451
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Lu X, Zhao BS, He C. TET family proteins: oxidation activity, interacting molecules, and functions in diseases. Chem Rev 2015; 115:2225-39. [PMID: 25675246 DOI: 10.1021/cr500470n] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Xingyu Lu
- †Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States.,‡Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
| | - Boxuan Simen Zhao
- †Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States.,‡Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
| | - Chuan He
- †Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States.,‡Howard Hughes Medical Institute, The University of Chicago, 929 East 57th Street, Chicago, Illinois 60637, United States
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452
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Jangiam W, Tungjai M, Rithidech KN. Induction of chronic oxidative stress, chronic inflammation and aberrant patterns of DNA methylation in the liver of titanium-exposed CBA/CaJ mice. Int J Radiat Biol 2015; 91:389-98. [PMID: 25565558 DOI: 10.3109/09553002.2015.1001882] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
PURPOSE To investigate the biological effects of titanium ((48)Ti, one of the important heavy ions found in space) in the liver of exposed-mice. MATERIALS AND METHODS We gave adult male CBA/CaJ mice a whole-body exposure to a total dose of 0, 0.1, 0.25 or 0.5 Gy of (48)Ti ions. The liver was collected at 1 week, 1 month, and 6 months post-irradiation (five mice per treatment-group at each harvest-time). Three biological endpoints were used for evaluating the effects of (48)Ti ions: Oxidative-stress, inflammatory responses, and DNA-methylation (5-methylcytosine and 5-hydroxymethylcytosine). RESULTS Our data clearly demonstrated dose-dependent increases in oxidative stress and inflammatory responses in the liver of exposed mice at all time-points (Analysis of Variance or ANOVA, p < 0.05). Significant dose-dependent increases in the levels of 5-methylcytosine were detected at 1 week and 1 month (ANOVA, p < 0.05). At 6 months post-irradiation, a significant increase in the level of 5-methylcytosine was found only in 0.5-Gy-(48)Ti-ion-exposed mice. In contrast, dose-dependent decreases in 5-hydroxymethylcytosine levels were found in the liver of exposed mice (ANOVA, p < 0.05) at all time-points. CONCLUSIONS Chronic oxidative-stress, chronic inflammation, and persistent aberrant DNA-methylation occurred in the liver of (48)Ti-exposed mice. Hence, exposure to (48)Ti ions in space may pose health risks.
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Affiliation(s)
- Witawat Jangiam
- Pathology Department, Stony Brook University , Stony Brook, NY , USA
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453
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5-Hydroxymethylcytosine expression in metastatic melanoma versus nodal nevus in sentinel lymph node biopsies. Mod Pathol 2015; 28:218-29. [PMID: 25081754 PMCID: PMC4312506 DOI: 10.1038/modpathol.2014.99] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 05/22/2014] [Accepted: 05/23/2014] [Indexed: 01/06/2023]
Abstract
Sentinel lymph node biopsies are conducted to stage patients with newly diagnosed melanomas that have histopathological attributes conferring defined levels of metastatic potential. Because benign nevic cells may also form 'deposits' in lymph nodes (nodal nevus), the pathological evaluation for metastatic melanoma within sentinel lymph nodes can be challenging. Twenty-eight sentinel lymph node biopsy cases containing either metastatic melanoma (N=18) or nodal nevi (N=10) were retrieved from the archives of the Brigham and Women's Hospital, Department of Pathology (2011-2014). In addition, two sentinel lymph node cases that were favored to represent metastatic disease but whose histopathological features were viewed as equivocal, with melanoma favored, were also included. Dual labeling for the melanocyte lineage marker, MART-1, and the epigenetic marker, 5-hydroxymethylcytosine, a functionally significant indicator that has been shown to distinguish benign nevi from melanoma, was performed on all cases using immunohistochemistry and/or direct immunofluorescence. All (18 of 18) metastatic melanoma cases showed complete loss of 5-hydroxymethylcytosine nuclear staining in MART-1-positive cells, and all (10 of 10) nodal nevus cases demonstrated 5-hydroxymethylcytosine nuclear staining in MART-1-positive cells. In addition, 5-hydroxymethylcytosine staining confirmed the favored diagnoses of metastatic melanoma in the two 'equivocal' cases. Thus, 5-hydroxymethylcytosine may be a useful adjunctive marker to distinguish between benign nodal nevi and metastatic melanoma during the evaluation of sentinel lymph node biopsies for metastatic melanoma.
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454
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Matsuda I, Imai Y, Hirota S. Distinct global DNA methylation status in B-cell lymphomas: immunohistochemical study of 5-methylcytosine and 5-hydroxymethylcytosine. J Clin Exp Hematop 2015; 54:67-73. [PMID: 24942948 DOI: 10.3960/jslrt.54.67] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Lymphomas are malignant neoplasms composed of lymphoid cells at various developmental stages and lineages. Recent advances in comprehensive genomic analyses in acute myeloid leukemia have revealed prevalent mutations in regulators of epigenetic phenomena including global DNA methylation status. The examples include mutations in isocitrate dehydrogenase 1 (IDH1), IDH2, and ten-eleven translocation 2. These mutations are proposed to inhibit conversion of 5-methylcytosine (5 mC) to 5-hydroxymethylcytosine (5 hmC), leading to global accumulation of 5 mC. These changes in global DNA methylation status can be visualized immunohistochemically using specific antibodies against 5 mC and 5 hmC. We examined the global DNA methylation status of B-cell lymphomas and that of their normal counterparts by immunohistochemistry for 5 mC and 5 hmC. Non-tumor lymphoid cells inside germinal centers (GC) in reactive lymphoid hyperplasia (RLH) were stained positive for 5 mC, but they were negative for 5 hmC. Similarly, follicular lymphomas, whose postulated normal counterparts are centrocytes in GCs, were 5 mC-positive but 5 hmC-negative by immunohistochemistry. This immunostaining pattern was also observed in Burkitt lymphoma. In contrast, non-tumor lymphoid cells in mantle zones were stained positive for 5 mC as well as for 5 hmC. Likewise, most mantle cell lymphomas, whose postulated normal counterparts are mantle zone B cells in RLH, were stained positive for 5 mC as well as for 5 hmC. This immunostaining pattern was also observed in chronic lymphocytic leukemia/small lymphocytic lymphoma. These results suggest that, in terms of 5 mC/5 hmC immunohistochemistry, B-cell lymphomas with different histological subtypes are associated with distinct global DNA methylation statuses that resemble those of their postulated normal counterparts.
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Affiliation(s)
- Ikuo Matsuda
- Department of Surgical Pathology, Hyogo College of Medicine
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455
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Scourzic L, Mouly E, Bernard OA. TET proteins and the control of cytosine demethylation in cancer. Genome Med 2015; 7:9. [PMID: 25632305 PMCID: PMC4308928 DOI: 10.1186/s13073-015-0134-6] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The discovery that ten-eleven translocation (TET) proteins are α-ketoglutarate-dependent dioxygenases involved in the conversion of 5-methylcytosines (5-mC) to 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine and 5-carboxycytosine has revealed new pathways in the cytosine methylation and demethylation process. The description of inactivating mutations in TET2 suggests that cellular transformation is in part caused by the deregulation of this 5-mC conversion. The direct and indirect deregulation of methylation control through mutations in DNA methyltransferase and isocitrate dehydrogenase (IDH) genes, respectively, along with the importance of cytosine methylation in the control of normal and malignant cellular differentiation have provided a conceptual framework for understanding the early steps in cancer development. Here, we review recent advances in our understanding of the cytosine methylation cycle and its implication in cellular transformation, with an emphasis on TET enzymes and 5-hmC. Ongoing clinical trials targeting the activity of mutated IDH enzymes provide a proof of principle that DNA methylation is targetable, and will trigger further therapeutic applications aimed at controlling both early and late stages of cancer development.
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Affiliation(s)
- Laurianne Scourzic
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité 1170, équipe labellisée Ligue Contre le Cancer, 94805 Villejuif, France ; Institut Gustave Roussy, 94805 Villejuif, France ; University Paris 11 Sud, 91405 Orsay, France
| | - Enguerran Mouly
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité 1170, équipe labellisée Ligue Contre le Cancer, 94805 Villejuif, France ; Institut Gustave Roussy, 94805 Villejuif, France ; University Paris 11 Sud, 91405 Orsay, France
| | - Olivier A Bernard
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité 1170, équipe labellisée Ligue Contre le Cancer, 94805 Villejuif, France ; Institut Gustave Roussy, 94805 Villejuif, France ; University Paris 11 Sud, 91405 Orsay, France
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456
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Shen L, Song CX, He C, Zhang Y. Mechanism and function of oxidative reversal of DNA and RNA methylation. Annu Rev Biochem 2015; 83:585-614. [PMID: 24905787 DOI: 10.1146/annurev-biochem-060713-035513] [Citation(s) in RCA: 246] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The importance of eukaryotic DNA methylation [5-methylcytosine (5mC)] in transcriptional regulation and development was first suggested almost 40 years ago. However, the molecular mechanism underlying the dynamic nature of this epigenetic mark was not understood until recently, following the discovery that the TET proteins, a family of AlkB-like Fe(II)/α-ketoglutarate-dependent dioxygenases, can oxidize 5mC to generate 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). Since then, several mechanisms that are responsible for processing oxidized 5mC derivatives to achieve DNA demethylation have emerged. Our biochemical understanding of the DNA demethylation process has prompted new investigations into the biological functions of DNA demethylation. Characterization of two additional AlkB family proteins, FTO and ALKBH5, showed that they possess demethylase activity toward N(6)-methyladenosine (m(6)A) in RNA, indicating that members of this subfamily of dioxygenases have a general function in demethylating nucleic acids. In this review, we discuss recent advances in this emerging field, focusing on the mechanism and function of TET-mediated DNA demethylation.
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Affiliation(s)
- Li Shen
- Howard Hughes Medical Institute and
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457
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Yin R, Mo J, Lu M, Wang H. Detection of Human Urinary 5-Hydroxymethylcytosine by Stable Isotope Dilution HPLC-MS/MS Analysis. Anal Chem 2015; 87:1846-52. [DOI: 10.1021/ac5038895] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Ruichuan Yin
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jiezhen Mo
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Meiling Lu
- Chemical
Analysis Group, Agilent Technologies, Beijing 100102, China
| | - Hailin Wang
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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458
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Dynamic switching of active promoter and enhancer domains regulates Tet1 and Tet2 expression during cell state transitions between pluripotency and differentiation. Mol Cell Biol 2015; 35:1026-42. [PMID: 25582196 DOI: 10.1128/mcb.01172-14] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The Tet 5-methylcytosine dioxygenases catalyze DNA demethylation by producing 5-hydroxymethylcytosine and further oxidized products. Tet1 and Tet2 are highly expressed in mouse pluripotent cells and downregulated to different extents in somatic cells, but the transcriptional mechanisms are unclear. Here we defined the promoter and enhancer domains in Tet1 and Tet2. Within a 15-kb "superenhancer" of Tet1, there are two transcription start sites (TSSs) with different activation patterns during development. A 6-kb promoter region upstream of the distal TSS is highly active in naive pluripotent cells, autonomously reports Tet1 expression in a transgenic system, and rapidly undergoes DNA methylation and silencing upon differentiation in cultured cells and native epiblast. A second TSS downstream, associated with a constitutively weak CpG-rich promoter, is activated by a neighboring enhancer in naive embryonic stem cells (ESCs) and primed epiblast-like cells (EpiLCs). Tet2 has a CpG island promoter with pluripotency-independent activity and an ESC-specific distal intragenic enhancer; the latter is rapidly downregulated in EpiLCs. Our study reveals distinct modes of transcriptional regulation at Tet1 and Tet2 during cell state transitions of early development. New transgenic reporters using Tet1 and Tet2 cis-regulatory domains may serve to distinguish nuanced changes in pluripotent states and the underlying epigenetic variations.
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459
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Kroeze LI, van der Reijden BA, Jansen JH. 5-Hydroxymethylcytosine: An epigenetic mark frequently deregulated in cancer. Biochim Biophys Acta Rev Cancer 2015; 1855:144-54. [PMID: 25579174 DOI: 10.1016/j.bbcan.2015.01.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 01/02/2015] [Accepted: 01/04/2015] [Indexed: 12/26/2022]
Abstract
The epigenetic mark 5-hydroxymethylcytosine (5hmC) has gained interest since 2009, when it was discovered that Ten-Eleven-Translocation (TET) proteins catalyze the conversion of 5-methylcytosine (5mC) into 5hmC. This conversion appears to be an intermediate step in the active DNA demethylation pathway. Factors that regulate DNA hydroxymethylation are frequently affected in cancer, leading to deregulated 5hmC levels. In this review, we will discuss the regulation of DNA hydroxymethylation, defects in this pathway in cancer, and novel therapies that may correct deregulated (hydroxy)methylation of DNA.
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Affiliation(s)
- Leonie I Kroeze
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center and Radboud Institute for Molecular Life Sciences, PO Box 9101, 6500 HB Nijmegen, The Netherlands.
| | - Bert A van der Reijden
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center and Radboud Institute for Molecular Life Sciences, PO Box 9101, 6500 HB Nijmegen, The Netherlands.
| | - Joop H Jansen
- Department of Laboratory Medicine, Laboratory of Hematology, Radboud University Medical Center and Radboud Institute for Molecular Life Sciences, PO Box 9101, 6500 HB Nijmegen, The Netherlands.
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460
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Huang JM, Hornyak TJ. Polycomb group proteins--epigenetic repressors with emerging roles in melanocytes and melanoma. Pigment Cell Melanoma Res 2015; 28:330-9. [PMID: 25475071 DOI: 10.1111/pcmr.12341] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Accepted: 11/28/2014] [Indexed: 12/21/2022]
Abstract
Melanocytes undergo rapid and significant changes in their gene expression programs at regular intervals during development and the hair follicle cycle. In melanoma, the gene expression pattern found in normal melanocytes is disrupted. These gene expression patterns are regulated in part by post-translational histone modifications catalyzed by Polycomb group (PcG) proteins, which play a major role in many developmental processes and are often altered in cancer. In this review, we discuss the role of the PcG proteins in stem cell and cancer biology, in general, as well as in melanocyte development and melanomagenesis. Highlights include the discussion of newly identified treatments that target the activity of PcG proteins as well as new developments in the understanding of the role that these proteins play in melanocyte biology.
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Affiliation(s)
- Jennifer M Huang
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, USA
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461
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Rawłuszko-Wieczorek AA, Siera A, Horbacka K, Horst N, Krokowicz P, Jagodziński PP. Clinical significance of DNA methylation mRNA levels of TET family members in colorectal cancer. J Cancer Res Clin Oncol 2015; 141:1379-92. [PMID: 25557833 PMCID: PMC4469774 DOI: 10.1007/s00432-014-1901-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 12/18/2014] [Indexed: 12/13/2022]
Abstract
Purpose
Ten eleven translocation (TET) enzyme activity is essential for active DNA demethylation in biological processes, and their altered expression has been observed in various malignancies. Therefore, we investigated DNA methylation and mRNA levels of all TETs in colorectal cancer (CRC) patients. Methods TET mRNA levels were evaluated using quantitative RT-PCR in primary cancerous and histopathologically unchanged colorectal tissues from patients who underwent radical surgical colon resection (n = 113). DNA methylation levels of the TET CpG island were assessed using bisulfite DNA sequencing and high-resolution melting analysis. Results We found reduced transcript levels of TET1, TET2 and TET3 in cancerous tissue compared with their histopathologically unchanged counterparts (p = 0.000011; p = 0.000001; p = 0.00031, respectively). Importantly, multivariate Cox regression analysis revealed favorable overall survival (OS) and disease-free survival (DFS) outcomes for patients with high TET2 mRNA levels in histopathologically unchanged tissue (HROS = 0.091, 95 % CI 0.011–0.77, p = 0.028; HRDFS = 0.21, 95 % CI 0.04–1.06, p = 0.059). Moreover, we found no DNA methylation in the TET2 and TET3 promoter regions in cancerous and histopathologically unchanged tissue. In contrast, we reported TET1 DNA hypermethylation in a small fraction of patients (n = 12/113). Conclusion To best of our knowledge, our study is the first to investigate TET mRNA levels in a cohort of CRC patients and correlate them with patients’ prognosis. Present study provides the evidence that TET2 mRNA expression may be an independent prognostic factor for disease recurrence and outcome. Additionally, our findings initially indicate the importance of DNA methylation in regulating TET1 expression. Electronic supplementary material The online version of this article (doi:10.1007/s00432-014-1901-2) contains supplementary material, which is available to authorized users.
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462
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Epigenetic deregulation in myeloid malignancies. Transl Res 2015; 165:102-14. [PMID: 24813528 DOI: 10.1016/j.trsl.2014.04.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 04/14/2014] [Accepted: 04/17/2014] [Indexed: 11/20/2022]
Abstract
Abnormal epigenetic patterning commonly is observed in cancer, including the myeloid malignancies acute myeloid leukemia and myelodysplastic syndromes. However, despite the universal nature of epigenetic deregulation, specific subtypes of myeloid disorders are associated with distinct epigenetic profiles, which accurately reflect the biologic heterogeneity of these disorders. In addition, mutations and genetic alterations of epigenetic-modifying enzymes frequently have been reported in these myeloid malignancies, emphasizing the importance of epigenetic deregulation in the initiation, progression, and outcome of these disorders. These aberrant epigenetic modifiers have become new targets for drug design, because their inhibition can potentially reverse the altered epigenetic landscapes that contribute to the development of the leukemia. In this review, we provide an overview of the role of epigenetic deregulation in leukemic transformation and their potential for therapeutic targeting.
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463
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Dong ZR, Zhang C, Cai JB, Zhang PF, Shi GM, Gao DM, Sun HC, Qiu SJ, Zhou J, Ke AW, Fan J. Role of 5-hydroxymethylcytosine level in diagnosis and prognosis prediction of intrahepatic cholangiocarcinoma. Tumour Biol 2014; 36:2763-71. [PMID: 25480415 DOI: 10.1007/s13277-014-2900-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 11/26/2014] [Indexed: 12/13/2022] Open
Abstract
The loss of 5-hydroxymethylcytosine (5-hmC) has been identified as an epigenetic hallmark in several malignancies. However, its role in intrahepatic cholangiocarcinoma (ICC) is still unknown. Our study aims to investigate the level of 5-hmC in diagnosis and prognosis prediction of ICC. The 5-hmC levels were detected using dot blot, tissue microarray technique and immunohistochemical method, and the correlation between 5-hmC level and ICC clinicopathological parameters was analysed. Compared with matched liver tissues, most of ICC tissues presented with the loss of 5-hmC. Furthermore, the subgroups of cirrhotic and poor differentiation tissues showed the lowest level of 5-hmC. We found that 5-hmC level in non-elevated ICC patients was significantly related to lymph node metastasis and TNM stage and not related to vessel invasion, sex, age, HBV, cirrhosis or degree of differentiation. ICC patients with high TNM stage (stages III and IV) and lymph node metastases had significantly lower 5-hmC level than those with low TNM stage (stages I and II) and no lymph node metastases. Further analysis showed that low 5-hmC level is significantly correlated with worse overall survival (OS) and disease-free survival (DFS). Importantly, multivariate analysis indicated that 5-hmC level, tumour diameter, lymphatic metastasis and tumour differentiation could be used as independent prognostic factors for ICC. The loss of 5-hmC is implicated in the progression of ICC. Our results can contribute to the diagnostic ability and postoperative surveillance of ICC patients.
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Affiliation(s)
- Zhao-Ru Dong
- Liver Cancer Institute and Zhongshan Hospital, Fudan University, 180 Fenglin Road, Shanghai, 200032, People's Republic of China
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464
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DNA hydroxymethylation profiling reveals that WT1 mutations result in loss of TET2 function in acute myeloid leukemia. Cell Rep 2014; 9:1841-1855. [PMID: 25482556 DOI: 10.1016/j.celrep.2014.11.004] [Citation(s) in RCA: 207] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 10/04/2014] [Accepted: 11/04/2014] [Indexed: 12/21/2022] Open
Abstract
Somatic mutations in IDH1/IDH2 and TET2 result in impaired TET2-mediated conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). The observation that WT1 inactivating mutations anticorrelate with TET2/IDH1/IDH2 mutations in acute myeloid leukemia (AML) led us to hypothesize that WT1 mutations may impact TET2 function. WT1 mutant AML patients have reduced 5hmC levels similar to TET2/IDH1/IDH2 mutant AML. These mutations are characterized by convergent, site-specific alterations in DNA hydroxymethylation, which drive differential gene expression more than alterations in DNA promoter methylation. WT1 overexpression increases global levels of 5hmC, and WT1 silencing reduced 5hmC levels. WT1 physically interacts with TET2 and TET3, and WT1 loss of function results in a similar hematopoietic differentiation phenotype as observed with TET2 deficiency. These data provide a role for WT1 in regulating DNA hydroxymethylation and suggest that TET2 IDH1/IDH2 and WT1 mutations define an AML subtype defined by dysregulated DNA hydroxymethylation.
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465
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Integrated analyses of DNA methylation and hydroxymethylation reveal tumor suppressive roles of ECM1, ATF5, and EOMES in human hepatocellular carcinoma. Genome Biol 2014; 15:533. [PMID: 25517360 PMCID: PMC4253612 DOI: 10.1186/s13059-014-0533-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 11/06/2014] [Indexed: 12/15/2022] Open
Abstract
Background Differences in 5-hydroxymethylcytosine, 5hmC, distributions may complicate previous observations of abnormal cytosine methylation statuses that are used for the identification of new tumor suppressor gene candidates that are relevant to human hepatocarcinogenesis. The simultaneous detection of 5-methylcytosine and 5-hydroxymethylcytosine is likely to stimulate the discovery of aberrantly methylated genes with increased accuracy in human hepatocellular carcinoma. Results Here, we performed ultra-performance liquid chromatography/tandem mass spectrometry and single-base high-throughput sequencing, Hydroxymethylation and Methylation Sensitive Tag sequencing, HMST-seq, to synchronously measure these two modifications in human hepatocellular carcinoma samples. After identification of differentially methylated and hydroxymethylated genes in human hepatocellular carcinoma, we integrate DNA copy-number alterations, as determined using array-based comparative genomic hybridization data, with gene expression to identify genes that are potentially silenced by promoter hypermethylation. Conclusions We report a high enrichment of genes with epigenetic aberrations in cancer signaling pathways. Six genes were selected as tumor suppressor gene candidates, among which, ECM1, ATF5 and EOMES are confirmed via siRNA experiments to have potential anti-cancer functions. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0533-9) contains supplementary material, which is available to authorized users.
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466
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Hattori N, Ushijima T. Compendium of aberrant DNA methylation and histone modifications in cancer. Biochem Biophys Res Commun 2014; 455:3-9. [DOI: 10.1016/j.bbrc.2014.08.140] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 08/26/2014] [Indexed: 12/20/2022]
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467
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Bachman M, Uribe-Lewis S, Yang X, Williams M, Murrell A, Balasubramanian S. 5-Hydroxymethylcytosine is a predominantly stable DNA modification. Nat Chem 2014; 6:1049-55. [PMID: 25411882 PMCID: PMC4382525 DOI: 10.1038/nchem.2064] [Citation(s) in RCA: 369] [Impact Index Per Article: 36.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 08/18/2014] [Indexed: 12/18/2022]
Abstract
5-Hydroxymethylcytosine (hmC) is an oxidation product of 5-methylcytosine which is present in the deoxyribonucleic acid (DNA) of most mammalian cells. Reduction of hmC levels in DNA is a hallmark of cancers. Elucidating the dynamics of this oxidation reaction and the lifetime of hmC in DNA is fundamental to understanding hmC function. Using stable isotope labelling of cytosine derivatives in the DNA of mammalian cells and ultrasensitive tandem liquid-chromatography mass spectrometry, we show that the majority of hmC is a stable modification, as opposed to a transient intermediate. In contrast with DNA methylation, which occurs immediately during replication, hmC forms slowly during the first 30 hours following DNA synthesis. Isotopic labelling of DNA in mouse tissues confirmed the stability of hmC in vivo and demonstrated a relationship between global levels of hmC and cell proliferation. These insights have important implications for understanding the states of chemically modified DNA bases in health and disease.
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Affiliation(s)
- Martin Bachman
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Santiago Uribe-Lewis
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Xiaoping Yang
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Michael Williams
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Adele Murrell
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
- Centre for Regenerative Medicine, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Shankar Balasubramanian
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
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468
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Nestin depletion induces melanoma matrix metalloproteinases and invasion. J Transl Med 2014; 94:1382-95. [PMID: 25365206 PMCID: PMC4419570 DOI: 10.1038/labinvest.2014.130] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Revised: 07/25/2014] [Accepted: 09/08/2014] [Indexed: 12/20/2022] Open
Abstract
Matrix metalloproteinases (MMPs) are key biological mediators of processes as diverse as wound healing, embryogenesis, and cancer progression. Although MMPs may be induced through multiple signaling pathways, the precise mechanisms for their regulation in cancer are incompletely understood. Because cytoskeletal changes are known to accompany MMP expression, we sought to examine the potential role of the poorly understood cytoskeletal protein, nestin, in modulating melanoma MMPs. Nestin knockdown (KD) upregulated the expression of specific MMPs and MMP-dependent invasion both through extracellular matrix barriers in vitro and in peritumoral connective tissue of xenografts in vivo. The development of three-dimensional melanospheres that in vitro partially recapitulate noninvasive tumorigenic melanoma growth was inhibited by nestin KD, although ECM invasion by aberrant melanospheres that did form was enhanced. Mechanistically, nestin KD-dependent melanoma invasion was associated with intracellular redistribution of phosphorylated focal adhesion kinase and increased melanoma cell responsiveness to transforming growth factor-beta, both implicated in pathways of melanoma invasion. The results suggest that the heretofore poorly understood intermediate filament, nestin, may serve as a novel mediator of MMPs critical to melanoma virulence.
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469
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Çelik S. Understanding the complexity of antigen retrieval of DNA methylation for immunofluorescence-based measurement and an approach to challenge. J Immunol Methods 2014; 416:1-16. [PMID: 25435341 DOI: 10.1016/j.jim.2014.11.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 10/31/2014] [Accepted: 11/21/2014] [Indexed: 12/28/2022]
Abstract
Cytosine methylation (5-methylcytosine, 5meC) in the CpG-rich regions of the mammalian genome is an important epigenetic mechanism playing roles in transcription regulation and genomic stability. The abnormalities in DNA methylation can occur in various types of cancer and some genetic diseases. The measurement of DNA methylation is therefore important and there is a range of methodologies used to detect DNA methylation. Many methods based on bisulfite treatment appeared with a lack of specificity after recent discoveries of various modifications of methylated cytosine, however there are new treatments developed to overcome this limitation. Immunofluorescence is currently known to be able to specifically detect DNA methylation as it uses different antibodies against 5meC and its derivatives, but it is a semi-quantitative method. Immunofluorescence protocols commonly include fixation of cells followed by permeabilisation, antigen retrieval, and treatments with antibodies. Establishing the strategy for antigen retrieval of immunofluorescence is important to unmask epitopes (i.e. 5meC) from other proteins, and therefore to access the antigen of interest. There are many approaches used for antigen retrieval induced by acid, enzyme and/or heat. The selection of antigen retrieval method can depend on a variety of such antigen-based or cell-based conditions, since the dynamic structure of DNA and chromatin accounts for the complexity of involved proteins to mask the epitope. This review aims to specifically focus on the complexity of in situ detection of DNA methylation by immunofluorescence-based methods using antigen retrieval with the current understanding of DNA methylation mechanism, and suggests conditions for antigenic retrieval of 5meC epitope.
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Affiliation(s)
- Selcen Çelik
- Human Reproduction and Development Unit, Kolling Institute for Medical Research, Sydney Medical School, University of Sydney, Sydney 2065, Australia.
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470
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Suppression of TET1-dependent DNA demethylation is essential for KRAS-mediated transformation. Cell Rep 2014; 9:1827-1840. [PMID: 25466250 DOI: 10.1016/j.celrep.2014.10.063] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 09/23/2014] [Accepted: 10/25/2014] [Indexed: 12/31/2022] Open
Abstract
Hypermethylation-mediated tumor suppressor gene (TSG) silencing is a central epigenetic alteration in RAS-dependent tumorigenesis. Ten-eleven translocation (TET) enzymes can depress DNA methylation by hydroxylation of 5-methylcytosine (5mC) bases to 5-hydroxymethylcytosine (5hmC). Here, we report that suppression of TET1 is required for KRAS-induced DNA hypermethylation and cellular transformation. In distinct nonmalignant cell lines, oncogenic KRAS promotes transformation by inhibiting TET1 expression via the ERK-signaling pathway. This reduces chromatin occupancy of TET1 at TSG promoters, lowers levels of 5hmC, and increases levels of 5mC and 5mC-dependent transcriptional silencing. Restoration of TET1 expression by ERK pathway inhibition or ectopic TET1 reintroduction in KRAS-transformed cells reactivates TSGs and inhibits colony formation. KRAS knockdown increases TET1 expression and diminishes colony-forming ability, whereas KRAS/TET1 double knockdown bypasses the KRAS dependence of KRAS-addicted cancer cells. Thus, suppression of TET1-dependent DNA demethylation is critical for KRAS-mediated transformation.
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471
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De Souza A, Tinguely M, Pfaltz M, Burghart DR, Kempf W. Loss of expression of 5-hydroxymethylcytosine in CD30-positive cutaneous lymphoproliferative disorders. J Cutan Pathol 2014; 41:901-6. [DOI: 10.1111/cup.12411] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 09/03/2014] [Accepted: 10/26/2014] [Indexed: 01/07/2023]
Affiliation(s)
- Aieska De Souza
- Department of Dermatology; Harvard Medical School; Boston MA USA
| | | | | | | | - Werner Kempf
- Kempf and Pfaltz; Histologische Diagnostik; Zürich Switzerland
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472
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Wescoe ZL, Schreiber J, Akeson M. Nanopores discriminate among five C5-cytosine variants in DNA. J Am Chem Soc 2014; 136:16582-7. [PMID: 25347819 PMCID: PMC4277752 DOI: 10.1021/ja508527b] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
Individual DNA molecules can be read
at single nucleotide precision
using nanopores coupled to processive enzymes. Discrimination among
the four canonical bases has been achieved, as has discrimination
among cytosine, 5-methylcytosine (mC), and 5-hydroxymethylcytosine
(hmC). Two additional modified cytosine bases, 5-carboxylcytosine
(caC) and 5-formylcytosine (fC), are produced during enzymatic conversion
of hmC to cytosine in mammalian cells. Thus, an accurate picture of
the cytosine epigenetic status in target cells should also include
these C5-cytosine variants. In the present study, we used a patch
clamp amplifier to acquire ionic current traces caused by phi29 DNA
polymerase-controlled translocation of DNA templates through the M2MspA
pore. Decision boundaries based on three consecutive ionic current
states were implemented to call mC, hmC, caC, fC, or cytosine at CG
dinucleotides in ∼4400 individual DNA molecules. We found that
the percentage of correct base calls for single pass reads ranged
from 91.6% to 98.3%. This accuracy depended upon the identity of nearest
neighbor bases surrounding the CG dinucleotide.
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Affiliation(s)
- Zachary L Wescoe
- Department of Biomolecular Engineering, Baskin School of Engineering, MS SOE2, University of California , Santa Cruz, California 95064, United States
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473
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Neri F, Dettori D, Incarnato D, Krepelova A, Rapelli S, Maldotti M, Parlato C, Paliogiannis P, Oliviero S. TET1 is a tumour suppressor that inhibits colon cancer growth by derepressing inhibitors of the WNT pathway. Oncogene 2014; 34:4168-76. [PMID: 25362856 DOI: 10.1038/onc.2014.356] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 08/22/2014] [Accepted: 09/16/2014] [Indexed: 12/17/2022]
Abstract
Ten eleven translocation (TET) enzymes catalyse the oxidative reactions of 5-methylcytosine (5mC) to promote the demethylation process. The reaction intermediate 5-hydroxymethylcytosine (5hmC) has been shown to be abundant in embryonic stem cells and tissues but strongly depleted in human cancers. Genetic mutations of TET2 gene were associated with leukaemia, whereas TET1 downregulation has been shown to promote malignancy in breast cancer. Here we report that TET1 is downregulated in colon tumours from the initial stage. TET1 silencing in primary epithelial colon cells increase their cellular proliferation while its re-expression in colon cancer cells inhibits their proliferation and the growth of tumour xenografts even at later stages. We found that TET1 binds to the promoter of the DKK gene inhibitors of the WNT signalling to maintain them hypomethylated. Downregulation of TET1 during colon cancer initiation leads to repression, by DNA methylation, the promoters of the inhibitors of the WNT pathway resulting in a constitutive activation of the WNT pathway. Thus the DNA hydroxymethylation mediated by TET1 controlling the WNT signalling is a key player of tumour growth. These results provide new insights for understanding how tumours escape cellular controls.
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Affiliation(s)
- F Neri
- Epigenetics, Human Genetics Foundation (HuGeF), Torino, Italy
| | - D Dettori
- Epigenetics, Human Genetics Foundation (HuGeF), Torino, Italy
| | - D Incarnato
- 1] Epigenetics, Human Genetics Foundation (HuGeF), Torino, Italy [2] Dipartimento di Biotecnologie Chimica e Farmacia, Università di Siena, Siena, Italy
| | - A Krepelova
- 1] Epigenetics, Human Genetics Foundation (HuGeF), Torino, Italy [2] Dipartimento di Biotecnologie Chimica e Farmacia, Università di Siena, Siena, Italy
| | - S Rapelli
- 1] Epigenetics, Human Genetics Foundation (HuGeF), Torino, Italy [2] Dipartimento di Biotecnologie Chimica e Farmacia, Università di Siena, Siena, Italy
| | - M Maldotti
- Epigenetics, Human Genetics Foundation (HuGeF), Torino, Italy
| | - C Parlato
- Epigenetics, Human Genetics Foundation (HuGeF), Torino, Italy
| | - P Paliogiannis
- Dipartimento di Scienze Chirurgiche, Microchirurgiche e Mediche, Università di Sassari, Sassari, Italy
| | - S Oliviero
- 1] Epigenetics, Human Genetics Foundation (HuGeF), Torino, Italy [2] Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università di Torino Torino, Italy
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474
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Navarro A, Yin P, Ono M, Monsivais D, Moravek MB, Coon JS, Dyson MT, Wei JJ, Bulun SE. 5-Hydroxymethylcytosine promotes proliferation of human uterine leiomyoma: a biological link to a new epigenetic modification in benign tumors. J Clin Endocrinol Metab 2014; 99:E2437-45. [PMID: 25057885 PMCID: PMC5393501 DOI: 10.1210/jc.2014-2264] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CONTEXT Uterine leiomyoma, or fibroids, represent the most common benign tumors of the female reproductive tract. A newly discovered epigenetic modification, 5-hydroxymethylation (5-hmC), and its regulators, the TET (Ten Eleven Translocation) enzymes, were implicated in the pathology of malignant tumors; however, their roles in benign tumors, including uterine fibroids, remain unknown. OBJECTIVE To determine the role of 5-hmC and TET proteins in the pathogenesis of leiomyoma using human uterine leiomyoma and normal matched myometrial tissues and primary cells. DESIGN 5-hmC levels were determined by ELISA and immunofluorescent staining in matched myometrial and leiomyoma tissues. TET expression was analyzed by quantitative RT-PCR and immunoblotting. TET1 or TET3 were silenced or inhibited by small interfering RNA or 2-hydroxyglutarate to study their effects on 5-hmC content and cell proliferation. RESULTS We demonstrated significantly higher 5-hmC levels in the genomic DNA of leiomyoma tissue compared to normal myometrial tissue. The increase in 5-hmC levels was associated with the up-regulation of TET1 or TET3 mRNA and protein expression in leiomyoma tissue. TET1 or TET3 knockdown significantly reduced 5-hmC levels in leiomyoma cells and decreased cell proliferation. Treatment with 2-hydroxyglutarate, a competitive TET enzyme inhibitor, significantly decreased both 5-hmC content and cell proliferation of leiomyoma cells. CONCLUSION An epigenetic imbalance in the 5-hmC content of leiomyoma tissue, caused by up-regulation of the TET1 and TET3 enzymes, might lead to discovery of new therapeutic targets in leiomyoma.
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Affiliation(s)
- Antonia Navarro
- Departments of Obstetrics and Gynecology (A.N., P.Y., M.O., D.M., M.B.M., J.S.C., M.T.D., J.-J.W., S.E.B.) and Pathology (J.-J.W.), Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611
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475
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Thomas NE, Slater NA, Edmiston SN, Zhou X, Kuan PF, Groben PA, Carson CC, Hao H, Parrish E, Moschos SJ, Berwick M, Ollila DW, Conway K. DNA methylation profiles in primary cutaneous melanomas are associated with clinically significant pathologic features. Pigment Cell Melanoma Res 2014; 27:1097-105. [PMID: 24986547 PMCID: PMC4211983 DOI: 10.1111/pcmr.12289] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 06/20/2014] [Indexed: 12/22/2022]
Abstract
DNA methylation studies have elucidated a methylation signature distinguishing primary melanomas from benign nevi and provided new insights about genes that may be important in melanoma development. However, it is unclear whether methylation differences among primary melanomas are related to tumor pathologic features with known clinical significance. We utilized the Illumina GoldenGate Cancer Panel array to investigate the methylation profiles of 47 primary cutaneous melanomas. Arraywide methylation patterns revealed a positive association of methylation with Breslow thickness and mutated BRAF, a negative association with mitotic rate, and a weak association with ulceration. Hierarchical clustering on CpG sites exhibiting the most variable methylation (n = 235) divided the melanoma samples into three clusters, including a highly methylated cluster that was positively associated with Breslow thickness and an intermediately methylated cluster associated with Breslow thickness and mitotic rate. Our findings provide support for the existence of methylation-defined subsets in melanomas with increased methylation associated with Breslow thickness.
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Affiliation(s)
- Nancy E. Thomas
- Department of Dermatology, University of North Carolina, Chapel
Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North
Carolina, Chapel Hill, NC, USA
| | - Nathaniel A. Slater
- Department of Dermatology, University of North Carolina, Chapel
Hill, NC, USA
| | - Sharon N. Edmiston
- Lineberger Comprehensive Cancer Center, University of North
Carolina, Chapel Hill, NC, USA
| | - Xin Zhou
- Department of Biostatistics, University of North Carolina, Chapel
Hill, NC, USA
| | - Pei-Fen Kuan
- Lineberger Comprehensive Cancer Center, University of North
Carolina, Chapel Hill, NC, USA
- Department of Biostatistics, University of North Carolina, Chapel
Hill, NC, USA
| | - Pamela A. Groben
- Department of Pathology and Laboratory Medicine, University of
North Carolina, Chapel Hill, NC, USA
| | - Craig C. Carson
- Department of Dermatology, University of North Carolina, Chapel
Hill, NC, USA
| | - Honglin Hao
- Department of Dermatology, University of North Carolina, Chapel
Hill, NC, USA
| | - Eloise Parrish
- Lineberger Comprehensive Cancer Center, University of North
Carolina, Chapel Hill, NC, USA
| | - Stergios J. Moschos
- Lineberger Comprehensive Cancer Center, University of North
Carolina, Chapel Hill, NC, USA
- Department of Medicine, University of North Carolina, Chapel
Hill, NC, USA
| | - Marianne Berwick
- Department of Medicine, Division of Epidemiology, University of
New Mexico, Albuquerque, NM, USA
| | - David W. Ollila
- Lineberger Comprehensive Cancer Center, University of North
Carolina, Chapel Hill, NC, USA
- Department of Surgery, University of North Carolina, Chapel Hill,
NC, USA
| | - Kathleen Conway
- Lineberger Comprehensive Cancer Center, University of North
Carolina, Chapel Hill, NC, USA
- Department of Epidemiology, University of North Carolina, Chapel
Hill, NC, USA
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476
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Davidsson J. The epigenetic landscape of aneuploidy: constitutional mosaicism leading the way? Epigenomics 2014; 6:45-58. [PMID: 24579946 DOI: 10.2217/epi.13.78] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The role of structural genetic changes in human disease has received substantial attention in recent decades, but surprisingly little is known about numerical chromosomal abnormalities, even though they have been recognized since the days of Boveri as partaking in different cellular pathophysiological processes such as cancer and genomic disorders. The current knowledge of the genetic and epigenetic consequences of aneuploidy is reviewed herein, with a special focus on using mosaic genetic syndromes to study the DNA methylation footprints and expressional effects associated with whole-chromosomal gains. Recent progress in understanding the debated role of aneuploidy as a driver or passenger in malignant transformation, as well as how the cell responds to and regulates excess genetic material in experimental settings, is also discussed in detail.
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Affiliation(s)
- Josef Davidsson
- Division of Molecular Medicine & Gene Therapy, Lund Stem Cell Center, Lund University, SE-221 84 Lund, Sweden
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477
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Laird A, Thomson JP, Harrison DJ, Meehan RR. 5-hydroxymethylcytosine profiling as an indicator of cellular state. Epigenomics 2014; 5:655-69. [PMID: 24283880 DOI: 10.2217/epi.13.69] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
DNA methylation is widely studied in the context of cancer. However, the rediscovery of 5-hydroxymethylation of DNA adds a new layer of complexity to understanding the epigenetic basis of development and disease, including carcinogenesis. There have been significant advances in techniques for the detection of 5-hydroxymethylcytosine and, with this, greater insight into the distribution, regulation and function of this mark, which are reviewed here. Better understanding of the associated pathways involved in regulation of, and by, 5-hydroxymethylcytosine may give promise to new therapeutic targets. We discuss evidence to support the view of 5-hydroxymethylcytosine as a unique and dynamic mark of cellular state. These 5-hydroxymethylcytosine profiles may offer optimism for the development of diagnostic, prognostic and predictive biomarkers.
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Affiliation(s)
- Alexander Laird
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
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478
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Chandola U, Das R, Panda B. Role of the N6-methyladenosine RNA mark in gene regulation and its implications on development and disease. Brief Funct Genomics 2014; 14:169-79. [PMID: 25305461 DOI: 10.1093/bfgp/elu039] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Epigenetics is a field that encompasses chemical modifications of DNA and histone proteins, both of which alter gene expression without changing the underlying nucleotide sequence. DNA methylation and modifications of histone tails have been studied in detail and are now known to be global gene regulatory mechanisms. An analogous post-transcriptional modification is chemical modification of specific nucleotides in RNA. Study of RNA modifications is a nascent field as yet, and the significance of these marks in controlling cell growth and differentiation is just beginning to be appreciated. The addition of a methyl group to adenosine (N-methyl-6-adenosine) or m6A is the most abundant modification in mammalian mRNAs. Though identified four decades ago, interest in this particular modification was set off by the discovery that the obesity gene FTO was an RNA demethylase. Since then, many studies have investigated m6A modification in different species. In this review, we summarize the current literature and hypotheses about the presence and function of this ubiquitous RNA modification in mammals, viruses, yeast and plants in terms of the consensus sequence and the methyltransferase/demethylation machinery identified thus far. We discuss its potential role in regulating molecular and physiological processes in each of these organisms, especially its role in RNA splicing, RNA degradation and development. We also enlist the methodologies developed so far, both locus-specific and transcriptome-wide, to study this modification. Lastly, we discuss whether m6A alterations have consequences on modulating disease aetiology, and speculate about its potential role in cancer.
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479
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Wang J, Tang J, Lai M, Zhang H. 5-Hydroxymethylcytosine and disease. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2014; 762:167-75. [PMID: 25475423 DOI: 10.1016/j.mrrev.2014.09.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 08/27/2014] [Accepted: 09/29/2014] [Indexed: 11/27/2022]
Abstract
Epigenetics is the study of inherited changes in phenotype or gene expression that do not alter DNA sequence. Recently, scientists have focused their attention on 5-hydroxymethylcytosine (5hmC), a newly discovered epigenetic marker, also known as sixth DNA base of the genome. In mammals, this novel epigenetic marker is derived from 5-methylcytosine (5mC) in a process catalyzed by ten-eleven translocation (TET) enzymes. Although 5hmC has only been subjected to study for a short while, a great deal of data has been accumulated regarding its generation, distribution, demethylation, function, and disease implications. All this information suggested that 5hmC acts not only as an intermediate in the DNA demethylation process but also as an independent epigenetic marker, playing an important role in the regulation of gene expression. This review focuses on recent progress in the study of the relationship between 5hmC and human diseases, such as cancer and Rett syndrome (RTT).
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Affiliation(s)
- Jingyu Wang
- Department of Pathology, School of Medicine, Zhejiang University, Zhejiang, PR China; Department of Pathology, The First Hospital of Jiaxing, Zhejiang, PR China
| | - Jinlong Tang
- Department of Pathology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang, PR China
| | - Maode Lai
- Department of Pathology, School of Medicine, Zhejiang University, Zhejiang, PR China; Key Laboratory of Disease Proteomics of Zhejiang Province, PR China.
| | - Honghe Zhang
- Department of Pathology, School of Medicine, Zhejiang University, Zhejiang, PR China; Key Laboratory of Disease Proteomics of Zhejiang Province, PR China.
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480
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Takai H, Masuda K, Sato T, Sakaguchi Y, Suzuki T, Suzuki T, Koyama-Nasu R, Nasu-Nishimura Y, Katou Y, Ogawa H, Morishita Y, Kozuka-Hata H, Oyama M, Todo T, Ino Y, Mukasa A, Saito N, Toyoshima C, Shirahige K, Akiyama T. 5-Hydroxymethylcytosine plays a critical role in glioblastomagenesis by recruiting the CHTOP-methylosome complex. Cell Rep 2014; 9:48-60. [PMID: 25284789 DOI: 10.1016/j.celrep.2014.08.071] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Revised: 07/29/2014] [Accepted: 08/27/2014] [Indexed: 11/28/2022] Open
Abstract
The development of cancer is driven not only by genetic mutations but also by epigenetic alterations. Here, we show that TET1-mediated production of 5-hydroxymethylcytosine (5hmC) is required for the tumorigenicity of glioblastoma cells. Furthermore, we demonstrate that chromatin target of PRMT1 (CHTOP) binds to 5hmC. We found that CHTOP is associated with an arginine methyltransferase complex, termed the methylosome, and that this promotes the PRMT1-mediated methylation of arginine 3 of histone H4 (H4R3) in genes involved in glioblastomagenesis, including EGFR, AKT3, CDK6, CCND2, and BRAF. Moreover, we found that CHTOP and PRMT1 are essential for the expression of these genes and that CHTOP is required for the tumorigenicity of glioblastoma cells. These results suggest that 5hmC plays a critical role in glioblastomagenesis by recruiting the CHTOP-methylosome complex to selective sites on the chromosome, where it methylates H4R3 and activates the transcription of cancer-related genes.
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Affiliation(s)
- Hiroki Takai
- Laboratory of Molecular and Genetic Information, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Koji Masuda
- Laboratory of Genome Structure and Function, Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Tomohiro Sato
- Laboratory of Molecular and Genetic Information, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Takeo Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Ryo Koyama-Nasu
- Laboratory of Molecular and Genetic Information, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Yukiko Nasu-Nishimura
- Laboratory of Molecular and Genetic Information, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Yuki Katou
- Laboratory of Genome Structure and Function, Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Haruo Ogawa
- Laboratory of Membrane Proteins, Center for Structural Biology of Challenging Proteins, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Yasuyuki Morishita
- Department of Molecular Pathology, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroko Kozuka-Hata
- Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Masaaki Oyama
- Medical Proteomics Laboratory, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Tomoki Todo
- Department of Neurosurgery, The University of Tokyo Hospital, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Yasushi Ino
- Department of Neurosurgery, The University of Tokyo Hospital, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Akitake Mukasa
- Department of Neurosurgery, The University of Tokyo Hospital, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Nobuhito Saito
- Department of Neurosurgery, The University of Tokyo Hospital, 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Chikashi Toyoshima
- Laboratory of Membrane Proteins, Center for Structural Biology of Challenging Proteins, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Katsuhiko Shirahige
- Laboratory of Genome Structure and Function, Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Tetsu Akiyama
- Laboratory of Molecular and Genetic Information, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
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481
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Pergoli L, Favero C, Ruth M. P, Tarantini L, Calista D, Cavalleri T, Angelici L, Consonni D, Pier A. B, Angela C. P, Maria T. L, Bollati V. Blood DNA methylation, nevi number, and the risk of melanoma. Melanoma Res 2014; 24:480-7. [PMID: 25026000 PMCID: PMC6857929 DOI: 10.1097/cmr.0000000000000112] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Germline mutations determining increased cutaneous malignant melanoma (CMM) risk have been identified in familial and sporadic CMM cases, but they account only for a small proportion of CMM cases. Recent evidence suggests that germline epimutations (e.g. DNA methylation alterations), which can be inherited similarly to genomic mutations and can be detected in normal body cells (including blood), might increase susceptibility to cancer. The aim of the study was to identify germline epimutations of genes that were found to be mutated in familial CMM (p16, p14, CDK4, MC1R, hTERT), immune and inflammatory genes (ICAM-1, TNFα), DNA mismatch repair gene (MLH1), and repetitive elements (ALU, LINE-1, HERV-w). We measured DNA methylation using bisulfite pyrosequencing in peripheral blood mononuclear cells from 167 CMM cases and 164 sex-matched and age-matched controls. We used multivariable logistic regression models to evaluate the association between methylation levels and CMM status or presence of dysplastic nevi. We found an association between the risk of CMM and peripheral blood mononuclear cell methylation levels of TNFα [odds ratio (OR)=1.11, 95% confidence interval (CI)=1.03-1.18], CDK4 (OR=0.76, 95% CI=0.64-0.91), and MLH1 (OR=1.12, 95% CI=1.02-1.22). In control participants, the risk of developing dysplastic nevi was associated with methylation levels of TNFα (OR=0.81, 95% CI=0.69-0.95), hTERT (OR=0.90, 95% CI=0.82-0.99), and ALU (OR=1.56, 95% CI=1.02-2.39). Epimutations in CMM susceptibility genes and in genes involved in response to oxidative damage are associated with the risk of developing CMM or dysplastic nevi. Further studies measuring methylation levels of these genes in prospectively collected samples are warranted to further elucidate their role in the development and progression of CMM.
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Affiliation(s)
- Laura Pergoli
- Center of Molecular and Genetic Epidemiology, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Chiara Favero
- Center of Molecular and Genetic Epidemiology, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Pfeiffer Ruth M.
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Letizia Tarantini
- Center of Molecular and Genetic Epidemiology, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | | | - Tommaso Cavalleri
- Center of Molecular and Genetic Epidemiology, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Laura Angelici
- Center of Molecular and Genetic Epidemiology, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Dario Consonni
- Epidemiology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Bertazzi Pier A.
- Center of Molecular and Genetic Epidemiology, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
- Epidemiology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Pesatori Angela C.
- Center of Molecular and Genetic Epidemiology, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
- Epidemiology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Landi Maria T.
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Valentina Bollati
- Center of Molecular and Genetic Epidemiology, Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
- Epidemiology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
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482
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Huang Y, Rao A. Connections between TET proteins and aberrant DNA modification in cancer. Trends Genet 2014; 30:464-74. [PMID: 25132561 PMCID: PMC4337960 DOI: 10.1016/j.tig.2014.07.005] [Citation(s) in RCA: 193] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 07/24/2014] [Accepted: 07/24/2014] [Indexed: 02/07/2023]
Abstract
DNA methylation has been linked to aberrant silencing of tumor suppressor genes in cancer, and an imbalance in DNA methylation-demethylation cycles is intimately implicated in the onset and progression of tumors. Ten-eleven translocation (TET) proteins are Fe(II)- and 2-oxoglutarate (2OG)-dependent dioxygenases that successively oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC), thereby mediating active DNA demethylation. In this review, we focus on the pathophysiological role of TET proteins and 5hmC in cancer. We present an overview of loss-of-function mutations and abnormal expression and regulation of TET proteins in hematological malignancies and solid tumors, and discuss the potential prognostic value of assessing TET mutations and 5hmC levels in cancer patients. We also address the crosstalk between TET and two critical enzymes involved in cell metabolism: O-linked β-N-acetylglucosamine transferase (OGT) and isocitrate dehydrogenase (IDH). Lastly, we discuss the therapeutic potential of targeting TET proteins and aberrant DNA methylation in cancer.
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Affiliation(s)
- Yun Huang
- La Jolla Institute, La Jolla, CA 92037, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA.
| | - Anjana Rao
- La Jolla Institute, La Jolla, CA 92037, USA; Sanford Consortium for Regenerative Medicine, La Jolla, CA 92037, USA.
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483
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Lezcano C, Kleffel S, Lee N, Larson AR, Zhan Q, DoRosario A, Wang LC, Schatton T, Murphy GF. Merkel cell carcinoma expresses vasculogenic mimicry: demonstration in patients and experimental manipulation in xenografts. J Transl Med 2014; 94:1092-102. [PMID: 25111691 PMCID: PMC4236190 DOI: 10.1038/labinvest.2014.99] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 06/24/2014] [Accepted: 06/27/2014] [Indexed: 12/31/2022] Open
Abstract
Merkel cell carcinoma (MCC) is a highly virulent cutaneous neoplasm that, like melanoma, is a frequent cause of patient morbidity and mortality. The cellular mechanisms responsible for the aggressive behavior of MCC remain unknown. Vasculogenic mimicry (VM) is a phenomenon associated with cancer virulence, including in melanoma, whereby anastomosing laminin networks form in association with tumor cells that express certain endothelial genes. To determine whether VM is a factor in MCC, we employed a relevant xenograft model using two independent human MCC lines. Experimentally induced tumors were remarkably similar histologically to patient MCC, and both contained laminin networks associated with vascular endothelial-cadherin (CD144) and vascular endothelial growth factor receptor 1, as well as Nodal expression typical of VM in melanoma. Moreover, two established chemotherapeutic agents utilized for human MCC, etoposide and carboplatin, induced necrosis in xenografts on systemic administration while enriching for laminin networks in apparently resistant viable tumor regions that persisted. These findings for the first time establish VM-like laminin networks as a biomarker in MCC, demonstrate the experimental utility of the MCC xenograft model, and suggest that VM-rich regions of MCC may be refractory to conventional chemotherapeutic agents.
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Affiliation(s)
- Cecilia Lezcano
- Department of Pathology, University of Pittsburgh Medical Center,
Pittsburgh, PA
| | - Sonja Kleffel
- Department of Dermatology, Brigham and Women’s Hospital,
Boston, MA,Harvard Medical School, Boston, MA
| | - Nayoung Lee
- Department of Dermatology, Brigham and Women’s Hospital,
Boston, MA,Harvard Medical School, Boston, MA
| | - Allison R. Larson
- Department of Dermatology, Brigham and Women’s Hospital,
Boston, MA,Harvard Medical School, Boston, MA
| | - Qian Zhan
- Harvard Medical School, Boston, MA,Department of Pathology, Brigham and Women’s Hospital,
Boston, MA
| | - Andrew DoRosario
- Harvard Medical School, Boston, MA,Center for Cutaneous Oncology, Dana-Farber/Brigham and
Women’s Cancer Center, Boston, MA
| | - Linda C. Wang
- Institute for Cancer Care, Mercy Medical Center, Baltimore,
MD
| | - Tobias Schatton
- Harvard Medical School, Boston, MA,Transplantation Research Center, Children’s Hospital
Boston, MA
| | - George F. Murphy
- Harvard Medical School, Boston, MA,Department of Pathology, Brigham and Women’s Hospital,
Boston, MA
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484
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Evaluation of stromal HGF immunoreactivity as a biomarker for melanoma response to RAF inhibitors. Mod Pathol 2014; 27:1193-202. [PMID: 24434899 PMCID: PMC4107197 DOI: 10.1038/modpathol.2013.226] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Revised: 10/12/2013] [Accepted: 10/13/2013] [Indexed: 12/13/2022]
Abstract
Of more than 150 000 published studies evaluating new biomarkers, fewer than 100 biomarkers have been implemented for patient care. One reason for this is lack of rigorous testing by the medical community to validate claims for biomarker clinical relevance, and potential reluctance to publish negative results when confirmation is not obtained. Here we sought to determine the utility and reproducibility of immunohistochemical detection of hepatocyte growth factor (HGF) in melanoma tissue, an approach of potential assistance in defining patients with innate resistance to BRAF inhibitor therapy. To this end, a published and a revised method that retained sensitivity but with greater specificity for HGF detection, were evaluated in cells known to endogenously express HGF, and in models where HGF is upregulated via cytokine induction and via overexpression by gene transfection. Consequent patient evaluation in collaboration with the Melanoma Institute Australia of a cohort of 41 melanoma specimens with extensive clinical annotation failed to validate HGF immunohistochemistry as a predictor of response to BRAF inhibitors. Targeted therapies for advanced melanoma and other cancers show great promise, and rigorous validation studies are thus indicated for approaches that seek to personalize such therapies to maximize therapeutic efficacy.
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485
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Bánhegyi G, Benedetti A, Margittai É, Marcolongo P, Fulceri R, Németh CE, Szarka A. Subcellular compartmentation of ascorbate and its variation in disease states. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1909-16. [DOI: 10.1016/j.bbamcr.2014.05.016] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Revised: 05/27/2014] [Accepted: 05/28/2014] [Indexed: 12/11/2022]
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486
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Ficz G, Gribben JG. Loss of 5-hydroxymethylcytosine in cancer: cause or consequence? Genomics 2014; 104:352-7. [PMID: 25179374 DOI: 10.1016/j.ygeno.2014.08.017] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 08/21/2014] [Accepted: 08/22/2014] [Indexed: 12/19/2022]
Abstract
Discovery of the enzymatic activity that catalyses oxidation of 5-methylcytosine (5mC) to generate 5-hydroxymethylcytosine (5hmC) mediated by the MLL (KMT2A) fusion partner TET1 has sparked intense research to understand the role this new DNA modification has in cancer. An unambiguous picture has emerged where tumours are depleted of 5hmC compared to corresponding normal tissue, but it is not known whether lack of 5hmC is a cause or a consequence of tumourigenesis. Experimental data reveals a dual tumour-suppressive and oncogenic role for TET proteins. Tet2 mutations are drivers in haematological malignancies but Tet1 had an oncogenic role in MLL-rearranged leukaemia, where Tet1 is overexpressed. Overexpression of Tet2 in melanoma cells re-established the 5hmC landscape and suppressed cancer progression but inhibiting Tet1 in non-transformed cells did not initiate cellular transformation. In this review we summarise recent findings that have shaped the current understanding on the role 5hmC plays in cancer.
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Affiliation(s)
- Gabriella Ficz
- Centre for Haemato-Oncology, Barts Cancer Institute, EC1M 6BQ London, UK.
| | - John G Gribben
- Centre for Haemato-Oncology, Barts Cancer Institute, EC1M 6BQ London, UK
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487
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Lian CG, Xu S, Guo W, Yan J, Frank MYM, Liu R, Liu C, Chen Y, Murphy GF, Chen T. Decrease of 5-hydroxymethylcytosine in rat liver with subchronic exposure to genotoxic carcinogens riddelliine and aristolochic acid. Mol Carcinog 2014; 54:1503-7. [PMID: 25154389 DOI: 10.1002/mc.22201] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 06/02/2014] [Accepted: 06/07/2014] [Indexed: 11/09/2022]
Abstract
The level of 5-hydroxymethylcytosine (5-hmC) converted by ten-eleven translocation (TET) family is decreased in cancers. However, whether 5-hmC level is perturbed in early stages of carcinogenesis caused by genotoxic carcinogens is not defined. 5-hmC levels and TET2 expression were measured in liver of rats treated with genotoxic carcinogens, riddelliine, or aristolochic acid. Levels of 5-hmC and TET2 expression decreased in the liver of the carcinogens-treated rats. Loss of 5-hmC correlates well with documented induction of genetic mutations by the carcinogens, suggesting that TET2-mediated 5-hydroxymethylation plays an epigenetic role in early state of carcinogenesis.
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Affiliation(s)
- Christine Guo Lian
- Program in Dermatopathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Shuyun Xu
- Program in Dermatopathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Weimin Guo
- Program in Dermatopathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jian Yan
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas
| | - Maximilian Y M Frank
- Program in Dermatopathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Robert Liu
- Program in Dermatopathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Cynthia Liu
- Program in Dermatopathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Ying Chen
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas
| | - George F Murphy
- Program in Dermatopathology, Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Tao Chen
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas
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488
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The potential role of O-GlcNAc modification in cancer epigenetics. Cell Mol Biol Lett 2014; 19:438-60. [PMID: 25141978 PMCID: PMC6275943 DOI: 10.2478/s11658-014-0204-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Accepted: 08/01/2014] [Indexed: 12/20/2022] Open
Abstract
There is no doubt that cancer is not only a genetic disease but that it can also occur due to epigenetic abnormalities. Diet and environmental factors can alter the scope of epigenetic regulation. The results of recent studies suggest that O-GlcNAcylation, which involves the addition of N-acetylglucosamine on the serine or threonine residues of proteins, may play a key role in the regulation of the epigenome in response to the metabolic status of the cell. Two enzymes are responsible for cyclic O-GlcNAcylation: O-GlcNAc transferase (OGT), which catalyzes the addition of the GlcNAc moiety to target proteins; and O-GlcNAcase (OGA), which removes the sugar moiety from proteins. Aberrant expression of O-GlcNAc cycling enzymes, especially OGT, has been found in all studied human cancers. OGT can link the cellular metabolic state and the epigenetic status of cancer cells by interacting with and modifying many epigenetic factors, such as HCF-1, TET, mSin3A, HDAC, and BAP1. A growing body of evidence from animal model systems also suggests an important role for OGT in polycomb-dependent repression of genes activity. Moreover, O-GlcNAcylation may be a part of the histone code: O-GlcNAc residues are found on all core histones.
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489
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Morin A, Letouzé E, Gimenez-Roqueplo AP, Favier J. Oncometabolites-driven tumorigenesis: From genetics to targeted therapy. Int J Cancer 2014; 135:2237-48. [DOI: 10.1002/ijc.29080] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 04/08/2014] [Accepted: 04/16/2014] [Indexed: 12/11/2022]
Affiliation(s)
- Aurélie Morin
- INSERM; UMR970, Paris-Cardiovascular Research Center at HEGP; Paris France
- Faculté de Médecine; Université Paris Descartes; Paris France
| | - Eric Letouzé
- Programme Cartes d'Identité des Tumeurs, Ligue Nationale Contre Le Cancer; Paris France
| | - Anne-Paule Gimenez-Roqueplo
- INSERM; UMR970, Paris-Cardiovascular Research Center at HEGP; Paris France
- Faculté de Médecine; Université Paris Descartes; Paris France
- Assistance Publique-Hôpitaux de Paris; Hôpital Européen Georges Pompidou, Service de Génétique; Paris France
| | - Judith Favier
- INSERM; UMR970, Paris-Cardiovascular Research Center at HEGP; Paris France
- Faculté de Médecine; Université Paris Descartes; Paris France
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490
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Yao Y, Des Marais TL, Costa M. Chromatin Memory in the Development of Human Cancers. GENE TECHNOLOGY 2014; 3:114. [PMID: 25606572 PMCID: PMC4297643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Cancer is a complex disease with acquired genomic and epigenomic alterations that affect cell proliferation, viability and invasiveness. Almost all the epigenetic mechanisms including cytosine methylation and hydroxymethylation, chromatin remodeling and non-coding RNAs have been found associate with carcinogenesis and cancer specific expression profile. Altered histone modification as an epigenetic hallmark is frequently found in tumors. Understanding the epigenetic alterations induced by carcinogens or infectious agents may help us understand early epigenetic changes prior to the development of cancer. In this review, we focus on chromatin remodeling and the associated histone modifiers in the development of cancer; the application of these modifiers as a cancer therapy target in different clinical trial phases is also discussed.
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Affiliation(s)
- Yixin Yao
- Department of Environmental Medicine New York University, New York, USA,Corresponding author: Yixin Yao, Department of Environmental Medicine, New York University, New York, USA; Tel: 845-731-3517;
| | | | - Max Costa
- Department of Environmental Medicine New York University, New York, USA,Department of Biochemistry and Molecular Pharmacology, New York University Langone Medical Center, Tuxedo, New York, USA
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491
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Mikoshiba Y, Ogawa E, Uchiyama R, Uchiyama A, Uhara H, Okuyama R. 5-Hydroxymethylcytosine is a useful marker to differentiate between dermatofibrosarcoma protuberans and dermatofibroma. J Eur Acad Dermatol Venereol 2014; 30:130-1. [PMID: 25087918 DOI: 10.1111/jdv.12614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Y Mikoshiba
- Department of Dermatology, Shinshu University School of Medicine, Matsumoto, Japan
| | - E Ogawa
- Department of Dermatology, Shinshu University School of Medicine, Matsumoto, Japan
| | - R Uchiyama
- Department of Dermatology, Shinshu University School of Medicine, Matsumoto, Japan
| | - A Uchiyama
- Department of Dermatology, Shinshu University School of Medicine, Matsumoto, Japan
| | - H Uhara
- Department of Dermatology, Shinshu University School of Medicine, Matsumoto, Japan
| | - R Okuyama
- Department of Dermatology, Shinshu University School of Medicine, Matsumoto, Japan
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492
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Abstract
Epigenetic modulations orchestrate with extracellular environmental cues to determine the spatial and temporal expression of key regulators in neural stem/progenitor cells to control their proliferation, fate specification, and differentiation. Here, Yao and Jin review the latest in our knowledge of epigenetic regulation in neurogenesis and offer a perspective for future studies. During embryonic and adult neurogenesis, neuronal stem cells follow a highly conserved path of differentiation to give rise to functional neurons at various developmental stages. Epigenetic regulation—including DNA modifications, histone modifications, and noncoding regulatory RNAs, such as microRNA (miRNA) and long noncoding RNA (lncRNA)—plays a pivotal role in embryonic and adult neurogenesis. Here we review the latest in our understanding of the epigenetic regulation in neurogenesis, with a particular focus on newly identified cytosine modifications and their dynamics, along with our perspective for future studies.
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Affiliation(s)
- Bing Yao
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Peng Jin
- Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia 30322, USA
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493
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Abstract
The ability of stem cells to self-renew and generate different lineages during development and organogenesis is a fundamental, tightly controlled, and generally unidirectional process, whereas the 'immortality' of cancer cells could be regarded as pathological self-renewal. The molecular mechanisms that underpin the generation of induced pluripotent stem cells are remarkably similar to those that are deregulated in cancer - so much so that aberrant reprogramming is tumorigenic. The similarities also suggest that mutations in genes implicated in DNA methylation dynamics might represent a hallmark of cancers with a stem cell origin, and they highlight an alternative view of cancer that may be of clinical benefit.
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Affiliation(s)
- Colin R Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, Old Road Campus Research Building, Old Road Campus, University of Oxford, Headington, Oxford OX3 7DQ, UK
| | - Duanqing Pei
- South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 510530 China
| | - Xin Lu
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, Old Road Campus Research Building, Old Road Campus, University of Oxford, Headington, Oxford OX3 7DQ, UK
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494
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Melanoma epigenetics: novel mechanisms, markers, and medicines. J Transl Med 2014; 94:822-38. [PMID: 24978641 PMCID: PMC4479581 DOI: 10.1038/labinvest.2014.87] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 04/30/2014] [Accepted: 05/08/2014] [Indexed: 02/07/2023] Open
Abstract
The incidence and mortality rates of cutaneous melanoma continue to increase worldwide, despite the deployment of targeted therapies. Recently, there has been rapid growth and development in our understanding of epigenetic mechanisms and their role in cancer pathobiology. Epigenetics--defined as the processes resulting in heritable changes in gene expression beyond those caused by alterations in the DNA sequence--likely contain the information that encodes for such phenotypic variation between individuals with identical genotypes. By altering the structure of chromatin through covalent modification of DNA bases or histone proteins, or by regulating mRNA translation through non-coding RNAs, the epigenome ultimately determines which genes are expressed and which are kept silent. While our understanding of epigenetic mechanisms is growing at a rapid pace, the field of melanoma epigenomics still remains in its infancy. In this Pathology in Focus, we will briefly review the basics of epigenetics to contextualize and critically examine the existing literature using melanoma as a cancer paradigm. Our understanding of how dysregulated DNA methylation and DNA demethylation/hydroxymethylation, histone modification, and non-coding RNAs affect cancer pathogenesis and melanoma virulence, in particular, provides us with an ever-expanding repertoire of potential diagnostic biomarkers, therapeutic targets, and novel pathogenic mechanisms. The evidence reviewed herein indicates the critical role of epigenetic mechanisms in melanoma pathobiology and provides evidence for future targets in the development of next-generation biomarkers and therapeutics.
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495
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Shahal T, Gilat N, Michaeli Y, Redy-Keisar O, Shabat D, Ebenstein Y. Spectroscopic quantification of 5-hydroxymethylcytosine in genomic DNA. Anal Chem 2014; 86:8231-7. [PMID: 25072105 DOI: 10.1021/ac501609d] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
5-Hydroxymethylcytosine (5hmC), a modified form of the DNA base cytosine, is an important epigenetic mark linked to regulation of gene expression in development, and tumorigenesis. We have developed a spectroscopic method for a global quantification of 5hmC in genomic DNA. The assay is performed within a multiwell plate, which allows simultaneous recording of up to 350 samples. Our quantification procedure of 5hmC is direct, simple, and rapid. It relies on a two-step protocol that consists of enzymatic glucosylation of 5hmC with an azide-modified glucose, followed by a "click reaction" with an alkyne-fluorescent tag. The fluorescence intensity recorded from the DNA sample is proportional to its 5hmC content and can be quantified by a simple plate reader measurement. This labeling technique is specific and highly sensitive, allowing detection of 5hmC down to 0.002% of the total nucleotides. Our results reveal significant variations in the 5hmC content obtained from different mouse tissues, in agreement with previously reported data.
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Affiliation(s)
- Tamar Shahal
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University , Tel Aviv, 6997801, Israel
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496
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Loriot A, Van Tongelen A, Blanco J, Klaessens S, Cannuyer J, van Baren N, Decottignies A, De Smet C. A novel cancer-germline transcript carrying pro-metastatic miR-105 and TET-targeting miR-767 induced by DNA hypomethylation in tumors. Epigenetics 2014; 9:1163-71. [PMID: 25089631 PMCID: PMC4164501 DOI: 10.4161/epi.29628] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Genome hypomethylation is a common epigenetic alteration in human tumors, where it often leads to aberrant activation of a group of germline-specific genes, commonly referred to as “cancer-germline” genes. The cellular functions and tumor promoting potential of these genes remain, however, largely uncertain. Here, we report identification of a novel cancer-germline transcript (CT-GABRA3) displaying DNA hypomethylation-dependent activation in various tumors, including melanoma and lung carcinoma. Importantly, CT-GABRA3 harbors a microRNA (miR-105), which has recently been identified as a promoter of cancer metastasis by its ability to weaken vascular endothelial barriers following exosomal secretion. CT-GABRA3 also carries a microRNA (miR-767) with predicted target sites in TET1 and TET3, two members of the ten-eleven-translocation family of tumor suppressor genes, which are involved in the conversion of 5-methylcytosines to 5-hydroxymethylcytosines (5hmC) in DNA. Decreased TET activity is a hallmark of cancer; here, we provide evidence that aberrant activation of miR-767 contributes to this phenomenon. We demonstrate that miR-767 represses TET1/3 mRNA and protein expression and regulates genomic 5hmC levels. Additionally, we show that high CT-GABRA3 transcription correlates with reduced TET1 mRNA levels in vivo in lung tumors. Together, our study identified a cancer-germline gene that produces microRNAs with oncogenic potential. Moreover, our data indicate that DNA hypomethylation in tumors can contribute to reduced 5hmC levels via activation of a TET-targeting microRNA.
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Affiliation(s)
- Axelle Loriot
- Group of Genetics and Epigenetics; de Duve Institute; Université Catholique de Louvain; Brussels, Belgium
| | - Aurélie Van Tongelen
- Group of Genetics and Epigenetics; de Duve Institute; Université Catholique de Louvain; Brussels, Belgium
| | - Jordi Blanco
- Group of Genetics and Epigenetics; de Duve Institute; Université Catholique de Louvain; Brussels, Belgium
| | - Simon Klaessens
- Group of Genetics and Epigenetics; de Duve Institute; Université Catholique de Louvain; Brussels, Belgium
| | - Julie Cannuyer
- Group of Genetics and Epigenetics; de Duve Institute; Université Catholique de Louvain; Brussels, Belgium
| | - Nicolas van Baren
- Ludwig Institute for Cancer Research Ltd; Centre du Cancer des Cliniques; Universitaires Saint-Luc; Brussels, Belgium
| | - Anabelle Decottignies
- Group of Genetics and Epigenetics; de Duve Institute; Université Catholique de Louvain; Brussels, Belgium
| | - Charles De Smet
- Group of Genetics and Epigenetics; de Duve Institute; Université Catholique de Louvain; Brussels, Belgium
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497
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Larson AR, Dresser K, Zhan Q, Lezcano C, Woda BA, Yosufi B, Thompson JF, Scolyer RA, Mihm MC, Shi YG, Murphy GF, Lian CG. Loss of 5-hydroxymethylcytosine correlates with increasing morphologic dysplasia in melanocytic tumors. Mod Pathol 2014; 27:936-44. [PMID: 24390216 PMCID: PMC4077910 DOI: 10.1038/modpathol.2013.224] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 10/16/2013] [Indexed: 12/31/2022]
Abstract
DNA methylation is the most well-studied epigenetic modification in cancer biology. 5-hydroxymethylcytosine is an epigenetic mark that can be converted from 5-methylcytosine by the ten-eleven translocation gene family. We recently reported the loss of 5-hydroxymethylcytosine in melanoma compared with benign nevi and suggested that loss of this epigenetic marker is correlated with tumor virulence based on its association with a worse prognosis. In this study, we further characterize the immunoreactivity patterns of 5-hydroxymethylcytosine in the full spectrum of melanocytic lesions to further validate the potential practical application of this epigenetic marker. One hundred and seventy-five cases were evaluated: 18 benign nevi, 20 dysplastic nevi (10 low-grade and 10 high-grade lesions), 10 atypical Spitz nevi, 20 borderline tumors, 5 melanomas arising within nevi, and 102 primary melanomas. Progressive loss of 5-hydroxymethylcytosine from benign dermal nevi to high-grade dysplastic nevi to borderline melanocytic neoplasms to melanoma was observed. In addition, an analysis of the relationship of nuclear diameter with 5-hydroxymethylcytosine staining intensity within lesional cells revealed a significant correlation between larger nuclear diameter and decreased levels of 5-hydroxymethylcytosine. Furthermore, borderline lesions uniquely exhibited a diverse spectrum of staining of each individual case. This study further substantiates the association of 5-hydroxymethylcytosine loss with dysplastic cytomorphologic features and tumor progression and supports the classification of borderline lesions as a biologically distinct category of melanocytic lesions.
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Affiliation(s)
- Allison R. Larson
- Program in Dermatopathology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School,Department of Dermatology, Brigham and Women’s Hospital, Harvard Medical School
| | - Karen Dresser
- Department of Pathology, University of Massachusetts Medical Center
| | - Qian Zhan
- Program in Dermatopathology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School
| | - Cecilia Lezcano
- Program in Dermatopathology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School
| | - Bruce A. Woda
- Department of Pathology, University of Massachusetts Medical Center
| | - Benafsha Yosufi
- Royal Prince Alfred Hospital, Melanoma Institute Australia and Sydney Medical School, The University of Sydney
| | - John F. Thompson
- Royal Prince Alfred Hospital, Melanoma Institute Australia and Sydney Medical School, The University of Sydney
| | - Richard A. Scolyer
- Royal Prince Alfred Hospital, Melanoma Institute Australia and Sydney Medical School, The University of Sydney
| | - Martin C. Mihm
- Department of Dermatology, Brigham and Women’s Hospital, Harvard Medical School
| | - Yujiang G. Shi
- Divison of Endocrinology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School
| | - George F. Murphy
- Program in Dermatopathology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School,Co-corresponding authors, George F. Murphy, MD, Program in Dermatopathology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Avenue, EBRC Suite 401, Boston MA 02115, , telephone 617-525-7484, fax 617-264-5149, Christine G. Lian, MD, Program in Dermatopathology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Avenue, EBRC Suite 401, Boston MA 02115, , telephone 617-525-7484, fax 617-264-5149
| | - Christine Guo Lian
- Program in Dermatopathology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School,Co-corresponding authors, George F. Murphy, MD, Program in Dermatopathology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Avenue, EBRC Suite 401, Boston MA 02115, , telephone 617-525-7484, fax 617-264-5149, Christine G. Lian, MD, Program in Dermatopathology, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, 221 Longwood Avenue, EBRC Suite 401, Boston MA 02115, , telephone 617-525-7484, fax 617-264-5149
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498
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Song F, Amos CI, Lee JE, Lian CG, Fang S, Liu H, MacGregor S, Iles MM, Law MH, Lindeman NI, Montgomery GW, Duffy DL, Cust AE, Jenkins MA, Whiteman DC, Kefford RF, Giles GG, Armstrong BK, Aitken JF, Hopper JL, Brown KM, Martin NG, Mann GJ, Bishop DT, Bishop JAN, Kraft P, Qureshi AA, Kanetsky PA, Hayward NK, Hunter DJ, Wei Q, Han J. Identification of a melanoma susceptibility locus and somatic mutation in TET2. Carcinogenesis 2014; 35:2097-101. [PMID: 24980573 DOI: 10.1093/carcin/bgu140] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Although genetic studies have reported a number of loci associated with melanoma risk, the complex genetic architecture of the disease is not yet fully understood. We sought to identify common genetic variants associated with melanoma risk in a genome-wide association study (GWAS) of 2298 cases and 6654 controls. Thirteen of 15 known loci were replicated with nominal significance. A total of 69 single-nucleotide polymorphisms (SNPs) were selected for in silico replication in two independent melanoma GWAS datasets (a total of 5149 cases and 12 795 controls). Seven novel loci were nominally significantly associated with melanoma risk. These seven SNPs were further genotyped in 234 melanoma cases and 238 controls. The SNP rs4698934 was nominally significantly associated with melanoma risk. The combined odds ratio per T allele = 1.18; 95% confidence interval (1.10-1.25); combined P = 7.70 × 10(-) (7). This SNP is located in the intron of the TET2 gene on chromosome 4q24. In addition, a novel somatic mutation of TET2 was identified by next-generation sequencing in 1 of 22 sporadic melanoma cases. TET2 encodes a member of TET family enzymes that oxidizes 5-methylcytosine to 5-hydroxymethylcytosine (5hmC). It is a putative epigenetic biomarker of melanoma as we previously reported, with observation of reduced TET2 transcriptional expression. This study is the first to implicate TET2 genetic variation and mutation in melanoma.
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Affiliation(s)
- Fengju Song
- Department of Epidemiology and Biostatistics, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center of Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, P.R. China
| | - Christopher I Amos
- Department of Community and Family Medicine, Center for Genomic Medicine, Geisel School of Medicine, Dartmouth College, Lebanon, NH 03755, USA
| | - Jeffrey E Lee
- Department of Surgical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Christine G Lian
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Shenying Fang
- Department of Surgical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hongliang Liu
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Stuart MacGregor
- Queensland Institute of Medical Research, Brisbane, Queensland 4029, Australia
| | - Mark M Iles
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds LS9 7TF, UK
| | - Matthew H Law
- Queensland Institute of Medical Research, Brisbane, Queensland 4029, Australia
| | - Neal I Lindeman
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Grant W Montgomery
- Queensland Institute of Medical Research, Brisbane, Queensland 4029, Australia
| | - David L Duffy
- Queensland Institute of Medical Research, Brisbane, Queensland 4029, Australia
| | - Anne E Cust
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, School of Population Health, University of Melbourne, Melbourne, Victoria 3052, Australia, Cancer Epidemiology and Services Research, Sydney School of Public Health, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Mark A Jenkins
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, School of Population Health, University of Melbourne, Melbourne, Victoria 3052, Australia
| | - David C Whiteman
- Queensland Institute of Medical Research, Brisbane, Queensland 4029, Australia
| | - Richard F Kefford
- Westmead Institute of Cancer Research, University of Sydney at Westmead Millennium Institute and Melanoma Institute Australia, Westmead, New South Wales 2145, Australia
| | - Graham G Giles
- Cancer Epidemiology Centre, The Cancer Council Victoria, Carlton, Victoria 3053, Australia
| | - Bruce K Armstrong
- Cancer Epidemiology and Services Research, Sydney School of Public Health, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Joanne F Aitken
- Viertel Centre for Research in Cancer Control, Cancer Council Queensland, Brisbane, Queensland 4004, Australia
| | - John L Hopper
- Centre for Molecular, Environmental, Genetic and Analytic Epidemiology, School of Population Health, University of Melbourne, Melbourne, Victoria 3052, Australia
| | - Kevin M Brown
- Laboratory of Translational Genomics, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD 20852, USA
| | - Nicholas G Martin
- Queensland Institute of Medical Research, Brisbane, Queensland 4029, Australia
| | - Graham J Mann
- Westmead Institute of Cancer Research, University of Sydney at Westmead Millennium Institute and Melanoma Institute Australia, Westmead, New South Wales 2145, Australia
| | - D Timothy Bishop
- Leeds Institute of Cancer and Pathology, University of Leeds, Leeds LS9 7TF, UK
| | | | | | - Peter Kraft
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
| | - Abrar A Qureshi
- Channing Division of Network Medicine and Department of Dermatology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Peter A Kanetsky
- Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nicholas K Hayward
- Oncogenomics Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Queensland 4029, Australia
| | - David J Hunter
- Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
| | - Qingyi Wei
- Duke Cancer Institute, Duke University Medical Center, Durham, NC 27710, USA,
| | - Jiali Han
- Department of Epidemiology and Biostatistics, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center of Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, P.R. China, Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA, Channing Division of Network Medicine and Department of Dermatology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA, Department of Epidemiology, Fairbanks School of Public Health, Indiana University, Indianapolis, IN 46202, USA, Simon Cancer Center, Indiana University, Indianapolis, IN 46202, USA and Department of Dermatology, School of Medicine, Indiana University, Indianapolis, IN 46202, USA
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499
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Putiri EL, Tiedemann RL, Thompson JJ, Liu C, Ho T, Choi JH, Robertson KD. Distinct and overlapping control of 5-methylcytosine and 5-hydroxymethylcytosine by the TET proteins in human cancer cells. Genome Biol 2014; 15:R81. [PMID: 24958354 PMCID: PMC4197818 DOI: 10.1186/gb-2014-15-6-r81] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 06/23/2014] [Indexed: 12/31/2022] Open
Abstract
Background The TET family of dioxygenases catalyze conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), but their involvement in establishing normal 5mC patterns during mammalian development and their contributions to aberrant control of 5mC during cellular transformation remain largely unknown. We depleted TET1, TET2, and TET3 in a pluripotent embryonic carcinoma cell model and examined the impact on genome-wide 5mC, 5hmC, and transcriptional patterns. Results TET1 depletion yields widespread reduction of 5hmC, while depletion of TET2 and TET3 reduces 5hmC at a subset of TET1 targets suggesting functional co-dependence. TET2 or TET3 depletion also causes increased 5hmC, suggesting these proteins play a major role in 5hmC removal. All TETs prevent hypermethylation throughout the genome, a finding dramatically illustrated in CpG island shores, where TET depletion results in prolific hypermethylation. Surprisingly, TETs also promote methylation, as hypomethylation was associated with 5hmC reduction. TET function is highly specific to chromatin environment: 5hmC maintenance by all TETs occurs at polycomb-marked chromatin and genes expressed at moderate levels; 5hmC removal by TET2 is associated with highly transcribed genes enriched for H3K4me3 and H3K36me3. Importantly, genes prone to hypermethylation in cancer become depleted of 5hmC with TET deficiency, suggesting that TETs normally promote 5hmC at these loci. Finally, all three TETs, but especially TET2, are required for 5hmC enrichment at enhancers, a condition necessary for expression of adjacent genes. Conclusions These results provide novel insight into the division of labor among TET proteins and reveal important connections between TET activity, the chromatin landscape, and gene expression.
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500
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Tung PY, Knoepfler PS. Epigenetic mechanisms of tumorigenicity manifesting in stem cells. Oncogene 2014; 34:2288-96. [PMID: 24931168 PMCID: PMC4268091 DOI: 10.1038/onc.2014.172] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 05/08/2014] [Accepted: 05/09/2014] [Indexed: 01/04/2023]
Abstract
One of the biggest roadblocks to using stem cells as the basis for regenerative medicine therapies is the tumorigenicity of stem cells. Unfortunately, the unique abilities of stem cells to self-renew and differentiate into a variety of cell types are also mechanistically linked to their tumorigenic behaviors. Understanding the mechanisms underlying the close relationship between stem cells and cancer cells has therefore become a primary goal in the field. In addition, knowledge gained from investigating the striking parallels between mechanisms orchestrating normal embryogenesis and those that invoke tumorigenesis may well serve as the foundation for developing novel cancer treatments. Emerging discoveries have demonstrated that epigenetic regulatory machinery plays important roles in normal stem cell functions, cancer development, and cancer stem cell identity. These studies provide valuable insights into both the shared and distinct mechanisms by which pluripotency and oncogenicity are established and regulated. In this review, the cancer-related epigenetic mechanisms found in pluripotent stem cells and cancer stem cells will be discussed, focusing on both the similarities and the differences.
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Affiliation(s)
- P-Y Tung
- 1] Department of Cell Biology and Human Anatomy, University of California Davis School of Medicine, Davis, CA, USA [2] UC Davis Genome Center, University of California Davis, Davis, CA, USA [3] UC Davis Comprehensive Cancer Center, Sacramento, CA, USA [4] Institute of Pediatric Regenerative Medicine, Shriners Hospital For Children Northern California, Sacramento, CA, USA
| | - P S Knoepfler
- 1] Department of Cell Biology and Human Anatomy, University of California Davis School of Medicine, Davis, CA, USA [2] UC Davis Genome Center, University of California Davis, Davis, CA, USA [3] UC Davis Comprehensive Cancer Center, Sacramento, CA, USA [4] Institute of Pediatric Regenerative Medicine, Shriners Hospital For Children Northern California, Sacramento, CA, USA
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