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Finet O, Yague-Sanz C, Marchand F, Hermand D. The Dihydrouridine landscape from tRNA to mRNA: a perspective on synthesis, structural impact and function. RNA Biol 2022; 19:735-750. [PMID: 35638108 PMCID: PMC9176250 DOI: 10.1080/15476286.2022.2078094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The universal dihydrouridine (D) epitranscriptomic mark results from a reduction of uridine by the Dus family of NADPH-dependent reductases and is typically found within the eponym D-loop of tRNAs. Despite its apparent simplicity, D is structurally unique, with the potential to deeply affect the RNA backbone and many, if not all, RNA-connected processes. The first landscape of its occupancy within the tRNAome was reported 20 years ago. Its potential biological significance was highlighted by observations ranging from a strong bias in its ecological distribution to the predictive nature of Dus enzymes overexpression for worse cancer patient outcomes. The exquisite specificity of the Dus enzymes revealed by a structure-function analyses and accumulating clues that the D distribution may expand beyond tRNAs recently led to the development of new high-resolution mapping methods, including Rho-seq that established the presence of D within mRNAs and led to the demonstration of its critical physiological relevance.
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Affiliation(s)
- Olivier Finet
- URPHYM-GEMO, The University of Namur, Namur, Belgium
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2
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BH +/MH +-matching method for discovery of cis-diol-containing modified nucleosides in urine by ribose-targeted solid phase extraction followed by dual-mass spectrometry platform identification. J Pharm Biomed Anal 2021; 210:114555. [PMID: 34974239 DOI: 10.1016/j.jpba.2021.114555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 12/23/2021] [Accepted: 12/25/2021] [Indexed: 12/18/2022]
Abstract
Profiling of new modified nucleosides from urine plays an important role in exploring biomarkers for cancer. However, limitations from the nature of the compound, bio-sample, instrumentation, and analytical method pose great challenges to achieving a comprehensive analysis of urinary nucleosides. Herein, a method of BH+/MH+-matching (BH+, protonated nucleobase ion; MH+, protonated precursor ion) was developed to discover novel modified nucleosides from human urine samples based on solid phase extraction targeted toward specific modified nucleosides combined with ultra-performance liquid chromatography coupled with dual-mass spectrometry platforms. Firstly, nucleosides containing 2,3-diol structure on ribose were effectively enriched by PBA (Phenylboronic Acid) cartridges. Secondly, a novel method, "BH+/MH+-matching" was established to achieve rapid screening of modified nucleosides. Based on the in-source fragmentation pattern of nucleosides, a series of putative modified nucleosides were rationally designed and characterized by matching the daughter ion BH+ and its parent ion MH+ in UPLC-MSE spectra. Finally, as a complement to UPLC Q-TOF/MS, UPLC Q-Trap/MS was employed to validate the structure of putative compounds by MRM-IDA-EPI mode. Using the strategy, 12 new cis-diol-containing nucleoside analogs were successfully characterized, which were formed by modified base (m1A, m6A, m2,2,7G, ac4C) and modified ribose containing C5'-O-formylation or C5'-O-methylation. Taken together, the results demonstrated our strategy could efficiently support the rapid discovery of cis-diol-containing nucleosides with modifications on either ribose or base moiety (or both), which exhibited a promising perspective in the future application of biochemical analysis and clinical diagnosis.
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3
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Nierenberg JL, He J, Li C, Gu X, Shi M, Razavi AC, Mi X, Li S, Bazzano LA, Anderson AH, He H, Chen W, Guralnik JM, Kinchen JM, Kelly TN. Serum metabolites associate with physical performance among middle-aged adults: Evidence from the Bogalusa Heart Study. Aging (Albany NY) 2020; 12:11914-11941. [PMID: 32482911 PMCID: PMC7343486 DOI: 10.18632/aging.103362] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 05/20/2020] [Indexed: 12/30/2022]
Abstract
Age-related declines in physical performance predict cognitive impairment, disability, chronic disease exacerbation, and mortality. We conducted a metabolome-wide association study of physical performance among Bogalusa Heart Study participants. Bonferroni corrected multivariate-adjusted linear regression was employed to examine cross-sectional associations between single metabolites and baseline gait speed (N=1,227) and grip strength (N=1,164). In a sub-sample of participants with repeated assessments of gait speed (N=282) and grip strength (N=201), significant metabolites from the cross-sectional analyses were tested for association with change in physical performance over 2.9 years of follow-up. Thirty-five and seven metabolites associated with baseline gait speed and grip strength respectively, including six metabolites that associated with both phenotypes. Three metabolites associated with preservation or improvement in gait speed over follow-up, including: sphingomyelin (40:2) (P=2.6×10-4) and behenoyl sphingomyelin (d18:1/22:0) and ergothioneine (both P<0.05). Seven metabolites associated with declines in gait speed, including: 1-carboxyethylphenylalanine (P=8.8×10-5), and N-acetylaspartate, N-formylmethionine, S-adenosylhomocysteine, N-acetylneuraminate, N2,N2-dimethylguanosine, and gamma-glutamylphenylalanine (all P<0.05). Two metabolite modules reflecting sphingolipid and bile acid metabolism associated with physical performance (minimum P=7.6×10-4). These results add to the accumulating evidence suggesting an important role of the human metabolome in physical performance and specifically implicate lipid, nucleotide, and amino acid metabolism in early physical performance decline.
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Affiliation(s)
- Jovia L Nierenberg
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA.,Department of Medicine, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA
| | - Changwei Li
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA.,Department of Epidemiology and Biostatistics, University of Georgia College of Public Health, Athens, GA 30606, USA
| | - Xiaoying Gu
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA.,Institute of Clinical Medical Sciences, China-Japan Friendship Hospital, National Clinical Research Center of Respiratory Diseases, Beijing, China
| | - Mengyao Shi
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA
| | - Alexander C Razavi
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA
| | - Xuenan Mi
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA
| | - Shengxu Li
- Children's Minnesota Research Institute, Children's Hospitals and Clinics of Minnesota, MN 55404, USA
| | - Lydia A Bazzano
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA
| | - Amanda H Anderson
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA
| | - Hua He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA
| | - Wei Chen
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA
| | - Jack M Guralnik
- Division of Gerontology, Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | | | - Tanika N Kelly
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA
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4
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Jinno D, Kanemitsu Y, Saitoh K, Nankumo S, Tsukamoto H, Matsumoto Y, Abe T, Tomioka Y. Rapid and selective simultaneous quantitative analysis of modified nucleosides using multi-column liquid chromatography-tandem mass spectrometry. J Anal Sci Technol 2017. [DOI: 10.1186/s40543-017-0110-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Jiang HP, Qi CB, Chu JM, Yuan BF, Feng YQ. Profiling of cis-diol-containing nucleosides and ribosylated metabolites by boronate-affinity organic-silica hybrid monolithic capillary liquid chromatography/mass spectrometry. Sci Rep 2015; 5:7785. [PMID: 25585609 PMCID: PMC4293604 DOI: 10.1038/srep07785] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 12/15/2014] [Indexed: 12/18/2022] Open
Abstract
RNA contains a large number of modified nucleosides. In the metabolic re-exchange of RNA, modified nucleosides cannot be recycled and are thus excreted from cells into biological fluids. Determination of endogenous modified nucleosides in biological fluids may serve as non-invasive cancers diagnostic methods. Here we prepared boronate-affinity organic-silica hybrid capillary monolithic column (BOHCMC) that exhibited excellent selectivity toward the cis-diol-containing compounds. We then used the prepared BOHCMC as the on-line solid-phase microextraction (SPME) column and developed an on-line SPME-LC-MS/MS method to comprehensively profile cis-diol-containing nucleosides and ribosylated metabolites in human urine. Forty-five cis-diol-containing nucleosides and ribosylated metabolites were successfully identified in human urine. And five ribose conjugates, for the first time, were identified existence in human urine in the current study. Furthermore, the relative quantification suggested 4 cis-diol-containing compounds (5′-deoxy-5′-methylthioadensine, N4-acetylcytidine, 1-ribosyl-N-propionylhistamine and N2,N2,7-trimethylguanosine) increased more than 1.5 folds in all the 3 types of examined cancers (lung cancer, colorectal cancer, and nasopharyngeal cancer) compared to healthy controls. The on-line SPME-LC-MS/MS method demonstrates a promising method for the comprehensive profiling of cis-diol-containing ribose conjugates in human urines, which provides an efficient strategy for the identification and discovery of biomarkers and may be used for the screening of cancers.
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Affiliation(s)
- Han-Peng Jiang
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Chu-Bo Qi
- 1] Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, China [2] Department of Pathology, Hubei Cancer Hospital, Wuhan 430079, China
| | - Jie-Mei Chu
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Bi-Feng Yuan
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, China
| | - Yu-Qi Feng
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Department of Chemistry, Wuhan University, Wuhan 430072, China
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Mikulska A, Inoue M, Kuroda K, Iwanowska A, Yusa SI, Nowakowska M, Szczubiałka K. Polymeric/silicagel hybrid molecularly photoimprinted adsorbents for adenosine and its derivatives. Eur Polym J 2014. [DOI: 10.1016/j.eurpolymj.2014.07.029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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7
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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]
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8
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Wang P, Sun H, Lv H, Sun W, Yuan Y, Han Y, Wang D, Zhang A, Wang X. Thyroxine and reserpine-induced changes in metabolic profiles of rat urine and the therapeutic effect of Liu Wei Di Huang Wan detected by UPLC-HDMS. J Pharm Biomed Anal 2010; 53:631-45. [DOI: 10.1016/j.jpba.2010.04.032] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2010] [Revised: 04/25/2010] [Accepted: 04/26/2010] [Indexed: 12/28/2022]
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Topp H, Fusch G, Schöch G, Fusch C. Noninvasive markers of oxidative DNA stress, RNA degradation and protein degradation are differentially correlated with resting metabolic rate and energy intake in children and adolescents. Pediatr Res 2008; 64:246-50. [PMID: 18437098 DOI: 10.1203/pdr.0b013e31817cfca6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Urinary excreted RNA and DNA catabolites are used as noninvasive markers for metabolic processes: 8-oxo-2'-deoxyguanosine (8-oxodG) potentially represents oxidative stress to DNA/deoxyribonucleotidetriphosphate pool, modified ribonucleoside pseudouridine (psi) originating mainly from degraded rRNA and tRNA reflects RNA turnover. Modified amino acid gamma-carboxyglutamic acid (Gla) stems from degraded proteins reflecting turnover of proteins. Aim of the present study was to investigate (44 healthy males, 3-18 y) how excretion rates of 8-oxodG, psi, and Gla are related to resting metabolic rate and energy intake. Excretion rates of 8-oxodG (pmol/kg/d), psi (micromol/kg/d), and Gla (micromol/kg/d) were significantly correlated with resting metabolic rate (kJ/kg/d): r = 0.108 (p = 0.029), 0.691 and 0.552 (p < 0.0001), respectively. Excretion rates of 8-oxodG, psi, and Gla were also significantly correlated with energy intake (kJ/kg/d): r = 0.108 (p = 0.036), 0.602 and 0.462 (p < 0.0001). 8-oxodG and Gla excretion was significantly correlated with psi excretion: r = 0.174 (p = 0.005) and 0.709 (p < 0.0001). These results indicate close relationships between whole-body RNA and protein degradation and metabolic rate. The relationship between 8-oxodG excretion and metabolic rate, however, is less strong suggesting that factors other than metabolic rate considerably affect the oxidative stress to DNA.
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Affiliation(s)
- Heinrich Topp
- Neonatology, University Children's Hospital, 17487 Greifswald, Germany
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Seidel A, Brunner S, Seidel P, Fritz GI, Herbarth O. Modified nucleosides: an accurate tumour marker for clinical diagnosis of cancer, early detection and therapy control. Br J Cancer 2006; 94:1726-33. [PMID: 16685264 PMCID: PMC2361309 DOI: 10.1038/sj.bjc.6603164] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Modified nucleosides, regarded as indicators for the whole-body turnover of RNAs, are excreted in abnormal amounts in the urine of patients with malignancies. To test their usefulness as tumour markers and to compare them with the conventional tumour markers, fractionated urine samples were analysed using chromatography. The excretion patterns of nucleosides of 68 cancer patients with malignant and benign tumours and 41 healthy controls have been studied. Significant elevations in the total sum and the concentrations of at least three (or four) of indicator nucleosides cytidine, pseudouridine, 2-pyridone-5-carboxamide-N1-ribofuranoside, N2,N2-dimethylguanine, 1-methylguanosine, 2-methylguanosine and 1-methyladenosine indicate a tumour with a sensitivity of 54% (77%) and a specificity of 86% (98%). Using an artificial neural network analysis, a sensitivity of 97% and a specificity of 85% were achieved in differentiating between tumour and control volunteers. The comparison with carcinoembryonic antigen, cancer antigen 15-3 und tissue polypeptide antigen indicates that urinary nucleosides may be useful tumour markers. This study suggests that the simultaneous determination of modified nucleosides and creatinine in urine samples of patients with cancer leads to an advantage to current methods and is a useful method to detect cancer early and to control the success of therapy.
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Affiliation(s)
- A Seidel
- Institute of Hygiene, Faculty of Medicine, University of Leipzig, Liebigstrasse 27, D-04103 Leipzig, Germany
| | - S Brunner
- Institute of Hygiene, Faculty of Medicine, University of Leipzig, Liebigstrasse 27, D-04103 Leipzig, Germany
| | - P Seidel
- Institute of Medical Biophysics and Physics, Faculty of Medicine, University of Leipzig, Liebigstrasse 27, D-04103 Leipzig, Germany
| | - G I Fritz
- Environmental Hygiene and Epidemiology (Environmental Medicine), Faculty of Medicine, University of Leipzig, Liebigstrasse 27, D-04103 Leipzig, Germany
| | - O Herbarth
- Department of Human Exposure Research and Epidemiology, UFZ – Centre for Environmental Research Leipzig-Halle, Permoserstrasse 15, D-04318 Leipzig, Germany
- Environmental Hygiene and Epidemiology (Environmental Medicine), Faculty of Medicine, University of Leipzig, Liebigstrasse 27, D-04103 Leipzig, Germany
- E-mail:
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11
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Cho SH, Jung BH, Lee SH, Lee WY, Kong G, Chung BC. Direct determination of nucleosides in the urine of patients with breast cancer using column-switching liquid chromatography–tandem mass spectrometry. Biomed Chromatogr 2006; 20:1229-36. [PMID: 16799933 DOI: 10.1002/bmc.689] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We developed an analytical method for a simple, sensitive and simultaneous determination of oxidized nucleosides in urine using column-switching liquid chromatography-electrospray/tandem mass spectrometry (LC-ESI/MS/MS). We connected two columns through a six-way switching valve and effectively separated nucleosides in the urine from the interference by column-switching liquid chromatography. We monitored separated nucleosides using positive ionization tandem mass spectrometry in selective reaction monitoring (SRM) mode. The calibration ranges of nucleosides were 0.2-100 nmol/mL. The linearity of the method was 0.994-0.999, and the limits-of-detection (LOD) at a signal-to-noise (S/N) ratio of 3 were 0.1-0.2 nmol/mL. The coefficients of variation were in the range 2.28-11.74% for within-day variation and 4.36-11.15% for day-to-day variation, respectively. To explore the relationship between breast cancer and the nucleosides level in human urine, we measured the concentrations of nucleosides in female patients with breast cancer (n = 30) and in normal female subjects (n = 30). The concentration of nucleosides was significantly increased in patients with breast cancer when compared with the normal controls (1-methyladenosine; p < 0.005, N(2),N(2)-dimethylguanosine; p < 0.01, 5-hydroxymethyl-2'-deoxyuridine; p < 0.001, 8-hydroxy-2-deoxyguanosine; p < 0.001). Therefore, the elevated levels of nucleosides could be used as an important biomarker for breast-cancer research.
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Affiliation(s)
- Sung-Hee Cho
- Bioanalysis and Biotransformation Research Center, KIST, Chengryang, Seoul 130-605, Korea
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12
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Liebich HM, Müller-Hagedorn S, Klaus F, Meziane K, Kim KR, Frickenschmidt A, Kammerer B. Chromatographic, capillary electrophoretic and matrix-assisted laser desorption ionization time-of-flight mass spectrometry analysis of urinary modified nucleosides as tumor markers. J Chromatogr A 2005; 1071:271-5. [PMID: 15865203 DOI: 10.1016/j.chroma.2004.12.055] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Modified nucleosides are formed posttranscriptionally in RNA. During RNA turnover free modified nucleosides are formed which circulate in the blood stream and are excreted in the urine. Their levels are increased in a number of malignant diseases, and they can be used in clinical chemistry as tumor markers. The analysis includes the isolation of the nucleosides from urine with phenylboronate gel and their separation and quantitation by HPLC on C18 columns or by capillary electrophoresis on uncoated columns applying a sodium dodecyl sulfate-borate-phosphate buffer. Identification of the nucleosides is performed with matrix-assisted laser desorption ionization time-of-flight mass spectrometry including post source decay spectra. In two clinical studies the diagnostic value of urinary modified nucleosides is investigated, in a study on children with leukemia and other malignant diseases and a study on women with breast cancer. Candidate markers are pseudouridine, 1-methylguanosine, N2-methylguanosine, 3-methyluridine and 1-methyl-inosine.
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Affiliation(s)
- H M Liebich
- a Medizinische Klinik, Universität Tübingen, Zentrallaboratorium, D-72076 Tübingen, Germany.
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Svoboda P, Kasai H. Simultaneous HPLC analysis of 8-hydroxydeoxyguanosine and 7-methylguanine in urine from humans and rodents. Anal Biochem 2004; 334:239-50. [PMID: 15494130 DOI: 10.1016/j.ab.2004.08.021] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2004] [Indexed: 12/13/2022]
Abstract
With a recently developed high-performance liquid chromatography (HPLC) method based on anion exchange chromatography, precise fraction collection, and reversed-phase chromatography, the oxidative DNA damage marker 8-hydroxydeoxyguanosine (8-OH-dG) was measured in human urine samples. The HPLC analysis was further modified to measure 8-OH-dG in rat and mouse urine samples. In addition, the urinary RNA degradation product 7-methylguanine (m7Gua) was analyzed simultaneously. The correlation coefficient (r) for the correlation between urinary creatinine and m7Gua was 0.9 for rats and 0.8 for humans and mice. Levels of 8-OH-dG in relation to urinary creatinine were compared and found to be similar for humans and rats and twice as high for mice. Urinary levels of m7Gua, as normalized to creatinine, were several-fold higher in rodents as compared with human levels, thereby correlating with the higher resting metabolic rate of rodents. The presented results show that 8-OH-dG and m7Gua can be analyzed simultaneously and reliably in urine from humans and rodents. In addition, m7Gua may be used as a reliable marker instead of creatinine for the normalization of 8-OH-dG in urine from rats and mice and also may be used in addition to normalization with creatinine in measurements of 8-OH-dG in human urine samples.
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Affiliation(s)
- Peter Svoboda
- Department of Environmental Oncology, Institute of Industrial Ecological Sciences, University of Occupational Environmental Health, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu 807-8555, Japan
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van Kuilenburg ABP, van Lenthe H, van Cruchten A, Kulik W. Quantification of 5,6-dihydrouracil by HPLC-electrospray tandem mass spectrometry. Clin Chem 2004; 50:236-8. [PMID: 14709662 DOI: 10.1373/clinchem.2003.026229] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- André B P van Kuilenburg
- Academic Medical Center, University of Amsterdam, Emma Children's Hospital and Department of Clinical Chemistry, PO Box 22700, 1100 DE Amsterdam, The Netherlands.
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Topp H, Armbrust S, Lengger C, Schöch G, Davies J, Stichler W, Manz F, Fusch C. Renal excretion of 8-oxo-7,8-dihydro-2(')-deoxyguanosine: degradation rates of RNA and metabolic rate in humans. Arch Biochem Biophys 2002; 402:31-7. [PMID: 12051680 DOI: 10.1016/s0003-9861(02)00034-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Renally excreted 8-oxo-7,8-dihydro-2(')-deoxyguanosine (oxo(8)dG) is a potential marker of oxidative DNA damage by reactive oxygen species. Whole-body degradation rates of t- and rRNA are potential indicators of the resting metabolic rate (RMR). Excretion rates of oxo(8)dG and degradation rates of t- and rRNA were determined in healthy non-smoking adults and children. RMR (indirect calorimetry; 14 children, 16 adults), total energy expenditure (TEE; doubly labelled water technique; 4 children, 6 adults), and lean body mass (LBM; dual-energy X-ray absorptiometry; 14 children, 16 adults) were also measured. Degradation of t- and rRNA (micromol/d/kg LBM; 4 children, 6 adults) was highly correlated with RMR (kJ/d/kg LBM), r=0.867 (p<0.005) and 0.959 (p<0.001), respectively. Excretion of oxo(8)dG (pmol/d/kg LBM; 14 children, 16 adults) was not significantly correlated with RMR (p>0.05). Neither excretion of oxo(8)dG nor degradation of RNA was significantly correlated with TEE (kJ/d/ kg LBM) (p>0.05). In healthy subjects further factors, other than the metabolic rate, seem to influence the excretion rate of oxo(8)dG. The degradation rates of t- and rRNA seem to be appropriate indicators of the RMR.
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Affiliation(s)
- Heinrich Topp
- Neonatology, University Children's Hospital, Soldtmannstr. 15, D-17487 Greifswald, Germany.
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16
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Liebich HM, Lehmann R, Xu G, Wahl HG, Häring HU. Application of capillary electrophoresis in clinical chemistry: the clinical value of urinary modified nucleosides. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL SCIENCES AND APPLICATIONS 2000; 745:189-96. [PMID: 10997714 DOI: 10.1016/s0378-4347(00)00263-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Urinary modified nucleosides were determined by capillary electrophoresis using a 300 mM SDS-25 mM sodium tetraborate-50 mM sodium dihydrogenphosphate buffer. The nucleosides were extracted from urine by phenylboronate affinity gel chromatography. In cancer patients the levels of the modified nucleosides are generally elevated. By an artificial neural network method breast cancer patients were differentiated from normal individuals, which indicates that the modified nucleosides could be of clinical value as tumor markers.
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Affiliation(s)
- H M Liebich
- Medizinische Universitaetsklinik, Abteilung IV, Zentrallabor, Tübingen, Germany
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18
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Topp H, Schöch G. Whole-body degradation rates of transfer-, ribosomal-, and messenger ribonucleic acids and resting metabolic rate in 3- to 18-year-old humans. Pediatr Res 2000; 47:163-8. [PMID: 10625098 DOI: 10.1203/00006450-200001000-00027] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Whole-body degradation rates of transfer, ribosomal, and messenger RNA were determined noninvasively in 3-, 6-, 10-, 14-, and 18-y-old female and male subjects (n = 14 per age group per sex) under normal living conditions. The method for determining the RNA degradation rates is based on measuring the renal excretion rates of special RNA catabolites (modified ribonucleosides and nucleobases) by HPLC. Resting metabolic rates were calculated for the same subjects by their body weights using formulas taken from literature. We found high correlations between the degradation rates of the different RNA classes (micromoles per day per kilogram body weight) and the resting metabolic rate (kilojoules per day per kilogram body weight): in females (n = 70), r = 0.75-0.82 and in males (n = 70), r = 0.68-0.79 (p<0.0001). We conclude that a causal relationship exists between the whole-body degradation rates of the different RNA classes and the resting metabolic rate. Therefore, in healthy subjects noninvasive determinations of RNA degradation rates could be very useful to assess the resting metabolic rate.
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Affiliation(s)
- H Topp
- Forschungsinstitut für Kinderernährung Dortmund and der Universität Witten/Herdecke, Germany
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Liebich HM, Xu G, Di Stefano C, Lehmann R. Capillary electrophoresis of urinary normal and modified nucleosides of cancer patients. J Chromatogr A 1998; 793:341-7. [PMID: 9474787 DOI: 10.1016/s0021-9673(97)00915-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
This paper gives a capillary electrophoretic method for the separation of 15 urinary normal and modified nucleosides from cancer patients in less than 40 min. A 500 mm x 50 microns uncoated capillary column (437.5 mm to window) was used. The effects of the voltage and the sodium dodecyl sulfate (SDS) concentration in the buffer on the separation were studied. With reproducibilities of migration times better than 1.2% (R.S.D.) and determined concentrations better than 5-25%, depending on the concentrations of nucleosides in the urine, the analytical characteristics of the method were good. Using this developed method, the concentrations of 13 normal and modified nucleosides, extracted on a phenyl boronic acid affinity chromatography column, in 25 urines from patients of 14 kinds of cancer were determined. The levels (nmol/mumol creatinine) of modified nucleosides in urines from cancer patients were increased as compared with those in normal urines.
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Affiliation(s)
- H M Liebich
- Medizinische Universitätsklinik, Department of Clinical Chemistry, Tübingen, Germany
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Topp H, Dörrenhaus A, Bolt H, Schöch G, Föllmann W. Determination of degradation rates of transfer and ribosomal ribonucleic acids in cultured rat hepatocytes by measuring N6-threoninocarbonyladenosine, dihydrouridine, and pseudouridine in medium using high-performance liquid chromatography. Anal Biochem 1997; 254:200-7. [PMID: 9417777 DOI: 10.1006/abio.1997.2409] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Modified ribonucleic acid catabolites excreted into the medium by primary cultures of rat hepatocytes (2.3 +/- 0.42 x 10(6) cells/dish) during a 24-h cultivation period were quantified by reversed-phase high-performance liquid chromatography (fmol/10(3) cells): 613 +/- 81 dihydrouridine, 46 +/- 6 N6-threoninocarbonyladenosine, 1879 +/- 220 pseudouridine. On the basis of these excretion rates and the average frequency of occurrence of these modified ribonucleosides per cytoplasmic transfer ribonucleic acid (residues: 2.6 dihydrouridine, 0.22 N6-threoninocarbonyladenosine, 3 pseudouridine) as well as per cytoplasmic ribosomal ribonucleic acid (residues: 95 pseudouridine), the degradation rates of transfer and ribosomal ribonucleic acids were calculated. The degradation rate of transfer ribonucleic acid (fmol/10(3) cells/24 h) was 236 +/- 31 (via dihydrouridine) and 211 +/- 28 (via N6-threoninocarbonyladenosine) and that of ribosomal ribonucleic acid (fmol/10(3) cells/24 h) was 13.1 +/- 1.7 (via pseudouridine and N6-threoninocarbonyladenosine).
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Affiliation(s)
- H Topp
- Forschungsinstitut für Kinderernährung, Federal Republic of Germany
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Abstract
Dihydrouridine is absent from the tRNA of almost all hyperthermophiles and most Archaea but is ubiquitous in the tRNA of Eubacteria and Eukaryotes. In order to investigate whether this could be due to instability, the rate of ring opening of dihydrouridine was measured between 25 and 120 degrees C. The dihydrouridine ring is stable at 25 degrees C, but the half-life at 100 degrees C and pH 7 is 9.1 h, which is comparable to the doubling time of hyperthermophiles. This suggests an explanation for the absence of dihydrouridine from the tRNA of hyperthermophiles. The rates of ring opening of dihydrouracil, dihydrothymine, and 1-N-methyldihydrouracil were measured at 100 degrees C and pH 6-9, as were the equilibrium constants for ring closure of the ureido acids to the dihydrouracils. The pH rate profiles for ring opening and ring closing were calculated from the data. Possible roles for dihydrouracils in the pre-RNA world are discussed.
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Affiliation(s)
- C H House
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla 92093-0506, USA
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