1
|
Tang Y, Zhang JL. Recent developments in DNA adduct analysis using liquid chromatography coupled with mass spectrometry. J Sep Sci 2019; 43:31-55. [PMID: 31573133 DOI: 10.1002/jssc.201900737] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 09/04/2019] [Accepted: 09/27/2019] [Indexed: 12/15/2022]
Abstract
The formation of DNA adducts by genotoxic agents is an early event in cancer development, and it may lead to gene mutations, thereby initiating tumor development. The measurement of DNA adducts can provide critical information about the genotoxic potential of a chemical and its mechanism of carcinogenesis. In recent decades, liquid chromatography coupled with mass spectrometry has become the most important technique for analyzing DNA adducts. The improvements in resolution achievable with new chromatographic separation techniques coupled with the high specificity and sensitivity and wide dynamic range of new mass spectrometry systems have been used for both qualitative and quantitative analyses of DNA adducts. This review discusses the challenges in qualitative and quantitative analyses of DNA adducts by liquid chromatography coupled with mass spectrometry and highlights recent developments towards overcoming the limitations of liquid chromatography coupled with mass spectrometry methods. The key steps and new solutions, such as sample preparation, mass spectrometry fragmentation, and method validation, are summarized. In addition, the fundamental principles and latest advances in DNA adductomic approaches are reviewed.
Collapse
Affiliation(s)
- Yu Tang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, P. R. China
| | - Jin-Lan Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing, P. R. China
| |
Collapse
|
2
|
Lagies S, Schlimpert M, Braun LM, Kather M, Plagge J, Erbes T, Wittel UA, Kammerer B. Unraveling altered RNA metabolism in pancreatic cancer cells by liquid-chromatography coupling to ion mobility mass spectrometry. Anal Bioanal Chem 2019; 411:6319-6328. [PMID: 31037374 DOI: 10.1007/s00216-019-01814-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/27/2019] [Accepted: 03/27/2019] [Indexed: 12/12/2022]
Abstract
Ion mobility coupling to mass spectrometry facilitates enhanced identification certitude. Further coupling to liquid chromatography results in multi-dimensional analytical methods, especially suitable for complex matrices with structurally similar compounds. Modified nucleosides represent a large group of very similar members linked to aberrant proliferation. Besides basal production under physiological conditions, they are increasingly excreted by transformed cells and subsequently discussed as putative biomarkers for various cancer types. Here, we report a method for modified nucleosides covering 37 species. We determined collisional cross-sections with high reproducibility from pure analytical standards. For sample purification, we applied an optimized phenylboronic acid solid-phase extraction on media obtained from four different pancreatic cancer cell lines. Our analysis could discriminate different subtypes of pancreatic cancer cell lines. Importantly, they could clearly be separated from a pancreatic control cell line as well as blank medium. m1A, m27G, and Asm were the most important features discriminating cancer cell lines derived from well-differentiated and poorly differentiated cancers. Eventually, we suggest the analytical method reported here for future tumor-marker identification studies. Graphical abstract.
Collapse
Affiliation(s)
- Simon Lagies
- Center for Biological Systems Analysis ZBSA, Albert-Ludwigs-University Freiburg, Habsburgerstr. 49, 79104, Freiburg, Germany.,Institute of Biology II, Albert-Ludwigs-University Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine, Albert-Ludwigs-University Freiburg, Albertstr. 19A, 79104, Freiburg, Germany
| | - Manuel Schlimpert
- Center for Biological Systems Analysis ZBSA, Albert-Ludwigs-University Freiburg, Habsburgerstr. 49, 79104, Freiburg, Germany.,Institute of Biology II, Albert-Ludwigs-University Freiburg, Schänzlestr. 1, 79104, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine, Albert-Ludwigs-University Freiburg, Albertstr. 19A, 79104, Freiburg, Germany
| | - Lukas M Braun
- Center for Biological Systems Analysis ZBSA, Albert-Ludwigs-University Freiburg, Habsburgerstr. 49, 79104, Freiburg, Germany.,Department of General- and Visceral Surgery, University of Freiburg Medical Center, Hugstetter Str. 55, 79106, Freiburg, Germany
| | - Michel Kather
- Center for Biological Systems Analysis ZBSA, Albert-Ludwigs-University Freiburg, Habsburgerstr. 49, 79104, Freiburg, Germany.,Faculty of Chemistry and Pharmacy, Albert-Ludwigs-University Freiburg, Hebelstr. 27, 79104, Freiburg, Germany.,Hermann Staudinger Graduate School, University of Freiburg, Hebelstr. 27, 79104, Freiburg, Germany
| | - Johannes Plagge
- Center for Biological Systems Analysis ZBSA, Albert-Ludwigs-University Freiburg, Habsburgerstr. 49, 79104, Freiburg, Germany
| | - Thalia Erbes
- Department of Gynecology and Obstetrics, Faculty of Medicine and Medical Center, University of Freiburg, Hugstetter Str. 55, 79106, Freiburg, Germany
| | - Uwe A Wittel
- Department of General- and Visceral Surgery, University of Freiburg Medical Center, Hugstetter Str. 55, 79106, Freiburg, Germany
| | - Bernd Kammerer
- Center for Biological Systems Analysis ZBSA, Albert-Ludwigs-University Freiburg, Habsburgerstr. 49, 79104, Freiburg, Germany. .,BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestr. 16, 79104, Freiburg, Germany.
| |
Collapse
|
3
|
Patejko M, Struck-Lewicka W, Siluk D, Waszczuk-Jankowska M, Markuszewski MJ. Urinary Nucleosides and Deoxynucleosides. Adv Clin Chem 2018; 83:1-51. [PMID: 29304899 DOI: 10.1016/bs.acc.2017.10.001] [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] [Indexed: 12/26/2022]
Abstract
Urinary nucleosides and deoxynucleosides are mainly known as metabolites of RNA turnover and oxidative damage of DNA. For several decades these metabolites have been examined for their potential use in disease states including cancer and oxidative stress. Subsequent improvements in analytical sensitivity and specificity have provided a reliable means to measure these unique molecules to better assess their relationship to physiologic and pathophysiologic conditions. In fact, some are currently used as antiviral and antitumor agents. In this review we provide insight into their molecular characteristics, highlight current separation techniques and detection methods, and explore potential clinical usefulness.
Collapse
|
4
|
Barroso M, Handy DE, Castro R. The Link Between Hyperhomocysteinemia and Hypomethylation. JOURNAL OF INBORN ERRORS OF METABOLISM AND SCREENING 2017. [DOI: 10.1177/2326409817698994] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- Madalena Barroso
- Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Diane E. Handy
- Cardiovascular Division, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Rita Castro
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
- Department of Biochemistry and Human Biology, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| |
Collapse
|
5
|
Lu Z, Wang Q, Wang M, Fu S, Zhang Q, Zhang Z, Zhao H, Liu Y, Huang Z, Xie Z, Yu H, Gao X. Using UHPLC Q-Trap/MS as a complementary technique to in-depth mine UPLC Q-TOF/MS data for identifying modified nucleosides in urine. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1051:108-117. [PMID: 28340480 DOI: 10.1016/j.jchromb.2017.03.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 02/27/2017] [Accepted: 03/01/2017] [Indexed: 12/25/2022]
Abstract
Modified nucleosides, metabolites of RNA, are potential biomarkers of cancer before the appearance of morphological abnormalities. It is of great significance to comprehensively detect and identify nucleosides in human urine for discovery of cancer biomarkers. However, the lower abundance, the greater polarity and the matrix effects make it difficult to detect urinary nucleosides. In this paper, an integrated method consisted of sample preparation followed by ultraperformance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC Q-TOF/MS) detection and primary identification, then ultra-high performance liquid chromatography coupled with hybrid triple quadrupole linear ion trap mass spectrometer (UHPLC Q-Trap/MS) further identification and validation were introduced. Firstly, to enrich the nucleosides and eliminate the urine matrix effects, different sorbent materials of solid phase extraction (SPE) and the elution conditions were screened. Secondly, UPLC Q-TOF/MS was used to acquire mass data in MSE mode. The structural formulas of nucleosides in urine sample were primarily identified according to retention time, accurate mass precursor ions and fragment ions from in-house database and online database. Thirdly, the preliminary identified nucleoside structures lacking of characteristic fragment ions were verified by UHPLC Q-Trap/MS in multiple reaction monitoring trigger enhanced product ion scan (MRM-EPI) and neutral loss scan (NL). At last, phenylboronic acid (PBA)-based SPE was utilized due to its higher MS signal and weaker matrix effects under optimized extraction conditions. Fifty-five nucleosides were primarily identified by UPLC Q-TOF/MS, among which 50 nucleosides were confirmed by UHPLC Q-Trap/MS. Five nucleosides, namely 4',5'-didehydro-5'-deoxyadenosine, 4',5'-didehydro-5'-deoxyinosine, isonicotinamide riboside, peroxywybutosine and hydroxywybutosine, were found from urine for the first time. The results will expand the Human Metabolome Database (HMDB).
Collapse
Affiliation(s)
- Zhiwei Lu
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, South of Wangjing Middle Ring Road, Chaoyang District, Beijing 100102, PR China.
| | - Qing Wang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, South of Wangjing Middle Ring Road, Chaoyang District, Beijing 100102, PR China.
| | - Meiling Wang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, South of Wangjing Middle Ring Road, Chaoyang District, Beijing 100102, PR China.
| | - Shuang Fu
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, South of Wangjing Middle Ring Road, Chaoyang District, Beijing 100102, PR China.
| | - Qingqing Zhang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, South of Wangjing Middle Ring Road, Chaoyang District, Beijing 100102, PR China.
| | - Zhixin Zhang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, South of Wangjing Middle Ring Road, Chaoyang District, Beijing 100102, PR China.
| | - Huizhen Zhao
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, South of Wangjing Middle Ring Road, Chaoyang District, Beijing 100102, PR China.
| | - Yuehong Liu
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, South of Wangjing Middle Ring Road, Chaoyang District, Beijing 100102, PR China.
| | - Zhenhai Huang
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, South of Wangjing Middle Ring Road, Chaoyang District, Beijing 100102, PR China.
| | - Ziye Xie
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, South of Wangjing Middle Ring Road, Chaoyang District, Beijing 100102, PR China.
| | - Honghong Yu
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, South of Wangjing Middle Ring Road, Chaoyang District, Beijing 100102, PR China.
| | - Xiaoyan Gao
- School of Chinese Pharmacy, Beijing University of Chinese Medicine, South of Wangjing Middle Ring Road, Chaoyang District, Beijing 100102, PR China.
| |
Collapse
|
6
|
Iwanowska A, Yusa SI, Nowakowska M, Szczubiałka K. Selective adsorption of modified nucleoside cancer biomarkers by hybrid molecularly imprinted adsorbents. J Sep Sci 2016; 39:3072-80. [DOI: 10.1002/jssc.201600132] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 05/31/2016] [Accepted: 06/01/2016] [Indexed: 12/21/2022]
Affiliation(s)
| | - Shin-Ichi Yusa
- Graduate School of Engineering, Department of Materials Science and Chemistry; University of Hyogo; Himeji Hyogo Japan
| | | | | |
Collapse
|
7
|
Abstract
Cells have developed molecular machineries, which can chemically modify DNA and RNA nucleosides. One particular and chemically simple modification, (cytosine-5) methylation (m(5)C), has been detected both in RNA and DNA suggesting universal use of m(5)C for the function of these nucleotide polymers. m(5)C can be reproducibly mapped to abundant noncoding RNAs (transfer RNA, tRNA and ribosomal RNA, rRNA), and recently, also nonabundant RNAs (including mRNAs) have been reported to carry this modification. Quantification of m(5)C content in total RNA preparations indicates that a limited number of RNAs carry this modification and suggests specific functions for (cytosine-5) RNA methylation. What exactly is the biological function of m(5)C in RNA? Before attempting to address this question, m(5)C needs to be mapped specifically and reproducibly, preferably on a transcriptome-wide scale. To facilitate the detection of m(5)C in its sequence context, RNA bisulfite sequencing (RNA-BisSeq) has been developed. This method relies on the efficient chemical deamination of nonmethylated cytosine, which can be read out as single nucleotide polymorphism (nonmethylated cytosine as thymine vs. methylated cytosine as cytosine), when differentially comparing cDNA libraries to reference sequences after DNA sequencing. Here, the basic protocol of RNA-BisSeq, its current applications and limitations are described.
Collapse
Affiliation(s)
- Matthias Schaefer
- Vienna Biocenter, Max F. Perutz Laboratories, Department of Biochemistry and Cell Biology, Universität Wien, Vienna, Austria.
| |
Collapse
|
8
|
Li S, Jin Y, Tang Z, Lin S, Liu H, Jiang Y, Cai Z. A novel method of liquid chromatography-tandem mass spectrometry combined with chemical derivatization for the determination of ribonucleosides in urine. Anal Chim Acta 2015; 864:30-8. [PMID: 25732424 DOI: 10.1016/j.aca.2015.01.044] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 01/20/2015] [Accepted: 01/28/2015] [Indexed: 11/30/2022]
Abstract
Ribonucleosides are the end products of RNA metabolism. These metabolites, especially the modified ribonucleosides, have been extensively evaluated as cancer-related biomarkers. However, the determination of urinary ribonucleosides is still a challenge due to their low abundance, high polarity and serious matrix interferences in urine samples. In this study, a derivatization method based on a chemical reaction between ribonucleosides and acetone to form acetonides was developed for the determination of urinary ribonucleosides. The derivative products, acetonides, were detected by using liquid chromatography-tandem mass spectrometry (LC-MS/MS). The methodological evaluation was performed by quantifying four nucleosides for linear range, average recovery, precision, accuracy and stability. The validated procedures were applied to screen modified ribonucleosides in urine samples. Improvement of separation and enhancement of sensitivity were obtained in the analysis. To identify ribonucleosides, inexpensive isotope labeling acetone (acetone-d6) and label-free acetone were applied to form ordinary and deuterated acetonides, respectively. The two groups of samples were separated with orthogonal partial least squares (OPLS). The ordinary and deuterated pairs of acetonides were symmetrically distributed in the S-plot for easy and visual signal identification. After structural confirmation, a total of 56 ribonucleosides were detected, 52 of which were modified ribonucleosides. The application of derivatization, deuterium-labeling and multivariate statistical analysis offers a new option for selective detection of ribonucleosides in biological samples.
Collapse
Affiliation(s)
- Shangfu Li
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, PR China
| | - Yibao Jin
- Shenzhen Institute for Drug Control, Shenzhen 518055, PR China; State Key Laboratory Breeding Base-Shenzhen Key Laboratory of Chemical Biology, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, PR China
| | - Zhi Tang
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, PR China
| | - Shuhai Lin
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, PR China
| | - Hongxia Liu
- State Key Laboratory Breeding Base-Shenzhen Key Laboratory of Chemical Biology, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, PR China; Key Laboratory of Metabolomics at Shenzhen, Shenzhen 518055, PR China
| | - Yuyang Jiang
- State Key Laboratory Breeding Base-Shenzhen Key Laboratory of Chemical Biology, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, PR China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Hong Kong, PR China.
| |
Collapse
|
9
|
Li Y, Yu H, Zhao W, Xu X, Zhou J, Xu M, Gao W, Yuan G. Analysis of urinary methylated nucleosides of patients with coronary artery disease by high-performance liquid chromatography/electrospray ionization tandem mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:2054-2058. [PMID: 25156594 DOI: 10.1002/rcm.6986] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Revised: 07/13/2014] [Accepted: 07/13/2014] [Indexed: 06/03/2023]
Abstract
RATIONALE In recent years, methylated nucleosides have been considered to be potential biomarkers to human diseases. The early diagnosis of coronary artery disease (CAD) is an unsolved problem in clinical cardiology. The aim of our study is to evaluate whether urinary methylated nucleosides can serve as useful biomarkers for CAD. METHODS A solid-phase extraction (SPE) column was used for extraction and purification of methylated nucleosides in urine, and high-performance liquid chromatography/electrospray ionization tandem mass spectrometry (HPLC/ESI-MS/MS) was employed for specific, sensitive and rapid determination of the urinary methylated nucleosides from patients with cardiac events. RESULTS We have analyzed six methylated nucleosides (N(3)-methylcytidine, N(1)-methyladenosine, N(6)-methyladenosine, N(2)-methylguanosine, N(1)-methylguanosine and N(2),N(2)-dimethylguanosine) in urine from 51 patients with CAD and 25 non-CAD controls by HPLC/ESI-MS/MS using selective reaction monitoring (SRM). Our results have shown that there were significant differences in the N(6)-methyladenosine levels from the patients and the non-CAD controls in the urine analyzed. CONCLUSIONS The results have indicated that HPLC/ESI-MS/MS is a highly specific and sensitive tool to measure urinary methylated nucleosides for analysis of CAD. Our result has revealed that the evaluation of urinary methylated nucleosides might be helpful in the analysis of CAD by liquid chromatography/mass spectrometry. Therefore, this N(6)-methyladenosine is worthy of further studies in the near future.
Collapse
Affiliation(s)
- Yanru Li
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | | | | | | | | | | | | | | |
Collapse
|
10
|
Dudley E, Bond L. Mass spectrometry analysis of nucleosides and nucleotides. MASS SPECTROMETRY REVIEWS 2014; 33:302-31. [PMID: 24285362 DOI: 10.1002/mas.21388] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 05/03/2013] [Accepted: 05/03/2013] [Indexed: 05/12/2023]
Abstract
Mass spectrometry has been widely utilised in the study of nucleobases, nucleosides and nucleotides as components of nucleic acids and as bioactive metabolites in their own right. In this review, the application of mass spectrometry to such analysis is overviewed in relation to various aspects regarding the analytical mass spectrometric and chromatographic techniques applied and also the various applications of such analysis.
Collapse
Affiliation(s)
- Ed Dudley
- Institute of Mass Spectrometry, College of Medicine, Swansea University, Singleton Park, Swansea, SA2 8PP, UK
| | | |
Collapse
|
11
|
Da Pieve C, Sahgal N, Moore SA, Velasco-Garcia MN. Development of a liquid chromatography/tandem mass spectrometry method to investigate the presence of biomarkers of DNA damage in urine related to red meat consumption and risk of colorectal cancer. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:2493-2503. [PMID: 24097406 DOI: 10.1002/rcm.6709] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 07/19/2013] [Accepted: 08/04/2013] [Indexed: 06/02/2023]
Abstract
RATIONALE The consumption of red meat is known to enhance the endogenous formation of N-nitroso compounds (NOCs), which are potent carcinogens. DNA damage related to NOCs, and hence red meat, has been detected in colorectal cells and in blood. We proposed to extend previous studies to a non-invasive approach for the detection of O(6)-carboxymethylguanine (O(6)CMG) and O(6)-carboxymethyl-2'-deoxyguanosine (O(6)CMdG) in urine in relation to red meat intake using liquid chromatography/tandem mass spectrometry (LC/MS/MS). The presence of the adduct in urine samples either as the free base or as 2'-deoxynucleoside could help in determining the repair mechanism involved when such lesions are produced. A non-invasive assessment of DNA adducts could also allow for large-scale analyses in the population and cancer prevention dietary strategies. METHODS An LC/MS/MS method for the quantitation of O(6)CMG and O(6)CMdG was developed. Urine samples collected from healthy volunteers on red meat and vegetarian diets were analysed either by direct injection or after purification by solid-phase extraction (SPE). A separate LC/MS/MS method for O(6)-methylguanine (O(6)MeG) and O(6)-methyl-2'-deoxyguanosine (O(6)MedG), which are possible hydrolysis products forming during the sample pre-treatment, was also developed. RESULTS The developed LC/MS/MS method allowed the simultaneous measurement of O(6)CMG and O(6)CMdG. The limits of detection (LODs) were 0.38 ng/mL for O(6)CMG and 0.18 ng/mL for O(6)CMdG. The direct injection analysis of the clinical samples showed low sensitivity due to high background signal that was improved by SPE purification. However, the concentrations of the adducts in clinical samples were still found to be below the LOD. CONCLUSIONS Novel, reproducible, and accurate LC/MS/MS methods were developed for the determination of the urinary content of O(6)CMG and O(6)CMdG, and of the possible formation of O(6)MeG and O(6)MedG by decarboxylation. Clinical samples from volunteers on different diets were analysed. Further studies are required to discover a link between the presence of these biomarkers in urine and red meat consumption.
Collapse
Affiliation(s)
- Chiara Da Pieve
- Department of Life, Health and Chemical Sciences, Faculty of Science, The Open University, Walton Hall, Milton Keynes, MK7 6AA, UK
| | | | | | | |
Collapse
|
12
|
Durdevic Z, Schaefer M. Dnmt2 methyltransferases and immunity: An ancient overlooked connection between nucleotide modification and host defense? Bioessays 2013; 35:1044-9. [DOI: 10.1002/bies.201300088] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Zeljko Durdevic
- Division of Epigenetics; DKFZ-ZMBH Alliance, German Cancer Research Center; Heidelberg Germany
| | - Matthias Schaefer
- Division of Epigenetics; DKFZ-ZMBH Alliance, German Cancer Research Center; Heidelberg Germany
| |
Collapse
|
13
|
Giessing AMB, Kirpekar F. Mass spectrometry in the biology of RNA and its modifications. J Proteomics 2012; 75:3434-49. [PMID: 22348820 DOI: 10.1016/j.jprot.2012.01.032] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 01/20/2012] [Accepted: 01/26/2012] [Indexed: 01/31/2023]
Abstract
Many powerful analytical techniques for investigation of nucleic acids exist in the average modern molecular biology lab. The current review will focus on questions in RNA biology that have been answered by the use of mass spectrometry, which means that new biological information is the purpose and outcome of most of the studies we refer to. The review begins with a brief account of the subject "MS in the biology of RNA" and an overview of the prevalent RNA modifications identified to date. Fundamental considerations about mass spectrometric analysis of RNA are presented with the aim of detailing the analytical possibilities and challenges relating to the unique chemical nature of nucleic acids. The main biological topics covered are RNA modifications and the enzymes that perform the modifications. Modifications of RNA are essential in biology, and it is a field where mass spectrometry clearly adds knowledge of biological importance compared to traditional methods used in nucleic acid research. The biological applications are divided into analyses exclusively performed at the building block (mainly nucleoside) level and investigations involving mass spectrometry at the oligonucleotide level. We conclude the review discussing aspects of RNA identification and quantifications, which are upcoming fields for MS in RNA research. This article is part of a Special Section entitled: Understanding genome regulation and genetic diversity by mass spectrometry.
Collapse
Affiliation(s)
- Anders M B Giessing
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, 5230 Odense M, Denmark
| | | |
Collapse
|
14
|
Study of retention behaviour and mass spectrometry compatibility in zwitterionic hydrophilic interaction chromatography for the separation of modified nucleosides and nucleobases. J Chromatogr A 2011; 1218:3994-4001. [DOI: 10.1016/j.chroma.2011.05.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 04/14/2011] [Accepted: 05/03/2011] [Indexed: 11/24/2022]
|
15
|
Kowalewska M, Nowak R, Chechlinska M. Implications of cancer-associated systemic inflammation for biomarker studies. Biochim Biophys Acta Rev Cancer 2010; 1806:163-71. [PMID: 20600631 DOI: 10.1016/j.bbcan.2010.06.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Revised: 06/16/2010] [Accepted: 06/17/2010] [Indexed: 12/19/2022]
Abstract
Highly sensitive molecular technologies provide new capacities for cancer biomarker research, but with sensitivity improvements marker specificity is significantly decreased, and too many false-positive results should disqualify the measurement from clinical use. Hence, of the thousands of potential cancer biomarkers only a few have found their way to clinical application. Differentiating false-positive results from true-positive (cancer-specific) results can indeed be difficult, if validation of a marker is performed against inadequate controls. We present examples of accumulating evidence that not only local but also systemic inflammatory reactions are implicated in cancer development and progression and interfere with the molecular image of cancer disease. We analyze several modern strategies of tumor marker discovery, namely, proteomics, metabonomics, studies on circulating tumor cells and circulating free nucleic acids, or their methylation degree, and provide examples of scarce, methodologically correct biomarker studies as opposed to numerous methodologically flawed biomarker studies, that examine cancer patients' samples against those of healthy, inflammation-free persons and present many inflammation-related biomarker alterations in cancer patients as cancer-specific. Inflammation as a cancer-associated condition should always be considered in cancer biomarker studies, and biomarkers should be validated against their expression in inflammatory conditions.
Collapse
Affiliation(s)
- Magdalena Kowalewska
- Department of Molecular Biology, Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology, Roentgena 5, 02-781 Warsaw, Poland
| | | | | |
Collapse
|
16
|
Abstract
Post-transcriptional ribonucleotide modification is a phenomenon best studied in tRNA, where it occurs most frequently and in great chemical diversity. This paper reviews the intrinsic network of modifications in the structural core of the tRNA, which governs structural flexibility and rigidity to fine-tune the molecule to peak performance and to regulate its steady-state level. Structural effects of RNA modifications range from nanometer-scale rearrangements to subtle restrictions of conformational space on the angstrom scale. Structural stabilization resulting from nucleotide modification results in increased thermal stability and translates into protection against unspecific degradation by bases and nucleases. Several mechanisms of specific degradation of hypomodified tRNA, which were only recently discovered, provide a link between structural and metabolic stability.
Collapse
Affiliation(s)
- Yuri Motorin
- Laboratoire ARN-RNP Maturation-Structure-Fonction, Enzymologie Moléculaire et Structurale (AREMS), UMR 7214 CNRS-UHP Faculté des Sciences et Techniques, Université Henri Poincaré, Nancy 1, Bld des Aiguillettes, BP 70239, 54506 Vandoeuvre-les-Nancy, France
| | | |
Collapse
|
17
|
Motorin Y, Lyko F, Helm M. 5-methylcytosine in RNA: detection, enzymatic formation and biological functions. Nucleic Acids Res 2009; 38:1415-30. [PMID: 20007150 PMCID: PMC2836557 DOI: 10.1093/nar/gkp1117] [Citation(s) in RCA: 240] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The nucleobase modification 5-methylcytosine (m5C) is widespread both in DNA and different cellular RNAs. The functions and enzymatic mechanisms of DNA m5C-methylation were extensively studied during the last decades. However, the location, the mechanism of formation and the cellular function(s) of the same modified nucleobase in RNA still remain to be elucidated. The recent development of a bisulfite sequencing approach for efficient m5C localization in various RNA molecules puts ribo-m5C in a highly privileged position as one of the few RNA modifications whose detection is amenable to PCR-based amplification and sequencing methods. Additional progress in the field also includes the characterization of several specific RNA methyltransferase enzymes in various organisms, and the discovery of a new and unexpected link between DNA and RNA m5C-methylation. Numerous putative RNA:m5C-MTases have now been identified and are awaiting characterization, including the identification of their RNA substrates and their related cellular functions. In order to bring these recent exciting developments into perspective, this review provides an ordered overview of the detection methods for RNA methylation, of the biochemistry, enzymology and molecular biology of the corresponding modification enzymes, and discusses perspectives for the emerging biological functions of these enzymes.
Collapse
Affiliation(s)
- Yuri Motorin
- Laboratoire ARN-RNP Maturation-Structure-Fonction, Enzymologie Moléculaire et Structurale (AREMS), UMR 7214 CNRS-UHP Faculté des Sciences et Techniques, Université Henri Poincaré, Nancy 1, Bld des Aiguillettes, BP 70239, 54506 Vandoeuvre-les-Nancy, France
| | | | | |
Collapse
|
18
|
Cataldi TRI, Bianco G, Abate S, Mattia D. Analysis of S-adenosylmethionine and related sulfur metabolites in bacterial isolates of Pseudomonas aeruginosa (BAA-47) by liquid chromatography/electrospray ionization coupled to a hybrid linear quadrupole ion trap and Fourier transform ion cyclotron resonance mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2009; 23:3465-3477. [PMID: 19813285 DOI: 10.1002/rcm.4274] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A comprehensive and highly selective method for detecting in bacterial supernatants a modified sulfur nucleoside, S-adenosyl-L-methionine (SAM), and its metabolites, i.e., S-adenosylhomocysteine (SAH), adenosine (Ado), 5'-deoxy-5'-methylthioadenosine (MTA), adenine (Ade), S-adenosyl-methioninamine (dcSAM), homocysteine (Hcy) and methionine (Met), was developed. The method is based on reversed-phase liquid chromatography with positive electrospray ionization (ESI+) coupled to a hybrid linear quadrupole ion trap (LTQ) and 7-T Fourier transform ion cyclotron resonance mass spectrometry (FTICRMS). A gradient elution was employed with a binary solvent of 0.05 M ammonium formate at pH 4 and acetonitrile. The assay involves a simultaneous cleanup of cell-free bacterial broths by solid-phase extraction and trace enrichment of metabolites with a 50-fold concentration factor by using immobilized phenylboronic and anion-exchange cartridges. While the quantitative determination of SAM was performed using stable-isotope-labeled SAM-d3 as an internal standard, in the case of Met and Ade, Met-13C and Ade-15N2 were employed as isotope-labeled internal standards, respectively. This method enabled the identification of SAM and its metabolites in cell-free culture of Pseudomonas aeruginosa grown in Davis minimal broth (formulation without sulphur organic compounds), with routine sub-ppm mass accuracies (-0.27 +/- 0.68 ppm). The resulting contents of S(C)S(S)-SAM, S(S)-dcSAM, MTA, Ado and Met in the free-cell supernatant of P. aeruginosa was 56.4 +/- 2.1 nM, 32.2 +/- 2.2 nM, 0.91 +/- 0.10 nM, 19.6 +/- 1.2 nM and 1.93 +/- 0.02 microM (mean +/- SD, n = 4 extractions), respectively. We report also the baseline separation (Rs > or = 1.5) of both diastereoisomeric forms of SAM (S(C)S(S) and S(C)R(S)) and dcSAM (S(S) and R(S)), which can be very useful to establish the relationship between the biologically active versus the inactive species, S(C)S(S)/S(C)R(S) and S(S)/R(S) of SAM and dcSAM, respectively. An additional confirmation of SAM-related metabolites was accomplished by a systematic study of their MS/MS spectra.
Collapse
Affiliation(s)
- Tommaso R I Cataldi
- Dipartimento di Chimica, Università degli Studi di Bari, Campus Universitario, Via E. Orabona 4, 70126 Bari, Italy.
| | | | | | | |
Collapse
|
19
|
Li HY, Wang SM, Liu HM, Bu SS, Li J, Han D, Zhang MZ, Wu GY. Separation and identification of purine nucleosides in the urine of patients with malignant cancer by reverse phase liquid chromatography/electrospray tandem mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2009; 44:641-51. [PMID: 19142897 DOI: 10.1002/jms.1539] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Urinary-modified nucleosides have a potential role as cancer biomarkers for a number of malignant diseases. High performance liquid chromatography (HPLC) was combined with full-scan mass spectrometry, MS/MS analysis and accurate mass measurements in order to identify purine nucleosides purified from urine. Potential purine nucleosides were assessed by their evident UV absorbance in the HPLC chromatogram and then further examined by the mass spectrometric techniques. In this manner, numerous modified purine nucleosides were identified in the urine samples from cancer patients including xanthine, adenosine, N1-methyladenosine, 5'-deoxy-5'-methylthioadenosine, 2-methyladenosine, N6-threonylcarbamoyladenosine, inosine, N1-methylinosine, guanosine, N1-methylguanosine, N7-methylguanine, N2-methylguanosine, N2,N2-dimethyguanosine, N2,N2,N7-trimethylguanosine. Furthermore, a number of novel purine nucleosides were tentatively identified via critical interpretation of the combined mass spectrometric data including N3-methyladenosine, N7-methyladenine, 5'-dehydro-2'-deoxyinosine, N3-methylguanine, O6-methylguanosine, N1,N2,N7-trimethylguanosine, N1-methyl-N2-ethylguanosine and N7-methyl-N1-ethylguanosine.
Collapse
Affiliation(s)
- Hua-Yu Li
- Department of Chemistry, Zhengzhou University, 100 Science Road, 450001 Zhengzhou, China
| | | | | | | | | | | | | | | |
Collapse
|