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da Conceição Braga L, Silva LM, Piedade JB, Traiman P, da Silva Filho AL. Epigenetic and expression analysis of TRAIL-R2 and BCL2: on the TRAIL to knowledge of apoptosis in ovarian tumors. Arch Gynecol Obstet 2013; 289:1061-9. [DOI: 10.1007/s00404-013-3060-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 10/15/2013] [Indexed: 02/07/2023]
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Hong SJ, Lee HJ, Oh JH, Jung SH, Min KO, Choi SW, Rhyu MG. Age-related methylation patterning of housekeeping genes and tissue-specific genes is distinct between the stomach antrum and body. Epigenomics 2013; 5:283-99. [PMID: 23750644 DOI: 10.2217/epi.13.17] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
AIM The methylation-variable sites around CpG islands are frequently overmethylated in Helicobacter pylori-infected stomachs. Age-related patterns of the overmethylation changes were compared between the fast-growing antrum cells and the slow-growing body cells. MATERIALS & METHODS A total of 316 H. pylori-positive tissues and 380 H. pylori-negative tissues were obtained by endoscopic biopsy. The methylation-variable sites of ten housekeeping genes and nine tissue-specific genes were semiquantitatively analyzed, based on the ten-level classification of methylation-specific PCR intensity. The overmethylated genes were scored when their methylation levels were higher than an intermediate level of each gene common in the H. pylori-negative mucosa. RESULTS The age-dependent methylation level of the inactive APC gene observed similarly in the antrum and the body was used as an age standard of methylation variation in a biopsy tissue. The overmethylation of housekeeping genes and stomach-specific genes rapidly increased to a high plateau frequency in the young-aged APC methylation cases (mean age: 43 years) in the H. pylori-positive antrum. In the H. pylori-positive body, most of the overmethylated housekeeping genes slowly increased to a peak frequency in the middle-aged APC methylation cases (mean age: 53 years). The housekeeping gene pairs showed high correlations (Spearman's correlation coefficient > 0.4) in both the antrum and the body. CONCLUSION The overmethylation of housekeeping genes rapidly and slowly increased to a high frequency in concordance with a rapid and slow growth of epithelial cells in the H. pylori-infected stomach.
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Affiliation(s)
- Seung-Jin Hong
- Department of Microbiology, College of Medicine, The Catholic University of Korea, 505 Banpo-dong Socho-gu, Seoul 137-701, Republic of Korea
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53
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Fukushige S, Horii A. DNA methylation in cancer: a gene silencing mechanism and the clinical potential of its biomarkers. TOHOKU J EXP MED 2013; 229:173-85. [PMID: 23419314 DOI: 10.1620/tjem.229.173] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Initiation and progression of human cancer not only depends on genetic alterations but also on epigenetic changes such as DNA methylation and histone modifications. Aberrant DNA hypermethylation in the promoter regions of genes is the most well-defined epigenetic change in tumors and is associated with inappropriate gene silencing. This feature can be utilized to search for tumor-specific DNA methylation biomarkers and to examine candidate DNA biomarkers for clinical use. DNA methylation biomarker is defined as a molecular target that undergoes DNA methylation changes in carcinogenesis. Such a biomarker is useful for early detection of cancer, predicting and/or monitoring the therapeutic response, and detection of recurrent cancer. In this review, we describe the mechanism that establishes and maintains DNA methylation patterns as well as the mechanism of aberrant gene silencing in cancer, and then we introduce methods to isolate the DNA methylation biomarkers. We also summarize the current status of clinical implementation for some of the most widely studied and well-validated DNA methylation biomarkers, including tissue factor pathway inhibitor 2 (TFPI2), septin 9 (SEPT9), glutathione S-transferase pi 1 (GSTP1), and O(6)-methylguanine-DNA methyltransferase (MGMT), and assess the clinical potential of these biomarkers for risk assessment, early diagnosis, prognosis, treatment, and the prevention of cancer. Finally we describe the possible involvement of 5-hydroxymethylcytosine in cancer; this is a recently discovered 5-methylcytosine oxidation derivative and might have a diagnostic potential in certain cancers. Abnormal DNA methylations are leading candidates for the development of specific markers for cancer diagnosis and therapy.
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Affiliation(s)
- Shinichi Fukushige
- Department of Molecular Pathology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan.
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54
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Rhyu MG, Oh JH, Hong SJ. Epigenetic implication of gene-adjacent retroelements in Helicobacter pylori-infected adults. Epigenomics 2013; 4:527-35. [PMID: 23130834 DOI: 10.2217/epi.12.51] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
A chronic inflammatory condition of gastric mucosa can facilitate the influx of new stem cells into the stomach. Epigenetic codes, such as DNA methylation, may be responsible for the stable maintenance of epigenetic phenotypes established in the new stomach-adapted stem cells. A number of hypotheses have been made for the role of CpG-island methylation, which is common in the Helicobacter pylori-infected stomach. However, they could not explain the plausible role of CpG-island methylation in the re-establishment of epigenetic phenotypes. These islands are highly repetitive sequences densely methylated throughout the human genome, the so-called parasitic retroelements, which expand a number of cDNA copies with reverse transcriptase. The densely methylated retroelements adjacent to the host genes can form the transitional-CpG sites around gene-control regions that are barely methylated. This review focuses on the putative role of transitional CpG methylation in the adaptive differentiation of new stem cells in the H. pylori-infected stomach.
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Affiliation(s)
- Mun-Gan Rhyu
- Department of Microbiology, College of Medicine, The Catholic University of Korea, 505 Banpo-dong Socho-gu, Seoul 137-701, Korea
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55
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Scarr E, Craig JM, Cairns MJ, Seo MS, Galati JC, Beveridge NJ, Gibbons A, Juzva S, Weinrich B, Parkinson-Bates M, Carroll AP, Saffery R, Dean B. Decreased cortical muscarinic M1 receptors in schizophrenia are associated with changes in gene promoter methylation, mRNA and gene targeting microRNA. Transl Psychiatry 2013; 3:e230. [PMID: 23423139 PMCID: PMC3594731 DOI: 10.1038/tp.2013.3] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Many studies have shown decreased cortical muscarinic M1 receptors (CHRM1) in schizophrenia (Sz), with one study showing Sz can be separated into two populations based on a marked loss of CHRM1 (-75%) in -25% of people (Def-Sz) with the disorder. To better understand the mechanism contributing to the loss of CHRM1 in Def-Sz, we measured specific markers of gene expression in the cortex of people with Sz as a whole, people differentiated into Def-Sz and people with Sz that do not have a deficit in cortical CHRM1 (Non-Def-Sz) and health controls. We now report that cortical CHRM1 gene promoter methylation and CHRM1 mRNA are decrease in Sz, Def-Sz and Non-Def-Sz but levels of the micro RNA (miR)-107, a CHRM1 targeting miR, are increased only in Def-Sz. We also report in vitro data strongly supporting the notion that miR-107 levels regulate CHRM1 expression. These data suggest there is a reversal of the expected inverse relationship between gene promoter methylation and CHRM1 mRNA in people with Sz and that a breakdown in gene promoter methylation control of CHRM1 expression is contributing to the global pathophysiology of the syndrome. In addition, our data argues that increased levels of at least one miR, miR-107, is contributing to the marked loss of cortical CHRM1 in Def-Sz and this may be a differentiating pathophysiology. These latter data continue to support the hypothesis that microRNAs (miRNA) have a role in the underlying neurobiology of Sz but argue they are differentially affected in subsets of people within that syndrome.
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Affiliation(s)
- E Scarr
- The Department of Psychiatry, The University of Melbourne, Parkville, Victoria, Australia
| | - J M Craig
- The Early Life Epigenetic Group, The Murdoch's Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria, Australia,The Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia
| | - M J Cairns
- The School of Biomedical Sciences and Pharmacy, and Hunter Medical Research Institute, University of Newcastle, Callaghan, New South Wales, Australia,The Schizophrenia Research Institute, University of Sydney, Sydney, New South Wales, Australia
| | - M S Seo
- The Department of Psychiatry, The University of Melbourne, Parkville, Victoria, Australia,The Molecular Psychiatry Laboratory, The Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - J C Galati
- The Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia,Department of Mathematics and Statistics, La Trobe University, Bundoora, Victoria, Australia
| | - N J Beveridge
- The School of Biomedical Sciences and Pharmacy, and Hunter Medical Research Institute, University of Newcastle, Callaghan, New South Wales, Australia,The Schizophrenia Research Institute, University of Sydney, Sydney, New South Wales, Australia
| | - A Gibbons
- The Department of Psychiatry, The University of Melbourne, Parkville, Victoria, Australia,The Molecular Psychiatry Laboratory, The Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - S Juzva
- The Molecular Psychiatry Laboratory, The Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia
| | - B Weinrich
- The Early Life Epigenetic Group, The Murdoch's Children's Research Institute, The Royal Children's Hospital, Parkville, Victoria, Australia
| | - M Parkinson-Bates
- The Cancer and the Developmental Epigenetics Group, The Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - A P Carroll
- The School of Biomedical Sciences and Pharmacy, and Hunter Medical Research Institute, University of Newcastle, Callaghan, New South Wales, Australia,The Schizophrenia Research Institute, University of Sydney, Sydney, New South Wales, Australia
| | - R Saffery
- The Department of Paediatrics, The University of Melbourne, Parkville, Victoria, Australia,The Cancer and the Developmental Epigenetics Group, The Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - B Dean
- The Department of Psychiatry, The University of Melbourne, Parkville, Victoria, Australia,The Molecular Psychiatry Laboratory, The Florey Institute of Neuroscience and Mental Health, Parkville, Victoria, Australia,Molecular Psychiatry Laboratory, The Mental Health Research Institute, The Kenneth Myer Building, The University of Melbourne, Genetics Lane, Parkville, Victoria 3010, Australia. E-mail:
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56
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De S, Shaknovich R, Riester M, Elemento O, Geng H, Kormaksson M, Jiang Y, Woolcock B, Johnson N, Polo JM, Cerchietti L, Gascoyne RD, Melnick A, Michor F. Aberration in DNA methylation in B-cell lymphomas has a complex origin and increases with disease severity. PLoS Genet 2013; 9:e1003137. [PMID: 23326238 PMCID: PMC3542081 DOI: 10.1371/journal.pgen.1003137] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 10/18/2012] [Indexed: 01/22/2023] Open
Abstract
Despite mounting evidence that epigenetic abnormalities play a key role in cancer biology, their contributions to the malignant phenotype remain poorly understood. Here we studied genome-wide DNA methylation in normal B-cell populations and subtypes of B-cell non-Hodgkin lymphoma: follicular lymphoma and diffuse large B-cell lymphomas. These lymphomas display striking and progressive intra-tumor heterogeneity and also inter-patient heterogeneity in their cytosine methylation patterns. Epigenetic heterogeneity is initiated in normal germinal center B-cells, increases markedly with disease aggressiveness, and is associated with unfavorable clinical outcome. Moreover, patterns of abnormal methylation vary depending upon chromosomal regions, gene density and the status of neighboring genes. DNA methylation abnormalities arise via two distinct processes: i) lymphomagenic transcriptional regulators perturb promoter DNA methylation in a target gene-specific manner, and ii) aberrant epigenetic states tend to spread to neighboring promoters in the absence of CTCF insulator binding sites. Follicular lymphomas and diffuse large B-cell lymphomas are the most common non-Hodgkin lymphomas. Although these diseases share many mutant alleles, the underlying cause of the different phenotypes remains unclear. We show that direct comparison of DNA methylation patterning provides insights about gene deregulation during lymphomagenesis and explains the nature of the different clinical behavior.
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MESH Headings
- B-Lymphocytes/metabolism
- B-Lymphocytes/pathology
- Binding Sites
- CCCTC-Binding Factor
- Cell Line, Tumor
- DNA Methylation/genetics
- Epigenesis, Genetic/genetics
- Gene Silencing
- Genome, Human
- Humans
- Insulator Elements/genetics
- Lymphoma, Follicular/genetics
- Lymphoma, Follicular/metabolism
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/metabolism
- Lymphoma, Large B-Cell, Diffuse/pathology
- Promoter Regions, Genetic
- Repressor Proteins/genetics
- Repressor Proteins/metabolism
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Affiliation(s)
- Subhajyoti De
- Department of Medicine, University of Colorado School of Medicine, Aurora, Colorado, United States of America
- Molecular Oncology Program, University of Colorado Cancer Center, Aurora, Colorado, United States of America
| | - Rita Shaknovich
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York, United States of America
- Division of Immunopathology, Department of Pathology, Weill Cornell Medical College, New York, New York, United States of America
| | - Markus Riester
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Olivier Elemento
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Huimin Geng
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York, United States of America
- Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Matthias Kormaksson
- Division of Biostatistics and Epidemiology, Department of Public Health, Weill Cornell Medical College, New York, New York, United States of America
| | - Yanwen Jiang
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York, United States of America
| | - Bruce Woolcock
- Centre for Lymphoid Cancers and Departments of Pathology and Experimental Therapeutics, British Columbia Cancer Agency, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Nathalie Johnson
- Centre for Lymphoid Cancers and Departments of Pathology and Experimental Therapeutics, British Columbia Cancer Agency, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Jose M. Polo
- Monash Immunology and Stem Cell Laboratories, Monash University, Clayton, Australia
| | - Leandro Cerchietti
- Division of Immunopathology, Department of Pathology, Weill Cornell Medical College, New York, New York, United States of America
| | - Randy D. Gascoyne
- Centre for Lymphoid Cancers and Departments of Pathology and Experimental Therapeutics, British Columbia Cancer Agency, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Ari Melnick
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York, United States of America
- * E-mail: (AM); (FM)
| | - Franziska Michor
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
- * E-mail: (AM); (FM)
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57
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DNA Hypomethylation and Hemimethylation in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 754:31-56. [DOI: 10.1007/978-1-4419-9967-2_2] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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58
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Price EM, Cotton AM, Peñaherrera MS, McFadden DE, Kobor MS, Robinson W. Different measures of "genome-wide" DNA methylation exhibit unique properties in placental and somatic tissues. Epigenetics 2012; 7:652-63. [PMID: 22531475 PMCID: PMC3398992 DOI: 10.4161/epi.20221] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
DNA methylation of CpGs located in two types of repetitive elements-LINE1 (L1) and Alu-is used to assess "global" changes in DNA methylation in studies of human disease and environmental exposure. L1 and Alu contribute close to 30% of all base pairs in the human genome and transposition of repetitive elements is repressed through DNA methylation. Few studies have investigated whether repetitive element DNA methylation is associated with DNA methylation at other genomic regions, or the biological and technical factors that influence potential associations. Here, we assess L1 and Alu DNA methylation by Pyrosequencing of consensus sequences and using subsets of probes included in the Illumina Infinium HumanMethylation27 BeadChip array. We show that evolutionary age and assay method affect the assessment of repetitive element DNA methylation. Additionally, we compare Pyrosequencing results for repetitive elements to average DNA methylation of CpG islands, as assessed by array probes classified into strong, weak and non-islands. We demonstrate that each of these dispersed sequences exhibits different patterns of tissue-specific DNA methylation. Correlation of DNA methylation suggests an association between L1 and weak CpG island DNA methylation in some of the tissues examined. We caution, however, that L1, Alu and CpG island DNA methylation are distinct measures of dispersed DNA methylation and one should not be used in lieu of another. Analysis of DNA methylation data is complex and assays may be influenced by environment and pathology in different or complementary ways.
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Affiliation(s)
- E Magda Price
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, BC, Canada
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59
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Zhang Y, Shu J, Si J, Shen L, Estecio MRH, Issa JPJ. Repetitive elements and enforced transcriptional repression co-operate to enhance DNA methylation spreading into a promoter CpG-island. Nucleic Acids Res 2012; 40:7257-68. [PMID: 22600741 PMCID: PMC3424568 DOI: 10.1093/nar/gks429] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Repression of many tumor suppressor genes in cancer is concurrent with aberrantly increased DNA methylation levels at promoter CpG islands (CGIs). About one-fourth of empirically defined human promoters are surrounded by or contain clustered repetitive elements. It was previously observed that a sharp transition of methylation exists between highly methylated repetitive elements and unmethylated promoter-CGIs in normal tissues. The factors that lead to aberrant CGI hypermethylation in cancer remain poorly understood. Here, we established a site-specific integration system with enforced local transcriptional repression in colorectal cancer cells and monitored the occurrence of initial de novo methylation at specific CG sites adjacent to the CGI of the INSL6 promoter, which could be accelerated by binding a KRAB-containing transcriptional factor. Additional repetitive elements from P16 and RIL (PDLIM4), if situated adjacent to the promoter of INSL6, could confer DNA methylation spreading into the CGI particularly in the setting of KRAB-factor binding. However, a repressive chromatin alone was not sufficient to initiate DNA methylation, which required specific DNA sequences and was integration-site (and/or cell-line) specific. Overall, these results demonstrate a requirement for specific DNA sequences to trigger de novo DNA methylation, and repetitive elements as cis-regulatory factors to cooperate with advanced transcriptional repression in promoting methylation spreading.
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Affiliation(s)
- Yan Zhang
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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60
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A regulatory potential of the Xist gene promoter in vole M. rossiaemeridionalis. PLoS One 2012; 7:e33994. [PMID: 22606223 PMCID: PMC3350511 DOI: 10.1371/journal.pone.0033994] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2011] [Accepted: 02/24/2012] [Indexed: 12/24/2022] Open
Abstract
X chromosome inactivation takes place in the early development of female mammals and depends on the Xist gene expression. The mechanisms of Xist expression regulation have not been well understood so far. In this work, we compared Xist promoter region of vole Microtus rossiaemeridionalis and other mammalian species. We observed three conserved regions which were characterized by computational analysis, DNaseI in vitro footprinting, and reporter construct assay. Regulatory factors potentially involved in Xist activation and repression in voles were determined. The role of CpG methylation in vole Xist expression regulation was established. A CTCF binding site was found in the 5' flanking region of the Xist promoter on the active X chromosome in both males and females. We suggest that CTCF acts as an insulator which defines an inactive Xist domain on the active X chromosome in voles.
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61
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De-Castro Arce J, Göckel-Krzikalla E, Rösl F. Silencing of multi-copy HPV16 by viral self-methylation and chromatin occlusion: a model for epigenetic virus-host interaction. Hum Mol Genet 2011; 21:1693-705. [PMID: 22210627 DOI: 10.1093/hmg/ddr604] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In the present study, we used the human papillomavirus type 16 (HPV16)-positive cervical carcinoma cell line CaSki as a paradigmatic model to understand epigenetic silencing of viral multi-copy genomes. We show that most of the hypermethylated HPV16 copies are kept as 'occluded' chromatin that defines a condition where genes were refractory in their response to trans-acting transcription factors and to external reactivation efforts. This provides the first example that viral genomes are silenced by such a host cell mechanism, hitherto only known for endogenous genes to preserve a stable and robust phenotype. Moreover, considering an adaptive cross-talk between viral proteins and the epigenetic modification machinery, we demonstrate that particularly E2-but also ectopically delivered E6/E7-can induce significant de novo methylation within the enhancer and, to a less extent, within the promoter region. These data suggest that under certain physiological conditions, HPV can down-regulate its own gene expression, regardless of the presence of transcriptional activators. We propose that self-methylation of multi-copy HPV could be the first event prior to heterochromatin formation. These processes favour an 'occluded' chromatin conformation, finally being unresponsive to transcriptional activation. The shift from potentially competent heterochromatin towards an occluded state is basically irreversible, possibly using the same mechanism described for lineage differentiation. Along this line, it is tempting to speculate that virus-cell interaction is able to 'sense' viral copy number and down-regulates excess of gene activity in order to guarantee cell viability.
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Affiliation(s)
- Johanna De-Castro Arce
- Division of Viral Transformation Mechanisms, Research Program: Infections and Cancer, Deutsches Krebsforschungszentrum, Heidelberg D-69120, Germany
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62
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Christensen BC, Marsit CJ. Epigenomics in environmental health. Front Genet 2011; 2:84. [PMID: 22303378 PMCID: PMC3268636 DOI: 10.3389/fgene.2011.00084] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Accepted: 11/04/2011] [Indexed: 12/29/2022] Open
Abstract
This review considers the emerging relationships between environmental factors and epigenetic alterations and the application of genome-wide assessments to better define these relationships. First we will briefly cover epigenetic programming in development, one-carbon metabolism, and exposures that may disrupt normal developmental programming of epigenetic states. In addition, because a large portion of epigenetic research has focused on cancer, we discuss exposures associated with carcinogenesis including asbestos, alcohol, radiation, arsenic, and air pollution. Research on other exposures that may affect epigenetic states such as endocrine disruptors is also described, and we also review the evidence for epigenetic alterations associated with aging that may reflect cumulative effects of exposures. From this evidence, we posit potential mechanisms by which exposures modify epigenetic states, noting that understanding the true effect of environmental exposures on the human epigenome will require additional research with appropriate epidemiologic studies and application of novel technologies. With a more comprehensive understanding of the affects of exposures on the epigenome, including consideration of genetic background, the prediction of the toxic potential of new compounds may be more readily achieved, and may lead to the development of more personalized disease prevention and treatment strategies.
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Affiliation(s)
- Brock C Christensen
- Section on Biostatistics and Epidemiology, Department of Community and Family Medicine, Dartmouth Medical School Hanover, NH, USA
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63
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Sigurdsson MI, Smith AV, Bjornsson HT, Jonsson JJ. Distribution of a marker of germline methylation differs between major families of transposon-derived repeats in the human genome. Gene 2011; 492:104-9. [PMID: 22093876 DOI: 10.1016/j.gene.2011.10.046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 10/18/2011] [Accepted: 10/27/2011] [Indexed: 11/18/2022]
Abstract
A potential relationship between transposon-derived repeats (TDR) and human germline methylation is of biological importance since many genes are flanked by TDR and methylation could affect the expression of nearby genes. Furthermore, DNA methylation has been suggested as a global defense mechanism against genome instability threatened by TDR. We studied the correlation between the density of HapMap methyl-associated SNPs (mSNPs), a marker of germline methylation, and proportion of TDR. After correcting for confounding variables, we found a negative correlation between proportion of Alu repeats and mSNP density for 125-1000 kb windows. Similar results were found for the most active subgroup of repeats. In contrast, a negative correlation between proportion of L1 repeats and mSNP density was found only in the larger 1000 kb windows. Using methylation data on germ cells (sperm) from the Human Epigenome Project, we found a lower proportion of Alu repeats adjacent (3-15 kb) to hypermethylated amplicons. On the contrary, there was a higher proportion of L1 repeats in the 3-5 kb of sequence flanking hypermethylated amplicons but not in the 10-15 kb flanks. Our data indicate a differential response to the major repeat families and that DNA methylation is unlikely to be a uniform global defense system against all TDR. It appears to play a role for the L1 subgroup, with sequences adjacent to L1 repeats methylated in response to their proximity. In contrast, sequences adjacent to Alu repeats appear to be hypomethylated, arguing against a role of methylation in germline defense against those elements.
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Affiliation(s)
- Martin I Sigurdsson
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Iceland, IS-101, and Department of Genetics and Molecular Medicine, Landspitali-University Hospital, Reykjavik, IS-101, Iceland
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64
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Uthup TK, Ravindran M, Bini K, Thakurdas S. Divergent DNA methylation patterns associated with abiotic stress in Hevea brasiliensis. MOLECULAR PLANT 2011; 4:996-1013. [PMID: 21705581 DOI: 10.1093/mp/ssr039] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Cytosine methylation is a fundamental epigenetic mechanism for gene-expression regulation and development in plants. Here, we report for the first time the identification of DNA methylation patterns and their putative relationship with abiotic stress in the tree crop Hevea brasiliensis (source of 99% of natural rubber in the world). Regulatory sequences of four major genes involved in the mevalonate pathway (rubber biosynthesis pathway) and one general defense-related gene of three high-yielding popular rubber clones grown at two different agroclimatic conditions were analyzed for the presence of methylation. We found several significant variations in the methylation pattern at core DNA binding motifs within all the five genes. Several consistent clone-specific and location-specific methylation patterns were identified. The differences in methylation pattern observed at certain pivotal cis-regulatory sites indicate the direct impact of stress on the genome and support the hypothesis of site-specific stress-induced DNA methylation. It is assumed that some of the methylation patterns observed may be involved in the stress-responsive mechanism in plants by which they adapt to extreme conditions. The study also provide clues towards the existence of highly divergent phenotypic characters among Hevea clones despite their very similar genetic make-up. Altogether, the observations from this study prove beyond doubt that there exist epigenetic variations in Hevea and environmental factors play a significant role in the induction of site-specific epigenetic mutations in its genome.
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Affiliation(s)
- Thomas K Uthup
- Genome Analysis Lab, Rubber Research Institute of India, Rubber Board PO, Kottayam, Kerala, 686009, India.
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65
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Coolen MW, Statham AL, Qu W, Campbell MJ, Henders AK, Montgomery GW, Martin NG, Clark SJ. Impact of the genome on the epigenome is manifested in DNA methylation patterns of imprinted regions in monozygotic and dizygotic twins. PLoS One 2011; 6:e25590. [PMID: 21991322 PMCID: PMC3184992 DOI: 10.1371/journal.pone.0025590] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Accepted: 09/06/2011] [Indexed: 01/13/2023] Open
Abstract
One of the best studied read-outs of epigenetic change is the differential expression of imprinted genes, controlled by differential methylation of imprinted control regions (ICRs). To address the impact of genotype on the epigenome, we performed a detailed study in 128 pairs of monozygotic (MZ) and 128 pairs of dizygotic (DZ) twins, interrogating the DNA methylation status of the ICRs of IGF2, H19, KCNQ1, GNAS and the non-imprinted gene RUNX1. While we found a similar overall pattern of methylation between MZ and DZ twins, we also observed a high degree of variability in individual CpG methylation levels, notably at the H19/IGF2 loci. A degree of methylation plasticity independent of the genome sequence was observed, with both local and regional CpG methylation changes, discordant between MZ and DZ individual pairs. However, concordant gains or losses of methylation, within individual twin pairs were more common in MZ than DZ twin pairs, indicating that de novo and/or maintenance methylation is influenced by the underlying DNA sequence. Specifically, for the first time we showed that the rs10732516 [A] polymorphism, located in a critical CTCF binding site in the H19 ICR locus, is strongly associated with increased hypermethylation of specific CpG sites in the maternal H19 allele. Together, our results highlight the impact of the genome on the epigenome and demonstrate that while DNA methylation states are tightly maintained between genetically identical and related individuals, there remains considerable epigenetic variation that may contribute to disease susceptibility.
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Affiliation(s)
- Marcel W. Coolen
- Epigenetics Research Group, Cancer Program, Garvan Institute of Medical Research, Sydney, Australia
- Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Aaron L. Statham
- Epigenetics Research Group, Cancer Program, Garvan Institute of Medical Research, Sydney, Australia
| | - Wenjia Qu
- Epigenetics Research Group, Cancer Program, Garvan Institute of Medical Research, Sydney, Australia
| | - Megan J. Campbell
- Genetic and Molecular Epidemiology Laboratories, Queensland Institute of Medical Research, Brisbane, Queensland, Australia
| | - Anjali K. Henders
- Genetic and Molecular Epidemiology Laboratories, Queensland Institute of Medical Research, Brisbane, Queensland, Australia
| | - Grant W. Montgomery
- Genetic and Molecular Epidemiology Laboratories, Queensland Institute of Medical Research, Brisbane, Queensland, Australia
| | - Nick G. Martin
- Genetic and Molecular Epidemiology Laboratories, Queensland Institute of Medical Research, Brisbane, Queensland, Australia
| | - Susan J. Clark
- Epigenetics Research Group, Cancer Program, Garvan Institute of Medical Research, Sydney, Australia
- St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, Australia
- * E-mail:
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66
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Lee HA, Lee DY, Lee HJ, Han HS, Kim I. Enrichment of (pro)renin receptor promoter with activating histone codes in the kidneys of spontaneously hypertensive rats. J Renin Angiotensin Aldosterone Syst 2011; 13:11-8. [PMID: 21803797 DOI: 10.1177/1470320311415738] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The (pro)renin receptor [(P)RR] non-proteolytically, through conformational change, activates prorenin which can convert angiotensinogen to angiotensin I in addition to the classic conversion of angiotensinogen to angiotensin I by circulating renin. Since renal (P)RR is upregulated in hypertension and implicated in the pathogenesis of malignant hypertension, we hypothesized that (pro)renin receptor promoter is enriched with activating histone codes in the kidney of spontaneously hypertensive rats (SHR). METHODS The mRNA and protein expression levels were measured by real-time polymerase chain reaction (PCR) and western blot, respectively. The DNA methylation status of (P)RR promoter region was analyzed by bisulfite sequencing. The histone modifications were determined by chromatin immunoprecipitation followed by real-time PCR. RESULTS The (P)RR mRNA expression in the kidney was about six times greater in SHR than in Wistar-Kyoto (WKY) rats. The (P)RR promoter was little methylated in the kidneys of both WKY and SHR. Acetylated histone H3 (H3Ac) and di-methylated histone H3 at lysine 4 (H3K4me2), activating histone codes, were about 25 and three times higher in SHR than in WKY, respectively. On the other hand, di-methylated histone H3 at lysine 9 (H3K9me2), a suppressive histone code, was 50 times lower in SHR than in WKY. CONCLUSION These results suggest that the (P)RR promoter is enriched with activating histone codes in the kidneys of SHR.
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Affiliation(s)
- Hae-Ahm Lee
- Department of Pharmacology, Kyungpook National University School of Medicine, Daegu, Korea
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Sipos F, Leiszter K, Tulassay Z. Effect of ageing on colonic mucosal regeneration. World J Gastroenterol 2011; 17:2981-6. [PMID: 21799643 PMCID: PMC3132248 DOI: 10.3748/wjg.v17.i25.2981] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Revised: 04/01/2011] [Accepted: 04/08/2011] [Indexed: 02/06/2023] Open
Abstract
The physiologic and pathologic cellular and molecular changes occurring with age in the human colon affect both the inflammatory process leading to mucosal injury and the regenerative capacity of the epithelium. On the one hand, age-related telomere shortening and inflamm-ageing may lead to the development of colonic inflammation, which results in epithelial damage. On the other hand, the altered migration and function of regenerative stem cells, the age-related methylation of mucosal healing-associated genes, together with the alterations of growth factor signaling with age, may be involved in delayed mucosal regeneration. The connections of these alterations to the process of ageing are not fully known. The understanding and custom-tailored modification of these mechanisms are of great clinical importance with regard to disease prevention and modern therapeutic strategies. Here, we aim to summarize the age-related microscopic and molecular changes of the human colon, as well as their role in altered mucosal healing.
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68
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Lin CI, Du J, Shen WT, Whang EE, Donner DB, Griff N, He F, Moore FD, Clark OH, Ruan DT. Mitogen-inducible gene-6 is a multifunctional adaptor protein with tumor suppressor-like activity in papillary thyroid cancer. J Clin Endocrinol Metab 2011; 96:E554-65. [PMID: 21190978 DOI: 10.1210/jc.2010-1800] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
CONTEXT Low tumoral expression of mitogen-inducible gene-6 (Mig-6) is associated with papillary thyroid cancer (PTC) recurrence after thyroidectomy. OBJECTIVE We hypothesize that Mig-6 behaves as a tumor suppressor in PTC. DESIGN Mig-6 expression and promoter methylation status were compared in 31 PTC specimens with matched normal thyroid tissue from the same patient. The impact of Mig-6 loss and gain of function on nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB) activation, global tyrosine kinase phosphorylation, and cellular invasion was determined in vitro. RESULTS Mig-6 protein was abundant in all normal thyroid specimens, whereas 77% of PTC had low Mig-6 expression. Mig-6 promoter methylation was found in 79% of PTC with low Mig-6 expression. Low Mig-6 expression in PTC specimens was associated with low NF-κB activity but high levels of epidermal growth factor receptor (EGFR) and ERK phosphorylation. Mig-6 expression inversely correlated with PTC size but had no association with other clinicopathological variables including age, extrathyroidal extension, lymphovascular invasion, or histological subtype. Mig-6 knockdown in thyroid cancer cell lines resulted in EGFR phosphorylation and diminished NF-κB activity, whereas Mig-6 overexpression had the opposite effects. Mig-6 knockdown activated ErbB2, Met, and Src phosphorylation. Furthermore, Mig-6 regulated ERK phosphorylation independent from its effects on EGFR. Mig-6 knockdown promoted cellular proliferation, as determined by clonogenic survival. Lastly, Mig-6 knockdown increased matrix metalloproteinase-2 and -9 activities and increased cellular invasion. CONCLUSIONS Mig-6 has tumor suppressor-like activity in PTC. In vivo studies are required to confirm that Mig-6 is a putative tumor suppressor in PTC, and future studies should investigate the utility of Mig-6 as a diagnostic marker.
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MESH Headings
- Adaptor Proteins, Signal Transducing/genetics
- Blotting, Western
- Carcinoma
- Carcinoma, Papillary/genetics
- Carcinoma, Papillary/pathology
- Cell Line, Tumor
- Cell Nucleus/chemistry
- Cells, Cultured
- Cytosol/chemistry
- DNA, Neoplasm/genetics
- DNA, Neoplasm/isolation & purification
- Diffusion Chambers, Culture
- Down-Regulation
- ErbB Receptors/metabolism
- Extracellular Signal-Regulated MAP Kinases/metabolism
- Genes, Tumor Suppressor/physiology
- Humans
- NF-kappa B/genetics
- Neoplasm Invasiveness/genetics
- Phosphorylation
- Reverse Transcriptase Polymerase Chain Reaction
- Thyroid Cancer, Papillary
- Thyroid Neoplasms/genetics
- Thyroid Neoplasms/pathology
- Tumor Stem Cell Assay
- Tumor Suppressor Proteins/genetics
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Affiliation(s)
- Chi-Iou Lin
- Department of Surgery, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
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69
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Argyros O, Wong SP, Fedonidis C, Tolmachov O, Waddington SN, Howe SJ, Niceta M, Coutelle C, Harbottle RP. Development of S/MAR minicircles for enhanced and persistent transgene expression in the mouse liver. J Mol Med (Berl) 2011; 89:515-29. [PMID: 21301798 DOI: 10.1007/s00109-010-0713-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Revised: 10/29/2010] [Accepted: 12/03/2010] [Indexed: 12/29/2022]
Abstract
We have previously described the development of a scaffold/matrix attachment region (S/MAR) episomal vector system for in vivo application and demonstrated its utility to sustain transgene expression in the mouse liver for at least 6 months following a single administration. Subsequently, we observed that transgene expression is sustained for the lifetime of the animal. The level of expression, however, does drop appreciably over time. We hypothesised that by eliminating the bacterial components in our vectors, we could improve their performance since bacterial sequences have been shown to be responsible for the immunotoxicity of the vector and the silencing of its expression when applied in vivo. We describe here the development of a minimally sized S/MAR vector, which is devoid of extraneous bacterial sequences. This minicircle vector comprises an expression cassette and an S/MAR moiety, providing higher and more sustained transgene expression for several months in the absence of selection, both in vitro and in vivo. In contrast to the expression of our original S/MAR plasmid vector, the novel S/MAR minicircle vectors mediate increased transgene expression, which becomes sustained at about twice the levels observed immediately after administration. These promising results demonstrate the utility of minimally sized S/MAR vectors for persistent, atoxic gene expression.
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Affiliation(s)
- Orestis Argyros
- Gene Therapy Research Group, Section of Molecular Medicine, National Heart and Lung Institute, Imperial College London, London, UK
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Abstract
Phenotypic robustness is a highly sought after goal for synthetic biology. There are many well-studied examples of robust systems in biology, and for the advancement of synthetic biology, particularly in performance-critical applications, fundamental understanding of how robustness is both achieved and maintained is very important. A synthetic circuit may fail to behave as expected for a multitude of reasons, and since many of these failures are difficult to predict a priori, a better understanding of a circuit's behavior as well as its possible failures are needed. In this chapter, we outline work that has been done in developing design principles for robust synthetic circuits, as well as sharing our experiences designing and constructing gene circuits.
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71
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Kravchenko-Balasha N, Klein S, Safrai M, Levitzki A. Contribution of gross chromosomal changes to HPV16-induced transformation. MOLECULAR BIOSYSTEMS 2011; 7:1501-11. [DOI: 10.1039/c0mb00284d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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72
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Schüttrumpf J, Milanov P, Abriss D, Roth S, Tonn T, Seifried E. Transgene Loss and Changes in the Promoter Methylation Status as Determinants for Expression Duration in Nonviral Gene Transfer for Factor IX. Hum Gene Ther 2011; 22:101-6. [DOI: 10.1089/hum.2009.212] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Jörg Schüttrumpf
- Institut für Transfusionsmedizin und Immunhämatologie, Klinikum der Johann Wolfgang Goethe Universität, DRK-Blutspendedienst Baden-Württemberg-Hessen, 60528 Frankfurt am Main, Germany
- Biomedical Research Institute, Georg-Speyer-Haus, D-60596 Frankfurt am Main
| | - Peter Milanov
- Institut für Transfusionsmedizin und Immunhämatologie, Klinikum der Johann Wolfgang Goethe Universität, DRK-Blutspendedienst Baden-Württemberg-Hessen, 60528 Frankfurt am Main, Germany
| | - Daniela Abriss
- Institut für Transfusionsmedizin und Immunhämatologie, Klinikum der Johann Wolfgang Goethe Universität, DRK-Blutspendedienst Baden-Württemberg-Hessen, 60528 Frankfurt am Main, Germany
| | - Stefanie Roth
- Institut für Transfusionsmedizin und Immunhämatologie, Klinikum der Johann Wolfgang Goethe Universität, DRK-Blutspendedienst Baden-Württemberg-Hessen, 60528 Frankfurt am Main, Germany
| | - Torsten Tonn
- Institut für Transfusionsmedizin und Immunhämatologie, Klinikum der Johann Wolfgang Goethe Universität, DRK-Blutspendedienst Baden-Württemberg-Hessen, 60528 Frankfurt am Main, Germany
| | - Erhard Seifried
- Institut für Transfusionsmedizin und Immunhämatologie, Klinikum der Johann Wolfgang Goethe Universität, DRK-Blutspendedienst Baden-Württemberg-Hessen, 60528 Frankfurt am Main, Germany
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Hong SJ, Oh JH, Jeon EJ, Min KO, Kang MI, Choi SW, Rhyu MG. The overmethylated genes in Helicobacter pylori-infected gastric mucosa are demethylated in gastric cancers. BMC Gastroenterol 2010; 10:137. [PMID: 21092120 PMCID: PMC2995475 DOI: 10.1186/1471-230x-10-137] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Accepted: 11/20/2010] [Indexed: 11/21/2022] Open
Abstract
Background The transitional-CpG sites between weakly methylated genes and densely methylated retroelements are overmethylated in the gastric mucosa infected with Helicobacter pylori (H. pylori) and they are undermethylated in the gastric cancers depending on the level of loss of heterozygosity (LOH) events. This study delineated the transitional-CpG methylation patterns of CpG-island-containing and -lacking genes in view of the retroelements. Methods The transitional-CpG sites of eight CpG-island-containing genes and six CpG-island-lacking genes were semi-quantitatively examined by performing radioisotope-labelling methylation-specific PCR under stringent conditions. The level of LOH in the gastric cancers was estimated using the 40 microsatellite markers on eight cancer-associated chromosomes. Each gene was scored as overmethylated or undermethylated based on an intermediate level of transitional-CpG methylation common in the H. pylori-negative gastric mucosa. Results The eight CpG-island genes examined were overmethylated depending on the proximity to the nearest retroelement in the H. pylori-positive gastric mucosa. The six CpG-island-lacking genes were similarly methylated in the H. pylori-positive and -negative gastric mucosa. In the gastric cancers, long transitional-CpG segments of the CpG-island genes distant from the retroelements remained overmethylated, whereas the overmethylation of short transitional-CpG segments close to the retroelements was not significant. Both the CpG-island-containing and -lacking genes tended to be decreasingly methylated in a LOH-level-dependent manner. Conclusions The overmethylated genes under the influence of retroelement methylation in the H. pylori-infected stomach are demethylated in the gastric cancers influenced by LOH.
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Affiliation(s)
- Seung-Jin Hong
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
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Oyer JA, Yates PA, Godsey S, Turker MS. Aberrantly silenced promoters retain a persistent memory of the silenced state after long-term reactivation. Mutat Res 2010; 706:21-7. [PMID: 21035468 DOI: 10.1016/j.mrfmmm.2010.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Revised: 10/10/2010] [Accepted: 10/20/2010] [Indexed: 10/18/2022]
Abstract
A hallmark of aberrant DNA methylation-associated silencing is reversibility. However, long-term stability of reactivated promoters has not been explored. To examine this issue, spontaneous reactivant clones were isolated from mouse embryonal carcinoma cells bearing aberrantly silenced Aprt alleles and re-silencing frequencies were determined as long as three months after reactivation occurred. Despite continuous selection for expression of the reactivated Aprt alleles, exceptionally high spontaneous re-silencing frequencies were observed. A DNA methylation analysis demonstrated retention of sporadic methylation of CpG sites in a protected region of the Aprt promoter in many reactivant alleles suggesting a role for these methylated sites in the re-silencing process. In contrast, a chromatin immunoprecipitation (ChIP) analysis for methyl-H3K4, acetyl-H3K9, and dimethyl-H3K9 levels failed to reveal a specific histone modification that could explain high frequency re-silencing. These results demonstrate that aberrantly silenced and reactivated promoters retain a persistent memory of having undergone the silencing process and suggest the failure to eliminate all CpG methylation as a potential contributing mechanism.
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Affiliation(s)
- Jon A Oyer
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
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Abstract
The identification of all epigenetic modifications implicated in gene expression is the next step for a better understanding of human biology in both normal and pathological states. This field is referred to as epigenomics, and it is defined as epigenetic changes (ie, DNA methylation, histone modifications and regulation by noncoding RNAs such as microRNAs) on a genomic scale rather than a single gene. Epigenetics modulate the structure of the chromatin, thereby affecting the transcription of genes in the genome. Different studies have already identified changes in epigenetic modifications in a few genes in specific pathways in cancers. Based on these epigenetic changes, drugs against different types of tumors were developed, which mainly target epimutations in the genome. Examples include DNA methylation inhibitors, histone modification inhibitors, and small molecules that target chromatin-remodeling proteins. However, these drugs are not specific, and side effects are a major problem; therefore, new DNA sequencing technologies combined with epigenomic tools have the potential to identify novel biomarkers and better molecular targets to treat cancers. The purpose of this review is to discuss current and emerging epigenomic tools and to address how these new technologies may impact the future of cancer management.
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Affiliation(s)
- Fabricio F Costa
- Cancer Biology and Epigenomics Program, Children's Memorial Research Center and Northwestern University's Feinberg School of Medicine, 2430 N. Halsted St, Box 220, Chicago, IL, USA
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76
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Genome-wide conserved consensus transcription factor binding motifs are hyper-methylated. BMC Genomics 2010; 11:519. [PMID: 20875111 PMCID: PMC2997012 DOI: 10.1186/1471-2164-11-519] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Accepted: 09/27/2010] [Indexed: 01/21/2023] Open
Abstract
Background DNA methylation can regulate gene expression by modulating the interaction between DNA and proteins or protein complexes. Conserved consensus motifs exist across the human genome ("predicted transcription factor binding sites": "predicted TFBS") but the large majority of these are proven by chromatin immunoprecipitation and high throughput sequencing (ChIP-seq) not to be biological transcription factor binding sites ("empirical TFBS"). We hypothesize that DNA methylation at conserved consensus motifs prevents promiscuous or disorderly transcription factor binding. Results Using genome-wide methylation maps of the human heart and sperm, we found that all conserved consensus motifs as well as the subset of those that reside outside CpG islands have an aggregate profile of hyper-methylation. In contrast, empirical TFBS with conserved consensus motifs have a profile of hypo-methylation. 40% of empirical TFBS with conserved consensus motifs resided in CpG islands whereas only 7% of all conserved consensus motifs were in CpG islands. Finally we further identified a minority subset of TF whose profiles are either hypo-methylated or neutral at their respective conserved consensus motifs implicating that these TF may be responsible for establishing or maintaining an un-methylated DNA state, or whose binding is not regulated by DNA methylation. Conclusions Our analysis supports the hypothesis that at least for a subset of TF, empirical binding to conserved consensus motifs genome-wide may be controlled by DNA methylation.
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77
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Kim K, Doi A, Wen B, Ng K, Zhao R, Cahan P, Kim J, Aryee MJ, Ji H, Ehrlich L, Yabuuchi A, Takeuchi A, Cunniff KC, Hongguang H, Mckinney-Freeman S, Naveiras O, Yoon TJ, Irizarry RA, Jung N, Seita J, Hanna J, Murakami P, Jaenisch R, Weissleder R, Orkin SH, Weissman IL, Feinberg AP, Daley GQ. Epigenetic memory in induced pluripotent stem cells. Nature 2010; 467:285-90. [PMID: 20644535 PMCID: PMC3150836 DOI: 10.1038/nature09342] [Citation(s) in RCA: 1635] [Impact Index Per Article: 116.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Accepted: 07/12/2010] [Indexed: 11/09/2022]
Abstract
Somatic cell nuclear transfer and transcription-factor-based reprogramming revert adult cells to an embryonic state, and yield pluripotent stem cells that can generate all tissues. Through different mechanisms and kinetics, these two reprogramming methods reset genomic methylation, an epigenetic modification of DNA that influences gene expression, leading us to hypothesize that the resulting pluripotent stem cells might have different properties. Here we observe that low-passage induced pluripotent stem cells (iPSCs) derived by factor-based reprogramming of adult murine tissues harbour residual DNA methylation signatures characteristic of their somatic tissue of origin, which favours their differentiation along lineages related to the donor cell, while restricting alternative cell fates. Such an 'epigenetic memory' of the donor tissue could be reset by differentiation and serial reprogramming, or by treatment of iPSCs with chromatin-modifying drugs. In contrast, the differentiation and methylation of nuclear-transfer-derived pluripotent stem cells were more similar to classical embryonic stem cells than were iPSCs. Our data indicate that nuclear transfer is more effective at establishing the ground state of pluripotency than factor-based reprogramming, which can leave an epigenetic memory of the tissue of origin that may influence efforts at directed differentiation for applications in disease modelling or treatment.
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Affiliation(s)
- K Kim
- Stem Cell Transplantation Program, Division of Pediatric Hematology/Oncology, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Children’s Hospital Boston and Dana Farber Cancer Institute; Division of Hematology, Brigham and Women’s Hospital; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Harvard Stem Cell Institute; Boston, MA 02115, USA
| | - A Doi
- Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - B Wen
- Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - K Ng
- Stem Cell Transplantation Program, Division of Pediatric Hematology/Oncology, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Children’s Hospital Boston and Dana Farber Cancer Institute; Division of Hematology, Brigham and Women’s Hospital; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Harvard Stem Cell Institute; Boston, MA 02115, USA
| | - R Zhao
- Stem Cell Transplantation Program, Division of Pediatric Hematology/Oncology, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Children’s Hospital Boston and Dana Farber Cancer Institute; Division of Hematology, Brigham and Women’s Hospital; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Harvard Stem Cell Institute; Boston, MA 02115, USA
| | - P Cahan
- Stem Cell Transplantation Program, Division of Pediatric Hematology/Oncology, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Children’s Hospital Boston and Dana Farber Cancer Institute; Division of Hematology, Brigham and Women’s Hospital; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Harvard Stem Cell Institute; Boston, MA 02115, USA
| | - J Kim
- Department of Pediatric Oncology, Howard Hughes Medical Institute, Children’s Hospital Boston and Dana Farber Cancer Institute; Boston, MA 02115, USA
| | - MJ Aryee
- Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, USA
| | - H Ji
- Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - L Ehrlich
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - A Yabuuchi
- Stem Cell Transplantation Program, Division of Pediatric Hematology/Oncology, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Children’s Hospital Boston and Dana Farber Cancer Institute; Division of Hematology, Brigham and Women’s Hospital; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Harvard Stem Cell Institute; Boston, MA 02115, USA
| | - A Takeuchi
- Stem Cell Transplantation Program, Division of Pediatric Hematology/Oncology, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Children’s Hospital Boston and Dana Farber Cancer Institute; Division of Hematology, Brigham and Women’s Hospital; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Harvard Stem Cell Institute; Boston, MA 02115, USA
| | - KC Cunniff
- Stem Cell Transplantation Program, Division of Pediatric Hematology/Oncology, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Children’s Hospital Boston and Dana Farber Cancer Institute; Division of Hematology, Brigham and Women’s Hospital; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Harvard Stem Cell Institute; Boston, MA 02115, USA
| | - H Hongguang
- Stem Cell Transplantation Program, Division of Pediatric Hematology/Oncology, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Children’s Hospital Boston and Dana Farber Cancer Institute; Division of Hematology, Brigham and Women’s Hospital; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Harvard Stem Cell Institute; Boston, MA 02115, USA
| | - S Mckinney-Freeman
- Stem Cell Transplantation Program, Division of Pediatric Hematology/Oncology, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Children’s Hospital Boston and Dana Farber Cancer Institute; Division of Hematology, Brigham and Women’s Hospital; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Harvard Stem Cell Institute; Boston, MA 02115, USA
| | - O Naveiras
- Stem Cell Transplantation Program, Division of Pediatric Hematology/Oncology, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Children’s Hospital Boston and Dana Farber Cancer Institute; Division of Hematology, Brigham and Women’s Hospital; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Harvard Stem Cell Institute; Boston, MA 02115, USA
| | - TJ Yoon
- Center for Systems Biology, Massachusetts General Hospital / Harvard Medical School, 185 Cambridge Street, CPZN 5206, Boston, MA 02114, USA
| | - RA Irizarry
- Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - N Jung
- Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - J Seita
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - J Hanna
- Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - P Murakami
- Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - R Jaenisch
- Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - R Weissleder
- Center for Systems Biology, Massachusetts General Hospital / Harvard Medical School, 185 Cambridge Street, CPZN 5206, Boston, MA 02114, USA
| | - SH Orkin
- Department of Pediatric Oncology, Howard Hughes Medical Institute, Children’s Hospital Boston and Dana Farber Cancer Institute; Boston, MA 02115, USA
| | - IL Weissman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - AP Feinberg
- Center for Epigenetics and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - GQ Daley
- Stem Cell Transplantation Program, Division of Pediatric Hematology/Oncology, Manton Center for Orphan Disease Research, Howard Hughes Medical Institute, Children’s Hospital Boston and Dana Farber Cancer Institute; Division of Hematology, Brigham and Women’s Hospital; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School; Harvard Stem Cell Institute; Boston, MA 02115, USA
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78
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Holz-Schietinger C, Reich NO. The inherent processivity of the human de novo methyltransferase 3A (DNMT3A) is enhanced by DNMT3L. J Biol Chem 2010; 285:29091-100. [PMID: 20630873 DOI: 10.1074/jbc.m110.142513] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Human DNMT3A is responsible for de novo DNA cytosine methylation patterning during development. Here we show that DNMT3A methylates 5-8 CpG sites on human promoters before 50% of the initially bound enzyme dissociates from the DNA. Processive methylation is enhanced 3-fold in the presence of DNMT3L, an inactive homolog of DNMT3A, therefore providing a mechanism for the previously described DNMT3L activation of DNMT3A. DNMT3A processivity on human promoters is also regulated by DNA topology, where a 2-fold decrease in processivity was observed on supercoiled DNA in comparison with linear DNA. These results are the first observation that DNMT3A utilizes this mechanism of increasing catalytic efficiency. Processive de novo DNA methylation provides a mechanism that ensures that multiple CpG sites undergo methylation for transcriptional regulation and silencing of newly integrated viral DNA.
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Affiliation(s)
- Celeste Holz-Schietinger
- Interdepartmental Program in Biomolecular Science and Engineering, University of California, Santa Barbara, California 93106-9510, USA
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79
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Combes AN, Whitelaw E. Epigenetic reprogramming: Enforcer or enabler of developmental fate? Dev Growth Differ 2010; 52:483-91. [DOI: 10.1111/j.1440-169x.2010.01185.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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80
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Abstract
Retrotransposons like L1 are silenced in somatic cells by a
variety of mechanisms acting at different levels. Protective
mechanisms include DNA methylation and packaging into inactive
chromatin to suppress transcription and prevent recombination,
potentially supported by cytidine deaminase editing of RNA.
Furthermore, DNA strand breaks arising during attempted
retrotranspositions ought to activate cellular checkpoints, and L1
activation outside immunoprivileged sites may elicit immune
responses. A number of observations indicate that L1 sequences
nevertheless become reactivated in human cancer. Prominently,
methylation of L1 sequences is diminished in many cancer types and
full-length L1 RNAs become detectable, although strong expression
is restricted to germ cell cancers. L1 elements have been found to
be enriched at sites of illegitimate recombination in many
cancers. In theory, lack of L1 repression in cancer might cause
transcriptional deregulation, insertional mutations, DNA breaks,
and an increased frequency of recombinations, contributing to
genome disorganization, expression changes, and chromosomal
instability. There is however little evidence that such effects
occur at a gross scale in human cancers. Rather, as a rule, L1
repression is only partly alleviated. Unfortunately, many
techniques commonly used to investigate genetic and epigenetic
alterations in cancer cells are not well suited to detect subtle
effects elicited by partial reactivation of retroelements like L1
which are present as abundant, but heterogeneous copies.
Therefore, effects of L1 sequences exerted on the local chromatin
structure, on the transcriptional regulation of individual genes,
and on chromosome fragility need to be more closely investigated
in normal and cancer cells.
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Affiliation(s)
- Wolfgang A. Schulz
- Department of Urology, Heinrich Heine University, Mooreustrasse 5, 40225 Düsseldorf, Germany
- *Wolfgang A. Schulz:
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81
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Sohn BH, Park IY, Lee JJ, Yang SJ, Jang YJ, Park KC, Kim DJ, Lee DC, Sohn HA, Kim TW, Yoo HS, Choi JY, Bae YS, Yeom YI. Functional switching of TGF-beta1 signaling in liver cancer via epigenetic modulation of a single CpG site in TTP promoter. Gastroenterology 2010; 138:1898-908. [PMID: 20038433 DOI: 10.1053/j.gastro.2009.12.044] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2009] [Revised: 11/16/2009] [Accepted: 12/17/2009] [Indexed: 12/19/2022]
Abstract
BACKGROUND & AIMS Acquisition of resistance to the antiproliferative effect of transforming growth factor (TGF)-beta1 is crucial for the malignant progression of cancers. In this study, we sought to determine whether deregulated expression of tristetrapolin (TTP), a negative posttranscriptional regulator of c-Myc, confers resistance to the antiproliferative effects of TGF-beta1 on liver cancer cells. METHODS The epigenetics of TTP promoter regulation and its effects on TGF-beta1 signaling were examined in hepatocellular carcinoma (HCC) cell lines and patient tissues. RESULTS TTP was down-regulated in HCC cell lines (10/11), compared with normal liver, as well as in tumor tissues (19/24) from paired HCC specimens. Methylation of a specific single CpG site located within the TGF-beta1-responsive region (TRR) of the TTP promoter was significantly associated with TTP down-regulation in both HCC cell lines and tumor tissues (r = -0.606383, P < .001). The singly methylated CpG site was specifically bound by a transcriptional repressor complex consisting of MECP2/c-Ski/DNMT3A and abolished the TGF-beta1-induced as well as basal-level expression of TTP. The epigenetic inactivation of TTP led to an increased half-life of c-Myc mRNA and blocked the cytostatic effect of TGF-beta1. Statistically significant correlations were observed between the single CpG site methylation and expression levels of TTP or c-Myc in clinical samples of HCC. CONCLUSIONS Abrogation of the post-transcriptional regulation of c-Myc via methylation of a specific single CpG site in the TTP promoter presents a novel mechanism for the gain of selective resistance to the antiproliferative signaling of TGF-beta1 in HCC.
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Affiliation(s)
- Bo Hwa Sohn
- Medical Genomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Korea
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82
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Promoter hypomethylation upregulates Na+-K+-2Cl- cotransporter 1 in spontaneously hypertensive rats. Biochem Biophys Res Commun 2010; 396:252-7. [PMID: 20406621 DOI: 10.1016/j.bbrc.2010.04.074] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Accepted: 04/13/2010] [Indexed: 12/16/2022]
Abstract
The Na(+)-K(+)-2Cl(-) cotransporter 1 (NKCC1) is one of several transporters that have been implicated for development of hypertension since NKCC1 activity is elevated in hypertensive aorta and vascular contractions are inhibited by bumetanide, an inhibitor of NKCC1. We hypothesized that promoter hypomethylation upregulates the NKCC1 in spontaneously hypertensive rats (SHR). Thoracic aortae and mesenteric arteries were excised, cut into rings, mounted in organ baths and subjected to vascular contraction. The expression levels of nkcc1 mRNA and protein in aortae and heart tissues were measured by real-time PCR and Western blot, respectively. The methylation status of nkcc1 promoter region was analyzed by combined bisulfite restriction assay (COBRA) and bisulfite sequencing. Phenylephrine-induced vascular contraction in a dose-dependent manner, which was inhibited by bumetanide. The inhibition of dose-response curves by bumetanide was much greater in SHR than in Wistar Kyoto (WKY) normotensive rats. The expression levels of nkcc1 mRNA and of NKCC1 protein in aortae and heart tissues were higher in SHR than in WKY. Nkcc1 gene promoter was hypomethylated in aortae and heart than those of WKY. These results suggest that promoter hypomethylation upregulates the NKCC1 expression in aortae and heart of SHR.
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83
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Hesson LB, Hitchins MP, Ward RL. Epimutations and cancer predisposition: importance and mechanisms. Curr Opin Genet Dev 2010; 20:290-8. [PMID: 20359882 DOI: 10.1016/j.gde.2010.02.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2009] [Revised: 01/31/2010] [Accepted: 02/20/2010] [Indexed: 01/24/2023]
Abstract
Germline sequence mutations in tumour suppressor genes can cause cancer predisposition syndromes. More recently, epimutations have also been proposed to cause at least one such syndrome, hereditary non-polyposis colorectal cancer (HNPCC). 'Epigenetic predisposition', is defined as an inherited propensity to an altered epigenetic state in normal tissues that confers a predisposition to disease. Genetic sequence variations acting in cis or trans may contribute to epigenetic variations. Understanding the origin of epimutations will inform cancer risk assessment and will also aid the design and application of new therapies that target the epigenome.
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Affiliation(s)
- Luke B Hesson
- Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Kensington, New South Wales, Australia
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84
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Mishiba KI, Yamasaki S, Nakatsuka T, Abe Y, Daimon H, Oda M, Nishihara M. Strict de novo methylation of the 35S enhancer sequence in gentian. PLoS One 2010; 5:e9670. [PMID: 20351783 PMCID: PMC2843634 DOI: 10.1371/journal.pone.0009670] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Accepted: 02/19/2010] [Indexed: 11/18/2022] Open
Abstract
A novel transgene silencing phenomenon was found in the ornamental plant, gentian (Gentiana triflora x G. scabra), in which the introduced Cauliflower mosaic virus (CaMV) 35S promoter region was strictly methylated, irrespective of the transgene copy number and integrated loci. Transgenic tobacco having the same vector did not show the silencing behavior. Not only unmodified, but also modified 35S promoters containing a 35S enhancer sequence were found to be highly methylated in the single copy transgenic gentian lines. The 35S core promoter (-90)-introduced transgenic lines showed a small degree of methylation, implying that the 35S enhancer sequence was involved in the methylation machinery. The rigorous silencing phenomenon enabled us to analyze methylation in a number of the transgenic lines in parallel, which led to the discovery of a consensus target region for de novo methylation, which comprised an asymmetric cytosine (CpHpH; H is A, C or T) sequence. Consequently, distinct footprints of de novo methylation were detected in each (modified) 35S promoter sequence, and the enhancer region (-148 to -85) was identified as a crucial target for de novo methylation. Electrophoretic mobility shift assay (EMSA) showed that complexes formed in gentian nuclear extract with the -149 to -124 and -107 to -83 region probes were distinct from those of tobacco nuclear extracts, suggesting that the complexes might contribute to de novo methylation. Our results provide insights into the phenomenon of sequence- and species- specific gene silencing in higher plants.
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Affiliation(s)
- Kei-ichiro Mishiba
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Osaka, Japan.
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85
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Hong SJ, Oh JH, Jung YC, Kim YH, Kim SJ, Kang SJ, Seo EJ, Choi SW, Kang MI, Rhyu MG. DNA methylation patterns of ulcer-healing genes associated with the normal gastric mucosa of gastric cancers. J Korean Med Sci 2010; 25:405-17. [PMID: 20191040 PMCID: PMC2826743 DOI: 10.3346/jkms.2010.25.3.405] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2009] [Accepted: 07/14/2009] [Indexed: 01/20/2023] Open
Abstract
Recent evidence suggests that gastric mucosal injury induces adaptive changes in DNA methylation. In this study, the methylation status of the key tissue-specific genes in normal gastric mucosa of healthy individuals and cancer patients was evaluated. The methylation-variable sites of 14 genes, including ulcer-healing genes (TFF1, TFF2, CDH1, and PPARG), were chosen from the CpG-island margins or non-island CpGs near the transcription start sites. The healthy individuals as well as the normal gastric mucosa of 23 ulcer, 21 non-invasive cancer, and 53 cancer patients were examined by semiquantitative methylation-specific polymerase chain reaction (PCR) analysis. The ulcer-healing genes were concurrently methylated with other genes depending on the presence or absence of CpG-islands in the normal mucosa of healthy individuals. Both the TFF2 and PPARG genes were frequently undermethylated in ulcer patients. The over- or intermediate-methylated TFF2 and undermethylated PPARG genes was more common in stage-1 cancer patients (71%) than in healthy individuals (10%; odds ratio [OR], 21.9) and non-invasive cancer patients (21%; OR, 8.9). The TFF2-PPARG methylation pattern of cancer patients was stronger in the older-age group (> or =55 yr; OR, 43.6). These results suggest that the combined methylation pattern of ulcer-healing genes serves as a sensitive marker for predicting cancer-prone gastric mucosa.
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Affiliation(s)
- Seung-Jin Hong
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jung-Hwan Oh
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Yu-Chae Jung
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Young-Ho Kim
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sung-Ja Kim
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Seok-Jin Kang
- Department of Clinical Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Eun-Joo Seo
- Department of Clinical Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sang-Wook Choi
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Moo-Il Kang
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Department of Clinical Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Mun-Gan Rhyu
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
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86
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Promotion of variant human mammary epithelial cell outgrowth by ionizing radiation: an agent-based model supported by in vitro studies. Breast Cancer Res 2010; 12:R11. [PMID: 20146798 PMCID: PMC2880432 DOI: 10.1186/bcr2477] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Revised: 01/20/2010] [Accepted: 02/10/2010] [Indexed: 01/25/2023] Open
Abstract
Introduction Most human mammary epithelial cells (HMEC) cultured from histologically normal breast tissues enter a senescent state termed stasis after 5 to 20 population doublings. These senescent cells display increased size, contain senescence associated β-galactosidase activity, and express cyclin-dependent kinase inhibitor, p16INK4A (CDKN2A; p16). However, HMEC grown in a serum-free medium, spontaneously yield, at low frequency, variant (v) HMEC that are capable of long-term growth and are susceptible to genomic instability. We investigated whether ionizing radiation, which increases breast cancer risk in women, affects the rate of vHMEC outgrowth. Methods Pre-stasis HMEC cultures were exposed to 5 to 200 cGy of sparsely (X- or γ-rays) or densely (1 GeV/amu 56Fe) ionizing radiation. Proliferation (bromodeoxyuridine incorporation), senescence (senescence-associated β-galactosidase activity), and p16 expression were assayed in subcultured irradiated or unirradiated populations four to six weeks following radiation exposure, when patches of vHMEC became apparent. Long-term growth potential and p16 promoter methylation in subsequent passages were also monitored. Agent-based modeling, incorporating a simple set of rules and underlying assumptions, was used to simulate vHMEC outgrowth and evaluate mechanistic hypotheses. Results Cultures derived from irradiated cells contained significantly more vHMEC, lacking senescence associated β-galactosidase or p16 expression, than cultures derived from unirradiated cells. As expected, post-stasis vHMEC cultures derived from both unirradiated and irradiated cells exhibited more extensive methylation of the p16 gene than pre-stasis HMEC cultures. However, the extent of methylation of individual CpG sites in vHMEC samples did not correlate with passage number or treatment. Exposure to sparsely or densely ionizing radiation elicited similar increases in the numbers of vHMEC compared to unirradiated controls. Agent-based modeling indicated that radiation-induced premature senescence of normal HMEC most likely accelerated vHMEC outgrowth through alleviation of spatial constraints. Subsequent experiments using defined co-cultures of vHMEC and senescent cells supported this mechanism. Conclusions Our studies indicate that ionizing radiation can promote the outgrowth of epigenetically altered cells with pre-malignant potential.
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87
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Gebhard C, Benner C, Ehrich M, Schwarzfischer L, Schilling E, Klug M, Dietmaier W, Thiede C, Holler E, Andreesen R, Rehli M. General Transcription Factor Binding at CpG Islands in Normal Cells Correlates with Resistance to De novo DNA Methylation in Cancer Cells. Cancer Res 2010; 70:1398-407. [DOI: 10.1158/0008-5472.can-09-3406] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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88
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Dickson J, Gowher H, Strogantsev R, Gaszner M, Hair A, Felsenfeld G, West AG. VEZF1 elements mediate protection from DNA methylation. PLoS Genet 2010; 6:e1000804. [PMID: 20062523 PMCID: PMC2795164 DOI: 10.1371/journal.pgen.1000804] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2009] [Accepted: 12/08/2009] [Indexed: 11/18/2022] Open
Abstract
There is growing consensus that genome organization and long-range gene regulation involves partitioning of the genome into domains of distinct epigenetic chromatin states. Chromatin insulator or barrier elements are key components of these processes as they can establish boundaries between chromatin states. The ability of elements such as the paradigm β-globin HS4 insulator to block the range of enhancers or the spread of repressive histone modifications is well established. Here we have addressed the hypothesis that a barrier element in vertebrates should be capable of defending a gene from silencing by DNA methylation. Using an established stable reporter gene system, we find that HS4 acts specifically to protect a gene promoter from de novo DNA methylation. Notably, protection from methylation can occur in the absence of histone acetylation or transcription. There is a division of labor at HS4; the sequences that mediate protection from methylation are separable from those that mediate CTCF-dependent enhancer blocking and USF-dependent histone modification recruitment. The zinc finger protein VEZF1 was purified as the factor that specifically interacts with the methylation protection elements. VEZF1 is a candidate CpG island protection factor as the G-rich sequences bound by VEZF1 are frequently found at CpG island promoters. Indeed, we show that VEZF1 elements are sufficient to mediate demethylation and protection of the APRT CpG island promoter from DNA methylation. We propose that many barrier elements in vertebrates will prevent DNA methylation in addition to blocking the propagation of repressive histone modifications, as either process is sufficient to direct the establishment of an epigenetically stable silent chromatin state. DNA sequences known as chromatin insulator or barrier elements are considered key components of genome organization as they can establish boundaries between transcriptionally permissive and repressive chromatin domains. Here we address the hypothesis that barrier elements in vertebrates can protect genes from transcriptional silencing that is marked by DNA methylation. We have found that the HS4 insulator element from the β-globin gene locus can protect a gene promoter from DNA methylation. Protection from DNA methylation is separable from other insulator activities and is mapped to three transcription factor binding sites occupied by the zinc finger protein VEZF1, a novel chromatin barrier protein. VEZF1 is a candidate factor for the protection of promoters from DNA methylation. We found that VEZF1-specific binding sites are sufficient to mediate demethylation and protection of the APRT gene promoter from DNA methylation. We propose that barrier elements in vertebrates must be capable of preventing DNA methylation in addition to blocking the propagation of silencing histone modifications, as either process is sufficient to direct the establishment of an inactive chromatin state.
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Affiliation(s)
- Jacqueline Dickson
- Section of Pathology and Gene Regulation, Faculty of Medicine, University of Glasgow, Western Infirmary, Glasgow, United Kingdom
| | - Humaira Gowher
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Ruslan Strogantsev
- Section of Pathology and Gene Regulation, Faculty of Medicine, University of Glasgow, Western Infirmary, Glasgow, United Kingdom
| | - Miklos Gaszner
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Alan Hair
- Section of Pathology and Gene Regulation, Faculty of Medicine, University of Glasgow, Western Infirmary, Glasgow, United Kingdom
| | - Gary Felsenfeld
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (AGW); (GF)
| | - Adam G. West
- Section of Pathology and Gene Regulation, Faculty of Medicine, University of Glasgow, Western Infirmary, Glasgow, United Kingdom
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (AGW); (GF)
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89
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90
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Lewandowska MA, Costa FF, Bischof JM, Williams SH, Soares MB, Harris A. Multiple mechanisms influence regulation of the cystic fibrosis transmembrane conductance regulator gene promoter. Am J Respir Cell Mol Biol 2009; 43:334-41. [PMID: 19855085 DOI: 10.1165/rcmb.2009-0149oc] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The cystic fibrosis transmembrane conductance regulator (CFTR) gene is driven by a promoter that cannot alone account for the temporal and tissue-specific regulation of the gene. This has led to the search for additional regulatory elements that cooperate with the basal promoter to achieve coordinated expression. We previously identified two alternative upstream exons of the gene that were mutually exclusive of the first exon, and one of which showed temporal regulation in the human and sheep lung. We now demonstrate that this alternative splice product generates a stable protein, which initiates translation at an ATG in exon 4, and thus lacks the N terminus of CFTR. The other splice variant inhibits translation of the protein. In a search for the promoter used by the upstream exons, we identified a novel element that contributes to the activity of the basal CFTR promoter in airway epithelial cells, but does not function independently. Finally, we demonstrate that, in primary airway cells, skin fibroblasts, and both airway and intestinal cell lines, the CFTR promoter is unmethylated, irrespective of CFTR expression status. Thus, methylation is not the main cause of inactivation of CFTR transcription.
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Affiliation(s)
- Marzena A Lewandowska
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60614, USA
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91
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Hong SJ, Kang MI, Oh JH, Jung YC, Kim YH, Kim SJ, Choi SH, Seo EJ, Choi SW, Rhyu MG. DNA methylation and expression patterns of key tissue-specific genes in adult stem cells and stomach tissues. J Korean Med Sci 2009; 24:918-29. [PMID: 19794993 PMCID: PMC2752778 DOI: 10.3346/jkms.2009.24.5.918] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2009] [Accepted: 07/01/2009] [Indexed: 11/25/2022] Open
Abstract
CpG-island margins and non-island-CpG sites round the transcription start sites of CpG-island-positive and -negative genes are methylated to various degrees in a tissue-specific manner. These methylation-variable CpG sites were analyzed to delineate a relationship between the methylation and transcription of the tissue-specific genes. The level of tissue-specific transcription was estimated by counting the number of the total transcripts in the SAGE (serial analysis of gene expression) database. The methylation status of 12 CpG-island margins and 21 non-island CpG sites near the key tissue-specific genes was examined in pluripotent stromal cells obtained from fat and bone marrow samples as well as in lineage-committed cells from marrow bulk, stomach, colon, breast, and thyroid samples. Of the 33 CpG sites examined, 10 non-island-CpG sites, but none of the CpG-island margins were undermethylated concurrent with tissue-specific expression of their nearby genes. The net methylation of the 33 CpG sites and the net amount of non-island-CpG gene transcripts were high in stomach tissues and low in stromal cells. The present findings suggest that the methylation of the non-island-CpG sites is inversely associated with the expression of the nearby genes, and the concert effect of transitional-CpG methylation is linearly associated with the stomach-specific genes lacking CpG-islands.
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Affiliation(s)
- Seung-Jin Hong
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Moo-Il Kang
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Jung-Hwan Oh
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Yu-Chae Jung
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Young-Ho Kim
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sung-Ja Kim
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Seung-Hye Choi
- Department of Surgery, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Eun-Joo Seo
- Department of Clinical Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sang-Wook Choi
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Mun-Gan Rhyu
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
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92
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Samuel MS, Suzuki H, Buchert M, Putoczki TL, Tebbutt NC, Lundgren-May T, Christou A, Inglese M, Toyota M, Heath JK, Ward RL, Waring PM, Ernst M. Elevated Dnmt3a activity promotes polyposis in Apc(Min) mice by relaxing extracellular restraints on Wnt signaling. Gastroenterology 2009; 137:902-13, 913.e1-11. [PMID: 19454286 DOI: 10.1053/j.gastro.2009.05.042] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2008] [Revised: 04/23/2009] [Accepted: 05/14/2009] [Indexed: 12/31/2022]
Abstract
BACKGROUND & AIMS Aberrant DNA methylation is a common early event in neoplasia, but it is unclear how this relates to dysregulation of DNA (cytosine-5) methyltransferases (Dnmts). Here we use knock-in transgenic mice to investigate the consequences of intestinal epithelium-specific overexpression of de novo Dnmt3a. METHODS A novel gene targeting strategy, based on the intestinal epithelium-specific, uniform expression of the A33 glycoprotein, is employed to restrict Dnmt3a overexpression in homozygous A33(Dnmt3a) mutant mice. RESULTS A33(Dnmt3a) mice infrequently develop spontaneous intestinal polyps. However, when genetically challenged, tumor multiplicity in A33(Dnmt3a);Apc(Min) compound mice is 3-fold higher than in Apc(Min) mice. Although we observe a requirement for spontaneous loss of heterozygosity of the adenomatous polyposis coli (Apc) gene to trigger tumorigenesis in Apc(Min) mice, lesions in A33(Dnmt3a);Apc(Min) mice frequently retain the wild-type Apc allele. However, epithelia from normal mucosa and polyps of A33(Dnmt3a);Apc(Min) mice show hypermethylation-mediated transcriptional silencing of the Wnt antagonists Sfrp5, and to a lesser extent, Sfrp1 and increased nuclear beta-catenin alongside activation of the Wnt-target gene Axin2/Conductin. Conversely, enforced Sfrp5 expression suppresses canonical Wnt-signaling more effectively in wild-type than in Apc(Min) cells. CONCLUSIONS Aberrant activation of the canonical Wnt pathway, either by mono-allelic Apc loss or transcriptional silencing of Sfrp5 is largely insufficient to promote polyposis, but epistatic interactions between these genetic and epigenetic events enables initiation and promotion of disease. This mechanism is likely to play a role in human colorectal cancer, because we also show that elevated DNMT3A expression coincides with repressed SFRP5 and enhanced AXIN2/CONDUCTIN expression in paired patient biopsies.
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Affiliation(s)
- Michael S Samuel
- Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Victoria, Australia
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Melotte V, Lentjes MHFM, van den Bosch SM, Hellebrekers DMEI, de Hoon JPJ, Wouters KAD, Daenen KLJ, Partouns-Hendriks IEJM, Stessels F, Louwagie J, Smits KM, Weijenberg MP, Sanduleanu S, Khalid-de Bakker CAJ, Oort FA, Meijer GA, Jonkers DMAE, Herman JG, de Bruïne AP, van Engeland M. N-Myc downstream-regulated gene 4 (NDRG4): a candidate tumor suppressor gene and potential biomarker for colorectal cancer. J Natl Cancer Inst 2009; 101:916-27. [PMID: 19535783 DOI: 10.1093/jnci/djp131] [Citation(s) in RCA: 161] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Identification of hypermethylated tumor suppressor genes in body fluids is an appealing strategy for the noninvasive detection of colorectal cancer. Here we examined the role of N-Myc downstream-regulated gene 4 (NDRG4) as a novel tumor suppressor and biomarker in colorectal cancer. METHODS NDRG4 promoter methylation was analyzed in human colorectal cancer cell lines, colorectal tissue, and noncancerous colon mucosa by using methylation-specific polymerase chain reaction (PCR) and bisulfite sequencing. NDRG4 mRNA and protein expression were studied using real-time-PCR and immunohistochemistry, respectively. Tumor suppressor functions of NDRG4 were examined by colony formation, cell proliferation, and migration and invasion assays in colorectal cancer cell lines that were stably transfected with an NDRG4 expression construct. Quantitative methylation-specific PCR was used to examine the utility of NDRG4 promoter methylation as a biomarker in fecal DNA from 75 colorectal cancer patients and 75 control subjects. All P values are two-sided. RESULTS The prevalence of NDRG4 promoter methylation in two independent series of colorectal cancers was 86% (71/83) and 70% (128/184) compared with 4% (2/48) in noncancerous colon mucosa (P < .001). NDRG4 mRNA and protein expression were decreased in colorectal cancer tissue compared with noncancerous colon mucosa. NDRG4 overexpression in colorectal cancer cell lines suppressed colony formation (P = .014), cell proliferation (P < .001), and invasion (P < .001). NDRG4 promoter methylation analysis in fecal DNA from a training set of colorectal cancer patients and control subjects yielded a sensitivity of 61% (95% confidence interval [CI] = 43% to 79%) and a specificity of 93% (95% CI = 90% to 97%). An independent test set of colorectal cancer patients and control subjects yielded a sensitivity of 53% (95% CI = 39% to 67%) and a specificity of 100% (95% CI = 86% to 100%). CONCLUSIONS NDRG4 is a candidate tumor suppressor gene in colorectal cancer whose expression is frequently inactivated by promoter methylation. NDRG4 promoter methylation is a potential biomarker for the noninvasive detection of colorectal cancer in stool samples.
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Affiliation(s)
- Veerle Melotte
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Center, The Netherlands
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94
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Abstract
DNA and histone methylation are linked and subjected to mitotic inheritance in mammals. Yet how methylation is propagated and maintained between successive cell divisions is not fully understood. A series of enzyme families that can add methylation marks to cytosine nucleobases, and lysine and arginine amino acid residues has been discovered. Apart from methyltransferases, there are also histone modification enzymes and accessory proteins, which can facilitate and/or target epigenetic marks. Several lysine and arginine demethylases have been discovered recently, and the presence of an active DNA demethylase is speculated in mammalian cells. A mammalian methyl DNA binding protein MBD2 and de novo DNA methyltransferase DNMT3A and DNMT3B are shown experimentally to possess DNA demethylase activity. Thus, complex mammalian epigenetic mechanisms appear to be dynamic yet reversible along with a well-choreographed set of events that take place during mammalian development.
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95
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Differences in DNA Methylation Patterns and Expression of the CCRK Gene in Human and Nonhuman Primate Cortices. Mol Biol Evol 2009; 26:1379-89. [DOI: 10.1093/molbev/msp046] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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96
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Oyer JA, Chu A, Brar S, Turker MS. Aberrant epigenetic silencing is triggered by a transient reduction in gene expression. PLoS One 2009; 4:e4832. [PMID: 19279688 PMCID: PMC2654015 DOI: 10.1371/journal.pone.0004832] [Citation(s) in RCA: 36] [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: 01/03/2009] [Accepted: 02/17/2009] [Indexed: 12/31/2022] Open
Abstract
Background Aberrant epigenetic silencing plays a major role in cancer formation by inactivating tumor suppressor genes. While the endpoints of aberrant silencing are known, i.e., promoter region DNA methylation and altered histone modifications, the triggers of silencing are not known. We used the tet-off system to test the hypothesis that a transient reduction in gene expression will sensitize a promoter to undergo epigenetic silencing. Methodology/Principal Findings The tet responsive promoter (PTRE) was used to drive expression of the selectable human HPRT cDNA in independent transfectants of an Hprt deficient mouse cell line. In this system, high basal HPRT expression is greatly reduced when doxycycline (Dox) is added to the culture medium. Exposure of the PTRE-HPRT transfectants to Dox induced HPRT deficient clones in a time dependent manner. A molecular analysis demonstrated promoter region DNA methylation, loss of histone modifications associated with expression (i.e., H3 lysine 9 and 14 acetylation and lysine 4 methylation), and acquisition of the repressive histone modification H3 lysine 9 methylation. These changes, which are consistent with aberrant epigenetic silencing, were not present in the Dox-treated cultures, with the exception of reduced H3 lysine 14 acetylation. Silenced alleles readily reactivated spontaneously or after treatment of cells with inhibitors of histone deacetylation and/or DNA methylation, but re-silencing of reactivated alleles did not require a new round of Dox exposure. Inhibition of histone deacetylation inhibited both the induction of silencing and re-silencing, whereas inhibition of DNA methylation had no such effect. Conclusions/Significance This study demonstrates that a transient reduction in gene expression triggers a pathway for aberrant silencing in mammalian cells and identifies histone deacetylation as a critical early step in this process. DNA methylation, in contrast, is a secondary step in the silencing pathway under study. A model to explain these observations is offered.
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Affiliation(s)
- Jon A. Oyer
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon, United States of America
| | - Adrian Chu
- Center for Research on Occupational and Environmental Toxicology (CROET), Oregon Health & Science University, Portland, Oregon, United States of America,
| | - Sukhmani Brar
- Center for Research on Occupational and Environmental Toxicology (CROET), Oregon Health & Science University, Portland, Oregon, United States of America,
| | - Mitchell S. Turker
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon, United States of America
- Center for Research on Occupational and Environmental Toxicology (CROET), Oregon Health & Science University, Portland, Oregon, United States of America,
- * E-mail:
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97
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Seniski GG, Camargo AA, Ierardi DF, Ramos EAS, Grochoski M, Ribeiro ESF, Cavalli IJ, Pedrosa FO, de Souza EM, Zanata SM, Costa FF, Klassen G. ADAM33 gene silencing by promoter hypermethylation as a molecular marker in breast invasive lobular carcinoma. BMC Cancer 2009; 9:80. [PMID: 19267929 PMCID: PMC2660367 DOI: 10.1186/1471-2407-9-80] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2008] [Accepted: 03/06/2009] [Indexed: 01/05/2023] Open
Abstract
Background ADAM33 protein is a member of the family of transmembrane glycoproteins composed of multidomains. ADAM family members have different activities, such as proteolysis and adhesion, making them good candidates to mediate the extracellular matrix remodelling and changes in cellular adhesion that characterise certain pathologies and cancer development. It was reported that one family member, ADAM23, is down-regulated by promoter hypermethylation. This seems to correlate with tumour progression and metastasis in breast cancer. In this study, we explored the involvement of ADAM33, another ADAM family member, in breast cancer. Methods First, we analysed ADAM33 expression in breast tumour cell lines by RT-PCR and western blotting. We also used 5-aza-2'-deoxycytidine (5azadCR) treatment and DNA bisulphite sequencing to study the promoter methylation of ADAM33 in breast tumour cell lines. We evaluated ADAM33 methylation in primary tumour samples by methylation specific PCR (MSP). Finally, ADAM33 promoter hypermethylation was correlated with clinicopathological data using the chi-square test and Fisher's exact test. Results The expression analysis of ADAM33 in breast tumour cell lines by RT-PCR revealed gene silencing in 65% of tumour cell lines. The corresponding lack of ADAM33 protein was confirmed by western blotting. We also used 5-aza-2'-deoxycytidine (5-aza-dCR) demethylation and bisulphite sequencing methodologies to confirm that gene silencing is due to ADAM33 promoter hypermethylation. Using MSP, we detected ADAM33 promoter hypermethylation in 40% of primary breast tumour samples. The correlation between methylation pattern and patient's clinicopathological data was not significantly associated with histological grade; tumour stage (TNM); tumour size; ER, PR or ERBB2 status; lymph node status; metastasis or recurrence. Methylation frequency in invasive lobular carcinoma (ILC) was 76.2% compared with 25.5% in invasive ductal carcinoma (IDC), and this difference was statistically significant (p = 0.0002). Conclusion ADAM33 gene silencing may be related to the discohesive histological appearance of ILCs. We suggest that ADAM33 promoter methylation may be a useful molecular marker for differentiating ILC and IDC.
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Affiliation(s)
- Gerusa G Seniski
- Department of Basic Pathology, Federal University of Parana, PR, Brazil.
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98
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Everhard S, Tost J, El Abdalaoui H, Crinière E, Busato F, Marie Y, Gut IG, Sanson M, Mokhtari K, Laigle-Donadey F, Hoang-Xuan K, Delattre JY, Thillet J. Identification of regions correlating MGMT promoter methylation and gene expression in glioblastomas. Neuro Oncol 2009; 11:348-56. [PMID: 19224763 DOI: 10.1215/15228517-2009-001] [Citation(s) in RCA: 130] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The O(6)-methylguanine-DNA methyltransferase gene (MGMT) is methylated in several cancers, including gliomas. However, the functional role of cysteine-phosphate-guanine (CpG) island (CGI) methylation in MGMT silencing is still controversial. The aim of this study was to investigate whether MGMT CGI methylation correlates inversely with RNA expression of MGMT in glioblastomas and to determine the CpG region whose methylation best reflects the level of expression. The methylation level of CpG sites that are potentially related to expression was investigated in 54 glioblastomas by pyrosequencing, a highly quantitative method, and analyzed with respect to their MGMT mRNA expression status. Three groups of patients were identified according to the methylation pattern of all 52 analyzed CpG sites. Overall, an 85% rate of concordance was observed between methylation and expression (p < 0.0001). When analyzing each CpG separately, six CpG sites were highly correlated with expression (p < 0.0001), and two CpG regions could be used as surrogate markers for RNA expression in 81.5% of the patients. This study indicates that there is good statistical agreement between MGMT methylation and expression, and that some CpG regions better reflect MGMT expression than do others. However, if transcriptional repression is the key mechanism in explaining the higher chemosensitivity of MGMT-methylated tumors, a substantial rate of discordance should lead clinicians to be cautious when deciding on a therapeutic strategy based on MGMT methylation status alone.
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Affiliation(s)
- Sibille Everhard
- INSERM, U711, Batiment de la nouvelle Pharmacie, 47 Bd de l'Hôpital, 75651 Paris Cedex 13, France.
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99
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Jung YC, Hong SJ, Kim YH, Kim SJ, Kang SJ, Choi SW, Rhyu MG. Chromosomal losses are associated with hypomethylation of the gene-control regions in the stomach with a low number of active genes. J Korean Med Sci 2008; 23:1068-89. [PMID: 19119454 PMCID: PMC2612760 DOI: 10.3346/jkms.2008.23.6.1068] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2007] [Accepted: 04/01/2008] [Indexed: 11/20/2022] Open
Abstract
Transitional-CpG methylation between unmethylated promoters and nearby methylated retroelements plays a role in the establishment of tissue-specific transcription. This study examined whether chromosomal losses reducing the active genes in cancers can change transitional-CpG methylation and the transcription activity in a cancer-type-dependent manner. The transitional-CpG sites at the CpG-island margins of nine genes and the non-island-CpG sites round the transcription start sites of six genes lacking CpG islands were examined by methylation-specific polymerase chain reaction (PCR) analysis. The number of active genes in normal and cancerous tissues of the stomach, colon, breast, and nasopharynx were analyzed using the public data in silico. The CpG-island margins and non-island CpG sites tended to be hypermethylated and hypomethylated in all cancer types, respectively. The CpG-island margins were hypermethylated and a low number of genes were active in the normal stomach compared with other normal tissues. In gastric cancers, the CpG-island margins and non-island-CpG sites were hypomethylated in association with high-level chromosomal losses, and the number of active genes increased. Colon, breast, and nasopharyngeal cancers showed no significant association between the chromosomal losses and methylation changes. These findings suggest that chromosomal losses in gastric cancers are associated with the hypomethylation of the gene-control regions and the increased number of active genes.
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Affiliation(s)
- Yu-Chae Jung
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Seung-Jin Hong
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Young-Ho Kim
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sung-Ja Kim
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Seok-Jin Kang
- Department of Clinical Pathology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Sang-Wook Choi
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Mun-Gan Rhyu
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
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100
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Aberrant methylation of the Adenomatous Polyposis Coli (APC) gene promoter is associated with the inflammatory breast cancer phenotype. Br J Cancer 2008; 99:1735-42. [PMID: 18841156 PMCID: PMC2584952 DOI: 10.1038/sj.bjc.6604705] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Aberrant methylation of the adenomatous polyposis coli (APC) gene promoter occurs in about 40% of breast tumours and has been correlated with reduced APC protein levels. To what extent epigenetic alterations of the APC gene may differ according to specific breast cancer phenotypes, remains to be elucidated. Our aim was to explore the role of APC methylation in the inflammatory breast cancer (IBC) phenotype. The status of APC gene promoter hypermethylation was investigated in DNA from normal breast tissues, IBC and non-IBC by both conventional and real-time quantitative methylation-specific PCR (MSP). APC methylation levels were compared with APC mRNA and protein levels. Hypermethylation of the APC gene promoter was present in 71% of IBC samples (n=21) and 43% of non-IBC samples (n=30) by conventional MSP (P=0.047). The APC gene also showed an increased frequency of high methylation levels in IBC (in 74% of cases, n=19) vs non-IBC (in 46% of cases, n=35) using a qMSP assay (P=0.048). We observed no significant association between APC methylation levels by qMSP and APC mRNA or protein expression levels. In conclusion, for the first time, we report the association of aberrant methylation of the APC gene promoter with the IBC phenotype, which might be of biological and clinical importance.
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