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Marchante-Gayón JM, Nicolás Carcelén J, Potes Rodríguez H, Pineda-Cevallos D, Rodas Sánchez L, González-Gago A, Rodríguez-González P, García Alonso JI. Quantification of modified nucleotides and nucleosides by isotope dilution mass spectrometry. MASS SPECTROMETRY REVIEWS 2024; 43:998-1018. [PMID: 37597182 DOI: 10.1002/mas.21865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/26/2023] [Accepted: 08/06/2023] [Indexed: 08/21/2023]
Abstract
Epigenetic modifications are closely related to certain disorders of the organism, including the development of tumors. One of the main epigenetic modifications is the methylation of DNA cytosines, 5-methyl-2'-deoxycycytidine. Furthermore, 5-mdC can be oxidized to form three new modifications, 5-(hydroxymethyl)-2'-deoxycytidine, 5-formyl-2'-deoxycytidine, and 5-carboxy-2'-deoxycytidine. The coupling of liquid chromatography with tandem mass spectrometry has been widely used for the total determination of methylated DNA cytosines in samples of biological and clinical interest. These methods are based on the measurement of the free compounds (e.g., urine) or after complete hydrolysis of the DNA (e.g., tissues) followed by a preconcentration, derivatization, and/or clean-up step. This review highlights the main advances in the quantification of modified nucleotides and nucleosides by isotope dilution using isotopically labeled analogs combined with liquid or gas chromatography coupled to mass spectrometry reported in the last 20 years. The different possible sources of labeled compounds are indicated. Special emphasis has been placed on the different types of chromatography commonly used (reverse phase and hydrophilic interaction liquid chromatography) and the derivatization methods developed to enhance chromatographic resolution and ionization efficiency. We have also revised the application of bidimensional chromatography and indicated significant biological and clinical applications of these determinations.
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Affiliation(s)
- Juan M Marchante-Gayón
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - Jesús Nicolás Carcelén
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - Helí Potes Rodríguez
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - Daniela Pineda-Cevallos
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - Laura Rodas Sánchez
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - Adriana González-Gago
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - Pablo Rodríguez-González
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
| | - Jose I García Alonso
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Oviedo, Spain
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2
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Zhao H, Zhang X, Zuo L, Li L, Yang H, Zhang M, Wang N, Jia Q, Liu Y. A new methodology to reveal potential nucleic acid modifications associated with the risk of endometrial cancer through dispersive solid-phase extraction coupled with UHPLC-QE-Orbitrap-MS/MS and HPLC-UV. Anal Bioanal Chem 2024; 416:2439-2452. [PMID: 38400939 DOI: 10.1007/s00216-024-05206-y] [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: 11/21/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/26/2024]
Abstract
Nucleic acid modifications have attracted increasing attention in recent years since they have been found to be related to a number of diseases including cancer. Previous studies have shown that the early development of endometrial cancer (EC) is often accompanied by changes in methylation levels of related genes, and the expression of related proteins that regulate reactive oxygen species (ROS) shows significant differences in EC cells and tissues. However, it has not been reported whether nucleic acid modifications related to methylation or ROS can serve as biomarkers for EC. Accurate quantification of these nucleic acid modifications still has challenges because their amounts in urine are very low and the interferences in urine are complicated. In this study, a novel dispersive solid-phase extraction (DSPE) method based on chitosan-carbon nanotube-Al2O3 (CS-CNT-Al2O3) has been established for the analysis of 5-hydroxymethyluracil (5 mU), 5-methyl-2'-deoxycytidine (5-mdC), 5-hydroxymethyl-2'-deoxycytidine (5-hmdC), 5-formyl-2'-deoxycytidine (5-fdC), and 8-hydroxy-2'-deoxyguanosine (8-OHdG) in EC patient urine samples coupled with UHPLC-QE-Orbitrap-MS/MS and HPLC-UV. Firstly, the synthesis of the CS-CNT-Al2O3 nanocomposite was conducted by a sono-coprecipitation method and was characterized by scanning electron microscope (SEM), energy dispersive spectrometer (EDS), and Fourier transform infrared (FTIR). Under the optimal extraction conditions of DSPE, we successfully quantified 5 mU, 5-mdC, 5-hmdC, 5-fdC, and 8-OHdG in urine samples from 37 EC patients and 39 healthy controls. The results showed that there were significant differences in the levels of 5-mdC, 5-hmdC, 5-fdC, and 8-OHdG in EC patients compared to the healthy control group. The receiver operator characteristic (ROC) curve analysis was carried out to evaluate the potential of 5-mdC, 5-hmdC, 5-fdC, and 8-OHdG to distinguish EC patients from healthy volunteers. The area under the curve (AUC) for 5-mdC, 5-hmdC, 5-fdC, and 8-OHdG was 0.7412, 0.667, 0.8438, and 0.7981, respectively. It indicated that 5-mdC, 5-hmdC, 5-fdC, and 8-OHdG had certain potential in distinguishing between EC patients and healthy volunteers and they could act as potential non-invasive biomarkers for early diagnosis of EC. Moreover, the present study would stimulate investigations of the effects of nucleic acid modifications on the initiation and progression of EC.
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Affiliation(s)
- Huanhuan Zhao
- Department of Obstetrics and Gynecology, Fourth Hospital of Hebei Medical University, Shijiazhuang, 050011, Hebei Province, People's Republic of China
| | - Xiaoguang Zhang
- Core Facilities and Centers, Hebei Medical University, Shijiazhuang, 050017, Hebei Province, People's Republic of China
| | - Lujie Zuo
- College of Pharmacy, Hebei Medical University, Shijiazhuang, 050017, Hebei Province, People's Republic of China
| | - Li Li
- Department of Obstetrics and Gynecology, Fourth Hospital of Hebei Medical University, Shijiazhuang, 050011, Hebei Province, People's Republic of China
| | - Hongfang Yang
- Department of Medical Laboratory, Fourth Hospital of Hebei Medical University, Shijiazhuang, 050011, Hebei Province, People's Republic of China
| | - Mengyu Zhang
- Department of Obstetrics and Gynecology, Fourth Hospital of Hebei Medical University, Shijiazhuang, 050011, Hebei Province, People's Republic of China
| | - Na Wang
- Department of Obstetrics and Gynecology, Fourth Hospital of Hebei Medical University, Shijiazhuang, 050011, Hebei Province, People's Republic of China
| | - Qingzhong Jia
- College of Pharmacy, Hebei Medical University, Shijiazhuang, 050017, Hebei Province, People's Republic of China.
| | - Yan Liu
- College of Pharmacy, Hebei Medical University, Shijiazhuang, 050017, Hebei Province, People's Republic of China.
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3
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Janoš T, Ottenbros I, Bláhová L, Šenk P, Šulc L, Pálešová N, Sheardová J, Vlaanderen J, Čupr P. Effects of pesticide exposure on oxidative stress and DNA methylation urinary biomarkers in Czech adults and children from the CELSPAC-SPECIMEn cohort. ENVIRONMENTAL RESEARCH 2023; 222:115368. [PMID: 36716809 PMCID: PMC10009299 DOI: 10.1016/j.envres.2023.115368] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 01/22/2023] [Accepted: 01/24/2023] [Indexed: 05/13/2023]
Abstract
Current-use pesticide (CUP) exposure occurs mainly through diet and environmental application in both agricultural and urban settings. While pesticide exposure has been associated with many adverse health outcomes, the intermediary molecular mechanisms are still not completely elucidated. Among others, their roles in epigenetics (DNA methylation) and DNA damage due to oxidative stress are presumed. Scientific evidence on urinary biomarkers of such body response in general population is limited, especially in children. A total of 440 urine samples (n = 110 parent-child pairs) were collected during the winter and summer seasons in order to describe levels of overall DNA methylation (5-mC, 5-mdC, 5-hmdC, 7-mG, 3-mA) and oxidative stress (8-OHdG) biomarkers and investigate their possible associations with metabolites of pyrethroids (3-PBA, t/c-DCCA), chlorpyrifos (TCPY), and tebuconazole (TEB-OH). Linear mixed-effects models accounting for intraindividual and intrahousehold correlations were utilized. We applied false discovery rate procedure to account for multiplicity and adjusted for potential confounding variables. Higher urinary levels of most biological response biomarkers were measured in winter samples. In adjusted repeated measures models, interquartile range (IQR) increases in pyrethroid metabolites were associated with higher oxidative stress. t/c-DCCA and TCPY were associated with higher urinary levels of cytosine methylation biomarkers (5-mC and/or 5-mdC). The most robust association was observed for tebuconazole metabolite with 3-mA (-15.1% change per IQR increase, 95% CI = -23.6, -5.69) suggesting a role of this pesticide in reduced demethylation processes through possible DNA glycosylase inhibition. Our results indicate an urgent need to extend the range of analyzed environmental chemicals such as azole pesticides (e.g. prothioconazole) in human biomonitoring studies. This is the first study to report urinary DNA methylation biomarkers in children and associations between CUP metabolites and a comprehensive set of biomarkers including methylated and oxidized DNA alterations. Observed associations warrant further large-scale research of these biomarkers and environmental pollutants including CUPs.
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Affiliation(s)
- Tomáš Janoš
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic
| | - Ilse Ottenbros
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands; Center for Sustainability, Environment and Health, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Lucie Bláhová
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic
| | - Petr Šenk
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic
| | - Libor Šulc
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic
| | - Nina Pálešová
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic
| | - Jessica Sheardová
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic
| | - Jelle Vlaanderen
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands
| | - Pavel Čupr
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic.
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Simultaneous Determination of Methylated Nucleosides by HILIC-MS/MS Revealed Their Alterations in Urine from Breast Cancer Patients. Metabolites 2022; 12:metabo12100973. [PMID: 36295875 PMCID: PMC9612034 DOI: 10.3390/metabo12100973] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/27/2022] [Accepted: 10/11/2022] [Indexed: 11/07/2022] Open
Abstract
RNA methylation plays a vital role in the pathogenesis of a variety of diseases including cancer, and aberrant levels of modified nucleosides in RNA were revealed to be related to cancer. Urine is a favored source for biomarker discovery due to the non-invasion to patients. Herein, we developed a sensitive hydrophilic interaction liquid chromatography tandem mass spectrometry (HILIC–MS/MS) method combined with stable isotope dilution for accurate quantification of methylated nucleosides in human urine. With this method, we successfully quantified ten methylated nucleosides in urine samples collected from healthy controls and breast cancer patients. We found N6-methyladenosine (m6A), 2′-O-methyladenosine (Am), N1-methyladenosine (m1A), N6,2′-O-dimethyladenosine (m6Am), N1-methylguanosine (m1G), 2′-O-methylguanosine (Gm), 5-methylcytidine (m5C) and 2′-O-methylcytidine (Cm) were all decreased in early-stage breast cancer patients, and a nomogram prediction model was constructed. Locally advanced breast cancer patients exhibited elevated levels of urinary 2′-O-methylated nucleosides in comparison to early-stage breast cancer patients. Together, we developed a robust method for the simultaneous determination of methylated nucleosides in human urine, and the results revealed an association between the contents of urinary methylated nucleosides and the occurrence of breast cancer, which may stimulate future studies about the regulatory roles of these methylated nucleosides in the initiation and progression of breast cancer.
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Lovreglio P, Stufano A, Andreoli R, Tomasi C, Cagnazzi P, Barbieri A, Soleo L, De Palma G. Urinary biomarkers of nucleic acid oxidation and methylation in workers exposed to low concentrations of benzene. Toxicol Lett 2020; 331:235-241. [PMID: 32562636 DOI: 10.1016/j.toxlet.2020.06.010] [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: 12/01/2019] [Revised: 06/10/2020] [Accepted: 06/16/2020] [Indexed: 11/24/2022]
Abstract
The study aims to investigate the influence of exposure to low concentrations of benzene on urinary biomarkers of nucleic acid oxidative damage and methylation. Benzene exposure was characterized for 93 coke production workers by measuring both airborne benzene and S-phenylmercapturic acid (SPMA) and unmodified benzene (U-B) in urine samples, collected at the end of the shift (ES) and at the next morning before shift (next BS). In the same urinary samples, biomarkers of nucleic acid oxidative damage and methylation were determined. Urinary concentrations of cotinine and creatinine were also determined to evaluate the smoking effect and to normalize urinary concentrations of analytes, respectively. The biomarkers of benzene internal dose, of oxidative damage (8-hydroxyy-7,8-dihydroguanine, 8-hydroxy-7,8-dihydroguanosine and 8-hydroxy-7,8-2'deoxyguanosine) and some of the biomarkers of nucleic acid methylation (5-Methyl-Cytosine, 1-Methyl-Guanine and 7-Methyl-Guanine) were higher in the ES than the next BS samples. Positive associations between ES 5-Methyl-Cytosine and both SPMA and U-B were found. In conclusion, occupational exposure to low levels of benzene seems to be related to urinary ES 5-Methyl-Cytosine that could be a possible biomarker to evaluate the changes of the nucleic acid methylation status.
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Affiliation(s)
- Piero Lovreglio
- Interdisciplinary Department of Medicine, Section of Occupational Medicine, University of Bari Aldo Moro, Bari, Italy.
| | - Angela Stufano
- Interdisciplinary Department of Medicine, Section of Occupational Medicine, University of Bari Aldo Moro, Bari, Italy
| | - Roberta Andreoli
- Department of Medicine and Surgery, Laboratory of Industrial Toxicology, University of Parma, Parma, Italy; Centre for Research in Toxicology (CERT), University of Parma, Parma, Italy
| | - Cesare Tomasi
- Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, Section of Public Health and Human Sciences, University of Brescia, Brescia, Italy
| | - Paola Cagnazzi
- Interdisciplinary Department of Medicine, Section of Occupational Medicine, University of Bari Aldo Moro, Bari, Italy
| | - Anna Barbieri
- Department of Medical and Surgical Science, Section of Public Health and Human Sciences, University of Bologna, Bologna, Italy
| | - Leonardo Soleo
- Interdisciplinary Department of Medicine, Section of Occupational Medicine, University of Bari Aldo Moro, Bari, Italy
| | - Giuseppe De Palma
- Department of Medical and Surgical Specialties, Radiological Sciences and Public Health, Section of Public Health and Human Sciences, University of Brescia, Brescia, Italy
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6
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MS Analysis of DNA Modifications in Urinary/Body Fluids. Methods Mol Biol 2020. [PMID: 32822026 DOI: 10.1007/978-1-0716-0876-0_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Analytical techniques based on mass spectrometry allow to analyze DNA modifications in body fluids. Here we describe two chromatographic methods that can be used for the simultaneous determination of the modified DNA bases and nucleosides in the same urine sample: isotope-dilution automated online two-dimensional ultraperformance liquid chromatography with tandem mass spectrometry (2D-UPLC-MS/MS) and high-performance liquid chromatography coupled with gas chromatography and mass spectrometry (HPLC/GC/MS).
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7
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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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Sun H, Wang H, Bai W, Bao L, Lin J, Li Y. Sensitive electrogenerated chemiluminescence biosensing method for the determination of DNA hydroxymethylation based on Ru(bpy)32+-doped silica nanoparticles labeling and MoS2-poly(acrylic acid) nanosheets modified electrode. Talanta 2019; 191:350-356. [DOI: 10.1016/j.talanta.2018.08.070] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 08/19/2018] [Accepted: 08/27/2018] [Indexed: 12/11/2022]
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Asenso J, Wang L, Du Y, Liu QH, Xu BJ, Guo MZ, Tang DQ. Advances in detection and quantification of methylcytosine and its derivatives. J Sep Sci 2018; 42:1105-1116. [PMID: 30575277 DOI: 10.1002/jssc.201801100] [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: 10/21/2018] [Revised: 11/21/2018] [Accepted: 12/16/2018] [Indexed: 11/08/2022]
Abstract
Methylation of the fifth carbon atom in cytosine is an epigenetic modification of deoxyribonucleic acid that plays important roles in numerous cellular processes and disease pathogenesis. Three additional states of cytosine, that is, 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine, have been identified and associated with the diagnosis and/or prognosis of diseases. However, accurate measurement of those intermediates is a challenge since their global levels are relatively low. A number of innovative methods have been developed to detect and quantify these compounds in biological samples, such as blood, tissue and urine, etc. This review focuses on recent advancement in detection and quantification of four cytosine modifications, based on which, the development, diagnosis, and prognosis of diseases could be monitored through non-invasive procedures.
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Affiliation(s)
- James Asenso
- Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China
| | - Liang Wang
- Department of Bioinformatics, School of Medical Informatics, Xuzhou Medical University, Xuzhou, P. R. China
| | - Yan Du
- Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China.,Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China
| | - Qing-Hua Liu
- Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China
| | - Bing-Ju Xu
- Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China
| | - Meng-Zhe Guo
- Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China.,Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China
| | - Dao-Quan Tang
- Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China.,Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China
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Guo C, Xie C, Chen Q, Cao X, Guo M, Zheng S, Wang Y. A novel malic acid-enhanced method for the analysis of 5-methyl-2'-deoxycytidine, 5-hydroxymethyl-2'-deoxycytidine, 5-methylcytidine and 5-hydroxymethylcytidine in human urine using hydrophilic interaction liquid chromatography-tandem mass spectrometry. Anal Chim Acta 2018; 1034:110-118. [PMID: 30193624 DOI: 10.1016/j.aca.2018.06.081] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 06/29/2018] [Accepted: 06/30/2018] [Indexed: 12/30/2022]
Abstract
5-Methyl-2'-deoxycytidine (5-mdC), 5-hydroxymethyl-2'-deoxycytidine (5-hmdC), 5-methylcytidine (5-mrC) and 5-hydroxymethylcytidine (5-hmrC) are epigenetic marks of DNA and RNA, and aberrant levels of these modified nucleosides were found to be associated with various cancers. Urine is a preferred source of biological fluid for biomarker discovery because the sample collection process is not invasive to patients. Herein, we developed a novel malic acid-enhanced hydrophilic interaction liquid chromatography-tandem mass spectrometry (HILIC-MS/MS) method for sensitive and simultaneous quantification of the modified cytosine nucleosides in human urine. Malic acid markedly increased the detection sensitivities of all four cytosine nucleosides, with the limits of detection (LODs) for 5-mdC, 5-hmdC, 5-mrC and 5-hmrC being 0.025, 0.025, 0.025 and 0.050 fmol, respectively. By using this method, we demonstrated, for the first time, the presence of 5-hmrC in human urine, and we successfully quantified 5-mdC, 5-hmdC, 5-mrC and 5-hmrC in urine samples collected from 90 patients with colorectal cancer (CRC) and 90 healthy controls. We found that the levels of 5-mdC, 5-hmdC, 5-mrC and 5-hmrC in urine were all substantially decreased in CRC patients, suggesting that these modified nucleosides might have great potential to be noninvasive biomarkers for early detection and prognosis of CRC. Together, we established a novel and sensitive method for detecting 5-methylated and 5-hydroxymethylated cytosine nucleosides in human urine and the results from this study may stimulate future investigations about the regulatory roles of these cytosine derivatives in the initiation and development of CRC.
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Affiliation(s)
- Cheng Guo
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China.
| | - Cong Xie
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China; College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, China
| | - Qin Chen
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Xiaoji Cao
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, China
| | - Mengzhe Guo
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical College, Xuzhou, Jiangsu, 221004, China
| | - Shu Zheng
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310009, China
| | - Yinsheng Wang
- Department of Chemistry, University of California, Riverside, CA, 92521, United States.
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11
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Guo M, Zhang L, Du Y, Du W, Liu D, Guo C, Pan Y, Tang D. Enrichment and Quantitative Determination of 5-(Hydroxymethyl)-2′-deoxycytidine, 5-(Formyl)-2′-deoxycytidine, and 5-(Carboxyl)-2′-deoxycytidine in Human Urine of Breast Cancer Patients by Magnetic Hyper-Cross-Linked Microporous Polymers Based on Polyionic Liquid. Anal Chem 2018; 90:3906-3913. [DOI: 10.1021/acs.analchem.7b04755] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Mengzhe Guo
- Jiangsu Key Laboratory
of New Drug Research and Clinical Pharmacy, Department of Pharmaceutical Analysis, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
| | - Liyan Zhang
- Jiangsu Key Laboratory
of New Drug Research and Clinical Pharmacy, Department of Pharmaceutical Analysis, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
| | - Yan Du
- Jiangsu Key Laboratory
of New Drug Research and Clinical Pharmacy, Department of Pharmaceutical Analysis, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
| | - Wencheng Du
- Jiangsu Key Laboratory
of New Drug Research and Clinical Pharmacy, Department of Pharmaceutical Analysis, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
| | - Dantong Liu
- Jiangsu Key Laboratory
of New Drug Research and Clinical Pharmacy, Department of Pharmaceutical Analysis, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
| | - Cheng Guo
- Cancer Institute,
The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Yuanjiang Pan
- Department of Chemistry, Zhejiang University, Hangzhou 310009, China
| | - Daoquan Tang
- Jiangsu Key Laboratory
of New Drug Research and Clinical Pharmacy, Department of Pharmaceutical Analysis, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
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12
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Pan Y, Wang X, Yeung LWY, Sheng N, Cui Q, Cui R, Zhang H, Dai J. Dietary exposure to di-isobutyl phthalate increases urinary 5-methyl-2'-deoxycytidine level and affects reproductive function in adult male mice. J Environ Sci (China) 2017; 61:14-23. [PMID: 29191310 DOI: 10.1016/j.jes.2017.04.036] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 04/27/2017] [Accepted: 04/28/2017] [Indexed: 06/07/2023]
Abstract
Phthalates are a large family of ubiquitous environmental pollutants suspected of being endocrine disruptors. Epidemiological studies have associated phthalate metabolites with decreased reproductive parameters and linked phthalate exposure with the level of urinary 5-methyl-2'-deoxycytidine (5mdC, a product of methylated DNA). In this study, adult male mice were exposed to 450mg di-isobutyl phthalate (DiBP)/(kg·day) via dietary exposure for 28days. Mono-isobutyl phthalate (MiBP, the urinary metabolite) and reproductive function parameters were determined. The levels of 5mdC and 5-hydroxymethyl-2'-deoxycytidine (5hmdC) were measured in urine to evaluate if their contents were also altered by DiBP exposure in this animal model. Results showed that DiBP exposure led to a significant increase in the urinary 5mdC level and significant decreases in sperm concentration and motility in the epididymis, accompanied with reduced testosterone levels and down-regulation of the P450 cholesterol side-chain cleavage enzyme (P450scc) gene in the mice testes. Our findings indicated that exposure to DiBP increased the urinary 5mdC levels, which supported our recent epidemiological study about the associations of urinary 5mdC with phthalate exposure in the male human population. In addition, DiBP exposure impaired male reproductive function, possibly by disturbing testosterone levels; P450scc might be a major steroidogenic enzyme targeted by DiBP or other phthalates.
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Affiliation(s)
- Yitao Pan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoyang Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Leo W Y Yeung
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Örebro, SE -70182, Sweden
| | - Nan Sheng
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qianqian Cui
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ruina Cui
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hongxia Zhang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiayin Dai
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
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13
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Prostate Cancer Patients-Negative Biopsy Controls Discrimination by Untargeted Metabolomics Analysis of Urine by LC-QTOF: Upstream Information on Other Omics. Sci Rep 2016; 6:38243. [PMID: 27910903 PMCID: PMC5133625 DOI: 10.1038/srep38243] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/04/2016] [Indexed: 01/06/2023] Open
Abstract
The existing clinical biomarkers for prostate cancer (PCa) diagnosis are far from ideal (e.g., the prostate specific antigen (PSA) serum level suffers from lack of specificity, providing frequent false positives leading to over-diagnosis). A key step in the search for minimum invasive tests to complement or replace PSA should be supported on the changes experienced by the biochemical pathways in PCa patients as compared to negative biopsy control individuals. In this research a comprehensive global analysis by LC–QTOF was applied to urine from 62 patients with a clinically significant PCa and 42 healthy individuals, both groups confirmed by biopsy. An unpaired t-test (p-value < 0.05) provided 28 significant metabolites tentatively identified in urine, used to develop a partial least squares discriminant analysis (PLS-DA) model characterized by 88.4 and 92.9% of sensitivity and specificity, respectively. Among the 28 significant metabolites 27 were present at lower concentrations in PCa patients than in control individuals, while only one reported higher concentrations in PCa patients. The connection among the biochemical pathways in which they are involved (DNA methylation, epigenetic marks on histones and RNA cap methylation) could explain the concentration changes with PCa and supports, once again, the role of metabolomics in upstream processes.
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14
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Rozalski R, Gackowski D, Siomek‐Gorecka A, Banaszkiewicz Z, Olinski R. Urinary Measurement of Epigenetic DNA Modifications: A Non-Invasive Assessment of the Whole-Body Epigenetic Status in Healthy Subjects and Colorectal Cancer Patients. ChemistryOpen 2016; 5:550-553. [PMID: 28032024 PMCID: PMC5167278 DOI: 10.1002/open.201600103] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Indexed: 11/24/2022] Open
Abstract
Active mechanism of DNA demethylation can be responsible for the activation of previously silenced genes. Products of 5-methylcytosine oxidation are released into the bloodstream and eventually excreted with urine. Therefore, whole-body epigenetic status can be assessed non-invasively on the basis of the urinary excretion of a broad spectrum of epigenetic modifications: 5-hydroxymethylcytosine (5-hmCyt), 5-formylcytosine (5-fCyt), 5-carboxycytosine (5-caCyt), and 5-hydroxymethyluracil (5-hmUra). We have developed a specific and sensitive, isotope-dilution, automated, online, two-dimensional ultra-performance liquid chromatography system with tandem mass spectrometry (2D UPLC-MS/MS) to measure 5-hmCyt, 5-fCyt, 5-caCyt, and their deoxynucleosides in the same urine sample. Human urine contains all of the modifications except from 5-formyl-2'-deoxycytidine (5-fdC) and 5-carboxy-2'-deoxycytidine (5-cadC). A highly significant difference in the urinary excretion of 5-(hydroxymethyl)-2'-deoxycytidine (5-hmdC) was found between healthy subjects and colorectal cancer patients (3.5 vs. 7.8 nmol mmol-1 creatinine, respectively), as well as strong correlations between the majority of analyzed compounds.
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Affiliation(s)
- Rafal Rozalski
- Department of Clinical BiochemistryFaculty of PharmacyNicolaus Copernicus University in ToruńCollegium Medicum in BydgoszczKarlowicza 2485-092BydgoszczPoland
| | - Daniel Gackowski
- Department of Clinical BiochemistryFaculty of PharmacyNicolaus Copernicus University in ToruńCollegium Medicum in BydgoszczKarlowicza 2485-092BydgoszczPoland
| | - Agnieszka Siomek‐Gorecka
- Department of Clinical BiochemistryFaculty of PharmacyNicolaus Copernicus University in ToruńCollegium Medicum in BydgoszczKarlowicza 2485-092BydgoszczPoland
| | - Zbigniew Banaszkiewicz
- Department of SurgeryFaculty of MedicineNicolaus Copernicus University in ToruńCollegium Medicum in BydgoszczUjejskiego 7585-168BydgoszczPoland
| | - Ryszard Olinski
- Department of Clinical BiochemistryFaculty of PharmacyNicolaus Copernicus University in ToruńCollegium Medicum in BydgoszczKarlowicza 2485-092BydgoszczPoland
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15
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Pan Y, Jing J, Yeung LWY, Sheng N, Zhang H, Yao B, Dai J. Associations of urinary 5-methyl-2'-deoxycytidine and 5-hydroxymethyl-2'-deoxycytidine with phthalate exposure and semen quality in 562 Chinese adult men. ENVIRONMENT INTERNATIONAL 2016; 94:583-590. [PMID: 27346742 DOI: 10.1016/j.envint.2016.06.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 06/14/2016] [Accepted: 06/16/2016] [Indexed: 05/27/2023]
Abstract
5-methyl-2'-deoxycytidine (5mdC) and 5-hydroxymethyl-2'-deoxycytidine (5hmdC), products of DNA methylation and hydroxymethylation processes, have been detected previously in human urine, but their associations with environmental chemicals or healthy outcomes are unclear. The present investigation explored the associations between urinary 5mdC and 5hmdC with phthalate exposure and semen quality. We assessed semen parameters including sperm concentration, motility, and morphology, before measuring urinary 5mdC, 5hmdC and 13 phthalate metabolites among 562 subfertile men from Nanjing, China. Urinary 5mdC and 5hmdC were positively associated with the levels of low molecular weight phthalate metabolites (Low-MWP), high molecular weight phthalate metabolites (High-MWP), and the sum of all phthalate metabolites (ΣPAEs), respectively. Urinary 5mdC was associated with below-reference sperm concentration (odds ratios for increasing quartiles=1.0, 2.2, 3.0, 2.0; p for trend =0.02), sperm motility (1.0, 1.1, 1.9, 1.3; p for trend =0.05), and sperm morphology (1.0, 1.4, 2.3, 1.5; p for trend =0.05). Sperm concentration was associated with the highest quartile of urinary 5hmdC [odds ratio=1.9 (95% CI: 1.1, 3.6)]. Our findings showed significant associations between urinary 5mdC and 5hmdC with phthalate metabolites and semen parameters, which suggested urinary 5mdC and 5hmdC may be promising biomarkers in future epidemiological studies.
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Affiliation(s)
- Yitao Pan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Jun Jing
- Reproductive Medical Center, Nanjing Jinling Hospital, Nanjing University, School of Medicine, Nanjing 210002, Jiangsu, PR China
| | - Leo W Y Yeung
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, SE-70182 Örebro, Sweden
| | - Nan Sheng
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Hongxia Zhang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Bing Yao
- Reproductive Medical Center, Nanjing Jinling Hospital, Nanjing University, School of Medicine, Nanjing 210002, Jiangsu, PR China.
| | - Jiayin Dai
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PR China.
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16
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Detection of 1,N2-propano-2′-deoxyguanosine in human urine by stable isotope dilution UHPLC–MS/MS analysis. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1023-1024:68-71. [DOI: 10.1016/j.jchromb.2016.04.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 04/15/2016] [Accepted: 04/16/2016] [Indexed: 11/18/2022]
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17
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Yin R, Mo J, Lu M, Wang H. Detection of Human Urinary 5-Hydroxymethylcytosine by Stable Isotope Dilution HPLC-MS/MS Analysis. Anal Chem 2015; 87:1846-52. [DOI: 10.1021/ac5038895] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Ruichuan Yin
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jiezhen Mo
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Meiling Lu
- Chemical
Analysis Group, Agilent Technologies, Beijing 100102, China
| | - Hailin Wang
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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18
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Podjava A, Kistkin S, Ausekle E, Mekss P, Zicmanis A. Zwitterionic sulfonates as m/z shift reagents for 5-methylcytosine detection in deoxyribonucleic acids (DNA) using flow injection analysis and electrospray ionization mass spectrometry. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2015; 21:659-667. [PMID: 26353988 DOI: 10.1255/ejms.1383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
5-Methylcytosine (5-MC) is an important epigenetic modification of DNA. Abnormally high concentrations of this substance appear because of the hypermethylation of cytosine. Therefore, the measurement of the quantity of this compound in mammals is of great importance. Recently, we reported that several imidazolium-based zwitterionic sulfonates form complexes with 5-MC in solution, which can be studied by electrospray ionisation mass spectrometry (ESI-MS). It is shown in this paper that such an association can be utilised for the detection of 5-MC in a DNA sample using high-throughput a flow injection analysis ESI-MS method. A variety of the sulfonate zwitterions have been tested as m/z shift reagents to increase the selectivity of the analysis. It is shown that either of the zwitterions can be used without the loss of sensitivity. The performance of the method was tested in terms of linearity range, sensitivity, intra- and between-day precision and accuracy, matrix effect and carryover. The method described is characterised by simplicity, a good limit of quantitation (1 pg injected) and low run times (at least 50 injections per hour). In addition, high-performance liquid chromatography and tandem mass spectrometry are not required. The possibility exists to widen the scope of the method to other amidine-containing compounds present in more complicated matrices.
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Affiliation(s)
- Anton Podjava
- Department of Chemistry, University of Latvia, Riga, Latvia.
| | | | - Elina Ausekle
- Department of Chemistry, University of Latvia, Riga, Latvia.
| | - Peteris Mekss
- Department of Chemistry, University of Latvia, Riga, Latvia.
| | - Andris Zicmanis
- Department of Chemistry, University of Latvia, Riga, Latvia.
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19
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Recent advances in the bioanalysis of modified nucleotides in epigenetic studies. Bioanalysis 2014; 5:2947-56. [PMID: 24295120 DOI: 10.4155/bio.13.270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Epigenetic alterations, such as DNA methylation, are involved in the pathogenesis of various diseases, the toxicity of diverse agents, the process of aging, the development of stem cells and numerous other mechanisms. DNA methylation is one of the most well-studied epigenetic alterations in mammals. Nevertheless, the scientific interest is now focusing on novel modified nucleotides with potential regulatory roles, such as 5-hydroxymethylcytosine. We currently present and discuss novel bioanalytical strategies developed for the determination of various modified nucleotides in epigenetic studies.
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20
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New validated LC-MS/MS method for the determination of three alkylated adenines in human urine and its application to the monitoring of alkylating agents in cigarette smoke. Anal Bioanal Chem 2014; 406:5293-302. [DOI: 10.1007/s00216-014-7979-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 06/08/2014] [Accepted: 06/16/2014] [Indexed: 01/26/2023]
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21
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Wood PL. Mass spectrometry strategies for clinical metabolomics and lipidomics in psychiatry, neurology, and neuro-oncology. Neuropsychopharmacology 2014; 39:24-33. [PMID: 23842599 PMCID: PMC3857645 DOI: 10.1038/npp.2013.167] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 07/04/2013] [Indexed: 12/14/2022]
Abstract
Metabolomics research has the potential to provide biomarkers for the detection of disease, for subtyping complex disease populations, for monitoring disease progression and therapy, and for defining new molecular targets for therapeutic intervention. These potentials are far from being realized because of a number of technical, conceptual, financial, and bioinformatics issues. Mass spectrometry provides analytical platforms that address the technical barriers to success in metabolomics research; however, the limited commercial availability of analytical and stable isotope standards has created a bottleneck for the absolute quantitation of a number of metabolites. Conceptual and financial factors contribute to the generation of statistically under-powered clinical studies, whereas bioinformatics issues result in the publication of a large number of unidentified metabolites. The path forward in this field involves targeted metabolomics analyses of large control and patient populations to define both the normal range of a defined metabolite and the potential heterogeneity (eg, bimodal) in complex patient populations. This approach requires that metabolomics research groups, in addition to developing a number of analytical platforms, build sufficient chemistry resources to supply the analytical standards required for absolute metabolite quantitation. Examples of metabolomics evaluations of sulfur amino-acid metabolism in psychiatry, neurology, and neuro-oncology and of lipidomics in neurology will be reviewed.
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Affiliation(s)
- Paul L Wood
- Metabolomics Unit, Department of Physiology and Pharmacology, DeBusk College of Osteopathic Medicine, Lincoln Memorial University, Math and Science 435, Harrogate, TN 37752, USA
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22
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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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23
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Affiliation(s)
- Natalia Tretyakova
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA.
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