1
|
Lee AV, Nestler KA, Chiappinelli KB. Therapeutic targeting of DNA methylation alterations in cancer. Pharmacol Ther 2024; 258:108640. [PMID: 38570075 DOI: 10.1016/j.pharmthera.2024.108640] [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: 12/13/2023] [Revised: 03/13/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024]
Abstract
DNA methylation is a critical component of gene regulation and plays an important role in the development of cancer. Hypermethylation of tumor suppressor genes and silencing of DNA repair pathways facilitate uncontrolled cell growth and synergize with oncogenic mutations to perpetuate cancer phenotypes. Additionally, aberrant DNA methylation hinders immune responses crucial for antitumor immunity. Thus, inhibiting dysregulated DNA methylation is a promising cancer therapy. Pharmacologic inhibition of DNA methylation reactivates silenced tumor suppressors and bolster immune responses through induction of viral mimicry. Now, with the advent of immunotherapies and discovery of the immune-modulatory effects of DNA methylation inhibitors, there is great interest in understanding how targeting DNA methylation in combination with other therapies can enhance antitumor immunity. Here, we describe the role of aberrant DNA methylation in cancer and mechanisms by which it promotes tumorigenesis and modulates immune responses. Finally, we review the initial discoveries and ongoing efforts to target DNA methylation as a cancer therapeutic.
Collapse
Affiliation(s)
- Abigail V Lee
- Department of Microbiology, Immunology, & Tropical Medicine, The George Washington University, Washington, DC, USA
| | - Kevin A Nestler
- Department of Microbiology, Immunology, & Tropical Medicine, The George Washington University, Washington, DC, USA
| | - Katherine B Chiappinelli
- Department of Microbiology, Immunology, & Tropical Medicine, The George Washington University, Washington, DC, USA.
| |
Collapse
|
2
|
Salazar M, Joly S, Anglada-Escudé G, Ribas L. Epigenetic and physiological alterations in zebrafish subjected to hypergravity. PLoS One 2024; 19:e0300310. [PMID: 38776274 PMCID: PMC11111069 DOI: 10.1371/journal.pone.0300310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/27/2024] [Indexed: 05/24/2024] Open
Abstract
Gravity is one of the most constant environmental factors across Earth's evolution and all organisms are adapted to it. Consequently, spatial exploration has captured the interest in studying the biological changes that physiological alterations are caused by gravity. In the last two decades, epigenetics has explained how environmental cues can alter gene functions in organisms. Although many studies addressed gravity, the underlying biological and molecular mechanisms that occur in altered gravity for those epigenetics-related mechanisms, are mostly inexistent. The present study addressed the effects of hypergravity on development, behavior, gene expression, and most importantly, on the epigenetic changes in a worldwide animal model, the zebrafish (Danio rerio). To perform hypergravity experiments, a custom-centrifuge simulating the large diameter centrifuge (100 rpm ~ 3 g) was designed and zebrafish embryos were exposed during 5 days post fertilization (dpf). Results showed a significant decrease in survival at 2 dpf but no significance in the hatching rate. Physiological and morphological alterations including fish position, movement frequency, and swimming behavior showed significant changes due to hypergravity. Epigenetic studies showed significant hypermethylation of the genome of the zebrafish larvae subjected to 5 days of hypergravity. Downregulation of the gene expression of three epigenetic-related genes (dnmt1, dnmt3, and tet1), although not significant, was further observed. Taken altogether, gravity alterations affected biological responses including epigenetics in fish, providing a valuable roadmap of the putative hazards of living beyond Earth.
Collapse
Affiliation(s)
- Marcela Salazar
- Department of Renewable Marine Resources, Institut de Ciències del Mar—Consejo Superior de Investigaciones Científicas (ICM-CSIC), Barcelona, Spain
| | - Silvia Joly
- Department of Renewable Marine Resources, Institut de Ciències del Mar—Consejo Superior de Investigaciones Científicas (ICM-CSIC), Barcelona, Spain
| | - Guillem Anglada-Escudé
- Department of Astrophysics, Institut de Ciències de l’Espai—Consejo Superior de Investigaciones Científicas (ICE-CSIC), UAB Campus at Cerdanyola del Vallès, Barcelona, Spain
- Institut d’Estudis Espacials de Catalunya–IEEC/CERCA, Gran Capità, 2–4, Edifici Nexus, Despatx 201, Barcelona, Spain
| | - Laia Ribas
- Department of Renewable Marine Resources, Institut de Ciències del Mar—Consejo Superior de Investigaciones Científicas (ICM-CSIC), Barcelona, Spain
| |
Collapse
|
3
|
Zhang X, Zhang Y, Wang C, Wang X. TET (Ten-eleven translocation) family proteins: structure, biological functions and applications. Signal Transduct Target Ther 2023; 8:297. [PMID: 37563110 PMCID: PMC10415333 DOI: 10.1038/s41392-023-01537-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 05/24/2023] [Accepted: 06/05/2023] [Indexed: 08/12/2023] Open
Abstract
Ten-eleven translocation (TET) family proteins (TETs), specifically, TET1, TET2 and TET3, can modify DNA by oxidizing 5-methylcytosine (5mC) iteratively to yield 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxycytosine (5caC), and then two of these intermediates (5fC and 5caC) can be excised and return to unmethylated cytosines by thymine-DNA glycosylase (TDG)-mediated base excision repair. Because DNA methylation and demethylation play an important role in numerous biological processes, including zygote formation, embryogenesis, spatial learning and immune homeostasis, the regulation of TETs functions is complicated, and dysregulation of their functions is implicated in many diseases such as myeloid malignancies. In addition, recent studies have demonstrated that TET2 is able to catalyze the hydroxymethylation of RNA to perform post-transcriptional regulation. Notably, catalytic-independent functions of TETs in certain biological contexts have been identified, further highlighting their multifunctional roles. Interestingly, by reactivating the expression of selected target genes, accumulated evidences support the potential therapeutic use of TETs-based DNA methylation editing tools in disorders associated with epigenetic silencing. In this review, we summarize recent key findings in TETs functions, activity regulators at various levels, technological advances in the detection of 5hmC, the main TETs oxidative product, and TETs emerging applications in epigenetic editing. Furthermore, we discuss existing challenges and future directions in this field.
Collapse
Affiliation(s)
- Xinchao Zhang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yue Zhang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Chaofu Wang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Xu Wang
- Department of Pathology, Ruijin Hospital and College of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| |
Collapse
|
4
|
Gattupalli M, Dey P, Poovizhi S, Patel RB, Mishra D, Banerjee S. The Prospects of RNAs and Common Significant Pathways in Cancer Therapy and Regenerative Medicine. Regen Med 2023. [DOI: 10.1007/978-981-19-6008-6_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
|
5
|
Yuan WB, Chen HQ, Li JZ, Zhou SM, Zeng Y, Fan J, Zhang Z, Liu JY, Cao J, Liu WB. TET1 mediated male reproductive toxicity induced by Bisphenol A through Catsper-Ca 2+ signaling pathway. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 296:118739. [PMID: 34953956 DOI: 10.1016/j.envpol.2021.118739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/15/2021] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
Abstract
Bisphenol A (BPA) exposure has many adverse effects on the reproductive system in animals and humans. Ten-eleven translocation 1 (TET1) is closely related to a variety of biological processes through regulating the dynamic balance of DNA demethylation and methylation. However, the role and mechanism of TET1 during BPA induced reproductive toxicity are largely unknown. In this study, mouse spermatogonia cell line GC-2 was treated with BPA in the final concentration of 0, 20, 40 and 80 μM for 72 h. The cell model of differential TET1 gene expression was established to explore the role and mechanism. We found that the growth rate of GC-2 cells, and the intracellular calcium level decreased significantly with the increase of BPA dose, while TET1 and Catsper1-4 expression level decrease with a dose-dependent relationship. Furthermore, TET1 overexpression promoted the proliferation of GC-2 cell, the increase of calcium ion concentration, and the expression level of Catsper1-4, while knockdown of TET1 leads to the opposite results. Mechanistically, TET1 expression promoted the hydroxymethylation of Catsper1-4 and reduced their methylation level. In addition, the expression level of Catsper1-4 was positively correlated with TET1 gene expression level in semen samples of the population. Our study revealed for the first time that TET1 gene regulates the expression of related molecules in the Catsper calcium signal pathway through its hydroxymethylation modification to affect the calcium level, thereby participating in the process of BPA induced damage. These results indicated that TET1 gene may be a potential biomarker of BPA induced male reproductive toxicity.
Collapse
Affiliation(s)
- Wen-Bo Yuan
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China; School of Public Health, Xinxiang Medical University, Xinxiang, Henan, 453003, PR China
| | - Hong-Qiang Chen
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China; Department of Environmental Health, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Jing-Zhi Li
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China; School of Public Health, Xinxiang Medical University, Xinxiang, Henan, 453003, PR China
| | - Shi-Meng Zhou
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China; School of Public Health, China Medical University, Shenyang, Liaoning, 110122, PR China
| | - Yong Zeng
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China; Department of Environmental Health, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Jun Fan
- Department of Breast and Thyroid Surgery, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing, 400042, PR China
| | - Zhe Zhang
- Department of Breast and Thyroid Surgery, Daping Hospital, Third Military Medical University (Army Medical University), Chongqing, 400042, PR China
| | - Jin-Yi Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Jia Cao
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China
| | - Wen-Bin Liu
- Institute of Toxicology, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China; Department of Environmental Health, College of Preventive Medicine, Third Military Medical University (Army Medical University), Chongqing, 400038, PR China.
| |
Collapse
|
6
|
Coker SJ, Smith-Díaz CC, Dyson RM, Vissers MCM, Berry MJ. The Epigenetic Role of Vitamin C in Neurodevelopment. Int J Mol Sci 2022; 23:ijms23031208. [PMID: 35163133 PMCID: PMC8836017 DOI: 10.3390/ijms23031208] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/16/2022] [Accepted: 01/17/2022] [Indexed: 02/07/2023] Open
Abstract
The maternal diet during pregnancy is a key determinant of offspring health. Early studies have linked poor maternal nutrition during gestation with a propensity for the development of chronic conditions in offspring. These conditions include cardiovascular disease, type 2 diabetes and even compromised mental health. While multiple factors may contribute to these outcomes, disturbed epigenetic programming during early development is one potential biological mechanism. The epigenome is programmed primarily in utero, and during this time, the developing fetus is highly susceptible to environmental factors such as nutritional insults. During neurodevelopment, epigenetic programming coordinates the formation of primitive central nervous system structures, neurogenesis, and neuroplasticity. Dysregulated epigenetic programming has been implicated in the aetiology of several neurodevelopmental disorders such as Tatton-Brown-Rahman syndrome. Accordingly, there is great interest in determining how maternal nutrient availability in pregnancy might affect the epigenetic status of offspring, and how such influences may present phenotypically. In recent years, a number of epigenetic enzymes that are active during embryonic development have been found to require vitamin C as a cofactor. These enzymes include the ten-eleven translocation methylcytosine dioxygenases (TETs) and the Jumonji C domain-containing histone lysine demethylases that catalyse the oxidative removal of methyl groups on cytosines and histone lysine residues, respectively. These enzymes are integral to epigenetic regulation and have fundamental roles in cellular differentiation, the maintenance of pluripotency and development. The dependence of these enzymes on vitamin C for optimal catalytic activity illustrates a potentially critical contribution of the nutrient during mammalian development. These insights also highlight a potential risk associated with vitamin C insufficiency during pregnancy. The link between vitamin C insufficiency and development is particularly apparent in the context of neurodevelopment and high vitamin C concentrations in the brain are indicative of important functional requirements in this organ. Accordingly, this review considers the evidence for the potential impact of maternal vitamin C status on neurodevelopmental epigenetics.
Collapse
Affiliation(s)
- Sharna J. Coker
- Perinatal & Developmental Physiology Group, Department of Paediatrics & Child Health, University of Otago, Wellington 6242, New Zealand; (S.J.C.); (R.M.D.)
| | - Carlos C. Smith-Díaz
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch 8140, New Zealand;
| | - Rebecca M. Dyson
- Perinatal & Developmental Physiology Group, Department of Paediatrics & Child Health, University of Otago, Wellington 6242, New Zealand; (S.J.C.); (R.M.D.)
| | - Margreet C. M. Vissers
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch 8140, New Zealand;
- Correspondence: (M.C.M.V.); (M.J.B.)
| | - Mary J. Berry
- Perinatal & Developmental Physiology Group, Department of Paediatrics & Child Health, University of Otago, Wellington 6242, New Zealand; (S.J.C.); (R.M.D.)
- Correspondence: (M.C.M.V.); (M.J.B.)
| |
Collapse
|
7
|
Fellous A, Wegner KM, John U, Mark FC, Shama LNS. Windows of opportunity: Ocean warming shapes temperature-sensitive epigenetic reprogramming and gene expression across gametogenesis and embryogenesis in marine stickleback. GLOBAL CHANGE BIOLOGY 2022; 28:54-71. [PMID: 34669228 DOI: 10.1111/gcb.15942] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/23/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
Rapid climate change is placing many marine species at risk of local extinction. Recent studies show that epigenetic mechanisms (e.g. DNA methylation, histone modifications) can facilitate both within and transgenerational plasticity to cope with changing environments. However, epigenetic reprogramming (erasure and re-establishment of epigenetic marks) during gamete and early embryo development may hinder transgenerational epigenetic inheritance. Most of our knowledge about reprogramming stems from mammals and model organisms, whereas the prevalence and extent of reprogramming among non-model species from wild populations is rarely investigated. Moreover, whether reprogramming dynamics are sensitive to changing environmental conditions is not well known, representing a key knowledge gap in the pursuit to identify mechanisms underlying links between parental exposure to changing climate patterns and environmentally adapted offspring phenotypes. Here, we investigated epigenetic reprogramming (DNA methylation/hydroxymethylation) and gene expression across gametogenesis and embryogenesis of marine stickleback (Gasterosteus aculeatus) under three ocean warming scenarios (ambient, +1.5 and +4°C). We found that parental acclimation to ocean warming led to dynamic and temperature-sensitive reprogramming throughout offspring development. Both global methylation/hydroxymethylation and expression of genes involved in epigenetic modifications were strongly and differentially affected by the increased warming scenarios. Comparing transcriptomic profiles from gonads, mature gametes and early embryonic stages showed sex-specific accumulation and temperature sensitivity of several epigenetic actors. DNA methyltransferase induction was primarily maternally inherited (suggesting maternal control of remethylation), whereas induction of several histone-modifying enzymes was shaped by both parents. Importantly, massive, temperature-specific changes to the epigenetic landscape occurred in blastula, a critical stage for successful embryo development, which could, thus, translate to substantial consequences for offspring phenotype resilience in warming environments. In summary, our study identified key stages during gamete and embryo development with temperature-sensitive reprogramming and epigenetic gene regulation, reflecting potential 'windows of opportunity' for adaptive epigenetic responses under future climate change.
Collapse
Affiliation(s)
- Alexandre Fellous
- Coastal Ecology Section, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Wadden Sea Station Sylt, List, Germany
| | - K Mathias Wegner
- Coastal Ecology Section, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Wadden Sea Station Sylt, List, Germany
| | - Uwe John
- Ecological Chemistry Section, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
| | - Felix C Mark
- Integrative Ecophysiology Section, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Lisa N S Shama
- Coastal Ecology Section, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Wadden Sea Station Sylt, List, Germany
| |
Collapse
|
8
|
Genetic Studies on Mammalian DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:111-136. [PMID: 36350508 PMCID: PMC9815518 DOI: 10.1007/978-3-031-11454-0_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Cytosine methylation at the C5-position-generating 5-methylcytosine (5mC)-is a DNA modification found in many eukaryotic organisms, including fungi, plants, invertebrates, and vertebrates, albeit its levels vary greatly in different organisms. In mammals, cytosine methylation occurs predominantly in the context of CpG dinucleotides, with the majority (60-80%) of CpG sites in their genomes being methylated. DNA methylation plays crucial roles in the regulation of chromatin structure and gene expression and is essential for mammalian development. Aberrant changes in DNA methylation and genetic alterations in enzymes and regulators involved in DNA methylation are associated with various human diseases, including cancer and developmental disorders. In mammals, DNA methylation is mediated by two families of DNA methyltransferases (Dnmts), namely Dnmt1 and Dnmt3 proteins. Over the last three decades, genetic manipulations of these enzymes, as well as their regulators, in mice have greatly contributed to our understanding of the biological functions of DNA methylation in mammals. In this chapter, we discuss genetic studies on mammalian Dnmts, focusing on their roles in embryogenesis, cellular differentiation, genomic imprinting, and human diseases.
Collapse
|
9
|
Martinez-Ruíz GU, Morales-Sánchez A, Bhandoola A. Transcriptional and epigenetic regulation in thymic epithelial cells. Immunol Rev 2022; 305:43-58. [PMID: 34750841 PMCID: PMC8766885 DOI: 10.1111/imr.13034] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 01/03/2023]
Abstract
The thymus is required for the development of both adaptive and innate-like T cell subsets. There is keen interest in manipulating thymic function for therapeutic purposes in circumstances of autoimmunity, immunodeficiency, and for purposes of immunotherapy. Within the thymus, thymic epithelial cells play essential roles in directing T cell development. Several transcription factors are known to be essential for thymic epithelial cell development and function, and a few transcription factors have been studied in considerable detail. However, the role of many other transcription factors is less well understood. Further, it is likely that roles exist for other transcription factors not yet known to be important in thymic epithelial cells. Recent progress in understanding of thymic epithelial cell heterogeneity has provided some new insight into transcriptional requirements in subtypes of thymic epithelial cells. However, it is unknown whether progenitors of thymic epithelial cells exist in the adult thymus, and consequently, developmental relationships linking putative precursors with differentiated cell types are poorly understood. While we do not presently possess a clear understanding of stage-specific requirements for transcription factors in thymic epithelial cells, new single-cell transcriptomic and epigenomic technologies should enable rapid progress in this field. Here, we review our current knowledge of transcription factors involved in the development, maintenance, and function of thymic epithelial cells, and the mechanisms by which they act.
Collapse
Affiliation(s)
- Gustavo Ulises Martinez-Ruíz
- T Cell Biology and Development Unit, Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Research Division, Faculty of Medicine, National Autonomous University of Mexico, Mexico City, Mexico
- Children’s Hospital of Mexico Federico Gomez, Mexico City, Mexico
| | - Abigail Morales-Sánchez
- T Cell Biology and Development Unit, Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Children’s Hospital of Mexico Federico Gomez, Mexico City, Mexico
| | - Avinash Bhandoola
- T Cell Biology and Development Unit, Laboratory of Genome Integrity, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| |
Collapse
|
10
|
Huo X, Jin S, Wang Y, Ma L. DNA methylation in chronic obstructive pulmonary disease. Epigenomics 2021; 13:1145-1155. [PMID: 34142873 DOI: 10.2217/epi-2021-0111] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD), a complex disease with polygenetic tendency, is one of the most important health problems in the world. Recently, in the study of the pathogenesis of the COPD, epigenetic changes caused by environmental factors, such as DNA methylation, started to attract more attention than genetic factors. In this review, we discuss the main features of DNA methylation, such as DNA methyltransferases and the methylation sites that modulate the DNA methylation level, and their roles in COPD progression. Finally, to promote new ideas for the prevention and treatment of COPD, we focus on the potential of DNA methylation as a COPD therapeutic target.
Collapse
Affiliation(s)
- XinXin Huo
- School of Public Health, Lanzhou University, Lanzhou, China
| | - SiHui Jin
- School of Public Health, Lanzhou University, Lanzhou, China
| | - YiGe Wang
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Li Ma
- School of Public Health, Lanzhou University, Lanzhou, China
| |
Collapse
|
11
|
Noncoding RNAs involved in DNA methylation and histone methylation, and acetylation in diabetic vascular complications. Pharmacol Res 2021; 170:105520. [PMID: 33639232 DOI: 10.1016/j.phrs.2021.105520] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 02/23/2021] [Indexed: 02/08/2023]
Abstract
Diabetes is a metabolic disorder and its incidence is still increasing. Diabetic vascular complications cause major diabetic mobility and include accelerated atherosclerosis, nephropathy, retinopathy, and neuropathy. Hyperglycemia contributes to the pathogenesis of diabetic vascular complications via numerous mechanisms including the induction of oxidative stress, inflammation, metabolic alterations, and abnormal proliferation of EC and angiogenesis. In the past decade, epigenetic modifications have attracted more attention as they participate in the progression of diabetic vascular complications despite controlled glucose levels and regulate gene expression without altering the genomic sequence. DNA methylation and histone methylation, and acetylation are vital epigenetic modifications and their underlying mechanisms in diabetic vascular complication are still urgently needed to be investigated. Non-coding RNAs (nc RNAs) such as micro RNAs (miRNAs), long non-coding RNA (lncRNAs), and circular RNAs (circ RNAs) were found to exert transcriptional regulation in diabetic vascular complication. Although nc RNAs are not considered as epigenetic components, they are involved in epigenetic modifications. In this review, we summarized the investigations of non-coding RNAs involved in DNA methylation and histone methylation and acetylation. Their cross-talks might offer novel insights into the pathology of diabetic vascular complications.
Collapse
|
12
|
STAT5 Regulation of Sex-Dependent Hepatic CpG Methylation at Distal Regulatory Elements Mapping to Sex-Biased Genes. Mol Cell Biol 2021; 41:MCB.00166-20. [PMID: 33199496 DOI: 10.1128/mcb.00166-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 11/05/2020] [Indexed: 12/19/2022] Open
Abstract
Growth hormone-activated STAT5b is an essential regulator of sex-differential gene expression in mouse liver; however, its impact on hepatic gene expression and epigenetic responses is poorly understood. Here, we found a substantial, albeit incomplete loss of liver sex bias in hepatocyte-specific STAT5a/STAT5b (collectively, STAT5)-deficient mouse liver. In male liver, many male-biased genes were downregulated in direct association with the loss of STAT5 binding; many female-biased genes, which show low STAT5 binding, were derepressed, indicating an indirect mechanism for repression by STAT5. Extensive changes in CpG methylation were seen in STAT5-deficient liver, where sex differences were abolished at 88% of ∼1,500 sex-differentially methylated regions, largely due to increased DNA methylation upon STAT5 loss. STAT5-dependent CpG hypomethylation was rarely found at proximal promoters of STAT5-dependent genes. Rather, STAT5 primarily regulated the methylation of distal enhancers, where STAT5 deficiency induced widespread hypermethylation at genomic regions enriched for accessible chromatin, enhancer histone marks (histone H3 lysine 4 monomethylation [H3K4me1] and histone H3 lysine 27 acetylation [H3K27ac]), STAT5 binding, and DNA motifs for STAT5 and other transcription factors implicated in liver sex differences. Thus, the sex-dependent binding of STAT5 to liver chromatin is closely linked to the sex-dependent demethylation of distal regulatory elements linked to STAT5-dependent genes important for liver sex bias.
Collapse
|
13
|
Mondal P, Natesh J, Penta D, Meeran SM. Progress and promises of epigenetic drugs and epigenetic diets in cancer prevention and therapy: A clinical update. Semin Cancer Biol 2020; 83:503-522. [PMID: 33309850 DOI: 10.1016/j.semcancer.2020.12.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 12/12/2022]
Abstract
Epigenetic modifications are heritable yet reversible, essential for normal physiological functions and biological development. Aberrant epigenetic modifications, including DNA methylation, histone modification, and non-coding RNA (ncRNA)-mediated gene regulation play a crucial role in cancer progression. In cellular reprogramming, irregular epigenomic modulations alter cell signaling pathways and the expression of tumor suppressor genes and oncogenes, resulting in cancer growth and metastasis. Therefore, alteration of epigenetic-status in cancer cells can be used as a potential target for cancer therapy. Several synthetic epigenetic inhibitors (epi-drugs) and natural epigenetic modulatory bioactives (epi-diets) have been shown to have the potential to alter the aberrant epigenetic status and inhibit cancer progression. Further, the use of combinatorial approaches with epigenetic drugs and diets has brought promising outcomes in cancer prevention and therapy. In this article, we have summarized the epigenetic modulatory activities of epi-drugs, epi-diets, and their combination against various cancers. We have also compiled the preclinical and clinical status of these epigenetic modulators in different cancers.
Collapse
Affiliation(s)
- Priya Mondal
- Department of Biochemistry, CSIR-Central Food Technological Research Institute, Mysore, 570020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Jagadish Natesh
- Department of Biochemistry, CSIR-Central Food Technological Research Institute, Mysore, 570020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Dhanamjai Penta
- Department of Biochemistry, CSIR-Central Food Technological Research Institute, Mysore, 570020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Syed Musthapa Meeran
- Department of Biochemistry, CSIR-Central Food Technological Research Institute, Mysore, 570020, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| |
Collapse
|
14
|
Kaur G, Batra S. Regulation of DNA methylation signatures on NF-κB and STAT3 pathway genes and TET activity in cigarette smoke extract-challenged cells/COPD exacerbation model in vitro. Cell Biol Toxicol 2020; 36:459-480. [PMID: 32342329 DOI: 10.1007/s10565-020-09522-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 03/19/2020] [Indexed: 02/08/2023]
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) is a global health problem. Currently, there is a lack of knowledge about the pathobiology of this disease and available therapies are ineffective. Cigarette smoking is the leading cause of COPD; however, not all smokers develop COPD. Exacerbations of COPD caused by microbes are common and detrimental. Approximately 20-50% of patient exacerbations are caused by bacterial colonization in the lower airways. It is generally accepted that epigenetic mechanisms, especially DNA methylation, play an important role during progression of COPD. Thus, we hypothesized that DNA methylation patterns vary significantly following smoke exposure and during exacerbations caused by bacterial infections. To test our hypothesis, we used an in vitro study model that mimics COPD exacerbations and performed extensive studies to understand the role of CpG promoter methylation of NF-κB and STAT3-mediated pathway genes. Both NF-κB and STAT3 transcription factors play critical roles in orchestrating inflammatory responses during cigarette smoke exposure. In brief, human lung adenocarcinoma cells with type II alveolar epithelium characteristics (A549) were challenged with cigarette smoke extract (CSE) or DMSO (control) followed by a 3-h challenge with bacterial lipopolysaccharide (LPS; from Pseudomonas aeruginosa) prior to the termination of CSE exposure (COPD exacerbation group). The production of cytokines/chemokines, regulation of transcription factors, and DNA methylation of specific genes were then assessed. We also studied changes in the expression and activity of ten-eleven translocases (TETs), the enzymes responsible for DNA demethylation, and assessed their role in regulating DNA methylation in the CSE-challenged group. RESULTS There was a significant increase in the release of cytokines/chemokines (IL-8, MCP-1, IL-6 and CCL5) in the COPD exacerbation group as compared to the control group. Hypomethylation of NF-κB-mediated pathway genes correlated with their induction in our COPD exacerbation study model. Further, we observed an important role of TET1/2 in regulating the DNA methylation of NF-κB, STAT3, IKK, and NIK genes and cytokine/chemokine production by A549 cells during CSE challenge. CONCLUSIONS Studies to further define the role of TETs in CSE-mediated epigenetic regulation may lead to the development of better and more effective therapeutic intervention strategies for COPD.
Collapse
Affiliation(s)
- Gagandeep Kaur
- Laboratory of Pulmonary Immunotoxicology, Department of Environmental Toxicology, Southern University and A&M College, Baton Rouge, LA, 70813, USA
| | - Sanjay Batra
- Laboratory of Pulmonary Immunotoxicology, Department of Environmental Toxicology, Southern University and A&M College, Baton Rouge, LA, 70813, USA.
| |
Collapse
|
15
|
Lu Y, Chan YT, Tan HY, Li S, Wang N, Feng Y. Epigenetic regulation in human cancer: the potential role of epi-drug in cancer therapy. Mol Cancer 2020; 19:79. [PMID: 32340605 PMCID: PMC7184703 DOI: 10.1186/s12943-020-01197-3] [Citation(s) in RCA: 231] [Impact Index Per Article: 57.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 04/08/2020] [Indexed: 12/15/2022] Open
Abstract
Epigenetics is dynamic and heritable modifications to the genome that occur independently of DNA sequence. It requires interactions cohesively with various enzymes and other molecular components. Aberrant epigenetic alterations can lead to inappropriate onset of genetic expressions and promote tumorigenesis. As the epigenetic modifiers are susceptible to extrinsic factors and reversible, they are becoming promising targets in multiple cancer therapies. Recently, various epi-drugs have been developed and implicated in clinical use. The use of epi-drugs alone, or in combination with chemotherapy or immunotherapy, has shown compelling outcomes, including augmentation of anti-tumoral effects, overcoming drug resistance, and activation of host immune response.
Collapse
Affiliation(s)
- Yuanjun Lu
- School of Chinese Medicine, The University of Hong Kong, 10 Sassoon Road, Pofulam, 000000, Hong Kong, Special Administrative Region of China
| | - Yau-Tuen Chan
- School of Chinese Medicine, The University of Hong Kong, 10 Sassoon Road, Pofulam, 000000, Hong Kong, Special Administrative Region of China
| | - Hor-Yue Tan
- School of Chinese Medicine, The University of Hong Kong, 10 Sassoon Road, Pofulam, 000000, Hong Kong, Special Administrative Region of China
| | - Sha Li
- School of Chinese Medicine, The University of Hong Kong, 10 Sassoon Road, Pofulam, 000000, Hong Kong, Special Administrative Region of China
| | - Ning Wang
- School of Chinese Medicine, The University of Hong Kong, 10 Sassoon Road, Pofulam, 000000, Hong Kong, Special Administrative Region of China.
| | - Yibin Feng
- School of Chinese Medicine, The University of Hong Kong, 10 Sassoon Road, Pofulam, 000000, Hong Kong, Special Administrative Region of China.
| |
Collapse
|
16
|
Bisserier M, Janostiak R, Lezoualc’h F, Hadri L. Targeting epigenetic mechanisms as an emerging therapeutic strategy in pulmonary hypertension disease. VASCULAR BIOLOGY (BRISTOL, ENGLAND) 2020; 2:R17-R34. [PMID: 32161845 PMCID: PMC7065685 DOI: 10.1530/vb-19-0030] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 12/17/2019] [Indexed: 12/12/2022]
Abstract
Pulmonary arterial hypertension (PAH) is a multifactorial cardiopulmonary disease characterized by an elevation of pulmonary artery pressure (PAP) and pulmonary vascular resistance (PVR), which can lead to right ventricular (RV) failure, multi-organ dysfunction, and ultimately to premature death. Despite the advances in molecular biology, the mechanisms underlying pulmonary hypertension (PH) remain unclear. Nowadays, there is no curative treatment for treating PH. Therefore, it is crucial to identify novel, specific therapeutic targets and to offer more effective treatments against the progression of PH. Increasing amounts of evidence suggest that epigenetic modification may play a critical role in the pathogenesis of PAH. In the presented paper, we provide an overview of the epigenetic mechanisms specifically, DNA methylation, histone acetylation, histone methylation, and ncRNAs. As the recent identification of new pharmacological drugs targeting these epigenetic mechanisms has opened new therapeutic avenues, we also discuss the importance of epigenetic-based therapies in the context of PH.
Collapse
Affiliation(s)
- Malik Bisserier
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Radoslav Janostiak
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Frank Lezoualc’h
- Inserm, UMR-1048, Institut des Maladies Métaboliques et Cardiovasculaires, University of Toulouse, Toulouse Cedex 4, France
| | - Lahouaria Hadri
- Cardiovascular Research Center, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| |
Collapse
|
17
|
Perera BP, Faulk C, Svoboda LK, Goodrich JM, Dolinoy DC. The role of environmental exposures and the epigenome in health and disease. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:176-192. [PMID: 31177562 PMCID: PMC7252203 DOI: 10.1002/em.22311] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 05/29/2019] [Accepted: 06/03/2019] [Indexed: 05/02/2023]
Abstract
The genetic material of every organism exists within the context of regulatory networks that govern gene expression, collectively called the epigenome. Epigenetics has taken center stage in the study of diseases such as cancer and diabetes, but its integration into the field of environmental health is still emerging. As the Environmental Mutagenesis and Genomics Society (EMGS) celebrates its 50th Anniversary this year, we have come together to review and summarize the seminal advances in the field of environmental epigenomics. Specifically, we focus on the role epigenetics may play in multigenerational and transgenerational transmission of environmentally induced health effects. We also summarize state of the art techniques for evaluating the epigenome, environmental epigenetic analysis, and the emerging field of epigenome editing. Finally, we evaluate transposon epigenetics as they relate to environmental exposures and explore the role of noncoding RNA as biomarkers of environmental exposures. Although the field has advanced over the past several decades, including being recognized by EMGS with its own Special Interest Group, recently renamed Epigenomics, we are excited about the opportunities for environmental epigenetic science in the next 50 years. Environ. Mol. Mutagen. 61:176-192, 2020. © 2019 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Bambarendage P.U. Perera
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Christopher Faulk
- Department of Animal Sciences, University of Minnesota, St. Paul, Minnesota
| | - Laurie K. Svoboda
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Jaclyn M. Goodrich
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Dana C. Dolinoy
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
- Correspondence to: Dana C. Dolinoy, Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan.
| |
Collapse
|
18
|
Mahmood AM, Dunwell JM. Evidence for novel epigenetic marks within plants. AIMS GENETICS 2019; 6:70-87. [PMID: 31922011 PMCID: PMC6949463 DOI: 10.3934/genet.2019.4.70] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 12/07/2019] [Indexed: 12/21/2022]
Abstract
Variation in patterns of gene expression can result from modifications in the genome that occur without a change in the sequence of the DNA; such modifications include methylation of cytosine to generate 5-methylcytosine (5mC) resulting in the generation of heritable epimutation and novel epialleles. This type of non-sequence variation is called epigenetics. The enzymes responsible for generation of such DNA modifications in mammals are named DNA methyltransferases (DNMT) including DNMT1, DNMT2 and DNMT3. The later stages of oxidations to these modifications are catalyzed by Ten Eleven Translocation (TET) proteins, which contain catalytic domains belonging to the 2-oxoglutarate dependent dioxygenase family. In various mammalian cells/tissues including embryonic stem cells, cancer cells and brain tissues, it has been confirmed that these proteins are able to induce the stepwise oxidization of 5-methyl cytosine to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and finally 5-carboxylcytosine (5caC). Each stage from initial methylation until the end of the DNA demethylation process is considered as a specific epigenetic mark that may regulate gene expression. This review discusses controversial evidence for the presence of such oxidative products, particularly 5hmC, in various plant species. Whereas some reports suggest no evidence for enzymatic DNA demethylation, other reports suggest that the presence of oxidative products is followed by the active demethylation and indicate the contribution of possible TET-like proteins in the regulation of gene expression in plants. The review also summarizes the results obtained by expressing the human TET conserved catalytic domain in transgenic plants.
Collapse
Affiliation(s)
- Asaad M Mahmood
- Department of Biology, College of Education, University of Garmian, Kalar, KRG/Iraq
| | - Jim M Dunwell
- School of School of Agriculture, Policy and Development, University of Reading, Reading, Berkshire, UK
| |
Collapse
|
19
|
Brandt B, Rashidiani S, Bán Á, Rauch TA. DNA Methylation-Governed Gene Expression in Autoimmune Arthritis. Int J Mol Sci 2019; 20:E5646. [PMID: 31718084 PMCID: PMC6888626 DOI: 10.3390/ijms20225646] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/05/2019] [Accepted: 11/08/2019] [Indexed: 12/17/2022] Open
Abstract
Rheumatoid arthritis (RA) is a chronic inflammatory autoimmune disease hallmarked by progressive and irreversible joint destruction. RA pathogenesis is a T cell-regulated and B cell-mediated process in which activated lymphocyte-produced chemokines and cytokines promote leukocyte infiltration that ultimately leads to destruction of the joints. There is an obvious need to discover new drugs for RA treatment that have different biological targets or modes of action than the currently employed therapeutics. Environmental factors such as cigarette smoke, certain diet components, and oral pathogens can significantly affect gene regulation via epigenetic factors. Epigenetics opened a new field for pharmacology, and DNA methylation and histone modification-implicated factors are feasible targets for RA therapy. Exploring RA pathogenesis involved epigenetic factors and mechanisms is crucial for developing more efficient RA therapies. Here we review epigenetic alterations associated with RA pathogenesis including DNA methylation and interacting factors. Additionally, we will summarize the literature revealing the involved molecular structures and interactions. Finally, potential epigenetic factor-based therapies will be discussed that may help in better management of RA in the future.
Collapse
Affiliation(s)
- Barbara Brandt
- Department of Medical Biology, Medical School, University of Pécs, Pécs 7624, Hungary; (B.B.); (S.R.)
| | - Shima Rashidiani
- Department of Medical Biology, Medical School, University of Pécs, Pécs 7624, Hungary; (B.B.); (S.R.)
| | - Ágnes Bán
- Department of Dentistry, Oral and Maxillofacial Surgery, Medical School, University of Pécs, Pécs 7621, Hungary;
| | - Tibor A. Rauch
- Department of Medical Biology, Medical School, University of Pécs, Pécs 7624, Hungary; (B.B.); (S.R.)
- Department of Biochemistry and Medical Chemistry, Medical School, University of Pécs, Pécs 7624, Hungary
| |
Collapse
|
20
|
Gaździcka J, Gołąbek K, Strzelczyk JK, Ostrowska Z. Epigenetic Modifications in Head and Neck Cancer. Biochem Genet 2019; 58:213-244. [PMID: 31712935 PMCID: PMC7113219 DOI: 10.1007/s10528-019-09941-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 10/24/2019] [Indexed: 12/17/2022]
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common human malignancy in the world, with high mortality and poor prognosis for patients. Among the risk factors are tobacco and alcohol intake, human papilloma virus, and also genetic and epigenetic modifications. Many studies show that epigenetic events play an important role in HNSCC development and progression, including DNA methylation, chromatin remodeling, histone posttranslational covalent modifications, and effects of non-coding RNA. Epigenetic modifications may influence silencing of tumor suppressor genes by promoter hypermethylation, regulate transcription by microRNAs and changes in chromatin structure, or induce genome instability through hypomethylation. Moreover, getting to better understand aberrant patterns of methylation may provide biomarkers for early detection and diagnosis, while knowledge about target genes of microRNAs may improve the therapy of HNSCC and extend overall survival. The aim of this review is to present recent studies which demonstrate the role of epigenetic regulation in the development of HNSCC.
Collapse
Affiliation(s)
- Jadwiga Gaździcka
- Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, Jordana 19 Str., 41-808, Zabrze, Katowice, Poland.
| | - Karolina Gołąbek
- Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, Jordana 19 Str., 41-808, Zabrze, Katowice, Poland
| | - Joanna Katarzyna Strzelczyk
- Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, Jordana 19 Str., 41-808, Zabrze, Katowice, Poland
| | - Zofia Ostrowska
- Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, Jordana 19 Str., 41-808, Zabrze, Katowice, Poland
| |
Collapse
|
21
|
Blanquart C, Linot C, Cartron PF, Tomaselli D, Mai A, Bertrand P. Epigenetic Metalloenzymes. Curr Med Chem 2019; 26:2748-2785. [PMID: 29984644 DOI: 10.2174/0929867325666180706105903] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 06/04/2018] [Accepted: 06/04/2018] [Indexed: 12/12/2022]
Abstract
Epigenetics controls the expression of genes and is responsible for cellular phenotypes. The fundamental basis of these mechanisms involves in part the post-translational modifications (PTMs) of DNA and proteins, in particular, the nuclear histones. DNA can be methylated or demethylated on cytosine. Histones are marked by several modifications including acetylation and/or methylation, and of particular importance are the covalent modifications of lysine. There exists a balance between addition and removal of these PTMs, leading to three groups of enzymes involved in these processes: the writers adding marks, the erasers removing them, and the readers able to detect these marks and participating in the recruitment of transcription factors. The stimulation or the repression in the expression of genes is thus the result of a subtle equilibrium between all the possibilities coming from the combinations of these PTMs. Indeed, these mechanisms can be deregulated and then participate in the appearance, development and maintenance of various human diseases, including cancers, neurological and metabolic disorders. Some of the key players in epigenetics are metalloenzymes, belonging mostly to the group of erasers: the zinc-dependent histone deacetylases (HDACs), the iron-dependent lysine demethylases of the Jumonji family (JMJ or KDM) and for DNA the iron-dependent ten-eleven-translocation enzymes (TET) responsible for the oxidation of methylcytosine prior to the demethylation of DNA. This review presents these metalloenzymes, their importance in human disease and their inhibitors.
Collapse
Affiliation(s)
- Christophe Blanquart
- CRCINA, INSERM, Universite d'Angers, Universite de Nantes, Nantes, France.,Réseau Epigénétique du Cancéropôle Grand Ouest, France
| | - Camille Linot
- CRCINA, INSERM, Universite d'Angers, Universite de Nantes, Nantes, France
| | - Pierre-François Cartron
- CRCINA, INSERM, Universite d'Angers, Universite de Nantes, Nantes, France.,Réseau Epigénétique du Cancéropôle Grand Ouest, France
| | - Daniela Tomaselli
- Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy
| | - Antonello Mai
- Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy.,Pasteur Institute - Cenci Bolognetti Foundation, Sapienza University of Rome, Rome, Italy
| | - Philippe Bertrand
- Réseau Epigénétique du Cancéropôle Grand Ouest, France.,Institut de Chimie des Milieux et Matériaux de Poitiers, UMR CNRS 7285, 4 rue Michel Brunet, TSA 51106, B27, 86073, Poitiers cedex 09, France
| |
Collapse
|
22
|
Puccini A, Loupakis F, Stintzing S, Cao S, Battaglin F, Togunaka R, Naseem M, Berger MD, Soni S, Zhang W, Mancao C, Salhia B, Mumenthaler SM, Weisenberger DJ, Liang G, Cremolini C, Heinemann V, Falcone A, Millstein J, Lenz HJ. Impact of polymorphisms within genes involved in regulating DNA methylation in patients with metastatic colorectal cancer enrolled in three independent, randomised, open-label clinical trials: a meta-analysis from TRIBE, MAVERICC and FIRE-3. Eur J Cancer 2019; 111:138-147. [PMID: 30852420 DOI: 10.1016/j.ejca.2019.01.105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 01/19/2019] [Accepted: 01/25/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND CpG island DNA hypermethylation and global DNA hypomethylation are hallmark characteristics of colorectal cancer (CRC). Therefore, we aim to explore the effect of genetic variations within the genes that regulate the DNA methylation and demethylation pathways on outcomes in patients with metastatic CRC (mCRC) treated with first-line therapy and enrolled in three independent, randomised, open-label clinical trials. METHODS A total of 884 patients with mCRC enrolled in TRIBE, MAVERICC and FIRE-3 trials were included. Single-nucleotide polymorphisms (SNPs) within genes involved in DNA methylation and demethylation pathways were analysed. The prognostic value of each SNP across all treatment arms was quantified using the inverse-variance-weighted effect size, a meta-analysis approach implemented in the METASOFT software. RESULTS In the meta-analysis, DNMT3A rs11681717 was significantly associated with overall survival (hazard ratio = 1.26; 95% confidence interval [CI] 1.08-1.46; P = 0.002; false discovery rate [FDR] = 0.016), accounting for seven tests in the DNA methylation pathway. In addition, there was suggestive evidence of association for ten-eleven translocation (TET) genes variance with tumour response (TET1 rs3814177, odds ratio [OR] = 0.76, 95% CI 0.59-0.97, P = 0.025, FDR = 0.087; TET3 rs7560668, OR = 1.44; 95% CI 1.10-1.89; P = 0.009; FDR = 0.062). CONCLUSIONS We showed that polymorphisms within the genes responsible for the DNA methylation and demethylation machineries are correlated with outcomes in patients with mCRC who were enrolled in three independent, randomised, open-label, phase II/III clinical trials. In addition, we demonstrated the feasibility of a meta-analysis approach to identify stronger and more convincing association between gene polymorphisms and outcome, potentially leading the way to a new method of analysis for similar data set.
Collapse
Affiliation(s)
- Alberto Puccini
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Fotios Loupakis
- Clinical and Experimental Oncology Department, Medical Oncology Unit 1, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Sebastian Stintzing
- Comprehensive Cancer Center, Ludwig-Maximilian-University of Munich, Munich, Germany
| | - Shu Cao
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Francesca Battaglin
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Clinical and Experimental Oncology Department, Medical Oncology Unit 1, Veneto Institute of Oncology IOV-IRCCS, Padua, Italy
| | - Ryuma Togunaka
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Madiha Naseem
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Martin D Berger
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shivani Soni
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Wu Zhang
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Christoph Mancao
- Oncology Biomarker Development, Genentech Inc., Basel, Switzerland
| | - Bodour Salhia
- Department of Translational Genomics, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shannon M Mumenthaler
- Lawrence J. Ellison Institute for Transformative Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Daniel J Weisenberger
- Department of Biochemistry and Molecular Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Gangning Liang
- Department of Urology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | | | - Volker Heinemann
- Comprehensive Cancer Center, Ludwig-Maximilian-University of Munich, Munich, Germany
| | - Alfredo Falcone
- Department of Medical Oncology, University of Pisa, Pisa, Italy
| | - Joshua Millstein
- Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, USA
| | - Heinz-Josef Lenz
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Department of Preventive Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, USA.
| |
Collapse
|
23
|
Lacal I, Ventura R. Epigenetic Inheritance: Concepts, Mechanisms and Perspectives. Front Mol Neurosci 2018; 11:292. [PMID: 30323739 PMCID: PMC6172332 DOI: 10.3389/fnmol.2018.00292] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 08/02/2018] [Indexed: 01/07/2023] Open
Abstract
Parents’ stressful experiences can influence an offspring’s vulnerability to many pathological conditions, including psychopathologies, and their effects may even endure for several generations. Nevertheless, the cause of this phenomenon has not been determined, and only recently have scientists turned to epigenetics to answer this question. There is extensive literature on epigenetics, but no consensus exists with regard to how and what can (and must) be considered to study and define epigenetics processes and their inheritance. In this work, we aimed to clarify and systematize these concepts. To this end, we analyzed the dynamics of epigenetic changes over time in detail and defined three types of epigenetics: a direct form of epigenetics (DE) and two indirect epigenetic processes—within (WIE) and across (AIE). DE refers to changes that occur in the lifespan of an individual, due to direct experiences with his environment. WIE concerns changes that occur inside of the womb, due to events during gestation. Finally, AIE defines changes that affect the individual’s predecessors (parents, grandparents, etc.), due to events that occur even long before conception and that are somehow (e.g., through gametes, the intrauterine environment setting) transmitted across generations. This distinction allows us to organize the main body of epigenetic evidence according to these categories and then focus on the latter (AIE), referring to it as a faster route of informational transmission across generations—compared with genetic inheritance—that guides human evolution in a Lamarckian (i.e., experience-dependent) manner. Of the molecular processes that are implicated in this phenomenon, well-known (methylation) and novel (non-coding RNA, ncRNA) regulatory mechanisms are converging. Our discussion of the chief methods that are used to study epigenetic inheritance highlights the most compelling technical and theoretical problems of this discipline. Experimental suggestions to expand this field are provided, and their practical and ethical implications are discussed extensively.
Collapse
Affiliation(s)
- Irene Lacal
- Department of Physiology and Pharmacology, Sapienza University of Rome, Rome, Italy
| | - Rossella Ventura
- Department of Psychology and "Daniel Bovet" Center, Sapienza University of Rome, Rome, Italy.,Fondazione Santa Lucia, IRCCS, Rome, Italy
| |
Collapse
|
24
|
Fellous A, Labed‐Veydert T, Locrel M, Voisin A, Earley RL, Silvestre F. DNA methylation in adults and during development of the self-fertilizing mangrove rivulus, Kryptolebias marmoratus. Ecol Evol 2018; 8:6016-6033. [PMID: 29988456 PMCID: PMC6024129 DOI: 10.1002/ece3.4141] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 03/18/2018] [Accepted: 04/04/2018] [Indexed: 12/18/2022] Open
Abstract
In addition to genetic variation, epigenetic mechanisms such as DNA methylation might make important contributions to heritable phenotypic diversity in populations. However, it is often difficult to disentangle the contributions of genetic and epigenetic variation to phenotypic diversity. Here, we investigated global DNA methylation and mRNA expression of the methylation-associated enzymes during embryonic development and in adult tissues of one natural isogenic lineage of mangrove rivulus fish, Kryptolebias marmoratus. Being the best-known self-fertilizing hermaphroditic vertebrate affords the opportunity to work with genetically identical individuals to examine, explicitly, the phenotypic effects of epigenetic variance. Using the LUminometric Methylation Assay (LUMA), we described variable global DNA methylation at CpG sites in adult tissues, which differed significantly between hermaphrodite ovotestes and male testes (79.6% and 87.2%, respectively). After fertilization, an immediate decrease in DNA methylation occurred to 15.8% in gastrula followed by re-establishment to 70.0% by stage 26 (liver formation). Compared to zebrafish, at the same embryonic stages, this reprogramming event seems later, deeper, and longer. Furthermore, genes putatively encoding DNA methyltransferases (DNMTs), Ten-Eleven Translocation (TET), and MeCP2 proteins showed specific regulation in adult gonad and brain, and also during early embryogenesis. Their conserved domains and expression profiles suggest that these proteins play important roles during reproduction and development. This study raises questions about mangrove rivulus' peculiar reprogramming period in terms of epigenetic transmission and physiological adaptation of individuals to highly variable environments. In accordance with the general-purpose genotype model, epigenetic mechanisms might allow for the expression of diverse phenotypes among genetically identical individuals. Such phenotypes might help to overcome environmental challenges, making the mangrove rivulus a valuable vertebrate model for ecological epigenetic studies. The mangrove rivulus, Kryptolebias marmoratus, is the best-known self-fertilizing hermaphroditic vertebrate that allows to work with genetically identical individuals to examine, explicitly, the phenotypic effects of epigenetic variance. The reprogramming event is later, more dramatic and longer than in other described vertebrates. High evolutionary conservation and expression patterns of DNMT, TET, and MeCP2 proteins in K. marmoratus suggest biological roles for each member in gametogenesis and development.
Collapse
Affiliation(s)
- Alexandre Fellous
- Laboratory of Evolutionary and Adaptive PhysiologyInstitute of Life, Earth and EnvironmentUniversity of NamurNamurBelgium
| | - Tiphaine Labed‐Veydert
- Laboratory of Evolutionary and Adaptive PhysiologyInstitute of Life, Earth and EnvironmentUniversity of NamurNamurBelgium
| | - Mélodie Locrel
- Laboratory of Evolutionary and Adaptive PhysiologyInstitute of Life, Earth and EnvironmentUniversity of NamurNamurBelgium
| | - Anne‐Sophie Voisin
- Laboratory of Evolutionary and Adaptive PhysiologyInstitute of Life, Earth and EnvironmentUniversity of NamurNamurBelgium
| | - Ryan L. Earley
- Department of Biological SciencesUniversity of AlabamaTuscaloosaAlabamaUSA
| | - Frederic Silvestre
- Laboratory of Evolutionary and Adaptive PhysiologyInstitute of Life, Earth and EnvironmentUniversity of NamurNamurBelgium
| |
Collapse
|
25
|
A network-based analysis of the human TET Gene Family. Biologia (Bratisl) 2018. [DOI: 10.2478/s11756-018-0041-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
26
|
Efimova OA, Pendina AA, Tikhonov AV, Baranov VS. The Evolution of Ideas on the Biological Role of 5-methylcytosine Oxidative Derivatives in the Mammalian Genome. ACTA ACUST UNITED AC 2018. [DOI: 10.1134/s2079059718010069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
27
|
Waryah CB, Moses C, Arooj M, Blancafort P. Zinc Fingers, TALEs, and CRISPR Systems: A Comparison of Tools for Epigenome Editing. Methods Mol Biol 2018. [PMID: 29524128 DOI: 10.1007/978-1-4939-7774-1_2] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The completion of genome, epigenome, and transcriptome mapping in multiple cell types has created a demand for precision biomolecular tools that allow researchers to functionally manipulate DNA, reconfigure chromatin structure, and ultimately reshape gene expression patterns. Epigenetic editing tools provide the ability to interrogate the relationship between epigenetic modifications and gene expression. Importantly, this information can be exploited to reprogram cell fate for both basic research and therapeutic applications. Three different molecular platforms for epigenetic editing have been developed: zinc finger proteins (ZFs), transcription activator-like effectors (TALEs), and the system of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated (Cas) proteins. These platforms serve as custom DNA-binding domains (DBDs), which are fused to epigenetic modifying domains to manipulate epigenetic marks at specific sites in the genome. The addition and/or removal of epigenetic modifications reconfigures local chromatin structure, with the potential to provoke long-lasting changes in gene transcription. Here we summarize the molecular structure and mechanism of action of ZF, TALE, and CRISPR platforms and describe their applications for the locus-specific manipulation of the epigenome. The advantages and disadvantages of each platform will be discussed with regard to genomic specificity, potency in regulating gene expression, and reprogramming cell phenotypes, as well as ease of design, construction, and delivery. Finally, we outline potential applications for these tools in molecular biology and biomedicine and identify possible barriers to their future clinical implementation.
Collapse
Affiliation(s)
- Charlene Babra Waryah
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, Australia
| | - Colette Moses
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, Australia
- School of Human Sciences, The University of Western Australia, Perth, WA, Australia
| | - Mahira Arooj
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, Australia
- School of Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Pilar Blancafort
- Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, Australia.
- School of Human Sciences, The University of Western Australia, Perth, WA, Australia.
| |
Collapse
|
28
|
Sepulveda H, Villagra A, Montecino M. Tet-Mediated DNA Demethylation Is Required for SWI/SNF-Dependent Chromatin Remodeling and Histone-Modifying Activities That Trigger Expression of the Sp7 Osteoblast Master Gene during Mesenchymal Lineage Commitment. Mol Cell Biol 2017; 37:e00177-17. [PMID: 28784721 PMCID: PMC5615189 DOI: 10.1128/mcb.00177-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 05/15/2017] [Accepted: 07/22/2017] [Indexed: 12/22/2022] Open
Abstract
Here we assess histone modification, chromatin remodeling, and DNA methylation processes that coordinately control the expression of the bone master transcription factor Sp7 (osterix) during mesenchymal lineage commitment in mammalian cells. We find that Sp7 gene silencing is mediated by DNA methyltransferase1/3 (DNMT1/3)-, histone deacetylase 1/2/4 (HDAC1/2/4)-, Setdb1/Suv39h1-, and Ezh1/2-containing complexes. In contrast, Sp7 gene activation involves changes in histone modifications, accompanied by decreased nucleosome enrichment and DNA demethylation mediated by SWI/SNF- and Tet1/Tet2-containing complexes, respectively. Inhibition of DNA methylation triggers changes in the histone modification profile and chromatin-remodeling events leading to Sp7 gene expression. Tet1/Tet2 silencing prevents Sp7 expression during osteoblast differentiation as it impairs DNA demethylation and alters the recruitment of histone methylase (COMPASS)-, histone demethylase (Jmjd2a/Jmjd3)-, and SWI/SNF-containing complexes to the Sp7 promoter. The dissection of these interconnected epigenetic mechanisms that govern Sp7 gene activation reveals a hierarchical process where regulatory components mediating DNA demethylation play a leading role.
Collapse
Affiliation(s)
- Hugo Sepulveda
- Center for Biomedical Research, Faculty of Biological Sciences and Faculty of Medicine, Universidad Andres Bello, Santiago, Chile
- FONDAP Center for Genome Regulation, Faculty of Biological Sciences and Faculty of Medicine, Universidad Andres Bello, Santiago, Chile
| | - Alejandro Villagra
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Martin Montecino
- Center for Biomedical Research, Faculty of Biological Sciences and Faculty of Medicine, Universidad Andres Bello, Santiago, Chile
- FONDAP Center for Genome Regulation, Faculty of Biological Sciences and Faculty of Medicine, Universidad Andres Bello, Santiago, Chile
| |
Collapse
|
29
|
Roche J, Gemmill RM, Drabkin HA. Epigenetic Regulation of the Epithelial to Mesenchymal Transition in Lung Cancer. Cancers (Basel) 2017; 9:cancers9070072. [PMID: 28672805 PMCID: PMC5532608 DOI: 10.3390/cancers9070072] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 06/17/2017] [Accepted: 06/17/2017] [Indexed: 12/24/2022] Open
Abstract
Lung cancer is the leading cause of cancer deaths worldwide. It is an aggressive and devastating cancer because of metastasis triggered by enhanced migration and invasion, and resistance to cytotoxic chemotherapy. The epithelial to mesenchymal transition (EMT) is a fundamental developmental process that is reactivated in wound healing and a variety of diseases including cancer where it promotes migration/invasion and metastasis, resistance to treatment, and generation and maintenance of cancer stem cells. The induction of EMT is associated with reprogramming of the epigenome. This review focuses on major mechanisms of epigenetic regulation mainly in lung cancer with recent data on EZH2 (enhancer of zeste 2 polycomb repressive complex 2 subunit ), the catalytic subunit of the PRC2 (Polycomb Group PcG), that behaves as an oncogene in lung cancer associated with gene repression, non-coding RNAs and the epitranscriptome.
Collapse
Affiliation(s)
- Joëlle Roche
- Laboratoire Ecologie et Biologie des Interactions, Equipe SEVE, Université de Poitiers, UMR CNRS 7267, F-86073 Poitiers, France.
| | - Robert M Gemmill
- Division of Hematology-Oncology, Medical University of South Carolina, 39 Sabin St., MSC 635, Charleston, SC 29425, USA.
| | - Harry A Drabkin
- Division of Hematology-Oncology, Medical University of South Carolina, 39 Sabin St., MSC 635, Charleston, SC 29425, USA.
| |
Collapse
|
30
|
Jin L, Lv M, Wei Y, Lu J, Min S. Reactivity of 5-carboxycytosine toward addition and hydrogen abstraction by ·OH in acetonitrile: a computational study. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1279286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Lingxia Jin
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi Sci-Tech University, Hanzhong, P.R. China
| | - Mengdan Lv
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi Sci-Tech University, Hanzhong, P.R. China
| | - Yawen Wei
- Periodical Offices of Chang’an University, Chang’an University, Xi’an, P.R. China
| | - Jiufu Lu
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi Sci-Tech University, Hanzhong, P.R. China
| | - Suotian Min
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi Sci-Tech University, Hanzhong, P.R. China
| |
Collapse
|
31
|
Vitamin C in Stem Cell Biology: Impact on Extracellular Matrix Homeostasis and Epigenetics. Stem Cells Int 2017; 2017:8936156. [PMID: 28512473 PMCID: PMC5415867 DOI: 10.1155/2017/8936156] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 03/05/2017] [Indexed: 12/30/2022] Open
Abstract
Transcription factors and signaling molecules are well-known regulators of stem cell identity and behavior; however, increasing evidence indicates that environmental cues contribute to this complex network of stimuli, acting as crucial determinants of stem cell fate. l-Ascorbic acid (vitamin C (VitC)) has gained growing interest for its multiple functions and mechanisms of action, contributing to the homeostasis of normal tissues and organs as well as to tissue regeneration. Here, we review the main functions of VitC and its effects on stem cells, focusing on its activity as cofactor of Fe+2/αKG dioxygenases, which regulate the epigenetic signatures, the redox status, and the extracellular matrix (ECM) composition, depending on the enzymes' subcellular localization. Acting as cofactor of collagen prolyl hydroxylases in the endoplasmic reticulum, VitC regulates ECM/collagen homeostasis and plays a key role in the differentiation of mesenchymal stem cells towards osteoblasts, chondrocytes, and tendons. In the nucleus, VitC enhances the activity of DNA and histone demethylases, improving somatic cell reprogramming and pushing embryonic stem cell towards the naive pluripotent state. The broad spectrum of actions of VitC highlights its relevance for stem cell biology in both physiology and disease.
Collapse
|
32
|
Abstract
Activation of oncogenes or the deactivation of tumor suppressor genes has long been established as the fundamental mechanism leading towards carcinogenesis. Although this age old axiom is vastly accurate, thorough study over the last 15years has given us unprecedented information on the involvement of epigenetic in cancer. Various biochemical pathways that are essential towards tumorigenesis are regulated by the epigenetic phenomenons like remodeling of nucleosome by histone modifications, DNA methylation and miRNA mediated targeting of various genes. Moreover the presence of mutations in the genes controlling the epigenetic players has further strengthened the association of epigenetics in cancer. This merger has opened up newer avenues for targeted anti-cancer drug therapy with numerous pharmaceutical industries focusing on expanding their research and development pipeline with epigenetic drugs. The information provided here elaborates the elementary phenomena of the various epigenetic regulators and discusses their alteration associated with the development of cancer. We also highlight the recent developments in epigenetic drugs combining preclinical and clinical data to signify this evolving field in cancer research.
Collapse
Affiliation(s)
- Subhankar Biswas
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal University, Manipal 576104, Karnataka, India
| | - C Mallikarjuna Rao
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal University, Manipal 576104, Karnataka, India.
| |
Collapse
|
33
|
Grzybek M, Golonko A, Walczak M, Lisowski P. Epigenetics of cell fate reprogramming and its implications for neurological disorders modelling. Neurobiol Dis 2016; 99:84-120. [PMID: 27890672 DOI: 10.1016/j.nbd.2016.11.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 11/03/2016] [Accepted: 11/21/2016] [Indexed: 02/06/2023] Open
Abstract
The reprogramming of human induced pluripotent stem cells (hiPSCs) proceeds in a stepwise manner with reprogramming factors binding and epigenetic composition changes during transition to maintain the epigenetic landscape, important for pluripotency. There arises a question as to whether the aberrant epigenetic state after reprogramming leads to epigenetic defects in induced stem cells causing unpredictable long term effects in differentiated cells. In this review, we present a comprehensive view of epigenetic alterations accompanying reprogramming, cell maintenance and differentiation as factors that influence applications of hiPSCs in stem cell based technologies. We conclude that sample heterogeneity masks DNA methylation signatures in subpopulations of cells and thus believe that beside a genetic evaluation, extensive epigenomic screening should become a standard procedure to ensure hiPSCs state before they are used for genome editing and differentiation into neurons of interest. In particular, we suggest that exploitation of the single-cell composition of the epigenome will provide important insights into heterogeneity within hiPSCs subpopulations to fast forward development of reliable hiPSC-based analytical platforms in neurological disorders modelling and before completed hiPSC technology will be implemented in clinical approaches.
Collapse
Affiliation(s)
- Maciej Grzybek
- Faculty of Veterinary Medicine, University of Life Sciences in Lublin, Akademicka 12, 20-950 Lublin, Poland; Department of Molecular Biology, Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Jastrzębiec, Postępu 36A, 05-552 Magdalenka, Poland.
| | - Aleksandra Golonko
- Department of Biotechnology, Faculty of Civil and Environmental Engineering, Bialystok University of Technology, Wiejska 45E, 15-351 Bialystok, Poland.
| | - Marta Walczak
- Department of Animal Behavior, Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Jastrzębiec, Postępu 36A, 05-552 Magdalenka, Poland.
| | - Pawel Lisowski
- Department of Molecular Biology, Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Jastrzębiec, Postępu 36A, 05-552 Magdalenka, Poland; iPS Cell-Based Disease Modelling Group, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Rössle-Str. 10, 13092 Berlin, Germany.
| |
Collapse
|
34
|
Zhang Y, Wu K, Shao Y, Sui F, Yang Q, Shi B, Hou P, Ji M. Decreased 5-Hydroxymethylcytosine (5-hmC) predicts poor prognosis in early-stage laryngeal squamous cell carcinoma. Am J Cancer Res 2016; 6:1089-1098. [PMID: 27294001 PMCID: PMC4889722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 04/18/2016] [Indexed: 06/06/2023] Open
Abstract
Accumulating evidences suggest that large-scale loss of 5-hydroxymethylcytosine (5-hmC) is an epigenetic hallmark in different cancers. However, the levels of 5-hmC in laryngeal squamous cell carcinoma (LSCC) and its prognostic value in this cancer remain largely unknown. Using dot-blot and quantitative RT-PCR assays, we investigate 5-hmC levels and expression of TET-1, -2 and -3 in LSCCs and explore the association of 5-hmC levels with clinicopathological characteristics and clinical outcome of LSCC patients. Our data showed that 5-hmC was significantly decreased in LSCCs as compared with matched normal tissues. We also found a strong link between decreased 5-hmC and the reduction of TET-1 gene expression, but not TET-2 or -3, suggesting that decreased TET-1 expression was implicated in 5-hmC loss in LSCC. Moreover, Mann-Whitney U tests showed that 5-hmC content was significantly associated with smoking (P = 0.039) and tumor invasion (P = 0.004). Importantly, we found that decreased 5-hmC was significantly associated with poor survival of early-stage LSCC patients (P = 0.043). Altogether, our findings implicate that decreased 5-hmC probaly caused by the reduction of TET-1 is crucial to the clinical pathology of LSCC and is a poor prognostic factor in ealry-stage LSCC patients.
Collapse
Affiliation(s)
- Yanfang Zhang
- Department of Endocrinology, The First Affiliated Hospital of Xi’an Jiaotong UniversityXi’an 710061, The People’s Republic of China
- Department of Endocrinology, Luoyang Central Hospital Affiliated to Zhengzhou UniversityLuoyang 471009, The People’s Republic of China
| | - Kexia Wu
- Department of Endocrinology, The First Affiliated Hospital of Xi’an Jiaotong UniversityXi’an 710061, The People’s Republic of China
| | - Yuan Shao
- Department of Otolaryngology, The First Affiliated Hospital of Xi’an Jiaotong UniversityXi’an 710061, The People’s Republic of China
| | - Fang Sui
- Department of Endocrinology, The First Affiliated Hospital of Xi’an Jiaotong UniversityXi’an 710061, The People’s Republic of China
| | - Qi Yang
- Department of Endocrinology, The First Affiliated Hospital of Xi’an Jiaotong UniversityXi’an 710061, The People’s Republic of China
| | - Bingyin Shi
- Department of Endocrinology, The First Affiliated Hospital of Xi’an Jiaotong UniversityXi’an 710061, The People’s Republic of China
| | - Peng Hou
- Department of Endocrinology, The First Affiliated Hospital of Xi’an Jiaotong UniversityXi’an 710061, The People’s Republic of China
| | - Meiju Ji
- Center for Translational Medicine, The First Affiliated Hospital of Xi’an Jiaotong UniversityXi’an 710061, The People’s Republic of China
| |
Collapse
|
35
|
Marholz LJ, Wang W, Zheng Y, Wang X. A Fluorescence Polarization Biophysical Assay for the Naegleria DNA Hydroxylase Tet1. ACS Med Chem Lett 2016; 7:167-171. [PMID: 27980707 PMCID: PMC5141568 DOI: 10.1021/acsmedchemlett.5b00366] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 12/07/2015] [Indexed: 01/23/2023] Open
Abstract
![]()
The discovery of the 5-methylcytosine
(5mC) oxidation by the ten–eleven
translocation (Tet) protein family was an important advancement in
our understanding of DNA-modified epigenetics. Potent inhibitors of
these proteins are greatly desired for both the understanding of the
functions of these enzymes and to serve as eventual therapeutic leads.
So far, the discovery of such small molecules with high affinity has
been quite limited. Original tools to screen for activity are greatly
needed in order to accelerate this process. Here we present a novel
fluorescent probe, and the results of a fluorescence polarization-based
binding assay for Naegleria Tet1, a homologue to
mammalian Tet. A fluorescence polarization-based competition assay
was also established and applied to the rapid and quantitative measurement
of the binding affinity of the cofactor αKG and several known
Tet1 inhibitors.
Collapse
Affiliation(s)
- Laura J. Marholz
- Department
of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - Wei Wang
- Department
of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - Yu Zheng
- RGENE Inc., 953 Indiana Street, San Francisco, California 94107, United States
| | - Xiang Wang
- Department
of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, United States
| |
Collapse
|
36
|
Bao J, Bedford MT. Epigenetic regulation of the histone-to-protamine transition during spermiogenesis. Reproduction 2016; 151:R55-70. [PMID: 26850883 DOI: 10.1530/rep-15-0562] [Citation(s) in RCA: 159] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 02/05/2016] [Indexed: 12/19/2022]
Abstract
In mammals, male germ cells differentiate from haploid round spermatids to flagella-containing motile sperm in a process called spermiogenesis. This process is distinct from somatic cell differentiation in that the majority of the core histones are replaced sequentially, first by transition proteins and then by protamines, facilitating chromatin hyper-compaction. This histone-to-protamine transition process represents an excellent model for the investigation of how epigenetic regulators interact with each other to remodel chromatin architecture. Although early work in the field highlighted the critical roles of testis-specific transcription factors in controlling the haploid-specific developmental program, recent studies underscore the essential functions of epigenetic players involved in the dramatic genome remodeling that takes place during wholesale histone replacement. In this review, we discuss recent advances in our understanding of how epigenetic players, such as histone variants and histone writers/readers/erasers, rewire the haploid spermatid genome to facilitate histone substitution by protamines in mammals.
Collapse
Affiliation(s)
- Jianqiang Bao
- Department of Epigenetics and Molecular CarcinogenesisThe University of Texas MD Anderson Cancer Center, Smithville, Texas, USA
| | - Mark T Bedford
- Department of Epigenetics and Molecular CarcinogenesisThe University of Texas MD Anderson Cancer Center, Smithville, Texas, USA
| |
Collapse
|
37
|
Dan J, Chen T. Genetic Studies on Mammalian DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:123-150. [PMID: 27826837 DOI: 10.1007/978-3-319-43624-1_6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Cytosine methylation at the C5-position, generating 5-methylcytosine (5mC), is a DNA modification found in many eukaryotic organisms, including fungi, plants, invertebrates, and vertebrates, albeit its levels vary greatly in different organisms. In mammals, cytosine methylation occurs predominantly in the context of CpG dinucleotides, with the majority (60-80 %) of CpG sites in their genomes being methylated. DNA methylation plays crucial roles in the regulation of chromatin structure and gene expression and is essential for mammalian development. Aberrant changes in DNA methylation levels and patterns are associated with various human diseases, including cancer and developmental disorders. DNA methylation is mediated by three active DNA methyltransferases (Dnmts), namely, Dnmt1, Dnmt3a, and Dnmt3b, in mammals. Over the last two decades, genetic manipulations of these enzymes, as well as their regulators, in mice have greatly contributed to our understanding of the biological functions of DNA methylation in mammals. In this chapter, we discuss genetic studies on mammalian Dnmts, focusing on their roles in embryogenesis, cellular differentiation, genomic imprinting, and X-chromosome inactivation.
Collapse
Affiliation(s)
- Jiameng Dan
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, 1808 Park Road 1C, Smithville, TX, 78957, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, 1808 Park Road 1C, Smithville, TX, 78957, USA
| | - Taiping Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, 1808 Park Road 1C, Smithville, TX, 78957, USA.
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, 1808 Park Road 1C, Smithville, TX, 78957, USA.
- Graduate School of Biomedical Sciences at Houston, Houston, TX, 77030, USA.
| |
Collapse
|
38
|
Akahori H, Guindon S, Yoshizaki S, Muto Y. Molecular Evolution of the TET Gene Family in Mammals. Int J Mol Sci 2015; 16:28472-85. [PMID: 26633372 PMCID: PMC4691057 DOI: 10.3390/ijms161226110] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 11/10/2015] [Accepted: 11/18/2015] [Indexed: 11/21/2022] Open
Abstract
Ten-eleven translocation (TET) proteins, a family of Fe2+- and 2-oxoglutarate-dependent dioxygenases, are involved in DNA demethylation. They also help regulate various cellular functions. Three TET paralogs have been identified (TET1, TET2, and TET3) in humans. This study focuses on the evolution of mammalian TET genes. Distinct patterns in TET1 and TET2 vs. TET3 were revealed by codon-based tests of positive selection. Results indicate that TET1 and TET2 genes have experienced positive selection more frequently than TET3 gene, and that the majority of codon sites evolved under strong negative selection. These findings imply that the selective pressure on TET3 may have been relaxed in several lineages during the course of evolution. Our analysis of convergent amino acid substitutions also supports the different evolutionary dynamics among TET gene subfamily members. All of the five amino acid sites that are inferred to have evolved under positive selection in the catalytic domain of TET2 are localized at the protein’s outer surface. The adaptive changes of these positively selected amino acid sites could be associated with dynamic interactions between other TET-interacting proteins, and positive selection thus appears to shift the regulatory scheme of TET enzyme function.
Collapse
Affiliation(s)
- Hiromichi Akahori
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1194, Japan.
| | - Stéphane Guindon
- Department of Statistics, the University of Auckland, Auckland 1010, New Zealand.
| | - Sumio Yoshizaki
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1194, Japan.
| | - Yoshinori Muto
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1194, Japan.
- Department of Functional Bioscience, Gifu University School of Medicine, 1-1 Yanagido, Gifu 501-1193, Japan.
| |
Collapse
|
39
|
King GJ. Crop epigenetics and the molecular hardware of genotype × environment interactions. FRONTIERS IN PLANT SCIENCE 2015; 6:968. [PMID: 26594221 PMCID: PMC4635209 DOI: 10.3389/fpls.2015.00968] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 10/22/2015] [Indexed: 05/04/2023]
Abstract
Crop plants encounter thermal environments which fluctuate on a diurnal and seasonal basis. Future climate resilient cultivars will need to respond to thermal profiles reflecting more variable conditions, and harness plasticity that involves regulation of epigenetic processes and complex genomic regulatory networks. Compartmentalization within plant cells insulates the genomic central processing unit within the interphase nucleus. This review addresses the properties of the chromatin hardware in which the genome is embedded, focusing on the biophysical and thermodynamic properties of DNA, histones and nucleosomes. It explores the consequences of thermal and ionic variation on the biophysical behavior of epigenetic marks such as DNA cytosine methylation (5mC), and histone variants such as H2A.Z, and how these contribute to maintenance of chromatin integrity in the nucleus, while enabling specific subsets of genes to be regulated. Information is drawn from theoretical molecular in vitro studies as well as model and crop plants and incorporates recent insights into the role epigenetic processes play in mediating between environmental signals and genomic regulation. A preliminary speculative framework is outlined, based on the evidence of what appears to be a cohesive set of interactions at molecular, biophysical and electrostatic level between the various components contributing to chromatin conformation and dynamics. It proposes that within plant nuclei, general and localized ionic homeostasis plays an important role in maintaining chromatin conformation, whilst maintaining complex genomic regulation that involves specific patterns of epigenetic marks. More generally, reversible changes in DNA methylation appear to be consistent with the ability of nuclear chromatin to manage variation in external ionic and temperature environment. Whilst tentative, this framework provides scope to develop experimental approaches to understand in greater detail the internal environment of plant nuclei. It is hoped that this will generate a deeper understanding of the molecular mechanisms underlying genotype × environment interactions that may be beneficial for long-term improvement of crop performance in less predictable climates.
Collapse
Affiliation(s)
- Graham J. King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW, Australia
- National Key Laboratory for Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
- Crops for the Future, Biotechnology and Breeding Systems, Semenyih, Malaysia
| |
Collapse
|
40
|
Hamidi T, Singh AK, Chen T. Genetic alterations of DNA methylation machinery in human diseases. Epigenomics 2015; 7:247-65. [PMID: 25942534 DOI: 10.2217/epi.14.80] [Citation(s) in RCA: 180] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
DNA methylation plays a critical role in the regulation of chromatin structure and gene expression and is involved in a variety of biological processes. The levels and patterns of DNA methylation are regulated by both DNA methyltransferases (DNMT1, DNMT3A and DNMT3B) and 'demethylating' proteins, including the ten-eleven translocation (TET) family of dioxygenases (TET1, TET2 and TET3). The effects of DNA methylation on chromatin and gene expression are largely mediated by methylated DNA 'reader' proteins, including MeCP2. Numerous mutations in DNMTs, TETs and MeCP2 have been identified in cancer and developmental disorders, highlighting the importance of the DNA methylation machinery in human development and physiology. In this review, we describe these mutations and discuss how they may lead to disease phenotypes.
Collapse
Affiliation(s)
- Tewfik Hamidi
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park - Research Division, 1808 Park Road 1C, P. O. Box 389, Smithville, TX 78957, USA
| | | | | |
Collapse
|
41
|
Epigenetic regulation of human adipose-derived stem cells differentiation. Mol Cell Biochem 2015; 410:111-20. [PMID: 26307369 DOI: 10.1007/s11010-015-2543-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 08/18/2015] [Indexed: 12/20/2022]
Abstract
Adult stem cells have more restricted differentiation potential than embryonic stem cells (ESCs), but upon appropriate stimulation can differentiate into cells of different germ layers. Epigenetic factors, including DNA modifications, take a significant part in regulation of pluripotency and differentiation of ESCs. Less is known about the epigenetic regulation of these processes in adult stem cells. Gene expression profile and location of DNA modifications in adipose-derived stem cells (ADSCs) and their osteogenically differentiated lineages were analyzed using Agilent microarrays. Methylation-specific PCR and restriction-based quantitative PCR were applied for 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) detection in selected loci. The level of DNA modifications in the POU5F1 locus was quantified with deep sequencing. Expression levels of selected genes were assayed by real-time PCR. ADSCs differentiation into osteogenic lineages involved marked changes in both 5mC and 5hmC profiles, but 5hmC changes were more abundant. 5mC losses and 5hmC gains were the main events observed during ADSCs differentiation, and were accompanied by increased expression of TET1 (P = 0.009). In ADSCs, POU5F1 was better expressed than NANOG or SOX2 (P ≤ 0.001). Both 5mC and 5hmC marks were present in the POU5F1 locus, but only hydroxymethylation of specific cytosine showed significant effect on the gene expression. In summary, the data of our study suggest significant involvement of changes in 5hmC profile during the differentiation of human adult stem cells.
Collapse
|
42
|
Shukla A, Sehgal M, Singh TR. Hydroxymethylation and its potential implication in DNA repair system: A review and future perspectives. Gene 2015; 564:109-18. [DOI: 10.1016/j.gene.2015.03.075] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 01/21/2015] [Accepted: 03/05/2015] [Indexed: 12/22/2022]
|
43
|
Nuclear and mitochondrial DNA alterations in newborns with prenatal exposure to cigarette smoke. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2015; 12:1135-55. [PMID: 25648174 PMCID: PMC4344659 DOI: 10.3390/ijerph120201135] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 01/13/2015] [Indexed: 12/17/2022]
Abstract
Newborns exposed to maternal cigarette smoke (CS) in utero have an increased risk of developing chronic diseases, cancer, and acquiring decreased cognitive function in adulthood. Although the literature reports many deleterious effects associated with maternal cigarette smoking on the fetus, the molecular alterations and mechanisms of action are not yet clear. Smoking may act directly on nuclear DNA by inducing mutations or epigenetic modifications. Recent studies also indicate that smoking may act on mitochondrial DNA by inducing a change in the number of copies to make up for the damage caused by smoking on the respiratory chain and lack of energy. In addition, individual genetic susceptibility plays a significant role in determining the effects of smoking during development. Furthermore, prior exposure of paternal and maternal gametes to cigarette smoke may affect the health of the developing individual, not only the in utero exposure. This review examines the genetic and epigenetic alterations in nuclear and mitochondrial DNA associated with smoke exposure during the most sensitive periods of development (prior to conception, prenatal and early postnatal) and assesses how such changes may have consequences for both fetal growth and development.
Collapse
|
44
|
O'Doherty AM, McGettigan PA. Epigenetic processes in the male germline. Reprod Fertil Dev 2015; 27:725-38. [DOI: 10.1071/rd14167] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 08/01/2014] [Indexed: 12/12/2022] Open
Abstract
Sperm undergo some of the most extensive chromatin modifications seen in mammalian biology. During male germline development, paternal DNA methylation marks are erased and established on a global scale through waves of demethylation and de novo methylation. As spermatogenesis progresses, the majority of the histones are removed and replaced by protamines, enabling a tighter packaging of the DNA and transcriptional shutdown. Following fertilisation, the paternal genome is rapidly reactivated, actively demethylated, the protamines are replaced with histones and the embryonic genome is activated. The development of new assays, made possible by high-throughput sequencing technology, has resulted in the revisiting of what was considered settled science regarding the state of DNA packaging in mammalian spermatozoa. Researchers have discovered that not all histones are replaced by protamines and, in certain experiments, various species of RNA have been detected in what was previously considered transcriptionally quiescent spermatozoa. Most controversially, several groups have suggested that environmental modifications of the epigenetic state of spermatozoa may operate as a non-DNA-based form of inheritance, a process known as ‘transgenerational epigenetic inheritance’. Other developments in the field include the increased focus on the involvement of short RNAs, such as microRNAs, long non-coding RNAs and piwi-interacting RNAs. There has also been an accumulation of evidence illustrating associations between defects in sperm DNA packaging and disease and fertility. In this paper we review the literature, recent findings and areas of controversy associated with epigenetic processes in the male germline, focusing on DNA methylation dynamics, non-coding RNAs, the biology of sperm chromatin packaging and transgenerational inheritance.
Collapse
|
45
|
Jin L, Zhao C, Zhang T, Wang Z, Min S, Wang W, Wei Y. Effects of an acid–alkaline environment on the reactivity of 5-carboxycytosine with hydroxyl radicals. RSC Adv 2015. [DOI: 10.1039/c5ra17393k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The addition of ˙OH to C5C6 double bond and abstraction of H5 from 5-caCyt are more favourable in neutral, acidic and alkaline conditions.
Collapse
Affiliation(s)
- Lingxia Jin
- Shaanxi Province Key Laboratory of Catalytic Fundamentals & Applications
- School of Chemical & Environment Science
- Shaanxi University of Technology
- Hanzhong
- China
| | - Caibin Zhao
- Shaanxi Province Key Laboratory of Catalytic Fundamentals & Applications
- School of Chemical & Environment Science
- Shaanxi University of Technology
- Hanzhong
- China
| | - Tianlei Zhang
- Shaanxi Province Key Laboratory of Catalytic Fundamentals & Applications
- School of Chemical & Environment Science
- Shaanxi University of Technology
- Hanzhong
- China
| | - Zhiyin Wang
- Shaanxi Province Key Laboratory of Catalytic Fundamentals & Applications
- School of Chemical & Environment Science
- Shaanxi University of Technology
- Hanzhong
- China
| | - Suotian Min
- Shaanxi Province Key Laboratory of Catalytic Fundamentals & Applications
- School of Chemical & Environment Science
- Shaanxi University of Technology
- Hanzhong
- China
| | - Wenliang Wang
- Key Laboratory for Macromolecular Science of Shaanxi Province
- School of Chemistry and Chemical Engineering
- Shaanxi Normal University
- Xi’an 710062
- China
| | - Yawen Wei
- Institute of Publication Science
- Chang’an University
- Xi’an 710064
- China
| |
Collapse
|
46
|
Ma JY, Zhang T, Shen W, Schatten H, Sun QY. Molecules and mechanisms controlling the active DNA demethylation of the mammalian zygotic genome. Protein Cell 2014; 5:827-36. [PMID: 25152302 PMCID: PMC4225482 DOI: 10.1007/s13238-014-0095-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Accepted: 07/21/2014] [Indexed: 12/02/2022] Open
Abstract
The active DNA demethylation in early embryos is essential for subsequent development. Although the zygotic genome is globally demethylated, the DNA methylation of imprinted regions, part of repeat sequences and some gamete-specific regions are maintained. Recent evidence has shown that multiple proteins and biological pathways participate in the regulation of active DNA demethylation, such as TET proteins, DNA repair pathways and DNA methyltransferases. Here we review the recent understanding regarding proteins associated with active DNA demethylation and the regulatory networks controlling the active DNA demethylation in early embryos.
Collapse
Affiliation(s)
- Jun-Yu Ma
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, 266109, China
| | | | | | | | | |
Collapse
|
47
|
Dao T, Cheng RYS, Revelo MP, Mitzner W, Tang W. Hydroxymethylation as a Novel Environmental Biosensor. Curr Environ Health Rep 2014; 1:1-10. [PMID: 24860723 PMCID: PMC4029614 DOI: 10.1007/s40572-013-0005-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Beyond the genome, epigenetics has become a promising approach in understanding the interactions between the gene and the environment. Epigenetic regulation includes DNA methylation, histone modifications, and non-coding RNAs. Among these, DNA methylation, which is the addition of a methyl group to the fifth base of cytosine to produce 5-methylcytosine (5-mC), is most commonly studied. Epigenetic regulation has changed given the discovery of 5-hydroxymethylcytosine (5-hmC), considered the "sixth base", and the nature of TET proteins to catalyze 5-mC oxidation to 5-hmC. 5-hydroxymethylation has been proposed to be a stable intermediate between methylation and demethylation and has raised questions about the functions of 5-hmC in gene regulation in cells, tissues, and organs in response to environmental exposure. Herein, we have provided an introduction to the chemistry of 5-hydroxymethylation, and the techniques for detection of 5-hydroxymethylation. In addition, we have reviewed current reports describing how 5-hmC responds to environmental factors, leading to the development of disease. And finally, we have discussed the potential use of 5-hmC in the study of disease development. All in all, it is our goal to provide innovative and convincing epigenetic studies for understanding the etiology of environmentally-related human disease, and translate these epigenetic findings into lifestyle recommendations and clinical practices to prevent and cure disease.
Collapse
Affiliation(s)
- T Dao
- Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States
| | - R Y S Cheng
- Radiation Biology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - M P Revelo
- Department of Pathology, University of Utah, Salt Lake City, Utah, United States
| | - W Mitzner
- Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States
| | - Wy Tang
- Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States
| |
Collapse
|
48
|
Logan PC, Mitchell MD, Lobie PE. DNA methyltransferases and TETs in the regulation of differentiation and invasiveness of extra-villous trophoblasts. Front Genet 2013; 4:265. [PMID: 24363660 PMCID: PMC3849743 DOI: 10.3389/fgene.2013.00265] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 11/15/2013] [Indexed: 01/21/2023] Open
Abstract
Specialized cell types of trophoblast cells form the placenta in which each cell type has particular properties of proliferation and invasion. The placenta sustains the growth of the fetus throughout pregnancy and any aberrant trophoblast differentiation or invasion potentially affects the future health of the child and adult. Recently, the field of epigenetics has been applied to understand differentiation of trophoblast lineages and embryonic stem cells (ESC), from fertilization of the oocyte onward. Each trophoblast cell-type has a distinctive epigenetic profile and we will concentrate on the epigenetic mechanism of DNA methyltransferases and TETs that regulate DNA methylation. Environmental factors affecting the mother potentially regulate the DNA methyltransferases in trophoblasts, and so do steroid hormones, cell cycle regulators, such as p53, and cytokines, especially interlukin-1β. There are interesting questions of why trophoblast genomes are globally hypomethylated yet specific genes can be suppressed by hypermethylation (in general, tumor suppressor genes, such as E-cadherin) and how invasive cell-types are liable to have condensed chromatin, as in metastatic cancer cells. Future work will attempt to understand the interactive nature of all epigenetic mechanisms together and their effect on the complex biological system of trophoblast differentiation and invasion in normal as well as pathological conditions.
Collapse
Affiliation(s)
- Philip C Logan
- The Liggins Institute, The University of Auckland Auckland, New Zealand
| | - Murray D Mitchell
- University of Queensland Centre for Clinical Research, University of Queensland Brisbane, QLD, Australia
| | - Peter E Lobie
- Cancer Science Institute of Singapore, National University of Singapore Singapore, Singapore
| |
Collapse
|
49
|
Getting rid of DNA methylation. Trends Cell Biol 2013; 24:136-43. [PMID: 24119665 DOI: 10.1016/j.tcb.2013.09.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 09/03/2013] [Accepted: 09/04/2013] [Indexed: 11/22/2022]
Abstract
Methylation of cytosine within DNA is associated with transcriptional repression and genome surveillance. In plants and animals, conserved pathways exist to establish and maintain this epigenetic mark. Mechanisms underlining its removal are, however, diverse and controversial and can depend on DNA synthesis (passive) or be independent of it (active). Ten-eleven translocation (Tet)-mediated conversion of 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) has recently been evoked as a possible mechanism in the initiation of active and passive DNA demethylation. This review discuses the recent progress in this exciting area.
Collapse
|
50
|
Cadet J, Wagner JR. TET enzymatic oxidation of 5-methylcytosine, 5-hydroxymethylcytosine and 5-formylcytosine. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2013; 764-765:18-35. [PMID: 24045206 DOI: 10.1016/j.mrgentox.2013.09.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Accepted: 09/04/2013] [Indexed: 12/14/2022]
Abstract
5-Methylcytosine and methylated histones have been considered for a long time as stable epigenetic marks of chromatin involved in gene regulation. This concept has been recently revisited with the detection of large amounts of 5-hydroxymethylcytosine, now considered as the sixth DNA base, in mouse embryonic stem cells, Purkinje neurons and brain tissues. The dioxygenases that belong to the ten eleven translocation (TET) oxygenase family have been shown to initiate the formation of this methyl oxidation product of 5-methylcytosine that is also generated although far less efficiently by radical reactions involving hydroxyl radical and one-electron oxidants. It was found as additional striking data that iterative TET-mediated oxidation of 5-hydroxymethylcytosine gives rise to 5-formylcytosine and 5-carboxylcytosine. This survey focuses on chemical and biochemical aspects of the enzymatic oxidation reactions of 5-methylcytosine that are likely to be involved in active demethylation pathways through the implication of enzymatic deamination of 5-methylcytosine oxidation products and/or several base excision repair enzymes. The high biological relevance of the latter modified bases explains why major efforts have been devoted to the design of a broad range of assays aimed at measuring globally or at the single base resolution, 5-hydroxymethylcytosine and the two other oxidation products in the DNA of cells and tissues. Another critical issue that is addressed in this review article deals with the assessment of the possible role of 5-methylcytosine oxidation products, when present in elevated amounts in cellular DNA, in terms of mutagenesis and interference with key cellular enzymes including DNA and RNA polymerases.
Collapse
Affiliation(s)
- Jean Cadet
- Direction des Sciences de la Matière, Institut Nanosciences et Cryogénie, CEA/Grenoble, 38054 Grenoble, France; Département de médecine nucléaire et radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Québec JIH 5N4, Canada.
| | - J Richard Wagner
- Département de médecine nucléaire et radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Québec JIH 5N4, Canada.
| |
Collapse
|