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Liao X, Bai X, Wang S, Liggins C, Pan L, Wang M, Tchounwou P, Mao J, Liu YM. A novel one-pot fluorescence tagging and depyrimidination strategy for quantification of global DNA methylation. Anal Chim Acta 2023; 1239:340636. [PMID: 36628742 PMCID: PMC9834644 DOI: 10.1016/j.aca.2022.340636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 11/22/2022]
Abstract
DNA methylation is intensively studied in medical science. Current HPLC methods for quantification of global DNA methylation involve digestion of a DNA sample and HPLC determination of both cytosine (C) and 5-methylcytosine (5mC) so that percentage of 5mC in total cytosine can be calculated as DNA methylation level. Herein we report a novel HPLC method based on a one-pot fluorescence tagging and depyrimidination reaction between DNA and chloroacetaldehyde (CAA) for highly sensitive quantification of global DNA methylation. In the one-pot reaction, C and 5mC residues in a DNA sequence react with CAA, forming fluorescent etheno-adducts that are then released from the sequence through depyrimidination. Interestingly, etheno-5mC (ε-5mC) is ∼20 times more fluorescent than ε-C and other ε-nucleobases resulting from the reaction, which greatly facilitates the quantification. Further, due to the tagging-induced increase in structural aromaticity, ε-nucleobases are far more separable by HPLC than intact nucleobases. The proposed HPLC method with fluorescence detection (HPLC-FD) is quick (i.e., < 1h per assay) and highly sensitive with a detection limit of 0.80 nM (or 250 fg on column) for 5mC. Using the method, DNA samples isolated from yeast, HCT-116 cells, and tissues were analyzed. Global DNA methylation was measured to be in the range from 0.35% to 2.23% in the samples analyzed. This sensitive method allowed accurate analyses of minute DNA samples (∼100 ng) isolated from milligrams of tissues.
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Affiliation(s)
- Xun Liao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Xiaolin Bai
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Shuguan Wang
- Department of Physics, Chemistry and Atmospheric Science, Jackson State University, Jackson, MS, 39217, USA
| | - Christany Liggins
- Department of Physics, Chemistry and Atmospheric Science, Jackson State University, Jackson, MS, 39217, USA
| | - Li Pan
- Department of Physics, Chemistry and Atmospheric Science, Jackson State University, Jackson, MS, 39217, USA
| | - Meiyuan Wang
- Department of Physics, Chemistry and Atmospheric Science, Jackson State University, Jackson, MS, 39217, USA
| | - Paul Tchounwou
- Department of Biology, Jackson State University, Jackson, MS, 39217, USA
| | - Jinghe Mao
- Department of Biology, Tougaloo College, Tugaloo, MS, 39174, USA
| | - Yi-Ming Liu
- Department of Physics, Chemistry and Atmospheric Science, Jackson State University, Jackson, MS, 39217, USA.
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Proskurina A, Nikolin V, Popova N, Varaksin N, Ryabicheva T, Ershova E, Kostyuk S, Leplina O, Ostanin A, Chernykh E, Bogachev S. Comparing the Biological Properties of Double-Stranded DNA Extracted from Human and Porcine Placenta and Salmon Sperm. Rep Biochem Mol Biol 2023; 11:577-589. [PMID: 37131888 PMCID: PMC10149128 DOI: 10.52547/rbmb.11.4.577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 10/09/2022] [Indexed: 05/04/2023]
Abstract
Background Double-stranded fragmented extracellular DNA is a participant, inducer, and indicator of various processes occurring in the organism. When investigating the properties of extracellular DNA, the question regarding the specificity of exposure to DNA from different sources has always been raised. The aim of this study was to perform comparative assessment of biological properties of double-stranded DNA obtained from the human placenta, porcine placenta and salmon sperm. Methods The intensity of leukocyte-stimulating effect of different dsDNA was assessed in mice after cyclophosphamide-induced cytoreduction. The stimulatory effect of different dsDNA on maturation and functions of human dendritic cells and the intensity of cytokine production by human whole blood cells was analyzed ex vivo. The oxidation level of the dsDNA was also compared. Results Human placental DNA exhibited the strongest leukocyte-stimulating effect. DNA extracted from human and porcine placenta exhibited similar stimulatory action on maturation of dendritic cells, allostimulatory capacity, and ability of dendritic cells to induce generation of cytotoxic CD8+CD107a+ T cells in the mixed leukocyte reaction. DNA extracted from salmon sperm stimulated the maturation of dendritic cells, while having no effect on their allostimulatory capacity. DNA extracted from human and porcine placenta was shown to exhibit a stimulatory effect on cytokine secretion by human whole blood cells. The observed differences between the DNA preparations can be caused by the total methylation level and are not related to differences in oxidation level of DNA molecules. Conclusions Human placental DNA exhibited the maximum combination of all biological effects.
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Affiliation(s)
- Anastasia Proskurina
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
| | - Valeriy Nikolin
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
| | - Nelly Popova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
| | - Nikolay Varaksin
- JSC “Vector-Best”, Koltsovo, Novosibirsk Region, 630559, Russia.
| | | | | | | | - Olga Leplina
- Research Institute of Fundamental and Clinical Immunology, Novosibirsk, 630099, Russia.
| | - Alexandr Ostanin
- Research Institute of Fundamental and Clinical Immunology, Novosibirsk, 630099, Russia.
| | - Elena Chernykh
- Research Institute of Fundamental and Clinical Immunology, Novosibirsk, 630099, Russia.
| | - Sergey Bogachev
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
- Corresponding author: Sergey Bogachev; Tel: +7 383 363 49 63; E-mail:
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Urine 5MedC, a Marker of DNA Methylation, in the Progression of Chronic Kidney Disease. DISEASE MARKERS 2019; 2019:5432453. [PMID: 31354889 PMCID: PMC6636573 DOI: 10.1155/2019/5432453] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 04/02/2019] [Accepted: 06/02/2019] [Indexed: 01/13/2023]
Abstract
Background Alterations in DNA methylation may be involved in disease progression in patients with chronic kidney disease (CKD). Recent studies have suggested that 5-methyl-2′-deoxycytidine (5MedC) may be a marker of hypermethylation of DNA. Currently, there is no information available regarding the urine levels of 5MedC and its association with the progression of CKD. Method We examined the urine levels of 5MedC in spot urine samples from 308 patients with CKD (median age: 56 years, male: 53.2%, and glomerulonephritis: 51.0%) using a competitive enzyme-linked immunosorbent assay and investigated the relationships among urine 5MedC, urine albumin, urine α1-microglobulin (α1MG), and the laboratory parameters associated with CKD. The patients were followed for three years to evaluate renal endpoints in a prospective manner. Results The urine 5MedC level was significantly increased in the later stages of CKD compared to the early to middle stages of CKD. In multiple logistic regression models, urine 5MedC was significantly associated with the prediction of later CKD stages. Urine 5MedC (median value, 65.9 μmol/gCr) was significantly able to predict a 30% decline in the estimated GFR or a development of end-stage renal disease when combined with macroalbuminuria or an increased level of urine α1MG (median value, 5.7 mg/gCr). Conclusion The present data demonstrate that the urine 5MedC level is associated with a reduced renal function and can serve as a novel and potent biomarker for predicting the renal outcome in CKD patients. Further studies will be necessary to elucidate the role of urine DNA methylation in the progression of CKD.
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de Oliveira AAF, de Oliveira TF, Dias MF, Medeiros MHG, Di Mascio P, Veras M, Lemos M, Marcourakis T, Saldiva PHN, Loureiro APM. Genotoxic and epigenotoxic effects in mice exposed to concentrated ambient fine particulate matter (PM 2.5) from São Paulo city, Brazil. Part Fibre Toxicol 2018; 15:40. [PMID: 30340610 PMCID: PMC6194750 DOI: 10.1186/s12989-018-0276-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 10/03/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The Metropolitan Area of São Paulo has a unique composition of atmospheric pollutants, and positive correlations between exposure and the risk of diseases and mortality have been observed. Here we assessed the effects of ambient fine particulate matter (PM2.5) on genotoxic and global DNA methylation and hydroxymethylation changes, as well as the activities of antioxidant enzymes, in tissues of AJ mice exposed whole body to ambient air enriched in PM2.5, which was concentrated in a chamber near an avenue of intense traffic in São Paulo City, Brazil. RESULTS Mice exposed to concentrated ambient PM2.5 (1 h daily, 3 months) were compared to in situ ambient air exposed mice as the study control. The concentrated PM2.5 exposed group presented increased levels of the oxidized nucleoside 8-oxo-7,8-dihydro-2'-deoxyguanosine in lung and kidney DNA and increased levels of the etheno adducts 1,N6-etheno-2'-deoxyadenosine and 1,N2-etheno-2'-deoxyguanosine in kidney and liver DNA, respectively. Apart from the genotoxic effects, the exposure to PM2.5 led to decreased levels of the epigenetic mark 5-hydroxymethylcytosine (5-hmC) in lung and liver DNA. Changes in lung, liver, and erythrocyte antioxidant enzyme activities were also observed. Decreased glutathione reductase and increased superoxide dismutase (SOD) activities were observed in the lungs, while the liver presented increased glutathione S-transferase and decreased SOD activities. An increase in SOD activity was also observed in erythrocytes. These changes are consistent with the induction of local and systemic oxidative stress. CONCLUSIONS Mice exposed daily to PM2.5 at a concentration that mimics 24-h exposure to the mean concentration found in ambient air presented, after 3 months, increased levels of DNA lesions related to the occurrence of oxidative stress in the lungs, liver, and kidney, in parallel to decreased global levels of 5-hmC in lung and liver DNA. Genetic and epigenetic alterations induced by pollutants may affect the genes committed to cell cycle control, apoptosis, and cell differentiation, increasing the chance of cancer development, which merits further investigation.
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Affiliation(s)
- Antonio Anax Falcão de Oliveira
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Av. Prof. Lineu Prestes 580, Bloco 13 B, São Paulo, CEP 05508-000 Brazil
| | - Tiago Franco de Oliveira
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Av. Prof. Lineu Prestes 580, Bloco 13 B, São Paulo, CEP 05508-000 Brazil
- Present address: Departamento de Farmacociências, Universidade Federal de Ciências da Saúde de Porto Alegre, Rua Sarmento Leite 245, Porto Alegre, Rio Grande do Sul CEP 90050-170 Brazil
| | - Michelle Francini Dias
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Av. Prof. Lineu Prestes 580, Bloco 13 B, São Paulo, CEP 05508-000 Brazil
| | - Marisa Helena Gennari Medeiros
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, CEP 05508-000 Brazil
| | - Paolo Di Mascio
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, CEP 05508-000 Brazil
| | - Mariana Veras
- Laboratório de Poluição Atmosférica Experimental – LIM05, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, Av. Dr. Arnaldo 455, São Paulo, CEP 01246903 Brazil
| | - Miriam Lemos
- Laboratório de Poluição Atmosférica Experimental – LIM05, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, Av. Dr. Arnaldo 455, São Paulo, CEP 01246903 Brazil
| | - Tania Marcourakis
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Av. Prof. Lineu Prestes 580, Bloco 13 B, São Paulo, CEP 05508-000 Brazil
| | - Paulo Hilário Nascimento Saldiva
- Laboratório de Poluição Atmosférica Experimental – LIM05, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, Av. Dr. Arnaldo 455, São Paulo, CEP 01246903 Brazil
- Instituto de Estudos Avançados, Universidade de São Paulo, R. do Anfiteatro, 513, São Paulo, CEP 05508060 Brazil
| | - Ana Paula Melo Loureiro
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Av. Prof. Lineu Prestes 580, Bloco 13 B, São Paulo, CEP 05508-000 Brazil
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Rastegar L, Mighani H, Ghassempour A. A comparison and column selection of Hydrophilic Interaction Liquid Chromatography and Reversed-Phase High-Performance Liquid Chromatography for detection of DNA methylation. Anal Biochem 2018; 557:123-130. [PMID: 30030996 DOI: 10.1016/j.ab.2018.07.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 07/11/2018] [Accepted: 07/16/2018] [Indexed: 01/08/2023]
Abstract
5-methylcytosine (5mC) is an epigenetic mark which has a profound effect on various fundamental processes in cells. In present study, at first Hydrophilic Interaction Liquid Chromatography (HILIC) was compared with Reversed-Phase High-Performance Liquid Chromatography (RP-HPLC) based on their selectivity (α), retention factor (k), and resolution (R) for cytosine (C) and 5mC nucleobases. We tried to justify the separation mechanism on the basis of mobile phase and solute polarity, structural characterization of solute and stationary phases, log Do/w, and pka under both modes. Then, these two modes were compared in order to select the best column for measurement of methylation level in two real samples with less analytical complexity (i.e. animal and bacteria) and a highly complex sample (i.e. plant), after chemical hydrolysis of DNA. In this favor, diol and cyano (CN) columns in HILIC mode as well as C8 and C18 in RP-HPLC were investigated. Optimum separation and the best validation parameters were obtained for CN column with Limit of Detection (LOD) of 1.4 pmol and Limit of Quantification (LOQ) of 4.8 pmol for 5mC. When the CN column was used in HILIC-UV procedure, separation of 5mC and C bases was achieved in all types of hydrolyzed DNA solutions.
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Affiliation(s)
- Leila Rastegar
- Department of Chemistry, Faculty of Science, Golestan University, Gorgan, Iran
| | - Hossein Mighani
- Department of Chemistry, Faculty of Science, Golestan University, Gorgan, Iran
| | - Alireza Ghassempour
- Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, G.C. Evin, Tehran, Iran.
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Wang LL, Yang CX, Yan XP. In Situ Growth of Covalent Organic Framework Shells on Silica Microspheres for Application in Liquid Chromatography. Chempluschem 2017; 82:933-938. [DOI: 10.1002/cplu.201700223] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 06/12/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Lu-Liang Wang
- College of Chemistry; Research Center for Analytical Sciences; Tianjin Key Laboratory of Molecular Recognition and Biosensing; State Key Laboratory of Medicinal Chemical Biology; Nankai University; 94 Weijin Road Tianjin 300071 China
| | - Cheng-Xiong Yang
- College of Chemistry; Research Center for Analytical Sciences; Tianjin Key Laboratory of Molecular Recognition and Biosensing; State Key Laboratory of Medicinal Chemical Biology; Nankai University; 94 Weijin Road Tianjin 300071 China
| | - Xiu-Ping Yan
- College of Chemistry; Research Center for Analytical Sciences; Tianjin Key Laboratory of Molecular Recognition and Biosensing; State Key Laboratory of Medicinal Chemical Biology; Nankai University; 94 Weijin Road Tianjin 300071 China
- Collaborative Innovation Center of Chemical Science and Engineering; 94 Weijin Road Tianjin 300071 China
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Li XL, Yuan J, Dong YS, Fu CH, Li MT, Yu LJ. Optimization of an HPLC Method for Determining the Genomic Methylation Levels of Taxus Cells. J Chromatogr Sci 2015; 54:200-5. [PMID: 26341490 DOI: 10.1093/chromsci/bmv129] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Indexed: 11/14/2022]
Abstract
An HPLC method for quantifying total DNA methylation in Taxus chinensis cells is described. Optimal conditions for the method were established as follows: DNA was hydrolyzed with DNA degradase at 37°C for 3 h. The mobile phase was a mixture of Solvent A [50 mM potassium dihydrogen phosphate/triethylamine (100:0.2, v/v)] and Solvent B (methanol); the gradient was 10% (v/v) solvent B. The calibration curves for deoxycytidine monophosphate (dCMP) and methylated dCMP were linear within 1.0-160.0 µg mL(-1), with correlation coefficients of 0.9996 and 0.9998. The limits of detection for dCMP and 5-mdCMP were 0.482 and 0.301 ng mL(-1), respectively, and the limits of quantification were 1.6 and 1.0 ng mL(-1), respectively. The method has been validated according to the current International Conference Harmonization guidelines. The method was able to quantify the content of dCMP and methylated dCMP specifically, accurately and precisely. The global DNA methylation level in different Taxus cells was measured using as little as 3 µg of DNA according to the optimized procedure. In addition, degradation of 5-methylcytosine was prevented.
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Affiliation(s)
- Xiao-li Li
- Department of Biotechnology, College of Life Science and Technology, Institute of Resource Biology and Biotechnology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Jie Yuan
- Department of Biotechnology, College of Life Science and Technology, Institute of Resource Biology and Biotechnology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yan-shan Dong
- Department of Biotechnology, College of Life Science and Technology, Institute of Resource Biology and Biotechnology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Chun-hua Fu
- Department of Biotechnology, College of Life Science and Technology, Institute of Resource Biology and Biotechnology, Huazhong University of Science and Technology, Wuhan 430074, China Key Laboratory of Molecular Biophysics of Ministry of Education, Wuhan 430074, China
| | - Mao-Teng Li
- Department of Biotechnology, College of Life Science and Technology, Institute of Resource Biology and Biotechnology, Huazhong University of Science and Technology, Wuhan 430074, China Key Laboratory of Molecular Biophysics of Ministry of Education, Wuhan 430074, China Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains, Huanggang, China
| | - Long-jiang Yu
- Department of Biotechnology, College of Life Science and Technology, Institute of Resource Biology and Biotechnology, Huazhong University of Science and Technology, Wuhan 430074, China Key Laboratory of Molecular Biophysics of Ministry of Education, Wuhan 430074, China
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Abstract
Fluoroquinolones (FQ) are powerful broad-spectrum antibiotics whose side effects include renal damage and, strangely, tendinopathies. The pathological mechanisms underlying these toxicities are poorly understood. Here, we show that the FQ drugs norfloxacin, ciprofloxacin, and enrofloxacin are powerful iron chelators comparable with deferoxamine, a clinically useful iron-chelating agent. We show that iron chelation by FQ leads to epigenetic effects through inhibition of α-ketoglutarate-dependent dioxygenases that require iron as a co-factor. Three dioxygenases were examined in HEK293 cells treated with FQ. At sub-millimolar concentrations, these antibiotics inhibited jumonji domain histone demethylases, TET DNA demethylases, and collagen prolyl 4-hydroxylases, leading to accumulation of methylated histones and DNA and inhibition of proline hydroxylation in collagen, respectively. These effects may explain FQ-induced nephrotoxicity and tendinopathy. By the same reasoning, dioxygenase inhibition by FQ was predicted to stabilize transcription factor HIF-1α by inhibition of the oxygen-dependent hypoxia-inducible transcription factor prolyl hydroxylation. In dramatic contrast to this prediction, HIF-1α protein was eliminated by FQ treatment. We explored possible mechanisms for this unexpected effect and show that FQ inhibit HIF-1α mRNA translation. Thus, FQ antibiotics induce global epigenetic changes, inhibit collagen maturation, and block HIF-1α accumulation. We suggest that these mechanisms explain the classic renal toxicities and peculiar tendinopathies associated with FQ antibiotics.
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Affiliation(s)
- Sujan Badal
- From the Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905
| | - Yeng F Her
- From the Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905
| | - L James Maher
- From the Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota 55905
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Bailey LB, Stover PJ, McNulty H, Fenech MF, Gregory JF, Mills JL, Pfeiffer CM, Fazili Z, Zhang M, Ueland PM, Molloy AM, Caudill MA, Shane B, Berry RJ, Bailey RL, Hausman DB, Raghavan R, Raiten DJ. Biomarkers of Nutrition for Development-Folate Review. J Nutr 2015; 145:1636S-1680S. [PMID: 26451605 PMCID: PMC4478945 DOI: 10.3945/jn.114.206599] [Citation(s) in RCA: 325] [Impact Index Per Article: 36.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 12/11/2014] [Accepted: 04/14/2015] [Indexed: 12/13/2022] Open
Abstract
The Biomarkers of Nutrition for Development (BOND) project is designed to provide evidence-based advice to anyone with an interest in the role of nutrition in health. Specifically, the BOND program provides state-of-the-art information and service with regard to selection, use, and interpretation of biomarkers of nutrient exposure, status, function, and effect. To accomplish this objective, expert panels are recruited to evaluate the literature and to draft comprehensive reports on the current state of the art with regard to specific nutrient biology and available biomarkers for assessing nutrients in body tissues at the individual and population level. Phase I of the BOND project includes the evaluation of biomarkers for 6 nutrients: iodine, iron, zinc, folate, vitamin A, and vitamin B-12. This review represents the second in the series of reviews and covers all relevant aspects of folate biology and biomarkers. The article is organized to provide the reader with a full appreciation of folate's history as a public health issue, its biology, and an overview of available biomarkers (serum folate, RBC folate, and plasma homocysteine concentrations) and their interpretation across a range of clinical and population-based uses. The article also includes a list of priority research needs for advancing the area of folate biomarkers related to nutritional health status and development.
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Affiliation(s)
- Lynn B Bailey
- Department of Foods and Nutrition, University of Georgia, Athens, GA;
| | - Patrick J Stover
- Division of Nutritional Sciences, Cornell University, Ithaca, NY
| | - Helene McNulty
- Northern Ireland Centre for Food and Health, Biomedical Sciences Research Institute, University of Ulster, Londonderry, United Kingdom
| | - Michael F Fenech
- Genome Health Nutrigenomics Laboratory, Food, Nutrition, and Bioproducts Flagship, Commonwealth Scientific and Industrial Research Organization, Adelaide, Australia
| | - Jesse F Gregory
- Food Science and Human Nutrition Department, University of Florida, Gainesville, FL
| | - James L Mills
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD
| | | | - Zia Fazili
- National Center for Environmental Health, CDC, Atlanta, GA
| | - Mindy Zhang
- National Center for Environmental Health, CDC, Atlanta, GA
| | - Per M Ueland
- Department of Clinical Science, Univeristy of Bergen, Bergen, Norway
| | - Anne M Molloy
- Institute of Molecular Medicine, Trinity College, Dublin, Ireland
| | - Marie A Caudill
- Division of Nutritional Sciences, Cornell University, Ithaca, NY
| | - Barry Shane
- Department of Nutritional Sciences and Toxicology, University of California-Berkeley, Berkeley, CA
| | - Robert J Berry
- National Center on Birth Defects and Developmental Disabilities, CDC, Atlanta, GA; and
| | | | - Dorothy B Hausman
- Department of Foods and Nutrition, University of Georgia, Athens, GA
| | - Ramkripa Raghavan
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD
| | - Daniel J Raiten
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD;
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Her YF, Nelson-Holte M, Maher LJ. Oxygen concentration controls epigenetic effects in models of familial paraganglioma. PLoS One 2015; 10:e0127471. [PMID: 25985299 PMCID: PMC4436181 DOI: 10.1371/journal.pone.0127471] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 04/15/2015] [Indexed: 01/14/2023] Open
Abstract
Familial paraganglioma (PGL) is a rare neuroendocrine cancer associated with defects in the genes encoding the subunits of succinate dehydrogenase (SDH), a tricarboxylic acid (TCA) cycle enzyme. For unknown reasons, a higher prevalence of PGL has been reported for humans living at higher altitude, with increased disease aggressiveness and morbidity. In this study, we evaluate the effects of oxygen on epigenetic changes due to succinate accumulation in three SDH loss cell culture models. We test the hypothesis that the mechanism of α-ketoglutarate (α-KG)-dependent dioxygenase enzymes explains the inhibitory synergy of hypoxia and succinate accumulation. We confirm that SDH loss leads to profound succinate accumulation. We further show that hypoxia and succinate accumulation synergistically inhibit α-KG-dependent dioxygenases leading to increased stabilization of transcription factor HIF1α, HIF2α, and hypermethylation of histones and DNA. Increasing oxygen suppresses succinate inhibition of α-KG-dependent dioxygenases. This result provides a possible explanation for the association between hypoxia and PGL, and suggests hyperoxia as a potential novel therapy.
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Affiliation(s)
- Yeng F. Her
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First St. SW, Rochester, MN, 55905, United States of America
- Mayo Graduate School, Mayo Medical School and the Mayo Clinic Medical Scientist Training Program, 200 First St. SW, Rochester, MN, 55905, United States of America
| | - Molly Nelson-Holte
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First St. SW, Rochester, MN, 55905, United States of America
| | - Louis James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First St. SW, Rochester, MN, 55905, United States of America
- * E-mail:
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11
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Iglesias T, Espina M, Montes-Bayón M, Sierra LM, Blanco-González E. Anion exchange chromatography for the determination of 5-methyl-2'-deoxycytidine: application to cisplatin-sensitive and cisplatin-resistant ovarian cancer cell lines. Anal Bioanal Chem 2014; 407:2423-31. [PMID: 25142048 DOI: 10.1007/s00216-014-8070-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 07/22/2014] [Accepted: 07/25/2014] [Indexed: 12/30/2022]
Abstract
Epigenetic alterations are increasingly implicated in the initiation and progression of cancer. Genome-wide (global) hypomethylation seems to occur in early neoplasia and is a feature of genomic DNA derived from solid tumour tissues like ovarian cancer. Thus, analytical methods that provide sensitive and quantitative information about cytosine methylation in DNA are currently required. In this work, we compare two different anion-exchange columns for the separation of methylated cytosine from the other DNA nucleotides: a silica-based (Tracer Extrasil SAX) column and a polystyrene/divinyl benzene-based (Mono-Q™) column. Under the optimised conditions, linearity range, precision and detection limits of the developed high-performance liquid chromatography (HPLC) method were evaluated and compared using conventional ultraviolet (UV) absorbance detection at 270 nm. Good separation of the five target nucleotides, including 5-methyl-2'-deoxycytidine monophosphate (5mdCMP) and 2'-deoxycytidine monophosphate (dCMP) was achieved on the Mono-Q™ column with a gradient elution of ammonium acetate buffer (1 M, pH 6.9) at a flow rate of 1 mL min(-1). The coupling of this column to inductively coupled plasma mass spectrometry (ICP-MS) permitted also phosphorous ((31)P) specific detection of the nucleotides. Both detection systems offered adequate analytical performance characteristics, with detection limits of 30 and 40 μg L(-1) for 5mdCMP by HPLC-UV and HPLC-ICP-MS, respectively. However, the latter method allowed the determination of the global DNA methylation level (%) without the need for external calibration. Different genomic DNA samples were analysed including calf thymus DNA and DNA from two human cancer cell lines (adenocarcinoma epithelial A549 and ovarian carcinoma A2780) using the proposed strategy. In the line A2780, the cisplatin-sensitive and cisplatin-resistant variants were analysed, finding no significant differences in the methylation percentage after treatment with cisplatin.
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Affiliation(s)
- Tamara Iglesias
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, C/ Julián Clavería 8, 33006, Oviedo, Spain
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13
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Unterberg M, Leffers L, Hübner F, Humpf HU, Lepikhov K, Walter J, Ebert F, Schwerdtle T. Toxicity of arsenite and thio-DMAV after long-term (21 days) incubation of human urothelial cells: cytotoxicity, genotoxicity and epigenetics. Toxicol Res (Camb) 2014. [DOI: 10.1039/c4tx00036f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
This study aims to further mechanistically understand toxic modes of action after chronic arsenic species exposure.
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Affiliation(s)
- Marlies Unterberg
- Graduate School of Chemistry
- WWU Muenster
- 48149 Muenster, Germany
- Institute of Nutritional Sciences
- University of Potsdam
| | - Larissa Leffers
- Graduate School of Chemistry
- WWU Muenster
- 48149 Muenster, Germany
| | - Florian Hübner
- Institute of Food Chemistry
- WWU Muenster
- 48149 Muenster, Germany
| | - Hans-Ulrich Humpf
- Graduate School of Chemistry
- WWU Muenster
- 48149 Muenster, Germany
- Institute of Food Chemistry
- WWU Muenster
| | - Konstantin Lepikhov
- Department of Genetics/Epigenetics
- Campus Saarbruecken
- Saarland University
- 66123 Saarbruecken, Germany
| | - Jörn Walter
- Department of Genetics/Epigenetics
- Campus Saarbruecken
- Saarland University
- 66123 Saarbruecken, Germany
| | - Franziska Ebert
- Institute of Nutritional Sciences
- University of Potsdam
- 14558 Nuthetal, Germany
| | - Tanja Schwerdtle
- Graduate School of Chemistry
- WWU Muenster
- 48149 Muenster, Germany
- Institute of Nutritional Sciences
- University of Potsdam
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14
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Abstract
Epigenetics has undergone an explosion in the past decade. DNA methylation, consisting of the addition of a methyl group at the fifth position of cytosine (5-methylcytosine, 5-mC) in a CpG dinucleotide, is a well-recognized epigenetic mark with important functions in cellular development and pathogenesis. Numerous studies have focused on the characterization of DNA methylation marks associated with disease development as they may serve as useful biomarkers for diagnosis, prognosis, and prediction of response to therapy. Recently, novel cytosine modifications with potential regulatory roles such as 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-foC), and 5-carboxylcytosine (5-caC) have been discovered. Study of the functions of 5-mC and its oxidation derivatives promotes the understanding of the mechanism underlying association of epigenetic modifications with disease biology. In this respect, much has been accomplished in the development of methods for the discovery, detection, and location analysis of 5-mC and its oxidation derivatives. In this review, we focus on the recent advances for the global detection and location study of 5-mC and its oxidation derivatives 5-hmC, 5-foC, and 5-caC.
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Abstract
The mouse is the first species in which genomic imprinting was studied. Imprinting research in farm species has lagged behind owing to a lack of sequencing and genetic background information, as well as long generation intervals and high costs in tissue collection. Since the creation of Dolly, the first cloned mammal from an adult sheep, studies on genomic imprinting in domestic species have accelerated because animals from cloning and other assisted reproductive technologies exhibit phenotypes of imprinting disruptions. Although this review focuses on new developments in farm animals, most of the imprinting mechanism information was derived from the mouse.
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Affiliation(s)
- Xiuchun Cindy Tian
- Department of Animal Science, Center for Regenerative Biology, University of Connecticut, Storrs, Connecticut 06269-4163;
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Hu CW, Lee H, Chen JL, Li YJ, Chao MR. Optimization of global DNA methylation measurement by LC-MS/MS and its application in lung cancer patients. Anal Bioanal Chem 2013; 405:8859-69. [PMID: 23978937 DOI: 10.1007/s00216-013-7305-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 08/10/2013] [Accepted: 08/13/2013] [Indexed: 01/03/2023]
Abstract
Global analyses of DNA methylation contribute important insights into biology and the wide-ranging role of DNA methylation. We describe the use of online solid-phase extraction and isotope-dilution liquid chromatography/tandem mass spectrometry (LC-MS/MS) for the simultaneous measurement of 5-methyl-2'-deoxycytidine (5-medC) and 2'-deoxycytidine (dC) in DNA. With the incorporation of isotope internal standards and online enrichment techniques, the detection limit of this method was estimated to be as low as 0.065 pg which enables human global DNA methylation detection using only picogram amounts of DNA. This method was applied to assess the optimal amounts of enzymes required for DNA digestion regarding an accurate global DNA methylation determination and completeness of digestion and to determine global methylation in human tumor adjacent lung tissue of 79 lung cancer patients. We further determined methylated (N7-methylguanine (N7-meG), O (6)-methylguanine (O (6)-meG), and N3-methyladenine (N3-meA)) and oxidized DNA lesions (8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG)) in lung cancer patients by LC-MS/MS. Optimization experiments revealed that dC was liberated from DNA much more readily than 5-medC by nuclease P1 and alkaline phosphatase (AP) in DNA, which could lead to an error in the global DNA methylation measurement following digestion with insufficient enzymes. Nuclease P1 showed more differential activity for 5-medC and dC than AP. Global DNA methylation levels in adenocarcinoma and squamous cell carcinoma patients were similar in the range of 3.16-4.01 %. Global DNA methylation levels were not affected by smoking and gender and were not correlated with N7-meG or 8-oxodG in lung cancer patients. Levels of O (6)-meG and N3-meA were however found to be undetectable in all lung tissue samples.
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Affiliation(s)
- Chiung-Wen Hu
- Department of Public Health, Chung Shan Medical University, Taichung, 402, Taiwan
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Ferrone A, Pesce M, Franceschelli S, Speranza L, De Lutiis MA, Grilli A, Felaco M, Patruno A. Analysis of genomic methylation level using micellar electrokinetic chromatography with UV detection. Electrophoresis 2013; 34:2275-80. [PMID: 23712818 DOI: 10.1002/elps.201300091] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 04/19/2013] [Accepted: 04/26/2013] [Indexed: 11/11/2022]
Abstract
Analytical methods for quantification of 5'-methylcytosine in genomes are important tools to investigate epigenetic changes in gene expression during development, differentiation, aging, or cancer. Here, we report a novel genomic methylation content assay based on enzymatic hydrolysis of DNA and MEKC separation of 5'-deoxyribonucleoside monophosphates (dNMP) using the cationic surfactant CTAB as pseudostationary phase. Calf Thymus DNA was used during method development to determine electrophoretic parameters and electrolyte composition for a complete separation between 2'-deoxycytosine-5'-monophosphate and 2'-deoxy-5'-methylcytosine 5'-monophosphate (d5mCMP). Methylated and not methylated oligonucleotides were used to confirm the identity of each peak and evaluate analytical parameters of the method. The LOD of the method was found to be 12.5 pmol/μL for d5mCMP.
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Affiliation(s)
- Alessio Ferrone
- Department of Medicine and Science of Aging, University G. D'Annunzio, Chieti, Italy
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18
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Chen ML, Liu YL, Xing XW, Zhou X, Feng YQ, Yuan BF. Preparation of a hyper-cross-linked polymer monolithic column and its application to the sensitive determination of genomic DNA methylation. Chemistry 2012. [PMID: 23180679 DOI: 10.1002/chem.201203129] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
A hyper-cross-linked polymer monolithic column, poly(methacrylatoethyl trimethyl ammonium-co-vinylbenzene chloride-co-divinylbenzene) (MATE-co-VBC-co-DVB) with phenyl and quaternary ammonium groups was successfully prepared in the current study. The prepared monolith possesses large specific surface area, narrow mesopore size distribution and high column efficiency. The poly(MATE-co-VBC-co-DVB) monolithic column was demonstrated to have strong anion exchange/reversed-phase (SAX/RP) mixed-mode retention for analytes on capillary liquid chromatography (cLC). By using this monolithic column, we developed a rapid and sensitive method for the detection of DNA methylation. Our results showed that six nucleobases (adenine, guanine, cytosine, thymine, uracil, and 5-methylcytosine (5-mC)) can be baseline separated within 15 min by electrostatic repulsion and hydrophobic interactions between nucleobases and the monolithic stationary phase. The limit of detection (LOD, signal/noise = 3) of 5-mC is 0.014 pmol and endogenous 5-mC can be distinctly detected by using only 10 ng genomic DNA, which is comparable to that obtained by mass spectrometry analysis. Furthermore, by using the method developed here, we found that DNA methylation inhibitor 5-azacytidine (5-aza-C) and 5-aza-2'-deoxycytidine (5-aza-CdR) could induce a significant decrease of genome-wide DNA methylation in human lung carcinoma cells (A549) and cervical carcinoma cells (HeLa).
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Affiliation(s)
- Ming-Luan Chen
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan, 430072, China
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Highly sensitive and quantitative profiling of acidic phytohormones using derivatization approach coupled with nano-LC-ESI-Q-TOF-MS analysis. J Chromatogr B Analyt Technol Biomed Life Sci 2012; 905:67-74. [PMID: 22917596 DOI: 10.1016/j.jchromb.2012.08.005] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 07/31/2012] [Accepted: 08/03/2012] [Indexed: 01/25/2023]
Abstract
In current study, we developed a highly sensitive method for the quantitative profiling of acidic phytohormones. Tandem solid-phase extraction (SPE) and liquid-liquid extraction (LLE) was employed to efficiently purify acidic phytohormones, which were further derived by 3-bromoactonyltrimethylammonium bromide (BTA) to increase the ionization efficiency in electrospray ionization-mass spectrometry detection. Additionally, fifteen BTA-derived acidic phytohormones, including ten gibberellins (GAs), were well separated with a salt gradient on poly(methacrylic acid-co-ethylene glycol dimethacrylate) (MAA-co-EDMA) monolithic column. By employing online trapping system, the signal intensities of the analytes were significantly improved. The limits of detection (LODs, Signal/Noise=3) of targeted phytohormones ranged from 1.05 to 122.4 pg/mL, which allowed the highly sensitive determination of low abundant acidic phytohormones with tiny amount plant sample. Good reproducibility was obtained by evaluating the intra- and inter-day precisions with relative standard deviations (RSDs) less than 10.9 and 11.9%, respectively. Recoveries of the target analytes from spiked rice leave samples ranged from 88.3 to 104.3%. By employing the method developed here, we were able to simultaneously determine 11 endogenous acidic phytohormones from only 5mg of rice leave sample, which dramatically decreased the required sample amount (three orders of magnitude lower) for the profiling of low abundant acidic phytohormones compared to previous reports. Taken together, the method provided a good solution for the highly sensitive and quantitative profiling of endogenous acidic phytohormones.
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Armstrong CA, Jones GD, Anderson R, Iyer P, Narayanan D, Sandhu J, Singh R, Talbot CJ, Tufarelli C. DNMTs are required for delayed genome instability caused by radiation. Epigenetics 2012; 7:892-902. [PMID: 22722331 PMCID: PMC3427285 DOI: 10.4161/epi.21094] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The ability of ionizing radiation to initiate genomic instability has been harnessed in the clinic where the localized delivery of controlled doses of radiation is used to induce cell death in tumor cells. Though very effective as a therapy, tumor relapse can occur in vivo and its appearance has been attributed to the radio-resistance of cells with stem cell-like features. The molecular mechanisms underlying these phenomena are unclear but there is evidence suggesting an inverse correlation between radiation-induced genomic instability and global hypomethylation. To further investigate the relationship between DNA hypomethylation, radiosensitivity and genomic stability in stem-like cells we have studied mouse embryonic stem cells containing differing levels of DNA methylation due to the presence or absence of DNA methyltransferases. Unexpectedly, we found that global levels of methylation do not determine radiosensitivity. In particular, radiation-induced delayed genomic instability was observed at the Hprt gene locus only in wild-type cells. Furthermore, absence of Dnmt1 resulted in a 10-fold increase in de novo Hprt mutation rate, which was unaltered by radiation. Our data indicate that functional DNMTs are required for radiation-induced genomic instability, and that individual DNMTs play distinct roles in genome stability. We propose that DNMTS may contribute to the acquirement of radio-resistance in stem-like cells.
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Evaluation of 5-methyl-2'-deoxycytidine stability in hydrolyzed and nonhydrolyzed DNA by HPLC-UV. Bioanalysis 2012; 4:367-72. [PMID: 22394137 DOI: 10.4155/bio.11.335] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Although the determination of 5-methyl-2'-deoxycytidine (5-MedC) in various biological samples is gaining increasing scientific interest, there are no data available regarding its stability. RESULTS We have currently evaluated the stability of 5-MedC and 2'-deoxycytidine (dC) at -20°C, both in hydrolyzed and nonhydrolyzed calf thymus DNA (CT DNA), as well as following repetitive freeze-thaw cycles. HPLC-UV was used for the accurate determination of the two 2'-deoxynucleosides. Statistical evaluation of the results revealed that 5-MedC and dC were stable in hydrolyzed CT DNA for at least 7 days and in nonhydrolyzed CT DNA for at least 65 days, when these were stored at -20°C. Furthermore, both 2'-deoxynucleosides were stable for at least three repetitive freeze-thaw cycles. CONCLUSION By using HPLC-UV, we have evaluated the stability of 5-MedC and dC under storage conditions and repetitive freeze-thaw cycles. Our results are informative about the way samples should be handled and stored in epigenetic studies.
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Falck E, Groenhagen A, Mühlisch J, Hempel G, Wünsch B. Genome-wide DNA methylation level analysis by micellar electrokinetic chromatography and laser-induced fluorescence detection after treatment of cell lines with azacytidine and antifolates. Anal Biochem 2012; 421:439-45. [DOI: 10.1016/j.ab.2011.09.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 09/26/2011] [Accepted: 09/28/2011] [Indexed: 11/28/2022]
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Torres AL, Barrientos EY, Wrobel K, Wrobel K. Selective derivatization of cytosine and methylcytosine moieties with 2-bromoacetophenone for submicrogram DNA methylation analysis by reversed phase HPLC with spectrofluorimetric detection. Anal Chem 2011; 83:7999-8005. [PMID: 21905673 DOI: 10.1021/ac2020799] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
In eukaryotes, actual DNA methylation patterns provide biologically important information, for which both, genome-wide and locus-specific methylation at cytosine residues have been extensively studied. The original contribution of this work relies on the selective derivatization of cytosine moieties with 2-bromoacetophenone for the determination of global DNA methylation by reversed phase high performance liquid chromatography with spectrofluorimetric detection. The important features of the proposed procedure are as follows: (1) no need for the elimination of RNA, (2) detection limits for cytidine, 2'-deoxycytidine, 5-methylcytidine, and 5-methyl-2'-deoxycytidine in the range of 14.4-22.7 fmol, (3) feasibility for the detection of 0.06% of methylation in a low amount of DNA (80 ng), (4) potential viability for the evaluation of RNA methylation, and (5) relative simplicity in terms of analytical instrumentation and personnel training. The results obtained in the analysis of salmon testes DNA and nucleic acids from plant, human blood, and earthworms demonstrate the utility of the proposed procedure in biological studies and, in particular, for evaluation of the potential effect of environmental factors on actual DNA methylation in different types of living organisms.
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Affiliation(s)
- Adolfo Lopez Torres
- Department of Chemistry, University of Guanajuato, L de Retana No. 5, 36000 Guanajuato, Mexico
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24
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Kato D, Goto K, Fujii SI, Takatsu A, Hirono S, Niwa O. Electrochemical DNA methylation detection for enzymatically digested CpG oligonucleotides. Anal Chem 2011; 83:7595-9. [PMID: 21905720 DOI: 10.1021/ac201761c] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We describe the electrochemical detection of DNA methylation through the direct oxidation of both 5-methylcytosine (mC) and cytosine (C) in 5'-CG-3' sequence (CpG) oligonucleotides using a sputtered nanocarbon film electrode after digesting a longer CpG oligonucleotide with endonuclease P1. Direct electrochemistry of the longer CpG oligonucleotides was insufficient for obtaining the oxidation currents of these bases because the CG rich sequence inhibited the direct oxidation of each base in the longer CpG oligonucleotides, owing to the conformational structure and its very low diffusion coefficient. To detect C methylation with better quantitativity and sensitivity in the relatively long CpG oligonucleotides, we successfully used an endonuclease P1 to digest the target CpG oligonucleotide and yield an identical mononucleotide 2'-deoxyribonucleoside 5'-monophosphate (5'-dNMP). Compared with results obtained without P1 treatment, we achieved 4.4 times higher sensitivity and a wider concentration range for mC detection with a resolution capable of detecting a subtle methylated cytosine difference in the CpG oligonucleotides (60mer).
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Affiliation(s)
- Dai Kato
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
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Lewandowska J, Bartoszek A. DNA methylation in cancer development, diagnosis and therapy--multiple opportunities for genotoxic agents to act as methylome disruptors or remediators. Mutagenesis 2011; 26:475-87. [PMID: 21551264 DOI: 10.1093/mutage/ger019] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The role of DNA methylation and recently discovered hydroxymethylation in the function of the human epigenome is currently one of the hottest topics in the life sciences. Progress in this field of research has been further accelerated by the discovery that alterations in the methylome are not only associated with key functions of cells and organisms, such as development, differentiation and gene expression, but may underlie a number of human diseases, including cancer. This review describes both well established and more recent observations concerning alterations in the methylome, i.e. the global and local distribution of 5-methylcytosines, involved in its normal functions. Then, the changes in DNA methylation pattern seen in cancer cells are discussed in the context of their utilisation in cancer diagnostics and treatment. On this basis, comparisons are made between natural covalent DNA modification and that induced by genotoxic agents, chemical carcinogens and antitumour drugs as regards their impact on epigenetic mechanisms. The available data suggest that DNA damage by genotoxins can mimic epigenetic markers and in consequence disrupt the proper function of the epigenome. On the other hand, the same processes in cancer cells, e.g. DNA demethylation as a result of DNA methyltransferase blocking or the induction of DNA repair by DNA adducts, may restore the activity of hypermethylated anticancer genes. The observed multiple mechanisms by which genotoxic agents directly affect methylome function suggest that chemical carcinogens act primarily as epigenome disruptors, whereas mutations are secondary events that occur at later stages of cancer development when genome-protecting mechanisms have already been deregulated.
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Affiliation(s)
- Joanna Lewandowska
- Chemical Faculty, Gdansk University of Technology, ul. Narutowicza 11/12, 80-233 Gdańsk, Poland
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Armstrong KM, Bermingham EN, Bassett SA, Treloar BP, Roy NC, Barnett MPG. Global DNA methylation measurement by HPLC using low amounts of DNA. Biotechnol J 2011; 6:113-7. [PMID: 21053336 DOI: 10.1002/biot.201000267] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Epigenetic changes in chromatin structure can influence gene expression without affecting the DNA sequence. The most commonly studied epigenetic modification, DNA methylation, has been implicated in normal tissue development and disease progression, and can be influenced by diet and other environmental factors. Current HPLC methods of determining DNA methylation may require relatively large amounts of DNA (50 μg); as many tissues have low DNA yields, this can be hard to achieve. We isolated DNA from mouse colon and liver in a study investigating post-natal supplementation with selenium and folic acid. After optimizing the methods to account for lower initial DNA amounts, we digested 3 μg of DNA to deoxynucleotide monophosphates, then purified and quantified it. Samples were analyzed by reversed-phase HPLC to determine global DNA methylation levels using commercial nucleotide standards. The HPLC column was cooled to 6(C (reducing run time), and detection was at 280 nm (UV). We showed that methylated cytosine can be accurately and reproducibly measured in as little as 3 μg of DNA using this HPLC analysis method (within-assay CV <2%). We also used this method to detect reduced DNA methylation in liver (P = 0.009) in response to post-natal supplementation with selenium and folate.
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Affiliation(s)
- Kelly M Armstrong
- Agri-Foods & Health, Food & Textiles Group, AgResearch Grasslands, Palmerston North, New Zealand
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27
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Wang X, Suo Y, Yin R, Shen H, Wang H. Ultra-performance liquid chromatography/tandem mass spectrometry for accurate quantification of global DNA methylation in human sperms. J Chromatogr B Analyt Technol Biomed Life Sci 2011; 879:1647-52. [PMID: 21536504 DOI: 10.1016/j.jchromb.2011.04.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Revised: 03/29/2011] [Accepted: 04/03/2011] [Indexed: 11/26/2022]
Abstract
Aberrant DNA methylation in human sperms has been proposed to be a possible mechanism associated with male infertility. We developed an ultra-performance liquid chromatography/tandem mass spectrometry (UPLC-MS/MS) method for rapid, sensitive, and specific detection of global DNA methylation level in human sperms. Multiple-reaction monitoring (MRM) mode was used in MS/MS detection for accurate quantification of DNA methylation. The intra-day and inter-day precision values of this method were within 1.50-5.70%. By using 2-deoxyguanosine as an internal standard, UPLC-MS/MS method was applied for the detection of global DNA methylation levels in three cultured cell lines. DNA methyltransferases inhibitor 5-aza-2'-deoxycytidine can significantly reduce global DNA methylation levels in treated cell lines, showing the reliability of our method. We further examined global DNA methylation levels in human sperms, and found that global methylation values varied from 3.79% to 4.65%. The average global DNA methylation level of sperm samples washed only by PBS (4.03%) was relatively lower than that of sperm samples in which abnormal and dead sperm cells were removed by density gradient centrifugation (4.25%), indicating the possible aberrant DNA methylation level in abnormal sperm cells. Clinical application of UPLC-MS/MS method in global DNA methylation detection of human sperms will be useful in human sperm quality evaluation and the study of epigenetic mechanisms responsible for male infertility.
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Affiliation(s)
- Xiaoli Wang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
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28
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Yang I, Fortin MC, Richardson JR, Buckley B. Fused-core silica column ultra-performance liquid chromatography-ion trap tandem mass spectrometry for determination of global DNA methylation status. Anal Biochem 2010; 409:138-43. [PMID: 20950581 DOI: 10.1016/j.ab.2010.10.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Accepted: 10/08/2010] [Indexed: 10/19/2022]
Abstract
Epigenetic modifications, such as DNA methylation, play key roles in transcriptional regulation of gene expression. More recently, global DNA methylation levels have been documented to be altered in several diseases, including cancer, and as the result of exposure to environmental toxicants. Based on the potential use of global DNA methylation status as a biomarker of disease status and exposure to environmental toxicants, we sought to develop a rapid, sensitive, and precise analytical method for the quantitative measurement of global DNA methylation status using ultra-performance liquid chromatography with detection by ion trap tandem mass spectrometry. Using a fused-core silica column, 2'-deoxyguanosine (2dG) and 5-methyl-2'-deoxycytidine (5mdC) were resolved in less than 1 min with detection limits of 0.54 and 1.47 fmol for 5mdC and 2dG, respectively. The accuracy of detection was 95% or higher, and the day-to-day coefficient of variation was found to be 3.8%. The method was validated by quantification of global DNA methylation status following treatment of cells with the DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine, which reduced DNA methylation from 3.1% in control cells to 1.1% in treated cells. The sensitivity and high throughput of this method rend it suitable for large-scale analysis of epidemiological and clinical DNA samples.
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Affiliation(s)
- Ill Yang
- Environmental and Occupational Health Sciences Institute, A Joint Institute of Rutgers University and the University of Medicine and Dentistry of New Jersey (UMDNJ), Piscataway, NJ 08854, USA
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29
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Wrobel K, Landero Figueroa JA, Zaina S, Lund G, Wrobel K. Phosphorus and osmium as elemental tags for the determination of global DNA methylation—A novel application of high performance liquid chromatography inductively coupled plasma mass spectrometry in epigenetic studies. J Chromatogr B Analyt Technol Biomed Life Sci 2010; 878:609-14. [DOI: 10.1016/j.jchromb.2010.01.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2009] [Accepted: 01/11/2010] [Indexed: 12/29/2022]
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