Quantification des pools de nucléotides à l'aide de la chromatographie liquide couplée à la spectrométrie de masse en tandem : applications à l'étude de la progression tumorale

Nucleotides, term including nucleoside mono-, di- and triphosphates, are endogenous compounds playing various roles in biology. They are components of nucleic acids, provide energy to metabolic reactions and act as carriers or second messenger. The study of endogenous nucleotides has become of great interest in physiological and pathological conditions. We developed a method for the quantification of endogenous nucleotides, using an on-line extraction on a WAX column coupled with LC-MS/MS. Analytical separation is performed on a Hypercarb column, without ion pairing agent in the mobile phase. The use of a triple quadrupole mass spectrometer following positive mode ionization allows the unambiguous identification of nucleotides presenting the same mass. Extraction and separation of nucleotides are achieved within 20 min and the method including re-equilibration of the two columns within 37 min. The method was validated for the quantification of nucleoside mono- and triphosphates, and could be applied to series of more than twenty biological samples. Secondly, in a study based on design of experiments, pre-analytical parameters influencing results of intracellular nucleotides were compared in four cell lines. We demonstrated that optimal pre-analytical parameters depend on cell lines. This clearly highlights the importance of pre- analytical conditions for the quantification of intracellular nucleotides to be as representative as possible of the real levels in cells. Then, thanks to experience acquired during the development and the validation of the analytical method, scientific collaborations have been established with several cancer research teams. For example, implication of nucleotide metabolism in replicative stress induced by oxidative stress or in the metabolic reprogramming in cancer cells was studied. Results obtained by our analytical approach were complementary to those obtained by other techniques. To conclude, our work consisted on the study of the entire workflow for the analysis of endogenous nucleotides in various biological samplesLes nucléotides, terme regroupant les nucléosides monophosphate, diphosphate et triphosphate, sont impliqués dans de nombreux processus cellulaires. Ils représentent les éléments constitutifs des acides nucléiques, fournissent de l'énergie à des réactions métaboliques, jouent le rôle de transporteurs et seconds messagers. L'exploration des pools nucléotidiques apparaît indispensable afin de connaître leur rôle précis dans des situations physiologiques ou pathologiques. Nous avons développé une méthode de dosage des nucléotides endogènes (formes mono-, di- et triphosphate) par extraction en ligne sur colonne WAX couplée à la LC-MS/MS. La séparation analytique est réalisée sur colonne Hypercarb, sans agent de paire d'ions dans la phase mobile. Grâce à l'utilisation d'un triple quadripôle et une ionisation en mode positif, les nucléotides endogènes sont identifiés sans équivoque, y compris ceux possédant la même masse molaire. L'extraction et la séparation des nucléotides sont réalisées en 20 min. L'ensemble de la méthode, en comptant la ré- équilibration des colonnes, dure 37 min. La méthode de dosage a été validée pour les formes mono- et triphosphate et est applicable à des séries d'une vingtaine d'échantillons biologiques. D'autre part, dans une étude pré-analytique basée sur les plans d'expériences, nous avons comparé les conditions de préparation d'échantillons en vue du dosage de nucléotides intracellulaires dans 4 lignées cellulaires : 2 adhérentes (Messa et NCI-H292) et 2 en suspension (RL et L1210). Nous avons montré que les conditions pré-analytiques optimales dépendent de la lignée cellulaire soulignant ainsi l'importance de cette phase dans l'analyse des nucléotides. Enfin, l'expérience et les connaissances acquises lors du développement de la méthode de dosage des nucléotides ainsi que la large palette de molécules analysables avec cette méthode (nucléosides, nucléotides sucrés, autres métabolites), nous ont permis de développer des collaborations dans le domaine de la cancérologie avec différentes équipes de recherche. Par exemple, nous avons étudié l'implication des pools nucléotidiques dans le stress réplicatif induit par le stress oxydant et dans la reprogrammation cellulaire observée dans les cellules cancéreuses. Ainsi, les informations apportées par notre approche analytique, complémentaires des autres approches utilisées, ont montré l'implication des pools nucléotidiques dans la tumorigénèse. En conclusion, ce travail a permis de développer une technique analytique et de mettre en place une méthode de travail pour le dosage des nucléotides endogènes dans différents milieux biologique

Quantification of nucleotides pools with liquid chromatography coupled with tandem mass spectrometry : applications in cancer research

Les nucléotides, terme regroupant les nucléosides monophosphate, diphosphate et triphosphate, sont impliqués dans de nombreux processus cellulaires. Ils représentent les éléments constitutifs des acides nucléiques, fournissent de l'énergie à des réactions métaboliques, jouent le rôle de transporteurs et seconds messagers. L'exploration des pools nucléotidiques apparaît indispensable afin de connaître leur rôle précis dans des situations physiologiques ou pathologiques. Nous avons développé une méthode de dosage des nucléotides endogènes (formes mono-, di- et triphosphate) par extraction en ligne sur colonne WAX couplée à la LC-MS/MS. La séparation analytique est réalisée sur colonne Hypercarb, sans agent de paire d'ions dans la phase mobile. Grâce à l'utilisation d'un triple quadripôle et une ionisation en mode positif, les nucléotides endogènes sont identifiés sans équivoque, y compris ceux possédant la même masse molaire. L'extraction et la séparation des nucléotides sont réalisées en 20 min. L'ensemble de la méthode, en comptant la ré- équilibration des colonnes, dure 37 min. La méthode de dosage a été validée pour les formes mono- et triphosphate et est applicable à des séries d'une vingtaine d'échantillons biologiques. D'autre part, dans une étude pré-analytique basée sur les plans d'expériences, nous avons comparé les conditions de préparation d'échantillons en vue du dosage de nucléotides intracellulaires dans 4 lignées cellulaires : 2 adhérentes (Messa et NCI-H292) et 2 en suspension (RL et L1210). Nous avons montré que les conditions pré-analytiques optimales dépendent de la lignée cellulaire soulignant ainsi l'importance de cette phase dans l'analyse des nucléotides. Enfin, l'expérience et les connaissances acquises lors du développement de la méthode de dosage des nucléotides ainsi que la large palette de molécules analysables avec cette méthode (nucléosides, nucléotides sucrés, autres métabolites), nous ont permis de développer des collaborations dans le domaine de la cancérologie avec différentes équipes de recherche. Par exemple, nous avons étudié l'implication des pools nucléotidiques dans le stress réplicatif induit par le stress oxydant et dans la reprogrammation cellulaire observée dans les cellules cancéreuses. Ainsi, les informations apportées par notre approche analytique, complémentaires des autres approches utilisées, ont montré l'implication des pools nucléotidiques dans la tumorigénèse. En conclusion, ce travail a permis de développer une technique analytique et de mettre en place une méthode de travail pour le dosage des nucléotides endogènes dans différents milieux biologiquesNucleotides, term including nucleoside mono-, di- and triphosphates, are endogenous compounds playing various roles in biology. They are components of nucleic acids, provide energy to metabolic reactions and act as carriers or second messenger. The study of endogenous nucleotides has become of great interest in physiological and pathological conditions. We developed a method for the quantification of endogenous nucleotides, using an on-line extraction on a WAX column coupled with LC-MS/MS. Analytical separation is performed on a Hypercarb column, without ion pairing agent in the mobile phase. The use of a triple quadrupole mass spectrometer following positive mode ionization allows the unambiguous identification of nucleotides presenting the same mass. Extraction and separation of nucleotides are achieved within 20 min and the method including re-equilibration of the two columns within 37 min. The method was validated for the quantification of nucleoside mono- and triphosphates, and could be applied to series of more than twenty biological samples. Secondly, in a study based on design of experiments, pre-analytical parameters influencing results of intracellular nucleotides were compared in four cell lines. We demonstrated that optimal pre-analytical parameters depend on cell lines. This clearly highlights the importance of pre- analytical conditions for the quantification of intracellular nucleotides to be as representative as possible of the real levels in cells. Then, thanks to experience acquired during the development and the validation of the analytical method, scientific collaborations have been established with several cancer research teams. For example, implication of nucleotide metabolism in replicative stress induced by oxidative stress or in the metabolic reprogramming in cancer cells was studied. Results obtained by our analytical approach were complementary to those obtained by other techniques. To conclude, our work consisted on the study of the entire workflow for the analysis of endogenous nucleotides in various biological sample

A Proposed Methodology to Deal with the Impact of In Vitro Cellular Matrix on the Analytical Performances of a Targeted Metabolomic LC-HRMS Method

Performances of metabolomic methods have been widely studied on biological matrices such as serum, plasma, and urine; but much less on in vitro cell extracts. While the impact of cell culture and sample preparation on results are well-described, the specific effect of the in vitro cellular matrix on the analytical performance remains uncertain. The aim of the present work was to study the impact of this matrix on the analytical performance of an LC-HRMS metabolomic method. For this purpose, experiments were performed on total extracts from two cell lines (MDA-MB-231 and HepaRG) using different cell numbers. Matrix effects, carryover, linearity, and variability of the method were studied. Results showed that the performances of the method depend on the nature of the endogenous metabolite, the cell number, and the nature of the cell line. These three parameters should, therefore, be considered for the processing of experiments and the interpretation of results depending on whether the study focuses on a limited number of metabolites or aims to establish a metabolic signature

Découverte fortuite d’une intoxication aiguë par vérapamil forme à libération prolongée : intérêt du criblage toxicologique

Objectifs : Un patient de 29 ans a été admis en soins intensifs pour hypotension résistante et anomalies du rythme cardiaque. Le service clinique suspectant une intoxication par bisoprolol, un criblage toxicologique par chromatographie liquide couplée à la spectrométrie de masse en tandem (LC-MS/MS) a été réalisé. Ce criblage n’a pas retrouvé de bisoprolol mais a mis en évidence une intoxication par vérapamil. Afin de confirmer l’intoxication, des dosages sanguins du vérapamil et de ses principaux métabolites ont été effectués quotidiennement. Méthodes : La recherche et les dosages ont été réalisés par LC-MS/MS. Les métabolites ont été préalablement identifiés après incubation du vérapamil avec des microsomes hépatiques de souris. Résultats : Sept métabolites ont été identifiés après incubation avec les microsomes hépatiques de souris. Cinq d’entre eux ont été retrouvés dans le sérum du patient. L’évolution des taux sanguins en vérapamil a montré une croissance le 1er jour (1,0 mg/L à J1, 1,7 mg/L à J2 ; valeurs thérapeutiques : 0,02 à 0,25 mg/L), un plateau pendant 3 jours puis une décroissance. Les cinétiques des principaux métabolites du vérapamil (norvérapamil et N-desalkylvérapamil) étaient comparables à celle de la molécule mère. Conclusion : Le criblage toxicologique a permis de diagnostiquer l’intoxication par vérapamil dans un contexte clinique complexe. La stagnation des taux sanguins pendant 3 jours était vraisemblablement due à une intoxication avec une forme à libération prolongée du vérapamil

Exploration urinaire du métabolisme : bilan nutritionnel, lithiase urinaire et tubulopathie

International audienceThe SFBC working group aimed to deal with biological tests outside the french nomenclature that may be useful in the context of urinary exploration of metabolism. This section will be divides into three parts: 1) nutritional assessment using urinary urea; 2) metabolic assessment of urolithiasis; 3) exploration of tubulopathies. National and international recommendations support the evaluation of nutritional status from urea measurements in urine and dialysate with the following indications: primary metabolic evaluation of urolithiasis patients, monitoring of protein intake in chronic renal failure stage 3 or stage 5D with residual diuresis. For the management of the urolithiasis disease, biomedical tests recommended by the national and international guidelines are the measurement of the urinary density using refractometry in the primary metabolic evaluation as well as the determination of oxalemia in the diagnosis (patients with GFR< 30 mL/min/1.73 m2) and follow-up (patients with GFR< 60 mL/min/1.73 m2) of primary hyperoxaluria. The determination of the bicarbonaturia is retained for the in depth exploration of urolithiasis and tubular acidosis. The measure of chlore in urine is used to evaluate the volume status during metabolic alkalosis and to calculate the urinary anionic gap during metabolic acidosis

Fully validated assay for the quantification of endogenous nucleoside mono- and triphosphates using online extraction coupled with liquid chromatography-tandem mass spectrometry.

International audienceAn 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

Use of designed experiments for the improvement of pre-analytical workflow for the quantification of intracellular nucleotides in cultured cell lines

International audienceThe 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

Singlet Oxygen-Mediated Oxidation during UVA Radiation Alters the Dynamic of Genomic DNA Replication.

UVA radiation (320-400 nm) is a major environmental agent that can exert its deleterious action on living organisms through absorption of the UVA photons by endogenous or exogenous photosensitizers. This leads to the production of reactive oxygen species (ROS), such as singlet oxygen (1O2) and hydrogen peroxide (H2O2), which in turn can modify reversibly or irreversibly biomolecules, such as lipids, proteins and nucleic acids. We have previously reported that UVA-induced ROS strongly inhibit DNA replication in a dose-dependent manner, but independently of the cell cycle checkpoints activation. Here, we report that the production of 1O2 by UVA radiation leads to a transient inhibition of replication fork velocity, a transient decrease in the dNTP pool, a quickly reversible GSH-dependent oxidation of the RRM1 subunit of ribonucleotide reductase and sustained inhibition of origin firing. The time of recovery post irradiation for each of these events can last from few minutes (reduction of oxidized RRM1) to several hours (replication fork velocity and origin firing). The quenching of 1O2 by sodium azide prevents the delay of DNA replication, the decrease in the dNTP pool and the oxidation of RRM1, while inhibition of Chk1 does not prevent the inhibition of origin firing. Although the molecular mechanism remains elusive, our data demonstrate that the dynamic of replication is altered by UVA photosensitization of vitamins via the production of singlet oxygen

Slow Replication Fork Velocity of Homologous Recombination-Defective Cells Results from Endogenous Oxidative Stress

International audienceReplications forks are routinely hindered by different endogenous stresses. Because homologous recombination plays a pivotal role in the reactivation of arrested replication forks, defects in homologous recombination reveal the initial endogenous stress(es). Homologous recombination-defective cells consistently exhibit a spontaneously reduced replication speed, leading to mitotic extra centrosomes. Here, we identify oxidative stress as a major endogenous source of replication speed deceleration in homologous recombination-defective cells. The treatment of homologous recombination-defective cells with the antioxidant N-acetyl-cysteine or the maintenance of the cells at low O2 levels (3%) rescues both the replication fork speed, as monitored by single-molecule analysis (molecular combing), and the associated mitotic extra centrosome frequency. Reciprocally, the exposure of wild-type cells to H2O2 reduces the replication fork speed and generates mitotic extra centrosomes. Supplying deoxynucleotide precursors to H2O2-exposed cells rescued the replication speed. Remarkably, treatment with N-acetyl-cysteine strongly expanded the nucleotide pool, accounting for the replication speed rescue. Remarkably, homologous recombination-defective cells exhibit a high level of endogenous reactive oxygen species. Consistently, homologous recombination-defective cells accumulate spontaneous γH2AX or XRCC1 foci that are abolished by treatment with N-acetyl-cysteine or maintenance at 3% O2. Finally, oxidative stress stimulated homologous recombination, which is suppressed by supplying deoxynucleotide precursors. Therefore, the cellular redox status strongly impacts genome duplication and transmission. Oxidative stress should generate replication stress through different mechanisms, including DNA damage and nucleotide pool imbalance. These data highlight the intricacy of endogenous replication and oxidative stresses, which are both evoked during tumorigenesis and senescence initiation, and emphasize the importance of homologous recombination as a barrier against spontaneous genetic instability triggered by the endogenous oxidative/replication stress axis

Oncolytic virotherapy with intratumoral injection of vaccinia virus TG6002 and 5-fluorocytosine administration in dogs with malignant tumors

International audienceTG6002 is an oncolytic vaccinia virus expressing FCU1 protein, which converts 5-fluorocytosine into 5-fluorouracil. The study objectives were to assess tolerance, viral replication, 5-fluorouracil synthesis, and tumor microenvironment modifications to treatment in dogs with spontaneous malignant tumors. Thirteen dogs received one to three weekly intratumoral injections of TG6002 and 5-fluorocytosine. The viral genome was assessed in blood and tumor biopsies by qPCR. 5-Fluorouracil concentrations were measured in serum and tumor biopsies by liquid chromatography or high-resolution mass spectrometry. Histological and immunohistochemical analyses were performed. The viral genome was detected in blood (7/13) and tumor biopsies (4/11). Viral replication was suspected in 6/13 dogs. The median intratumoral concentration of 5-fluorouracil was 314 pg/mg. 5-Fluorouracil was not detected in the blood. An increase in necrosis (6/9) and a downregulation of intratumoral regulatory T lymphocytes (6/6) were observed. Viral replication, 5-fluorouracil synthesis, and tumor microenvironment changes were more frequently observed with higher TG6002 doses. This study confirmed the replicative properties, targeted chemotherapy synthesis, and reversion of the immunosuppressive tumor microenvironment in dogs with spontaneous malignant tumors treated with TG6002 and 5-fluorocytosine