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Warneboldt J, Haller F, Horstmann O, Danner BC, Füzesi L, Doenecke D, Happel N. Histone H1x is highly expressed in human neuroendocrine cells and tumours. BMC Cancer 2008; 8:388. [PMID: 19108733 PMCID: PMC2631592 DOI: 10.1186/1471-2407-8-388] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2008] [Accepted: 12/24/2008] [Indexed: 11/14/2022] Open
Abstract
Background Histone H1x is a ubiquitously expressed member of the H1 histone family. H1 histones, also called linker histones, stabilize compact, higher order structures of chromatin. In addition to their role as structural proteins, they actively regulate gene expression and participate in chromatin-based processes like DNA replication and repair. The epigenetic contribution of H1 histones to these mechanisms makes it conceivable that they also take part in malignant transformation. Methods Based on results of a Blast data base search which revealed an accumulation of expressed sequence tags (ESTs) of H1x in libraries from neuroendocrine tumours (NETs), we evaluated the expression of H1x in NETs from lung and the gastrointestinal tract using immunohistochemisty. Relative protein and mRNA levels of H1x were analysed by Western blot analysis and quantitative real-time RT-PCR, respectively. Since several reports describe a change of the expression level of the replacement subtype H1.0 during tumourigenesis, the analysis of this subtype was included in this study. Results We found an increased expression of H1x but not of H1.0 in NET tissues in comparison to corresponding normal tissues. Even though the analysed NETs were heterogenous regarding their grade of malignancy, all except one showed a considerably higher protein amount of H1x compared with corresponding non-neoplastic tissue. Furthermore, double-labelling of H1x and chromogranin A in sections of pancreas and small intestine revealed that H1x is highly expressed in neuroendocrine cells of these tissues. Conclusion We conclude that the high expression of histone H1x in NETs is probably due to the abundance of this protein in the cells from which these tumours originate.
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Affiliation(s)
- Julia Warneboldt
- Institute for Biochemistry and Molecular Cell Biology, University of Göttingen, Humboldtallee 23, D-37073 Göttingen, Germany.
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Lebedev IN, Sazhenova EA. Epimutations of imprinted genes in the human genome: Classification, causes, association with hereditary pathology. RUSS J GENET+ 2008. [DOI: 10.1134/s1022795408100062] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Migliore L, Coppedè F. Environmental-induced oxidative stress in neurodegenerative disorders and aging. Mutat Res 2008; 674:73-84. [PMID: 18952194 DOI: 10.1016/j.mrgentox.2008.09.013] [Citation(s) in RCA: 237] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Accepted: 09/23/2008] [Indexed: 12/29/2022]
Abstract
The aetiology of most neurodegenerative disorders is multifactorial and consists of an interaction between environmental factors and genetic predisposition. Free radicals derived primarily from molecular oxygen have been implicated and considered as associated risk factors for a variety of human disorders including neurodegenerative diseases and aging. Damage to tissue biomolecules, including lipids, proteins and DNA, by free radicals is postulated to contribute importantly to the pathophysiology of oxidative stress. The potential of environmental exposure to metals, air pollution and pesticides as well as diet as risk factors via the induction of oxidative stress for neurodegenerative diseases and aging is discussed. The role of genetic background is discussed on the light of the oxidative stress implication, focusing on both complex neurodegenerative diseases (Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis) and monogenic neurological disorders (Huntington's disease, Ataxia telangiectasia, Friedreich Ataxia and others). Emphasis is given to role of the repair mechanisms of oxidative DNA damage in delaying aging and protecting against neurodegeneration. The emerging interplay between environmental-induced oxidative stress and epigenetic modifications of critical genes for neurodegeneration is also discussed.
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Affiliation(s)
- Lucia Migliore
- Department of Human and Environmental Sciences, University of Pisa, Faculty of Medicine, Via S. Giuseppe 22, 56126 Pisa, Italy.
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Lu K, Boysen G, Gao L, Collins LB, Swenberg JA. Formaldehyde-induced histone modifications in vitro. Chem Res Toxicol 2008; 21:1586-93. [PMID: 18656964 DOI: 10.1021/tx8000576] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Numerous experiments have demonstrated the genotoxic and mutagenic effects of formaldehyde, including DNA-protein cross-links (DPC). Histone was reported to be involved in the formation of DPC in which the epsilon-amino groups of lysine and exocyclic amino groups of DNA were thought to be cross-linked through multiple step reactions. Using mass spectrometry, the N-terminus of histone and lysine residues located in both the histone N-terminal tail and the globular fold domain were identified as binding sites for formaldehyde in the current study. The observation that only lysine residues without post-translational modification (PTM) can be attacked by formaldehyde indicates that PTM blocks the reaction between lysine and formaldehyde. Additionally, we found that formaldehyde-induced Schiff bases on lysine residues could inhibit the formation of PTM on histone, raising the possibility that formaldehyde might alter epigenetic regulation.
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Affiliation(s)
- Kun Lu
- Curriculum in Applied Science & Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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Yu Y, Zhang H, Tian F, Zhang W, Fang H, Song J. An integrated epigenetic and genetic analysis of DNA methyltransferase genes (DNMTs) in tumor resistant and susceptible chicken lines. PLoS One 2008; 3:e2672. [PMID: 18648519 PMCID: PMC2481300 DOI: 10.1371/journal.pone.0002672] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2008] [Accepted: 06/12/2008] [Indexed: 11/20/2022] Open
Abstract
Both epigenetic alterations and genetic variations play essential roles in tumorigenesis. The epigenetic modification of DNA methylation is catalyzed and maintained by the DNA methyltransferases (DNMT3a, DNMT3b and DNMT1). DNA mutations and DNA methylation profiles of DNMTs themselves and their relationships with chicken neoplastic disease resistance and susceptibility are not yet defined. In the present study, we analyzed the complexity of the DNA methylation variations and DNA mutations in the first exon of three DNMTs genes over generations, tissues, and ages among chickens of two highly inbred White Leghorn lines, Marek's disease-resistant line 6(3) and -susceptible line 7(2), and six recombinant congenic strains (RCSs). Among them, tissue-specific methylation patterns of DNMT3a were disclosed in spleen, liver, and hypothalamus in lines 6(3) and 7(2). The methylation level of DNMT3b on four CpG sites was not significantly different among four tissues of the two lines. However, two line-specific DNA transition mutations, CpG-->TpG (Chr20:10203733 and 10203778), were discovered in line 7(2) compared to the line 6(3) and RCSs. The methylation contents of DNMT1 in blood cell showed significant epimutations in the first CpG site among the two inbred lines and the six RCSs (P<0.05). Age-specific methylation of DNMT1 was detected in comparisons between 15 month-old and 2 month-old chickens in both lines except in spleen samples from line 7(2). No DNA mutations were discovered on the studied regions of DNMT1 and DNMT3a among the two lines and the six RCSs. Moreover, we developed a novel method that can effectively test the significance of DNA methylation patterns consisting of continuous CpG sites. Taken together, these results highlight the potential of epigenetic alterations in DNMT1 and DNMT3a, as well as the DNA mutations in DNMT3b, as epigenetic and genetic factors to neoplastic diseases of chickens.
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Affiliation(s)
- Ying Yu
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland, United State of America
| | - Huanmin Zhang
- Agriculture Research Service (ARS), United States Department of Agriculture (USDA), Avian Disease and Oncology Laboratory, East Lansing, Michigan, United State of America
| | - Fei Tian
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland, United State of America
| | - Wensheng Zhang
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland, United State of America
| | - Hongbin Fang
- Division of Biostatistics of The University of Maryland Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland, United State of America
| | - Jiuzhou Song
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland, United State of America
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Chango A, Nour AA, Bousserouel S, Eveillard D, Anton PM, Guéant JL. Time course gene expression in the one-carbon metabolism network using HepG2 cell line grown in folate-deficient medium. J Nutr Biochem 2008; 20:312-20. [PMID: 18602821 DOI: 10.1016/j.jnutbio.2008.04.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2007] [Revised: 02/11/2008] [Accepted: 04/01/2008] [Indexed: 11/15/2022]
Abstract
The integrated view of the expression of genes involved in folate-dependent one-carbon metabolism (FOCM) under folate deficiency remains unknown. Dynamics of changes in the transcriptional expression of 28 genes involved in the FOCM network were evaluated at different time points (0, 2, 4, 6, 12, 24 and 48 h) in human hepatoma HepG2 cell line. Combined experimental and computational approaches were conducted for emphasizing characteristic patterns in the gene expression changes produced by cellular folate deficiency. Bivariate analysis showed that folate deficiency (0.3 nmol/L of folate vs. 2.27 mumol/L in control medium) displayed rapid and coordinated regulation during the first 2 h with differential expression for hRfc1 (increased by 69%) and Ahcy (decreased by 437%). Density analysis through the time points gave evidence of differential expression for five genes (Ahcy, Cth, Gnmt, Mat1A, Mtrr and hRfc1). Differential expression of Ahcy, Gnmt, Mat1A and Mtrr was confirmed by time-series analysis gene expression. We also found a marked differential expression of Mtrr. Qualitative analysis of genes allowed identifying four clusters of gene that was coexpressed. Two of these clusters were consistent with specific metabolic functions as they associated genes involved in the remethylation (Mthfr and Mtrr) and in the transmethylation (Dnmt1and Dnmt3B) pathways. The study shows a strong influence of folate status on Mtrr transcription in HepG2 cells. It suggests also that folate deficiency produces transcription changes that particularly involve the clusters of genes related with the remethylation and the transmethylation pathways.
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Affiliation(s)
- Abalo Chango
- Institut Polytechnique LaSalle, EGEAL, F-60026 Beauvais Cedex, France.
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Iliopoulos D, Malizos KN, Tsezou A. Epigenetic regulation of leptin affects MMP-13 expression in osteoarthritic chondrocytes: possible molecular target for osteoarthritis therapeutic intervention. Ann Rheum Dis 2007; 66:1616-21. [PMID: 17502362 PMCID: PMC2095321 DOI: 10.1136/ard.2007.069377] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2007] [Indexed: 12/20/2022]
Abstract
OBJECTIVE To investigate whether epigenetic mechanisms can regulate leptin's expression and affect its downstream targets as metalloproteinases 3,9,13 in osteoarthritic chondrocytes. METHODS DNA methylation in leptin promoter was measured by DNA bisulfite sequencing, and mRNA expression levels were measured by real-time quantitative PCR in osteoarthritic as well as in normal cartilage. Osteoarthritic articular cartilage samples were obtained from two distinct locations of the knee (n = 15); from the main defective area of maximum load (advanced osteoarthritis (OA)) and from adjacent macroscopically intact regions (minimal OA). Using small interference RNA, we tested if leptin downregulation would affect matrix metalloproteinase (MMP)-13 activity. We also evaluated the effect of the demethylating agent, 5'-Aza-2-deoxycytidine (AZA) and of the histone deacetylase inhibitor trichostatin A (TSA) on leptin expression in chondrocyte cultures. Furthermore, we performed chromatin immunoprecipitation in leptin's promoter area. RESULTS We found a correlation between leptin expression and DNA methylation and also that leptin controls MMP-13 activity in chondrocytes. Leptin's downregulation with small interference RNA inhibited MMP-13 expression dramatically. After 5-AZA application in normal chondrocytes, leptin's methylation was decreased, while its expression was upregulated, and MMP-13 was activated. Furthermore, TSA application in normal chondrocyte cultures increased leptin's expression. Also, chromatin immunoprecipitation in leptin's promoter after TSA treatment revealed that histone H3 lysines 9 and 14 were acetylated. CONCLUSION We found that epigenetic mechanisms regulate leptin's expression in chondrocytes affecting its downstream target MMP-13. Small interference RNA against leptin deactivated directly MMP-13, which was upregulated after leptin's epigenetic reactivation, raising the issue of leptin's therapeutic potential for osteoarthritis.
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Affiliation(s)
- D Iliopoulos
- University of Thessalia, Medical School, Department of Biology, 22 Papakyriazi str. 41 222 Larisa, Greece
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Clark SJ. Action at a distance: epigenetic silencing of large chromosomal regions in carcinogenesis. Hum Mol Genet 2007; 16 Spec No 1:R88-95. [PMID: 17613553 DOI: 10.1093/hmg/ddm051] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Despite the completion of the Human Genome Project, we are still far from understanding the molecular events underlying epigenetic change in cancer. Cancer is a disease of the DNA with both genetic and epigenetic changes contributing to changes in gene expression. Epigenetics involves the interplay between DNA methylation, histone modifications and expression of non-coding RNAs in the regulation of gene transcription. We now know that tumour suppressor genes, with CpG island-associated promoters, are commonly hypermethylated and silenced in cancer, but we do not understood what triggers this process or when it occurs during carcinogenesis. Epigenetic gene silencing has always been envisaged as a local event silencing discrete genes, but recent data now indicates that large regions of chromosomes can be co-coordinately suppressed; a process termed long range epigenetic silencing (LRES). LRES can span megabases of DNA and involves broad heterochromatin formation accompanied by hypermethylation of clusters of contiguous CpG islands within the region. It is not clear if LRES is initiated by one critical gene target that spreads and conscripts innocent bystanders, analogous to large genetic deletions or if coordinate silencing of multiple genes is important in carcinogenesis? Over the next decade with the exciting new genomic approaches to epigenome analysis and the initiation of a Human Epigenome Project, we will understand more about the interplay between DNA methylation and chromatin modifications and the expression of non-coding RNAs, promising a new range of molecular diagnostic cancer markers and molecular targets for cancer epigenetic therapy.
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Affiliation(s)
- Susan J Clark
- Cancer Program, Garvan Institute of Medical Research, Darlinghurst Sydney, 2010 NSW, Australia.
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Smith LT, Otterson GA, Plass C. Unraveling the epigenetic code of cancer for therapy. Trends Genet 2007; 23:449-56. [PMID: 17681396 DOI: 10.1016/j.tig.2007.07.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2006] [Revised: 06/06/2007] [Accepted: 07/24/2007] [Indexed: 01/03/2023]
Abstract
Alterations in the genome and the epigenome are common in most cancers. Changes in epigenetic signatures, including aberrant DNA methylation and histone deacetylation, are among the most prevalent modifications in cancer and lead to dramatic changes in gene expression patterns. Because DNA methylation and histone deacetylation are reversible processes, they have become attractive as targets for cancer epigenetic therapy, both as single agents and as 'enhancing' agents for other treatment strategies. In this review we discuss our current view of the mammalian epigenome, this view has changed over the years because of the availability of novel technologies. We further demonstrate how the profound understanding of epigenetic alterations in cancer will help develop novel strategies for epigenetic therapies.
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Affiliation(s)
- Laura T Smith
- Division of Human Cancer Genetics, Department of Molecular Virology, Immunology and Medical Genetics, OH, USA
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Abstract
The correlation between epigenetic aberrations and disease underscores the importance of epigenetic mechanisms. Here, we review recent findings regarding chromatin modifications and their relevance to cancer.
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Affiliation(s)
- Miryam Ducasse
- Institute for Biomedical Research Georg-Speyer-Haus, 60596 Frankfurt, Germany
| | - Mark A Brown
- Section of Molecular Genetics and Microbiology and Institute for Cellular and Molecular Biology, The University of Texas at Austin, 1 University Station A5000, Austin TX 78712, USA
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