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Boycott C, Beetch M, Yang T, Lubecka K, Ma Y, Zhang J, Kurzava Kendall L, Ullmer M, Ramsey BS, Torregrosa-Allen S, Elzey BD, Cox A, Lanman NA, Hui A, Villanueva N, de Conti A, Huan T, Pogribny I, Stefanska B. Epigenetic aberrations of gene expression in a rat model of hepatocellular carcinoma. Epigenetics 2022; 17:1513-1534. [PMID: 35502615 PMCID: PMC9586690 DOI: 10.1080/15592294.2022.2069386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/22/2022] [Accepted: 04/14/2022] [Indexed: 11/15/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is mostly triggered by environmental and life-style factors and may involve epigenetic aberrations. However, a comprehensive documentation of the link between the dysregulated epigenome, transcriptome, and liver carcinogenesis is lacking. In the present study, Fischer-344 rats were fed a choline-deficient (CDAA, cancer group) or choline-sufficient (CSAA, healthy group) L-amino acid-defined diet. At the end of 52 weeks, transcriptomic alterations in livers of rats with HCC tumours and healthy livers were investigated by RNA sequencing. DNA methylation and gene expression were assessed by pyrosequencing and quantitative reverse-transcription PCR (qRT-PCR), respectively. We discovered 1,848 genes that were significantly differentially expressed in livers of rats with HCC tumours (CDAA) as compared with healthy livers (CSAA). Upregulated genes in the CDAA group were associated with cancer-related functions, whereas macronutrient metabolic processes were enriched by downregulated genes. Changes of highest magnitude were detected in numerous upregulated genes that govern key oncogenic signalling pathways, including Notch, Wnt, Hedgehog, and extracellular matrix degradation. We further detected perturbations in DNA methylating and demethylating enzymes, which was reflected in decreased global DNA methylation and increased global DNA hydroxymethylation. Four selected upregulated candidates, Mmp12, Jag1, Wnt4, and Smo, demonstrated promoter hypomethylation with the most profound decrease in Mmp12. MMP12 was also strongly overexpressed and hypomethylated in human HCC HepG2 cells as compared with primary hepatocytes, which coincided with binding of Ten-eleven translocation 1 (TET1). Our findings provide comprehensive evidence for gene expression changes and dysregulated epigenome in HCC pathogenesis, potentially revealing novel targets for HCC prevention/treatment.
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Affiliation(s)
- Cayla Boycott
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada
| | - Megan Beetch
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada
| | - Tony Yang
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada
| | - Katarzyna Lubecka
- Department of Biomedical Chemistry, Faculty of Health Sciences, Medical University of Lodz, Lodz, Poland
| | - Yuexi Ma
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jiaxi Zhang
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada
| | - Lucinda Kurzava Kendall
- Department of Nutrition Science, College of Health and Human Sciences, Purdue University, Indiana, USA
- Department of Internal Medicine, Ascension St. Vincent Hospital, Indianapolis, Indiana, USA
| | - Melissa Ullmer
- Department of Anatomy, Cell Biology and Physiology, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Benjamin S. Ramsey
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Sandra Torregrosa-Allen
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
| | - Bennett D. Elzey
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, Indiana, USA
| | - Abigail Cox
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, Indiana, USA
| | - Nadia Atallah Lanman
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, Indiana, USA
| | - Alisa Hui
- Department of Chemistry, Faculty of Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nathaniel Villanueva
- Department of Chemistry, Faculty of Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Aline de Conti
- Division of Biochemical Toxicology, FDA-National Center for Toxicological Research, Jefferson, Arkansas, USA
| | - Tao Huan
- Department of Chemistry, Faculty of Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Igor Pogribny
- Division of Biochemical Toxicology, FDA-National Center for Toxicological Research, Jefferson, Arkansas, USA
| | - Barbara Stefanska
- Food, Nutrition and Health Program, Faculty of Land and Food Systems, University of British Columbia, Vancouver, British Columbia, Canada
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Protein Arginine Methyltransferases in Cardiovascular and Neuronal Function. Mol Neurobiol 2019; 57:1716-1732. [PMID: 31823198 DOI: 10.1007/s12035-019-01850-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 12/01/2019] [Indexed: 12/16/2022]
Abstract
The methylation of arginine residues by protein arginine methyltransferases (PRMTs) is a type of post-translational modification which is important for numerous cellular processes, including mRNA splicing, DNA repair, signal transduction, protein interaction, and transport. PRMTs have been extensively associated with various pathologies, including cancer, inflammation, and immunity response. However, the role of PRMTs has not been well described in vascular and neurological function. Aberrant expression of PRMTs can alter its metabolic products, asymmetric dimethylarginine (ADMA), and symmetric dimethylarginine (SDMA). Increased ADMA levels are recognized as an independent risk factor for cardiovascular disease and mortality. Recent studies have provided considerable advances in the development of small-molecule inhibitors of PRMTs to study their function under normal and pathological states. In this review, we aim to elucidate the particular roles of PRMTs in vascular and neuronal function as a potential target for cardiovascular and neurological diseases.
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Auta J, Zhang H, Pandey SC, Guidotti A. Chronic Alcohol Exposure Differentially Alters One-Carbon Metabolism in Rat Liver and Brain. Alcohol Clin Exp Res 2017; 41:1105-1111. [PMID: 28369960 DOI: 10.1111/acer.13382] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 03/22/2017] [Indexed: 01/13/2023]
Abstract
BACKGROUND Epigenetic mechanisms such as DNA methylation play an important role in regulating the pathophysiology of alcoholism. Chronic alcohol exposure leads to behavioral changes as well as decreased expression of genes associated with synaptic plasticity. In the liver, it has been documented that chronic alcohol exposure impairs methionine synthase (Ms) activity leading to a decrease in S-adenosyl methionine/S-adenosyl homocysteine (SAM/SAH) ratio which results in DNA hypomethylation; however, it is not known whether similar alterations of SAM and SAH levels are also produced in brain. METHODS Male adult Sprague Dawley rats were fed chronically with Lieber-DeCarli ethanol (EtOH) (9% v/v) or control diet. The EtOH-diet-fed rats were withdrawn for 0 and 24 hours. The cerebellum and liver tissues were dissected and used to investigate changes in one-carbon metabolism, SAM, and SAH levels. RESULTS We found that chronic EtOH exposure decreased SAM levels, SAM/SAH ratio, Ms, methylene tetrahydrofolate reductase, and betaine homocysteine methyltransferase (Bhmt) expression and increased methionine adenosyltransferase-2b (Mat2b) but not Mat2a expression in the liver. In contrast, chronic EtOH exposure decreased SAH levels, increased SAM/SAH ratio and the expression of Mat2a and S-adenosyl homocysteine hydrolase, while the levels of SAM or Bhmt expression in cerebellum remained unaltered. However, in both liver and cerebellum, chronic EtOH exposure decreased the expression of Ms and increased Mat2b expression. All chronic EtOH-induced changes of one-carbon metabolism in cerebellum, but not liver, returned to near-normal levels during EtOH withdrawal. CONCLUSIONS These results indicate a decreased "methylation index" in liver and an increased "methylation index" in cerebellum. The opposing changes of the "methylation index" suggest altered DNA methylation in liver and cerebellum, thus implicating one-carbon metabolism in the pathophysiology of alcoholism.
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Affiliation(s)
- James Auta
- Center for Alcohol Research in Epigenetics , Department of Psychiatry, College of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Huaibo Zhang
- Center for Alcohol Research in Epigenetics , Department of Psychiatry, College of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Subhash C Pandey
- Center for Alcohol Research in Epigenetics , Department of Psychiatry, College of Medicine, University of Illinois at Chicago, Chicago, Illinois.,Jesse Brown VA Medical Center , Chicago, Illinois
| | - Alessandro Guidotti
- Center for Alcohol Research in Epigenetics , Department of Psychiatry, College of Medicine, University of Illinois at Chicago, Chicago, Illinois
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Wang X, Pan C, Gong J, Liu X, Li H. Enhancing the Enrichment of Pharmacophore-Based Target Prediction for the Polypharmacological Profiles of Drugs. J Chem Inf Model 2016; 56:1175-83. [PMID: 27187084 DOI: 10.1021/acs.jcim.5b00690] [Citation(s) in RCA: 175] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
PharmMapper is a web server for drug target identification by reversed pharmacophore matching the query compound against an annotated pharmacophore model database, which provides a computational polypharmacology prediction approach for drug repurposing and side effect risk evaluation. But due to the inherent nondiscriminative feature of the simple fit scores used for prediction results ranking, the signal/noise ratio of the prediction results is high, posing a challenge for predictive reliability. In this paper, we improved the predictive accuracy of PharmMapper by generating a ligand-target pairwise fit score matrix from profiling all the annotated pharmacophore models against corresponding ligands in the original complex structures that were used to extract these pharmacophore models. The matrix reflects the noise baseline of fit score distribution of the background database, thus enabling estimation of the probability of finding a given target randomly with the calculated ligand-pharmacophore fit score. Two retrospective tests were performed which confirmed that the probability-based ranking score outperformed the simple fit score in terms of identification of both known drug targets and adverse drug reaction related off-targets.
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Affiliation(s)
- Xia Wang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, and ‡School of Information Science and Engineering, East China University of Science and Technology , Shanghai 200237, China
| | - Chenxu Pan
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, and ‡School of Information Science and Engineering, East China University of Science and Technology , Shanghai 200237, China
| | - Jiayu Gong
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, and ‡School of Information Science and Engineering, East China University of Science and Technology , Shanghai 200237, China
| | - Xiaofeng Liu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, and ‡School of Information Science and Engineering, East China University of Science and Technology , Shanghai 200237, China
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, and ‡School of Information Science and Engineering, East China University of Science and Technology , Shanghai 200237, China
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Torres N, Guevara-Cruz M, Velázquez-Villegas LA, Tovar AR. Nutrition and Atherosclerosis. Arch Med Res 2015; 46:408-26. [DOI: 10.1016/j.arcmed.2015.05.010] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 05/12/2015] [Indexed: 12/15/2022]
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D’Elia PQ, dos Santos AA, Bianco B, Barbosa CP, Christofolini DM, Aoki T. MTHFR polymorphisms C677T and A1298C and associations with IVF outcomes in Brazilian women. Reprod Biomed Online 2014; 28:733-8. [DOI: 10.1016/j.rbmo.2014.02.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 02/04/2014] [Accepted: 02/05/2014] [Indexed: 11/27/2022]
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Zhang H, Wang Y, Sang Y, Zhang Y, Hua S. Combination of S-adenosylhomocysteine and scriptaid, a non-toxic epigenetic modifying reagent, modulates the reprogramming of bovine somatic-cell nuclear transfer embryos. Mol Reprod Dev 2013; 81:87-97. [PMID: 24347442 DOI: 10.1002/mrd.22287] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 11/20/2013] [Indexed: 11/07/2022]
Abstract
The goal of this study was to improve the development of bovine somatic-cell nuclear transfer (SCNT) embryos by optimizing the combination of DNA methyltransferases inhibitor S-adenosylhomocysteine (SAH) and histone deacetylase inhibitor Scriptaid (SPD). A. 4 × 4-factor design of different drug combinations (0, 0.75, 1.0, and 1.5 mM SAH and 0, 5, 250, and 500 nM SPD) was used to identify an optimal combination of 0.75 mM SAH and 250 nM SPD that improved the developmental competence of bovine SCNT embryos. Further experiments using this combination revealed that methylation levels of CpG islands near exon 1 of the pluripotent gene SOX2; the epigenetic-related gene HDAC3 and DNMT3a; imprinted genes XIST and PEG3; as well as apoptosis-related genes BCL2 and BAX were returned to levels similar to those of in vitro fertilized (IVF) embryo after treatment, which also normalized transcript levels for these genes. This combination also returned global DNA methylation to a normal level, correcting H4K12ac levels while enhancing H3K9ac levels. Thus, the combined application of 0.75 mM SAH and 250 nM SPD can significantly improve the reprogramming of bovine SCNT embryos by stabilizing how embryos utilize their genomes.
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Affiliation(s)
- Hui Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi Province, People's Republic of China; Key Laboratory of Biological Technology, Ministry of Agriculture, Yangling, China
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Glier MB, Green TJ, Devlin AM. Methyl nutrients, DNA methylation, and cardiovascular disease. Mol Nutr Food Res 2013; 58:172-82. [PMID: 23661599 DOI: 10.1002/mnfr.201200636] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 03/08/2013] [Accepted: 03/13/2013] [Indexed: 12/22/2022]
Abstract
Diet plays an important role in the development and prevention of cardiovascular disease (CVD), but the molecular mechanisms are not fully understood. DNA methylation has been implicated as an underlying molecular mechanism that may account for the effect of dietary factors on the development and prevention of CVD. DNA methylation is an epigenetic process that provides "marks" in the genome by which genes are set to be transcriptionally activated or silenced. Epigenomic marks are heritable but are also responsive to environmental shifts, such as changes in nutritional status, and are especially vulnerable during development. S-adenosylmethionine is the methyl group donor for DNA methylation and several nutrients are required for the production of S-adenosylmethionine. These methyl nutrients include vitamins (folate, riboflavin, vitamin B12, vitamin B6, choline) and amino acids (methionine, cysteine, serine, glycine). As such, imbalances in the metabolism of these nutrients have the potential to affect DNA methylation. The focus of this review is to provide an overview on the current understanding of the relationship between methyl nutrient status and DNA methylation patterns and the potential role of this interaction in CVD pathology.
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Affiliation(s)
- Melissa B Glier
- Department of Pathology and Laboratory Medicine, Child and Family Research Institute, University of British Columbia, Vancouver, Canada
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Glier MB, Ngai YF, Sulistyoningrum DC, Aleliunas RE, Bottiglieri T, Devlin AM. Tissue-specific relationship of S-adenosylhomocysteine with allele-specific H19/Igf2 methylation and imprinting in mice with hyperhomocysteinemia. Epigenetics 2012; 8:44-53. [PMID: 23221482 DOI: 10.4161/epi.23063] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
DNA methylation is linked to homocysteine metabolism through the generation of S-adenosylmethionine (AdoMet) and S-Adenosylhomocysteine (AdoHcy). The ratio of AdoMet/AdoHcy is often considered an indicator of tissue methylation capacity. The goal of this study is to determine the relationship of tissue AdoMet and AdoHcy concentrations to allele-specific methylation and expression of genomically imprinted H19/Igf2. Expression of H19/Igf2 is regulated by a differentially methylated domain (DMD), with H19 paternally imprinted and Igf2 maternally imprinted. F1 hybrid C57BL/6J x Castaneous/EiJ (Cast) mice with (+/-), and without (+/+), heterozygous disruption of cystathionine-β-synthase (Cbs) were fed a control diet or a diet (called HH) to induce hyperhomocysteinemia and changes in tissue AdoMet and AdoHcy. F1 Cast x Cbs+/- mice fed the HH diet had significantly higher plasma total homocysteine concentrations, higher liver AdoHcy, and lower AdoMet/AdoHcy ratios and this was accompanied by lower liver maternal H19 DMD allele methylation, lower liver Igf2 mRNA levels, and loss of Igf2 maternal imprinting. In contrast, we found no significant differences in AdoMet and AdoHcy in brain between the diet groups but F1 Cast x Cbs+/- mice fed the HH diet had higher maternal H19 DMD methylation and lower H19 mRNA levels in brain. A significant negative relationship between AdoHcy and maternal H19 DMD allele methylation was found in liver but not in brain. These findings suggest the relationship of AdoMet and AdoHcy to gene-specific DNA methylation is tissue-specific and that changes in DNA methylation can occur without changes in AdoMet and AdoHcy.
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Affiliation(s)
- Melissa B Glier
- Department of Pathology and Laboratory Medicine, University of British Columbia, Child & Family Research Institute, Vancouver, BC, Canada
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Sappok A, Mahlknecht U. Ribavirin restores ESR1 gene expression and tamoxifen sensitivity in ESR1 negative breast cancer cell lines. Clin Epigenetics 2011; 3:8. [PMID: 22414275 PMCID: PMC3305339 DOI: 10.1186/1868-7083-3-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 12/05/2011] [Indexed: 11/10/2022] Open
Abstract
Tumor growth is estrogen independent in approximately one-third of all breast cancers, which makes these patients unresponsive to hormonal treatment. This unresponsiveness to hormonal treatment may be explained through the absence of the estrogen receptor alpha (ESR1). The ESR1 gene re-expression through epigenetic modulators such as DNA methyltransferase inhibitors and/or histone deacetylase inhibitors restores tamoxifen sensitivity in ESR1 negative breast cancer cell lines and opens new treatment horizons in patients who were previously associated with a poor prognosis.In the study presented herein, we tested the ability of ribavirin, which shares some structural similarities with the DNA-methyltransferase inhibitor 5-azacytidine and which is widely known as an anti-viral agent in the treatment of hepatitis C, to restore ESR1 gene re-expression in ESR1 negative breast cancer cell lines.In our study we identified ribavirin to restore ESR1 gene re-expression alone and even more in combination with suberoylanilide hydroxamic acid (SAHA - up to 276 fold induction).Ribavirin and analogs could pave the way to novel translational research projects that aim to restore ESR1 gene re-expression and thus the susceptibility to tamoxifen-based endocrine treatment strategies.
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Affiliation(s)
- Anne Sappok
- Saarland University Medical Center, Department of Internal Medicine, Division of Immunotherapy and Gene Therapy, Homburg/Saar, Germany.
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Jafari S, Hosseini MS, Hajian M, Forouzanfar M, Jafarpour F, Abedi P, Ostadhosseini S, Abbasi H, Gourabi H, Shahverdi AH, Dizaj AVT, Anjomshoaa M, Haron W, Noorshariza N, Yakub H, Nasr-Esfahani MH. Improved in vitro development of cloned bovine embryos using S-adenosylhomocysteine, a non-toxic epigenetic modifying reagent. Mol Reprod Dev 2011; 78:576-84. [PMID: 21721066 DOI: 10.1002/mrd.21344] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Accepted: 05/23/2011] [Indexed: 11/08/2022]
Abstract
In this study, fibroblast cells were stably transfected with mouse POU5F1 promoter-driven enhanced green fluorescent protein (EGFP) to investigate the effect of S-adenosylhomocysteine (SAH), the reversible non-toxic inhibitor of DNA-methyltransferases (DNMTs), at different intervals post-fusion on in vitro development of cloned bovine embryos. Treatment with SAH for 12 hr resulted in 54.6 ± 7.7% blastocyst production, which was significantly greater than in vitro fertilized embryos (IVF: 37.2 ± 2.7%), cloned embryos treated with SAH for 72 hr (31.0 ± 7.6%), and control cloned embryos (34.6 ± 3.6%). The fluorescence intensities of the EGFP-POU5F1 reporter gene at all intervals of SAH treatment, except of 72 hr, were significantly higher than control somatic cell nuclear transfers (SCNT) embryos. The intensity of DNA-methylation in cloned embryos treated with SAH for 48 hr was similar to that of IVF embryos, and was significantly lower than the other SCNT groups. The levels of H3K9 acetylation in all SCNT groups were significantly lower than IVF embryos. Real-time PCR analysis of gene expression revealed significantly higher expression of POU5F1 in cloned versus IVF blastocysts. Neither embryo production method (SCNT vs. IVF) nor the SAH treatment interval affected expression of the BCL2 gene. Cloned embryos at all intervals of SAH treatment, except for 24 hr, had significantly increased VEGF transcript compared to IVF and control SCNT embryos. It was suggested that the time interval of DNMT inhibition may have important consequences on different in vitro features of bovine SCNT, and the improving effects of DNMT inhibition on developmental competency of cloned embryos are restricted to a specific period of time preceding de novo methylation.
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Affiliation(s)
- Shahram Jafari
- Faculty of Agriculture, Department of Animal Science, University Putra of Malayasia, Kualalumpur, Malaysia
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Tryndyak VP, Han T, Muskhelishvili L, Fuscoe JC, Ross SA, Beland FA, Pogribny IP. Coupling global methylation and gene expression profiles reveal key pathophysiological events in liver injury induced by a methyl-deficient diet. Mol Nutr Food Res 2010; 55:411-8. [PMID: 20938992 DOI: 10.1002/mnfr.201000300] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2010] [Revised: 07/31/2010] [Accepted: 08/17/2010] [Indexed: 01/23/2023]
Abstract
SCOPE A methyl-deficient diet induces liver injury similar to human nonalcoholic steatohepatitis, one of the main risk factors for the development of hepatocellular carcinoma. Previous studies have demonstrated that this diet perturbs DNA methylation by causing a profound loss of global cytosine methylation, predominantly at heavily methylated repetitive sequences. However, whether methyl deficiency affects the methylation status of gene promoters has not been explored. METHODS AND RESULTS Mouse gene expression and CpG island microarrays were used to characterize the gene expression and CpG island methylation profiles in the livers of C57BL/6J mice fed a methyl-deficient diet. We detected 164 genes that were differentially expressed and exhibited an inverse relationship between the gene expression and the extent of CpG island methylation. Furthermore, these genes were associated with altered lipid and glucose metabolism, DNA damage and repair, apoptosis, the development of fibrosis, and liver tissue remodeling. Although there were both increased and decreased levels of CpG island methylation, the number of hypomethylated genes was substantially greater than the number of hypermethylated genes. CONCLUSION The results this study demonstrate that pairing methylation profiles with gene expression profiles is a powerful approach to identify dysregulated high-priority fundamental pathophysiological pathways associated with disease development.
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Affiliation(s)
- Volodymyr P Tryndyak
- Division of Biochemical Toxicology, National Center for Toxicological Research, Jefferson, AR 72079, USA
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Jeon BG, Coppola G, Perrault SD, Rho GJ, Betts DH, King WA. S-adenosylhomocysteine treatment of adult female fibroblasts alters X-chromosome inactivation and improves in vitro embryo development after somatic cell nuclear transfer. Reproduction 2008; 135:815-28. [DOI: 10.1530/rep-07-0442] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The poor outcome of somatic cell nuclear transfer (SCNT) is thought to be a consequence of incomplete reprogramming of the donor cell. The objective of this study was to investigate the effects of treatment withS-adenosylhomocysteine (SAH) a DNA demethylation agent, on DNA methylation levels and X-chromosome inactivation status of bovine female fibroblast donor cells and the subsequent impact on developmental potential after SCNT. Compared with non-treated controls, the cells treated with SAH revealed (i) significantly (P<0.05) reduced global DNA methylation, (ii) significantly (∼1.5-fold) increased telomerase activity, (iii) diminished distribution signals of methylated histones H3-3mK9 and H3-3mK27 on the presumptive inactive X-chromosome (Xi), (iv) alteration in the replication pattern of the Xi, and (v) elevation of transcript levels for X-chromosome linked genes,ANT3,MECP2,XIAP,XIST, andHPRT. SCNT embryos produced with SAH-treated donor cells compared with those derived from untreated donor cells revealed (i) similar cleavage frequencies, (ii) significant elevation in the frequencies of development of cleaved embryos to hatched blastocyst stage, and (iii) 1.5-fold increase in telomerase activity. We concluded that SAH induces global DNA demethylation that partially reactivates the Xi, and that a hypomethylated genome may facilitate the nuclear reprogramming process.
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Lin HC, Yang CM, Liu CL, Hu ML. Synergistic effects of homocysteine, S-adenosylhomocysteine and adenosine on apoptosis in BV-2 murine microglial cells. Biofactors 2008; 34:81-95. [PMID: 19706975 DOI: 10.1002/biof.5520340201] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Homocysteine (Hcy), S-adenosylhomocysteine (SAH) and adenosine (Ado) are methionine metabolism intermediates that may act synergistically in certain disease. In this study, we examined whether HCy, SAH and Ado may synergistically induce neuronal apoptosis of BV-2 microglial cells. We found that an incubation of BV-2 cells with 1 mM Hcy, 1 muM SAH and 100 muM Ado (SAH + Hcy + Ado) led to marked apoptosis of BV-2 cells, as evidenced by several markers of apoptosis. A synergistic effect of SAH + Hcy + Ado on apoptosis (2.55-fold, P < 0.05) was obtained, as calculated using the data of Annexin V-positive cells. This combination markedly induced intracellular levels of reactive oxygen species (ROS) starting at 6 h and significantly decreased the mitochondrial potential starting at 12 h. The combination significantly elevated caspase-9 and caspase-3 activities at 24 and 48 h. The combination also induced hypomethylation (at 24 and 48 h), as indicated by significantly decreased 5-methyldeoxycytidine levels and SAM/SAH ratios. Pre-incubation of cells with alpha-tocopherol (30 muM) reduced the increase of ROS (at 6 h) and significantly restored cell viability (at 24 and 48~h) in the SAH + Hcy + Ado group. Overall, the present study demonstrates that SAH, Hcy and Ado synergistically induce BV-2 apoptosis, possibly by generation of ROS and induction of intracellular hypomethylation.
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Affiliation(s)
- Hung-Chi Lin
- Department of Food Science and Biotechnology, National Chung Hsing University, Taiwan
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Lin PY, Yang TH, Lin HG, Hu ML. Synergistic effects of S-adenosylhomocysteine and homocysteine on DNA damage in a murine microglial cell line. Clin Chim Acta 2007; 379:139-44. [PMID: 17300772 DOI: 10.1016/j.cca.2007.01.007] [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] [Received: 10/16/2006] [Revised: 01/05/2007] [Accepted: 01/07/2007] [Indexed: 11/23/2022]
Abstract
BACKGROUND Homocysteine (Hcy) and S-adenosylhomocysteine (SAH) are 2 major metabolites of methionine. However, little is known about their interactions in human diseases. METHODS We determined the interaction of Hcy with SAH on DNA damage (measured as comet formation) and DNA hypomethylation (assayed as 5-methyldeoxycytidine, 5-mdc) in BV-2 cells (immortalized murine microglia). RESULTS Hcy at 100 micromol/l and SAH at 4 micromol/l alone caused little DNA strand breaks, whereas 100 micromol/l Hcy in combination with 0.5 to 4 micromol/l SAH led to marked DNA damage and uracil misincorporation. The combination of 100 micromol/l Hcy with 4 micromol/l SAH (SAH+Hcy) significantly increased intracellular H(2)O(2), and the DNA damage induced by SAH+Hcy was strongly inhibited by addition of superoxide dismutase, catalase or desferrioxamine, suggesting the involvement of reactive oxygen species. DNA damage induced by SAH+Hcy may also involve DNA hypomethylation (i.e., decreased %5-mdc) because of the high correlation between them. The effects induced by SAH+Hcy were specific to SAH but not to Hcy because they were markedly decreased by replacing SAH with adenosine (4.0 micromol/l) but was not affected by replacing Hcy with cysteine (100 micromol/l). CONCLUSION SAH in combination with Hcy can cause synergistic DNA damage in BV-2 cells. It remains to be seen whether some of the Hcy-related diseases may be caused by a collaborative action of Hcy with SAH.
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Affiliation(s)
- Pei-Ying Lin
- Department of Food Science and Biotechnology, National Chung-Hsing University, 250 Kuo-Kuang Road, Taichung, 402, Taiwan, ROC
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16
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Tchetina EV, Kobayashi M, Yasuda T, Meijers T, Pidoux I, Poole AR. Chondrocyte hypertrophy can be induced by a cryptic sequence of type II collagen and is accompanied by the induction of MMP-13 and collagenase activity: implications for development and arthritis. Matrix Biol 2007; 26:247-58. [PMID: 17306969 DOI: 10.1016/j.matbio.2007.01.006] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2006] [Revised: 12/05/2006] [Accepted: 01/11/2007] [Indexed: 11/24/2022]
Abstract
The objective of this study was to determine whether a peptide of type II collagen which can induce collagenase activity can also induce chondrocyte terminal differentiation (hypertrophy) in articulate cartilage. Full depth explants of normal adult bovine articular cartilage were cultured with or without a 24 mer synthetic peptide of type II collagen (residues 195-218) (CB12-II). Peptide CB12-II lacks any RGD sequence and is derived from the CB12 fragment of type II collagen. Type II collagen cleavage by collagenase was measured by ELISA in cartilage and medium. Real-time RT-PCR was used to analyze gene expression of the chondrocyte hypertrophy markers COL10A1 and MMP-13. Immunostaining for anti-Ki67, anti-PCNA, (proliferation markers), type X collagen, cleavage of type II collagen by collagenases (hypertrophy markers) and TUNEL staining (hypertrophy and apoptosis markers) were used to detect progressive maturational stages of chondrocyte hypertrophy. At high but naturally occurring concentrations (10 microM and up) the collagen peptide CB12-II induced an increase in the expression of MMP-13 (24 h) and cleavage of type II collagen by collagenase in the mid zone (day 4) and also in the superficial zone (day 6). Furthermore the peptide induced an increase in proliferation on day 1 in the mid and deep zones extending to the superficial zone by day 4. There was also upregulation of COL10A1 expression at day 4 and of type X staining in the mid zone extending to the superficial zone by day 6. Apoptotic cell death was increased by day 4 in the lower deep zone and also in the superficial zone at day 7. The increase in apoptosis in the deep zone was also seen in controls. Our results show that the induction of collagenase activity by a cryptic peptide sequence of type II collagen, is accompanied by chondrocyte hypertrophy and associated with cellular and matrix changes. This induction occurs in the mid and superficial zones of previously healthy articular cartilage. This response of the chondrocyte to a cryptic sequence of denatured type II collagen may play a role in naturally occurring hypertrophy in endochondral ossification and in the development of cartilage pathology in osteoarthritis.
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Affiliation(s)
- Elena V Tchetina
- Joint Diseases Laboratory, Shriners Hospitals for Children and Department of Surgery, McGill University, Montreal, Quebec, Canada
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17
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Park JH, Lee HC, Jeong YM, Chung TG, Kim HJ, Kim NK, Lee SH, Lee S. MTHFR C677T polymorphism associates with unexplained infertile male factors. J Assist Reprod Genet 2005; 22:361-8. [PMID: 16247718 DOI: 10.1007/s10815-005-6795-0] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2004] [Accepted: 05/10/2004] [Indexed: 10/25/2022] Open
Abstract
PURPOSE To determine whether 5,10-methylenetetrahydrofolate reductase (MTHFR C677T and A1298C) genotype is associated with male infertility. METHODS Analysis of cytogenetic, Y chromosomal microdeletion assay (Yq), and the C677T and A1298C polymorphisms of the MTHFR gene by pyrosequencing and PCR-Restriction Fragment Length Polymorphism (RFLP) method. SAS 8.1 assessed the statistical risk of MTHFR genotype. RESULTS The homozygous (T/T) C677T polymorphism of the MTHFR gene was present at a statistically high significance in unexplained infertile men with normal karyotype, instead at no significance in explained infertile men with chromosomal abnormality or Y chromosome deletion. There was no statistically significance of A1298C variation in infertile males. CONCLUSIONS The MTHFR 677TT genotype may be a genetic risk factor for male infertility, especially with severe OAT and non-obstructive azoospermia in unexplained infertile males.
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Affiliation(s)
- Jung Hoon Park
- Functional Genomics Lab, Graduate School of Life Science and Biotechnology, CHA Research Institute, College of Medicine, Pochon CHA University, Bundang Campus, Seoul, Korea
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18
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Nieto M, Samper E, Fraga MF, González de Buitrago G, Esteller M, Serrano M. The absence of p53 is critical for the induction of apoptosis by 5-aza-2'-deoxycytidine. Oncogene 2004; 23:735-43. [PMID: 14737108 DOI: 10.1038/sj.onc.1207175] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The absence of functional p53 has complex consequences on the cellular responses to cytotoxic drugs. Here, we have examined the role of p53 in the response to 5-aza-2'-deoxycytidine (5-aza-dC or decitabine). Primary mouse embryonic fibroblasts deficient for p53 undergo apoptosis after treatment with 5-aza-dC. When compared with other demethylating drugs or chemotherapeutic treatments, 5-aza-dC showed the highest selectivity ratio for triggering apoptosis in p53-deficient cells relative to wild-type cells. Moreover, the apoptotic efficacy of 5-aza-dC is proprietary of p53-deficient cells, not being observed in cells lacking other cell-cycle regulators, such as p19ARF, p16INK4a, p21(CIP1/WAF1), E2F-1, or E2F-2. Interestingly, treatment with 5-aza-dC results in the same degree of global genomic hypomethylation in wild-type and p53-null cells. However, wild-type cells activate p53 and arrest at G2/M, whereas p53-null cells accumulate severe chromosomal aberrations and undergo apoptosis. Significantly, the impact of p53-deficiency on the response to 5-aza-dC is not exclusive of primary non-neoplastic cells, but it is also present in neoplastically transformed cells. Finally, treatment of mice bearing genetically defined tumors with nontoxic doses of 5-aza-dC results in therapeutical responses only on tumors lacking p53, but not on tumors lacking p19ARF. Together, our results put forward the hypothesis that the absence of p53 may determine a higher chemotherapeutic index for 5-aza-dC.
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Affiliation(s)
- María Nieto
- Department of Immunology and Oncology, Spanish National Center of Biotechnology (CNB), Madrid, Spain
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19
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Altintas E, Sezgin O. S-adenosylhomocysteine hydrolase, S-adenosylmethionine, S-adenosylhomocysteine: correlations with ribavirin induced anemia. Med Hypotheses 2004; 63:834-7. [PMID: 15488656 DOI: 10.1016/j.mehy.2004.03.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2004] [Accepted: 03/05/2004] [Indexed: 11/23/2022]
Abstract
Objective is to speculate on the ribavirin induced anemia by inhibiting S-adenosylhomocysteine (SAH)-hydrolase activity. The major toxicity associated with the use of ribavirin is hemolytic anemia. This adverse effect has been ascribed to the accumulation of ribavirin triphosphate in the erythrocyte, which interferes with erythrocyte function. Ribavirin has been found to inhibit SAH-hydrolase activity in erythrocyte. SAH is further hydrolyzed to adenosine and homocysteine by SAH-hydrolase. The formation of S-adenosylmethionine (SAM) is then demethylated to SAH. SAH, the metabolite of SAM, on the other hand is a powerful inhibitor of methyltransferase enzymes, competing for the SAM binding site. A concurrent decrease in SAM and an increase in SAH levels would inhibit methylation of many tissue components including proteins, DNA, RNA, phospholipids and other small molecules. The enzyme protein carboxyl methyltransferase type II has been recently shown to play a crucial role in the repair of damaged proteins. SAM is the methyl donor of the reaction, and its demethylated product, SAH is the natural inhibitor of this reaction, as well as of most SAM-dependent methylations. The biological function of this transmethylation reaction is related to the repair or degradation of age-damaged proteins. Methyl ester formation in erythrocyte membrane proteins has been used as a marker reaction to tag these abnormal residues and to monitor their increase associated with erythrocyte ageing diseases. Liver disease is complicated by cholesterol deposition in hepatic and extrahepatic membranes. Erythrocyte membrane fluidity has been improved with the administration of SAM and correlated with the cholesterol/phospholipid ratio of the membranes. The levels of SAH-hydrolase activity were also found to undergo a sharp decrease with red cell ageing. The similarity of these alterations with certain morphofunctional characteristics of erythrocyte in some conditions as chronic renal failure, liver disease and hereditary spherocytosis makes it possible to hypothesize that the inhibition of SAH-hydrolase could constitute at least a part of ribavirin induced hemolytic anemia.
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Affiliation(s)
- Engin Altintas
- Division of Gastroenterology, School of Medicine, Mersin University, Zeytinli Bahce Cad. Eski Otogar Yani, 33079 Mersin, Turkey.
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20
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van der Velden PA, Zuidervaart W, Hurks MHMH, Pavey S, Ksander BR, Krijgsman E, Frants RR, Tensen CP, Willemze R, Jager MJ, Gruis NA. Expression profiling reveals that methylation of TIMP3 is involved in uveal melanoma development. Int J Cancer 2003; 106:472-479. [PMID: 12845640 DOI: 10.1002/ijc.11262] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Uveal melanoma is associated with a high tumor-related mortality due to the propensity to develop metastases. The mechanisms that are responsible for malignant dissemination are largely unknown and need to be explored to facilitate diagnosis and treatment of metastases. To identify molecules involved in dissemination, we used cell lines derived from a primary uveal melanoma and 2 liver metastases from the same patient as a model for tumor progression. Using a microarray representing 1,176 genes, we identified 63 differentially expressed genes. Forty genes showed a higher expression and 23 showed a lower expression in the primary cell line compared to the metastasis cell lines. These genes are involved in processes like angiogenesis, apoptosis, macrophage stimulation, and extracellular matrix regulation. In contrast, the 2 liver metastasis cell lines produced nearly identical expression profiles. Demethylation of the primary melanoma cell line by 5-aza-2'deoxycytidine treatment revealed that 19 genes were suppressed by hypermethylation. An important finding was the 5-fold decreased expression of TIMP3 in the metastatic cell lines, a molecule involved in extracellular matrix degradation. We demonstrate in the cell lines that TIMP3 expression is regulated by methylation. These observations were confirmed in primary uveal melanoma and suggests a role for TIMP3 in uveal melanoma development.
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Affiliation(s)
| | - Wieke Zuidervaart
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
| | - Monique H M H Hurks
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
| | - Sandra Pavey
- Queensland Institute of Medical Research, Brisbane, Australia
| | - Bruce R Ksander
- Schepens Eye Research Institute and the Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Elise Krijgsman
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
| | - Rune R Frants
- Center for Human and Clinical Genetics section Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Cornelis P Tensen
- Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Rein Willemze
- Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Martine J Jager
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
| | - Nelleke A Gruis
- Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands
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21
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Fu W, Dudman NP, Perry MA, Young K, Wang XL. Interrelations between plasma homocysteine and intracellular S-adenosylhomocysteine. Biochem Biophys Res Commun 2000; 271:47-53. [PMID: 10777679 DOI: 10.1006/bbrc.2000.2587] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
S-Adenosylhomocysteine, a potent intracellular methylation inhibitor, is suggested as a potential mediator for hyperhomocysteinemia-related vascular changes. We investigated the effect of acute and chronic hyperhomocysteinemia on intracellular S-adenosylhomocysteine and S-adenosylmethionine in rats and humans. Elevated plasma homocysteine in rats infused with homocysteine produced an increase in S-adenosylhomocysteine (P < 0.001) but not S-adenosylmethionine levels (P > 0.05) in various rat tissues. However intraerythrocyte S-adenosylhomocysteine and S-adenosylmethionine levels were not changed in homocysteine-infused rats and human subjects with experimentally acute hyperhomocysteinemia by methionine loading test. In contrast, erythrocyte S-adenosylhomocysteine levels were significantly higher in chronic renal failure patients, who had chronically elevated plasma homocysteine levels, than in either vascular disease patients or healthy controls (P < 0.05). In conclusion, acute hyperhomocysteinemia can increase intracellular S-adenosylhomocysteine levels in tissues actively involved in homocysteine metabolism. The findings are relevant to homocysteine-related endothelial dysfunction since S-adenosylhomocysteine modulates endothelial cell apoptosis.
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Affiliation(s)
- W Fu
- Department of Medicine, Prince Henry/Prince of Wales Hospital and Center for Thrombosis and Vascular Biology, University of New South Wales, Sydney, Australia
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22
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James SJ, Pogribna M, Pogribny IP, Melnyk S, Hine RJ, Gibson JB, Yi P, Tafoya DL, Swenson DH, Wilson VL, Gaylor DW. Abnormal folate metabolism and mutation in the methylenetetrahydrofolate reductase gene may be maternal risk factors for Down syndrome. Am J Clin Nutr 1999; 70:495-501. [PMID: 10500018 DOI: 10.1093/ajcn/70.4.495] [Citation(s) in RCA: 304] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Down syndrome, or trisomy 21, is a complex genetic disease resulting from the presence of 3 copies of chromosome 21. The origin of the extra chromosome is maternal in 95% of cases and is due to the failure of normal chromosomal segregation during meiosis. Although advanced maternal age is a major risk factor for trisomy 21, most children with Down syndrome are born to mothers <30 y of age. OBJECTIVE On the basis of evidence that abnormal folate and methyl metabolism can lead to DNA hypomethylation and abnormal chromosomal segregation, we hypothesized that the C-to-T substitution at nucleotide 677 (677C-->T) mutation of the methylenetetrahydrofolate reductase (MTHFR) gene may be a risk factor for maternal meiotic nondisjunction and Down syndrome in young mothers. DESIGN The frequency of the MTHFR 677C-->T mutation was evaluated in 57 mothers of children with Down syndrome and in 50 age-matched control mothers. Ratios of plasma homocysteine to methionine and lymphocyte methotrexate cytotoxicity were measured as indicators of functional folate status. RESULTS A significant increase in plasma homocysteine concentrations and lymphocyte methotrexate cytotoxicity was observed in the mothers of children with Down syndrome, consistent with abnormal folate and methyl metabolism. Mothers with the 677C-->T mutation had a 2.6-fold higher risk of having a child with Down syndrome than did mothers without the T substitution (odds ratio: 2.6; 95% CI: 1.2, 5.8; P < 0.03). CONCLUSION The results of this initial study indicate that folate metabolism is abnormal in mothers of children with Down syndrome and that this may be explained, in part, by a mutation in the MTHFR gene.
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Affiliation(s)
- S J James
- Food and Drug Administration-National Center for Toxicological Research, the Division of Biochemical Toxicology, Jefferson, AR 72079,USA.
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