control of mutations have been documented. Vitamin C plays a vital role in hematopoiesis by controlling regulation and prevent dysfunction of hematopoietic stem cells. Scurvy deficiency has been a silent growing clinical problem which needs a high index of suspicion for a clinician to pick it. It should be considered as one among potential differential diagnosis of leukemia and aplastic anemia especially in the pediatric population. History of any dietary restriction should be obtained and addressed properly. Serum vitamin C should be among the essential laboratory workout in diagnosis of both leukemia and aplastic anemia. All patients suspected to have such conditions should be screened and supplemented for vitamin C deficiency irrespective of positive confirmatory test results of leukemia or aplastic anemia since the probability of co-occurrence is likely also. Moreover, studies should be conducted to explore the clinical link, if any, between vitamin C deficiency or insufficiency and development of leukemia and aplastic anemia among the pediatric population given its physiological and genomic role in hematopoiesis. Furthermore, the potential pharmacological therapeutic use of vitamin C in treatment of leukemia and aplastic anemia should be determined clinically.
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Affiliation(s)
- Harold L Mashauri
- Department of Pediatrics and Child Health Kilimanjaro Christian Medical University College Moshi Tanzania
- Department of Internal Medicine Kilimanjaro Christian Medical University College Moshi Tanzania
- Department of Epidemiology and Biostatistics Kilimanjaro Christian Medical University College Moshi Tanzania
- Department of Physiology Kilimanjaro Christian Medical University College Moshi Tanzania
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4
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Desaulniers D, Vasseur P, Jacobs A, Aguila MC, Ertych N, Jacobs MN. Integration of Epigenetic Mechanisms into Non-Genotoxic Carcinogenicity Hazard Assessment: Focus on DNA Methylation and Histone Modifications. Int J Mol Sci 2021; 22:10969. [PMID: 34681626 PMCID: PMC8535778 DOI: 10.3390/ijms222010969] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 12/15/2022] Open
Abstract
Epigenetics involves a series of mechanisms that entail histone and DNA covalent modifications and non-coding RNAs, and that collectively contribute to programing cell functions and differentiation. Epigenetic anomalies and DNA mutations are co-drivers of cellular dysfunctions, including carcinogenesis. Alterations of the epigenetic system occur in cancers whether the initial carcinogenic events are from genotoxic (GTxC) or non-genotoxic (NGTxC) carcinogens. NGTxC are not inherently DNA reactive, they do not have a unifying mode of action and as yet there are no regulatory test guidelines addressing mechanisms of NGTxC. To fil this gap, the Test Guideline Programme of the Organisation for Economic Cooperation and Development is developing a framework for an integrated approach for the testing and assessment (IATA) of NGTxC and is considering assays that address key events of cancer hallmarks. Here, with the intent of better understanding the applicability of epigenetic assays in chemical carcinogenicity assessment, we focus on DNA methylation and histone modifications and review: (1) epigenetic mechanisms contributing to carcinogenesis, (2) epigenetic mechanisms altered following exposure to arsenic, nickel, or phenobarbital in order to identify common carcinogen-specific mechanisms, (3) characteristics of a series of epigenetic assay types, and (4) epigenetic assay validation needs in the context of chemical hazard assessment. As a key component of numerous NGTxC mechanisms of action, epigenetic assays included in IATA assay combinations can contribute to improved chemical carcinogen identification for the better protection of public health.
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Affiliation(s)
- Daniel Desaulniers
- Environmental Health Sciences and Research Bureau, Hazard Identification Division, Health Canada, AL:2203B, Ottawa, ON K1A 0K9, Canada
| | - Paule Vasseur
- CNRS, LIEC, Université de Lorraine, 57070 Metz, France;
| | - Abigail Jacobs
- Independent at the Time of Publication, Previously US Food and Drug Administration, Rockville, MD 20852, USA;
| | - M. Cecilia Aguila
- Toxicology Team, Division of Human Food Safety, Center for Veterinary Medicine, US Food and Drug Administration, Department of Health and Human Services, Rockville, MD 20852, USA;
| | - Norman Ertych
- German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277 Berlin, Germany;
| | - Miriam N. Jacobs
- Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton OX11 0RQ, UK;
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5
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Functional Interplay between Methyltransferases and Inflammasomes in Inflammatory Responses and Diseases. Int J Mol Sci 2021; 22:ijms22147580. [PMID: 34299198 PMCID: PMC8306412 DOI: 10.3390/ijms22147580] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/07/2021] [Accepted: 07/13/2021] [Indexed: 02/08/2023] Open
Abstract
An inflammasome is an intracellular protein complex that is activated in response to a pathogenic infection and cellular damage. It triggers inflammatory responses by promoting inflammatory cell death (called pyroptosis) and the secretion of pro-inflammatory cytokines, interleukin (IL)-1β and IL-18. Many types of inflammasomes have been identified and demonstrated to play a central role in inducing inflammatory responses, leading to the onset and progression of numerous inflammatory diseases. Methylation is a biological process by which methyl groups are transferred from methyl donors to proteins, nucleic acids, and other cellular molecules. Methylation plays critical roles in various biological functions by modulating gene expression, protein activity, protein localization, and molecular stability, and aberrant regulation of methylation causes deleterious outcomes in various human diseases. Methylation is a key determinant of inflammatory responses and diseases. This review highlights the current understanding of the functional relationship between inflammasome regulation and methylation of cellular molecules in inflammatory responses and diseases.
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6
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Fathi E, Farahzadi R, Montazersaheb S, Bagheri Y. Epigenetic Modifications in Acute Lymphoblastic Leukemia: From Cellular Mechanisms to Therapeutics. Curr Gene Ther 2021; 21:60-71. [PMID: 33183201 DOI: 10.2174/1566523220999201111194554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 10/23/2020] [Accepted: 11/02/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Epigenetic modification pattern is considered as a characteristic feature in blood malignancies. Modifications in the DNA methylation modulators are recurrent in lymphoma and leukemia, so that the distinct methylation pattern defines different types of leukemia. Generally, the role of epigenetics is less understood, and most investigations are focused on genetic abnormalities and cytogenic studies to develop novel treatments for patients with hematologic disorders. Recently, understanding the underlying mechanism of acute lymphoblastic leukemia (ALL), especially epigenetic alterations as a driving force in the development of ALL opens a new era of investigation for developing promising strategy, beyond available conventional therapy. OBJECTIVE This review will focus on a better understanding of the epigenetic mechanisms in cancer development and progression, with an emphasis on epigenetic alterations in ALL including, DNA methylation, histone modification, and microRNA alterations. Other topics that will be discussed include the use of epigenetic alterations as a promising therapeutic target in order to develop novel, well-suited approaches against ALL. CONCLUSION According to the literature review, leukemogenesis of ALL is extensively influenced by epigenetic modifications, particularly DNA hyper-methylation, histone modification, and miRNA alteration.
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Affiliation(s)
- Ezzatollah Fathi
- Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Tabriz, Tabriz, Iran
| | - Raheleh Farahzadi
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Soheila Montazersaheb
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yasin Bagheri
- Young Researchers and Elite Club, Tabriz Branch, Islamic Azad University, Tabriz, Iran
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7
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Iwanami N, Takeshita K, Lawir DF, Suetake I, Tajima S, Sikora K, Trancoso I, ÓMeara C, Siamishi I, Takahama Y, Furutani-Seiki M, Kondoh H, Yonezawa Y, Schorpp M, Boehm T. Epigenetic Protection of Vertebrate Lymphoid Progenitor Cells by Dnmt1. iScience 2020; 23:101260. [PMID: 32585597 PMCID: PMC7322073 DOI: 10.1016/j.isci.2020.101260] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/28/2020] [Accepted: 06/08/2020] [Indexed: 11/27/2022] Open
Abstract
DNA methylation is a universal epigenetic mechanism involved in regulation of gene expression and genome stability. The DNA maintenance methylase DNMT1 ensures that DNA methylation patterns are faithfully transmitted to daughter cells during cell division. Because loss of DNMT1 is lethal, a pan-organismic analysis of DNMT1 function is lacking. We identified new recessive dnmt1 alleles in medaka and zebrafish and, guided by the structures of mutant proteins, generated a recessive variant of mouse Dnmt1. Each of the three missense mutations studied here distorts the catalytic pocket and reduces enzymatic activity. Because all three DNMT1 mutant animals are viable, it was possible to examine their phenotypes throughout life. The consequences of genome-wide hypomethylation of DNA of somatic tissues in the Dnmt1 mutants are surprisingly mild but consistently affect the development of the lymphoid lineage. Our findings indicate that developing lymphocytes in vertebrates are sensitive to perturbations of DNA maintenance methylation. Genetic screens identified recessive viable missense alleles of dnmt1 in teleosts A viable mouse Dnmt1 mutant generated by structure-guided precision mutagenesis Missense mutations distort the catalytic pocket and reduce enzymatic activity DNA hypomethylation consistently affects development of the lymphoid lineage
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Affiliation(s)
- Norimasa Iwanami
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany.
| | | | - Divine-Fondzenyuy Lawir
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Isao Suetake
- Laboratory of Epigenetics, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
| | - Shoji Tajima
- Laboratory of Epigenetics, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita-shi, Osaka 565-0871, Japan
| | - Katarzyna Sikora
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Inês Trancoso
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Connor ÓMeara
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Iliana Siamishi
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Yousuke Takahama
- Thymus Biology Section, Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Division of Experimental Immunology, Institute of Advanced Medical Sciences, University of Tokushima, 3-18-15 Kuramoto, Tokushima 770-8503, Japan
| | - Makoto Furutani-Seiki
- Systems Biochemistry in Pathology and Regeneration, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi 755-8505, Japan
| | - Hisato Kondoh
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-ku, Kyoto 603-8555, Japan
| | - Yasushige Yonezawa
- High Pressure Protein Research Center, Institute of Advanced Technology, Kindai University, 930 Nishimitani, Kinokawa, Wakayama 649-6493, Japan
| | - Michael Schorpp
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany
| | - Thomas Boehm
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108 Freiburg, Germany.
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8
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Crosstalk between DNA methylation and gene expression in colorectal cancer, a potential plasma biomarker for tracing this tumor. Sci Rep 2020; 10:2813. [PMID: 32071364 PMCID: PMC7028731 DOI: 10.1038/s41598-020-59690-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 02/03/2020] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC), the second leading cause of cancer mortality, constitutes a significant global health burden. An accurate, noninvasive detection method for CRC as complement to colonoscopy could improve the effectiveness of treatment. In the present study, SureSelectXT Methyl-Seq was performed on cancerous and normal colon tissues and CLDN1, INHBA and SLC30A10 were found as candidate methylated genes. MethyLight assay was run on formalin-fixed paraffin-embedded (FFPE) and fresh case and control tissues to validate the methylation of the selected gene. The methylation was significantly different (p-values < 2.2e-16) with a sensitivity of 87.17%; at a specificity cut-off of 100% in FFPE tissues. Methylation studies on fresh tissues, indicated a sensitivity of 82.14% and a specificity cut-off of 92% (p-values = 1.163e-07). The biomarker performance was robust since, normal tissues indicated a significant 22.1-fold over-expression of the selected gene as compared to the corresponding CRC tissues (p-value < 2.2e-16) in the FFPE expression assay. In our plasma pilot study, evaluation of the tissue methylation marker in the circulating cell-free DNA, demonstrated that 9 out of 22 CRC samples and 20 out of 20 normal samples were identified correctly. In summary, there is a clinical feasibility that the offered methylated gene could serve as a candidate biomarker for CRC diagnostic purpose, although further exploration of our candidate gene is warranted.
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Age-Associated TET2 Mutations: Common Drivers of Myeloid Dysfunction, Cancer and Cardiovascular Disease. Int J Mol Sci 2020; 21:ijms21020626. [PMID: 31963585 PMCID: PMC7014315 DOI: 10.3390/ijms21020626] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/10/2020] [Accepted: 01/13/2020] [Indexed: 02/06/2023] Open
Abstract
Acquired, inactivating mutations in Tet methylcytosine dioxygenase 2 (TET2) are detected in peripheral blood cells of a remarkable 5%–10% of adults greater than 65 years of age. They impart a hematopoietic stem cell advantage and resultant clonal hematopoiesis of indeterminate potential (CHIP) with skewed myelomonocytic differentiation. CHIP is associated with an overall increased risk of transformation to a hematological malignancy, especially myeloproliferative and myelodysplastic neoplasms (MPN, MDS) and acute myeloid leukemia (AML), of approximately 0.5% to 1% per year. However, it is becoming increasingly possible to identify individuals at greatest risk, based on CHIP mutational characteristics. CHIP, and particularly TET2-mutant CHIP, is also a novel, significant risk factor for cardiovascular diseases, related in part to hyper-inflammatory, progeny macrophages carrying TET2 mutations. Therefore, somatic TET2 mutations contribute to myeloid expansion and innate immune dysregulation with age and contribute to prevalent diseases in the developed world—cancer and cardiovascular disease. Herein, we describe the impact of detecting TET2 mutations in the clinical setting. We also present the rationale and promise for targeting TET2-mutant and other CHIP clones, and their inflammatory environment, as potential means of lessening risk of myeloid cancer development and dampening CHIP-comorbid inflammatory diseases.
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10
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Wang F, Zhang J, Qi J. Ten-eleven translocation-2 affects the fate of cells and has therapeutic potential in digestive tumors. Chronic Dis Transl Med 2020; 5:267-272. [PMID: 32055786 PMCID: PMC7004935 DOI: 10.1016/j.cdtm.2019.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Indexed: 02/07/2023] Open
Abstract
Ten-eleven translocation (TET) methylcytosine dioxygenases catalyze the oxidative reactions of 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-fC), and 5-carboxylcytosine (5-caC), which are intermediate steps during DNA demethylation. It is reported that somatic mutations of TET2 gene are identified in a variety of human tumors, especially in hematological malignancies. The tendency and mechanism of cellular differentiation in different systems are affected by TET2 via regulation of associated gene expression or maintenance of demethylated state. TET2 acts as a critical driver of tumorigenesis through the conversion of 5-mC to 5-hmC and successive oxidation products. Sometimes, it requires special interactions and cofactors. Here, we reviewed recent advances in understanding the function of TET2 proteins in regulating cell differentiation, and its role in various tumors focusing on several digestive cancers.
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Affiliation(s)
- Feng Wang
- Department of Gastroenterology, Zhongnan Hospital, Wuhan University, Wuhan, Hubei 430071, China
| | - Jing Zhang
- Department of Gastroenterology, Zhongnan Hospital, Wuhan University, Wuhan, Hubei 430071, China
| | - Jian Qi
- Department of Gastroenterology, Zhongnan Hospital, Wuhan University, Wuhan, Hubei 430071, China
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11
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Potential role of TET2 in gastric cancer cisplatin resistance. Pathol Res Pract 2019; 215:152637. [DOI: 10.1016/j.prp.2019.152637] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/26/2019] [Accepted: 09/15/2019] [Indexed: 01/27/2023]
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12
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Jeltsch A, Broche J, Bashtrykov P. Molecular Processes Connecting DNA Methylation Patterns with DNA Methyltransferases and Histone Modifications in Mammalian Genomes. Genes (Basel) 2018; 9:genes9110566. [PMID: 30469440 PMCID: PMC6266221 DOI: 10.3390/genes9110566] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 11/13/2018] [Accepted: 11/16/2018] [Indexed: 12/20/2022] Open
Abstract
DNA methylation is an essential part of the epigenome chromatin modification network, which also comprises several covalent histone protein post-translational modifications. All these modifications are highly interconnected, because the writers and erasers of one mark, DNA methyltransferases (DNMTs) and ten eleven translocation enzymes (TETs) in the case of DNA methylation, are directly or indirectly targeted and regulated by other marks. Here, we have collected information about the genomic distribution and variability of DNA methylation in human and mouse DNA in different genomic elements. After summarizing the impact of DNA methylation on genome evolution including CpG depletion, we describe the connection of DNA methylation with several important histone post-translational modifications, including methylation of H3K4, H3K9, H3K27, and H3K36, but also with nucleosome remodeling. Moreover, we present the mechanistic features of mammalian DNA methyltransferases and their associated factors that mediate the crosstalk between DNA methylation and chromatin modifications. Finally, we describe recent advances regarding the methylation of non-CpG sites, methylation of adenine residues in human cells and methylation of mitochondrial DNA. At several places, we highlight controversial findings or open questions demanding future experimental work.
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Affiliation(s)
- Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany.
| | - Julian Broche
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany.
| | - Pavel Bashtrykov
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany.
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13
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Gowher H, Jeltsch A. Mammalian DNA methyltransferases: new discoveries and open questions. Biochem Soc Trans 2018; 46:1191-1202. [PMID: 30154093 PMCID: PMC6581191 DOI: 10.1042/bst20170574] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/12/2018] [Accepted: 07/13/2018] [Indexed: 11/17/2022]
Abstract
As part of the epigenetic network, DNA methylation is a major regulator of chromatin structure and function. In mammals, it mainly occurs at palindromic CpG sites, but asymmetric methylation at non-CpG sites is also observed. Three enzymes are involved in the generation and maintenance of DNA methylation patterns. DNMT1 has high preference for hemimethylated CpG sites, and DNMT3A and DNMT3B equally methylate unmethylated and hemimethylated DNA, and also introduce non-CpG methylation. Here, we review recent observations and novel insights into the structure and function of mammalian DNMTs (DNA methyltransferases), including new structures of DNMT1 and DNMT3A, data on their mechanism, regulation by post-translational modifications and on the function of DNMTs in cells. In addition, we present news findings regarding the allosteric regulation and targeting of DNMTs by chromatin modifications and chromatin proteins. In combination, the recent publications summarized here impressively illustrate the intensity of ongoing research in this field. They provide a deeper understanding of key mechanistic properties of DNMTs, but they also document still unsolved issues, which need to be addressed in future research.
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Affiliation(s)
- Humaira Gowher
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, U.S.A
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Stuttgart, Germany
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14
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Norvil AB, Petell CJ, Alabdi L, Wu L, Rossie S, Gowher H. Dnmt3b Methylates DNA by a Noncooperative Mechanism, and Its Activity Is Unaffected by Manipulations at the Predicted Dimer Interface. Biochemistry 2018; 57:4312-4324. [PMID: 27768276 PMCID: PMC5992102 DOI: 10.1021/acs.biochem.6b00964] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The catalytic domains of the de novo DNA methyltransferases Dnmt3a-C and Dnmt3b-C are highly homologous. However, their unique biochemical properties could potentially contribute to differences in the substrate preferences or biological functions of these enzymes. Dnmt3a-C forms tetramers through interactions at the dimer interface, which also promote multimerization on DNA and cooperativity. Similar to the case for processive enzymes, cooperativity allows Dnmt3a-C to methylate multiple sites on the same DNA molecule; however, it is unclear whether Dnmt3b-C methylates DNA by a cooperative or processive mechanism. The importance of the tetramer structure and cooperative mechanism is emphasized by the observation that the R882H mutation in the dimer interface of DNMT3A is highly prevalent in acute myeloid leukemia and leads to a substantial loss of its activity. Under conditions that distinguish between cooperativity and processivity, we show that in contrast to that of Dnmt3a-C, the activity of Dnmt3b-C is not cooperative and confirm the processivity of Dnmt3b-C and the full length Dnmt3b enzyme. Whereas the R878H mutation (mouse homologue of R882H) led to the loss of cooperativity of Dnmt3a-C, the activity and processivity of the analogous Dnmt3b-C R829H variant were comparable to those of the wild-type enzyme. Additionally, buffer acidification that attenuates the dimer interface interactions of Dnmt3a-C had no effect on Dnmt3b-C activity. Taken together, these results demonstrate an important mechanistic difference between Dnmt3b and Dnmt3a and suggest that interactions at the dimer interface may play a limited role in regulating Dnmt3b-C activity. These new insights have potential implications for the distinct biological roles of Dnmt3a and Dnmt3b.
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Affiliation(s)
- Allison B. Norvil
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Christopher J. Petell
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Lama Alabdi
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Lanchen Wu
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Sandra Rossie
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Humaira Gowher
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
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Li W, Huang Y, Sargsyan D, Khor TO, Guo Y, Shu L, Yang AY, Zhang C, Paredes-Gonzalez X, Verzi M, Hart RP, Kong AN. Epigenetic alterations in TRAMP mice: epigenome DNA methylation profiling using MeDIP-seq. Cell Biosci 2018; 8:3. [PMID: 29344347 PMCID: PMC5767006 DOI: 10.1186/s13578-018-0201-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 01/05/2018] [Indexed: 01/15/2023] Open
Abstract
Purpose We investigated the genomic DNA methylation profile of prostate cancer in transgenic adenocarcinoma of the mouse prostate (TRAMP) cancer model and to analyze the crosstalk among targeted genes and the related functional pathways. Methods Prostate DNA samples from 24-week-old TRAMP and C57BL/6 male mice were isolated. The DNA methylation profiles were analyzed by methylated DNA immunoprecipitation (MeDIP) followed by next-generation sequencing (MeDIP-seq). Canonical pathways, diseases and function and network analyses of the different samples were then performed using the Ingenuity® Pathway Analysis (IPA) software. Some target genes with significant difference in methylation were selected for validation using methylation specific primers (MSP) and qPCR. Results TRAMP mice undergo extensive aberrant CpG hyper- and hypo-methylation. There were 2147 genes with a significant (log2-change ≥ 2) change in CpG methylation between the two groups, as mapped by the IPA software. Among these genes, the methylation of 1105 and 1042 genes was significantly decreased and increased, respectively, in TRAMP prostate tumors. The top associated disease identified by IPA was adenocarcinoma; however, the cAMP response element-binding protein (CREB)-, histone deacetylase 2 (HDAC2)-, glutathione S-transferase pi (GSTP1)- and polyubiquitin-C (UBC)-related pathways showed significantly altered methylation profiles based on the canonical pathway and network analyses. MSP and qPCR results of genes of interests corroborated with MeDIP-seq findings. Conclusions This is the first MeDIP-seq with IPA analysis of the TRAMP model to provide novel insight into the genome-wide methylation profile of prostate cancer. Studies on epigenetics, such as DNA methylation, will potentially provide novel avenues and strategies for further development of biomarkers targeted for treatment and prevention approaches for prostate cancer.
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Affiliation(s)
- Wenji Li
- 1Center for Phytochemical Epigenome Studies, Ernest Mario School of Pharmacy, The State University of New Jersey, Piscataway, NJ 08854 USA.,2Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ 08854 USA
| | - Ying Huang
- 1Center for Phytochemical Epigenome Studies, Ernest Mario School of Pharmacy, The State University of New Jersey, Piscataway, NJ 08854 USA.,2Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ 08854 USA.,3Graduate Program in Pharmaceutical Sciences, Ernest Mario School of Pharmacy, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Davit Sargsyan
- 1Center for Phytochemical Epigenome Studies, Ernest Mario School of Pharmacy, The State University of New Jersey, Piscataway, NJ 08854 USA.,2Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ 08854 USA.,3Graduate Program in Pharmaceutical Sciences, Ernest Mario School of Pharmacy, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Tin Oo Khor
- 1Center for Phytochemical Epigenome Studies, Ernest Mario School of Pharmacy, The State University of New Jersey, Piscataway, NJ 08854 USA.,2Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ 08854 USA
| | - Yue Guo
- 1Center for Phytochemical Epigenome Studies, Ernest Mario School of Pharmacy, The State University of New Jersey, Piscataway, NJ 08854 USA.,2Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ 08854 USA.,3Graduate Program in Pharmaceutical Sciences, Ernest Mario School of Pharmacy, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Limin Shu
- 1Center for Phytochemical Epigenome Studies, Ernest Mario School of Pharmacy, The State University of New Jersey, Piscataway, NJ 08854 USA.,2Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ 08854 USA
| | - Anne Yuqing Yang
- 1Center for Phytochemical Epigenome Studies, Ernest Mario School of Pharmacy, The State University of New Jersey, Piscataway, NJ 08854 USA.,2Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ 08854 USA.,3Graduate Program in Pharmaceutical Sciences, Ernest Mario School of Pharmacy, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Chengyue Zhang
- 1Center for Phytochemical Epigenome Studies, Ernest Mario School of Pharmacy, The State University of New Jersey, Piscataway, NJ 08854 USA.,2Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ 08854 USA.,3Graduate Program in Pharmaceutical Sciences, Ernest Mario School of Pharmacy, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Ximena Paredes-Gonzalez
- 1Center for Phytochemical Epigenome Studies, Ernest Mario School of Pharmacy, The State University of New Jersey, Piscataway, NJ 08854 USA.,2Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ 08854 USA.,3Graduate Program in Pharmaceutical Sciences, Ernest Mario School of Pharmacy, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Michael Verzi
- 4Department of Genetics, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Ronald P Hart
- 5Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Ah-Ng Kong
- 1Center for Phytochemical Epigenome Studies, Ernest Mario School of Pharmacy, The State University of New Jersey, Piscataway, NJ 08854 USA.,2Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ 08854 USA
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Yassi M, Shams Davodly E, Mojtabanezhad Shariatpanahi A, Heidari M, Dayyani M, Heravi-Moussavi A, Moattar MH, Kerachian MA. DMRFusion: A differentially methylated region detection tool based on the ranked fusion method. Genomics 2018; 110:366-374. [PMID: 29309841 DOI: 10.1016/j.ygeno.2017.12.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 11/05/2017] [Accepted: 12/11/2017] [Indexed: 12/11/2022]
Abstract
DNA methylation is an important epigenetic modification involved in many biological processes and diseases. Computational analysis of differentially methylated regions (DMRs) could explore the underlying reasons of methylation. DMRFusion is presented as a useful tool for comprehensive DNA methylation analysis of DMRs on methylation sequencing data. This tool is designed base on the integration of several ranking methods; Information gain, Between versus within Class scatter ratio, Fisher ratio, Z-score and Welch's t-test. In this study, DMRFusion on reduced representation bisulfite sequencing (RRBS) data in chronic lymphocytic leukemia cancer displayed 30 nominated regions and CpG sites with a maximum methylation difference detected in the hypermethylation DMRs. We realized that DMRFusion is able to process methylation sequencing data in an efficient and accurate manner and to provide annotation and visualization for DMRs with high fold difference score (p-value and FDR<0.05 and type I error: 0.04).
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Affiliation(s)
- Maryam Yassi
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran
| | - Ehsan Shams Davodly
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran
| | | | - Mehdi Heidari
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran
| | - Mahdieh Dayyani
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran
| | - Alireza Heravi-Moussavi
- Canada's Michael Smith Genome Sciences Center, BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | - Mohammad Amin Kerachian
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran; Cancer Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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Rahmani M, Talebi M, Hagh MF, Feizi AAH, Solali S. Aberrant DNA methylation of key genes and Acute Lymphoblastic Leukemia. Biomed Pharmacother 2017; 97:1493-1500. [PMID: 29793312 DOI: 10.1016/j.biopha.2017.11.033] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2017] [Revised: 10/27/2017] [Accepted: 11/03/2017] [Indexed: 02/06/2023] Open
Abstract
DNA methylation is a dynamic process influencing gene expression by altering either coding or non-coding loci. Despite advances in treatment of Acute Lymphoblastic Leukemia (ALL); relapse occurs in approximately 20% of patients. Nowadays, epigenetic factors are considered as one of the most effective mechanisms in pathogenesis of malignancies. These factors are reversible elements which can be potentially regarded as therapy targets and disease prognosis. DNA methylation, which primarily serves as transcriptional suppressor, mostly occurs in CpG islands of the gene promoter regions. This was shown as a key epigenetic factor in inactivating various tumor suppressor genes during cancer initiation and progression. We aimed to review methylation status of key genes involved in hematopoietic malignancies such as IKZF1, CDKN2B, TET2, CYP1B1, SALL4, DLC1, DLX family, TP73, PTPN6, and CDKN1C; and their significance in pathogenesis of ALL. The DNA methylation alterations in promoter regions of the genes have been shown to play crucial roles in tumorigenesis. Methylation -based inactivation of these genes has also been reported as associated with prognosis in acute leukemia. In this review, we also addressed the association of gene expression and methylation pattern in ALL patients.
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Affiliation(s)
- Mina Rahmani
- Department of Immunology, Division of Hematology and Transfusion Medicine, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Stem cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehdi Talebi
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Majid Farshdousti Hagh
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Saeed Solali
- Department of Immunology, Division of Hematology and Transfusion Medicine, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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Abstract
Metabolic cues and (epi-)genetic factors are emerging regulators of hematopoietic stem cell (HSC) potency. Two new studies in Nature and Cell, from Agathocleous et al. (2017) and Cimmino et al. (2017), respectively, show that vitamin C regulates HSC function and suppresses leukemogenesis by modulating Tet2 activity.
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Abstract
PURPOSE OF REVIEW Hematopoietic stem cells (HSCs) possess two fundamental characteristics, the capacity for self-renewal and the sustained production of all blood cell lineages. The fine balance between HSC expansion and lineage specification is dynamically regulated by the interplay between external and internal stimuli. This review introduces recent advances in the roles played by the stem cell niche, regulatory transcriptional networks, and metabolic pathways in governing HSC self-renewal, commitment, and lineage differentiation. We will further focus on discoveries made by studying hematopoiesis at single-cell resolution. RECENT FINDINGS HSCs require the support of an interactive milieu with their physical position within the perivascular niche dynamically regulating HSC behavior. In these microenvironments, transcription factor networks and nutrient-mediated regulation of energy resources, signaling pathways, and epigenetic status govern HSC quiescence and differentiation. Once HSCs begin their lineage specification, single-cell analyses show that they do not become oligopotent but rather, differentiate directly into committed unipotent progenitors. SUMMARY The diversity of transcriptional networks and metabolic pathways in HSCs and their downstream progeny allows a high level of plasticity in blood differentiation. The intricate interactions between these pathways, within the perivascular niche, broaden the specification of HSCs in pathological and stressed conditions.
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20
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Bartosch C, Lopes JM, Jerónimo C. Epigenetics in endometrial carcinogenesis - part 1: DNA methylation. Epigenomics 2017; 9:737-755. [PMID: 28470096 DOI: 10.2217/epi-2016-0166] [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] [Indexed: 12/18/2022] Open
Abstract
Carcinogenesis is a multistep multifactorial process that involves the accumulation of genetic and epigenetic alterations. In the past two decades, there has been an exponential growth of knowledge establishing the importance of epigenetic changes in cancer. Our work focused on reviewing the main role of epigenetics in the pathogenesis of endometrial carcinoma, highlighting the reported results concerning each epigenetic mechanistic layer. The present review is the first part of this work, in which we examined the contribution of DNA methylation alterations for endometrial carcinogenesis.
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Affiliation(s)
- Carla Bartosch
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO-Porto), Porto, Portugal.,Cancer Biology & Epigenetics Group, Research Center (CI-IPOP), Portuguese Oncology Institute of Porto, Porto, Portugal.,Department of Pathology & Oncology, Medical Faculty, University of Porto, Porto, Portugal.,Porto Comprehensive Cancer Center (P.ccc), Porto, Portugal
| | - José Manuel Lopes
- Department of Pathology & Oncology, Medical Faculty, University of Porto, Porto, Portugal.,Department of Pathology, Centro Hospitalar São João (CHSJ), Porto, Portugal.,IPATIMUP - Institute of Molecular Pathology & Immunology, University of Porto, Porto, Portugal.,I3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology & Epigenetics Group, Research Center (CI-IPOP), Portuguese Oncology Institute of Porto, Porto, Portugal.,Porto Comprehensive Cancer Center (P.ccc), Porto, Portugal.,Department of Pathology & Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
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Nawrocki MJ, Majewski D, Puszczewicz M, Jagodziński PP. Decreased mRNA expression levels of DNA methyltransferases type 1 and 3A in systemic lupus erythematosus. Rheumatol Int 2017; 37:775-783. [PMID: 28349196 PMCID: PMC5397457 DOI: 10.1007/s00296-017-3711-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 03/20/2017] [Indexed: 11/30/2022]
Abstract
OBJECTIVES Systemic lupus erythematosus (SLE) is a chronic relapsing autoimmune disease characterized by the presence of autoantibodies directed against nuclear antigens and by chronic inflammation. Although the etiology of SLE remains unclear, the influence of environment factors, which is largely reflected by the epigenetic mechanisms, with DNA methylation changes in particular, is generally considered as main players in the pathogenesis of SLE. We studied DNA methyltransferases' (DNMTs) type 1, 3A and 3B transcript levels in peripheral blood mononuclear cells from patients diagnosed with systemic lupus erythematosus and from the healthy control subjects. Furthermore, the association of DNMT1, DNMT3A, and DNMT3B mRNA levels with gender, age, and major clinical manifestations was analyzed. METHODS Peripheral blood mononuclear cells (PBMCs) were isolated from 32 SLE patients and 40 healthy controls. Reverse transcription and real-time quantitative polymerase chain reaction (RT-qPCR) analyses were used to determine DNMT1, DNMT3A, and DNMT3B mRNA expression levels. RESULTS Significantly lower DNMT1 (p = 0.015543) and DNMT3A (p = 0.003652) transcript levels in SLE patients were observed compared with healthy controls. Nevertheless, the DNMT3B mRNA expression levels were markedly lower compared with DNMT1 and DNMT3A, both in PBMCs from affected patients and those from control subjects. Furthermore, the DNMT1 transcript levels were positively correlated with SLE disease activity index (SLEDAI) (r s = 0.4087, p = 0.020224), while the DNMT3A transcript levels were negatively correlated with patients age (r s = -0.3765, p = 0.03369). CONCLUSIONS Our analyses confirmed the importance of epigenetic alterations in SLE etiology. Moreover, our results suggest that the presence of some clinical manifestations, such as phototosensitivity and arthritis, might be associated with the dysregulation of DNA methyltransferases' mRNA expression levels.
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Affiliation(s)
- Mariusz J Nawrocki
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences, 6 Święcickiego St., 60-781, Poznań, Poland.
| | - Dominik Majewski
- Department of Rheumatology and Internal Diseases, Poznań University of Medical Science, 135/147 28 Czerwca 1956 r. St., 61-545, Poznań, Poland
| | - Mariusz Puszczewicz
- Department of Rheumatology and Internal Diseases, Poznań University of Medical Science, 135/147 28 Czerwca 1956 r. St., 61-545, Poznań, Poland
| | - Paweł P Jagodziński
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences, 6 Święcickiego St., 60-781, Poznań, Poland
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[Modification of DNA methylation in leukemia development]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2016; 37:1003-1007. [PMID: 27995891 PMCID: PMC7348520 DOI: 10.3760/cma.j.issn.0253-2727.2016.11.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Impact of combinatorial dysfunctions of Tet2 and Ezh2 on the epigenome in the pathogenesis of myelodysplastic syndrome. Leukemia 2016; 31:861-871. [DOI: 10.1038/leu.2016.268] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 08/31/2016] [Accepted: 09/06/2016] [Indexed: 12/11/2022]
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CTNNA1 hypermethylation, a frequent event in acute myeloid leukemia, is independently associated with an adverse outcome. Oncotarget 2016; 7:31454-65. [PMID: 27129146 PMCID: PMC5058770 DOI: 10.18632/oncotarget.8962] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 04/12/2016] [Indexed: 11/25/2022] Open
Abstract
The aim of this study is to evaluate the frequency of CTNNA1 hypermethylation in acute myeloid leukemia (AML) patients in an attempt to improve molecular prognostic model. CTNNA1 promoter methylation levels in 319 newly diagnosed AML patients were detected using quantitative methylation-specific polymerase chain reaction (qMS-PCR). Furthermore, hematological characteristics, cytogenetic abnormalities, and genetic mutation status were analyzed, followed by assessment of clinical impact. Our findings demonstrated that CTNNA1 hypermethylation was observed in 25% AML patients. Hypermethylation of the CTNNA1 promoter was associated with unfavorable karyotype, and also possessed the higher frequency of coexisting with ASXL1 and RUNX1 mutations. Patients with CTNNA1 hypermethylation exhibited the shorter relapse-free survival (RFS) and overall survival (OS) in the whole AML and non-M3 AML patients. Moreover, patients with the higher methylation levels had more aggressive course than those with relative lower levels. In multivariate analyses, CTNNA1 hypermethylation was an independent factor predicting for poor RFS, but not for OS. In conclusion, CTNNA1 hypermethylation may be a reliable factor for improving prognostic molecular model for AML.
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Abou Zahr A, Bernabe Ramirez C, Wozney J, Prebet T, Zeidan AM. New Insights into the Pathogenesis of MDS and the rational therapeutic opportunities. Expert Rev Hematol 2016; 9:377-88. [DOI: 10.1586/17474086.2016.1135047] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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26
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Ruiz MA, Rivers A, Ibanez V, Vaitkus K, Mahmud N, DeSimone J, Lavelle D. Hydroxymethylcytosine and demethylation of the γ-globin gene promoter during erythroid differentiation. Epigenetics 2016; 10:397-407. [PMID: 25932923 PMCID: PMC4622718 DOI: 10.1080/15592294.2015.1039220] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The mechanism responsible for developmental stage-specific regulation of γ-globin gene expression involves DNA methylation. Previous results have shown that the γ-globin promoter is nearly fully demethylated during fetal liver erythroid differentiation and partially demethylated during adult bone marrow erythroid differentiation. The hypothesis that 5-hydroxymethylcytosine (5hmC), a known intermediate in DNA demethylation pathways, is involved in demethylation of the γ-globin gene promoter during erythroid differentiation was investigated by analyzing levels of 5-methylcytosine (5mC) and 5hmC at a CCGG site within the 5′ γ-globin gene promoter region in FACS-purified cells from baboon bone marrow and fetal liver enriched for different stages of erythroid differentiation. Our results show that 5mC and 5hmC levels at the γ-globin promoter are dynamically modulated during erythroid differentiation with peak levels of 5hmC preceding and/or coinciding with demethylation. The Tet2 and Tet3 dioxygenases that catalyze formation of 5hmC are expressed during early stages of erythroid differentiation and Tet3 expression increases as differentiation proceeds. In baboon CD34+ bone marrow-derived erythroid progenitor cell cultures, γ-globin expression was positively correlated with 5hmC and negatively correlated with 5mC at the γ-globin promoter. Supplementation of culture media with Vitamin C, a cofactor of the Tet dioxygenases, reduced γ-globin promoter DNA methylation and increased γ-globin expression when added alone and in an additive manner in combination with either DNA methyltransferase or LSD1 inhibitors. These results strongly support the hypothesis that the Tet-mediated 5hmC pathway is involved in developmental stage-specific regulation of γ-globin expression by mediating demethylation of the γ-globin promoter.
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Hewitt KJ, Johnson KD, Gao X, Keles S, Bresnick EH. The Hematopoietic Stem and Progenitor Cell Cistrome: GATA Factor-Dependent cis-Regulatory Mechanisms. Curr Top Dev Biol 2016; 118:45-76. [PMID: 27137654 PMCID: PMC8572122 DOI: 10.1016/bs.ctdb.2016.01.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Transcriptional regulators mediate the genesis and function of the hematopoietic system by binding complex ensembles of cis-regulatory elements to establish genetic networks. While thousands to millions of any given cis-element resides in a genome, how transcriptional regulators select these sites and how site attributes dictate functional output is not well understood. An instructive system to address this problem involves the GATA family of transcription factors that control vital developmental and physiological processes and are linked to multiple human pathologies. Although GATA factors bind DNA motifs harboring the sequence GATA, only a very small subset of these abundant motifs are occupied in genomes. Mechanistic studies revealed a unique configuration of a GATA factor-regulated cis-element consisting of an E-box and a downstream GATA motif separated by a short DNA spacer. GATA-1- or GATA-2-containing multiprotein complexes at these composite elements control transcription of genes critical for hematopoietic stem cell emergence in the mammalian embryo, hematopoietic progenitor cell regulation, and erythroid cell maturation. Other constituents of the complex include the basic helix-loop-loop transcription factor Scl/TAL1, its heterodimeric partner E2A, and the Lim domain proteins LMO2 and LDB1. This chapter reviews the structure/function of E-box-GATA composite cis-elements, which collectively constitute an important sector of the hematopoietic stem and progenitor cell cistrome.
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Affiliation(s)
- Kyle J. Hewitt
- University of Wisconsin School of Medicine and Public Health, Department of Cell and Regenerative Biology, Carbone Cancer Center, Madison, WI 53705,UW-Madison Blood Research Program
| | - Kirby D. Johnson
- University of Wisconsin School of Medicine and Public Health, Department of Cell and Regenerative Biology, Carbone Cancer Center, Madison, WI 53705,UW-Madison Blood Research Program
| | - Xin Gao
- University of Wisconsin School of Medicine and Public Health, Department of Cell and Regenerative Biology, Carbone Cancer Center, Madison, WI 53705,UW-Madison Blood Research Program
| | - Sunduz Keles
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health
| | - Emery H. Bresnick
- University of Wisconsin School of Medicine and Public Health, Department of Cell and Regenerative Biology, Carbone Cancer Center, Madison, WI 53705,UW-Madison Blood Research Program,Corresponding author:
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Paul F, Arkin Y, Giladi A, Jaitin DA, Kenigsberg E, Keren-Shaul H, Winter D, Lara-Astiaso D, Gury M, Weiner A, David E, Cohen N, Lauridsen FKB, Haas S, Schlitzer A, Mildner A, Ginhoux F, Jung S, Trumpp A, Porse BT, Tanay A, Amit I. Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors. Cell 2015; 163:1663-77. [PMID: 26627738 DOI: 10.1016/j.cell.2015.11.013] [Citation(s) in RCA: 651] [Impact Index Per Article: 72.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 09/30/2015] [Accepted: 11/05/2015] [Indexed: 11/29/2022]
Abstract
Within the bone marrow, stem cells differentiate and give rise to diverse blood cell types and functions. Currently, hematopoietic progenitors are defined using surface markers combined with functional assays that are not directly linked with in vivo differentiation potential or gene regulatory mechanisms. Here, we comprehensively map myeloid progenitor subpopulations by transcriptional sorting of single cells from the bone marrow. We describe multiple progenitor subgroups, showing unexpected transcriptional priming toward seven differentiation fates but no progenitors with a mixed state. Transcriptional differentiation is correlated with combinations of known and previously undefined transcription factors, suggesting that the process is tightly regulated. Histone maps and knockout assays are consistent with early transcriptional priming, while traditional transplantation experiments suggest that in vivo priming may still allow for plasticity given strong perturbations. These data establish a reference model and general framework for studying hematopoiesis at single-cell resolution.
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Affiliation(s)
- Franziska Paul
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ya'ara Arkin
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Amir Giladi
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Ephraim Kenigsberg
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Hadas Keren-Shaul
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Deborah Winter
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - David Lara-Astiaso
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Meital Gury
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Assaf Weiner
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Eyal David
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Nadav Cohen
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Felicia Kathrine Bratt Lauridsen
- The Finsen Laboratory, Rigshospitalet, University of Copenhagen, Copenhagen 2200, Denmark; Biotech Research and Innovation Centre (BRIC), Copenhagen 2200, Denmark; Danish Stem Cell Centre (DanStem) Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Simon Haas
- Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany
| | - Andreas Schlitzer
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), BIOPOLIS 138648, Singapore; Genomics and Immunoregulation, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53115 Bonn, Germany
| | - Alexander Mildner
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Florent Ginhoux
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A(∗)STAR), BIOPOLIS 138648, Singapore
| | - Steffen Jung
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Andreas Trumpp
- Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ), 69120 Heidelberg, Germany
| | - Bo Torben Porse
- The Finsen Laboratory, Rigshospitalet, University of Copenhagen, Copenhagen 2200, Denmark; Biotech Research and Innovation Centre (BRIC), Copenhagen 2200, Denmark; Danish Stem Cell Centre (DanStem) Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Amos Tanay
- Department of Computer Science and Applied Mathematics and Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel.
| | - Ido Amit
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel.
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Abstract
Cancer genome sequencing has created an opportunity for precision medicine. Thus far, genetic alterations can only be used to guide treatment for small subsets of certain cancer types with these key alterations. Similar to mutations, epigenetic events are equally suitable for personalized medicine. DNA methylation alterations have been used to identify tumor-specific drug responsive markers. Methylation of MGMT sensitizes gliomas to alkylating agents is an example of epigenetic personalized medicine. Recent studies have revealed that 5-azacytidine and decitabine show activity in myelodysplasia, lung and other cancers. There are currently at least 20 kinds of histone deacetylase inhibitors in clinical testing. Inhibitors targeting other epigenetic regulators are being clinically tested, such as EZH2 inhibitor EPZ-6438.
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Affiliation(s)
- Wenji Yan
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing 100853, China
| | - James G Herman
- The Hillman Cancer Center, University of Pittsburgh Cancer Institute, 5117 Centre Avenue, Suite 2.18/Research, Pittsburgh, PA 15213, USA
| | - Mingzhou Guo
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing 100853, China
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30
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Abou Zahr A, Saad Aldin E, Barbarotta L, Podoltsev N, Zeidan AM. The clinical use of DNA methyltransferase inhibitors in myelodysplastic syndromes. Expert Rev Anticancer Ther 2015; 15:1019-36. [DOI: 10.1586/14737140.2015.1061936] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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31
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Pan F, Weeks O, Yang FC, Xu M. The TET2 interactors and their links to hematological malignancies. IUBMB Life 2015; 67:438-45. [PMID: 26099018 DOI: 10.1002/iub.1389] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 05/14/2015] [Indexed: 12/19/2022]
Abstract
Ten-eleven translocation (TET) family proteins are dioxygenases that oxidize 5-methylcytosine to 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine in DNA, early steps of active DNA demethylation. TET2, the second member of TET protein family, is frequently mutated in patients with hematological malignancies, leading to aberrant DNA methylation profiling and decreased 5hmC levels. Located in the nucleus and acting as a DNA-modifying enzyme, TET2 is thought to exert its function via TET2-containing protein complexes. Identifying the interactome network of TET2 likely holds the key to uncover the mechanisms by which TET2 exerts its function in cells. Here, we review recent literature on TET2 interactors and discuss their possible roles in TET2 loss-mediated dysregulation of hematopoiesis and pathogenesis of hematological malignancies.
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Affiliation(s)
- Feng Pan
- Department of Biological Sciences, Florida International University, Miami, FL, USA.,Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Ophelia Weeks
- Department of Biological Sciences, Florida International University, Miami, FL, USA
| | - Feng-Chun Yang
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, USA.,Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Mingjiang Xu
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, USA.,Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
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32
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Cerón-Maldonado R, Martínez-Tovar A, Ramos-Peñafiel C, Miranda-Peralta E, Mendoza-Salas I, Mendoza-García E, Rozen-Fuller E, Kassack-Ipiña J, Collazo-Jaloma J, Martínez-Herrera A, Olarte-Carrillo I. Detection and analysis of tumour biomarkers to strengthen the diagnosis of acute and chronic leukaemias. REVISTA MÉDICA DEL HOSPITAL GENERAL DE MÉXICO 2015. [DOI: 10.1016/j.hgmx.2015.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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33
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Koyanagi KO. Inferring cell differentiation processes based on phylogenetic analysis of genome-wide epigenetic information: hematopoiesis as a model case. Genome Biol Evol 2015; 7:699-705. [PMID: 25638259 PMCID: PMC5322552 DOI: 10.1093/gbe/evv024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
How cells divide and differentiate is a fundamental question in organismal development; however, the discovery of differentiation processes in various cell types is laborious and sometimes impossible. Phylogenetic analysis is typically used to reconstruct evolutionary processes based on inherent characters. It could also be used to reconstruct developmental processes based on the developmental changes that occur during cell proliferation and differentiation. In this study, DNA methylation information from differentiated hematopoietic cells was used to perform phylogenetic analyses. The results were assessed for their validity in inferring hierarchical differentiation processes of hematopoietic cells and DNA methylation processes of differentiating progenitor cells. Overall, phylogenetic analyses based on DNA methylation information facilitated inferences regarding hematopoiesis.
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Affiliation(s)
- Kanako O Koyanagi
- Graduate School of Information Science and Technology, Hokkaido University, Sapporo, Japan
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34
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Plutzky J. Emerging epigenetic maps in atherosclerosis. CIRCULATION. CARDIOVASCULAR GENETICS 2014; 7:573-575. [PMID: 25518042 DOI: 10.1161/circgenetics.114.000829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Affiliation(s)
- Jorge Plutzky
- From the Division of Cardiovascular Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.
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