501
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Besaratinia A, Tommasi S. Epigenetics of human melanoma: promises and challenges. J Mol Cell Biol 2014; 6:356-67. [PMID: 24895357 DOI: 10.1093/jmcb/mju027] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Melanoma is the deadliest form of skin cancer with rising incidence and mortality rates. Although early-stage melanoma is highly curable, advanced-stage melanoma is refractory to treatment. This underscores the importance of prevention and early detection as well as the need to improve treatment and prognostication of human melanoma. Elucidating the underlying mechanisms of the initiation and progression of human melanoma can help identify potential targets of intervention for prevention, diagnosis, therapy, and prognosis of this disease. Aberrant DNA methylation and histone modifications are the best-established epigenetic mechanisms of carcinogenesis. The occurrence of epigenetic changes prior to clinical diagnosis of cancer and their reversibility through pharmacologic/genetic approaches offer a promising avenue for basic and translational research on human melanoma. Candidate gene(s) or genome-wide aberrant DNA methylation and histone modifications have been observed in human melanoma tumor tissues and cell lines, and correlated to cellular and functional characteristics and/or clinicopathological features of this malignancy. The present review summarizes the published researches on aberrant DNA methylation and histone modifications in connection with human melanoma. Representative studies are highlighted to set forth the current state of knowledge, gaps in the knowledgebase, and future directions in these epigenetic fields of research. Examples of epigenetic therapy applied for human melanoma in vitro, and the challenges of its in vivo application for clinical treatment of solid tumors are discussed.
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Affiliation(s)
- Ahmad Besaratinia
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, M/C 9603, Los Angeles, CA 90033, USA
| | - Stella Tommasi
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, M/C 9603, Los Angeles, CA 90033, USA
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502
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Insights from Genetic Models of Melanoma in Fish. CURRENT PATHOBIOLOGY REPORTS 2014. [DOI: 10.1007/s40139-014-0043-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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503
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Ecsedi S, Hernandez-Vargas H, Lima SC, Vizkeleti L, Toth R, Lazar V, Koroknai V, Kiss T, Emri G, Herceg Z, Adany R, Balazs M. DNA methylation characteristics of primary melanomas with distinct biological behaviour. PLoS One 2014; 9:e96612. [PMID: 24832207 PMCID: PMC4022506 DOI: 10.1371/journal.pone.0096612] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 04/09/2014] [Indexed: 12/29/2022] Open
Abstract
In melanoma, the presence of promoter related hypermethylation has previously been reported, however, no methylation-based distinction has been drawn among the diverse melanoma subtypes. Here, we investigated DNA methylation changes associated with melanoma progression and links between methylation patterns and other types of somatic alterations, including the most frequent mutations and DNA copy number changes. Our results revealed that the methylome, presenting in early stage samples and associated with the BRAF(V600E) mutation, gradually decreased in the medium and late stages of the disease. An inverse relationship among the other predefined groups and promoter methylation was also revealed except for histologic subtype, whereas the more aggressive, nodular subtype melanomas exhibited hypermethylation as well. The Breslow thickness, which is a continuous variable, allowed for the most precise insight into how promoter methylation decreases from stage to stage. Integrating our methylation results with a high-throughput copy number alteration dataset, local correlations were detected in the MYB and EYA4 genes. With regard to the effects of DNA hypermethylation on melanoma patients' survival, correcting for clinical cofounders, only the KIT gene was associated with a lower overall survival rate. In this study, we demonstrate the strong influence of promoter localized DNA methylation changes on melanoma initiation and show how hypermethylation decreases in melanomas associated with less favourable clinical outcomes. Furthermore, we establish the methylation pattern as part of an integrated apparatus of somatic DNA alterations.
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Affiliation(s)
- Szilvia Ecsedi
- Department of Preventive Medicine, Faculty of Public Health, University of Debrecen, Debrecen, Hungary
- MTA-DE- Public Health Research Group, University of Debrecen, Debrecen, Hungary
| | - Hector Hernandez-Vargas
- International Agency for Research on Cancer, Section of Mechanisms of Carcinogenesis, Epigenetics Group, Lyon, France
| | - Sheila C. Lima
- International Agency for Research on Cancer, Section of Mechanisms of Carcinogenesis, Epigenetics Group, Lyon, France
| | - Laura Vizkeleti
- Department of Preventive Medicine, Faculty of Public Health, University of Debrecen, Debrecen, Hungary
- MTA-DE- Public Health Research Group, University of Debrecen, Debrecen, Hungary
| | - Reka Toth
- Department of Preventive Medicine, Faculty of Public Health, University of Debrecen, Debrecen, Hungary
| | - Viktoria Lazar
- Department of Preventive Medicine, Faculty of Public Health, University of Debrecen, Debrecen, Hungary
| | - Viktoria Koroknai
- Department of Preventive Medicine, Faculty of Public Health, University of Debrecen, Debrecen, Hungary
| | - Timea Kiss
- Department of Preventive Medicine, Faculty of Public Health, University of Debrecen, Debrecen, Hungary
| | - Gabriella Emri
- Department of Dermatology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Zdenko Herceg
- International Agency for Research on Cancer, Section of Mechanisms of Carcinogenesis, Epigenetics Group, Lyon, France
| | - Roza Adany
- Department of Preventive Medicine, Faculty of Public Health, University of Debrecen, Debrecen, Hungary
- MTA-DE- Public Health Research Group, University of Debrecen, Debrecen, Hungary
| | - Margit Balazs
- Department of Preventive Medicine, Faculty of Public Health, University of Debrecen, Debrecen, Hungary
- MTA-DE- Public Health Research Group, University of Debrecen, Debrecen, Hungary
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504
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Abstract
Methylation of the fifth carbon of cytosine was the first epigenetic modification to be discovered in DNA. Recently, three new DNA modifications have come to light: hydroxymethylcytosine, formylcytosine, and carboxylcytosine, all generated by oxidation of methylcytosine by Ten Eleven Translocation (TET) enzymes. These modifications can initiate full DNA demethylation, but they are also likely to participate, like methylcytosine, in epigenetic signalling per se. A scenario is emerging in which coordinated regulation at multiple levels governs the participation of TETs in a wide range of physiological functions, sometimes via a mechanism unrelated to their enzymatic activity. Although still under construction, a sophisticated picture is rapidly forming where, according to the function to be performed, TETs ensure epigenetic marking to create specific landscapes, and whose improper build-up can lead to diseases such as cancer and neurodegenerative disorders.
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Affiliation(s)
- Benjamin Delatte
- Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles, Brussels, Belgium
| | - Rachel Deplus
- Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles, Brussels, Belgium
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, Université Libre de Bruxelles, Brussels, Belgium
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505
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Calvo X, Nomdedeu M, Navarro A, Tejero R, Costa D, Muñoz C, Pereira A, Peña O, Risueño RM, Monzó M, Esteve J, Nomdedeu B. High levels of global DNA methylation are an independent adverse prognostic factor in a series of 90 patients with de novo myelodysplastic syndrome. Leuk Res 2014; 38:874-81. [PMID: 24880536 DOI: 10.1016/j.leukres.2014.04.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 04/23/2014] [Accepted: 04/27/2014] [Indexed: 12/31/2022]
Abstract
The prognostic impact of global DNA methylation and hydroxymethylation was assessed in 90 patients with de novo myelodysplastic syndrome (MDS). DNA was isolated from bone marrow samples obtained at diagnosis and global methylation and hydroxymethylation were determined by ELISA. Patients with a percentage of methylated DNA above 2.73% had a shorter overall survival than those with lower levels (P=0.018) and presented a negative trend in terms of leukemia-free survival (P=0.084), that was statistically significant after censoring 9 patients that received disease-modifying treatments both in univariate and multivariate analyses. Similarly, the low-risk MDS patients defined by the IPSS, WPSS and IPSS-R with 5-mC percentage in total DNA above 2.73% had a shorter overall survival (P=0.032; P=0.023; P=0.031). No cut-off value for the 5-hydroxymethylcytosine percentage with statistical significance for overall or leukemia-free survival was obtained. This study suggests that global DNA methylation predicts overall survival in myelodysplastic syndromes.
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Affiliation(s)
- Xavier Calvo
- Hematopathology Unit, Department of Pathology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain.
| | - Meritxell Nomdedeu
- Hematology Department, Hospital Clínic, IDIBAPS, University of Barcelona, Barcelona, Spain; Josep Carreras Leukaemia Research Institute, Barcelona, Spain
| | - Alfons Navarro
- Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, School of Medicine, University of Barcelona, IDIBAPS, Barcelona, Spain
| | - Rut Tejero
- Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, School of Medicine, University of Barcelona, IDIBAPS, Barcelona, Spain
| | - Dolors Costa
- Hematopathology Unit, Department of Pathology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Concha Muñoz
- Hematopathology Unit, Department of Pathology, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Arturo Pereira
- Department of Hemotherapy and Hemostasis, Hospital Clínic, IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Oscar Peña
- Hematology Department, Hospital Clínic, IDIBAPS, University of Barcelona, Barcelona, Spain
| | - Ruth M Risueño
- Josep Carreras Leukaemia Research Institute, Barcelona, Spain
| | - Mariano Monzó
- Molecular Oncology and Embryology Laboratory, Human Anatomy Unit, School of Medicine, University of Barcelona, IDIBAPS, Barcelona, Spain
| | - Jordi Esteve
- Hematology Department, Hospital Clínic, IDIBAPS, University of Barcelona, Barcelona, Spain; Josep Carreras Leukaemia Research Institute, Barcelona, Spain
| | - Benet Nomdedeu
- Hematology Department, Hospital Clínic, IDIBAPS, University of Barcelona, Barcelona, Spain.
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506
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Pfeifer GP, Xiong W, Hahn MA, Jin SG. The role of 5-hydroxymethylcytosine in human cancer. Cell Tissue Res 2014; 356:631-41. [PMID: 24816989 DOI: 10.1007/s00441-014-1896-7] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 04/10/2014] [Indexed: 12/22/2022]
Abstract
The patterns of DNA methylation in human cancer cells are highly abnormal and often involve the acquisition of DNA hypermethylation at hundreds or thousands of CpG islands that are usually unmethylated in normal tissues. The recent discovery of 5-hydroxymethylcytosine (5hmC) as an enzymatic oxidation product of 5-methylcytosine (5mC) has led to models and experimental data in which the hypermethylation and 5mC oxidation pathways seem to be connected. Key discoveries in this setting include the findings that several genes coding for proteins involved in the 5mC oxidation reaction are mutated in human tumors, and that a broad loss of 5hmC occurs across many types of cancer. In this review, we will summarize current knowledge and discuss models of the potential roles of 5hmC in human cancer biology.
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Affiliation(s)
- Gerd P Pfeifer
- Beckman Research Institute, City of Hope Medical Center, 1500 East Duarte Road, Duarte, CA 91010, USA,
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507
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McNally B, Linder M, Valdes R. Epigenetic primer for diagnostic applications: a window into personalized medicine. Per Med 2014; 11:323-337. [DOI: 10.2217/pme.14.21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Epigenetic testing, primarily in the form of DNA methylation analysis, is currently being used in healthcare settings to help identify and manage disease conditions and to develop and select drugs that specifically target epigenetic machinery. Yet, the clinical application of epigenetic analysis is still in its infancy. With a number of large-scale national and international epigenomic consortia projects in progress to identify tissue-specific epigenomes in normal and disease conditions, we are now poised for a new era of understanding disease processes based upon genetic changes that do not involve alterations to the DNA sequence. The developing epigenetic knowledge base will significantly advance the practice of personalized medicine and precision therapeutics. In this article, we provide a primer on the fundamentals of epigenetics with an emphasis on DNA methylation and review the prospective uses of epigenetic testing in advancing healthcare.
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Affiliation(s)
| | - Mark Linder
- PGXL Laboratories, Louisville, KY 40202, USA
- Department of Pathology & Laboratory Medicine, University of Louisville School of Medicine, MDR Building, 511 S Flloyd Street, Room 222, Louisville KY 40292, USA
| | - Roland Valdes
- PGXL Laboratories, Louisville, KY 40202, USA
- Department of Pathology & Laboratory Medicine, University of Louisville School of Medicine, MDR Building, 511 S Flloyd Street, Room 222, Louisville KY 40292, USA
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508
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Crichton JH, Dunican DS, MacLennan M, Meehan RR, Adams IR. Defending the genome from the enemy within: mechanisms of retrotransposon suppression in the mouse germline. Cell Mol Life Sci 2014; 71:1581-605. [PMID: 24045705 PMCID: PMC3983883 DOI: 10.1007/s00018-013-1468-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 08/27/2013] [Accepted: 08/29/2013] [Indexed: 12/15/2022]
Abstract
The viability of any species requires that the genome is kept stable as it is transmitted from generation to generation by the germ cells. One of the challenges to transgenerational genome stability is the potential mutagenic activity of transposable genetic elements, particularly retrotransposons. There are many different types of retrotransposon in mammalian genomes, and these target different points in germline development to amplify and integrate into new genomic locations. Germ cells, and their pluripotent developmental precursors, have evolved a variety of genome defence mechanisms that suppress retrotransposon activity and maintain genome stability across the generations. Here, we review recent advances in understanding how retrotransposon activity is suppressed in the mammalian germline, how genes involved in germline genome defence mechanisms are regulated, and the consequences of mutating these genome defence genes for the developing germline.
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Affiliation(s)
- James H. Crichton
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU UK
| | - Donncha S. Dunican
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU UK
| | - Marie MacLennan
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU UK
| | - Richard R. Meehan
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU UK
| | - Ian R. Adams
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU UK
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509
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Liu WR, Tian MX, Jin L, Yang LX, Ding ZB, Shen YH, Peng YF, Zhou J, Qiu SJ, Dai Z, Fan J, Shi YH. High expression of 5-hydroxymethylcytosine and isocitrate dehydrogenase 2 is associated with favorable prognosis after curative resection of hepatocellular carcinoma. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2014; 33:32. [PMID: 24716838 PMCID: PMC4081660 DOI: 10.1186/1756-9966-33-32] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 03/27/2014] [Indexed: 12/17/2022]
Abstract
BACKGROUND The expression of 5-hydroxymethylcytosine (5-hmC) and isocitrate dehydrogenase 2 (IDH2) is frequently downregulated in numerous cancers. 5-hmC and IDH2 expression in hepatocellular carcinoma (HCC) has yet to be determined. METHODS The immunohistochemical expression of 5-hmC and IDH2 were analyzed in tissue microarrays containing samples from 646 patients who had undergone hepatectomy for histologically proven HCC. The prognostic value of 5-hmC and IDH2 were evaluated by Cox regression and Kaplan-Meier analyses. RESULTS We discovered that low 5-hmC and IDH2 expression was associated with malignant behaviors. Low 5-hmC or IDH2 expression alone and combined 5-hmC and IDH2 expression were associated with lower overall survival (OS) rates and higher cumulative recurrence rates. Multivariate analysis indicated that 5-hmC or IDH2 and 5-hmC/IDH2 were independent prognostic indicators for OS and time to recurrence (TTR), which was confirmed in an independent validation cohort. CONCLUSIONS 5-hmC and IDH2 correlate with less aggressive tumor behavior in HCC. When 5-hmC and IDH2 are considered together, they serve as a prognostic marker in patients with surgically resected HCCs.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Jia Fan
- Department of Liver Surgery, Liver Cancer Institute, Zhongshan Hospital, Fudan University, 180 FengLin Road, Shanghai 200032, China.
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510
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Wu H, Zhang Y. Reversing DNA methylation: mechanisms, genomics, and biological functions. Cell 2014; 156:45-68. [PMID: 24439369 DOI: 10.1016/j.cell.2013.12.019] [Citation(s) in RCA: 753] [Impact Index Per Article: 75.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Indexed: 12/28/2022]
Abstract
Methylation of cytosines in the mammalian genome represents a key epigenetic modification and is dynamically regulated during development. Compelling evidence now suggests that dynamic regulation of DNA methylation is mainly achieved through a cyclic enzymatic cascade comprised of cytosine methylation, iterative oxidation of methyl group by TET dioxygenases, and restoration of unmodified cytosines by either replication-dependent dilution or DNA glycosylase-initiated base excision repair. In this review, we discuss the mechanism and function of DNA demethylation in mammalian genomes, focusing particularly on how developmental modulation of the cytosine-modifying pathway is coupled to active reversal of DNA methylation in diverse biological processes.
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Affiliation(s)
- Hao Wu
- Howard Hughes Medical Institute, Harvard Medical School, WAB-149G, 200 Longwood Avenue, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, WAB-149G, 200 Longwood Avenue, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, WAB-149G, 200 Longwood Avenue, Boston, MA 02115, USA; Harvard Stem Cell Institute, Harvard Medical School, WAB-149G, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Yi Zhang
- Howard Hughes Medical Institute, Harvard Medical School, WAB-149G, 200 Longwood Avenue, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, WAB-149G, 200 Longwood Avenue, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, WAB-149G, 200 Longwood Avenue, Boston, MA 02115, USA; Harvard Stem Cell Institute, Harvard Medical School, WAB-149G, 200 Longwood Avenue, Boston, MA 02115, USA.
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511
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Taylor SEB, Smeriglio P, Dhulipala L, Rath M, Bhutani N. A global increase in 5-hydroxymethylcytosine levels marks osteoarthritic chondrocytes. Arthritis Rheumatol 2014; 66:90-100. [PMID: 24449578 DOI: 10.1002/art.38200] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 09/12/2013] [Indexed: 12/24/2022]
Abstract
OBJECTIVE To investigate the role of the newly discovered epigenetic mark 5-hydroxymethylcytosine (5hmC) and its regulators in altered gene expression in osteoarthritis (OA). METHODS Cartilage was obtained from OA patients undergoing total knee arthroplasty and from control patients undergoing anterior cruciate ligament reconstruction. Global levels of 5hmC and 5-methylcytosine (5mC) were investigated using immunoblotting, enzyme-linked immunosorbent assays, and cellular staining. Gene expression changes were monitored by quantitative polymerase chain reaction (PCR) analysis. Levels of locus-specific 5hmC and 5mC at CpG sites in the matrix metalloproteinase 1 (MMP-1), MMP-3, ADAMTS-5, and hypoxanthine guanine phosphoribosyltransferase 1 (HPRT-1) promoters were quantified using a glucosylation and enzyme digestion-based method followed by quantitative PCR analysis. Global and locus-specific 5hmC levels and gene expression changes were monitored in normal chondrocytes stimulated with inflammatory cytokines to identify the effect of joint inflammation. RESULTS A global 5-6-fold increase in 5hmC concomitant with a loss of TET1 was observed in human OA chondrocytes compared to normal chondrocytes. Enrichment of 5hmC was observed in promoters of enzymes critical to OA pathology, MMP-1 and MMP-3. Short-term treatment of normal chondrocytes with inflammatory cytokines induced a rapid decrease in TET1 expression but no global or locus-specific 5hmC enrichment. CONCLUSION This study provides the first evidence of an epigenetic imbalance of the 5hmC homeostasis in OA leading to TET1 down-regulation and 5hmC accumulation. Our experiments identify 5hmC and its regulators as potential diagnostic and therapeutic targets in OA.
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512
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Abstract
Epigenetic alterations are associated with all aspects of cancer, from tumor initiation to cancer progression and metastasis. It is now well understood that both losses and gains of DNA methylation as well as altered chromatin organization contribute significantly to cancer-associated phenotypes. More recently, new sequencing technologies have allowed the identification of driver mutations in epigenetic regulators, providing a mechanistic link between the cancer epigenome and genetic alterations. Oncogenic activating mutations are now known to occur in a number of epigenetic modifiers (i.e. IDH1/2, EZH2, DNMT3A), pinpointing epigenetic pathways that are involved in tumorigenesis. Similarly, investigations into the role of inactivating mutations in chromatin modifiers (i.e. KDM6A, CREBBP/EP300, SMARCB1) implicate many of these genes as tumor suppressors. Intriguingly, a number of neoplasms are defined by a plethora of mutations in epigenetic regulators, including renal, bladder, and adenoid cystic carcinomas. Particularly striking is the discovery of frequent histone H3.3 mutations in pediatric glioma, a particularly aggressive neoplasm that has long remained poorly understood. Cancer epigenetics is a relatively new, promising frontier with much potential for improving cancer outcomes. Already, therapies such as 5-azacytidine and decitabine have proven that targeting epigenetic alterations in cancer can lead to tangible benefits. Understanding how genetic alterations give rise to the cancer epigenome will offer new possibilities for developing better prognostic and therapeutic strategies.
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513
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Affiliation(s)
- Padmaja Mummaneni
- Office of Clinical Pharmacology; Office of Translational Sciences; Center for Drug Evaluation and Research; United States Food and Drug Administration; Silver Spring Maryland
| | - Stacy S. Shord
- Office of Clinical Pharmacology; Office of Translational Sciences; Center for Drug Evaluation and Research; United States Food and Drug Administration; Silver Spring Maryland
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514
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Tsagaratou A, Rao A. TET proteins and 5-methylcytosine oxidation in the immune system. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2014; 78:1-10. [PMID: 24619230 DOI: 10.1101/sqb.2013.78.020248] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DNA methylation in the form of 5-methylcytosine (5mC) is essential for normal development in mammals and influences a variety of biological processes, including transcriptional regulation, imprinting, and the maintenance of genomic stability. The recent discovery of TET proteins, which oxidize 5mC to 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine, has changed our understanding of the process of DNA demethylation. Here, we summarize our current knowledge of the roles of DNA methylation and TET proteins in cell differentiation and function. The intensive research on this subject has so far focused primarily on embryonic stem (ES) cells and neurons. In addition, we summarize what is known about DNA methylation in T-cell function.
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Affiliation(s)
- Ageliki Tsagaratou
- La Jolla Institute for Allergy and Immunology, La Jolla, California 92037
| | - Anjana Rao
- La Jolla Institute for Allergy and Immunology, La Jolla, California 92037 Department of Pharmacology, University of California, San Diego, La Jolla, California 92093-0636 Sanford Consortium for Regenerative Medicine, La Jolla, California 92037
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515
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Bacolla A, Cooper DN, Vasquez KM. Mechanisms of base substitution mutagenesis in cancer genomes. Genes (Basel) 2014; 5:108-46. [PMID: 24705290 PMCID: PMC3978516 DOI: 10.3390/genes5010108] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 02/07/2014] [Accepted: 02/11/2014] [Indexed: 01/24/2023] Open
Abstract
Cancer genome sequence data provide an invaluable resource for inferring the key mechanisms by which mutations arise in cancer cells, favoring their survival, proliferation and invasiveness. Here we examine recent advances in understanding the molecular mechanisms responsible for the predominant type of genetic alteration found in cancer cells, somatic single base substitutions (SBSs). Cytosine methylation, demethylation and deamination, charge transfer reactions in DNA, DNA replication timing, chromatin status and altered DNA proofreading activities are all now known to contribute to the mechanisms leading to base substitution mutagenesis. We review current hypotheses as to the major processes that give rise to SBSs and evaluate their relative relevance in the light of knowledge acquired from cancer genome sequencing projects and the study of base modifications, DNA repair and lesion bypass. Although gene expression data on APOBEC3B enzymes provide support for a role in cancer mutagenesis through U:G mismatch intermediates, the enzyme preference for single-stranded DNA may limit its activity genome-wide. For SBSs at both CG:CG and YC:GR sites, we outline evidence for a prominent role of damage by charge transfer reactions that follow interactions of the DNA with reactive oxygen species (ROS) and other endogenous or exogenous electron-abstracting molecules.
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Affiliation(s)
- Albino Bacolla
- Dell Pediatric Research Institute, Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA.
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK.
| | - Karen M Vasquez
- Dell Pediatric Research Institute, Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA.
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516
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Dao T, Cheng RYS, Revelo MP, Mitzner W, Tang W. Hydroxymethylation as a Novel Environmental Biosensor. Curr Environ Health Rep 2014; 1:1-10. [PMID: 24860723 PMCID: PMC4029614 DOI: 10.1007/s40572-013-0005-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Beyond the genome, epigenetics has become a promising approach in understanding the interactions between the gene and the environment. Epigenetic regulation includes DNA methylation, histone modifications, and non-coding RNAs. Among these, DNA methylation, which is the addition of a methyl group to the fifth base of cytosine to produce 5-methylcytosine (5-mC), is most commonly studied. Epigenetic regulation has changed given the discovery of 5-hydroxymethylcytosine (5-hmC), considered the "sixth base", and the nature of TET proteins to catalyze 5-mC oxidation to 5-hmC. 5-hydroxymethylation has been proposed to be a stable intermediate between methylation and demethylation and has raised questions about the functions of 5-hmC in gene regulation in cells, tissues, and organs in response to environmental exposure. Herein, we have provided an introduction to the chemistry of 5-hydroxymethylation, and the techniques for detection of 5-hydroxymethylation. In addition, we have reviewed current reports describing how 5-hmC responds to environmental factors, leading to the development of disease. And finally, we have discussed the potential use of 5-hmC in the study of disease development. All in all, it is our goal to provide innovative and convincing epigenetic studies for understanding the etiology of environmentally-related human disease, and translate these epigenetic findings into lifestyle recommendations and clinical practices to prevent and cure disease.
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Affiliation(s)
- T Dao
- Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States
| | - R Y S Cheng
- Radiation Biology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - M P Revelo
- Department of Pathology, University of Utah, Salt Lake City, Utah, United States
| | - W Mitzner
- Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States
| | - Wy Tang
- Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States
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517
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Zhao X, Dai J, Ma Y, Mi Y, Cui D, Ju G, Macklin WB, Jin W. Dynamics of ten-eleven translocation hydroxylase family proteins and 5-hydroxymethylcytosine in oligodendrocyte differentiation. Glia 2014; 62:914-26. [PMID: 24615693 DOI: 10.1002/glia.22649] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 02/07/2014] [Accepted: 02/07/2014] [Indexed: 12/21/2022]
Abstract
The ten-eleven translocation (TET) family of methylcytosine dioxygenases catalyze oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) and promote DNA demethylation. Despite the abundance of 5hmC and TET proteins in the brain, little is known about their role in oligodendrocytes (OLs). Here, we analyzed TET expression during OL development in vivo and in vitro, and found that three TET family members possess unique subcellular and temporal expression patterns. Furthermore, the level of 5hmC exhibits dynamic changes during OL maturation, which implies that 5hmC modification may play a role in the expression of critical genes necessary for OL maturation. siRNA-mediated silencing of the TET family proteins in OLs demonstrated that each of the TET proteins is required for OL differentiation. However, based on their unique domain structures, we speculate that the three TET members may function by different mechanisms. In summary, we have established the temporal expression of TET proteins and the dynamic level of 5hmC during OL development and demonstrate that all three TET members are necessary for OL differentiation.
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Affiliation(s)
- Xianghui Zhao
- Institute of Neuroscience, Fourth Military Medical University, Xi'an, China
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518
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Sun W, Guan M, Li X. 5-hydroxymethylcytosine-mediated DNA demethylation in stem cells and development. Stem Cells Dev 2014; 23:923-30. [PMID: 24400731 DOI: 10.1089/scd.2013.0428] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The pursuit of DNA demethylation has a colorful history, but it was not until 2009 that the stars of this story, the Ten-eleven-translocation (Tet) family of proteins, were really identified. Tet proteins convert 5-methylcytosine to 5-hydroxymethylcytosine (5hmC), which can be further oxidized to 5-formylcytosine and 5-cyboxycytosine by Tet proteins to achieve DNA demethylation. Recent studies have revealed that 5hmC-mediated DNA demethylation can play essential roles in diverse biological processes, including development and diseases. Here, we review recent discoveries in 5hmC-mediated DNA demethylation in the context of stem cells and development.
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Affiliation(s)
- Wenjia Sun
- 1 The Children's Hospital, School of Medicine, Zhejiang University , Hangzhou, China
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519
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Uchiyama R, Uhara H, Uchiyama A, Ogawa E, Takazawa Y, Ashida A, Koga H, Hayashi K, Kiniwa Y, Okuyama R. 5-Hydroxymethylcytosine as a useful marker to differentiate between malignant melanomas and benign melanocytic nevi. J Dermatol Sci 2014; 73:161-3. [DOI: 10.1016/j.jdermsci.2013.09.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 09/27/2013] [Accepted: 09/30/2013] [Indexed: 10/26/2022]
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520
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Tampe B, Tampe D, Müller CA, Sugimoto H, LeBleu V, Xu X, Müller GA, Zeisberg EM, Kalluri R, Zeisberg M. Tet3-mediated hydroxymethylation of epigenetically silenced genes contributes to bone morphogenic protein 7-induced reversal of kidney fibrosis. J Am Soc Nephrol 2014; 25:905-12. [PMID: 24480825 DOI: 10.1681/asn.2013070723] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Methylation of CpG island promoters is an epigenetic event that can effectively silence transcription over multiple cell generations. Hypermethylation of the Rasal1 promoter contributes to activation of fibroblasts and progression of kidney fibrosis. Here, we explored whether such causative hypermethylation could be reversed through endogenous mechanisms and whether such reversal of hypermethylation is a constituent of the antifibrotic activity of bone morphogenic protein 7 (BMP7). We show that successful inhibition of experimental kidney fibrosis through administration of BMP7 associates with normalization of Rasal1 promoter hypermethylation. Furthermore, this reversal of pathologic hypermethylation was achieved specifically through Tet3-mediated hydroxymethylation. Collectively, our findings reveal a new mechanism that may be exploited to facilitate therapeutic DNA demethylation to reverse kidney fibrosis.
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Affiliation(s)
- Björn Tampe
- Departments of Nephrology and Rheumatology, and
| | | | - Claudia A Müller
- Departments of Nephrology and Rheumatology, and Department of Transplantation, Immunology and Immunohematology, Tübingen University Medical Center, Eberhard Karls University, Tübingen, Germany
| | - Hikaru Sugimoto
- Department of Cancer Biology and the Metastasis Research Center, University of Texas MD Anderson Cancer Center, Houston, Texas; and
| | - Valerie LeBleu
- Department of Cancer Biology and the Metastasis Research Center, University of Texas MD Anderson Cancer Center, Houston, Texas; and
| | - Xingbo Xu
- Cardiology and Pneumology, Göttingen University Medical Center, Georg August University, Göttingen, Germany; German Center for Cardiovascular Research (DZHK), Göttingen, Germany
| | | | - Elisabeth M Zeisberg
- Cardiology and Pneumology, Göttingen University Medical Center, Georg August University, Göttingen, Germany; German Center for Cardiovascular Research (DZHK), Göttingen, Germany
| | - Raghu Kalluri
- Department of Cancer Biology and the Metastasis Research Center, University of Texas MD Anderson Cancer Center, Houston, Texas; and
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521
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Haseeb A, Makki MS, Haqqi TM. Modulation of ten-eleven translocation 1 (TET1), Isocitrate Dehydrogenase (IDH) expression, α-Ketoglutarate (α-KG), and DNA hydroxymethylation levels by interleukin-1β in primary human chondrocytes. J Biol Chem 2014; 289:6877-6885. [PMID: 24469454 DOI: 10.1074/jbc.m113.512269] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
5-Hydroxymethylcytosine (5-hmC) generated by ten-eleven translocation 1-3 (TET1-3) enzymes is an epigenetic mark present in many tissues with different degrees of abundance. IL-1β and TNF-α are the two major cytokines present in arthritic joints that modulate the expression of many genes associated with cartilage degradation in osteoarthritis. In the present study, we investigated the global 5-hmC content, the effects of IL-1β and TNF-α on 5-hmC content, and the expression and activity of TETs and isocitrate dehydrogenases in primary human chondrocytes. The global 5-hmC content was found to be ∼0.1% of the total genome. There was a significant decrease in the levels of 5-hmC and the TET enzyme activity upon treatment of chondrocytes with IL-1β alone or in combination with TNF-α. We observed a dramatic (10-20-fold) decrease in the levels of TET1 mRNA expression and a small increase (2-3-fold) in TET3 expression in chondrocytes stimulated with IL-1β and TNF-α. IL-1β and TNF-α significantly suppressed the activity and expression of IDHs, which correlated with the reduced α-ketoglutarate levels. Whole genome profiling showed an erasure effect of IL-1β and TNF-α, resulting in a significant decrease in hydroxymethylation in a myriad of genes including many genes that are important in chondrocyte physiology. Our data demonstrate that DNA hydroxymethylation is modulated by pro-inflammatory cytokines via suppression of the cytosine hydroxymethylation machinery. These data point to new mechanisms of epigenetic control of gene expression by pro-inflammatory cytokines in human chondrocytes.
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Affiliation(s)
- Abdul Haseeb
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, Ohio 44272
| | - Mohammad Shahidul Makki
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, Ohio 44272
| | - Tariq M Haqqi
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, Ohio 44272.
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522
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Odagiri H, Kadomatsu T, Endo M, Masuda T, Morioka MS, Fukuhara S, Miyamoto T, Kobayashi E, Miyata K, Aoi J, Horiguchi H, Nishimura N, Terada K, Yakushiji T, Manabe I, Mochizuki N, Mizuta H, Oike Y. The secreted protein ANGPTL2 promotes metastasis of osteosarcoma cells through integrin α5β1, p38 MAPK, and matrix metalloproteinases. Sci Signal 2014; 7:ra7. [PMID: 24448647 DOI: 10.1126/scisignal.2004612] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The tumor microenvironment can enhance the invasive capacity of tumor cells. We showed that expression of angiopoietin-like protein 2 (ANGPTL2) in osteosarcoma (OS) cell lines increased and the methylation of its promoter decreased with time when grown as xenografts in mice compared with culture. Compared with cells grown in normal culture conditions, the expression of genes encoding DNA demethylation-related enzymes increased in tumor cells implanted into mice or grown in hypoxic, serum-starved culture conditions. ANGPTL2 expression in OS cell lines correlated with increased tumor metastasis and decreased animal survival by promoting tumor cell intravasation mediated by the integrin α5β1, p38 mitogen-activated protein kinase, and matrix metalloproteinases. The tolloid-like 1 (TLL1) protease cleaved ANGPTL2 into fragments in vitro that did not enhance tumor progression when overexpressed in xenografts. Expression of TLL1 was weak in OS patient tumors, suggesting that ANGPTL2 may not be efficiently cleaved upon secretion from OS cells. These findings demonstrate that preventing ANGPTL2 signaling stimulated by the tumor microenvironment could inhibit tumor cell migration and metastasis.
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Affiliation(s)
- Haruki Odagiri
- 1Department of Molecular Genetics, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto 860-8556, Japan
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523
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Frycz BA, Murawa D, Borejsza-Wysocki M, Marciniak R, Murawa P, Drews M, Kołodziejczak A, Tomela K, Jagodziński PP. Decreased expression of ten-eleven translocation 1 protein is associated with some clinicopathological features in gastric cancer. Biomed Pharmacother 2014; 68:209-12. [PMID: 24507562 DOI: 10.1016/j.biopha.2013.12.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 12/31/2013] [Indexed: 12/22/2022] Open
Abstract
A decrease in ten-eleven translocation 1 (TET1) transcript and 5-Hydroxymethylcytosine (5hmC) levels has recently been demonstrated in primary gastric cancer (GC). However, little is known about TET1 protein levels in gastric tumoral and nontumoral tissue. Therefore, using reverse transcription, real-time quantitative polymerase chain reaction and western blotting analysis, we determined the TET1 transcript and protein levels in tumoral and nontumoral tissue from 38 patients with GC. We also assessed the association between the decrease in TET1 transcript and protein levels and some clinicopathological features in primary GC. We found significantly decreased levels of TET1 transcript (P=0.0023) and protein (P=0.00024) in primary tumoral tissues as compared to nontumoral tissues in patients with GC. Moreover, we also observed significantly lower amounts of TET1 transcript (P=0.03) and protein (P=0.00018) in tumoral tissues in patients aged>60. We also found significant lowered TET1 protein levels in male patients (P=0.0014), stomach (P=0.044) and cardia (P=0.013) tumor localization, T3 depth of invasion (P=0.019), N1 (P=0.012) and N3 lymph node metastasis (P=0.013) and G3 histological grade (P=0.0012). There were also significant decreases in TET1 transcript levels in female patients (P=0.042), intestinal histological types (P=0.0079) and T4 depth of invasion (P=0.037). Our results demonstrated that a decrease in TET1 transcript and protein levels is associated with some clinicopathological features in GC.
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Affiliation(s)
- Bartosz Adam Frycz
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences, Poznań, Poland
| | - Dawid Murawa
- First Department of Surgical Oncology and General Surgery, Wielkopolska Cancer Center, Poznań, Poland
| | - Maciej Borejsza-Wysocki
- Department of General Surgery, Oncologic Gastroenterological and Plastic Surgery, Poznań University of Medical Sciences, Poznań, Poland
| | - Ryszard Marciniak
- Department of General Surgery, Oncologic Gastroenterological and Plastic Surgery, Poznań University of Medical Sciences, Poznań, Poland
| | - Paweł Murawa
- First Department of Surgical Oncology and General Surgery, Wielkopolska Cancer Center, Poznań, Poland
| | - Michał Drews
- Department of General Surgery, Oncologic Gastroenterological and Plastic Surgery, Poznań University of Medical Sciences, Poznań, Poland
| | - Anna Kołodziejczak
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences, Poznań, Poland
| | - Katarzyna Tomela
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences, Poznań, Poland
| | - Paweł Piotr Jagodziński
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences, Poznań, Poland.
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524
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Distinct roles of the methylcytosine oxidases Tet1 and Tet2 in mouse embryonic stem cells. Proc Natl Acad Sci U S A 2014; 111:1361-6. [PMID: 24474761 DOI: 10.1073/pnas.1322921111] [Citation(s) in RCA: 194] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Dioxygenases of the Ten-Eleven Translocation (TET) family are 5-methylcytosine oxidases that convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) and further oxidation products in DNA. We show that Tet1 and Tet2 have distinct roles in regulating 5hmC in mouse embryonic stem cells (mESC). Tet1 depletion diminishes 5hmC levels at transcription start sites (TSS), whereas Tet2 depletion is predominantly associated with decreased 5hmC in gene bodies. Enrichment of 5hmC is observed at the boundaries of exons that are highly expressed, and Tet2 depletion results in substantial loss of 5hmC at these boundaries. In contrast, at promoter/TSS regions, Tet2 depletion results in increased 5hmC, potentially because of the redundant activity of Tet1. Together, the data point to a complex interplay between Tet1 and Tet2 in mESC, and to distinct roles for these two proteins in regulating promoter, exon, and polyadenylation site usage in cells.
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525
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Zhang Q, Lei X, Lu H. Alterations of epigenetic signatures in hepatocyte nuclear factor 4α deficient mouse liver determined by improved ChIP-qPCR and (h)MeDIP-qPCR assays. PLoS One 2014; 9:e84925. [PMID: 24427299 PMCID: PMC3888413 DOI: 10.1371/journal.pone.0084925] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 11/19/2013] [Indexed: 02/07/2023] Open
Abstract
Hepatocyte nuclear factor 4α (HNF4α) is a liver-enriched transcription factor essential for liver development and function. In hepatocytes, HNF4α regulates a large number of genes important for nutrient/xenobiotic metabolism and cell differentiation and proliferation. Currently, little is known about the epigenetic mechanism of gene regulation by HNF4α. In this study, the global and specific alterations at the selected gene loci of representative histone modifications and DNA methylations were investigated in Hnf4a-deficient female mouse livers using the improved MeDIP-, hMeDIP- and ChIP-qPCR assay. Hnf4a deficiency significantly increased hepatic total IPed DNA fragments for histone H3 lysine-4 dimethylation (H3K4me2), H3K4me3, H3K9me2, H3K27me3 and H3K4 acetylation, but not for H3K9me3, 5-methylcytosine,or 5-hydroxymethylcytosine. At specific gene loci, the relative enrichments of histone and DNA modifications were changed to different degree in Hnf4a-deficient mouse liver. Among the epigenetic signatures investigated, changes in H3K4me3 correlated the best with mRNA expression. Additionally, Hnf4a-deficient livers had increased mRNA expression of histone H1.2 and H3.3 as well as epigenetic modifiers Dnmt1, Tet3, Setd7, Kmt2c, Ehmt2, and Ezh2. In conclusion, the present study provides convenient improved (h)MeDIP- and ChIP-qPCR assays for epigenetic study. Hnf4a deficiency in young-adult mouse liver markedly alters histone methylation and acetylation, with fewer effects on DNA methylation and 5-hydroxymethylation. The underlying mechanism may be the induction of epigenetic enzymes responsible for the addition/removal of the epigenetic signatures, and/or the loss of HNF4αper se as a key coordinator for epigenetic modifiers.
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Affiliation(s)
- Qinghao Zhang
- Department of Pharmacology, SUNY Upstate Medical University, Syracuse, New York, United States of America
| | - Xiaohong Lei
- Department of Pharmacology, SUNY Upstate Medical University, Syracuse, New York, United States of America
| | - Hong Lu
- Department of Pharmacology, SUNY Upstate Medical University, Syracuse, New York, United States of America
- * E-mail:
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526
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Tseng PT, Lin PY, Lee Y, Hung CF, Lung FW, Chen CS, Chong MY. Age-associated decrease in global DNA methylation in patients with major depression. Neuropsychiatr Dis Treat 2014; 10:2105-14. [PMID: 25419133 PMCID: PMC4235206 DOI: 10.2147/ndt.s71997] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Evidence has supported a role of DNA methylation in the pathophysiology of mood disorders. The purpose of the current study is to examine 5-methylcytosine (5-mc) and 5-hydroxymethylcytosine (5-hmc) levels in patients with major depressive disorder (MDD) at different disease states. METHODS Forty-nine patients with MDD and 25 healthy control subjects were included. The severity in the disease was assessed by using the 17-item Hamilton Rating Scale of Depression (HAM-D) (HAM-D ≥19 for severe MDD and HAM-D ≤7 for remitted MDD). The 5-mc and 5-hmc levels in leukocyte DNA were measured using an enzyme-linked immunosorbent assay-based method. RESULTS We found a significant decrease in 5-hmc and trends of decreasing 5-mc levels in patients with severe MDD compared to healthy controls (P=0.059 for 5-mc and P=0.013 for 5-hmc). The decrease in the level exists only in the older age group (P=0.035 for 5-mc and P=0.002 for 5-hmc) but not in the younger age group (P=0.077 for 5-mc and P=0.620 for 5-hmc). In addition, the 5-mc level was found to be inversely correlated with disease severity (P=0.011). CONCLUSION Our results support a decrease in global DNA methylation associated with age in patients with severe depression. Further studies are needed to clarify the role of the methylation level as a disease marker of depression and whether antidepressant treatment changes the methylation profiles.
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Affiliation(s)
- Ping-Tao Tseng
- Department of Psychiatry, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan ; Department of Psychiatry, Tsyr-Huey Mental Hospital, Kaohsiung Jen-Ai's Home, Taiwan
| | - Pao-Yen Lin
- Department of Psychiatry, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan ; Center for Translational Research in Biomedical Sciences, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Yu Lee
- Department of Psychiatry, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chi-Fa Hung
- Department of Psychiatry, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - For-Wey Lung
- Taipei City Psychiatric Center, Taipei City Hospital, Taipei, Taiwan ; Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan
| | - Cheng-Sheng Chen
- Department of Psychiatry, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan ; Department of Psychiatry, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Mian-Yoon Chong
- Department of Psychiatry, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
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527
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Bastian BC. The molecular pathology of melanoma: an integrated taxonomy of melanocytic neoplasia. ANNUAL REVIEW OF PATHOLOGY 2014; 9:239-71. [PMID: 24460190 PMCID: PMC4831647 DOI: 10.1146/annurev-pathol-012513-104658] [Citation(s) in RCA: 312] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Melanomas comprise multiple biologically distinct categories, which differ in cell of origin, age of onset, clinical and histologic presentation, pattern of metastasis, ethnic distribution, causative role of UV radiation, predisposing germ-line alterations, mutational processes, and patterns of somatic mutations. Neoplasms are initiated by gain-of-function mutations in one of several primary oncogenes, which typically lead to benign melanocytic nevi with characteristic histologic features. The progression of nevi is restrained by multiple tumor-suppressive mechanisms. Secondary genetic alterations override these barriers and promote intermediate or overtly malignant tumors along distinct progression trajectories. The current knowledge about the pathogenesis and clinical, histologic, and genetic features of primary melanocytic neoplasms is reviewed and integrated into a taxonomic framework.
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Affiliation(s)
- Boris C Bastian
- Departments of Dermatology and Pathology, Cardiovascular Research Institute, University of California, San Francisco, California 94158-9001;
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528
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Abstract
The zebrafish has emerged as a powerful model system to study human diseases, including a variety of neoplasms. Principal components that have contributed to the rise in use of this vertebrate model system are its high fecundity, ease of genetic manipulation, and low cost of maintenance. Vital imaging of the zebrafish is possible from the transparent embryonic stage through adulthood, the latter enabled by a number of mutant lines that ablate pigmentation. As a result, high-resolution analyses of tumor progression can be accomplished in vivo. Straightforward transgenesis of zebrafish has been employed to develop numerous tumor models that recapitulate many aspects of human neoplastic disease, both in terms of pathologic and molecular conservation. The small size of zebrafish embryos has enabled screens for novel chemotherapeutic agents. Its facile genetics have been exploited in studies that extend beyond modeling cancer to investigations that define new cancer genes and mechanisms of cancer progression. Together, these attributes have established the zebrafish as a robust and versatile model system for investigating cancer. In this chapter we describe methods that are used to study a gene's impact on melanoma progression. We detail methods for making transgenic animals and screening for tumor onset as well as methods to investigate tumor invasion and propagation.
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Affiliation(s)
- Corrie A Painter
- Program in Molecular Medicine, Department of Cancer Biology, Program in Cell and Developmental Dynamics, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01605, USA
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529
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Nettersheim D, Heukamp LC, Fronhoffs F, Grewe MJ, Haas N, Waha A, Honecker F, Waha A, Kristiansen G, Schorle H. Analysis of TET expression/activity and 5mC oxidation during normal and malignant germ cell development. PLoS One 2013; 8:e82881. [PMID: 24386123 PMCID: PMC3873252 DOI: 10.1371/journal.pone.0082881] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 10/28/2013] [Indexed: 02/06/2023] Open
Abstract
During mammalian development the fertilized zygote and primordial germ cells lose their DNA methylation within one cell cycle leading to the concept of active DNA demethylation. Recent studies identified the TET hydroxylases as key enzymes responsible for active DNA demethylation, catalyzing the oxidation of 5-methylcytosine to 5-hydroxymethylcytosine. Further oxidation and activation of the base excision repair mechanism leads to replacement of a modified cytosine by an unmodified one. In this study, we analyzed the expression/activity of TET1-3 and screened for the presence of 5 mC oxidation products in adult human testis and in germ cell cancers. By analyzing human testis sections, we show that levels of 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine are decreasing as spermatogenesis proceeds, while 5-methylcytosine levels remain constant. These data indicate that during spermatogenesis active DNA demethylation becomes downregulated leading to a conservation of the methylation marks in mature sperm. We demonstrate that all carcinoma in situ and the majority of seminomas are hypomethylated and hypohydroxymethylated compared to non-seminomas. Interestingly, 5-formylcytosine and 5-carboxylcytosine were detectable in all germ cell cancer entities analyzed, but levels did not correlate to the 5-methylcytosine or 5-hydroxymethylcytosine status. A meta-analysis of gene expression data of germ cell cancer tissues and corresponding cell lines demonstrates high expression of TET1 and the DNA glycosylase TDG, suggesting that germ cell cancers utilize the oxidation pathway for active DNA demethylation. During xenograft experiments, where seminoma-like TCam-2 cells transit to an embryonal carcinoma-like state DNMT3B and DNMT3L where strongly upregulated, which correlated to increasing 5-methylcytosine levels. Additionally, 5-hydroxymethylcytosine levels were elevated, demonstrating that de novo methylation and active demethylation accompanies this transition process. Finally, mutations of IDH1 (IDH1 (R132)) and IDH2 (IDH2 (R172)) leading to production of the TET inhibiting oncometabolite 2-hydroxyglutarate in germ cell cancer cell lines were not detected.
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Affiliation(s)
- Daniel Nettersheim
- Institute of Pathology, Department of Developmental Pathology, University Hospital, Bonn, Germany
| | | | | | - Marc J. Grewe
- Institute of Pathology, University Hospital, Bonn, Germany
| | - Natalie Haas
- Institute of Pathology, Department of Developmental Pathology, University Hospital, Bonn, Germany
| | - Anke Waha
- Institute of Neuropathology, University Hospital, Bonn, Germany
| | - Friedemann Honecker
- Department of Oncology, Haematology and Bone Marrow Transplantation with Section Pneumology, Hubertus Wald-Tumorzentrum, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andreas Waha
- Institute of Neuropathology, University Hospital, Bonn, Germany
| | | | - Hubert Schorle
- Institute of Pathology, Department of Developmental Pathology, University Hospital, Bonn, Germany
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530
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Hu L, Li Z, Cheng J, Rao Q, Gong W, Liu M, Shi YG, Zhu J, Wang P, Xu Y. Crystal structure of TET2-DNA complex: insight into TET-mediated 5mC oxidation. Cell 2013; 155:1545-55. [PMID: 24315485 DOI: 10.1016/j.cell.2013.11.020] [Citation(s) in RCA: 297] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Revised: 11/14/2013] [Accepted: 11/15/2013] [Indexed: 12/27/2022]
Abstract
TET proteins oxidize 5-methylcytosine (5mC) on DNA and play important roles in various biological processes. Mutations of TET2 are frequently observed in myeloid malignance. Here, we present the crystal structure of human TET2 bound to methylated DNA at 2.02 Å resolution. The structure shows that two zinc fingers bring the Cys-rich and DSBH domains together to form a compact catalytic domain. The Cys-rich domain stabilizes the DNA above the DSBH core. TET2 specifically recognizes CpG dinucleotide and shows substrate preference for 5mC in a CpG context. 5mC is inserted into the catalytic cavity with the methyl group orientated to catalytic Fe(II) for reaction. The methyl group is not involved in TET2-DNA contacts so that the catalytic cavity allows TET2 to accommodate 5mC derivatives for further oxidation. Mutations of Fe(II)/NOG-chelating, DNA-interacting, and zinc-chelating residues are frequently observed in human cancers. Our studies provide a structural basis for understanding the mechanisms of TET-mediated 5mC oxidation.
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Affiliation(s)
- Lulu Hu
- Fudan University Shanghai Cancer Center, Department of Oncology and Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China; State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Ze Li
- Fudan University Shanghai Cancer Center, Department of Oncology and Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Jingdong Cheng
- Fudan University Shanghai Cancer Center, Department of Oncology and Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Qinhui Rao
- Fudan University Shanghai Cancer Center, Department of Oncology and Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Wei Gong
- Fudan University Shanghai Cancer Center, Department of Oncology and Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Mengjie Liu
- Fudan University Shanghai Cancer Center, Department of Oncology and Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yujiang Geno Shi
- Fudan University Shanghai Cancer Center, Department of Oncology and Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China; Division of Endocrinology, Diabetes and Hypertension, Department of Medicine and Department of Biological Chemistry & Molecular Pharmacology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Jiayu Zhu
- Fudan University Shanghai Cancer Center, Department of Oncology and Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Ping Wang
- Fudan University Shanghai Cancer Center, Department of Oncology and Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Department of Oncology and Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China; State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China.
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531
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Logan PC, Mitchell MD, Lobie PE. DNA methyltransferases and TETs in the regulation of differentiation and invasiveness of extra-villous trophoblasts. Front Genet 2013; 4:265. [PMID: 24363660 PMCID: PMC3849743 DOI: 10.3389/fgene.2013.00265] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 11/15/2013] [Indexed: 01/21/2023] Open
Abstract
Specialized cell types of trophoblast cells form the placenta in which each cell type has particular properties of proliferation and invasion. The placenta sustains the growth of the fetus throughout pregnancy and any aberrant trophoblast differentiation or invasion potentially affects the future health of the child and adult. Recently, the field of epigenetics has been applied to understand differentiation of trophoblast lineages and embryonic stem cells (ESC), from fertilization of the oocyte onward. Each trophoblast cell-type has a distinctive epigenetic profile and we will concentrate on the epigenetic mechanism of DNA methyltransferases and TETs that regulate DNA methylation. Environmental factors affecting the mother potentially regulate the DNA methyltransferases in trophoblasts, and so do steroid hormones, cell cycle regulators, such as p53, and cytokines, especially interlukin-1β. There are interesting questions of why trophoblast genomes are globally hypomethylated yet specific genes can be suppressed by hypermethylation (in general, tumor suppressor genes, such as E-cadherin) and how invasive cell-types are liable to have condensed chromatin, as in metastatic cancer cells. Future work will attempt to understand the interactive nature of all epigenetic mechanisms together and their effect on the complex biological system of trophoblast differentiation and invasion in normal as well as pathological conditions.
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Affiliation(s)
- Philip C Logan
- The Liggins Institute, The University of Auckland Auckland, New Zealand
| | - Murray D Mitchell
- University of Queensland Centre for Clinical Research, University of Queensland Brisbane, QLD, Australia
| | - Peter E Lobie
- Cancer Science Institute of Singapore, National University of Singapore Singapore, Singapore
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532
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Wielscher M, Liou W, Pulverer W, Singer CF, Rappaport-Fuerhauser C, Kandioler D, Egger G, Weinhäusel A. Cytosine 5-Hydroxymethylation of the LZTS1 Gene Is Reduced in Breast Cancer. Transl Oncol 2013; 6:715-21. [PMID: 24466374 PMCID: PMC3890706 DOI: 10.1593/tlo.13523] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 09/06/2013] [Accepted: 09/09/2013] [Indexed: 02/07/2023] Open
Abstract
Change of DNA cytosine methylation (5mC) is an early event in the development of cancer, and the recent discovery of a 5-hydroxymethylated form (5hmC) of cytosine suggests a regulatory epigenetic role that might be different from 5-methylcytosine. Here, we aimed at elucidating the role of 5hmC in breast cancer. To interrogate the 5hmC levels of the leucine zipper, putative tumor suppressor 1 (LZTS1) gene in detail, we analyzed 75 primary breast cancer tissue samples from initial diagnosis and 12 normal breast tissue samples derived from healthy persons. Samples were subjected to 5hmC glucosyltransferase treatment followed by restriction digestion and segment-specific amplification of 11 polymerase chain reaction products. Nine of the 11 5'LZTS1 fragments showed significantly lower (fold change of 1.61-6.01, P < .05) 5hmC content in primary breast cancer tissue compared to normal breast tissue samples. No significant differences were observed for 5mC DNA methylation. Furthermore, both LZTS1 and TET1 mRNA expressions were significantly reduced in tumor samples (n = 75, P < .001, Student's t test), which correlated significantly with 5hmC levels in samples. 5hmC levels in breast cancer tissues were associated with unfavorable histopathologic parameters such as lymph node involvement (P < .05, Student's t test). A decrease of 5hmC levels of LZTS1, a classic tumor suppressor gene known to influence metastasis in breast cancer progression, is correlated to down-regulation of LZTS1 mRNA expression in breast cancer and might epigenetically enhance carcinogenesis. The study provides support for the novel hypothesis that suggests a strong influence of 5hmC on mRNA expression. Finally, one may also consider 5hmC as a new biomarker.
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Affiliation(s)
- Matthias Wielscher
- Molecular Diagnostics Unit, Health and Environment Department, Austrian Institute of Technology, Vienna, Austria
| | - Willy Liou
- Molecular Diagnostics Unit, Health and Environment Department, Austrian Institute of Technology, Vienna, Austria
| | - Walter Pulverer
- Molecular Diagnostics Unit, Health and Environment Department, Austrian Institute of Technology, Vienna, Austria
| | - Christian F Singer
- Department of Obstetrics and Gynecology and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | | | | | - Gerda Egger
- Clinical Institute of Pathology, Medical University of Vienna, Vienna, Austria
| | - Andreas Weinhäusel
- Molecular Diagnostics Unit, Health and Environment Department, Austrian Institute of Technology, Vienna, Austria
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533
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Abstract
DNA methylation at the 5 position of cytosine (5-mC) has emerged as a key epigenetic marker that plays essential roles in various biological and pathological processes. 5-mC can be converted to 5-hydroxymethylcytosine (5-hmC) by the ten-eleven translocation (TET) family proteins, which is now widely recognized as the "sixth base" in the mammalian genome, following 5-mC, the "fifth base". 5-hmC is detected to be abundant in brain and embryonic stem cells, and is also distributed in many different human tissues. Emerging evidence has shown that 5-hmC and TET family might serve unique biological roles in many biological processes such as gene control mechanisms, DNA methylation regulation, and involved in many diseases, especially cancers. In this paper we provide an overview of the role of 5-hmC as a new sight of epigenetics in human cancer.
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Affiliation(s)
- Chao Ye
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; School of Medicine; First Affiliated Hospital; Zhejiang University; Hangzhou, Zhejiang, PR China
| | - Lan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases; School of Medicine; First Affiliated Hospital; Zhejiang University; Hangzhou, Zhejiang, PR China
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534
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Li L, Lorzadeh A, Hirst M. Regulatory variation: an emerging vantage point for cancer biology. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2013; 6:37-59. [DOI: 10.1002/wsbm.1250] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Luolan Li
- Centre for High-Throughput Biology, Department of Microbiology & Immunology; University of British Columbia; Vancouver, British Columbia Canada
| | - Alireza Lorzadeh
- Centre for High-Throughput Biology, Department of Microbiology & Immunology; University of British Columbia; Vancouver, British Columbia Canada
| | - Martin Hirst
- Centre for High-Throughput Biology, Department of Microbiology & Immunology; University of British Columbia; Vancouver, British Columbia Canada
- Canada's Michael Smith Genome Sciences Centre; BC Cancer Agency; Vancouver, British Columbia Canada
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535
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Solary E, Bernard OA, Tefferi A, Fuks F, Vainchenker W. The Ten-Eleven Translocation-2 (TET2) gene in hematopoiesis and hematopoietic diseases. Leukemia 2013; 28:485-96. [PMID: 24220273 DOI: 10.1038/leu.2013.337] [Citation(s) in RCA: 203] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 10/14/2013] [Indexed: 12/17/2022]
Abstract
Ten-Eleven Translocation-2 (TET2) inactivation through loss-of-function mutation, deletion and IDH1/2 (Isocitrate Dehydrogenase 1 and 2) gene mutation is a common event in myeloid and lymphoid malignancies. TET2 gene mutations similar to those observed in myeloid and lymphoid malignancies also accumulate with age in otherwise healthy subjects with clonal hematopoiesis. TET2 is one of the three proteins of the TET (Ten-Eleven Translocation) family, which are evolutionarily conserved dioxygenases that catalyze the conversion of 5-methyl-cytosine (5-mC) to 5-hydroxymethyl-cytosine (5-hmC) and promote DNA demethylation. TET dioxygenases require 2-oxoglutarate, oxygen and Fe(II) for their activity, which is enhanced in the presence of ascorbic acid. TET2 is the most expressed TET gene in the hematopoietic tissue, especially in hematopoietic stem cells. In addition to their hydroxylase activity, TET proteins recruit the O-linked β-D-N-acetylglucosamine (O-GlcNAc) transferase (OGT) enzyme to chromatin, which promotes post-transcriptional modifications of histones and facilitates gene expression. The TET2 level is regulated by interaction with IDAX, originating from TET2 gene fission during evolution, and by the microRNA miR-22. TET2 has pleiotropic roles during hematopoiesis, including stem-cell self-renewal, lineage commitment and terminal differentiation of monocytes. Analysis of Tet2 knockout mice, which are viable and fertile, demonstrated that Tet2 functions as a tumor suppressor whose haploinsufficiency initiates myeloid and lymphoid transformations. This review summarizes the recently identified TET2 physiological and pathological functions and discusses how this knowledge influences our therapeutic approaches in hematological malignancies and possibly other tumor types.
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Affiliation(s)
- E Solary
- 1] Hematology Department, Gustave Roussy, Villejuif, France [2] Inserm UMR1009, Gustave Roussy, Villejuif cedex, France [3] Faculty of Medicine, University Paris-Sud, Le Kremlin-Bicêtre, France
| | - O A Bernard
- 1] Hematology Department, Gustave Roussy, Villejuif, France [2] Faculty of Medicine, University Paris-Sud, Le Kremlin-Bicêtre, France [3] Inserm UMR985, Gustave Roussy, Villejuif, France
| | - A Tefferi
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - F Fuks
- Faculty of Medicine, Laboratory of Cancer Epigenetics, Université Libre de Bruxelles, Brussels, Belgium
| | - W Vainchenker
- 1] Hematology Department, Gustave Roussy, Villejuif, France [2] Inserm UMR1009, Gustave Roussy, Villejuif cedex, France [3] Faculty of Medicine, University Paris-Sud, Le Kremlin-Bicêtre, France
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536
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Thomson JP, Hunter JM, Nestor CE, Dunican DS, Terranova R, Moggs JG, Meehan RR. Comparative analysis of affinity-based 5-hydroxymethylation enrichment techniques. Nucleic Acids Res 2013; 41:e206. [PMID: 24214958 PMCID: PMC3905904 DOI: 10.1093/nar/gkt1080] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The epigenetic modification of 5-hydroxymethylcytosine (5hmC) is receiving great attention due to its potential role in DNA methylation reprogramming and as a cell state identifier. Given this interest, it is important to identify reliable and cost-effective methods for the enrichment of 5hmC marked DNA for downstream analysis. We tested three commonly used affinity-based enrichment techniques; (i) antibody, (ii) chemical capture and (iii) protein affinity enrichment and assessed their ability to accurately and reproducibly report 5hmC profiles in mouse tissues containing high (brain) and lower (liver) levels of 5hmC. The protein-affinity technique is a poor reporter of 5hmC profiles, delivering 5hmC patterns that are incompatible with other methods. Both antibody and chemical capture-based techniques generate highly similar genome-wide patterns for 5hmC, which are independently validated by standard quantitative PCR (qPCR) and glucosyl-sensitive restriction enzyme digestion (gRES-qPCR). Both antibody and chemical capture generated profiles reproducibly link to unique chromatin modification profiles associated with 5hmC. However, there appears to be a slight bias of the antibody to bind to regions of DNA rich in simple repeats. Ultimately, the increased specificity observed with chemical capture-based approaches makes this an attractive method for the analysis of locus-specific or genome-wide patterns of 5hmC.
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Affiliation(s)
- John P Thomson
- Chromosomes and Gene Expression, MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK, Member of MARCAR Consortium, The Centre for Individualized Medication, Linköping University Hospital, Linköping University, Linköping SE-58185, Sweden and Discovery and Investigative Safety, Preclinical Safety, Novartis Institutes for Biomedical Research, Klybeckstrasse, Basel CH-4002, Switzerland
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537
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Mason EF, Hornick JL. Succinate dehydrogenase deficiency is associated with decreased 5-hydroxymethylcytosine production in gastrointestinal stromal tumors: implications for mechanisms of tumorigenesis. Mod Pathol 2013; 26:1492-7. [PMID: 23743927 DOI: 10.1038/modpathol.2013.86] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 03/25/2013] [Accepted: 03/26/2013] [Indexed: 01/09/2023]
Abstract
Gastrointestinal stromal tumors (GISTs) usually harbor activating mutations in KIT or PDGFRA, which promote tumorigenesis through activation of growth factor receptor signaling pathways. Around 15% of GISTs in adults and >90% in children lack such mutations ('wild-type' GISTs). Most gastric wild-type GISTs show loss of function of the Krebs cycle enzyme complex succinate dehydrogenase (SDH). However, the mechanism by which SDH deficiency drives tumorigenesis is unclear. Loss of SDH leads to succinate accumulation, which is thought to inhibit α-ketoglutarate-dependent dioxygenase enzymes, such as the TET family of DNA hydroxylases. TET proteins catalyze the conversion of 5-methylcytosine to 5-hydroxymethylcytosine (5-hmC), which is required for subsequent DNA demethylation. Thus, TET-mediated 5-hmC production alters global DNA methylation patterns and may thereby influence gene expression. We investigated 5-hmC levels in a cohort of genotyped GISTs to determine whether loss of SDH was associated with inhibition of TET activity. 5-hmC levels were examined via immunohistochemistry in a cohort of 30 genotyped GISTs, including 10 SDH-deficient tumors (5 SDHA mutant; 1 SDHB mutant; 1 SDHC mutant; 3 unknown), 14 tumors with KIT mutations (10 in exon 11; 3 in exon 9; 1 in exon 17), and 6 tumors with PDGFRA mutations (all in exon 18). Staining for 5-hmC was negative in 9 of 10 (90%) SDH-deficient GISTs, 3 of 14 (21%) KIT-mutant GISTs, and 1 of 6 (17%) PDGFRA-mutant GISTs. The other SDH-deficient GIST showed weak staining for 5-hmC. Thus, 5-hmC was absent in nearly all SDH-deficient GISTs. These findings suggest that SDH deficiency may promote tumorigenesis through accumulation of succinate and inhibition of dioxygenase enzymes. Inhibition of TET activity may, in turn, alter global DNA methylation and gene expression in SDH-deficient tumors.
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Affiliation(s)
- Emily F Mason
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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538
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Cheng J, Guo S, Chen S, Mastriano SJ, Liu C, D’Alessio AC, Hysolli E, Guo Y, Yao H, Megyola CM, Li D, Liu J, Pan W, Roden CA, Zhou XL, Heydari K, Chen J, Park IH, Ding Y, Zhang Y, Lu J. An extensive network of TET2-targeting MicroRNAs regulates malignant hematopoiesis. Cell Rep 2013; 5:471-81. [PMID: 24120864 PMCID: PMC3834864 DOI: 10.1016/j.celrep.2013.08.050] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 07/30/2013] [Accepted: 08/29/2013] [Indexed: 02/05/2023] Open
Abstract
The Ten-Eleven-Translocation 2 (TET2) gene, which oxidates 5-methylcytosine in DNA to 5-hydroxylmethylcytosine (5hmC), is a key tumor suppressor frequently mutated in hematopoietic malignancies. However, the molecular regulation of TET2 expression is poorly understood. We show that TET2 is under extensive microRNA (miRNA) regulation, and such TET2 targeting is an important pathogenic mechanism in hematopoietic malignancies. Using a high-throughput 3' UTR activity screen, we identify >30 miRNAs that inhibit TET2 expression and cellular 5hmC. Forced expression of TET2-targeting miRNAs in vivo disrupts normal hematopoiesis, leading to hematopoietic expansion and/or myeloid differentiation bias, whereas coexpression of TET2 corrects these phenotypes. Importantly, several TET2-targeting miRNAs, including miR-125b, miR-29b, miR-29c, miR-101, and miR-7, are preferentially overexpressed in TET2-wild-type acute myeloid leukemia. Our results demonstrate the extensive roles of miRNAs in functionally regulating TET2 and cellular 5hmC and reveal miRNAs with previously unrecognized oncogenic potential. Our work suggests that TET2-targeting miRNAs might be exploited in cancer diagnosis.
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Affiliation(s)
- Jijun Cheng
- Department of Genetics and Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
- Yale Cancer Center and Center for RNA Science and Medicine, Yale University, New Haven, CT 06520, USA
| | - Shangqin Guo
- Department of Genetics and Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
- Department of Cell Biology, Yale University, New Haven, CT 06520, USA
| | - Suning Chen
- Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, China
| | - Stephen J. Mastriano
- Department of Genetics and Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
- Yale Cancer Center and Center for RNA Science and Medicine, Yale University, New Haven, CT 06520, USA
| | - Chaochun Liu
- Wadsworth Center, New York State Department of Health, 150 New Scotland Avenue, Albany, NY 12201, USA
| | - Ana C. D’Alessio
- Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Eriona Hysolli
- Department of Genetics and Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
| | - Yanwen Guo
- Department of Genetics and Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
- Yale Cancer Center and Center for RNA Science and Medicine, Yale University, New Haven, CT 06520, USA
| | - Hong Yao
- Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, China
| | - Cynthia M. Megyola
- Department of Genetics and Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
- Yale Cancer Center and Center for RNA Science and Medicine, Yale University, New Haven, CT 06520, USA
| | - Dan Li
- Department of Genetics and Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
- Yale Cancer Center and Center for RNA Science and Medicine, Yale University, New Haven, CT 06520, USA
| | - Jun Liu
- Department of Genetics and Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
- Yale Cancer Center and Center for RNA Science and Medicine, Yale University, New Haven, CT 06520, USA
| | - Wen Pan
- Department of Genetics and Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
- Yale Cancer Center and Center for RNA Science and Medicine, Yale University, New Haven, CT 06520, USA
| | - Christine A. Roden
- Department of Genetics and Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
- Yale Cancer Center and Center for RNA Science and Medicine, Yale University, New Haven, CT 06520, USA
| | - Xiao-Ling Zhou
- Department of Genetics and Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
- Department of Cell Biology and Genetics, Shantou University Medical College, Guangdong 515041, China
| | - Kartoosh Heydari
- Yale Cancer Center and Center for RNA Science and Medicine, Yale University, New Haven, CT 06520, USA
| | - Jianjun Chen
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - In-Hyun Park
- Department of Genetics and Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
| | - Ye Ding
- Wadsworth Center, New York State Department of Health, 150 New Scotland Avenue, Albany, NY 12201, USA
| | - Yi Zhang
- Howard Hughes Medical Institute, Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Jun Lu
- Department of Genetics and Yale Stem Cell Center, Yale University, New Haven, CT 06520, USA
- Yale Cancer Center and Center for RNA Science and Medicine, Yale University, New Haven, CT 06520, USA
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539
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Cancer development, progression, and therapy: an epigenetic overview. Int J Mol Sci 2013; 14:21087-113. [PMID: 24152442 PMCID: PMC3821660 DOI: 10.3390/ijms141021087] [Citation(s) in RCA: 182] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 09/27/2013] [Accepted: 10/04/2013] [Indexed: 11/17/2022] Open
Abstract
Carcinogenesis involves uncontrolled cell growth, which follows the activation of oncogenes and/or the deactivation of tumor suppression genes. Metastasis requires down-regulation of cell adhesion receptors necessary for tissue-specific, cell-cell attachment, as well as up-regulation of receptors that enhance cell motility. Epigenetic changes, including histone modifications, DNA methylation, and DNA hydroxymethylation, can modify these characteristics. Targets for these epigenetic changes include signaling pathways that regulate apoptosis and autophagy, as well as microRNA. We propose that predisposed normal cells convert to cancer progenitor cells that, after growing, undergo an epithelial-mesenchymal transition. This process, which is partially under epigenetic control, can create a metastatic form of both progenitor and full-fledged cancer cells, after which metastasis to a distant location may occur. Identification of epigenetic regulatory mechanisms has provided potential therapeutic avenues. In particular, epigenetic drugs appear to potentiate the action of traditional therapeutics, often by demethylating and re-expressing tumor suppressor genes to inhibit tumorigenesis. Epigenetic drugs may inhibit both the formation and growth of cancer progenitor cells, thus reducing the recurrence of cancer. Adopting epigenetic alteration as a new hallmark of cancer is a logical and necessary step that will further encourage the development of novel epigenetic biomarkers and therapeutics.
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540
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Murphy GF, Wilson BJ, Girouard SD, Frank NY, Frank MH. Stem cells and targeted approaches to melanoma cure. Mol Aspects Med 2013; 39:33-49. [PMID: 24145241 DOI: 10.1016/j.mam.2013.10.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 10/08/2013] [Accepted: 10/09/2013] [Indexed: 12/24/2022]
Abstract
Melanoma stem cells, also known as malignant melanoma-initiating cells, are identifiable through expression of specific biomarkers such as ABCB5 (ATP-binding cassette, sub-family B (MDR/TAP), member 5), NGFR (nerve growth factor receptor, CD271) and ALDH (aldehyde dehydrogenase), and drive melanoma initiation and progression based on prolonged self-renewal capacity, vasculogenic differentiation and immune evasion. As we will review here, specific roles of these aggressive subpopulations have been documented in tumorigenic growth, metastatic dissemination, therapeutic resistance, and malignant recurrence. Moreover, recent findings have provided pre-clinical proof-of-concept for the potential therapeutic utility of the melanoma stem cell concept. Therefore, melanoma stem cell-directed therapeutic approaches represent promising novel strategies to improve therapy of this arguably most virulent human cancer.
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Affiliation(s)
- George F Murphy
- Department of Pathology, Brigham & Women's Hospital, Boston, MA, USA.
| | - Brian J Wilson
- Transplantation Research Center, Children's Hospital Boston, Boston, MA, USA; Department of Dermatology, Brigham & Women's Hospital, Boston, MA, USA
| | - Sasha D Girouard
- Dermatology Residency Program, Harvard Medical School, Boston, MA, USA
| | - Natasha Y Frank
- Department of Medicine, VA Boston Healthcare System, Boston, MA, USA
| | - Markus H Frank
- Transplantation Research Center, Children's Hospital Boston, Boston, MA, USA; Department of Dermatology, Brigham & Women's Hospital, Boston, MA, USA.
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541
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Tarayrah L, Chen X. Epigenetic regulation in adult stem cells and cancers. Cell Biosci 2013; 3:41. [PMID: 24172544 PMCID: PMC3852361 DOI: 10.1186/2045-3701-3-41] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 09/05/2013] [Indexed: 12/23/2022] Open
Abstract
Adult stem cells maintain tissue homeostasis by their ability to both self-renew and differentiate to distinct cell types. Multiple signaling pathways have been shown to play essential roles as extrinsic cues in maintaining adult stem cell identity and activity. Recent studies also show dynamic regulation by epigenetic mechanisms as intrinsic factors in multiple adult stem cell lineages. Emerging evidence demonstrates intimate crosstalk between these two mechanisms. Misregulation of adult stem cell activity could lead to tumorigenesis, and it has been proposed that cancer stem cells may be responsible for tumor growth and metastasis. However, it is unclear whether cancer stem cells share commonalities with normal adult stem cells. In this review, we will focus on recent discoveries of epigenetic regulation in multiple adult stem cell lineages. We will also discuss how epigenetic mechanisms regulate cancer stem cell activity and probe the common and different features between cancer stem cells and normal adult stem cells.
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Affiliation(s)
- Lama Tarayrah
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA.
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542
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Liu R, Jin Y, Tang WH, Qin L, Zhang X, Tellides G, Hwa J, Yu J, Martin KA. Ten-eleven translocation-2 (TET2) is a master regulator of smooth muscle cell plasticity. Circulation 2013; 128:2047-57. [PMID: 24077167 DOI: 10.1161/circulationaha.113.002887] [Citation(s) in RCA: 212] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
BACKGROUND Smooth muscle cells (SMCs) are remarkably plastic. Their reversible differentiation is required for growth and wound healing but also contributes to pathologies such as atherosclerosis and restenosis. Although key regulators of the SMC phenotype, including myocardin (MYOCD) and KLF4, have been identified, a unifying epigenetic mechanism that confers reversible SMC differentiation has not been reported. METHODS AND RESULTS Using human SMCs, human arterial tissue, and mouse models, we report that SMC plasticity is governed by the DNA-modifying enzyme ten-eleven translocation-2 (TET2). TET2 and its product, 5-hydroxymethylcytosine (5-hmC), are enriched in contractile SMCs but reduced in dedifferentiated SMCs. TET2 knockdown inhibits expression of key procontractile genes, including MYOCD and SRF, with concomitant transcriptional upregulation of KLF4. TET2 knockdown prevents rapamycin-induced SMC differentiation, whereas TET2 overexpression is sufficient to induce a contractile phenotype. TET2 overexpression also induces SMC gene expression in fibroblasts. Chromatin immunoprecipitation demonstrates that TET2 coordinately regulates phenotypic modulation through opposing effects on chromatin accessibility at the promoters of procontractile versus dedifferentiation-associated genes. Notably, we find that TET2 binds and 5-hmC is enriched in CArG-rich regions of active SMC contractile promoters (MYOCD, SRF, and MYH11). Loss of TET2 and 5-hmC positively correlates with the degree of injury in murine models of vascular injury and human atherosclerotic disease. Importantly, localized TET2 knockdown exacerbates injury response, and local TET2 overexpression restores the 5-hmC epigenetic landscape and contractile gene expression and greatly attenuates intimal hyperplasia in vivo. CONCLUSIONS We identify TET2 as a novel and necessary master epigenetic regulator of SMC differentiation.
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Affiliation(s)
- Renjing Liu
- Department of Internal Medicine, Yale Cardiovascular Research Center, Section of Cardiovascular Medicine (R.L., Y.J., W.T., X.Z., J.H., J.Y., K.A.M.), Department of Surgery (Cardiac Surgery) (L.Q., G.T.), and Department of Pharmacology (K.A.M.), Yale University, New Haven, CT
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543
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Cadet J, Wagner JR. TET enzymatic oxidation of 5-methylcytosine, 5-hydroxymethylcytosine and 5-formylcytosine. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2013; 764-765:18-35. [PMID: 24045206 DOI: 10.1016/j.mrgentox.2013.09.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Accepted: 09/04/2013] [Indexed: 12/14/2022]
Abstract
5-Methylcytosine and methylated histones have been considered for a long time as stable epigenetic marks of chromatin involved in gene regulation. This concept has been recently revisited with the detection of large amounts of 5-hydroxymethylcytosine, now considered as the sixth DNA base, in mouse embryonic stem cells, Purkinje neurons and brain tissues. The dioxygenases that belong to the ten eleven translocation (TET) oxygenase family have been shown to initiate the formation of this methyl oxidation product of 5-methylcytosine that is also generated although far less efficiently by radical reactions involving hydroxyl radical and one-electron oxidants. It was found as additional striking data that iterative TET-mediated oxidation of 5-hydroxymethylcytosine gives rise to 5-formylcytosine and 5-carboxylcytosine. This survey focuses on chemical and biochemical aspects of the enzymatic oxidation reactions of 5-methylcytosine that are likely to be involved in active demethylation pathways through the implication of enzymatic deamination of 5-methylcytosine oxidation products and/or several base excision repair enzymes. The high biological relevance of the latter modified bases explains why major efforts have been devoted to the design of a broad range of assays aimed at measuring globally or at the single base resolution, 5-hydroxymethylcytosine and the two other oxidation products in the DNA of cells and tissues. Another critical issue that is addressed in this review article deals with the assessment of the possible role of 5-methylcytosine oxidation products, when present in elevated amounts in cellular DNA, in terms of mutagenesis and interference with key cellular enzymes including DNA and RNA polymerases.
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Affiliation(s)
- Jean Cadet
- Direction des Sciences de la Matière, Institut Nanosciences et Cryogénie, CEA/Grenoble, 38054 Grenoble, France; Département de médecine nucléaire et radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Québec JIH 5N4, Canada.
| | - J Richard Wagner
- Département de médecine nucléaire et radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Québec JIH 5N4, Canada.
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544
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SIRT5-mediated lysine desuccinylation impacts diverse metabolic pathways. Mol Cell 2013; 50:919-30. [PMID: 23806337 DOI: 10.1016/j.molcel.2013.06.001] [Citation(s) in RCA: 682] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 04/19/2013] [Accepted: 06/04/2013] [Indexed: 12/31/2022]
Abstract
Protein function is regulated by diverse posttranslational modifications. The mitochondrial sirtuin SIRT5 removes malonyl and succinyl moieties from target lysines. The spectrum of protein substrates subject to these modifications is unknown. We report systematic profiling of the mammalian succinylome, identifying 2,565 succinylation sites on 779 proteins. Most of these do not overlap with acetylation sites, suggesting differential regulation of succinylation and acetylation. Our analysis reveals potential impacts of lysine succinylation on enzymes involved in mitochondrial metabolism; e.g., amino acid degradation, the tricarboxylic acid cycle (TCA) cycle, and fatty acid metabolism. Lysine succinylation is also present on cytosolic and nuclear proteins; indeed, we show that a substantial fraction of SIRT5 is extramitochondrial. SIRT5 represses biochemical activity of, and cellular respiration through, two protein complexes identified in our analysis, pyruvate dehydrogenase complex and succinate dehydrogenase. Our data reveal widespread roles for lysine succinylation in regulating metabolism and potentially other cellular functions.
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545
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Dickson KM, Gustafson CB, Young JI, Züchner S, Wang G. Ascorbate-induced generation of 5-hydroxymethylcytosine is unaffected by varying levels of iron and 2-oxoglutarate. Biochem Biophys Res Commun 2013; 439:522-7. [PMID: 24021282 DOI: 10.1016/j.bbrc.2013.09.010] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 09/02/2013] [Indexed: 12/31/2022]
Abstract
Tet (ten-eleven translocation) methylcytosine dioxygenases, which belong to the iron and 2-oxoglutarate (2OG)-dependent dioxygenase superfamily, convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) in DNA. We recently reported that ascorbate (vitamin C) induces Tet-mediated generation of 5hmC. To initially delineate the role of ascorbate on 5hmC generation, we analyzed whether the effect of ascorbate is dependent upon the conditions of other components involved in the hydroxylation of 5mC catalyzed by Tet. We found that removing iron from the culture medium did not affect the induction of 5hmC by ascorbate (10 μM) in mouse embryonic fibroblasts (MEFs). The effect of ascorbate did not involve an increased expression of Tet1-3 or isocitrate dehydrogenases (IDH1-2), the enzymes responsible for producing 2OG. Interestingly, MEFs cultured with different concentrations of glucose, a major precursor of 2OG, exhibited nearly identical responses to ascorbate treatment. Further, blocking the uptake of the reduced form of vitamin C, ascorbic acid, through the sodium-dependent vitamin C transporters (SVCTs) inhibited the effect of ascorbate on 5hmC. However, inhibition of the facilitative glucose transporters (GLUTs), which mediate the incorporation of the oxidized form of vitamin C, dehydroascorbic acid (DHA), did not modify the ability of ascorbate to induce 5hmC generation. These results indicate that the effect of ascorbate on 5hmC is not dependent upon iron uptake, the expression of Tet and IDH, or the production of 2OG, suggesting that ascorbate may directly participate in the generation of 5hmC, most likely as a cofactor of Tet.
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Affiliation(s)
- Kevin M Dickson
- John P. Hussman Institute for Human Genomics, Dr. John T. Macdonald Foundation, Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, USA
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546
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Thomson JP, Moggs JG, Wolf CR, Meehan RR. Epigenetic profiles as defined signatures of xenobiotic exposure. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2013; 764-765:3-9. [PMID: 24001620 DOI: 10.1016/j.mrgentox.2013.08.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 08/24/2013] [Indexed: 01/01/2023]
Abstract
With the advent of high resolution sequencing technologies there has been increasing interest in the study of genome-wide epigenetic modification patterns that govern the underlying gene expression events of a particular cell or tissue type. There is now mounting evidence that perturbations to the epigenetic landscape occur during a host of cellular processes including normal proliferation/differentiation and aberrant outcomes such as carcinogenesis. Furthermore, epigenetic perturbations have been associated with exposure to a range of drugs and toxicants, including non-genotoxic carcinogens (NGCs). Although a variety of epigenetic modifications induced by NGCs have been studied previously, recent genome-wide integrated epigenomic and transcriptomic studies reveal for the first time the extent and dynamic nature of the epigenetic perturbations resulting from xenobiotic exposure. The interrogation and integration of one such epigenetic mark, the newly discovered 5-hydroxymethylcytosine (5hmC) modification, reveals that drug treatment associated perturbations of the epigenome can result in unique epigenetic signatures. This review focuses on how recent advances in the field of epigenetics can enhance our mechanistic understanding of xenobiotic exposure and provide novel safety biomarkers.
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Affiliation(s)
- John P Thomson
- MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK
| | - Jonathan G Moggs
- Discovery & Investigative Safety, Investigative Toxicology, Preclinical Safety, Translational Sciences, Novartis Institutes for Biomedical Research, Basel, Switzerland
| | - C Roland Wolf
- Medical Research Institute, University of Dundee, Ninewells Hospital & Medical School, Dundee, DD1 9SY, UK
| | - Richard R Meehan
- MRC Human Genetics Unit at the Institute of Genetics and Molecular Medicine at the University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK.
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547
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Neri F, Incarnato D, Krepelova A, Rapelli S, Pagnani A, Zecchina R, Parlato C, Oliviero S. Genome-wide analysis identifies a functional association of Tet1 and Polycomb repressive complex 2 in mouse embryonic stem cells. Genome Biol 2013; 14:R91. [PMID: 23987249 PMCID: PMC4053938 DOI: 10.1186/gb-2013-14-8-r91] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 08/10/2013] [Accepted: 08/29/2013] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Ten-Eleven Translocation (TETs)proteins mediate the oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). Tet1 is expressed at high levels in mouse embryonic stem cells (ESCs), where it mediates the induction of 5hmC decoration on gene-regulatory elements. While the function of Tet1 is known, the mechanisms of its specificity remain unclear. RESULTS We perform a genome-wide comparative analysis of 5hmC in pluripotent ESCs, as well as in differentiated embryonic and adult cells. We find that 5hmC co-localization with Polycomb repressive complex 2 (PRC2) is specific to ESCs and is absent in differentiated cells. Tet1 in ESCs is distributed on bivalent genes in two independent pools: one with Sin3a centered at non-hydroxymethylated transcription start sites and another centered downstream from these sites. This latter pool of Tet1 co-localizes with 5hmC and PRC2. Through co-immunoprecipitation experiments, we show that Tet1 forms a complex with PRC2 specifically in ESCs. Genome-wide analysis of 5hmC profiles in ESCs following knockdown of the PRC2 subunit Suz12 shows a reduction of 5hmC within promoter sequences, specifically at H3K27me3-positive regions of bivalent promoters. CONCLUSIONS In ESCs, PRC2 recruits Tet1 to chromatin at H3K27me3 positive regions of the genome, with 5hmC enriched in a broad peak centered 455 bp after the transcription start site and dependent on the PRC2 component Suz12. These results suggest that PRC2-dependent recruitment of Tet1 contributes to epigenetic plasticity throughout cell differentiation.
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Affiliation(s)
- Francesco Neri
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126, Torino, Italy
| | - Danny Incarnato
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126, Torino, Italy
- Dipartimento di Biotecnologie Chimica e Farmacia Università degli Studi di Siena. Via Fiorentina 1, 53100 Siena, Italy
| | - Anna Krepelova
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126, Torino, Italy
- Dipartimento di Biotecnologie Chimica e Farmacia Università degli Studi di Siena. Via Fiorentina 1, 53100 Siena, Italy
| | - Stefania Rapelli
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126, Torino, Italy
- Dipartimento di Biotecnologie Chimica e Farmacia Università degli Studi di Siena. Via Fiorentina 1, 53100 Siena, Italy
| | - Andrea Pagnani
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126, Torino, Italy
- Politecnico di Torino, Corso Duca degli Abruzzi 24, I-10129 Torino, Italy
| | - Riccardo Zecchina
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126, Torino, Italy
- Politecnico di Torino, Corso Duca degli Abruzzi 24, I-10129 Torino, Italy
| | - Caterina Parlato
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126, Torino, Italy
| | - Salvatore Oliviero
- Human Genetics Foundation (HuGeF), via Nizza 52, 10126, Torino, Italy
- Dipartimento di Biotecnologie Chimica e Farmacia Università degli Studi di Siena. Via Fiorentina 1, 53100 Siena, Italy
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548
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Ivanov M, Kals M, Kacevska M, Barragan I, Kasuga K, Rane A, Metspalu A, Milani L, Ingelman-Sundberg M. Ontogeny, distribution and potential roles of 5-hydroxymethylcytosine in human liver function. Genome Biol 2013; 14:R83. [PMID: 23958281 PMCID: PMC4054829 DOI: 10.1186/gb-2013-14-8-r83] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 07/30/2013] [Accepted: 08/19/2013] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Interindividual differences in liver functions such as protein synthesis, lipid and carbohydrate metabolism and drug metabolism are influenced by epigenetic factors. The role of the epigenetic machinery in such processes has, however, been barely investigated. 5-hydroxymethylcytosine (5hmC) is a recently re-discovered epigenetic DNA modification that plays an important role in the control of gene expression. RESULTS In this study, we investigate 5hmC occurrence and genomic distribution in 8 fetal and 7 adult human liver samples in relation to ontogeny and function. LC-MS analysis shows that in the adult liver samples 5hmC comprises up to 1% of the total cytosine content, whereas in all fetal livers it is below 0.125%. Immunohistostaining of liver sections with a polyclonal anti-5hmC antibody shows that 5hmC is detected in most of the hepatocytes. Genome-wide mapping of the distribution of 5hmC in human liver samples by next-generation sequencing shows significant differences between fetal and adult livers. In adult livers, 5hmC occupancy is overrepresented in genes involved in active catabolic and metabolic processes, whereas 5hmC elements which are found in genes exclusively in fetal livers and disappear in the adult state, are more specific to pathways for differentiation and development. CONCLUSIONS Our findings suggest that 5-hydroxymethylcytosine plays an important role in the development and function of the human liver and might be an important determinant for development of liver diseases as well as of the interindividual differences in drug metabolism and toxicity.
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Affiliation(s)
- Maxim Ivanov
- Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Nanna Svartz väg 2, 17177 Stockholm, Sweden
| | - Mart Kals
- Estonian Genome Center, University of Tartu, Riia 23b, 51010 Tartu, Estonia
| | - Marina Kacevska
- Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Nanna Svartz väg 2, 17177 Stockholm, Sweden
| | - Isabel Barragan
- Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Nanna Svartz väg 2, 17177 Stockholm, Sweden
| | - Kie Kasuga
- Cancer Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet Science Park, Tomtebodavägen 23A, 17165 Solna, Sweden
| | - Anders Rane
- Division of Clinical Pharmacology, Department of Laboratory Medicine, Karolinska University Hospital at Huddinge, Medicingatan 5, 14186 Stockholm, Sweden
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Riia 23b, 51010 Tartu, Estonia
- Estonian Biocentre, Riia 23b, 51010 Tartu, Estonia
- AQ2 Institute of Molecular and Cell Biology, University of Tartu, Riia 23b, 51010 Tartu, Estonia
| | - Lili Milani
- Estonian Genome Center, University of Tartu, Riia 23b, 51010 Tartu, Estonia
- AQ2 Institute of Molecular and Cell Biology, University of Tartu, Riia 23b, 51010 Tartu, Estonia
| | - Magnus Ingelman-Sundberg
- Section of Pharmacogenetics, Department of Physiology and Pharmacology, Karolinska Institutet, Nanna Svartz väg 2, 17177 Stockholm, Sweden
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549
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Segura MF, Fontanals-Cirera B, Gaziel-Sovran A, Guijarro MV, Hanniford D, Zhang G, González-Gomez P, Morante M, Jubierre L, Zhang W, Darvishian F, Ohlmeyer M, Osman I, Zhou MM, Hernando E. BRD4 sustains melanoma proliferation and represents a new target for epigenetic therapy. Cancer Res 2013; 73:6264-76. [PMID: 23950209 DOI: 10.1158/0008-5472.can-13-0122-t] [Citation(s) in RCA: 177] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Metastatic melanoma remains a mostly incurable disease. Although newly approved targeted therapies are efficacious in a subset of patients, resistance and relapse rapidly ensue. Alternative therapeutic strategies to manipulate epigenetic regulators and disrupt the transcriptional program that maintains tumor cell identity are emerging. Bromodomain and extraterminal domain (BET) proteins are epigenome readers known to exert key roles at the interface between chromatin remodeling and transcriptional regulation. Here, we report that BRD4, a BET family member, is significantly upregulated in primary and metastatic melanoma tissues compared with melanocytes and nevi. Treatment with BET inhibitors impaired melanoma cell proliferation in vitro and tumor growth and metastatic behavior in vivo, effects that were mostly recapitulated by individual silencing of BRD4. RNA sequencing of BET inhibitor-treated cells followed by Gene Ontology analysis showed a striking impact on transcriptional programs controlling cell growth, proliferation, cell-cycle regulation, and differentiation. In particular, we found that, rapidly after BET displacement, key cell-cycle genes (SKP2, ERK1, and c-MYC) were downregulated concomitantly with the accumulation of cyclin-dependent kinase (CDK) inhibitors (p21 and p27), followed by cell-cycle arrest. Importantly, BET inhibitor efficacy was not influenced by BRAF or NRAS mutational status, opening the possibility of using these small-molecule compounds to treat patients for whom no effective targeted therapy exists. Collectively, our study reveals a critical role for BRD4 in melanoma tumor maintenance and renders it a legitimate and novel target for epigenetic therapy directed against the core transcriptional program of melanoma.
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Affiliation(s)
- Miguel F Segura
- Authors' Affiliations: Departments of Pathology and Dermatology, New York University School of Medicine; Interdisciplinary Melanoma Cooperative Group, New York University Cancer Institute, New York University Langone Medical Center; Departments of Structural and Chemical Biology and Medicine, Icahn School of Medicine at Mount Sinai, New York, New York; Instituto de Salud Carlos III, Majadahonda, Madrid; and Laboratory of Translational Research in Childhood Cancer, Vall d'Hebrón Institut de Recerca (VHIR), Barcelona, Spain
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550
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Stepanenko AA, Vassetzky YS, Kavsan VM. Antagonistic functional duality of cancer genes. Gene 2013; 529:199-207. [PMID: 23933273 DOI: 10.1016/j.gene.2013.07.047] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 05/08/2013] [Accepted: 07/09/2013] [Indexed: 12/21/2022]
Abstract
Cancer evolution is a stochastic process both at the genome and gene levels. Most of tumors contain multiple genetic subclones, evolving in either succession or in parallel, either in a linear or branching manner, with heterogeneous genome and gene alterations, extensively rewired signaling networks, and addicted to multiple oncogenes easily switching with each other during cancer progression and medical intervention. Hundreds of discovered cancer genes are classified according to whether they function in a dominant (oncogenes) or recessive (tumor suppressor genes) manner in a cancer cell. However, there are many cancer "gene-chameleons", which behave distinctly in opposite way in the different experimental settings showing antagonistic duality. In contrast to the widely accepted view that mutant NADP(+)-dependent isocitrate dehydrogenases 1/2 (IDH1/2) and associated metabolite 2-hydroxyglutarate (R)-enantiomer are intrinsically "the drivers" of tumourigenesis, mutant IDH1/2 inhibited, promoted or had no effect on cell proliferation, growth and tumorigenicity in diverse experiments. Similar behavior was evidenced for dozens of cancer genes. Gene function is dependent on genetic network, which is defined by the genome context. The overall changes in karyotype can result in alterations of the role and function of the same genes and pathways. The diverse cell lines and tumor samples have been used in experiments for proving gene tumor promoting/suppressive activity. They all display heterogeneous individual karyotypes and disturbed signaling networks. Consequently, the effect and function of gene under investigation can be opposite and versatile in cells with different genomes that may explain antagonistic duality of cancer genes and the cell type- or the cellular genetic/context-dependent response to the same protein. Antagonistic duality of cancer genes might contribute to failure of chemotherapy. Instructive examples of unexpected activity of cancer genes and "paradoxical" effects of different anticancer drugs depending on the cellular genetic context/signaling network are discussed.
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Affiliation(s)
- A A Stepanenko
- State Key Laboratory of Molecular and Cellular Biology, Institute of Molecular Biology and Genetics, 150 Zabolotnogo Street, Kyiv 03680, Ukraine.
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