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Sharma S, Kong Z, Jia S, Tran P, Nilsson AK, Chabes A. Quantitative Analysis of Nucleoside Triphosphate Pools in Mouse Muscle Using Hydrophilic Interaction Liquid Chromatography Coupled with Tandem Mass Spectrometry Detection. Methods Mol Biol 2023; 2615:267-280. [PMID: 36807798 DOI: 10.1007/978-1-0716-2922-2_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Defects in deoxyribonucleoside triphosphate (dNTP) metabolism are associated with a number of mitochondrial DNA (mtDNA) depletion syndromes (MDS). These disorders affect the muscles, liver, and brain, and the concentrations of dNTPs in these tissues are already normally low and are, therefore, difficult to measure. Thus, information about the concentrations of dNTPs in tissues of healthy animals and animals with MDS are important for mechanistic studies of mtDNA replication, analysis of disease progression, and the development of therapeutic interventions. Here, we present a sensitive method for the simultaneous analysis of all four dNTPs as well as all four ribonucleoside triphosphates (NTPs) in mouse muscles using hydrophilic interaction liquid chromatography coupled with triple quadrupole mass spectrometry. The simultaneous detection of NTPs allows them to be used as internal standards for the normalization of dNTP concentrations. The method can be applied for measuring dNTP and NTP pools in other tissues and organisms.
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Affiliation(s)
- Sushma Sharma
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Ziqing Kong
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Shaodong Jia
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Phong Tran
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Anna Karin Nilsson
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden.
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2
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Frańska M, Stȩżycka O, Jankowski W, Hoffmann M. Gas-Phase Internal Ribose Residue Loss from Mg-ATP and Mg-ADP Complexes: Experimental and Theoretical Evidence for Phosphate-Mg-Adenine Interaction. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1474-1479. [PMID: 35796751 PMCID: PMC9354248 DOI: 10.1021/jasms.2c00071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Gas-phase decompositions of magnesium complexes with adenosine-5'-triphosphate (ATP) and adenosine-5'-diphosphate (ADP) were studied by using electrospray ionization-collision-induced dissociation-tandem mass spectrometry, in the negative ion mode. The loss of internal ribose residue was observed and was found to occur directly from the [ADP-3H+Mg]- ion. The occurrence of this process indicates the presence of a strong phosphate-Mg-adenine interaction. The performed quantum mechanics calculations confirmed the occurrence of this interaction in the [ADP-3H+Mg]- ion, namely the presence of Mg-N7 bond and hydrogen bond between the phosphate oxygen atom and amino group. Although the finding concerns the gas phase, it indicates that phosphate-Mg-adenine interaction may be also of importance for biological processes. The loss of an internal ribose residue was also observed for calcium and zinc complexes with ATP/ADP as well as for magnesium complexes with guanosine-5'-triphosphate (GTP) or guanosine-5'-diphosphate (GDP). Therefore, it is reasonable to conclude that the presence of the phosphate-metal-nucleobase interaction is a feature of gas phase [NDP-3H+metal]- ion (NDP, nucleoside-5'-diphosphate) and may also be important for biological processes.
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Affiliation(s)
- Magdalena Frańska
- Institute
of Chemistry and Technical Electrochemistry, Poznań University of Technology, Berdychowo 4, 60-965 Poznań, Poland
| | - Olga Stȩżycka
- Institute
of Chemistry and Technical Electrochemistry, Poznań University of Technology, Berdychowo 4, 60-965 Poznań, Poland
| | - Wojciech Jankowski
- Faculty of
Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego
8, 61-614 Poznań, Poland
| | - Marcin Hoffmann
- Faculty of
Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego
8, 61-614 Poznań, Poland
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3
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Wang X, Luo X. Precursor Quantitation Methods for Next Generation Food Production. Front Bioeng Biotechnol 2022; 10:849177. [PMID: 35360389 PMCID: PMC8960114 DOI: 10.3389/fbioe.2022.849177] [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] [Received: 01/05/2022] [Accepted: 02/22/2022] [Indexed: 11/21/2022] Open
Abstract
Food is essential for human survival. Nowadays, traditional agriculture faces challenges in balancing the need of sustainable environmental development and the rising food demand caused by an increasing population. In addition, in the emerging of consumers' awareness of health related issues bring a growing trend towards novel nature-based food additives. Synthetic biology, using engineered microbial cell factories for production of various molecules, shows great advantages for generating food alternatives and additives, which not only relieve the pressure laid on tradition agriculture, but also create a new stage in healthy and sustainable food supplement. The biosynthesis of food components (protein, fats, carbohydrates or vitamins) in engineered microbial cells often involves cellular central metabolic pathways, where common precursors are processed into different proteins and products. Quantitation of the precursors provides information of the metabolic flux and intracellular metabolic state, giving guidance for precise pathway engineering. In this review, we summarized the quantitation methods for most cellular biosynthetic precursors, including energy molecules and co-factors involved in redox-reactions. It will also be useful for studies worked on pathway engineering of other microbial-derived metabolites. Finally, advantages and limitations of each method are discussed.
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Affiliation(s)
- Xinran Wang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xiaozhou Luo
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Shenzhen Institute of Advanced Technology, Shenzhen, China
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4
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Enhancing the Antiviral Potency of Nucleobases for Potential Broad-Spectrum Antiviral Therapies. Viruses 2021; 13:v13122508. [PMID: 34960780 PMCID: PMC8705664 DOI: 10.3390/v13122508] [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] [Received: 10/26/2021] [Revised: 11/29/2021] [Accepted: 12/08/2021] [Indexed: 11/16/2022] Open
Abstract
Broad-spectrum antiviral therapies hold promise as a first-line defense against emerging viruses by blunting illness severity and spread until vaccines and virus-specific antivirals are developed. The nucleobase favipiravir, often discussed as a broad-spectrum inhibitor, was not effective in recent clinical trials involving patients infected with Ebola virus or SARS-CoV-2. A drawback of favipiravir use is its rapid clearance before conversion to its active nucleoside-5′-triphosphate form. In this work, we report a synergistic reduction of flavivirus (dengue, Zika), orthomyxovirus (influenza A), and coronavirus (HCoV-OC43 and SARS-CoV-2) replication when the nucleobases favipiravir or T-1105 were combined with the antimetabolite 6-methylmercaptopurine riboside (6MMPr). The 6MMPr/T-1105 combination increased the C-U and G-A mutation frequency compared to treatment with T-1105 or 6MMPr alone. A further analysis revealed that the 6MMPr/T-1105 co-treatment reduced cellular purine nucleotide triphosphate synthesis and increased conversion of the antiviral nucleobase to its nucleoside-5′-monophosphate, -diphosphate, and -triphosphate forms. The 6MMPr co-treatment specifically increased production of the active antiviral form of the nucleobases (but not corresponding nucleosides) while also reducing levels of competing cellular NTPs to produce the synergistic effect. This in-depth work establishes a foundation for development of small molecules as possible co-treatments with nucleobases like favipiravir in response to emerging RNA virus infections.
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5
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Wang HY, Hsin P, Huang CY, Chang ZF. A Convenient and Sensitive Method for Deoxynucleoside Triphosphate Quantification by the Combination of Rolling Circle Amplification and Quantitative Polymerase Chain Reaction. Anal Chem 2021; 93:14247-14255. [PMID: 34633808 DOI: 10.1021/acs.analchem.1c03236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Measurement of four dNTP pools is important for investigating metabolism, genome stability, and drug action. In this report, we developed a two-step method for quantitating dNTPs by the combination of rolling circle amplification (RCA) and quantitative polymerase chain reaction (qPCR). We used CircLigase to generate a single-strand DNA in circular monomeric configuration, which was then used for the first step of RCA reaction that contained three dNTPs in excess for quantification of one dNTP at limiting levels. The second step is the amplification of RCA products by qPCR, in which one primer was designed to be completely annealed with the polymeric ssDNA product but not the monomeric template DNA. Using 1 amol of the template in the assay, each dNTP from 0.02 to 2.5 pmol gave a linearity with r2 > 0.99, and the quantification was not affected by the presence of rNTPs. We further found that the preparation of biological samples for the RCA reaction required methanol and chloroform extraction. The method was so sensitive that 1 × 104 cells were sufficient for dNTP quantification with the results similar to those determined by a radio-isotope method using 2 × 105 cells. Thus, the RCA/qPCR method is convenient, cost-effective, and highly sensitive for dNTP quantification.
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Affiliation(s)
- Hsin-Yen Wang
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, No. 1, Section 1, Jen-Ai Road, Taipei 100, Taiwan, R.O.C.,Center of Precision Medicine, College of Medicine, National Taiwan University, No. 1, Section 1, Jen-Ai Road, Taipei 100, Taiwan, R.O.C
| | - Peng Hsin
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, No. 1, Section 1, Jen-Ai Road, Taipei 100, Taiwan, R.O.C.,Center of Precision Medicine, College of Medicine, National Taiwan University, No. 1, Section 1, Jen-Ai Road, Taipei 100, Taiwan, R.O.C
| | - Chang-Yu Huang
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, No. 1, Section 1, Jen-Ai Road, Taipei 100, Taiwan, R.O.C.,Center of Precision Medicine, College of Medicine, National Taiwan University, No. 1, Section 1, Jen-Ai Road, Taipei 100, Taiwan, R.O.C
| | - Zee-Fen Chang
- Institute of Molecular Medicine, College of Medicine, National Taiwan University, No. 1, Section 1, Jen-Ai Road, Taipei 100, Taiwan, R.O.C.,Center of Precision Medicine, College of Medicine, National Taiwan University, No. 1, Section 1, Jen-Ai Road, Taipei 100, Taiwan, R.O.C
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6
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Straube H, Niehaus M, Zwittian S, Witte CP, Herde M. Enhanced nucleotide analysis enables the quantification of deoxynucleotides in plants and algae revealing connections between nucleoside and deoxynucleoside metabolism. THE PLANT CELL 2021; 33:270-289. [PMID: 33793855 PMCID: PMC8136904 DOI: 10.1093/plcell/koaa028] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/12/2020] [Indexed: 05/02/2023]
Abstract
Detecting and quantifying low-abundance (deoxy)ribonucleotides and (deoxy)ribonucleosides in plants remains difficult; this is a major roadblock for the investigation of plant nucleotide (NT) metabolism. Here, we present a method that overcomes this limitation, allowing the detection of all deoxy- and ribonucleotides as well as the corresponding nucleosides from the same plant sample. The method is characterized by high sensitivity and robustness enabling the reproducible detection and absolute quantification of these metabolites even if they are of low abundance. Employing the new method, we analyzed Arabidopsis thaliana null mutants of CYTIDINE DEAMINASE, GUANOSINE DEAMINASE, and NUCLEOSIDE HYDROLASE 1, demonstrating that the deoxyribonucleotide (dNT) metabolism is intricately interwoven with the catabolism of ribonucleosides (rNs). In addition, we discovered a function of rN catabolic enzymes in the degradation of deoxyribonucleosides in vivo. We also determined the concentrations of dNTs in several mono- and dicotyledonous plants, a bryophyte, and three algae, revealing a correlation of GC to AT dNT ratios with genomic GC contents. This suggests a link between the genome and the metabolome previously discussed but not experimentally addressed. Together, these findings demonstrate the potential of this new method to provide insight into plant NT metabolism.
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Affiliation(s)
- Henryk Straube
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
| | - Markus Niehaus
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
| | - Sarah Zwittian
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
| | - Claus-Peter Witte
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
| | - Marco Herde
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
- Author for correspondence:
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Straube H, Witte CP, Herde M. Analysis of Nucleosides and Nucleotides in Plants: An Update on Sample Preparation and LC-MS Techniques. Cells 2021; 10:689. [PMID: 33804650 PMCID: PMC8003640 DOI: 10.3390/cells10030689] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 02/06/2023] Open
Abstract
Nucleotides fulfill many essential functions in plants. Compared to non-plant systems, these hydrophilic metabolites have not been adequately investigated in plants, especially the less abundant nucleotide species such as deoxyribonucleotides and modified or damaged nucleotides. Until recently, this was mainly due to a lack of adequate methods for in-depth analysis of nucleotides and nucleosides in plants. In this review, we focus on the current state-of-the-art of nucleotide analysis in plants with liquid chromatography coupled to mass spectrometry and describe recent major advances. Tissue disruption, quenching, liquid-liquid and solid-phase extraction, chromatographic strategies, and peculiarities of nucleotides and nucleosides in mass spectrometry are covered. We describe how the different steps of the analytical workflow influence each other, highlight the specific challenges of nucleotide analysis, and outline promising future developments. The metabolite matrix of plants is particularly complex. Therefore, it is likely that nucleotide analysis methods that work for plants can be applied to other organisms as well. Although this review focuses on plants, we also discuss advances in nucleotide analysis from non-plant systems to provide an overview of the analytical techniques available for this challenging class of metabolites.
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Affiliation(s)
| | - Claus-Peter Witte
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, 30419 Hannover, Germany;
| | - Marco Herde
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, 30419 Hannover, Germany;
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8
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Hu W, Chang L, Ke C, Xie Y, Shen J, Tan B, Liu J. Challenges and stepwise fit-for-purpose optimization for bioanalyses of remdesivir metabolites nucleotide monophosphate and triphosphate in mouse tissues using LC-MS/MS. J Pharm Biomed Anal 2020; 194:113806. [PMID: 33280995 PMCID: PMC7703390 DOI: 10.1016/j.jpba.2020.113806] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 01/18/2023]
Abstract
A robust and reliable LC–MS/MS method for the quantification of RMP and RTP was optimized and validated. The novel method solved the major challenges of direct determination of RMP and RTP in biological matrix through improvement of LC retention, stability and recovery. The method was validated and successfully applied to mouse tissue distribution study. This method provides useful information for further study of remdesivir as well as extends the approach for phosphate determination. The method solved the major challenges for determining RMP and RTP in biological matrix such as LC retention, stability and recovery.
Remdesivir is a prodrug of the nucleotide analogue and used for COVID-19 treatment. However, the bioanalysis of the active metabolites remdesivir nucleotide triphosphate (RTP) and its precursor remdesivir nucleotide monophosphate (RMP) is very challenging. Herein, we established a novel method to separate RTP and RMP on a BioBasic AX column and quantified them by high-performance liquid chromatography-tandem mass spectrometry in positive electrospray ionization mode. Stepwise, we optimized chromatographic retention on an anion exchange column, improved stability in matrix through the addition of 5,5′-dithiobis-(2nitrobenzoic acid) and PhosSTOP EASYpack, and increased recovery by dissociation of tight protein binding with 2 % formic acid aqueous solution. The method allowed lower limit of quantification of 20 nM for RMP and 10 nM for RTP. Method validation demonstrated acceptable accuracy (93.6%–103% for RMP, 94.5%–107% for RTP) and precision (RSD < 11.9 % for RMP, RSD < 11.4 % for RTP), suggesting that it was sensitive and robust for simultaneous quantification of RMP and RTP. The method was successfully applied to analyze RMP and RTP in mouse tissues. In general, the developed method is suitable to monitor RMP and RTP, and provides a useful approach for exploring more detailed effects of remdesivir in treating diseases.
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Affiliation(s)
- Wenjuan Hu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Lu Chang
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Changqiang Ke
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Yuanchao Xie
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Jingshan Shen
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Bo Tan
- Clinical Pharmacokinetic Laboratory, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| | - Jia Liu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
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Feliu C, Peyret H, Vautier D, Djerada Z. Simultaneous quantification of 8 nucleotides and adenosine in cells and their medium using UHPLC-HRMS. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1148:122156. [PMID: 32446186 DOI: 10.1016/j.jchromb.2020.122156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/10/2020] [Accepted: 05/11/2020] [Indexed: 10/24/2022]
Abstract
Purinergic signalling is involved in physiological processes, particularly during ischemia-reperfusion injuries for which it has a protective effect. The purpose of this work was to develop a method for simultaneous quantification of eight nucleotides and adenosine in biological matrices by liquid chromatography coupled with high-resolution mass spectrometry. A method was developed that was sufficiently robust to quantify the targeted analytes in 20 min with good sensitivity. Analysis of extracellular media from cultured endothelial cells detected the release of nucleotides and adenosine during 2 h of hypoxia. The quantification of cylic adenosine monophosphate (cAMP) allowed to establish a dose-response curve after receptor stimulation. Therefore, our method allows us to study the involvement of nucleotides in various processes in both the intracellular and extracellular compartment.
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Affiliation(s)
- Catherine Feliu
- Department of Pharmacology, E.A.3801, SFR CAP-santé, Reims University Hospital, 51, rue Cognacq-Jay, 51095 Reims Cedex, France
| | - Hélène Peyret
- Department of Pharmacology, E.A.3801, SFR CAP-santé, Reims University Hospital, 51, rue Cognacq-Jay, 51095 Reims Cedex, France
| | - Damien Vautier
- Department of Pharmacology, E.A.3801, SFR CAP-santé, Reims University Hospital, 51, rue Cognacq-Jay, 51095 Reims Cedex, France
| | - Zoubir Djerada
- Department of Pharmacology, E.A.3801, SFR CAP-santé, Reims University Hospital, 51, rue Cognacq-Jay, 51095 Reims Cedex, France.
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10
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Feliu C, Peyret H, Brassart-Pasco S, Oszust F, Poitevin G, Nguyen P, Millart H, Djerada Z. Ticagrelor Prevents Endothelial Cell Apoptosis through the Adenosine Signalling Pathway in the Early Stages of Hypoxia. Biomolecules 2020; 10:biom10050740. [PMID: 32397519 PMCID: PMC7277469 DOI: 10.3390/biom10050740] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/05/2020] [Accepted: 05/07/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Several studies have reported the beneficial effects of anti-platelet drugs in cardioprotection against ischaemia-reperfusion injuries. To date, no studies have focused on the indirect cytoprotective effects of ticagrelor via adenosine receptor on the endothelium. METHOD By evaluating cell viability and cleaved caspase 3 expression, we validated a model of endothelial cell apoptosis induced by hypoxia. In hypoxic endothelial cells treated with ticagrelor, we quantified the extracellular concentration of adenosine, and then we studied the involvement of adenosine pathways in the cytoprotective effect of ticagrelor. RESULTS Our results showed that 10 µM ticagrelor induced an anti-apoptotic effect in our model associated with an increase of extracellular adenosine concentration. Similar experiments were conducted with cangrelor but did not demonstrate an anti-apoptotic effect. We also found that A2B and A3 adenosine receptors were involved in the anti-apoptotic effect of ticagrelor in endothelial cells exposed to 2 h of hypoxia stress. CONCLUSION we described an endothelial cytoprotective mechanism of ticagrelor against hypoxia stress, independent of blood elements. We highlighted a mechanism triggered mainly by the increased extracellular bioavailability of adenosine, which activates A2B and A3 receptors on the endothelium.
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Affiliation(s)
- Catherine Feliu
- Department of Pharmacology, Hémostase et Remodelage Vasculaire post-Ischémie (HERVI) E.A.3801, SFR CAP-santé, Reims University Hospital, 51, rue Cognacq-Jay, 51095 Reims CEDEX, France; (C.F.); (H.P.); (F.O.); (H.M.)
| | - Hélène Peyret
- Department of Pharmacology, Hémostase et Remodelage Vasculaire post-Ischémie (HERVI) E.A.3801, SFR CAP-santé, Reims University Hospital, 51, rue Cognacq-Jay, 51095 Reims CEDEX, France; (C.F.); (H.P.); (F.O.); (H.M.)
| | - Sylvie Brassart-Pasco
- UMR CNRS/URCA 7369, Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Reims University Hospital, SFR CAP-santé, 51, rue Cognacq-Jay, 51095 Reims CEDEX, France;
| | - Floriane Oszust
- Department of Pharmacology, Hémostase et Remodelage Vasculaire post-Ischémie (HERVI) E.A.3801, SFR CAP-santé, Reims University Hospital, 51, rue Cognacq-Jay, 51095 Reims CEDEX, France; (C.F.); (H.P.); (F.O.); (H.M.)
| | - Gaël Poitevin
- Laboratory of Hematology, E.A.3801, SFR CAP-santé, Reims University Hospital, 51, rue Cognacq-Jay, 51095 Reims CEDEX, France; (G.P.); (P.N.)
| | - Philippe Nguyen
- Laboratory of Hematology, E.A.3801, SFR CAP-santé, Reims University Hospital, 51, rue Cognacq-Jay, 51095 Reims CEDEX, France; (G.P.); (P.N.)
| | - Hervé Millart
- Department of Pharmacology, Hémostase et Remodelage Vasculaire post-Ischémie (HERVI) E.A.3801, SFR CAP-santé, Reims University Hospital, 51, rue Cognacq-Jay, 51095 Reims CEDEX, France; (C.F.); (H.P.); (F.O.); (H.M.)
| | - Zoubir Djerada
- Department of Pharmacology, Hémostase et Remodelage Vasculaire post-Ischémie (HERVI) E.A.3801, SFR CAP-santé, Reims University Hospital, 51, rue Cognacq-Jay, 51095 Reims CEDEX, France; (C.F.); (H.P.); (F.O.); (H.M.)
- Correspondence: ; Tel.: +33-3-26-83-27-82; Fax: +33-3-26-78-84-56
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11
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Direct and indirect quantification of phosphate metabolites of nucleoside analogs in biological samples. J Pharm Biomed Anal 2019; 178:112902. [PMID: 31610397 DOI: 10.1016/j.jpba.2019.112902] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/22/2019] [Accepted: 09/29/2019] [Indexed: 12/19/2022]
Abstract
Nucleoside reverse transcriptase inhibitors (NRTIs) are prodrugs that require intracellular phosphorylation to active triphosphate nucleotide metabolites (NMs) for their pharmacological activity. However, monitoring these pharmacologically active NMs is challenging due to their instability, high hydrophilicity, and their low concentrations in blood and tissues. Liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) is the gold standard technique for the quantification of NRTIs and their phosphorylated NMs. In this review, an overview of the publications describing the quantitative analysis of intracellular and total tissue concentration of NMs is presented. The focus of this review is the comparison of the different approaches and challenges associated with sample collection, tissue homogenization, cell lysis, cell counting, analyte extraction, sample storage conditions, and LC-MS analysis. Quantification methods of NMs via LC-MS can be categorized into direct and indirect methods. In the direct LC-MS methods, chromatographic retention of the NMs is accomplished by ion-exchange (IEX), ion-pairing (IP), hydrophilic interaction (HILIC), porous graphitic carbon (PGC) chromatography, or capillary electrophoresis (CE). In indirect methods, parent nucleosides are 1st generated from the dephosphorylation of NMs during sample preparation and are then quantified by reverse phase LC-MS as surrogates for their corresponding NMs. Both approaches have advantages and disadvantages associated with them, which are discussed in this review.
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12
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Kong Z, Jia S, Chabes AL, Appelblad P, Lundmark R, Moritz T, Chabes A. Simultaneous determination of ribonucleoside and deoxyribonucleoside triphosphates in biological samples by hydrophilic interaction liquid chromatography coupled with tandem mass spectrometry. Nucleic Acids Res 2019; 46:e66. [PMID: 29554314 PMCID: PMC6009580 DOI: 10.1093/nar/gky203] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 03/08/2018] [Indexed: 11/13/2022] Open
Abstract
Information about the intracellular concentration of dNTPs and NTPs is important for studies of the mechanisms of DNA replication and repair, but the low concentration of dNTPs and their chemical similarity to NTPs present a challenge for their measurement. Here, we describe a new rapid and sensitive method utilizing hydrophilic interaction liquid chromatography coupled with tandem mass spectrometry for the simultaneous determination of dNTPs and NTPs in biological samples. The developed method showed linearity (R2 > 0.99) in wide concentration ranges and could accurately quantify dNTPs and NTPs at low pmol levels. The intra-day and inter-day precision were below 13%, and the relative recovery was between 92% and 108%. In comparison with other chromatographic methods, the current method has shorter analysis times and simpler sample pre-treatment steps, and it utilizes an ion-pair-free mobile phase that enhances mass-spectrometric detection. Using this method, we determined dNTP and NTP concentrations in actively dividing and quiescent mouse fibroblasts.
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Affiliation(s)
- Ziqing Kong
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
| | - Shaodong Jia
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
| | - Anna Lena Chabes
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
| | - Patrik Appelblad
- Department of Pharmacology and Clinical Neuroscience, Umeå University, SE-901 87, Umeå, Sweden.,Merck Chemicals and Life Science AB, SE 169-03 Solna, Sweden
| | - Richard Lundmark
- Dept. of Integrative Medical Biology, Umeå University, SE-901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87 Umeå, Sweden
| | - Thomas Moritz
- Umeå Plant Science Centre (UPSC), Dept. of Forest Genetics and Plant Physiology, SLU, SE-901 87 Umeå, Sweden
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87 Umeå, Sweden
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13
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Feliu C, Peyret H, Poitevin G, Cazaubon Y, Oszust F, Nguyen P, Millart H, Djerada Z. Complementary Role of P2 and Adenosine Receptors in ATP Induced-Anti-Apoptotic Effects Against Hypoxic Injury of HUVECs. Int J Mol Sci 2019; 20:ijms20061446. [PMID: 30909368 PMCID: PMC6470483 DOI: 10.3390/ijms20061446] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 03/16/2019] [Accepted: 03/20/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Vascular endothelial injury during ischemia generates apoptotic cell death and precedes apoptosis of underlying tissues. We aimed at studying the role of extracellular adenosine triphosphate (ATP) on endothelial cells protection against hypoxia injury. METHODS In a hypoxic model on endothelial cells, we quantified the extracellular concentration of ATP and adenosine. The expression of mRNA (ectonucleotidases, adenosine, and P2 receptors) was measured. Apoptosis was evaluated by the expression of cleaved caspase 3. The involvement of P2 and adenosine receptors and signaling pathways was investigated using selective inhibitors. RESULTS Hypoxic stress induced a significant increase in extracellular ATP and adenosine. After a 2-h hypoxic injury, an increase of cleaved caspase 3 was observed. ATP anti-apoptotic effect was prevented by suramin, pyridoxalphosphate-6-azophenyl-2',4'-disulfonic acid (PPADS), and CGS15943, as well as by selective A2A, A2B, and A3 receptor antagonists. P2 receptor-mediated anti-apoptotic effect of ATP involved phosphoinositide 3-kinase (PI3K), extracellular signal-regulated kinases (ERK1/2), mitoKATP, and nitric oxide synthase (NOS) pathways whereas adenosine receptor-mediated anti-apoptotic effect involved ERK1/2, protein kinase A (PKA), and NOS. CONCLUSIONS These results suggest a complementary role of P2 and adenosine receptors in ATP-induced protective effects against hypoxia injury of endothelial. This could be considered therapeutic targets to limit the development of ischemic injury of organs such as heart, brain, and kidney.
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Affiliation(s)
- Catherine Feliu
- Department of Pharmacology, E.A.3801, SFR CAP-santé, Reims University Hospital, 51, rue Cognacq-Jay, 51095 Reims CEDEX, France.
| | - Hélène Peyret
- Department of Pharmacology, E.A.3801, SFR CAP-santé, Reims University Hospital, 51, rue Cognacq-Jay, 51095 Reims CEDEX, France.
| | - Gael Poitevin
- Laboratory of Hematology, E.A.3801, SFR CAP-santé, Reims University Hospital, 51, rue Cognacq-Jay, 51095 Reims CEDEX, France.
| | - Yoann Cazaubon
- Department of Pharmacology, E.A.3801, SFR CAP-santé, Reims University Hospital, 51, rue Cognacq-Jay, 51095 Reims CEDEX, France.
| | - Floriane Oszust
- Department of Pharmacology, E.A.3801, SFR CAP-santé, Reims University Hospital, 51, rue Cognacq-Jay, 51095 Reims CEDEX, France.
| | - Philippe Nguyen
- Laboratory of Hematology, E.A.3801, SFR CAP-santé, Reims University Hospital, 51, rue Cognacq-Jay, 51095 Reims CEDEX, France.
| | - Hervé Millart
- Department of Pharmacology, E.A.3801, SFR CAP-santé, Reims University Hospital, 51, rue Cognacq-Jay, 51095 Reims CEDEX, France.
| | - Zoubir Djerada
- Department of Pharmacology, E.A.3801, SFR CAP-santé, Reims University Hospital, 51, rue Cognacq-Jay, 51095 Reims CEDEX, France.
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14
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Zhang Q, Zhou DD, Li F, Wang YZ, Yang FQ. Extraction of nucleobases, nucleosides and nucleotides by employing a magnetized graphene oxide functionalized with hydrophilic phytic acid and titanium(IV) ions. Mikrochim Acta 2019; 186:187. [PMID: 30771073 DOI: 10.1007/s00604-019-3308-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 02/04/2019] [Indexed: 12/26/2022]
Abstract
A magnetite@graphene oxide nanocomposite was first coated with polyethylenimine and then modified with phytic acid and titanium(IV) ions. The high loading with Ti(IV) and the good hydrophilicity of PEI and PA result in a material that can be applied to the efficient extraction of highly polar nucleobases, nucleosides and nucleotides. The physicochemical properties of the composite were investigated by scanning electron microscopy, transmission electron microscopy, energy dispersive X-ray spectroscopy, Fourier transform infrared spectroscopy, water contact angle measurements, thermogravimetric analysis, and vibrating sample magnetometry. A series of parameters that affect extraction and elution under the conditions of immobilized metal affinity chromatography (IMAC) and hydrophilic interaction liquid chromatography (HILIC) were examined. The analytes were eluted from the nanocomposites using 10 mM trisodium phosphate as the elution solution in the IMAC mode, and 50% methanol-water as elution solution in the HILIC mode. Figures of merit include (a) an intra-day precision of 0.1-1.0% in the IMAC mode; (b) an intra-day precision of 0.4%-0.8% in the HILIC mode; (c) detection limits between 1.8-2.8 ng mL-1 in the IMAC mode; and (d) detection limits of 4.0-10.5 ng mL-1 in the HILIC mode. The method was applied to the extraction of the nucleotides cytidine-5'-monophosphate (CMP), uridine-5'-monophosphate (UMP), guanosine-5'-monophosphate (GMP), and adenosine-5'-monophosphate (AMP), and the nucleobases and nucleosides hypoxanthine, adenosine, cytosine, inosine and cytidine from Cordyceps sinensis, Lentinus edodes and plasma samples. Graphical abstract Schematic presentation of the workflow for the extraction of nucleobases, nucleosides and nucleotides using phytic acid-Ti(IV) functionalized magnetite@graphene oxide nanocomposites under two distinct modes.
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Affiliation(s)
- Qian Zhang
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331, People's Republic of China
| | - Dong-Dong Zhou
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331, People's Republic of China
| | - Fan Li
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331, People's Republic of China
| | - Yin-Zhen Wang
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331, People's Republic of China
| | - Feng-Qing Yang
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 401331, People's Republic of China.
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15
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Kuskovsky R, Buj R, Xu P, Hofbauer S, Doan MT, Jiang H, Bostwick A, Mesaros C, Aird KM, Snyder NW. Simultaneous isotope dilution quantification and metabolic tracing of deoxyribonucleotides by liquid chromatography high resolution mass spectrometry. Anal Biochem 2018; 568:65-72. [PMID: 30605633 DOI: 10.1016/j.ab.2018.12.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/26/2018] [Accepted: 12/29/2018] [Indexed: 12/21/2022]
Abstract
Quantification of cellular deoxyribonucleoside mono- (dNMP), di- (dNDP), triphosphates (dNTPs) and related nucleoside metabolites are difficult due to their physiochemical properties and widely varying abundance. Involvement of dNTP metabolism in cellular processes including senescence and pathophysiological processes including cancer and viral infection make dNTP metabolism an important bioanalytical target. We modified a previously developed ion pairing reversed phase chromatography-mass spectrometry method for the simultaneous quantification and 13C isotope tracing of dNTP metabolites. dNMPs, dNDPs, and dNTPs were chromatographically resolved to avoid mis-annotation of in-source fragmentation. We used commercially available 13C15N-stable isotope labeled analogs as internal standards and show that this isotope dilution approach improves analytical figures of merit. At sufficiently high mass resolution achievable on an Orbitrap mass analyzer, stable isotope resolved metabolomics allows simultaneous isotope dilution quantification and 13C isotope tracing from major substrates including 13C-glucose. As a proof of principle, we quantified dNMP, dNDP and dNTP pools from multiple cell lines. We also identified isotopologue enrichment from glucose corresponding to ribose from the pentose-phosphate pathway in dNTP metabolites.
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Affiliation(s)
- Rostislav Kuskovsky
- AJ Drexel Autism Institute, Drexel University, 3020 Market St Suite 560, Philadelphia, PA, 19104, USA
| | - Raquel Buj
- Department of Cellular and Molecular Physiology, Penn State College of Medicine, Hershey, PA, USA
| | - Peining Xu
- AJ Drexel Autism Institute, Drexel University, 3020 Market St Suite 560, Philadelphia, PA, 19104, USA
| | - Samuel Hofbauer
- Centers for Cancer Pharmacology and Excellence in Environmental Toxicology, Department of Pharmacology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Mary T Doan
- AJ Drexel Autism Institute, Drexel University, 3020 Market St Suite 560, Philadelphia, PA, 19104, USA
| | - Helen Jiang
- AJ Drexel Autism Institute, Drexel University, 3020 Market St Suite 560, Philadelphia, PA, 19104, USA
| | - Anna Bostwick
- AJ Drexel Autism Institute, Drexel University, 3020 Market St Suite 560, Philadelphia, PA, 19104, USA
| | - Clementina Mesaros
- Centers for Cancer Pharmacology and Excellence in Environmental Toxicology, Department of Pharmacology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Katherine M Aird
- Department of Cellular and Molecular Physiology, Penn State College of Medicine, Hershey, PA, USA
| | - Nathaniel W Snyder
- AJ Drexel Autism Institute, Drexel University, 3020 Market St Suite 560, Philadelphia, PA, 19104, USA.
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16
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Li Z, Zhang HX, Li Y, Lam CWK, Wang CY, Zhang WJ, Wong VKW, Pang SS, Yao MC, Zhang W. Method for Quantification of Ribonucleotides and Deoxyribonucleotides in Human Cells Using (Trimethylsilyl)diazomethane Derivatization Followed by Liquid Chromatography-Tandem Mass Spectrometry. Anal Chem 2018; 91:1019-1026. [PMID: 30525455 DOI: 10.1021/acs.analchem.8b04281] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Investigation into intracellular ribonucleotides (RNs) and deoxyribonucleotides (dRNs) is important for studies of the mechanism of many biological processes, such as RNA and DNA synthesis and DNA repair, as well as metabolic and therapeutic efficacy of nucleoside analogues. However, current methods are still unsatisfactory for determination of nucleotides in complex matrixes. Here we describe a novel method for the determination of RN and dRN pools in cells based on fast derivatization with (trimethylsilyl)diazomethane (TMSD) followed by quantification using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Derivatization was accomplished in 3 min, and each derivatized nucleotide not only had a sufficient retention on reversed-phase column by introduction of methyl groups but also exhibited a unique ion transition which consequently eliminated mutual interference in LC-MS/MS. Chromatographic separation was performed on a C18 column with a simple acetonitrile-water gradient elution system, which avoided contamination and ion suppression caused by ion-pairing reagents. The developed method was fully validated and applied to the analysis of RNs and dRNs in cell samples. Moreover, results demonstrated that the applicability of this method could be extended to nucleoside analogues and their metabolites and could facilitate many applications in future studies.
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Affiliation(s)
- Zheng Li
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health , Macau University of Science and Technology , Taipa , Macau , China
| | - Hui-Xia Zhang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health , Macau University of Science and Technology , Taipa , Macau , China
| | - Yan Li
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health , Macau University of Science and Technology , Taipa , Macau , China
| | - Christopher Wai Kei Lam
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health , Macau University of Science and Technology , Taipa , Macau , China
| | - Cai-Yun Wang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health , Macau University of Science and Technology , Taipa , Macau , China
| | - Wei-Jia Zhang
- School of Pharmaceutical Sciences , Sun Yat-Sen University , Guang Zhou 510275 , China
| | - Vincent Kam Wai Wong
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health , Macau University of Science and Technology , Taipa , Macau , China
| | - Su-Seng Pang
- Louisiana State University , Baton Rouge , Louisiana 70803 , United States
| | - Mei-Cun Yao
- School of Pharmaceutical Sciences , Sun Yat-Sen University , Guang Zhou 510275 , China
| | - Wei Zhang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health , Macau University of Science and Technology , Taipa , Macau , China
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17
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Li N, El Zahar NM, Saad JG, van der Hage ERE, Bartlett MG. Alkylamine ion-pairing reagents and the chromatographic separation of oligonucleotides. J Chromatogr A 2018; 1580:110-119. [PMID: 30409418 DOI: 10.1016/j.chroma.2018.10.040] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 10/11/2018] [Accepted: 10/19/2018] [Indexed: 11/17/2022]
Abstract
Alkylamines are commonly used to improve both chromatographic and mass spectral performance of electrospray ionization liquid chromatography mass spectrometry based methods for the analysis of oligonucleotides. Recently several new alkylamines have been introduced to enhance the electrospray mass spectral response for oligonucleotides; however, the chromatographic properties of these new alkylamines have not been rigorously assessed. We have investigated the retention, peak width, resolution and general chromatographic performance of fifteen different alkylamines for the separation of a model DNA, RNA and an antisense therapeutic oligonucleotide. Eleven of the fifteen alkylamines were shown to provide similar chromatographic performance across all three classes of oligonucleotides. Based on these findings, a model for the mechanism of retention of oligonucleotides using alkylamines and hexafluoroisopropanol mobile phases is proposed. Depending on the concentrations of alkylamines and pH adjustment, oligonucleotides can be retained by micellar chromatography and not the generally held ion-pairing mechanism. This conclusion is supported by light scattering, transmission electron microscopy and ion mobility experiments detecting three micron aggregates in the mobile phase at concentrations that are routinely used for LC-MS analysis of oligonucleotides. These aggregates are not detected at lower alkylamine concentrations where the retention mechanism follows an ion-pairing mechanism. The formation of these aggregates appears to be dependent on the pH of the mobile phase.
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Affiliation(s)
- Ning Li
- Department of Pharmaceutical Analysis, School of Pharmacy, Shenyang Pharmaceutical University, 103 Wenhua Road, Shenyang, 110016, China; Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 W. Green Street, Athens, GA, 30602-2352, USA
| | - N M El Zahar
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 W. Green Street, Athens, GA, 30602-2352, USA; Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Ain Shams University, Organization of African Unity Street, Abassia, Cairo, 11566, Egypt
| | - Jack G Saad
- Micromeritics Instrument Company, 4356 Communications Drive, Norcross, GA, 30093, USA
| | | | - Michael G Bartlett
- Department of Pharmaceutical and Biomedical Sciences, The University of Georgia College of Pharmacy, 250 W. Green Street, Athens, GA, 30602-2352, USA.
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18
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Hayama T, Ohyama K. Recent development and trends in sample extraction and preparation for mass spectrometric analysis of nucleotides, nucleosides, and proteins. J Pharm Biomed Anal 2018; 161:51-60. [PMID: 30145449 DOI: 10.1016/j.jpba.2018.08.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 08/02/2018] [Accepted: 08/16/2018] [Indexed: 12/20/2022]
Abstract
This review describes the recent developments in sample extraction and preparation techniques for mass spectrometric analysis of nucleotides, nucleosides, and proteins. Unique materials and techniques have been developed for highly selective extraction of nucleotides and nucleosides by solid-phase extraction strategies using various affinities. However, for proteins, the analysis of small-scale sections of diseased tissues (formalin-fixed, paraffin-embedded tissues) and the direct analysis of an exact lesion on the surface of diseased tissues (liquid extraction surface analysis) have become important advances in this field. In this review, we focus on the latest developments of these techniques and strategies.
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Affiliation(s)
- Tadashi Hayama
- Faculty of Pharmaceutical Sciences, Fukuoka University, 8-19-1 Nanakuma, Johnan, Fukuoka 814-0180, Japan
| | - Kaname Ohyama
- Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto-machi, Nagasaki 852-8588, Japan.
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19
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Jin H, Lao YM, Zhou J, Zhang HJ, Cai ZH. A rapid UHPLC-HILIC method for algal guanosine 5'-diphosphate 3'-diphosphate (ppGpp) and the potential separation mechanism. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1096:143-153. [PMID: 30170292 DOI: 10.1016/j.jchromb.2018.08.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 06/20/2018] [Accepted: 08/16/2018] [Indexed: 10/28/2022]
Abstract
A fast and facile hydrophilic interaction liquid chromatography (HILIC) method was developed and applied to quantify physiologically important ppGpp and its analogues in a tough sample, the astaxanthin-accumulating alga Hameatococcus pluvialis. The method is able to analyze simultaneously seven nucleotides, including ppGpp at the order of pmol g-1 cells within 12 min. Mechanism on the elution order was investigated. It was found that 1) phosphate salt competed for the amide groups on the HILIC column with the phosphate groups of the nucleotides; 2) intramolecular hydrogen bonds might contribute to the elution order by offsetting and reducing the number of free hydrogen acceptor/donor of the nucleotide molecules interacting with the amide groups. This is the first HILIC method for ppGpp, which is feasible and applicable to a wide range of samples, especially tough samples, e.g., algae and plants.
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Affiliation(s)
- Hui Jin
- Shenzhen Public Platform of Screening & Application of Marine Microbial Resources, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, PR China; Shenzhen Key Laboratory for Coastal Ocean Dynamic and Environment, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, PR China
| | - Yong Min Lao
- Shenzhen Public Platform of Screening & Application of Marine Microbial Resources, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, PR China; Shenzhen Key Laboratory for Coastal Ocean Dynamic and Environment, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, PR China
| | - Jin Zhou
- Shenzhen Public Platform of Screening & Application of Marine Microbial Resources, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, PR China; Shenzhen Key Laboratory for Coastal Ocean Dynamic and Environment, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, PR China
| | - Huai Jin Zhang
- School of Life Sciences, Tsinghua University, Beijing 100084, PR China
| | - Zhong Hua Cai
- Shenzhen Public Platform of Screening & Application of Marine Microbial Resources, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, PR China; Shenzhen Key Laboratory for Coastal Ocean Dynamic and Environment, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, PR China.
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20
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Kiyokawa E, Hayama T, Yoshida H, Yamaguchi M, Nohta H. Fluorous-assisted metal chelate affinity extraction for nucleotides followed by HILIC-MS/MS analysis. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1074-1075:86-90. [PMID: 29334633 DOI: 10.1016/j.jchromb.2017.12.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 12/26/2017] [Accepted: 12/29/2017] [Indexed: 11/26/2022]
Abstract
We herein developed a selective method for the determination of nucleotides by fluorous-assisted metal chelate affinity extraction followed by hydrophilic interaction liquid chromatography (HILIC) combined with tandem mass spectrometric (MS/MS) analysis. In this study, the nucleotides were selectively chelated by Fe(III)-immobilized perfluoroalkyliminodiacetic acid, and the resulting chelates were subsequently extracted into a fluorous solvent. The nucleotides present in the fluorous solvent were then back-extracted into a non-fluorous solution, such as a solution of ammonia in aqueous acetonitrile. The resulting non-fluorous solution containing the nucleotides was then directly injected into an amide-type HILIC column using a mixture of acetonitrile and aqueous ammonium bicarbonate as the mobile phase for gradient elution, and the nucleotides were detected using the negative electrospray ionization MS/MS mode. In this method, the extraction recoveries of the nucleotides ranged from 43.2 to 94.7% within a relative standard deviation of 17%. This method enabled the determination of intracellular concentrations of nucleotides.
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Affiliation(s)
- Ena Kiyokawa
- Faculty of Pharmaceutical Sciences, Fukuoka University, 8-19-1 Nanakuma, Johnan, Fukuoka 814-0180, Japan
| | - Tadashi Hayama
- Faculty of Pharmaceutical Sciences, Fukuoka University, 8-19-1 Nanakuma, Johnan, Fukuoka 814-0180, Japan
| | - Hideyuki Yoshida
- Faculty of Pharmaceutical Sciences, Fukuoka University, 8-19-1 Nanakuma, Johnan, Fukuoka 814-0180, Japan
| | - Masatoshi Yamaguchi
- Faculty of Pharmaceutical Sciences, Fukuoka University, 8-19-1 Nanakuma, Johnan, Fukuoka 814-0180, Japan
| | - Hitoshi Nohta
- Faculty of Pharmaceutical Sciences, Fukuoka University, 8-19-1 Nanakuma, Johnan, Fukuoka 814-0180, Japan.
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21
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Zhu B, Wei H, Wang Q, Li F, Dai J, Yan C, Cheng Y. A simultaneously quantitative method to profiling twenty endogenous nucleosides and nucleotides in cancer cells using UHPLC-MS/MS. Talanta 2017; 179:615-623. [PMID: 29310284 DOI: 10.1016/j.talanta.2017.11.054] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 11/08/2017] [Accepted: 11/26/2017] [Indexed: 12/31/2022]
Abstract
Endogenous nucleosides and nucleotides in biosamples are frequently highlighted as the most differential metabolites in recent metabolomics studies. We developed a rapid, sensitive, high-throughput and reliable quantitative method to simultaneously profile 20 endogenous nucleosides and nucleotides in cancer cell lines based on ultra-high performance liquid chromatography-electrospray tandem mass spectrometry (UHPLC- MS/MS) by using a porous graphitic carbon column and basic mobile phase. The results indicated that high pH value of mobile phase containing 0.12% diethylamine (DEA) and 5mM NH4OAC (pH 11.5) was the critical factor to prevent the adsorption of multi-phosphorylated species, and significantly improved peak shape and sensitivity. The optimized method was successfully validated with satisfactory linearity, sensitivity, accuracy, precision, matrix effects, recovery and stability for all analytes. The limit of quantification (LOQ) was in the range of 0.6-6nM (6-60 fmol on column). The validated method was applied to the extract of three epithelial cancer cell lines, and the significant difference in the profiling of the nucleosides and nucleotides among the cancer cell lines enables discrimination of breast cancer cell line from the colon cancer cell line and the lung cancer cell line. This quantified analytical method of 20 endogenous nucleosides and nucleotides in cancer cell lines meets the requirement of quantification in specific expanded metabolomics studies, with good selectivity and sensitivity.
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Affiliation(s)
- Bangjie Zhu
- School of Chemistry and molecular engineering, East China Normal University, Shanghai 200241, China; School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hai Wei
- Center for Chinese Medical Therapy and Systems Biology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Qingjiang Wang
- School of Chemistry and molecular engineering, East China Normal University, Shanghai 200241, China
| | - Fugang Li
- DMPK Department, HD Biosciences (China) Co., Ltd., Shanghai 201201, China
| | - Jieyu Dai
- DMPK Department, HD Biosciences (China) Co., Ltd., Shanghai 201201, China
| | - Chao Yan
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Yu Cheng
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China.
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22
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Olafsson S, Whittington D, Murray J, Regnier M, Moussavi-Harami F. Fast and sensitive HPLC-MS/MS method for direct quantification of intracellular deoxyribonucleoside triphosphates from tissue and cells. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1068-1069:90-97. [PMID: 29032043 DOI: 10.1016/j.jchromb.2017.10.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 09/26/2017] [Accepted: 10/04/2017] [Indexed: 01/31/2023]
Abstract
Deoxyribonucleoside triphosphates (dNTPs) are used in DNA synthesis and repair. Even slight imbalances can have adverse biological effects. This study validates a fast and sensitive HPLC-MS/MS method for direct quantification of intracellular dNTPs from tissue. Equal volumes of methanol and water were used for nucleotide extraction from mouse heart and gastrocnemius muscle and isolated cardiomyocytes followed by centrifugation to remove particulates. The resulting supernatant was analyzed on a porous graphitic carbon chromatography column using an elution gradient of ammonium acetate in water and ammonium hydroxide in acetonitrile with a run time of just 10min. Calibration curves of all dNTPs ranged from 62.5 to 2500fmol injections and demonstrated excellent linearity (r2>0.99). The within day and between day precision, as measured by the coefficient of variation (CV (%)), was <25% for all points, including the lower limit of quantification (LLOQ). The inter-day accuracy was within 12% of expected concentration for the LLOQ and within 7% for all other points on the calibration curve. The intra-day accuracy was within 22% for the LLOQ and within 11% for all points on the curve. Compared to existing methods, this study presents a faster and more sensitive method for dNTP quantification.
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Affiliation(s)
- Sigurast Olafsson
- Division of Cardiology, Department of Medicine, University of Washington, Seattle, WA 98109, United States
| | - Dale Whittington
- Department of Medicinal Chemistry, University of Washington, Box 357610 H172, Health Science Building, Seattle, WA 98195-7610, United States
| | - Jason Murray
- Department of Physiology and Biophysics, University of Washington, 1705 NE Pacific Street, HSB Room G424, Box 357290, Seattle, WA 98195-7290, United States
| | - Michael Regnier
- Department of Bioengineering, University of Washington, Box 355061, Seattle, WA 98195-5061, United States
| | - Farid Moussavi-Harami
- Division of Cardiology, Department of Medicine, University of Washington, Seattle, WA 98109, United States.
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23
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Dong J, Wu T, Xiao Y, Chen L, Xu L, Li M, Zhao M. Target-triggered transcription machinery for ultra-selective and sensitive fluorescence detection of nucleoside triphosphates in one minute. Biosens Bioelectron 2017; 100:333-340. [PMID: 28942346 DOI: 10.1016/j.bios.2017.09.030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 09/06/2017] [Accepted: 09/17/2017] [Indexed: 01/02/2023]
Abstract
Nucleoside triphosphates (NTPs) play important roles in living organisms. However, no fluorescent assays are currently available to simply and rapidly detect multiple NTPs with satisfactory selectivity, sensitivity and low cost. Here we demonstrate for the first time a target-triggered in-vitro transcription machinery for ultra-selective, sensitive and instant fluorescence detection of multiple NTPs. The machinery assembles RNA polymerase, DNA template and non-target NTPs to convert the target NTP into equivalent RNA signal sequences which are monitored by the fluorescence enhancement of molecular beacon. The machinery offers excellent selectivity for the target NTP against NDP, NMP and dNTP. Notably, to accelerate the kinetics of the machinery while maintain its high specificity, we investigated the sequence of DNA templates systematically and established a set of guidelines for the design of the optimum DNA templates, which allowed for instant detection of the target NTP at fmol level in less than 1min. Furthermore, the machinery could be transformed into logic gates to study the coeffects of two NTPs in biosynthesis and real-time monitoring systems to reflect the distribution of NTP in nucleotide pools. These results provide very useful and low-cost tools for both biochemical tests and point-of-care analysis.
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Affiliation(s)
- Jiantong Dong
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Tongbo Wu
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yu Xiao
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Lu Chen
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Lei Xu
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Mengyuan Li
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
| | - Meiping Zhao
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
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24
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Ouyang B, Zhou F, Zhen L, Peng Y, Sun J, Chen Q, Jin X, Wang G, Zhang J. Simultaneous determination of tenofovir alafenamide and its active metabolites tenofovir and tenofovir diphosphate in HBV-infected hepatocyte with a sensitive LC-MS/MS method. J Pharm Biomed Anal 2017; 146:147-153. [PMID: 28881311 DOI: 10.1016/j.jpba.2017.08.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 08/14/2017] [Accepted: 08/18/2017] [Indexed: 11/30/2022]
Abstract
Tenofovir (TFV), a first-line anti-viral agent, has been prepared as various forms of prodrugs for better bioavailability, lower systemic exposure and higher target cells loading of TFV to enhance efficacy and reduce toxicity. TFV undergoes intracellular phosphorylation to form TFV diphosphate (TFV-DP) in target cell to inhibit viral DNA replication. Hence, TFV-DP is the key active metabolite that exhibits anti-virus activity, its intracellular exposure and half-life determine the final activity. Therefore, simultaneous monitoring prodrug, TFV and TFV-DP in target cells will comprehensively evaluate TFV prodrugs, both considering the stability of ester prodrug, and the intracellular exposure of TFV-DP. Thus we intended to develop a convenient general analytical method, taking tenofovir alafenamide (TAF) as a representative of TFV prodrugs. A sensitive LC-MS/MS method was developed, and TAF, TFV and TFV-DP were separated on a XSelect HSS T3 column (4.6mm×150mm, 3.5μm, Waters) with gradient elution after protein precipitation. The method provided good linearity for all the compounds (2-500nM for TFV and TAF; 20-5000nM for TFV-DP) with the correlation coefficients (r) greater than 0.999. Intra- and inter-day accuracies (in terms of relative error, RE<10.4%) and precisions (in terms of coefficient of variation, CV<14.1%) satisfied the standard of validation. The matrix effect, recovery and stability were also within acceptable criteria. Finally, we investigated the intracellular pharmacokinetics of TAF and its active metabolites in HepG2.2.15 cells with this method.
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Affiliation(s)
- Bingchen Ouyang
- Key Lab of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Fang Zhou
- Key Lab of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Le Zhen
- Key Lab of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Ying Peng
- Key Lab of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Jianguo Sun
- Key Lab of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Qianying Chen
- Key Lab of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Xiaoliang Jin
- Key Lab of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Guangji Wang
- Key Lab of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, China.
| | - Jingwei Zhang
- Key Lab of Drug Metabolism and Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, Jiangsu, China.
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25
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Determination and quantification of intracellular fludarabine triphosphate, cladribine triphosphate and clofarabine triphosphate by LC-MS/MS in human cancer cells. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1053:101-110. [PMID: 28415014 DOI: 10.1016/j.jchromb.2017.03.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 03/02/2017] [Accepted: 03/22/2017] [Indexed: 11/21/2022]
Abstract
Purine nucleoside analogues are widely used in the treatment of haematological malignancies, and their biological activity is dependent on the intracellular accumulation of their triphosphorylated metabolites. In this context, we developed and validated a liquid chromatography tandem mass spectrometry (LC-MS/MS) method to study the formation of 5'-triphosphorylated derivatives of cladribine, fludarabine, clofarabine and 2'-deoxyadenosine in human cancer cells. Br-ATP was used as internal standard. Separation was achieved on a hypercarb column. Analytes were eluted with a mixture of hexylamine (5 mM), DEA (0.4%, v/v, pH 10.5) and acetonitrile, in a gradient mode at a flow rate of 0.3mLmin-1. Multiple reactions monitoring (MRM) and electrospray ionization in negative mode (ESI-) were used for detection. The application of this method to the quantification of these phosphorylated cytotoxic compounds in a human follicular lymphoma cell line, showed that it was suitable for the study of relevant biological samples.
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26
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Yoo S, Kim S, Eom MS, Kang S, Lim SH, Han MS. Development of a highly sensitive colorimetric thymidine triphosphate chemosensor using gold nanoparticles and the p-xylyl-bis(Hg2+-cyclen) complex: improved selectivity by metal ion tuning. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.08.075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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27
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Chen X, McAllister KJ, Klein B, Bushman LR, Anderson PL. Development and validation of an LC-MS/MS quantitative method for endogenous deoxynucleoside triphosphates in cellular lysate. Biomed Chromatogr 2016; 31. [PMID: 27557296 DOI: 10.1002/bmc.3820] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 08/11/2016] [Accepted: 08/20/2016] [Indexed: 01/07/2023]
Abstract
The endogenous deoxynucleoside triphosphate (dNTP) pool includes deoxyadenosine triphosphate (dATP), deoxycytidine triphosphate (dCTP), deoxyguanosine triphosphate (dGTP) and thymidine triphosphate (TTP). The endogenous dNTP pool is regulated by complex enzymatic pathways that can be targeted by drugs, such as antimetabolites. In addition, these components compete with antiviral nucleos(t)ide analog triphosphates, contributing to the mechanism of pharmacologic action. This communication describes the development and validation of a sensitive method to quantify the intracellular dNTP pool in cellular lysates. The extraction process was optimized for dNTPs using an indirect strategy - the separation of mono-, di- and triphosphate moieties by strong anion exchange, dephosphorylation of target fractions to molar equivalent nucleosides - followed by sensitive quantitation using liquid chromatography-tandem mass spectrometry. The validated analytical range was 50-2500 fmol/sample for each dNTP. The assay was used to quantify dNTPs in peripheral blood mononuclear cells from 40 clinical research participants (n = 279 samples). Median (interquartile range) concentrations were 143 (116, 169) for dATP, 737 (605, 887) for dCTP, 237 (200, 290) for dGTP and 315 (220, 456) for TTP, in femtomoles per million cells. This method allows for future studies of endogenous dNTP disposition in subjects receiving antimetabolites or nucleos(t)ide analogs, or for other clinical scenarios.
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Affiliation(s)
- Xinhui Chen
- University of Colorado, Skaggs School of Pharmacy and Pharmaceutical Sciences, Aurora, CO, USA
| | | | - Brandon Klein
- University of Colorado, Skaggs School of Pharmacy and Pharmaceutical Sciences, Aurora, CO, USA
| | - Lane R Bushman
- University of Colorado, Skaggs School of Pharmacy and Pharmaceutical Sciences, Aurora, CO, USA
| | - Peter L Anderson
- University of Colorado, Skaggs School of Pharmacy and Pharmaceutical Sciences, Aurora, CO, USA
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28
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Rawson JMO, Roth ME, Xie J, Daly MB, Clouser CL, Landman SR, Reilly CS, Bonnac L, Kim B, Patterson SE, Mansky LM. Synergistic reduction of HIV-1 infectivity by 5-azacytidine and inhibitors of ribonucleotide reductase. Bioorg Med Chem 2016; 24:2410-2422. [PMID: 27117260 DOI: 10.1016/j.bmc.2016.03.052] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 03/18/2016] [Accepted: 03/27/2016] [Indexed: 11/29/2022]
Abstract
Although many compounds have been approved for the treatment of human immunodeficiency type-1 (HIV-1) infection, additional anti-HIV-1 drugs (particularly those belonging to new drug classes) are still needed due to issues such as long-term drug-associated toxicities, transmission of drug-resistant variants, and development of multi-class resistance. Lethal mutagenesis represents an antiviral strategy that has not yet been clinically translated for HIV-1 and is based on the use of small molecules to induce excessive levels of deleterious mutations within the viral genome. Here, we show that 5-azacytidine (5-aza-C), a ribonucleoside analog that induces the lethal mutagenesis of HIV-1, and multiple inhibitors of the enzyme ribonucleotide reductase (RNR) interact in a synergistic fashion to more effectively reduce the infectivity of HIV-1. In these drug combinations, RNR inhibitors failed to significantly inhibit the conversion of 5-aza-C to 5-aza-2'-deoxycytidine, suggesting that 5-aza-C acts primarily as a deoxyribonucleoside even in the presence of RNR inhibitors. The mechanism of antiviral synergy was further investigated for the combination of 5-aza-C and one specific RNR inhibitor, resveratrol, as this combination improved the selectivity index of 5-aza-C to the greatest extent. Antiviral synergy was found to be primarily due to the reduced accumulation of reverse transcription products rather than the enhancement of viral mutagenesis. To our knowledge, these observations represent the first demonstration of antiretroviral synergy between a ribonucleoside analog and RNR inhibitors, and encourage the development of additional ribonucleoside analogs and RNR inhibitors with improved antiretroviral activity.
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Affiliation(s)
- Jonathan M O Rawson
- Institute for Molecular Virology, University of Minnesota, 18-242 Moos Tower, 515 Delaware Street SE, Minneapolis, MN 55455, USA; Molecular, Cellular, Developmental Biology & Genetics Graduate Program, University of Minnesota, 321 Church Street SE, Minneapolis, MN 55455, USA
| | - Megan E Roth
- Institute for Molecular Virology, University of Minnesota, 18-242 Moos Tower, 515 Delaware Street SE, Minneapolis, MN 55455, USA; Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, 515 Delaware Street SE, Minneapolis, MN 55455, USA
| | - Jiashu Xie
- Center for Drug Design, Academic Health Center, University of Minnesota, 516 Delaware Street SE, Minneapolis, MN 55455, USA
| | - Michele B Daly
- Emory Center for AIDS Research, Emory University, 1518 Clifton Road NE, Suite 8050, Atlanta, GA 30322, USA
| | - Christine L Clouser
- Institute for Molecular Virology, University of Minnesota, 18-242 Moos Tower, 515 Delaware Street SE, Minneapolis, MN 55455, USA; Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, 515 Delaware Street SE, Minneapolis, MN 55455, USA
| | - Sean R Landman
- Department of Computer Science and Engineering, University of Minnesota, 4-192 Keller Hall, 200 Union Street SE, Minneapolis, MN 55455, USA
| | - Cavan S Reilly
- Institute for Molecular Virology, University of Minnesota, 18-242 Moos Tower, 515 Delaware Street SE, Minneapolis, MN 55455, USA; Division of Biostatistics, School of Public Health, University of Minnesota, 420 Delaware Street SE, Minneapolis, MN 55455, USA
| | - Laurent Bonnac
- Center for Drug Design, Academic Health Center, University of Minnesota, 516 Delaware Street SE, Minneapolis, MN 55455, USA
| | - Baek Kim
- Emory Center for AIDS Research, Emory University, 1518 Clifton Road NE, Suite 8050, Atlanta, GA 30322, USA
| | - Steven E Patterson
- Institute for Molecular Virology, University of Minnesota, 18-242 Moos Tower, 515 Delaware Street SE, Minneapolis, MN 55455, USA; Center for Drug Design, Academic Health Center, University of Minnesota, 516 Delaware Street SE, Minneapolis, MN 55455, USA
| | - Louis M Mansky
- Institute for Molecular Virology, University of Minnesota, 18-242 Moos Tower, 515 Delaware Street SE, Minneapolis, MN 55455, USA; Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, 515 Delaware Street SE, Minneapolis, MN 55455, USA; Department of Microbiology and Immunology, Medical School, University of Minnesota, 689 23rd Avenue SE, Minneapolis, MN 55455, USA; Molecular, Cellular, Developmental Biology & Genetics Graduate Program, University of Minnesota, 321 Church Street SE, Minneapolis, MN 55455, USA; Center for Drug Design, Academic Health Center, University of Minnesota, 516 Delaware Street SE, Minneapolis, MN 55455, USA.
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29
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5-Azacytidine Enhances the Mutagenesis of HIV-1 by Reduction to 5-Aza-2'-Deoxycytidine. Antimicrob Agents Chemother 2016; 60:2318-25. [PMID: 26833151 DOI: 10.1128/aac.03084-15] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 01/25/2016] [Indexed: 11/20/2022] Open
Abstract
5-Azacytidine (5-aza-C) is a ribonucleoside analog that induces the lethal mutagenesis of human immunodeficiency virus type 1 (HIV-1) by causing predominantly G-to-C transversions during reverse transcription. 5-Aza-C could potentially act primarily as a ribonucleotide (5-aza-CTP) or as a deoxyribonucleotide (5-aza-2'-deoxycytidine triphosphate [5-aza-dCTP]) during reverse transcription. In order to determine the primary form of 5-aza-C that is active against HIV-1, Illumina sequencing was performed using proviral DNA from cells treated with 5-aza-C or 5-aza-dC. 5-Aza-C and 5-aza-dC were found to induce highly similar patterns of mutation in HIV-1 in terms of the types of mutations observed, the magnitudes of effects, and the distributions of mutations at individual sequence positions. Further, 5-aza-dCTP was detected by liquid chromatography-tandem mass spectrometry in cells treated with 5-aza-C, demonstrating that 5-aza-C was a substrate for ribonucleotide reductase. Notably, levels of 5-aza-dCTP were similar in cells treated with equivalent effective concentrations of 5-aza-C or 5-aza-dC. Lastly, HIV-1 reverse transcriptase was found to incorporate 5-aza-CTPin vitroat least 10,000-fold less efficiently than 5-aza-dCTP. Taken together, these data support the model that 5-aza-C enhances the mutagenesis of HIV-1 primarily after reduction to 5-aza-dC, which can then be incorporated during reverse transcription and lead to G-to-C hypermutation. These findings may have important implications for the design of new ribonucleoside analogs directed against retroviruses.
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30
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Daly MB, Roth ME, Bonnac L, Maldonado JO, Xie J, Clouser CL, Patterson SE, Kim B, Mansky LM. Dual anti-HIV mechanism of clofarabine. Retrovirology 2016; 13:20. [PMID: 27009333 PMCID: PMC4806454 DOI: 10.1186/s12977-016-0254-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 03/17/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND HIV-1 replication kinetics inherently depends on the availability of cellular dNTPs for viral DNA synthesis. In activated CD4(+) T cells and other rapidly dividing cells, the concentrations of dNTPs are high and HIV-1 reverse transcription occurs in an efficient manner. In contrast, nondividing cells such as macrophages have lower dNTP pools, which restricts efficient reverse transcription. Clofarabine is an FDA approved ribonucleotide reductase inhibitor, which has shown potent antiretroviral activity in transformed cell lines. Here, we explore the potency, toxicity and mechanism of action of clofarabine in the human primary HIV-1 target cells: activated CD4(+) T cells and macrophages. RESULTS Clofarabine is a potent HIV-1 inhibitor in both activated CD4(+) T cells and macrophages. Due to its minimal toxicity in macrophages, clofarabine displays a selectivity index over 300 in this nondividing cell type. The anti-HIV-1 activity of clofarabine correlated with a significant decrease in both cellular dNTP levels and viral DNA synthesis. Additionally, we observed that clofarabine triphosphate was directly incorporated into DNA by HIV-1 reverse transcriptase and blocked processive DNA synthesis, particularly at the low dNTP levels found in macrophages. CONCLUSIONS Taken together, these data provide strong mechanistic evidence that clofarabine is a dual action inhibitor of HIV-1 replication that both limits dNTP substrates for viral DNA synthesis and directly inhibits the DNA polymerase activity of HIV-1 reverse transcriptase.
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Affiliation(s)
- Michele B Daly
- Center for Drug Discovery, Department of Pediatrics, Emory Center for AIDS Research, Emory University, Children's Healthcare of Atlanta, 1760 Haygood Dr., Atlanta, GA, 30322, USA
| | - Megan E Roth
- Institute for Molecular Virology, University of Minnesota, 18-242 Moos Tower, 515 Delaware St SE, Minneapolis, MN, 55455, USA.,Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN, 55455, USA.,Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Laurent Bonnac
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - José O Maldonado
- Institute for Molecular Virology, University of Minnesota, 18-242 Moos Tower, 515 Delaware St SE, Minneapolis, MN, 55455, USA.,Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN, 55455, USA.,Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Jiashu Xie
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Christine L Clouser
- Institute for Molecular Virology, University of Minnesota, 18-242 Moos Tower, 515 Delaware St SE, Minneapolis, MN, 55455, USA
| | - Steven E Patterson
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Baek Kim
- Center for Drug Discovery, Department of Pediatrics, Emory Center for AIDS Research, Emory University, Children's Healthcare of Atlanta, 1760 Haygood Dr., Atlanta, GA, 30322, USA.
| | - Louis M Mansky
- Institute for Molecular Virology, University of Minnesota, 18-242 Moos Tower, 515 Delaware St SE, Minneapolis, MN, 55455, USA. .,Department of Diagnostic and Biological Sciences, School of Dentistry, University of Minnesota, Minneapolis, MN, 55455, USA. .,Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, 55455, USA. .,Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, USA.
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31
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Derissen EJB, Jacobs BAW, Huitema ADR, Rosing H, Schellens JHM, Beijnen JH. Exploring the intracellular pharmacokinetics of the 5-fluorouracil nucleotides during capecitabine treatment. Br J Clin Pharmacol 2016; 81:949-57. [PMID: 26718616 DOI: 10.1111/bcp.12877] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Revised: 12/11/2015] [Accepted: 12/24/2015] [Indexed: 12/26/2022] Open
Abstract
AIM Three intracellularly formed metabolites are responsible for the antineoplastic effect of capecitabine: 5-fluorouridine 5'-triphosphate (FUTP), 5-fluoro-2'-deoxyuridine 5'-triphosphate (FdUTP), and 5-fluoro-2'-deoxyuridine 5'-monophosphate (FdUMP). The objective of this study was to explore the pharmacokinetics of these intracellular metabolites during capecitabine treatment. METHODS Serial plasma and peripheral blood mononuclear cell (PBMC) samples were collected from 13 patients treated with capecitabine 1000 mg QD (group A) and eight patients receiving capecitabine 850 mg m(-2) BID for fourteen days, every three weeks (group B). Samples were collected on day 1 and, for four patients of group B, also on day 14. The capecitabine and 5-fluorouracil (5-FU) plasma concentrations and intracellular metabolite concentrations were determined using LC-MS/MS. Pharmacokinetic parameters were estimated using non-compartmental analysis. RESULTS Only FUTP could be measured in the PBMC samples. The FdUTP and FdUMP concentrations were below the detection limits (LOD). No significant correlation was found between the plasma 5-FU and intracellular FUTP exposure. The FUTP concentration-time profiles demonstrated considerable inter-individual variation and accumulation of the metabolite in PBMCs. FUTP levels ranged between <LOD and 1.0 μM on day 1, and from 0.64 to 14 μM on day 14. The area under the FUTP concentration-time curve was significantly increased on day 14 of the treatment compared to day 1 (mean ± SD: 28 ± 19 μM h vs. 2.0 ± 1.9 μM h). CONCLUSIONS To our knowledge, this is the first time that intracellular FUTP concentrations were measured in patients treated with capecitabine. During 14 days of treatment with capecitabine twice daily, intracellular accumulation of FUTP occurs.
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Affiliation(s)
- Ellen J B Derissen
- Department of Pharmacy & Pharmacology, Antoni van Leeuwenhoek Hospital - The Netherlands Cancer Institute and MC Slotervaart, Louwesweg 6, 1066 EC, Amsterdam, The Netherlands
| | - Bart A W Jacobs
- Department of Pharmacy & Pharmacology, Antoni van Leeuwenhoek Hospital - The Netherlands Cancer Institute and MC Slotervaart, Louwesweg 6, 1066 EC, Amsterdam, The Netherlands
| | - Alwin D R Huitema
- Department of Pharmacy & Pharmacology, Antoni van Leeuwenhoek Hospital - The Netherlands Cancer Institute and MC Slotervaart, Louwesweg 6, 1066 EC, Amsterdam, The Netherlands
| | - Hilde Rosing
- Department of Pharmacy & Pharmacology, Antoni van Leeuwenhoek Hospital - The Netherlands Cancer Institute and MC Slotervaart, Louwesweg 6, 1066 EC, Amsterdam, The Netherlands
| | - Jan H M Schellens
- Department of Clinical Pharmacology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.,Science Faculty, Utrecht Institute for Pharmaceutical Sciences (UIPS), Division of Pharmaco-Epidemiology & Clinical Pharmacology, Utrecht University, P.O. Box 80082, 3508 TB, Utrecht, The Netherlands
| | - Jos H Beijnen
- Department of Pharmacy & Pharmacology, Antoni van Leeuwenhoek Hospital - The Netherlands Cancer Institute and MC Slotervaart, Louwesweg 6, 1066 EC, Amsterdam, The Netherlands.,Science Faculty, Utrecht Institute for Pharmaceutical Sciences (UIPS), Division of Pharmaco-Epidemiology & Clinical Pharmacology, Utrecht University, P.O. Box 80082, 3508 TB, Utrecht, The Netherlands
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32
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Wu J, Zhang Y, Wiegand R, Wang J, Bepler G, Li J. Quantitative analysis of intracellular nucleoside triphosphates and other polar metabolites using ion pair reversed-phase liquid chromatography coupled with tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 1006:167-178. [PMID: 26551209 DOI: 10.1016/j.jchromb.2015.10.030] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 09/11/2015] [Accepted: 10/22/2015] [Indexed: 11/17/2022]
Abstract
Simultaneous, quantitative determination of intracellular nucleoside triphosphates and other polar metabolites using liquid chromatography with electrospray ionization tandem mass spectrometry (LC-MS/MS) represents a bioanalytic challenge because of charged, highly hydrophilic analytes presented at a large concentration range in a complex matrix. In this study, an ion pair LC-MS/MS method using triethylamine (TEA)-hexafluoroisopropanol (HFIP) ion-pair mobile phase was optimized and validated for simultaneous and unambiguous determination of 8 nucleoside triphosphates (including ATP, CTP, GTP, UTP, dATP, dCTP, dGTP, and dTTP) in cellular samples. Compared to the the less volatile ion-pair reagent, triethylammonium acetate (100mM, pH 7.0), the combination of HFIP (100mM) and TEA (8.6mM) increased the MS signal intensity by about 50-fold, while retaining comparable chromatographic resolution. The isotope-labeled internal standard method was used for the quantitation. Lower limits of quantitation were determined at 0.5nM for CTP, UTP, dATP, dCTP, and dTTP, at 1nM for ATP, and at 5nM for GTP and dGTP. The intra- and inter-day precision and accuracy were within the generally accepted criteria for bioanalytical method validation (<15%). While the present method was validated for the quantitation of intracellular nucleoside triphosphates, it had a broad application potential for quantitative profiling of nucleoside mono- and bi-phosphates as well as other polar, ionic metabolic intermediates (including carbohydrate derivatives, carboxylic acid derivatives, co-acyl A derivatives, fatty acyls, and others) in biological samples.
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Affiliation(s)
- Jianmei Wu
- Karmanos Cancer Institute, Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, United States
| | - Yingtao Zhang
- Karmanos Cancer Institute, Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, United States
| | - Richard Wiegand
- Karmanos Cancer Institute, Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, United States
| | - Jian Wang
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI 48201, United States
| | - Gerold Bepler
- Karmanos Cancer Institute, Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, United States
| | - Jing Li
- Karmanos Cancer Institute, Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, United States.
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Kamčeva T, Bjånes T, Svardal A, Riedel B, Schjøtt J, Eide T. Liquid chromatography/tandem mass spectrometry method for simultaneous quantification of eight endogenous nucleotides and the intracellular gemcitabine metabolite dFdCTP in human peripheral blood mononuclear cells. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 1001:212-20. [PMID: 26281773 DOI: 10.1016/j.jchromb.2015.07.041] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 07/17/2015] [Accepted: 07/18/2015] [Indexed: 01/12/2023]
Abstract
Quantification of endogenous nucleotides is of interest for investigation of numerous cellular biochemical processes, such as energy metabolism and signal transduction, and may also be applied in cancer and antiretroviral therapies in which nucleoside analogues are used. For these purposes we developed and validated a sensitive and high accuracy ion-pair liquid chromatography tandem mass spectrometry (IP LC-MS/MS) method for simultaneous quantification of eight endogenous nucleotides (ATP, CTP, GTP, UTP, dATP, dCTP, dGTP, dTTP) and 2',2'-difluoro-2'-deoxycytidine triphosphate (dFdCTP), an intracellular metabolite of the nucleoside analogue gemcitabine. The assay was validated using 200μL aliquots of peripheral blood mononuclear cell (20×10(6)cells/ml, 4×10(6)cells) extracts, pretreated with activated charcoal and spiked with unlabeled nucleotides, deoxynucleotides and dFdCTP. Analytes were extracted by simple precipitation with cold 60% methanol containing isotope labeled internal standards and separated on a porous graphitic carbon column. For method validation, the concentration ranges were: 0.125-20.8pmol injected for deoxynucleotides, 0.25-312.5pmol injected for dFdCTP and 5-3200pmol injected for nucleotides. The highest coefficients of variation (CV) were 12.1% for within run assay and 11.4% for between run assay, both representing the precision at the lowest analyte concentrations. The method was applied to monitor dFdCTP and changes in endogenous nucleotides in patients who were receiving gemcitabine infusions.
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Affiliation(s)
- Tina Kamčeva
- Laboratory of Clinical Biochemistry, Section of Clinical Pharmacology, Haukeland University Hospital, 5020 Bergen, Norway.
| | - Tormod Bjånes
- Laboratory of Clinical Biochemistry, Section of Clinical Pharmacology, Haukeland University Hospital, 5020 Bergen, Norway.
| | - Asbjørn Svardal
- Faculty of Medicine and Dentistry, Institute of Clinical Science, University of Bergen, 5021 Bergen, Norway.
| | - Bettina Riedel
- Laboratory of Clinical Biochemistry, Section of Clinical Pharmacology, Haukeland University Hospital, 5020 Bergen, Norway; Faculty of Medicine and Dentistry, Institute of Clinical Science, University of Bergen, 5021 Bergen, Norway.
| | - Jan Schjøtt
- Laboratory of Clinical Biochemistry, Section of Clinical Pharmacology, Haukeland University Hospital, 5020 Bergen, Norway; Faculty of Medicine and Dentistry, Institute of Clinical Science, University of Bergen, 5021 Bergen, Norway.
| | - Torunn Eide
- Faculty of Medicine and Dentistry, Institute of Clinical Science, University of Bergen, 5021 Bergen, Norway.
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Use of designed experiments for the improvement of pre-analytical workflow for the quantification of intracellular nucleotides in cultured cell lines. J Chromatogr A 2015; 1405:116-25. [PMID: 26094139 DOI: 10.1016/j.chroma.2015.05.069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 05/26/2015] [Accepted: 05/30/2015] [Indexed: 11/21/2022]
Abstract
The present study is focused on the development of a pre-analytical strategy for the quantification of intracellular nucleotides from cultured cell lines. Different protocols, including cell recovery, nucleotide extraction and purification, were compared on a panel of nucleoside mono-, di- and triphosphates from four cell lines (adherent and suspension cells). The quantification of nucleotides was performed using a validated technique with on-line solid-phase extraction coupled with liquid chromatography-triple quadrupole tandem mass spectrometry (LC-MS/MS). Designed experiments were implemented to investigate, in a rigorous and limited-testing experimental approach, the influence of several operating parameters. Results showed that the technique used to harvest adherent cells drastically affected the amounts of intracellular nucleotides. Scraping cells was deleterious because of a major leakage (more than 70%) of intracellular nucleotides during scraping. Moreover, some other tested conditions should be avoided, such as using pure methanol as extraction solvent (decrease over 50% of intracellular nucleotides extracted from NCI-H292 cells) or adding a purification step with chloroform. Designed experiments allowed identifying an interaction between the percentage of methanol and the presence of chloroform. The mixture methanol/water (70/30, v/v) was considered as the best compromise according to the nucleoside mono-, di-, or triphosphates and the four cell lines studied. This work highlights the importance of pre-analytical step combined with the cell lines studied associated to sensitive and validated assay for the quantification of nucleotides in biological matrices.
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Ihara Y, Ohta H, Masuda S. A highly sensitive quantification method for the accumulation of alarmone ppGpp in Arabidopsis thaliana using UPLC-ESI-qMS/MS. JOURNAL OF PLANT RESEARCH 2015; 128:511-8. [PMID: 25752614 DOI: 10.1007/s10265-015-0711-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 01/04/2015] [Indexed: 05/09/2023]
Abstract
Recently, a bacterial second messenger, guanosine 5'-diphosphate 3'-diphosphate (ppGpp), has been detected in chloroplasts. However, because ppGpp concentration in plants is much lower than that in bacteria, detailed analysis of ppGpp in plants has not been performed. A highly sensitive quantification method is required for further characterization of ppGpp function in chloroplasts. Here, we report a new method that allows for the highly sensitive and selective high-throughput quantification of ppGpp by ultra-performance liquid chromatography (UPLC) coupled with a tandem quadrupole mass spectrometer (qMS/MS) equipped with an electrospray interface (ESI). This method requires only ~100 mg of plant tissue for ppGpp quantification. We used this method to measure ppGpp levels in Arabidopsis thaliana under different light conditions. A. thaliana accumulated ppGpp during dark periods. This method will be helpful to further characterize the stringent response in higher plants.
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Affiliation(s)
- Yuta Ihara
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
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Wang F, Liu X, Liu C, Liu Z, Sun L. Effects of antibiotic antitumor drugs on nucleotide levels in cultured tumor cells: an exploratory method to distinguish the mechanisms of antitumor drug action based on targeted metabolomics. Acta Pharm Sin B 2015; 5:223-30. [PMID: 26579450 PMCID: PMC4629260 DOI: 10.1016/j.apsb.2015.03.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 12/19/2014] [Accepted: 03/14/2015] [Indexed: 12/29/2022] Open
Abstract
Nucleotide pools in mammalian cells change due to the influence of antitumor drugs, which may help in evaluating the drug effect and understanding the mechanism of drug action. In this study, an ion-pair RP-HPLC method was used for a simple, sensitive and simultaneous determination of the levels of 12 nucleotides in mammalian cells treated with antibiotic antitumor drugs (daunorubicin, epirubicin and dactinomycin D). Through the use of this targeted metabolomics approach to find potential biomarkers, UTP and ATP were verified to be the most appropriate biomarkers. Moreover, a holistic statistical approach was put forward to develop a model which could distinguish 4 categories of drugs with different mechanisms of action. This model can be further validated by evaluating drugs with different mechanisms of action. This targeted metabolomics study may provide a novel approach to predict the mechanism of action of antitumor drugs.
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Key Words
- ADP, adenosine diphosphate
- AMP, adenosine monophosphate
- ANOVA, analysis of variance
- ATP, adenosine triphosphate
- AUC, area under the curve
- Antibiotic anticancer drugs
- CDP, cytidine diphosphate
- CTP, cytidine triphosphate
- DMEM, Dulbecco׳s modified eagle׳s cell culture media
- DMSO, dimethyl sulfoxide
- DNA, deoxyribonucleic acid
- EC, energy charge
- EDTA, ethylene diamine tetra-acetic acid
- FCS, fetal calf serum
- GDP, guanosine diphosphate
- GMP, guanosine monophosphate
- GTP, guanosine triphosphate
- HEPES, 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
- Ion-pair HPLC
- MTT, 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide
- Mechanisms of antitumor drug action
- Nucleotides
- PBS, phosphate buffered saline
- PCA, principal component analysis
- Potential biomarkers
- Principal component analysis
- RNA, ribonucleic acid
- ROC, receiver operating characteristic
- RPMI-1640, Roswell Park Memorial Institute-1640
- TBAHS, tetrabutylammonium hydrogen sulfate
- TCA, trichloroacetic acid
- Targeted metabolomics analysis
- Tumor cells
- UDP, uridine diphosphate
- UTP, uridine triphosphate
- dATP, deoxyadenosine triphosphate
- dCDP, deoxycytidine diphosphate
- dCTP, deoxycytidine triphosphate
- dGMP, deoxyribonucleic monophosphate
- dGTP, deoxyguanosine triphosphate
- dUDP, deoxyuridine diphpsphate
- dUTP, deoxyuridine triphosphate
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Affiliation(s)
- Fang Wang
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Xi Liu
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Cuichai Liu
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Zheng Liu
- School of Life Science and Bio-pharmaceutics Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Lixin Sun
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang 110016, China
- Corresponding author. Tel.: +86 24 23986365; fax: +86 24 23986259.
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Villaño D, Vilaplana C, Medina S, Cejuela-Anta R, Martínez-Sanz JM, Gil P, Genieser HG, Ferreres F, Gil-Izquierdo A. Effect of elite physical exercise by triathletes on seven catabolites of DNA oxidation. Free Radic Res 2015; 49:973-83. [PMID: 25786325 DOI: 10.3109/10715762.2015.1025388] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The oxidized nucleoside 8-hydroxy-2'-deoxyguanosine has been widely studied as a marker of DNA oxidation; however, data on the occurrence of other metabolites in plasma that are related to DNA damage are scarce. We have applied an improved, sensitive, robust, and reliable method, involving solid phase extraction and ultrahigh-performance liquid chromatography (UHPLC)-tandem mass spectrometry (MS/MS), to the precise quantitation of seven metabolites in the plasma of 15 elite triathletes after a 2-week training program. All compounds were eluted in the first 1.6 min, with limits of detection and quantification ranging between 0.001 and 0.3 ng.mL(-1) and 0.009 and 0.6 ng.mL(-1), respectively. Four compounds were detected in plasma: guanosine-3'-5'-cyclic monophosphate, 8-hydroxyguanine, 8-hydroxy-2'-deoxyguanosine, and 8-nitroguanosine. After two weeks of training, 8-hydroxyguanine exhibited the highest increase (from 0.031 ± 0.008 nM to 0.036 ± 0.012 nM) (p < 0.05), which could be related to the enhanced activity of DNA-repairing enzymes that excise this oxidized base. Increased levels of guanosine-3'-5'-cyclic monophosphate and 8-hydroxy-2'-deoxyguanosine were also observed. In contrast, levels of 8-nitroguanosine (p < 0.05) were significantly reduced, which might be a protective measure as this compound strongly stimulates the generation of superoxide radicals, and its excess is related to pathologies such as microbial (viral) infections and other inflammatory and degenerative disorders. The results obtained indicate an induced adaptive response to the increased oxidative stress related to elite training, and point to the benefits associated with regular exercise.
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Affiliation(s)
- D Villaño
- Department of Food Science and Technology, CEBAS-CSIC , Murcia , Spain
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Derissen EJB, Hillebrand MJX, Rosing H, Schellens JHM, Beijnen JH. Development of an LC-MS/MS assay for the quantitative determination of the intracellular 5-fluorouracil nucleotides responsible for the anticancer effect of 5-fluorouracil. J Pharm Biomed Anal 2015; 110:58-66. [PMID: 25804433 DOI: 10.1016/j.jpba.2015.02.051] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 01/26/2015] [Accepted: 02/28/2015] [Indexed: 11/19/2022]
Abstract
5-Fluorouracil (5-FU) and its oral prodrug capecitabine are among the most widely used chemotherapeutics. For cytotoxic activity, 5-FU requires cellular uptake and intracellular metabolic activation. Three intracellular formed metabolites are responsible for the antineoplastic effect of 5-FU: 5-fluorouridine 5'-triphosphate (FUTP), 5-fluoro-2'-deoxyuridine 5'-triphosphate (FdUTP) and 5-fluoro-2'-deoxyuridine 5'-monophosphate (FdUMP). In this paper, we describe the development of an LC-MS/MS assay for quantification of these active 5-FU nucleotides in peripheral blood mononuclear cells (PBMCs). Because the intracellular 5-FU nucleotide concentrations were very low, maximization of the release from the cell matrix and minimization of interference were critical factors. Therefore, a series of experiments was performed to select the best method for cell lysis and nucleotide extraction. Chromatography was optimized to obtain separation from endogenous nucleotides, and the effect of different cell numbers was examined. The assay was validated for the following concentration ranges in PBMC lysate: 0.488-19.9 nM for FUTP, 1.66-67.7 nM for FdUTP and 0.748-30.7 nM for FdUMP. Accuracies were between -2.2 and 7.0% deviation for all analytes, and the coefficient of variation values were ≤ 4.9%. The assay was successfully applied to quantify 5-FU nucleotides in PBMC samples from patients treated with capecitabine and patients receiving 5-FU intravenously. FUTP amounts up to 3054 fmol/10(6) PBMCs and FdUMP levels up to 169 fmol/10(6) PBMCs were measured. The FdUTP concentrations were below the lower limit of quantification. To our knowledge, this is the first time that 5-FU nucleotides were quantified in cells from patients treated with 5-FU or capecitabine without using a radiolabel.
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Affiliation(s)
- Ellen J B Derissen
- Department of Pharmacy & Pharmacology, Antoni van Leeuwenhoek Hospital - The Netherlands Cancer Institute, Louwesweg 6, 1066 EC Amsterdam, The Netherlands.
| | - Michel J X Hillebrand
- Department of Pharmacy & Pharmacology, Antoni van Leeuwenhoek Hospital - The Netherlands Cancer Institute, Louwesweg 6, 1066 EC Amsterdam, The Netherlands
| | - Hilde Rosing
- Department of Pharmacy & Pharmacology, Antoni van Leeuwenhoek Hospital - The Netherlands Cancer Institute, Louwesweg 6, 1066 EC Amsterdam, The Netherlands
| | - Jan H M Schellens
- Department of Clinical Pharmacology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands; Science Faculty, Utrecht Institute for Pharmaceutical Sciences (UIPS), Division of Pharmaco-epidemiology & Clinical Pharmacology, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands
| | - Jos H Beijnen
- Department of Pharmacy & Pharmacology, Antoni van Leeuwenhoek Hospital - The Netherlands Cancer Institute, Louwesweg 6, 1066 EC Amsterdam, The Netherlands; Science Faculty, Utrecht Institute for Pharmaceutical Sciences (UIPS), Division of Pharmaco-epidemiology & Clinical Pharmacology, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands
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Quantitation of endogenous nucleoside triphosphates and nucleosides in human cells by liquid chromatography tandem mass spectrometry. Anal Bioanal Chem 2015; 407:3693-704. [PMID: 25749797 DOI: 10.1007/s00216-015-8588-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 02/06/2015] [Accepted: 02/20/2015] [Indexed: 10/23/2022]
Abstract
Nucleosides and nucleoside triphosphates are the building blocks of nucleic acids and important bioactive metabolites, existing in all living cells. In the present study, two liquid chromatography tandem mass spectrometry methods were developed to quantify both groups of compounds from the same sample with a shared extraction procedure. After a simple protein precipitation with methanol, the nucleosides were separated with reversed phase chromatography on an Atlantis T3 column while for the separation of the nucleoside triphosphates, an anion exchange column (BioBasic AX) was used. No addition of ion pair reagent was required. A 5500 QTrap was used as analyzer, operating as triple quadrupole. The analytical method for the nucleoside triphosphates has been validated according to the guidelines of the US Food and Drug Administration. The lower limit of quantification values were determined as 10 pg on column (0.5 ng/mL in the injection solution) for deoxyadenosine triphosphate and deoxyguanosine triphosphate, 20 pg (1 ng/mL) for deoxycytidine triphosphate and thymidine triphosphate, 100 pg (5 ng/mL) for cytidine triphosphate and guanosine triphosphate, and 500 pg (25 ng/mL) for adenosine triphosphate und uridine triphosphate respectively. This methodology has been applied to the quantitation of nucleosides and nucleoside triphosphates in primary human CD4 T lymphocytes and macrophages. As expected, the concentrations for ribonucleosides and ribonucleoside triphophates were considerably higher than those obtained for the deoxy derivatives. Upon T cell receptor activation, the levels of all analytes, with the notable exceptions of deoxyadenosine triphosphate and deoxyguanosine triphosphate, were found to be elevated in CD4 T cells.
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Abstract
DNA methylation and histone modification are epigenetic mechanisms that result in altered gene expression and cellular phenotype. The exact role of methylation in myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML) remains unclear. However, aberrations (e.g. loss-/gain-of-function or up-/down-regulation) in components of epigenetic transcriptional regulation in general, and of the methylation machinery in particular, have been implicated in the pathogenesis of these diseases. In addition, many of these components have been identified as therapeutic targets for patients with MDS/AML, and are also being assessed as potential biomarkers of response or resistance to hypomethylating agents (HMAs). The HMAs 5-azacitidine (AZA) and 2'-deoxy-5-azacitidine (decitabine, DAC) inhibit DNA methylation and have shown significant clinical benefits in patients with myeloid malignancies. Despite being viewed as mechanistically similar drugs, AZA and DAC have differing mechanisms of action. DAC is incorporated 100% into DNA, whereas AZA is incorporated into RNA (80-90%) as well as DNA (10-20%). As such, both drugs inhibit DNA methyltransferases (DNMTs; dependently or independently of DNA replication) resulting in the re-expression of tumor-suppressor genes; however, AZA also has an impact on mRNA and protein metabolism via its inhibition of ribonucleotide reductase, resulting in apoptosis. Herein, we first give an overview of transcriptional regulation, including DNA methylation, post-translational histone-tail modifications, the role of micro-RNA and long-range epigenetic gene silencing. We place special emphasis on epigenetic transcriptional regulation and discuss the implication of various components in the pathogenesis of MDS/AML, their potential as therapeutic targets, and their therapeutic modulation by HMAs and other substances (if known). The main focus of this review is laid on dissecting the rapidly evolving knowledge of AZA and DAC with a special focus on their differing mechanisms of action, and the effect of HMAs on transcriptional regulation.
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Affiliation(s)
- Lisa Pleyer
- 3rd Medical Department with Hematology and Medical Oncology, Hemostaseology, Rheumatology and Infectious Diseases, Laboratory for Immunological and Molecular Cancer Research, Oncologic Center, Paracelsus Medical University Hospital Salzburg, Center for Clinical Cancer and Immunology Trials at Salzburg Cancer Research Institute , Salzburg , Austria
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Jia S, Marjavaara L, Buckland R, Sharma S, Chabes A. Determination of deoxyribonucleoside triphosphate concentrations in yeast cells by strong anion-exchange high-performance liquid chromatography coupled with ultraviolet detection. Methods Mol Biol 2015; 1300:113-121. [PMID: 25916709 DOI: 10.1007/978-1-4939-2596-4_8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
DNA polymerase assays are commonly used for the detection of deoxyribonucleoside triphosphates (dNTPs) in biological samples. For better specificity and accuracy, high-performance liquid chromatography (HPLC) methods have been developed for the analysis of the four dNTPs in complex samples. Here we describe a simple method using isocratic strong anion-exchange (SAX) chromatographic separation coupled with ultraviolet detection (UV) for the analysis of the four dNTPs in budding yeast Saccharomyces cerevisiae. This method can be applied to other species of yeast or bacteria.
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Affiliation(s)
- Shaodong Jia
- Department of Medical Biochemistry and Biophysics, Umeå University, KBC-Building, 6th Floor, Umeå, 901 87, Sweden
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42
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Boissan M, Montagnac G, Shen Q, Griparic L, Guitton J, Romao M, Sauvonnet N, Lagache T, Lascu I, Raposo G, Desbourdes C, Schlattner U, Lacombe ML, Polo S, van der Bliek AM, Roux A, Chavrier P. Membrane trafficking. Nucleoside diphosphate kinases fuel dynamin superfamily proteins with GTP for membrane remodeling. Science 2014; 344:1510-5. [PMID: 24970086 PMCID: PMC4601533 DOI: 10.1126/science.1253768] [Citation(s) in RCA: 127] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Dynamin superfamily molecular motors use guanosine triphosphate (GTP) as a source of energy for membrane-remodeling events. We found that knockdown of nucleoside diphosphate kinases (NDPKs) NM23-H1/H2, which produce GTP through adenosine triphosphate (ATP)-driven conversion of guanosine diphosphate (GDP), inhibited dynamin-mediated endocytosis. NM23-H1/H2 localized at clathrin-coated pits and interacted with the proline-rich domain of dynamin. In vitro, NM23-H1/H2 were recruited to dynamin-induced tubules, stimulated GTP-loading on dynamin, and triggered fission in the presence of ATP and GDP. NM23-H4, a mitochondria-specific NDPK, colocalized with mitochondrial dynamin-like OPA1 involved in mitochondria inner membrane fusion and increased GTP-loading on OPA1. Like OPA1 loss of function, silencing of NM23-H4 but not NM23-H1/H2 resulted in mitochondrial fragmentation, reflecting fusion defects. Thus, NDPKs interact with and provide GTP to dynamins, allowing these motor proteins to work with high thermodynamic efficiency.
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Affiliation(s)
- Mathieu Boissan
- Institut Curie, Research Center, Paris, France. Membrane and Cytoskeleton Dynamics, CNRS UMR 144, Paris, France. Université Pierre et Marie Curie, University Paris 06, Paris, France. Saint-Antoine Research Center, INSERM UMR-S 938, Paris, France.
| | - Guillaume Montagnac
- Institut Curie, Research Center, Paris, France. Membrane and Cytoskeleton Dynamics, CNRS UMR 144, Paris, France
| | - Qinfang Shen
- Department of Biological Chemistry, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, USA
| | - Lorena Griparic
- Department of Biological Chemistry, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, USA
| | - Jérôme Guitton
- Hospices Civils de Lyon, Pierre Bénite, France. Université de Lyon, Lyon, France
| | - Maryse Romao
- Institut Curie, Research Center, Paris, France. Structure and Membrane Compartments, CNRS UMR 144, Paris, France
| | - Nathalie Sauvonnet
- Institut Pasteur, Unité de Biologie des Interactions Cellulaires, Paris, France
| | - Thibault Lagache
- Quantitative Image Analysis Unit, Institut Pasteur, Paris, France
| | - Ioan Lascu
- Institut de Biochimie et Génétique Cellulaires-CNRS, Université Bordeaux 2, Bordeaux, France
| | - Graça Raposo
- Institut Curie, Research Center, Paris, France. Structure and Membrane Compartments, CNRS UMR 144, Paris, France
| | - Céline Desbourdes
- Université Grenoble Alpes, Laboratory of Fundamental and Applied Bioenergetics, Grenoble, France. Inserm, U1055, Grenoble, France
| | - Uwe Schlattner
- Université Grenoble Alpes, Laboratory of Fundamental and Applied Bioenergetics, Grenoble, France. Inserm, U1055, Grenoble, France
| | - Marie-Lise Lacombe
- Université Pierre et Marie Curie, University Paris 06, Paris, France. Saint-Antoine Research Center, INSERM UMR-S 938, Paris, France
| | - Simona Polo
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy. Dipartimento di Scienze della Salute, Universita' degli Studi di Milano, Milan, Italy
| | - Alexander M van der Bliek
- Department of Biological Chemistry, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, USA
| | - Aurélien Roux
- Biochemistry Department, University of Geneva, & Swiss National Center for Competence in Research Program Chemical Biology, Geneva, Switzerland
| | - Philippe Chavrier
- Institut Curie, Research Center, Paris, France. Membrane and Cytoskeleton Dynamics, CNRS UMR 144, Paris, France.
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Antiretroviral therapy-induced mitochondrial toxicity: potential mechanisms beyond polymerase-γ inhibition. Clin Pharmacol Ther 2014; 96:110-20. [PMID: 24637942 PMCID: PMC4065195 DOI: 10.1038/clpt.2014.64] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 03/10/2014] [Indexed: 12/29/2022]
Abstract
We hypothesized that competition between nucleotide reverse-transcriptase inhibitor triphosphate and endogenous deoxyribonucleotide triphosphate (dNTP) may lead to depletion of dNTP pools and mitochondrial dysfunction independent of polymerase-γ (pol-γ) inhibition. We collected peripheral blood mononuclear cells from 75 adults (25 cases: HIV-infected patients with mitochondrial toxicity, 25 HIV-infected positive controls, and 25 HIV-negative controls). We observed statistically significant individual and group differences in ribonucleotide (RN) and deoxyribonucleotide (dRN) pools. The median values for the RN pools were 10,062 (interquartile range (IQR): 7,090-12,590), 4,360 (IQR: 3,058-6,838), and 2,968 (IQR: 2,538-4,436) pmol/10(6) cells for negative controls, positive controls, and cases, respectively. Cases had significantly higher absolute mitochondrial DNA copy number as compared with negative controls (P < 0.05). Moreover, cases had significantly higher expression levels of pol-γ, nucleotide transporters, cellular kinases, and adenosine triphosphate (ATP)-binding cassette (ABC) proteins as compared with controls. Antiretroviral therapy (ART) perturbs RN and dRN pools. Depletion of RN and dRN pools may be associated with ART-induced mitochondrial toxicity independent of pol-γ inhibition.
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Machon C, Jordheim LP, Puy JY, Lefebvre I, Dumontet C, Guitton J. Fully validated assay for the quantification of endogenous nucleoside mono- and triphosphates using online extraction coupled with liquid chromatography-tandem mass spectrometry. Anal Bioanal Chem 2014; 406:2925-41. [PMID: 24633509 DOI: 10.1007/s00216-014-7711-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 02/13/2014] [Accepted: 02/19/2014] [Indexed: 11/29/2022]
Abstract
An analytical method coupling online solid-phase extraction (SPE) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) was developed to quantify 16 endogenous nucleoside mono- and triphosphates in cellular samples. Separation was achieved on a porous graphitic carbon (PGC) column without ion-pairing agent in the mobile phase. Low levels of the ion-pairing agent diethylamine (DEA) added to the reconstitution solution were necessary to prevent peak tailing of nucleoside triphosphates. The mass spectrometer, a triple quadrupole with an electrospray ionisation source, was operated in positive mode. Two multiple reaction monitoring (MRM) segments were programmed, each an internal standard. Extraction and separation of nucleoside mono- and triphosphates were obtained within 20 min. The total duration of a single run was 37 min. Calibration curves, performed with labelled nucleotides added to the sample matrix, ranged from 0.29 to 18.8 pmol injected for deoxyribonucleotides and from 3.9 to 3,156 pmol for ribonucleotides. Accuracy did not deviate more than -14.6 and 10.2 % from nominal values for all compounds at all levels. CV results were all lower than 17.0 % for the LLOQ level and 14.6 % for the other levels. Quality control (QC) samples were also in agreement with acceptance criteria, except for the lower QC of GMP. Ion suppression, matrix effect, extraction recoveries and stability were assessed. After validation, the method was applied to the evaluation of the effects of gemcitabine and hydroxyurea on nucleotide pools in Messa cells.
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Affiliation(s)
- Christelle Machon
- Laboratoire de Biochimie et Toxicologie, Hospices Civils de Lyon, Centre Hospitalier Lyon-Sud, 69495, Pierre-Bénite, France
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Nathanson DA, Armijo AL, Tom M, Li Z, Dimitrova E, Austin WR, Nomme J, Campbell DO, Ta L, Le TM, Lee JT, Darvish R, Gordin A, Wei L, Liao HI, Wilks M, Martin C, Sadeghi S, Murphy JM, Boulos N, Phelps ME, Faull KF, Herschman HR, Jung ME, Czernin J, Lavie A, Radu CG. Co-targeting of convergent nucleotide biosynthetic pathways for leukemia eradication. ACTA ACUST UNITED AC 2014; 211:473-86. [PMID: 24567448 PMCID: PMC3949575 DOI: 10.1084/jem.20131738] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Co-targeting of both de novo and salvage pathways for dCTP biosynthesis shows efficacy in T-ALL and B-ALL. Pharmacological targeting of metabolic processes in cancer must overcome redundancy in biosynthetic pathways. Deoxycytidine (dC) triphosphate (dCTP) can be produced both by the de novo pathway (DNP) and by the nucleoside salvage pathway (NSP). However, the role of the NSP in dCTP production and DNA synthesis in cancer cells is currently not well understood. We show that acute lymphoblastic leukemia (ALL) cells avoid lethal replication stress after thymidine (dT)-induced inhibition of DNP dCTP synthesis by switching to NSP-mediated dCTP production. The metabolic switch in dCTP production triggered by DNP inhibition is accompanied by NSP up-regulation and can be prevented using DI-39, a new high-affinity small-molecule inhibitor of the NSP rate-limiting enzyme dC kinase (dCK). Positron emission tomography (PET) imaging was useful for following both the duration and degree of dCK inhibition by DI-39 treatment in vivo, thus providing a companion pharmacodynamic biomarker. Pharmacological co-targeting of the DNP with dT and the NSP with DI-39 was efficacious against ALL models in mice, without detectable host toxicity. These findings advance our understanding of nucleotide metabolism in leukemic cells, and identify dCTP biosynthesis as a potential new therapeutic target for metabolic interventions in ALL and possibly other hematological malignancies.
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Affiliation(s)
- David A Nathanson
- Department of Molecular and Medical Pharmacology; 2 Ahmanson Translational Imaging Division; 3 Department of Biomathematics; 4 The Pasarow Mass Spectrometry Laboratory, Department of Psychiatry and Biobehavioral Sciences and the Semel Institute for Neuroscience and Human Behavior; 5 Department of Biological Chemistry; and 6 Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095
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Zhang G, Walker AD, Lin Z, Han X, Blatnik M, Steenwyk RC, Groeber EA. Strategies for quantitation of endogenous adenine nucleotides in human plasma using novel ion-pair hydrophilic interaction chromatography coupled with tandem mass spectrometry. J Chromatogr A 2013; 1325:129-36. [PMID: 24377733 DOI: 10.1016/j.chroma.2013.12.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 12/03/2013] [Accepted: 12/04/2013] [Indexed: 11/25/2022]
Abstract
We present here a novel and highly sensitive ion-pair hydrophilic interaction chromatography-tandem mass spectrometry (IP-HILIC-MS/MS) method for quantitation of highly polar acid metabolites like adenine nucleotides. A mobile phase based on diethylamine (DEA) and hexafluoro-2-isopropanol (HFIP) and an aminopropyl (NH2) column were applied for a novel chromatographic separation for the determination of AMP, ADP and ATP in biological matrices. This novel IP-HILIC mechanism could be hypothesized by the ion-pairing reagent (DEA) in the mobile phase forming neutral and hydrophilic complexes with the analytes of polar organic acids. The IP-HILIC-MS/MS assay for adenine nucleotides was successfully validated with satisfactory linearity, sensitivity, accuracy, reproducibility and matrix effects. The lower limit of quantitation (LLOQ) at 2.00ng/mL obtained for ATP showed a least 10-fold higher sensitivity than previous LC-MS/MS assays except nano-LC-MS/MS assay. In summary, this novel IP-HILIC-MS/MS assay provides a sensitive method for nucleotides bioanalysis and shows great potential to determine a number of organic acids in biological matrices.
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Affiliation(s)
- Guodong Zhang
- Biomarker Research, Pharmacokinetics, Dynamics and Metabolism, Pfizer Global Research and Development, Groton, CT 06340, USA.
| | - Annie D Walker
- Cardiovascular, Metabolic, and Endocrine Diseases Research Unit, Pfizer Global Research and Development, Cambridge, MA 02139, USA
| | - Zhaosheng Lin
- Biomarker Research, Pharmacokinetics, Dynamics and Metabolism, Pfizer Global Research and Development, Groton, CT 06340, USA
| | - Xiaogang Han
- Biomarker Research, Pharmacokinetics, Dynamics and Metabolism, Pfizer Global Research and Development, Groton, CT 06340, USA
| | - Matthew Blatnik
- Biomarker Research, Pharmacokinetics, Dynamics and Metabolism, Pfizer Global Research and Development, Groton, CT 06340, USA
| | - Rick C Steenwyk
- Biomarker Research, Pharmacokinetics, Dynamics and Metabolism, Pfizer Global Research and Development, Groton, CT 06340, USA
| | - Elizabeth A Groeber
- Biomarker Research, Pharmacokinetics, Dynamics and Metabolism, Pfizer Global Research and Development, Groton, CT 06340, USA
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Quantitative determination of azacitidine triphosphate in peripheral blood mononuclear cells using liquid chromatography coupled with high-resolution mass spectrometry. J Pharm Biomed Anal 2013; 90:7-14. [PMID: 24317024 DOI: 10.1016/j.jpba.2013.11.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 11/07/2013] [Accepted: 11/09/2013] [Indexed: 11/22/2022]
Abstract
Azacitidine is a cytidine analog used in the treatment of myelodysplastic syndromes, chronic myelomonocytic leukemia and acute myeloid leukemia. The pharmacological effect of azacitidine arises after incorporation into the DNA and RNA. To this end, the drug first has to be converted into its triphosphate forms. This paper describes the development of an assay for quantitative determination of azacitidine triphosphate (aza-CTP) in peripheral blood mononuclear cells (PBMCs). To quantify aza-CTP, separation from the endogenous nucleotides cytidine triphosphate (CTP) and uridine triphosphate (UTP) is required. This was a challenge as the structures of these nucleotides are highly similar and the monoisotopic molecular masses of aza-CTP, UTP and the naturally occurring [(13)C]- and [(15)N]-isotopes of CTP differ less than 0.02 Da. Efforts to select a specific MS(2)-fragment for aza-CTP using a triple quadrupole mass spectrometer remained without success. Therefore, we investigated the feasibility to separate these highly resembling nucleotides based on accurate mass spectrometry using a linear trap quadrupole (LTQ) coupled with an Orbitrap. The LTQ-Orbitrap was able to differentiate between aza-CTP and the endogenous nucleotides UTP and [(13)C]-CTP. There was no baseline resolution between aza-CTP and [(15)N]-CTP, but the [(15)N]-CTP interference was low. For quantification, extracted ion chromatograms were obtained for the accurate m/z window of the aza-CTP product ion. The assay was able to determine aza-CTP concentrations in PBMC lysate from 40.7 to 281 nM. Assuming that an average cell suspension extracted from 16 mL blood contains 10 to 42 million PBMCs per mL, this range corresponds with 2.58/10.9-17.8/74.9 pmol aza-CTP per million PBMCs. Intra-assay accuracies were between -1.1 and 9.5% deviation and coefficient of variation values were ≤13.2%. The assay was successfully applied to quantify aza-CTP in samples from two patients treated with azacitidine. Aza-CTP concentrations up to 19.0 pmol per million PBMCs were measured. This is the first time that aza-CTP concentrations were quantified in PBMCs from patients treated with azacitidine.
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Zhang C, Liu Z, Liu X, Wei L, Liu Y, Yu J, Sun L. Targeted metabolic analysis of nucleotides and identification of biomarkers associated with cancer in cultured cell models. Acta Pharm Sin B 2013. [DOI: 10.1016/j.apsb.2013.06.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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Guo S, Duan JA, Qian D, Wang H, Tang Y, Qian Y, Wu D, Su S, Shang E. Hydrophilic interaction ultra-high performance liquid chromatography coupled with triple quadrupole mass spectrometry for determination of nucleotides, nucleosides and nucleobases in Ziziphus plants. J Chromatogr A 2013; 1301:147-55. [PMID: 23800804 DOI: 10.1016/j.chroma.2013.05.074] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 05/20/2013] [Accepted: 05/29/2013] [Indexed: 02/06/2023]
Abstract
In this study, a rapid and sensitive analytical method was developed for the determination of 20 nucleobases, nucleosides and nucleotides in Ziziphus plants at trace levels by using hydrophilic interaction ultra-high performance liquid chromatography coupled with triple-quadrupole tandem mass spectrometry (HILIC-UHPLC-TQ-MS/MS) in multiple-reaction monitoring (MRM) mode. Under the optimized chromatographic conditions, good separation for 20 target compounds were obtained on a UHPLC Amide column with sub-2μm particles within 10min. The overall LODs and LOQs were between 0.11-3.12ngmL(-1) and 0.29-12.48ngmL(-1) for the 20 analytes, respectively. It is the first report about simultaneous analysis of nucleobases, nucleosides and nucleotides in medicinal plants using HILIC-UHPLC-TQ-MS/MS method, which affords good linearity, precision, repeatability and accuracy. The developed method was successfully applied to Ziziphus plant (Z. jujuba, Z. jujuba var. spinosa and Z. mauritiana) samples. The analysis showed that the fruits and leaves of Ziziphus plants are rich in nucleosides and nucleobases as well as nucleotides, and could be selected as the healthy food resources. Our results in present study suggest that HILIC-UHPLC-TQ-MS/MS method could be employed as a useful tool for quality assessment of the samples from the Ziziphus plants as well as other medicinal plants or food samples using nucleotides, nucleosides and nucleobases as markers.
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Affiliation(s)
- Sheng Guo
- Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing 210023, China
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Faria M, Halquist MS, Kindt E, Li W, Karnes HT, O'Brien PJ. Liquid chromatography-tandem mass spectrometry method for quantification of thymidine kinase activity in human serum by monitoring the conversion of 3'-deoxy-3'-fluorothymidine to 3'-deoxy-3'-fluorothymidine monophosphate. J Chromatogr B Analyt Technol Biomed Life Sci 2012; 907:13-20. [PMID: 22995377 DOI: 10.1016/j.jchromb.2012.08.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Revised: 08/16/2012] [Accepted: 08/19/2012] [Indexed: 10/28/2022]
Abstract
Thymidine kinase 1 (TK1) is an enzyme involved in DNA synthesis whose activity in serum is indicative of tumor proliferation and the severity of blood malignancies. 3'-deoxy-3'-fluorothymidine (FLT), a specific exogenous substrate for TK1, is phosphorylated by TK1 in the presence of a phosphorylating buffer, therefore the conversion of FLT to 3'-deoxy-3'-fluorothymidine monophosphate (FLT-MP) can be measured to assess serum TK1 activity. Here we describe a liquid chromatography-MS/MS (LC-MS/MS) method for quantification of FLT and FLT-MP from serum using protein precipitation and column switching followed by detection on an Applied Biosystems SCIEX API 4000 QTrap mass spectrometer. The method was linear over the range of 0.5-500 ng/mL for FLT and 2.5-2000 ng/mL for FLT-MP with a mean correlation coefficient of 0.9964 and 0.9935 for FLT and FLT-MP, respectively. The lower limit of quantification was 0.5 ng/mL for FLT and 2.5 ng/mL for FLT-MP. Intra-assay accuracy and inter-assay accuracy was within ±12% for both FLT and FLT-MP. Intra-assay precision was 2.8% to 7.7% for FLT and 3.3% to 5.8% for FLT-MP. Inter-assay precision was 4.6% to 14.9% for FLT and 4.9% to 14.6% for FLT-MP. Serum TK1 activity was measured in serum from hepatocellular carcinoma patients and age-matched controls under standardized conditions. Elevated TK1 activity was detected in 26.3% of hepatocellular carcinoma samples compared to controls. This method provides a robust alternative to radiometric and immunochemical assays of serum TK1 activity.
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Affiliation(s)
- Morse Faria
- Department of Pharmaceutics, Virginia Commonwealth University, Richmond, VA 23298, USA
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