101
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Nagarajan RP, Costello JF. Epigenetic mechanisms in glioblastoma multiforme. Semin Cancer Biol 2009; 19:188-97. [PMID: 19429483 DOI: 10.1016/j.semcancer.2009.02.005] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2008] [Accepted: 02/11/2009] [Indexed: 11/26/2022]
Abstract
Glioblastoma multiforme (GBM) is an aggressive and lethal cancer, accounting for the majority of primary brain tumors in adults. GBMs are characterized by genetic alterations large and small, affecting genes that control cell growth, apoptosis, angiogenesis, and invasion. Epigenetic alterations also affect the expression of cancer genes alone, or in combination with genetic mechanisms. For example, in each GBM, hundreds of genes are subject to DNA hypermethylation at their CpG island promoters. A subset of GBMs is also characterized by locus-specific and genome-wide decrease in DNA methylation, or DNA hypomethylation. Other epigenetic alterations, such as changes in the position of histone variants and changes in histone modifications are also likely important in the molecular pathology of GBM, but somewhat surprisingly there are very limited data about these in GBM. Alterations in histone modifications are especially important to understand, given that histone deacetylases are targets for drugs that are in clinical trial for GBMs. The technological wave of next-generation sequencing will accelerate GBM epigenome profiling, allowing the direct integration of DNA methylation, histone modification and gene expression profiles. Ultimately, genomic and epigenomic data should provide new predictive markers of response and lead to more effective therapies for GBM.
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Affiliation(s)
- Raman P Nagarajan
- Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94143, USA
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102
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Huang J. Current progress in epigenetic research for hepatocarcinomagenesis. ACTA ACUST UNITED AC 2009; 52:31-42. [PMID: 19152082 DOI: 10.1007/s11427-009-0014-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2008] [Accepted: 10/08/2008] [Indexed: 12/19/2022]
Abstract
Hepatocellular carcinoma is the main type of primary liver cancer, and also one of the most malignant tumors. At present, the pathogenesis mechanisms of liver cancer are not entirely clear. It has been shown that inactivation of tumor suppressor genes and activation of oncogenes play a significant role in carcinogenesis, caused by the genetic and epigenetic aberrance. In the past, people generally thought that genetic mutation is a key event of tumor pathogenesis, and somatic mutation of tumor suppressor genes is in particular closely associated with oncogenesis. With deeper understanding of tumors in recent years, increasing evidence has shown that epigenetic silencing of those genes, as a result of aberrant hypermethylation of CpG islands in promoters and histone modification, is essential to carcinogenesis and metastasis. The term epigenetics refers to heritable changes in gene expression caused by regulation mechanisms, other than changes in the underlying DNA sequence. Specific epigenetic processes include DNA methylation, genome imprinting, chromotin remodeling, histone modification and microRNA regulations. This paper reviews recent epigenetics research progress in the hepatocellular carcinoma study, and tries to depict the relationships between hepatocellular carcinomagenesis and DNA methylation as well as microRNA regulation.
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Affiliation(s)
- Jian Huang
- National Human Genome Research Center at Shanghai-Ministry of Science and Technology to build a healthy and disease Genomics Laboratory, Shanghai, 201203, China.
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103
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Fan H, Cheng J, Zhao ZJ. Inhibition of de novo Methyltransferase 3B is a Potential Therapy for Hepatocellular Carcinoma. Gastroenterology Res 2008; 1:33-39. [PMID: 27994704 PMCID: PMC5154213 DOI: 10.4021/gr2008.10.1240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2008] [Accepted: 11/06/2008] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Aberrant epigenetic patterns, including inactivation of tumor suppressor genes due to DNA methylation, have been described in many human cancers. Epigenetic therapeutic is a new and rapidly developing area of tumor treatment because DNA methyltransferase (DNMT) inhibitors can reverse its changes. We attempted to identify potential approach for epigenetic therapy of hepatocellular carcinoma. METHODS We knocked down the expression of DNMT 1 or DNMT 3B by siRNA, and inhibited DNA methyltranferases by 5-Aza-2'-deoxycytidine. We used high-density oligonucleotide gene expression microarrays to examine the induced genes in human hepatocellular carcinoma cell line SMMC-7721 after suppressing DNA methyltranferases. The 5' ends of up-regulated genes were analyzed by BLAST database to determine whether they have promoter CpG islands, and then the identical induced genes were compared among different inhibition of DNA methyltranferases. RESULTS Our results show that 9 genes were found to be over expressed by more than two-fold induced by DNMT1 siRNA and 5-Aza-CdR, and 30 genes were found to be over expressed by more than two-fold induced by DNMT3B siRNA and 5-Aza-CdR in SMMC-7721. Among them, 76.6% up-regulated genes conjectural contained 5' CpG islands. The DNMT3B siRNA could induce more genes identical to demethylation agent in SMMC-7721. CONCLUSIONS DNMT3B might be a new potential target for therapy of hepatocellular carcinoma.
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Affiliation(s)
- Hong Fan
- Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Southeast University; Department of Genetics and Development, Southeast University Medical School. 87 Dingjiaqiao, Nanjing 210009, Jiangsu Province, China
| | - Jian Cheng
- Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Southeast University; Department of Genetics and Development, Southeast University Medical School. 87 Dingjiaqiao, Nanjing 210009, Jiangsu Province, China
| | - Zhu Jiang Zhao
- Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Southeast University; Department of Genetics and Development, Southeast University Medical School. 87 Dingjiaqiao, Nanjing 210009, Jiangsu Province, China
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104
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Abstract
Alterations of DNA methylation can account for the histological heterogeneity, reflected in the stepwise progression and complex biological characteristics of human cancers, that genetic alterations alone cannot explain. Analysis of DNA methylation status in tissue samples can be an aid to understanding the molecular mechanisms of multistage carcinogenesis. Human cancer cells show a drastic change in DNA methylation status, that is, overall DNA hypomethylation and regional DNA hypermethylation, which results in chromosomal instability and silencing of tumor-suppressor genes. Overexpression of DNA methyltransferase (DNMT) 1 is not a secondary result of increased cell proliferative activity but may underline the CpG island methylator phenotype of cancers. Splicing alteration of DNMT3B may result in chromosomal instability through DNA hypomethylation of pericentromeric satellite regions. Alterations of DNA methylation are observed even in the precancerous stage frequently associated with chronic inflammation and/or persistent viral infection or with cigarette smoking. Precancerous conditions showing alterations of DNA methylation may generate more malignant cancers. Aberrant DNA methylation is significantly associated with aggressiveness of cancers and poorer outcome of cancer patients. Genome-wide analysis of DNA methylation status based on array-based technology may identify DNA methylation profiles that can be used as appropriate indicators for carcinogenetic risk estimation and prognostication.
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Affiliation(s)
- Yae Kanai
- Pathology Division, National Cancer Center Research Institute, Tokyo, Japan.
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105
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Wang SH, Liu NH, Wang J, Bai H, Mao L. Critical role of deltaDNMT3B4/2 in regulating RASSF1A promoter-specific DNA methylation in non-small cell lung cancer. Chin Med J (Engl) 2008; 121:1712-1721. [PMID: 19024105 DOI: 10.1097/00029330-200809010-00024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND DeltaDNMT3B (a new DNMT3B subfamily) expression is initiated through a novel promoter. We identified at least 7 transcription variants of deltaDNMT3B as a result of alternative pre-mRNA processing. The aim of this study was to detect the expression pattern of deltaDNMT3B variants in non-small cell lung cancer (NSCLC) and to explore the role of deltaDNMT3B variants in regulating the promoter-specific DNA methylation. METHODS Specific polymerase chain reaction (PCR) primer sets were designed to distinguish individual deltaDNMT3B variants according to their splicing patterns. The expressions of seven deltaDNMT3B variants were measured in 13 cell lines, 109 NSCLC patients, and the corresponding normal lung tissues using reverse transcription-PCR (RT-PCR). The status of the p16 and RASSF1A promoter methylations in the tumors was detected using a methylation specific PCR (MSP). The relationships of the expression patterns of the deltaDNMT3B variants were analyzed by observing the status of p16 and RASSF1A promoter methylations in the tumors. The siRNA and the anti-sense oligo-dioxynucleotide specifically targeting the junction of exon 5 and 7 of deltaDNMT3B were designed and transfected by lipofectmane 2000 into H1299 and H358 cell lines. RASSF1A promoter methylation from cells treated by siRNA-deltaDNMT3B4/2 was detected using MSP and Bisulfite sequencing, and Western blotting was used to detect the protein expression of DNMT3B and ADNMT3B. Cell growth and cell cycle distribution were measured by applying real-time cell growth analysis and flowcytometry, respectively. RESULTS ADNMT3B variants, not DNMT3B, were the predominant transcripts in both NSCLC cell lines and primary tumors. The expression of deltaDNMT3B4 strongly correlated to the promoter methylation status of RASSF1A in a primary NSCLC. The knockdown of deltaDNMT3B4/2 by RNA-interference or anti-sense approaches resulted in a complete demethylation of RASSF1A promoter with the reactivation of a RASSF1A gene expression in less than 12 hours, but no effect resulted from the p16(INK4a) promoter in the NSCLC cell lines. CONCLUSIONS These results demonstrate an important role of deltaDNMT3B4/2 in the maintenance of promoter-specific DNA methylation in a cell type specific manner and provide a novel cell model for the study of the regulation of replication-independent DNA methylation.
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Affiliation(s)
- Shu-Hang Wang
- Department of Thoracic Medical Oncology, Peking University School of Oncology, Beijing Cancer Hospital, Beijing Institute for Cancer Research, Beijing 100036, China
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106
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Gowher H, Stuhlmann H, Felsenfeld G. Vezf1 regulates genomic DNA methylation through its effects on expression of DNA methyltransferase Dnmt3b. Genes Dev 2008; 22:2075-84. [PMID: 18676812 PMCID: PMC2492749 DOI: 10.1101/gad.1658408] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2008] [Accepted: 06/03/2008] [Indexed: 01/08/2023]
Abstract
The zinc finger protein vascular endothelial zinc finger 1 (Vezf1) has been implicated in the development of the blood vascular and lymphatic system in mice, and has been characterized as a transcriptional activator in some systems. The chicken homolog, BGP1, has binding sites in the beta-globin locus, including the upstream insulator element. We report that in a mouse embryonic stem cell line deletion of both copies of Vezf1 results in loss of DNA methylation at widespread sites in the genome, including Line1 elements and minor satellite repeats, some imprinted genes, and several CpG islands. Loss of methylation appears to arise from a substantial decrease in the abundance of the de novo DNA methyltransferase, Dnmt3b. These results suggest that naturally occurring mutations in Vezf1/BGP1 might have widespread effects on DNA methylation patterns and therefore on epigenetic regulation of gene expression.
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Affiliation(s)
- Humaira Gowher
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Heidi Stuhlmann
- Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, New York 10021, USA
| | - Gary Felsenfeld
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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107
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Fan H, Zhang F, Hu J, Liu D, Zhao Z. Promoter polymorphisms of DNMT3B and the risk of colorectal cancer in Chinese: a case-control study. J Exp Clin Cancer Res 2008; 27:24. [PMID: 18662374 PMCID: PMC2515831 DOI: 10.1186/1756-9966-27-24] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Accepted: 07/28/2008] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA-methyltransferase-3B (DNMT3B), which plays a role in DNA methylation, is usually aberrant expression involved in carcinogenesis. Polymorphisms of the DNMT3B gene may influence DNMT3B activity on DNA methylation in several cancers, thereby modulating the susceptibility to cancer. METHODS DNMT3B -579G>T genotypes and -149C>T were determined by PCR-RFLP and sequencing in 137 colorectal cancer patients and 308 controls matched for age and sex, who did not receive radiotherapy or chemotherapy for newly diagnosed and histopathologically confirmed colorectal cancer. The association between two SNPs of the DNMT3B promoter and the risk of the development of colorectal cancer was analyzed in a population of Chinese. RESULTS The allele frequency of -149C >T among patients and controls was 0.73% versus 0.65%, respectively. The allele frequency of -597G>T for patients and controls was 6.57% versus 11.53%, respectively. Individuals with at least one -149C>T allele were no at a significantly increase risk of colorectal cancer compared with those having a -149TT genotype. However, Individuals with at least one 579G>T allele were decreased risk of colorectal cancer compared with those having a -579TT genotype. CONCLUSION The relative distribution of -149C>T DNMT3B SNPs among a Chinese population can not be used as a stratification marker to predict an individual's susceptibility to colorectal cancer. However, the DNMT3B -579G>T polymorphism may contribute to the genetic susceptibility to colorectal cancer.
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Affiliation(s)
- Hong Fan
- Key Laboratory of Developmental genes and Human diseases, Ministry of Education, Southeast University, 210009, Nanjing, PR China
- Department of Genetics & Developmental Biology, The School of Basic Medical Sciences, Southeast University, 210009, Nanjing, PR China
| | - Feng Zhang
- Key Laboratory of Developmental genes and Human diseases, Ministry of Education, Southeast University, 210009, Nanjing, PR China
| | - Jiabo Hu
- School of Medicine, Jiangsu University, 212001, Zhenjiang, PR China
| | - Dongsheng Liu
- Key Laboratory of Developmental genes and Human diseases, Ministry of Education, Southeast University, 210009, Nanjing, PR China
| | - Zhujiang Zhao
- Key Laboratory of Developmental genes and Human diseases, Ministry of Education, Southeast University, 210009, Nanjing, PR China
- Department of Genetics & Developmental Biology, The School of Basic Medical Sciences, Southeast University, 210009, Nanjing, PR China
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108
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Duursma AM, Kedde M, Schrier M, le Sage C, Agami R. miR-148 targets human DNMT3b protein coding region. RNA (NEW YORK, N.Y.) 2008; 14:872-7. [PMID: 18367714 PMCID: PMC2327368 DOI: 10.1261/rna.972008] [Citation(s) in RCA: 433] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2007] [Accepted: 02/06/2008] [Indexed: 05/24/2023]
Abstract
MicroRNAs (miRNAs) are small noncoding RNA molecules of 20-24 nucleotides that regulate gene expression. In animals, miRNAs form imperfect interactions with sequences in the 3' Untranslated region (3'UTR) of mRNAs, causing translational inhibition and mRNA decay. In contrast, plant miRNAs mostly associate with protein coding regions. Here we show that human miR-148 represses DNA methyltransferase 3b (Dnmt3b) gene expression through a region in its coding sequence. This region is evolutionary conserved and present in the Dnmt3b splice variants Dnmt3b1, Dnmt3b2, and Dnmt3b4, but not in the abundantly expressed Dnmt3b3. Whereas overexpression of miR-148 results in decreased DNMT3b1 expression, short-hairpin RNA-mediated miR-148 repression leads to an increase in DNMT3b1 expression. Interestingly, mutating the putative miR-148 target site in Dnmt3b1 abolishes regulation by miR-148. Moreover, endogenous Dnmt3b3 mRNA, which lacks the putative miR-148 target site, is resistant to miR-148-mediated regulation. Thus, our results demonstrate that the coding sequence of Dnmt3b mediates regulation by the miR-148 family. More generally, we provide evidence that coding regions of human genes can be targeted by miRNAs, and that such a mechanism might play a role in determining the relative abundance of different splice variants.
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Affiliation(s)
- Anja M Duursma
- Division of Tumor Biology, The Netherlands Cancer Institute, 1066 CX Amsterdam, The Netherlands
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109
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Fan H, Liu DS, Zhang SH, Hu JB, Zhang F, Zhao ZJ. DNMT3B 579 G>T promoter polymorphism and risk of esophagus carcinoma in Chinese. World J Gastroenterol 2008; 14:2230-4. [PMID: 18407600 PMCID: PMC2703851 DOI: 10.3748/wjg.14.2230] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Revised: 02/04/2008] [Indexed: 02/06/2023] Open
Abstract
AIM To investigate the relationship between 579 G>T polymorphisms in the DNMT3B gene, which is involved in de novo methylation and associated with the risk of esophagus cancer (EC) in Chinese. METHODS DNMT3B 579 G>T genotypes were determined by PCR-RFLP in 194 EC patients and 210 healthy controls matched for age and sex, who did not receive radiotherapy or chemotherapy for newly diagnosed and histopathologically confirmed EC. RESULTS In control subjects, the frequency of T/T and G/T genotypes, and T and G alleles was 81.4%, 18.1%, 90.05% and 9.55%, respectively. The distribution of genotypes and allelotypes in the EC patients was not significantly different from that in the controls. When stratified by sex and age, there was still no significant association between the risks of EC and GT and GG genotypes. This study also showed a distinct difference in the distribution of DNMT3B and single nucleotide polymorphism (SNP) between Chinese and Koreans. CONCLUSION DNMT3B 579 G>T polymorphism may not be a stratification marker to predict the susceptibility to EC, at least in Chinese. DNMT3B promoter SNP is diverse in ethnic populations.
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110
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Abstract
As for many other tumors, development of hepatocellular carcinoma (HCC) must be understood as a multistep process with accumulation of genetic and epigenetic alterations in regulatory genes, leading to activation of oncogenes and inactivation or loss of tumor suppressor genes (TSG). In the last decades, in addition to genetic alterations, epigenetic inactivation of (tumor suppressor) genes by promoter hypermethylation has been recognized as an important and alternative mechanism in tumorigenesis. In HCC, aberrant methylation of promoter sequences occurs not only in advanced tumors, it has been also observed in premalignant conditions just as chronic viral hepatitis B or C and cirrhotic liver. This review discusses the epigenetic alterations in hepatocellular carcinoma focusing DNA methylation.
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111
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Klinck R, Bramard A, Inkel L, Dufresne-Martin G, Gervais-Bird J, Madden R, Paquet ER, Koh C, Venables JP, Prinos P, Jilaveanu-Pelmus M, Wellinger R, Rancourt C, Chabot B, Abou Elela S. Multiple alternative splicing markers for ovarian cancer. Cancer Res 2008; 68:657-63. [PMID: 18245464 DOI: 10.1158/0008-5472.can-07-2580] [Citation(s) in RCA: 126] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Intense efforts are currently being directed toward profiling gene expression in the hope of developing better cancer markers and identifying potential drug targets. Here, we present a sensitive new approach for the identification of cancer signatures based on direct high-throughput reverse transcription-PCR validation of alternative splicing events. This layered and integrated system for splicing annotation (LISA) fills a gap between high-throughput microarray studies and high-sensitivity individual gene investigations, and was created to monitor the splicing of 600 cancer-associated genes in 25 normal and 21 serous ovarian cancer tissues. Out of >4,700 alternative splicing events screened, the LISA identified 48 events that were significantly associated with serous ovarian tumor tissues. In a further screen directed at 39 ovarian tissues containing cancer pathologies of various origins, our ovarian cancer splicing signature successfully distinguished all normal tissues from cancer. High-volume identification of cancer-associated splice forms by the LISA paves the way for the use of alternative splicing profiling to diagnose subtypes of cancer.
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Affiliation(s)
- Roscoe Klinck
- Laboratoire de génomique fonctionnelle de l'Université de Sherbrooke, Université de Sherbrooke, Sherbrooke, Québec, Canada
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112
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Wang J, Bhutani M, Pathak AK, Lang W, Ren H, Jelinek J, He R, Shen L, Issa JP, Mao L. Delta DNMT3B variants regulate DNA methylation in a promoter-specific manner. Cancer Res 2007; 67:10647-52. [PMID: 18006804 DOI: 10.1158/0008-5472.can-07-1337] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
DNA methyltransferase 3B (DNMT3B) is critical in de novo DNA methylation during development and tumorigenesis. We recently reported the identification of a DNMT3B subfamily, DeltaDNMT3B, which contains at least seven variants, resulting from alternative pre-mRNA splicing. DeltaDNMT3Bs are the predominant expression forms of DNMT3B in human lung cancer. A strong correlation was observed between the promoter methylation of RASSF1A gene but not p16 gene (both frequently inactivated by promoter methylation in lung cancer) and expression of DeltaDNMT3B4 in primary lung cancer, suggesting a role of DeltaDNMT3B in regulating promoter-specific methylation of common tumor suppressor genes in tumorigenesis. In this report, we provide first experimental evidence showing a direct involvement of DeltaDNMT3B4 in regulating RASSF1A promoter methylation in human lung cancer cells. Knockdown of DeltaDNMT3B4 expression by small interfering RNA resulted in a rapid demethylation of RASSF1A promoter and reexpression of RASSF1A mRNA but had no effect on p16 promoter in the lung cancer cells. Conversely, normal bronchial epithelial cells with stably transfected DeltaDNMT3B4 gained an increased DNA methylation in RASSF1A promoter but not p16 promoter. We conclude that promoter DNA methylation can be differentially regulated and DeltaDNMT3Bs are involved in regulation of such promoter-specific de novo DNA methylation.
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Affiliation(s)
- Jie Wang
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030, USA
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113
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Calvisi DF, Ladu S, Gorden A, Farina M, Lee JS, Conner EA, Schroeder I, Factor VM, Thorgeirsson SS. Mechanistic and prognostic significance of aberrant methylation in the molecular pathogenesis of human hepatocellular carcinoma. J Clin Invest 2007. [PMID: 17717605 DOI: 10.1172/jci31457ds1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the fifth most common cancer worldwide, accounting for an estimated 600,000 deaths annually. Aberrant methylation, consisting of DNA hypomethylation and/or promoter gene CpG hypermethylation, is implicated in the development of a variety of solid tumors, including HCC. We analyzed the global levels of DNA methylation as well as the methylation status of 105 putative tumor suppressor genes and found that the extent of genome-wide hypomethylation and CpG hypermethylation correlates with biological features and clinical outcome of HCC patients. We identified activation of Ras and downstream Ras effectors (ERK, AKT, and RAL) due to epigenetic silencing of inhibitors of the Ras pathway in all HCC. Further, selective inactivation of SPRY1 and -2, DAB2, and SOCS4 and -5 genes and inhibitors of angiogenesis (BNIP3, BNIP3L, IGFBP3, and EGLN2) was associated with poor prognosis. Importantly, several epigenetically silenced putative tumor suppressor genes found in HCC were also inactivated in the nontumorous liver. Our results assign both therapeutic and chemopreventive significance to methylation patterns in human HCC and open the possibility of using molecular targets, including those identified in this study, to effectively inhibit HCC development and progression.
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Affiliation(s)
- Diego F Calvisi
- Laboratory of Experimental Carcinogenesis, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892-4262, USA
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114
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Calvisi DF, Ladu S, Gorden A, Farina M, Lee JS, Conner EA, Schroeder I, Factor VM, Thorgeirsson SS. Mechanistic and prognostic significance of aberrant methylation in the molecular pathogenesis of human hepatocellular carcinoma. J Clin Invest 2007; 117:2713-22. [PMID: 17717605 PMCID: PMC1950459 DOI: 10.1172/jci31457] [Citation(s) in RCA: 305] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2007] [Accepted: 06/12/2007] [Indexed: 12/13/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the fifth most common cancer worldwide, accounting for an estimated 600,000 deaths annually. Aberrant methylation, consisting of DNA hypomethylation and/or promoter gene CpG hypermethylation, is implicated in the development of a variety of solid tumors, including HCC. We analyzed the global levels of DNA methylation as well as the methylation status of 105 putative tumor suppressor genes and found that the extent of genome-wide hypomethylation and CpG hypermethylation correlates with biological features and clinical outcome of HCC patients. We identified activation of Ras and downstream Ras effectors (ERK, AKT, and RAL) due to epigenetic silencing of inhibitors of the Ras pathway in all HCC. Further, selective inactivation of SPRY1 and -2, DAB2, and SOCS4 and -5 genes and inhibitors of angiogenesis (BNIP3, BNIP3L, IGFBP3, and EGLN2) was associated with poor prognosis. Importantly, several epigenetically silenced putative tumor suppressor genes found in HCC were also inactivated in the nontumorous liver. Our results assign both therapeutic and chemopreventive significance to methylation patterns in human HCC and open the possibility of using molecular targets, including those identified in this study, to effectively inhibit HCC development and progression.
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Affiliation(s)
- Diego F. Calvisi
- Laboratory of Experimental Carcinogenesis, Center for Cancer
Research, National Cancer Institute, NIH, Bethesda, Maryland, USA.
Department of Biomedical Sciences, Division of Experimental
Pathology and Oncology, University of Sassari, Sassari, Italy
| | - Sara Ladu
- Laboratory of Experimental Carcinogenesis, Center for Cancer
Research, National Cancer Institute, NIH, Bethesda, Maryland, USA.
Department of Biomedical Sciences, Division of Experimental
Pathology and Oncology, University of Sassari, Sassari, Italy
| | - Alexis Gorden
- Laboratory of Experimental Carcinogenesis, Center for Cancer
Research, National Cancer Institute, NIH, Bethesda, Maryland, USA.
Department of Biomedical Sciences, Division of Experimental
Pathology and Oncology, University of Sassari, Sassari, Italy
| | - Miriam Farina
- Laboratory of Experimental Carcinogenesis, Center for Cancer
Research, National Cancer Institute, NIH, Bethesda, Maryland, USA.
Department of Biomedical Sciences, Division of Experimental
Pathology and Oncology, University of Sassari, Sassari, Italy
| | - Ju-Seog Lee
- Laboratory of Experimental Carcinogenesis, Center for Cancer
Research, National Cancer Institute, NIH, Bethesda, Maryland, USA.
Department of Biomedical Sciences, Division of Experimental
Pathology and Oncology, University of Sassari, Sassari, Italy
| | - Elizabeth A. Conner
- Laboratory of Experimental Carcinogenesis, Center for Cancer
Research, National Cancer Institute, NIH, Bethesda, Maryland, USA.
Department of Biomedical Sciences, Division of Experimental
Pathology and Oncology, University of Sassari, Sassari, Italy
| | - Insa Schroeder
- Laboratory of Experimental Carcinogenesis, Center for Cancer
Research, National Cancer Institute, NIH, Bethesda, Maryland, USA.
Department of Biomedical Sciences, Division of Experimental
Pathology and Oncology, University of Sassari, Sassari, Italy
| | - Valentina M. Factor
- Laboratory of Experimental Carcinogenesis, Center for Cancer
Research, National Cancer Institute, NIH, Bethesda, Maryland, USA.
Department of Biomedical Sciences, Division of Experimental
Pathology and Oncology, University of Sassari, Sassari, Italy
| | - Snorri S. Thorgeirsson
- Laboratory of Experimental Carcinogenesis, Center for Cancer
Research, National Cancer Institute, NIH, Bethesda, Maryland, USA.
Department of Biomedical Sciences, Division of Experimental
Pathology and Oncology, University of Sassari, Sassari, Italy
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115
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Benbrahim-Tallaa L, Waterland RA, Dill AL, Webber MM, Waalkes MP. Tumor suppressor gene inactivation during cadmium-induced malignant transformation of human prostate cells correlates with overexpression of de novo DNA methyltransferase. ENVIRONMENTAL HEALTH PERSPECTIVES 2007; 115:1454-9. [PMID: 17938735 PMCID: PMC2022656 DOI: 10.1289/ehp.10207] [Citation(s) in RCA: 140] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Accepted: 07/19/2007] [Indexed: 05/18/2023]
Abstract
BACKGROUND Aberrant DNA methylation is common in carcinogenesis. The typical pattern appears to involve reduced expression of maintenance DNA methyltransferase, DNMT1, inducing genomic hypomethylation, whereas increased expression of de novo DNMT3a or 3b causes gene-specific hypermethylation. OBJECTIVES During cadmium-induced malignant transformation, an unusual pattern of genomic hypermethylation occurred that we studied to provide insight into the roles of specific DNMTs in oncogenesis. METHODS Gene expression and DNA methylation were assessed in control and chronic cadmium-transformed prostate epithelial cells (CTPE) using reverse transcription-polymerase chain reaction (RT-PCR), Western blot analysis, methylation-specific PCR, and methyl acceptance assay. RESULTS During the 10-weeks of cadmium exposure that induced malignant transformation, progressive increases in generalized DNMT enzymatic activity occurred that were associated with over-expression of DNMT3b without changes in DNMT1 expression. Increased DNMT3b expression preceded increased DNMT enzymatic activity. Procainamide, a specific DNMT1 inhibitor, reversed cadmium-induced genomic DNA hypermethylation. Reduced expression of the tumor suppressor genes, RASSF1A and p16, began about the time DNMT3b overexpression first occurred and progressively decreased thereafter. RASSF1A and p16 promoter regions were heavily methylated in CTPE cells, indicating silencing by hypermethylation, while the DNA demethylating agent, 5-aza-2'-deoxycytidine, reversed this silencing. DNMT1 inhibition only modestly increased RASSF1A and p16 expression in CTPE cells and did not completely reverse silencing. CONCLUSIONS These data indicate that DNMT3b overexpression can result in generalized DNA hypermethylation and gene silencing but that DNMT1 is required to maintain these effects. The pattern of genomic DNA hypermethylation together with up-regulation of DNMT3b may provide a unique set of biomarkers to specifically identify cadmium-induced human prostate cancers.
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Affiliation(s)
- Lamia Benbrahim-Tallaa
- Inorganic Carcinogenesis Section, Laboratory of Comparative Carcinogenesis, National Cancer Institute at the National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Robert A. Waterland
- Departments of Pediatrics and Molecular and Human Genetics, Baylor College of Medicine, Children’s Nutrition Research Center, Houston, Texas, USA
| | - Anna L. Dill
- Inorganic Carcinogenesis Section, Laboratory of Comparative Carcinogenesis, National Cancer Institute at the National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - Mukta M. Webber
- Department of Medicine and Department of Zoology, Michigan State University, East Lansing, Michigan, USA
| | - Michael P. Waalkes
- Inorganic Carcinogenesis Section, Laboratory of Comparative Carcinogenesis, National Cancer Institute at the National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
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116
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Ostler KR, Davis EM, Payne SL, Gosalia BB, Expósito-Céspedes J, Le Beau MM, Godley LA. Cancer cells express aberrant DNMT3B transcripts encoding truncated proteins. Oncogene 2007; 26:5553-63. [PMID: 17353906 PMCID: PMC2435620 DOI: 10.1038/sj.onc.1210351] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2006] [Revised: 01/17/2007] [Accepted: 01/17/2007] [Indexed: 12/21/2022]
Abstract
Cancer cells display an altered distribution of DNA methylation relative to normal cells. Certain tumor suppressor gene promoters are hypermethylated and transcriptionally inactivated, whereas repetitive DNA is hypomethylated and transcriptionally active. Little is understood about how the abnormal DNA methylation patterns of cancer cells are established and maintained. Here, we identify over 20 DNMT3B transcripts from many cancer cell lines and primary acute leukemia cells that contain aberrant splicing at the 5' end of the gene, encoding truncated proteins lacking the C-terminal catalytic domain. Many of these aberrant transcripts retain intron sequences. Although the aberrant transcripts represent a minority of the DNMT3B transcripts present, Western blot analysis demonstrates truncated DNMT3B isoforms in the nuclear protein extracts of cancer cells. To test if expression of a truncated DNMT3B protein could alter the DNA methylation patterns within cells, we expressed DNMT3B7, the most frequently expressed aberrant transcript, in 293 cells. DNMT3B7-expressing 293 cells have altered gene expression as identified by microarray analysis. Some of these changes in gene expression correlate with altered DNA methylation of corresponding CpG islands. These results suggest that truncated DNMT3B proteins could play a role in the abnormal distribution of DNA methylation found in cancer cells.
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Affiliation(s)
- KR Ostler
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA and
| | - EM Davis
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA and
| | - SL Payne
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA and
| | - BB Gosalia
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA and
| | - J Expósito-Céspedes
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA and
| | - MM Le Beau
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA and
- University of Chicago Cancer Research Center, University of Chicago, Chicago, IL, USA
| | - LA Godley
- Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL, USA and
- University of Chicago Cancer Research Center, University of Chicago, Chicago, IL, USA
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117
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Fanelli M, Caprodossi S, Ricci-Vitiani L, Porcellini A, Tomassoni-Ardori F, Amatori S, Andreoni F, Magnani M, De Maria R, Santoni A, Minucci S, Pelicci PG. Loss of pericentromeric DNA methylation pattern in human glioblastoma is associated with altered DNA methyltransferases expression and involves the stem cell compartment. Oncogene 2007; 27:358-65. [PMID: 17653095 DOI: 10.1038/sj.onc.1210642] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Cancer is generally characterized by loss of CG dinucleotides methylation resulting in a global hypomethylation and the consequent genomic instability. The major contribution to the general decreased methylation levels seems to be due to demethylation of heterochromatin repetitive DNA sequences. In human immunodeficiency, centromeric instability and facial anomalies syndrome, demethylation of pericentromeric satellite 2 DNA sequences has been correlated to functional mutations of the de novo DNA methyltransferase 3b (DNMT3b), but the mechanism responsible for the hypomethylated status in tumors is poorly known. Here, we report that human glioblastoma is affected by strong hypomethylation of satellite 2 pericentromeric sequences that involves the stem cell compartment. Concomitantly with the integrity of the DNMTs coding sequences, we report aberrations in DNA methyltrasferases expression showing upregulation of the DNA methyltransferase 1 (DNMT1) and downregulation of the de novo DNA methyltransferase 3a (DNMT3a). Moreover, we show that DNMT3a is the major de novo methyltransferase expressed in normal neural progenitor cells (NPCs) and its forced re-expression is sufficient to partially recover the methylation levels of satellite 2 repeats in glioblastoma cell lines. Thus, we speculate that DNMT3a decreased expression may be involved in the early post-natal inheritance of an epigenetically altered NPC population that could be responsible for glioblastoma development later in adult life.
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Affiliation(s)
- M Fanelli
- Centre of Biotechnology, University of Urbino, Fano, Italy.
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118
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Pogribny IP, Tryndyak VP, Woods CG, Witt SE, Rusyn I. Epigenetic effects of the continuous exposure to peroxisome proliferator WY-14,643 in mouse liver are dependent upon peroxisome proliferator activated receptor alpha. Mutat Res 2007; 625:62-71. [PMID: 17586532 PMCID: PMC2111058 DOI: 10.1016/j.mrfmmm.2007.05.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2007] [Revised: 05/08/2007] [Accepted: 05/10/2007] [Indexed: 01/17/2023]
Abstract
Peroxisome proliferators are potent rodent liver carcinogens that act via a non-genotoxic mechanism. The mode of action of these agents in rodent liver includes increased cell proliferation, decreased apoptosis, secondary oxidative stress and other events; however, it is not well understood how peroxisome proliferators are triggering the plethora of the molecular signals leading to cancer. Epigenetic changes have been implicated in the mechanism of liver carcinogenesis by a number of environmental agents. Short-term treatment with peroxisome proliferators and other non-genotoxic carcinogens leads to global and locus-specific DNA hypomethylation in mouse liver, events that were suggested to correlate with a burst of cell proliferation. In the current study, we investigated the effects of long-term exposure to a model peroxisome proliferator WY-14,643 on DNA and histone methylation. Male SV129mice were fed a control or WY-14,643-containing (1000ppm) diet for one week, five weeks or five months. Treatment with WY-14,643 led to progressive global hypomethylation of liver DNA as determined by an HpaII-based cytosine extension assay with the maximum effect reaching over 200% at five months. Likewise, trimethylation of histone H4 lysine 20 and H3 lysine 9 was significantly decreased at all time points. The majority of cytosine methylation in mammals resides in repetitive DNA sequences. In view of this, we measured the effect of WY-14,643 on the methylation status of major and minor satellites, as well as in IAP, LINE1 and LINE2 elements in liver DNA. Exposure to WY-14,643 resulted in a gradual loss of cytosine methylation in major and minor satellites, IAP, LINE1 and LINE2 elements. The epigenetic changes correlated with the temporal effects of WY-14,643 on cell proliferation rates in liver, but no sustained effect on c-Myc promoter methylation was observed. Finally, WY-14,643 had no effect on DNA and histone methylation status in Pparalpha-null mice at any of the time points considered in this study. These data indicate the importance of epigenetic alterations in the mechanism of action of peroxisome proliferators and the key role of Pparalpha.
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Affiliation(s)
- Igor P. Pogribny
- Division of Biochemical Toxicology, National Center for Toxicological Research, Jefferson, AR 72079, USA
| | - Volodymyr P. Tryndyak
- Division of Biochemical Toxicology, National Center for Toxicological Research, Jefferson, AR 72079, USA
| | - Courtney G. Woods
- Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Sarah E. Witt
- Division of Biochemical Toxicology, National Center for Toxicological Research, Jefferson, AR 72079, USA
| | - Ivan Rusyn
- Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, NC 27599, USA
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119
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Moss TJ, Wallrath LL. Connections between epigenetic gene silencing and human disease. Mutat Res 2007; 618:163-74. [PMID: 17306846 PMCID: PMC1892579 DOI: 10.1016/j.mrfmmm.2006.05.038] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2006] [Accepted: 05/25/2006] [Indexed: 04/15/2023]
Abstract
Alterations in epigenetic gene regulation are associated with human disease. Here, we discuss connections between DNA methylation and histone methylation, providing examples in which defects in these processes are linked with disease. Mutations in genes encoding DNA methyltransferases and proteins that bind methylated cytosine residues cause changes in gene expression and alterations in the patterns of DNA methylation. These changes are associated with cancer and congenital diseases due to defects in imprinting. Gene expression is also controlled through histone methylation. Altered levels of methyltransferases that modify lysine 27 of histone H3 (K27H3) and lysine 9 of histone H3 (K9H3) correlate with changes in Rb signaling and disruption of the cell cycle in cancer cells. The K27H3 mark recruits a Polycomb complex involved in regulating stem cell pluripotency, silencing of developmentally regulated genes, and controlling cancer progression. The K9H3 methyl mark recruits HP1, a structural protein that plays a role in heterochromatin formation, gene silencing, and viral latency. Cells exhibiting altered levels of HP1 are predicted to show a loss of silencing at genes regulating cancer progression. Gene silencing through K27H3 and K9H3 can involve histone deacetylation and DNA methylation, suggesting cross talk between epigenetic silencing systems through direct interactions among the various players. The reversible nature of these epigenetic modifications offers therapeutic possibilities for a wide spectrum of disease.
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Affiliation(s)
- Timothy J Moss
- Department of Biochemistry, 3136 MERF, University of Iowa, Iowa City, IA 52242, USA
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120
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Kubarek Ł, Jagodzinski PP. Epigenetic up-regulation of CXCR4 and CXCL12 expression by 17 beta-estradiol and tamoxifen is associated with formation of DNA methyltransferase 3B4 splice variant in Ishikawa endometrial adenocarcinoma cells. FEBS Lett 2007; 581:1441-8. [PMID: 17362937 DOI: 10.1016/j.febslet.2007.02.070] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2006] [Accepted: 02/28/2007] [Indexed: 01/30/2023]
Abstract
Increased risk for the development of endometrial cancer has been associated with unopposed oestrogen exposure, hyperoestrogenic factors, and a history of breast cancer treated long-term with tamoxifen (Tam). Stromal cell-derived factor-1, currently named as CXCL12, is a chemokine that, via binding to CXCR4 receptor, activates several downstream effectors and signalling pathways responsible for proliferation, survival, and migration of cancer cells. We observed that 17beta-estradiol (E2) and tamoxifen (Tam) increase the expression of CXCR4 and CXCL12 transcripts and proteins in oestrogen receptor positive (ER(+)) but not in negative (ER(-)02) Ishikawa endometrial adenocarcinoma (ISH) cell lines. However, the demethylating agent 5-Aza-2'-deoxycytidine profoundly elevated CXCR4 and CXCL12 expression in both ER(+) and ER(-)02 ISH cells. Bisulfite sequencing revealed that E2 and Tam up-regulate expression via demethylation of cytosine in the cytosine-guanosine dinucleotide island of CXCR4 and CXCL12 promoters. We also found that E2 and Tam significantly increased, for several hours, the expression of DNA methyltransferase 3B4 enzymatically inactive splice variant in ER(+) but not in ER(-)02 ISH cells. Our results suggest that E2 and Tam, through their ability for gene-transcription regulation, change the cellular milieu that maintains the hypermethylated stage of CpG islands of CXCR4 and CXCL12 promoters.
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Affiliation(s)
- Ł Kubarek
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Sciences, 6 Swiecickiego St., 60-781 Pozań, Poland
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121
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Tang SH, Yang DH, Huang W, Zhou HK, Lu XH, Ye G. Hypomethylated P4 promoter induces expression of the insulin-like growth factor-II gene in hepatocellular carcinoma in a Chinese population. Clin Cancer Res 2007; 12:4171-7. [PMID: 16857788 DOI: 10.1158/1078-0432.ccr-05-2261] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE The expression of human insulin-like growth factor-II (IGF-II) is regulated by the activation of four promoters (P1-P4) acting in a development-dependent, tissue-specific manner. IGF-II overexpression associated with P3 and P4 activation is observed in animal and human hepatocarcinogenesis. We correlated P4 epigenetic alteration with P4 transcript activation and clinicopathologic features. EXPERIMENTAL DESIGN We analyzed P4 epigenetic alteration using methylation-specific PCR in 34 hepatocellular carcinoma (HCC) specimens, 34 matched adjacent nontumor specimens, and 8 normal adult liver specimens. The data were correlated with activation of P4 transcription by using reverse transcription-PCR. Epigenetic alteration was compared with patients' clinicopathologic features. RESULTS Compared with normal liver tissue, hypomethylation of P4 CpG islands was significantly more frequent in HCC (P = 0.03) and matched tissues (P = 0.047). P4 mRNA levels in HCC with unmethylated alleles were significantly higher than in HCC without unmethylated alleles (P = 0.001); P4 mRNA levels in matched nontumor tissues with unmethylated alleles were significantly higher than in matched nontumor tissues without unmethylated alleles (P = 0.005). P4 hypomethylation in HCC was associated with portal vein tumor embolus (P = 0.017) and poorer tumor differentiation (P = 0.025). CONCLUSIONS These findings suggest that IGF-II P4 hypomethylation may be an early and frequent event and that it may contribute to P4 transcription expression activation during the transformation of a premalignant liver lesion to HCC. Furthermore, aberrant hypomethylation of P4 CpG islands not only may play an important role during hepatocarcinogenesis but might also be a useful biomarker for poor prognosis of patients with HCC.
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Affiliation(s)
- Shao Hui Tang
- Department of Gastroenterology, First Affiliated Hospital of Jinan University, Guangzhou, China
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122
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Sawada M, Kanai Y, Arai E, Ushijima S, Ojima H, Hirohashi S. Increased expression of DNA methyltransferase 1 (DNMT1) protein in uterine cervix squamous cell carcinoma and its precursor lesion. Cancer Lett 2006; 251:211-9. [PMID: 17196739 DOI: 10.1016/j.canlet.2006.11.023] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2006] [Revised: 11/17/2006] [Accepted: 11/21/2006] [Indexed: 12/31/2022]
Abstract
Aberrant DNA methylation has been shown to play important roles during multistage carcinogenesis in various human organs. The aim of this study was to evaluate the significance of DNA methyltransferase 1 (DNMT1) protein expression during cervical carcinogenesis. We carried out an immunohistochemical examination for DNMT1 in 34 samples of histologically normal squamous epithelium, 36 samples of low-grade cervical intraepithelial neoplasia (CIN), 61 samples of higher-grade CIN and 30 samples of squamous cell carcinoma of the uterine cervix. The DNMT1 protein expression score, reflecting the intensity and incidence of DNMT1 nuclear immunoreactivity, was increased even in low-grade CIN (P<0.0001) in comparison with histologically normal squamous epithelium and was further increased in higher-grade CIN (P<0.0001 compared to low-grade CIN). The DNMT1 protein expression score remained at a plateau in microinvasive carcinoma (Stage IA, P=0.0690 compared to higher-grade CIN) and then decreased with cancer invasion (Stage IB or more, P=0.0176 compared to Stage IA), whereas the proliferating cell nuclear antigen (PCNA) labeling index did not decrease with cancer invasion (P=0.8259 between Stage IA and Stage IB or more). Thus, the DNMT1 protein expression score and the PCNA labeling index were not mutually correlated in squamous cell carcinoma of the uterine cervix (P=0.2304). These data suggest that progressively increasing expression of DNMT1 protein is not entirely a secondary result of increased cell proliferative activity, but is associated with an early step of multistage cervical carcinogenesis.
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Affiliation(s)
- Morio Sawada
- Pathology Division, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
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123
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Jenkins RB, Blair H, Ballman KV, Giannini C, Arusell RM, Law M, Flynn H, Passe S, Felten S, Brown PD, Shaw EG, Buckner JC. A t(1;19)(q10;p10) mediates the combined deletions of 1p and 19q and predicts a better prognosis of patients with oligodendroglioma. Cancer Res 2006; 66:9852-61. [PMID: 17047046 DOI: 10.1158/0008-5472.can-06-1796] [Citation(s) in RCA: 500] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Combined deletion of chromosomes 1p and 19q is associated with improved prognosis and responsiveness to therapy in patients with anaplastic oligodendroglioma. The deletions usually involve whole chromosome arms, suggesting a t(1;19)(q10;p10). Using stem cell medium, we cultured a few tumors. Paraffin-embedded tissue was obtained from 21 Mayo Clinic patients and 98 patients enrolled in 2 North Central Cancer Treatment Group (NCCTG) low-grade glioma trials. Interphase fusion of CEP1 and 19p12 probes detected the t(1;19). 1p/19q deletions were evaluated by fluorescence in situ hybridization. Upon culture, one oligodendroglioma contained an unbalanced 45,XX,t(1;19)(q10;p10). CEP1/19p12 fusion was observed in all metaphases and 74% of interphase nuclei. Among Mayo Clinic oligodendrogliomas, the prevalence of fusion was 81%. Among NCCTG patients, CEP1/19p12 fusion prevalence was 55%, 47%, and 0% among the oligodendrogliomas, mixed oligoastrocytomas, and astrocytomas, respectively. Ninety-one percent of NCCTG gliomas with 1p/19q deletion and 12% without 1p/19q deletion had CEP1/19p12 fusion (P < 0.001, chi(2) test). The median overall survival (OS) for all patients was 8.1 years without fusion and 11.9 years with fusion (P = 0.003). The median OS for patients with low-grade oligodendroglioma was 9.1 years without fusion and 13.0 years with fusion (P = 0.01). Similar significant median OS differences were observed for patients with combined 1p/19q deletions. The absence of alterations was associated with a significantly shorter OS for patients who received higher doses of radiotherapy. Our results strongly suggest that a t(1;19)(q10;p10) mediates the combined 1p/19q deletion in human gliomas. Like combined 1p/19q deletion, the 1;19 translocation is associated with superior OS and progression-free survival in low-grade glioma patients.
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124
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Peyrin-Biroulet L, Barraud H, Darfeuil F, Lefebvre M, Bigard MA, Gueant JL, Bronowicki JP. Anomalies épigénétiques et carcinogenèse hépatique. ACTA ACUST UNITED AC 2006; 30:1354-9. [PMID: 17211332 DOI: 10.1016/s0399-8320(06)73554-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The molecular mechanisms involved in liver carcinogenesis are poorly understood. Over the past decade, epigenetic changes (DNA methylation) have received increasing attention for their potential involvement in the development of hepatocarcinoma. The DNA methylation level is influenced by environmental factors (folate and methionine diet), as well as by genetic factors (methylenetetrahydrofolate reductase/MTHFR polymorphisms). These findings provide new insight into the understanding of liver carcinogenesis. Interventional studies are now required to determine the role of folate supplementation in the development of liver tumors in targeted patients.
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Affiliation(s)
- Laurent Peyrin-Biroulet
- Service d'Hépato-Gastroentérologie et Laboratoire de Pathologie Cellulaire et Moléculaire en Nutrition-INSERM U724, CHU Nancy, Vandoeuvre-les-Nancy.
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125
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Wang J, Walsh G, Liu DD, Lee JJ, Mao L. Expression of Delta DNMT3B variants and its association with promoter methylation of p16 and RASSF1A in primary non-small cell lung cancer. Cancer Res 2006; 66:8361-6. [PMID: 16951144 DOI: 10.1158/0008-5472.can-06-2031] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Despite the role of DNMT3B in de novo DNA methylation, a correlation between DNMT3B expression and promoter DNA methylation has not being established in tumors. We recently reported DeltaDNMT3B, a subfamily of DNMT3B, with seven variants, as the predominant expression forms in non-small cell lung cancer (NSCLC). We hypothesized that expression of the DeltaDNMT3B variants plays a role in promoter methylation formation during lung tumorigenesis. Expression of seven DeltaDNMT3B variants was measured in 119 NSCLCs and the corresponding normal lungs using reverse transcription-PCR. The expression patterns of DeltaDNMT3B variants were analyzed with the status of p16 and RASSF1A promoter methylation in the tumors as well as in patients' clinical variables, including outcomes. Expression of DeltaDNMT3B variants was detected in 94 of 119 (80%) tumors but in only 22 (18%) of the corresponding normal lungs (P < 0.0001). DeltaDNMT3B1, DeltaDNMT3B2, and DeltaDNMT3B4 were the most frequently detected transcripts in the tumors (62%, 76%, and 46%, respectively). The expression of DeltaDNMT3B variants was associated with p16 and RASSF1A promoter methylation in the tumors, but the strongest association was between DeltaDNMT3B4 and RASSF1A. Forty-two of 46 (91%) tumors with RASSF1A promoter methylation expressed DeltaDNMT3B4 compared with only 13 of 73 (18%) tumors without the promoter methylation (P < 0.0001). Strong associations were also observed between expression of the variants in the tumors and in patients' clinical outcomes. Expression of DeltaDNMT3B variants is common in NSCLC and may play an important role in the development of promoter methylation.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Carcinoma, Non-Small-Cell Lung/enzymology
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/pathology
- DNA (Cytosine-5-)-Methyltransferases/genetics
- DNA Methylation
- DNA, Neoplasm/genetics
- DNA, Neoplasm/isolation & purification
- Genes, p16
- Genetic Variation
- Humans
- Lung Neoplasms/enzymology
- Lung Neoplasms/genetics
- Lung Neoplasms/pathology
- Middle Aged
- Neoplasm Staging
- Promoter Regions, Genetic
- RNA, Neoplasm/genetics
- RNA, Neoplasm/isolation & purification
- Reverse Transcriptase Polymerase Chain Reaction
- Tumor Suppressor Proteins/genetics
- DNA Methyltransferase 3B
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Affiliation(s)
- Jie Wang
- Molecular Biology Laboratory, Department of Thoracic/Head and Neck Medical Oncology, Department of Thoracic, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
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126
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Wilson AS, Power BE, Molloy PL. DNA hypomethylation and human diseases. Biochim Biophys Acta Rev Cancer 2006; 1775:138-62. [PMID: 17045745 DOI: 10.1016/j.bbcan.2006.08.007] [Citation(s) in RCA: 327] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2006] [Revised: 08/24/2006] [Accepted: 08/27/2006] [Indexed: 12/14/2022]
Abstract
Changes in human DNA methylation patterns are an important feature of cancer development and progression and a potential role in other conditions such as atherosclerosis and autoimmune diseases (e.g., multiple sclerosis and lupus) is being recognised. The cancer genome is frequently characterised by hypermethylation of specific genes concurrently with an overall decrease in the level of 5 methyl cytosine. This hypomethylation of the genome largely affects the intergenic and intronic regions of the DNA, particularly repeat sequences and transposable elements, and is believed to result in chromosomal instability and increased mutation events. This review examines our understanding of the patterns of cancer-associated hypomethylation, and how recent advances in understanding of chromatin biology may help elucidate the mechanisms underlying repeat sequence demethylation. It also considers how global demethylation of repeat sequences including transposable elements and the site-specific hypomethylation of certain genes might contribute to the deleterious effects that ultimately result in the initiation and progression of cancer and other diseases. The use of hypomethylation of interspersed repeat sequences and genes as potential biomarkers in the early detection of tumors and their prognostic use in monitoring disease progression are also examined.
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Affiliation(s)
- Ann S Wilson
- Preventative Health National Research Flagship, North Ryde, NSW, Australia
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127
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Simão TDA, Simões GLDBA, Ribeiro FS, Cidade DADP, Andreollo NA, Lopes LR, Macedo JMB, Acatauassu R, Teixeira AMR, Felzenszwalb I, Pinto LFR, Albano RM. Lower expression of p14ARF and p16INK4a correlates with higher DNMT3B expression in human oesophageal squamous cell carcinomas. Hum Exp Toxicol 2006; 25:515-22. [PMID: 17017004 DOI: 10.1191/0960327106het649oa] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Oesophageal squamous cell carcinoma (ESCC) is one of the most common malignancies and is the sixth cause of cancer-related death in the world. Inactivation of cell-cycle regulating genes, such as p14ARF and p16INK4a, and cell adhesion genes, such as E-cadherin, is common in cancer, and results from genetic and/or epigenetic alterations. Therefore, we have analysed the mRNA expression of p14ARF, p16INK4a and E-cadherin in 17 matched ESCC and normal mucosal samples obtained from Brazilian patients by semi-quantitative RT-PCR. The expression of p14ARF and p16INK4a was absent or reduced in several ESCC samples. Hypermethylation of CpG islands, caused by the action of DNA methyltransferases (DNMTs), is a major form of epigenetic inactivation of the p14ARF and p16INK4a genes in tumours. Hence, we also investigated the mRNA expression of the human DNA methyltransferases in normal oesophageal mucosa and in the tumour matched samples. All DNMTs were constitutively expressed in the normal oesophageal mucosa but a significantly higher expression of DNMT3B was observed in the tumours. Data analysis by the Spearman rank test showed that the expression of DNMT3B was inversely correlated with that of p14ARF and p16INK4a. Our results suggest that DNMT3B over-expression may be involved in the suppression or lower expression of p14ARF and p16INK4a observed in ESCC.
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Affiliation(s)
- Tatiana de Almeida Simão
- Departamento de Bioquímica, IBRAG, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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128
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Ehrlich M. Cancer-linked DNA hypomethylation and its relationship to hypermethylation. Curr Top Microbiol Immunol 2006; 310:251-74. [PMID: 16909914 DOI: 10.1007/3-540-31181-5_12] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
It is not surprising that cancer, a kind of derangement of development, hijacks DNA methylation, which is necessary for normal mammalian embryogenesis. Both decreases and increases in DNA methylation are a frequent characteristic of a wide variety of cancers. There is often more hypomethylation than hypermethylation of DNA during carcinogenesis, leading to a net decrease in the genomic 5-methylcytosine content. Although the exact methylation changes between different cancers of the same type are not the same, there are cancer type-specific differences in the frequency of hypermethylation or hypomethylation of certain genomic sequences. These opposite types of DNA methylation changes appear to be mostly independent of one another, although they may arise because of a similar abnormality leading to long-lasting epigenetic instability in cancers. Both tandem and interspersed DNA repeats often exhibit cancer-associated hypomethylation. However, one of these repeated sequences (NBL2) displayed predominant increases in methylation in some ovarian carcinomas and Wilms tumors and decreases in others. Furthermore, decreases and increases in CpG methylation can be interspersed within a small subregion of the 1.4-kb repeat unit of these tandem arrays. While the transcription-silencing role of DNA hypermethylation at promoters of many tumor-suppressor genes is clear, the biological effects of cancer-linked hypomethylation of genomic DNA are less well understood. Evidence suggests that DNA hypomethylation functions in direct or indirect control of transcription and in destabilizing chromosomal integrity. Recent studies of cancer-linked DNA hypomethylation indicate that changes to DNA methylation during tumorigenesis and tumor progression have a previously underestimated plasticity and dynamic nature.
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Affiliation(s)
- M Ehrlich
- Human Genetics Program, Department of Biochemistry, and Tulane Cancer Center, Tulane Medical School, New Orleans, LA 70112, USA.
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129
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La Salle S, Trasler JM. Dynamic expression of DNMT3a and DNMT3b isoforms during male germ cell development in the mouse. Dev Biol 2006; 296:71-82. [PMID: 16725135 DOI: 10.1016/j.ydbio.2006.04.436] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2005] [Revised: 02/27/2006] [Accepted: 04/04/2006] [Indexed: 11/28/2022]
Abstract
In the male germ line, sequence-specific methylation patterns are initially acquired prenatally in diploid gonocytes and are further consolidated after birth during spermatogenesis. It is still unclear how DNA methyltransferases are involved in establishing and/or maintaining these patterns in germ cells, or how their activity is regulated. We compared the temporal expression patterns of the postulated de novo DNA methyltransferases DNMT3a and DNMT3b in murine male germ cells. Mitotic, meiotic and post-meiotic male germ cells were isolated, and expression of various transcript variants and isoforms of Dnmt3a and Dnmt3b was examined using Quantitative RT-PCR and Western blotting. We found that proliferating and differentiating male germ cells were marked by distinctive expression profiles. Dnmt3a2 and Dnmt3b transcripts were at their highest levels in type A spermatogonia, decreased dramatically in type B spermatogonia and preleptotene spermatocytes and rose again in leptotene/zygotene spermatocytes, while Dnmt3a expression was mostly constant, except in type B spermatogonia where it increased. In all cases, expression declined as pachynema progressed. At the protein level, DNMT3a was the predominant isoform in type B spermatogonia, while DNMT3a2, DNMT3b2, and DNMT3b3 were expressed throughout most of spermatogenesis, except in pachytene spermatocytes. We also detected DNMT3a2 and DNMT3b2 in round spermatids. Taken together, these data highlight the tightly regulated expression of these genes during spermatogenesis and provide evidence that DNMTs may be contributing differentially to the establishment and/or maintenance of methylation patterns in male germ cells.
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Affiliation(s)
- Sophie La Salle
- Department of Pharmacology and Therapeutics, and Montreal Children's Hospital Research Institute, McGill University, Montreal, QC, Canada H3H 1P3
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130
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Ehrlich M, Woods CB, Yu MC, Dubeau L, Yang F, Campan M, Weisenberger DJ, Long T, Youn B, Fiala ES, Laird PW. Quantitative analysis of associations between DNA hypermethylation, hypomethylation, and DNMT RNA levels in ovarian tumors. Oncogene 2006; 25:2636-45. [PMID: 16532039 PMCID: PMC1449872 DOI: 10.1038/sj.onc.1209145] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
How hypermethylation and hypomethylation of different parts of the genome in cancer are related to each other and to DNA methyltransferase (DNMT) gene expression is ill defined. We used ovarian epithelial tumors of different malignant potential to look for associations between 5'-gene region or promoter hypermethylation, satellite, or global DNA hypomethylation, and RNA levels for ten DNMT isoforms. In the quantitative MethyLight assay, six of the 55 examined gene loci (LTB4R, MTHFR, CDH13, PGR, CDH1, and IGSF4) were significantly hypermethylated relative to the degree of malignancy (after adjustment for multiple comparisons; P < 0.001). Importantly, hypermethylation of these genes was associated with degree of malignancy independently of the association of satellite or global DNA hypomethylation with degree of malignancy. Cancer-related increases in methylation of only two studied genes, LTB4R and MTHFR, which were appreciably methylated even in control tissues, were associated with DNMT1 RNA levels. Cancer-linked satellite DNA hypomethylation was independent of RNA levels for all DNMT3B isoforms, despite the ICF syndrome-linked DNMT3B deficiency causing juxtacentromeric satellite DNA hypomethylation. Our results suggest that there is not a simple association of gene hypermethylation in cancer with altered DNMT RNA levels, and that this hypermethylation is neither the result nor the cause of satellite and global DNA hypomethylation.
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MESH Headings
- Adenocarcinoma, Mucinous/genetics
- Adenocarcinoma, Mucinous/pathology
- Adolescent
- Adult
- Aged
- Carcinoma, Endometrioid/genetics
- Carcinoma, Endometrioid/pathology
- Cystadenoma, Serous/genetics
- Cystadenoma, Serous/pathology
- DNA (Cytosine-5-)-Methyltransferase 1
- DNA (Cytosine-5-)-Methyltransferases/genetics
- DNA Methylation
- DNA Methyltransferase 3A
- DNA, Neoplasm
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Middle Aged
- Neoplasm Proteins/genetics
- Ovarian Neoplasms/genetics
- Ovarian Neoplasms/pathology
- RNA, Neoplasm/genetics
- RNA, Neoplasm/metabolism
- Tumor Suppressor Proteins
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Affiliation(s)
- M Ehrlich
- Tulane Cancer Center, Department of Biochemistry, and Human Genetics Program, Tulane Medical School, New Orleans, LA 70112, USA.
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131
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Ghoshal K, Li X, Datta J, Bai S, Pogribny I, Pogribny M, Huang Y, Young D, Jacob ST. A folate- and methyl-deficient diet alters the expression of DNA methyltransferases and methyl CpG binding proteins involved in epigenetic gene silencing in livers of F344 rats. J Nutr 2006; 136:1522-7. [PMID: 16702315 PMCID: PMC2237890 DOI: 10.1093/jn/136.6.1522] [Citation(s) in RCA: 144] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Aberrations in methylation profile of the genome occur in human cancers induced by folate deficiency. To elucidate the underlying mechanism, male F344 rats were fed a diet deficient in l-methionine and devoid of folic acid and choline (FMD diet), which is known to induce hepatocellular carcinomas. We investigated changes in the DNA methylation machinery, namely, de novo DNA methyltransferases (Dnmt3a and 3b), maintenance DNA methyltransferase (Dnmt1), and methyl CpG binding proteins (MBDs), in rat livers during early stages of tumorigenesis. RT-PCR and Western blot analyses revealed differential expression of these proteins in the livers of rats fed the FMD diet. Although the hepatic Dnmt1 mRNA level declined with age (P < 0.001), it was elevated (P < 0.001) in deficient rats compared with controls. The changes in hepatic Dnmt1 protein level with the diet correlated with its mRNA levels (r = 0.60, P = 0.002). Similarly, the Dnmt3a mRNA level was elevated in rats fed the FMD diet (P < 0.001), whereas the Dnmt3b level (mRNA and protein) was not affected by diet or age. Compared with controls, hepatic MBD1-3 RNA levels increased (P < 0.001) and the protein levels of MBD1, 2, and 4 were elevated (P < 0.001) in the deficient rats. In both diet groups, hepatic MBD2 protein decreased (P < 0.001), whereas MeCP2 protein increased (P < 0.001) with age. These results demonstrate that a combined folate and methyl deficiency alters components of the DNA methylation machinery by both transcriptional and posttranscriptional mechanisms during early stages of hepatocarcinogenesis.
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Affiliation(s)
- Kalpana Ghoshal
- Department of Molecular and Cellular Biochemistry, Ohio State University, Columbus, OH 43210
- To whom correspondence should be addressed. E-mail: or
| | - Xin Li
- Department of Molecular and Cellular Biochemistry, Ohio State University, Columbus, OH 43210
| | - Jharna Datta
- Department of Molecular and Cellular Biochemistry, Ohio State University, Columbus, OH 43210
| | - Shoumei Bai
- Department of Molecular and Cellular Biochemistry, Ohio State University, Columbus, OH 43210
| | - Igor Pogribny
- Division of Biochemical Toxicology, Food and Drug Administration, National Center for Toxicological Research, Jefferson, AR 72079
| | - Marta Pogribny
- Division of Biochemical Toxicology, Food and Drug Administration, National Center for Toxicological Research, Jefferson, AR 72079
| | - Yan Huang
- Department of Molecular and Cellular Biochemistry, Ohio State University, Columbus, OH 43210
| | - Donn Young
- Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210
| | - Samson T. Jacob
- Department of Molecular and Cellular Biochemistry, Ohio State University, Columbus, OH 43210
- Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210
- Department of Internal Medicine, Ohio State University, Columbus, OH 43210
- To whom correspondence should be addressed. E-mail: or
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132
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Costa FF, Paixão VA, Cavalher FP, Ribeiro KB, Cunha IW, Rinck JA, O'Hare M, Mackay A, Soares FA, Brentani RR, Camargo AA. SATR-1 hypomethylation is a common and early event in breast cancer. ACTA ACUST UNITED AC 2006; 165:135-43. [PMID: 16527607 DOI: 10.1016/j.cancergencyto.2005.07.023] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2005] [Revised: 07/15/2005] [Accepted: 07/21/2005] [Indexed: 01/26/2023]
Abstract
Genome stability and normal gene expression are maintained by a fixed and predetermined DNA methylation pattern, which becomes abnormal in malignant cells. Hypomethylation of satellite DNA sequences is frequently found in tumors and has been associated with an increased frequency of DNA rearrangements and chromosome instability. In this work, we used methylation-sensitive arbitrarily primed polymerase chain reaction (MSAP-PCR) to identify differentially methylated DNA fragments in normal and tumor breast samples. We identified a novel differentially methylated fragment located on chromosome 5 with high similarity to a SATR-1 satellite sequence. This fragment was found to be hypomethylated in 63% of breast tumor cell lines and in 86% of breast tumors relative to normal breast tissue. We found that normal tissue adjacent to breast tumors displayed a variable decrease in methylation and that the decrease observed for most of these adjacent samples was higher than observed for normal breast tissue derived from reduction mammoplasty. The methylation decrease was, however, significantly higher in tumor samples than in adjacent tissue (chi2= 154, 1 df, P < 10(-4)), suggesting that SATR-1 hypomethylation frequently occurs in the early stages of tumor development. Our results highlight the importance of global DNA hypomethylation as a contributing factor in breast tumorigenesis.
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Affiliation(s)
- Fabrício F Costa
- Laboratory of Molecular Biology and Genomics, Ludwig Institute for Cancer Research, Rua Prof. Antonio Prudente, 109, 4th floor, 01509-010 São Paulo, SP Brazil
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133
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Lin H, Yamada Y, Nguyen S, Linhart H, Jackson-Grusby L, Meissner A, Meletis K, Lo G, Jaenisch R. Suppression of intestinal neoplasia by deletion of Dnmt3b. Mol Cell Biol 2006; 26:2976-83. [PMID: 16581773 PMCID: PMC1446955 DOI: 10.1128/mcb.26.8.2976-2983.2006] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2005] [Revised: 12/22/2005] [Accepted: 01/11/2006] [Indexed: 12/31/2022] Open
Abstract
Aberrant gene silencing accompanied by DNA methylation is associated with neoplastic progression in many tumors that also show global loss of DNA methylation. Using conditional inactivation of de novo methyltransferase Dnmt3b in Apc(Min/+) mice, we demonstrate that the loss of Dnmt3b has no impact on microadenoma formation, which is considered the earliest stage of intestinal tumor formation. Nevertheless, we observed a significant decrease in the formation of macroscopic colonic adenomas. Interestingly, many large adenomas showed regions with Dnmt3b inactivation, indicating that Dnmt3b is required for initial outgrowth of macroscopic adenomas but is not required for their maintenance. These results support a role for Dnmt3b in the transition stage between microadenoma formation and macroscopic colonic tumor growth and further suggest that Dnmt3b, and by extension de novo methylation, is not required for maintaining tumor growth after this transition stage has occurred.
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Affiliation(s)
- Haijiang Lin
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02141, USA
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134
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Abstract
The upper gastrointestinal (GI) cancers have various carcinogenic pathways and precursor lesions, such as dysplasia for esophageal squamous cell carcinoma, Barrett esophagus for esophageal adenocarcinoma, and intestinal metaplasia for the intestinal-type of gastric cancer. Recently, many epigenetic events in carcinogenic pathways have been revealed, along with genomic and genetic alterations. This information has provided deeper insight into an understanding of the mechanisms of upper GI carcinogenesis. Moreover, detection methods of aberrant methylation have been applied to clinical fields to stratify high-risk groups, detect early cancer, and to predict clinical outcomes. In this review, a variety of information is summarized regarding gene hypermethylation in esophageal and gastric cancer.
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Affiliation(s)
- Fumiaki Sato
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA.
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135
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DNA methylation and cancer-associated genetic instability. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2006; 570:363-92. [PMID: 18727508 DOI: 10.1007/1-4020-3764-3_13] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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136
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Chan GC, Fish JE, Mawji IA, Leung DD, Rachlis AC, Marsden PA. Epigenetic basis for the transcriptional hyporesponsiveness of the human inducible nitric oxide synthase gene in vascular endothelial cells. THE JOURNAL OF IMMUNOLOGY 2005; 175:3846-61. [PMID: 16148131 DOI: 10.4049/jimmunol.175.6.3846] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A marked difference exists in the inducibility of inducible NO synthase (iNOS) between humans and rodents. Although important cis and trans factors in the murine and human iNOS promoters have been characterized using episomal-based approaches, a compelling molecular explanation for why human iNOS is resistant to induction has not been reported. In this study we present evidence that the hyporesponsiveness of the human iNOS promoter is based in part on epigenetic silencing, specifically hypermethylation of CpG dinucleotides and histone H3 lysine 9 methylation. Using bisulfite sequencing, we demonstrated that the iNOS promoter was heavily methylated at CpG dinucleotides in a variety of primary human endothelial cells and vascular smooth muscle cells, all of which are notoriously resistant to iNOS induction. In contrast, in human cell types capable of iNOS induction (e.g., A549 pulmonary adenocarcinoma, DLD-1 colon adenocarcinoma, and primary hepatocytes), the iNOS promoter was relatively hypomethylated. Treatment of human cells, such as DLD-1, with a DNA methyltransferase inhibitor (5-azacytidine) induced global and iNOS promoter DNA hypomethylation. Importantly, 5-azacytidine enhanced the cytokine inducibility of iNOS. Using chromatin immunoprecipitation, we found that the human iNOS promoter was basally enriched with di- and trimethylation of H3 lysine 9 in endothelial cells, and this did not change with cytokine addition. This contrasted with the absence of lysine 9 methylation in inducible cell types. Importantly, chromatin immunoprecipitation demonstrated the selective presence of the methyl-CpG-binding transcriptional repressor MeCP2 at the iNOS promoter in endothelial cells. Collectively, our work defines a role for chromatin-based mechanisms in the control of human iNOS gene expression.
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MESH Headings
- Cell Line, Tumor
- Cells, Cultured
- Chromatin
- CpG Islands
- DNA Methylation
- Endothelial Cells/metabolism
- Endothelium, Vascular/cytology
- Endothelium, Vascular/metabolism
- Epigenesis, Genetic
- Gene Silencing
- Histones
- Humans
- Lysine
- Methyl-CpG-Binding Protein 2/analysis
- Methyl-CpG-Binding Protein 2/physiology
- Methylation
- Muscle, Smooth, Vascular/cytology
- Muscle, Smooth, Vascular/metabolism
- Promoter Regions, Genetic
- Species Specificity
- Transcription, Genetic
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Affiliation(s)
- Gary C Chan
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
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137
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Roman-Gomez J, Jimenez-Velasco A, Agirre X, Cervantes F, Sanchez J, Garate L, Barrios M, Castillejo JA, Navarro G, Colomer D, Prosper F, Heiniger A, Torres A. Promoter hypomethylation of the LINE-1 retrotransposable elements activates sense/antisense transcription and marks the progression of chronic myeloid leukemia. Oncogene 2005; 24:7213-23. [PMID: 16170379 DOI: 10.1038/sj.onc.1208866] [Citation(s) in RCA: 185] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2005] [Revised: 04/20/2005] [Accepted: 05/20/2005] [Indexed: 01/05/2023]
Abstract
Aberrant genome-wide hypomethylation is thought to be related to tumorigenesis by promoting genomic instability. Since DNA methylation is considered an important mechanism for the silencing of retroelements, hypomethylation in human tumors may lead to their reactivation. However, the role of DNA hypomethylation in chronic myeloid leukemia (CML) remains to be elucidated. In this study, the methylation status of the LINE-1 (L1) retrotransposon promoter was analysed in CML samples from the chronic-phase (CP, n=140) and the blast crisis (BC, n=47). L1 hypomethylation was significantly more frequent in BC (74.5%) than in CP (38%) (P<0.0001). Furthermore, L1 hypomethylation led to activation of both ORF1 sense transcription (P<0.0001) and c-MET gene antisense transcription (P<0.0001), and was significantly associated with high levels of BCR-ABL (P=0.02) and DNMT3b4 (P=0.001) transcripts. Interestingly, in CP-CML, extensive L1 hypomethylation was associated with poorer prognosis in terms of cytogenetic response to interferon (P=0.004) or imatinib (P=0.034) and progression-free survival (P=0.005). The above results strongly suggest that activation of both sense and antisense transcriptions by aberrant promoter hypomethylation of the L1 elements plays a role in the progression and clinical behavior of the CML.
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MESH Headings
- Adult
- Antineoplastic Agents/therapeutic use
- Benzamides
- Blast Crisis/genetics
- Blast Crisis/pathology
- CpG Islands
- DNA (Cytosine-5-)-Methyltransferases/metabolism
- DNA Methylation
- Disease Progression
- Female
- Humans
- Imatinib Mesylate
- Interferons/therapeutic use
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/mortality
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/therapy
- Leukemia, Myeloid, Chronic-Phase/genetics
- Leukemia, Myeloid, Chronic-Phase/pathology
- Leukemia, Myeloid, Chronic-Phase/therapy
- Long Interspersed Nucleotide Elements/genetics
- Male
- Middle Aged
- Multivariate Analysis
- Open Reading Frames
- Piperazines/therapeutic use
- Promoter Regions, Genetic
- Proto-Oncogene Proteins c-abl/metabolism
- Proto-Oncogene Proteins c-met/metabolism
- Pyrimidines/therapeutic use
- Regression Analysis
- Retroelements/genetics
- Transcription, Genetic/drug effects
- Treatment Outcome
- DNA Methyltransferase 3B
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Affiliation(s)
- Jose Roman-Gomez
- Hematology Department, Reina Sofia Hospital, Avda. Menendez Pidal s/n. 14004, Cordoba, Spain.
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138
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Schneider-Stock R, Roessner A, Ullrich O. Methyltransferases in apoptosis and cancer. ACTA ACUST UNITED AC 2005. [DOI: 10.1002/sita.200400047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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139
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Kloeckener-Gruissem B, Betts DR, Zankl A, Berger W, Güngör T. A new and a reclassified ICF patient without mutations in DNMT3B and its interacting proteins SUMO-1 and UBC9. Am J Med Genet A 2005; 136:31-7. [PMID: 15952214 DOI: 10.1002/ajmg.a.30767] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The ICF syndrome (immunodeficiency, centromeric instability, facial anomalies) (OMIM#242860) is a rare autosomal, recessively inherited disorder. Another rare condition, ischiadic hypoplasia, renal dysgenesis, immunodeficiency, and polydactyly (IHRDIP, OMIM#243340), displays features that resemble those of the ICF syndrome. Due to the overlapping symptoms in both syndromes, we asked whether a shared underlying molecular defect exists. Two patients, each with the clinical characteristics of one of these syndromes, were subjected to conventional cytogenetic analysis and the determination of the methylation state of satellite II DNA. We found that both displayed the two hallmark features of the ICF syndrome, namely hypomethylation and centromeric instability of chromosomes 1 and 16. Therefore, we reclassified the patient previously diagnosed with the IHRDIP syndrome as an ICF patient. Since the majority of ICF patients are carriers of mutations in the methytransferase gene DNMT3B, we determined the sequence of its coding, splice site, and putative promoter region and analyzed its transcripts in both patients, without detecting any alterations. Similarly, the coding region of two DNMT3B-interacting proteins, SUMO-1 and UBC9, did not reveal mutations. With this study, the published number of patients that lack mutations in DNMT3B coding region increases to almost 40% of all ICF patients reported. It is, therefore, implied that a significant subset of ICF patients will have a yet unknown, alternative alteration, which may include the involvement of DNMT3B-interacting factors or aberrations of an independent pathway.
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Affiliation(s)
- Barbara Kloeckener-Gruissem
- Division of Medical Molecular Genetics and Gene Diagnostics, Institute of Medical Genetics, University of Zurich, Switzerland.
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140
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Kim Y, Sills RC, Houle CD. Overview of the molecular biology of hepatocellular neoplasms and hepatoblastomas of the mouse liver. Toxicol Pathol 2005; 33:175-80. [PMID: 15805069 DOI: 10.1080/01926230590522130] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The molecular pathogenesis of chemically induced hepatocellular neoplasms and hepatoblastomas in the B6C3FI mouse is unclear but may involve alterations in the fi-catenin/Wnt signaling pathway as was recently described for human liver neoplasms. The objectives of this research were to characterize the mutation frequency and spectrum of P-catenin mutations and the intracellular localization of I-catenin protein accumulation in chemically induced hepatoblastomas and hepatocellular neoplasms. In the majority of the hepatoblastomas examined by immunohistochemical methods, both nuclear and cytoplasmic localization of P-catenin protein were detected, whereas in hepatocellular adenomas and carcinomas and normal liver only membrane staining was observed. Genomic DNA was isolated from paraffin sections of each liver tumor. P-catenin exon 2 (corresponds to exon 3 in humans) genetic alterations were identified in the majority of hepatoblastomas from exposed mice. Deletion mutations were identified more frequently than point mutations in hepatoblastomas. Hepatocellular adenomas and carcinomas from treated mice had mutations in exon 2 of the B-catenin gene which ranged from 32-43%, while 10% P-catenin mutations were detected in spontaneous neoplasms. By immunohistochemical methods cyclin Dl was observed in most nuclei of hepatoblastomas and strong expression of cyclin Dl was confirmed by Western analysis regardless of treatment. The cumulative data suggests that P-catenin mutations with upregulation of the B-catenin protein and Wnt signaling most likely increased cyclin Dl expression. Cyclin D1 may provide an advantage during tumor progression of hepatocellular neoplasms and hepatoblastomas. The review will also focus on other genes which are important in mouse and human liver tumors.
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MESH Headings
- Adenoma, Liver Cell/chemically induced
- Adenoma, Liver Cell/genetics
- Adenoma, Liver Cell/metabolism
- Animals
- Carcinoma, Hepatocellular/chemically induced
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/metabolism
- Cytoskeletal Proteins/metabolism
- Intercellular Signaling Peptides and Proteins/metabolism
- Liver Neoplasms/chemically induced
- Liver Neoplasms/genetics
- Liver Neoplasms/metabolism
- Liver Neoplasms, Experimental/chemically induced
- Liver Neoplasms, Experimental/genetics
- Liver Neoplasms, Experimental/metabolism
- Mice
- Mice, Inbred Strains
- Molecular Biology
- Mutation
- Trans-Activators/metabolism
- Wnt Proteins
- beta Catenin
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Affiliation(s)
- Yongbaek Kim
- Laboratory of Experimental Pathology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA
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141
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142
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Missiaglia E, Donadelli M, Palmieri M, Crnogorac-Jurcevic T, Scarpa A, Lemoine NR. Growth delay of human pancreatic cancer cells by methylase inhibitor 5-aza-2'-deoxycytidine treatment is associated with activation of the interferon signalling pathway. Oncogene 2005; 24:199-211. [PMID: 15637593 DOI: 10.1038/sj.onc.1208018] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Alteration of methylation status has been recognized as a possible epigenetic mechanism of selection during tumorigenesis in pancreatic cancer. This type of cancer is characterized by poor prognosis partly due to resistance to conventional drug treatments. We have used microarray technology to investigate the changes in global gene expression observed after treatment of different pancreatic cancer cell lines with the methylase inhibitor 5-aza-2'-deoxycytidine (5-aza-CdR). We have observed that this agent is able to inhibit to various degrees the growth of three pancreatic cancer cell lines. In particular, this inhibition was associated with induction of interferon (IFN)-related genes, as observed in other tumour types. Thus, expression of STAT1 seems to play a key role in the cellular response to treatment with the cytosine analogue. Moreover, we found increased p21(WAF1) and gadd45A expression to be associated with the efficacy of the treatment; this induction may correlate with activation of the IFN signalling pathway. Expression of the p16(INK) protein was also linked to the ability of cells to respond to 5-aza-CdR. Finally, genome-wide demethylation induced sensitization that significantly increased response to further treatment with various chemotherapy agents.
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Affiliation(s)
- Edoardo Missiaglia
- Cancer Research UK, Molecular Oncology Unit, Imperial College School of Medicine at Hammersmith Campus, London, UK
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143
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Jiang YL, Rigolet M, Bourc'his D, Nigon F, Bokesoy I, Fryns JP, Hultén M, Jonveaux P, Maraschio P, Mégarbané A, Moncla A, Viegas-Péquignot E. DNMT3B mutations and DNA methylation defect define two types of ICF syndrome. Hum Mutat 2005; 25:56-63. [PMID: 15580563 DOI: 10.1002/humu.20113] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
ICF syndrome is a rare autosomal recessive disease characterized by variable immunodeficiency, centromeric instability, and facial abnormalities. Mutations in the catalytic domain of DNMT3B, a gene encoding a de novo DNA methyltransferase, have been recognized in a subset of patients. ICF syndrome is a genetic disease directly related to a genomic methylation defect that mainly affects classical satellites 2 and 3, both components of constitutive heterochromatin. The variable incidence of DNMT3B mutations and the differential methylation defect of alpha satellites allow the identification of two types of patients, both showing an undermethylation of classical satellite DNA. This classification illustrates the specificity of the methylation process and raises questions about the genetic heterogeneity of the ICF syndrome.
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Affiliation(s)
- Y L Jiang
- E367 Inserm, Institut Jacques Monod, Paris, France
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144
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Abstract
Pre-mRNA splicing is a sophisticated and ubiquitous nuclear process, which is a natural source of cancer-causing errors in gene expression. Intronic splice site mutations of tumor suppressor genes often cause exon-skipping events that truncate proteins just like classical nonsense mutations. Also, many studies over the last 20 years have reported cancer-specific alternative splicing in the absence of genomic mutations. Affected proteins include transcription factors, cell signal transducers, and components of the extracellular matrix. Antibodies against alternatively spliced products on cancer cells are currently in clinical trials, and competitive reverse transcription-PCR across regions of alternative splicing is being used as a simple diagnostic test. As well as being associated with cancer, the nature of the alternative gene products is usually consistent with an active role in cancer; therefore, the alternative splicing process itself is a potential target for gene therapy.
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Affiliation(s)
- Julian P Venables
- University of Newcastle-upon-Tyne, Institute of Human Genetics, International Centre for Life, Central Parkway, Newcastle-upon-Tyne, United Kingdom.
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145
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Kanai Y, Saito Y, Ushijima S, Hirohashi S. Alterations in gene expression associated with the overexpression of a splice variant of DNA methyltransferase 3b, DNMT3b4, during human hepatocarcinogenesis. J Cancer Res Clin Oncol 2004; 130:636-44. [PMID: 15490234 DOI: 10.1007/s00432-004-0586-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2004] [Accepted: 04/23/2004] [Indexed: 02/06/2023]
Abstract
PURPOSE Overexpression of a splice variant of DNA methyltransferase 3b, DNMT3b4, correlates significantly with DNA hypomethylation in pericentromeric satellite regions, which is known to result in centromeric decondensation and enhanced chromosomal recombination in precancerous conditions and hepatocellular carcinomas (HCCs). We aimed to elucidate further the significance of DNMT3b4 during human hepatocarcinogenesis. METHODS DNMT3b4-transfected human epithelial 293 cells were characterized using growth rate measurements, gene expression microarray, and quantitative reverse transcription-polymerase chain reaction (RT-PCR) analyses. RT-PCR was also performed on eight normal liver specimens, 45 noncancerous liver specimens showing chronic hepatitis or cirrhosis, which are considered to be precancerous conditions, and 56 HCCs. RESULTS The growth rate of the DNMT3b4 transfectants was about double that of mock-transfectants. Induction of signal transducer and activator of transcription 1 (STAT1), an effector of interferon signaling, and of a set of downstream genes implicated in such signaling, was observed in the DNMT3b4 transfectants. There was significant correlation between the mRNA expression levels of DNMT3b4 and STAT1 in HCCs. mRNA expression levels of STAT1 and the three downstream genes examined were all significantly elevated in the chronic hepatitis and cirrhosis specimens compared with the normal liver specimens. Among the HCCs, the mRNA expression levels of STAT1 and the downstream genes were higher in tumors without portal vein involvement than in more malignant HCCs with portal vein involvement. Significant correlations between the mRNA expression levels of STAT1 and each of the downstream genes were observed in the tissue samples. CONCLUSIONS Overexpression of DNMT3b4 is involved in human hepatocarcinogenesis, even at the precancerous stages, not only by inducing chromosomal instability but also by affecting the expression of specific genes.
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Affiliation(s)
- Yae Kanai
- Pathology Division, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, 104-0045, Tokyo, Japan.
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146
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Murata H, Tsuji S, Tsujii M, Sakaguchi Y, Fu HY, Kawano S, Hori M. Promoter hypermethylation silences cyclooxygenase-2 (Cox-2) and regulates growth of human hepatocellular carcinoma cells. J Transl Med 2004; 84:1050-9. [PMID: 15156159 DOI: 10.1038/labinvest.3700118] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Cyclooxygenase-2 (COX-2) upregulation is recognized to confer advantage in progression in a wide variety of cancers, with colorectal cancer most intensively investigated. Epidemiologically, chemopreventive effects of COX-2 inhibitors have been proven on numerous cancers, but not on hepatocellular carcinoma (HCC). Although the antiapoptotic feature of COX-2 generally supports cancer cell growth, previous reports have shown that COX-2 expression, upregulated in early HCC, is downregulated in advanced HCC. Therefore, COX-2 downregulation may be somehow advantageous and specific for HCC development. However, its mechanism remains unclear. Since promoter hypermethylation often silences the gene expression, we hypothesized that the epigenetic mechanism might regulate COX-2 expression in HCC. We examined the methylation status of the Cox-2 promoter in six human HCC cell lines (Hep3B, HepG2, SK-Hep1, HuH7, PLC, and FLC-7 cells) using methylation-specific PCR. The promoter was remarkably hypermethylated in Hep3B and FLC-7 cells and moderately in HepG2 and SK-Hep1 cells, but not in HuH7 and PLC cells. In Hep3B cells, coincubation with 5-aza-2'-deoxycytidine, a demethylator, demethylated the promoter and upregulated COX-2 expression as well as prostaglandin E2 production dose dependently. On the other hand, no such effects were observed in HuH7 cells. Additionally, the methylator suppressed growth of Hep3B cells dose dependently, accompanied by cyclin D1 downregulation, and the growth suppression was abrogated by potent COX-2 inhibition with a COX-2 selective inhibitor celecoxib, but these responses were not found in HuH7 cells. These results indicated that cell growth was largely retarded by Cox-2 upregulation via promoter demethylation, rather than the potentially reactivated genes concurrently demethylated by 5-aza-2'-deoxycytidine. In conclusion, promoter hypermethylation transcriptionally silences Cox-2 in HCC cells. Epigenetic alteration of Cox-2, at least in part, modulates the growth of HCC cells.
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Affiliation(s)
- Hiroaki Murata
- Department of Internal Medicine and Therapeutics, School of Allied Health Sciences, Osaka University Graduate School of Medicine, Osaka, Japan
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147
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Pogribny IP, James SJ, Jernigan S, Pogribna M. Genomic hypomethylation is specific for preneoplastic liver in folate/methyl deficient rats and does not occur in non-target tissues. Mutat Res 2004; 548:53-9. [PMID: 15063136 DOI: 10.1016/j.mrfmmm.2003.12.014] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2003] [Revised: 12/18/2003] [Accepted: 12/30/2003] [Indexed: 01/22/2023]
Abstract
Chronic dietary insufficiency of the lipotropic nutrients choline and methionine is hepatocarcinogenic in male rats and certain mouse strains. Despite the fact that DNA hypomethylation is a hallmark of most cancer genomes, the tissue-specific consequences of this alternation with respect to tumorigenesis remain to be determined. In the present study, the folate/methyl deficient model of multistage hepatocarcinogenesis was used to evaluate in vivo alterations in DNA methylation in the liver, the carcinogenesis target tissue, and in non-target tissues, including pancreas, spleen, kidney, and thymus, of male F344 rats. By utilizing the HpaII/MspI-based cytosine extension assay, we demonstrated that the percent of CpG sites that lost methyl groups on both strands progressively increased in liver tissue after 9, 18, and 36 weeks of folate/methyl deficiency. The endogenous activity of DNA methyltransferase in liver of rats fed with folate/methyl deficient diet for the 36-week period gradually increased with time. In contrast, non-target tissues displayed no changes in DNA methylation level or activity of DNA methyltransferase. The failure of DNA methyltransferase to restore and maintain DNA methylation patterns in preneoplastic liver tissue may lead to the establishment of tumor-specific DNA methylation and DNA methyltransferase profiles that are not expressed in normal liver. These results provide additional information about alterations in DNA methylation during early preneoplastic stages of carcinogenesis. They also demonstrate that DNA hypomethylation is localized to tissue that undergoes carcinogenesis, and is not altered in non-target tissues.
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Affiliation(s)
- Igor P Pogribny
- Division of Biochemical Toxicology, FDA-National Center for Toxicological Research, NCTR, 3900 NCTR Road, Jefferson, AR 72079, USA.
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148
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Affiliation(s)
- Andrew P Feinberg
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
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149
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Abstract
Abstract
Several alternatively spliced variants of DNA methyltransferase (DNMT) 3b have been described. Here, we identified new murine Dnmt3b mRNA isoforms and found that mouse embryonic stem (ES) cells expressed only Dnmt3b transcripts that contained exons 10 and 11, whereas the Dnmt3b transcripts in somatic cells lacked these exons, suggesting that this region is important for embryonic development. DNMT3b2 and 3b3 were the major isoforms expressed in human cell lines and the mRNA levels of these isoforms closely correlated with their protein levels. Although DNMT3b3 may be catalytically inactive, it still may be biologically important because D4Z4 and satellites 2 and 3 repeat sequences, all known DNMT3b target sequences, were methylated in cells that predominantly expressed DNMT3b3. Treatment of cells with the mechanism-based inhibitor 5-aza-2′-deoxycytidine (5-Aza-CdR) caused a complete depletion of DNMT1, 3a, 3b1, and 3b2 proteins. Human DNMT3b3 and the murine Dnmt3b3-like isoform, Dnmt3b6, were also depleted although less efficiently, suggesting that DNMT3b3 also may be capable of DNA binding. Moreover, de novo methylation of D4Z4 in T24 cancer cells after 5-Aza-CdR treatment only occurred when DNMT3b3 was expressed, reinforcing its role as a contributing factor of DNA methylation. The expression of either DNMT3b2 or 3b3, however, was not sufficient to explain the abnormal methylation of DNMT3b target sequences in human cancers, which may therefore be dependent on factors that affect DNMT3b targeting. Methylation analyses of immunodeficiency, chromosomal instabilities, and facial abnormalities cells revealed that an Alu repeat sequence was highly methylated, suggesting that Alu sequences are not DNMT3b targets.
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150
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Abstract
DNA methylation is a common epigenetic modification found in eukaryotic organisms ranging from fungi to mammals. Over the past 15 years, a number of eukaryotic DNA methyltransferases have been identified from various model organisms. These enzymes exhibit distinct biochemical properties and biological functions, partly due to their structural differences. The highly variable N-terminal extensions of these enzymes harbor various evolutionarily conserved domains and motifs, some of which have been shown to be involved in functional specializations. DNA methylation has divergent functions in different organisms, consistent with the notion that it is a dynamically evolving mechanism that can be adapted to fulfill various functions. Genetic studies using model organisms have provided evidence suggesting the progressive integration of DNA methylation into eukaryotic developmental programs during evolution.
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Affiliation(s)
- Taiping Chen
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Charlestown, Massachusetts 02129, USA
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