New insights into sulfur metabolism in yeasts as revealed by studies of Yarrowia lipolytica.

Yarrowia lipolytica, located at the frontier of hemiascomycetous yeasts and fungi, is an excellent candidate for studies of metabolism evolution. This yeast, widely recognized for its technological applications, in particular produces volatile sulfur compounds (VSCs) that fully contribute to the flavor of smear cheese. We report here a relevant global vision of sulfur metabolism in Y. lipolytica based on a comparison between high- and low-sulfur source supplies (sulfate, methionine, or cystine) by combined approaches (transcriptomics, metabolite profiling, and VSC analysis). The strongest repression of the sulfate assimilation pathway was observed in the case of high methionine supply, together with a large accumulation of sulfur intermediates. A high sulfate supply seems to provoke considerable cellular stress via sulfite production, resulting in a decrease of the availability of the glutathione pathway's sulfur intermediates. The most limited effect was observed for the cystine supply, suggesting that the intracellular cysteine level is more controlled than that of methionine and sulfate. Using a combination of metabolomic profiling and genetic experiments, we revealed taurine and hypotaurine metabolism in yeast for the first time. On the basis of a phylogenetic study, we then demonstrated that this pathway was lost by some of the hemiascomycetous yeasts during evolution.

Pathophysiology of sickle cell disease is mirrored by the red blood cell metabolome.

Emerging metabolomic tools can now be used to establish metabolic signatures of specialized circulating hematopoietic cells in physiologic or pathologic conditions and in human hematologic diseases. To determine metabolomes of normal and sickle cell erythrocytes, we used an extraction method of erythrocytes metabolites coupled with a liquid chromatography-mass spectrometry-based metabolite profiling method. Comparison of these 2 metabolomes identified major changes in metabolites produced by (1) endogenous glycolysis characterized by accumulation of many glycolytic intermediates; (2) endogenous glutathione and ascorbate metabolisms characterized by accumulation of ascorbate metabolism intermediates, such as diketogulonic acid and decreased levels of both glutathione and glutathione disulfide; (3) membrane turnover, such as carnitine, or membrane transport characteristics, such as amino acids; and (4) exogenous arginine and NO metabolisms, such as spermine, spermidine, or citrulline. Finally, metabolomic analysis of young and old normal red blood cells indicates metabolites whose levels are directly related to sickle cell disease. These results show the relevance of metabolic profiling for the follow-up of sickle cell patients or other red blood cell diseases and pinpoint the importance of metabolomics to further depict the pathophysiology of human hematologic diseases.

Validation of a standardised method for determining beryllium in human urine at nanogram level.

The potential toxicity of beryllium at low levels of exposure means that a biological and/or air monitoring strategy may be required to monitor the exposure of subjects. The main objective of the work presented in this manuscript was to develop and validate a sensitive and reproducible method for determining levels of beryllium in human urine and to establish reference values in workers and in non-occupationally exposed people. A chelate of beryllium acetylacetonate formed from beryllium(II) in human urine was pre-concentrated on a SPE C18 cartridge and eluted with methanol. After drying the eluate, the residue was solubilised in nitric acid and analysed by atomic absorption spectrometry and/or inductively coupled plasma mass spectrometry. The proposed method is 4 to 100 times more sensitive than other methods currently in routine use. The new method was validated with the concordance correlation coefficient test for beryllium concentrations ranging from 10 to 100 ng/L. Creatinine concentration, urine pH, interfering compounds and freeze-thaw cycles were found to have only slight effects on the performance of the method (less than 6%). The effectiveness of the two analytical techniques was compared statistically with each other and to direct analysis techniques. Even with a detection limit of 0.6 ng/L (obtained with inductively coupled plasma mass spectrometry), the method is not sensitive enough to detect levels in non-occupationally exposed persons. The method performance does however appear to be suitable for monitoring worker exposure in some industrial settings and it could therefore be of use in biological monitoring strategies.

Annotation of the human adult urinary metabolome and metabolite identification using ultra high performance liquid chromatography coupled to a linear quadrupole ion trap-Orbitrap mass spectrometer.

Metabolic profiles of biofluids obtained by atmospheric pressure ionization mass spectrometry-based technologies contain hundreds to thousands of features, most of them remaining unknown or at least not characterized in analytical systems. We report here on the annotation of the human adult urinary metabolome and metabolite identification from electrospray ionization mass spectrometry (ESI-MS)-based metabolomics data sets. Features of biological interest were first of all annotated using the ESI-MS database of the laboratory. They were also grouped, thanks to software tools, and annotated using public databases. Metabolite identification was achieved using two complementary approaches: (i) formal identification by matching chromatographic retention times, mass spectra, and also product ion spectra (if required) of metabolites to be characterized in biological data sets to those of reference compounds and (ii) putative identification from biological data thanks to MS/MS experiments for metabolites not available in our chemical library. By these means, 384 metabolites corresponding to 1484 annotated features (659 in negative ion mode and 825 in positive ion mode) were characterized in human urine samples. Of these metabolites, 192 and 66 were formally and putatively identified, respectively, and 54 are reported in human urine for the first time. These lists of features could be used by other laboratories to annotate their ESI-MS metabolomics data sets.

Global regulation of the response to sulfur availability in the cheese-related bacterium Brevibacterium aurantiacum.

In this study, we combined metabolic reconstruction, growth assays, and metabolome and transcriptome analyses to obtain a global view of the sulfur metabolic network and of the response to sulfur availability in Brevibacterium aurantiacum. In agreement with the growth of B. aurantiacum in the presence of sulfate and cystine, the metabolic reconstruction showed the presence of a sulfate assimilation pathway, thiolation pathways that produce cysteine (cysE and cysK) or homocysteine (metX and metY) from sulfide, at least one gene of the transsulfuration pathway (aecD), and genes encoding three MetE-type methionine synthases. We also compared the expression profiles of B. aurantiacum ATCC 9175 during sulfur starvation or in the presence of sulfate. Under sulfur starvation, 690 genes, including 21 genes involved in sulfur metabolism and 29 genes encoding amino acids and peptide transporters, were differentially expressed. We also investigated changes in pools of sulfur-containing metabolites and in expression profiles after growth in the presence of sulfate, cystine, or methionine plus cystine. The expression of genes involved in sulfate assimilation and cysteine synthesis was repressed in the presence of cystine, whereas the expression of metX, metY, metE1, metE2, and BL613, encoding a probable cystathionine-γ-synthase, decreased in the presence of methionine. We identified three ABC transporters: two operons encoding transporters were transcribed more strongly during cysteine limitation, and one was transcribed more strongly during methionine depletion. Finally, the expression of genes encoding a methionine γ-lyase (BL929) and a methionine transporter (metPS) was induced in the presence of methionine in conjunction with a significant increase in volatile sulfur compound production.

Alterations of red blood cell metabolome in overhydrated hereditary stomatocytosis.

Overhydrated hereditary stomatocytosis, clinically characterized by hemolytic anemia, is a rare disorder of the erythrocyte membrane permeability to monovalent cations, associated with mutations in the Rh-associated glycoprotein gene. We assessed the red blood cell metabolome of 4 patients with this disorder and showed recurrent metabolic abnormalities associated with this disease but not due to the diminished half-life of their erythrocytes. Glycolysis is exhausted with accumulation of ADP, pyruvate, lactate, and malate. Ascorbate metabolic pathway is altered probably due to a limited entry of dehydroascorbate. Although no major oxydative stress has been reported in patients with overhydrated hereditary stomatocytosis, we found decreased amounts of oxydized glutathione, creatine and ergothioneine, suggesting transporter abnormalities and/or uncharacterized oxydative stress. These results pinpoint major metabolic defects of overhydrated hereditary stomatocytosis erythrocytes and emphasize the relevance of red blood cell metabolomics for a better understanding of the pathophysiological bases of hemolytic anemia associated with erythrocyte abnormalities.

Exploration of sulfur metabolism in the yeast Kluyveromyces lactis.

Hemiascomycetes are separated by considerable evolutionary distances and, as a consequence, the mechanisms involved in sulfur metabolism in the extensively studied yeast, Saccharomyces cerevisiae, could be different from those of other species of the phylum. This is the first time that a global view of sulfur metabolism is reported in the biotechnological yeast Kluyveromyces lactis. We used combined approaches based on transcriptome analysis, metabolome profiling, and analysis of volatile sulfur compounds (VSCs). A comparison between high and low sulfur source supplies, i.e., sulfate, methionine, or cystine, was carried out in order to identify key steps in the biosynthetic and catabolic pathways of the sulfur metabolism. We found that sulfur metabolism of K. lactis is mainly modulated by methionine. Furthermore, since sulfur assimilation is highly regulated, genes coding for numerous transporters, key enzymes involved in sulfate assimilation and the interconversion of cysteine to methionine pathways are repressed under conditions of high sulfur supply. Consequently, as highlighted by metabolomic results, intracellular pools of homocysteine and cysteine are maintained at very low concentrations, while the cystathionine pool is highly expandable. Moreover, our results suggest a new catabolic pathway for methionine to VSCs in this yeast: methionine is transaminated by the ARO8 gene product into 4-methylthio-oxobutyric acid (KMBA), which could be exported outside of the cell by the transporter encoded by PDR12 and demethiolated by a spontaneous reaction into methanethiol and its derivatives.

Evaluation of accurate mass and relative isotopic abundance measurements in the LTQ-orbitrap mass spectrometer for further metabolomics database building.

Recently, high-resolution mass spectrometry has been largely employed for compound identification, thanks to accurate mass measurements. As additional information, relative isotope abundance (RIA) is often needed to reduce the number of candidates prior to tandem MS(n). Here, we report on the evaluation of the LTQ-Orbitrap, in terms of accurate mass and RIA measurements for building further metabolomics spectral databases. Accurate mass measurements were achieved in the ppm range, using external calibration within 24 h, and remained at <5 ppm over a one-week period. The experimental relative abundances of (M+1) isotopic ions were evaluated in different data sets. First of all, 137 solutions of commercial compounds were analyzed by flow injection analysis in both the positive and negative ion modes. It was found that the ion abundance was the main factor impacting the accuracy of RIA measurements. It was possible to define some intensity thresholds above which errors were systematically <20% of their theoretical values. The same type of results were obtained with analyses from two biological media. Otherwise, no significant effect of ion transmission between the LTQ ion trap and the Orbitrap analyzer on RIA measurement errors was found, whereas the reliability of RIA measurements was dramatically improved by reducing the mass detection window. It was also observed that the signal integration method had a significant impact on RIA measurement errors, with the most-reliable results being obtained with peak height integrations. Finally, automatic integrations using the data preprocessing software XCMS and MZmine gave results similar to those obtained by manual integration, suggesting that it is relevant to use the RIA information in automatic elemental composition determination software from metabolomic peak tables.

Mass spectrometry for the identification of the discriminating signals from metabolomics: current status and future trends.

The metabolome is characterized by a large number of molecules exhibiting a high diversity of chemical structures and abundances, requiring complementary analytical platforms to reach its extensive coverage. Among them, atmospheric pressure ionization mass spectrometry (API-MS)-based technologies, and especially those using electrospray ionization are now very popular. In this context, this review deals with strengths, limitations and future trends in the identification of signals highlighted by API-MS-based metabolomics. It covers the identification process from the determination of the molecular mass and/or its elemental composition to the confirmation of structural hypotheses. Furthermore, some tools that were developed in order to address the MS signal redundancy and some approaches that could facilitate identification by improving the visualization and organization of complex data sets are also reported and discussed.

Organochlorines and endometriosis: a mini-review.

Organochlorines (polychlorinated biphenyls and dioxin-like compounds) are suspected to play a role in the etiopathogenesis of endometriosis. This hypothesis, based on experimental data, has been circulating for years in the scientific community and several epidemiologic surveys have attempted to obtain confirmatory human data. The purpose of this mini-review is to provide an overview of the twelve epidemiological studies that have assessed the relationship between endometriosis and organochlorine exposure. Several studies did not observe a significant association between peritoneal endometriosis and organochlorines. The deep nodular form of endometriosis appears associated with a higher serum level of both dioxin-like compounds and polychlorobiphenyls. The type of control women, the nature of the chemicals measured, and the definition of the disease could modulate the ability to detect the possible relationship between endometriosis and organochlorine exposure.

Impact of iron and steel industry and waste incinerators on human exposure to dioxins, PCBs, and heavy metals: results of a cross-sectional study in Belgium.

We evaluated the impact of two iron and steel plants and two municipal solid waste incinerators (MSWI) in Wallonia (Belgium) on the exposure of residents to dioxins, polychlorinated biphenyls (PCBs), and heavy metals. In total, 142 volunteers living around these facilities were recruited and compared with 63 referents from a rural area with no industrial source of pollution. Information about smoking habits, dietary habits, anthropometric characteristics, residential history, and health status was obtained from a self-administered questionnaire. The volunteers provided blood under fasting conditions in order to evaluate the body burden of dioxins (17 polychlorinated dibenzo-p-dioxins/dibenzofurans [PCDD/Fs] congeners) and PCBs. Samples of blood and urine were also taken for the determination of cadmium, mercury, and lead. After adjustment for covariates, concentrations of cadmium, mercury, and lead in urine or blood were not increased in subjects living in the vicinity of MSWIs or sinter plants by comparison with referents. Residents around the sinter plants and the MSWI located in the industrial area had concentrations of dioxins and PCBs in serum similar to that of referents. By contrast, subjects living in the vicinity of the MSWI in the rural area showed significantly higher serum levels of dioxins (geometric mean, 38 vs. 24 pg TEQ/g fat) and coplanar PCBs (geometric mean, 10.8 vs. 7.0 pg TEQ/g fat). Although age-adjusted dioxin levels in referents did not vary with local animal fat consumption, concentrations of dioxins in subjects living around the incinerators correlated positively with their intake of local animal fat, with almost a doubling in subjects with the highest fat intake. These results indicate that dioxins and coplanar PCBs emitted by MSWIs can indeed accumulate in the body of residents who regularly consume animal products of local origin.

Serum dioxin-like compounds and aromatase (CYP19) expression in endometriotic tissues.

Dioxin-like compounds (DLCs) are suspected etiological factors of endometriosis but their potential mechanisms of action remain elusive. Because endometriosis is an estrogen-dependent disease and since aromatase (CYP19), a key enzyme in estrogen biosynthesis, was recently demonstrated to be expressed in endometriotic lesions, we hypothesized that dioxin-like compounds could modulate local estrogen production through an up-regulation of aromatase. We tested this hypothesis by examining the correlation between serum DLC levels and CYP19 expression in endometriotic tissue obtained from 47 patients with peritoneal, ovarian endometriosis and/or deep endometriotic nodules of the rectovaginal septum. Aromatase expression was assessed by real-time RT-PCR in biopsied endometriotic tissues [peritoneal (n=19), ovarian (n=17) endometriosis and deep endometriotic nodules of the recto-vaginal septum (n=29)]. The relationship between aromatase expression and DLCs was traced by simple regression analysis. DLCs did not appear to be significant determinants of aromatase expression. CYP1A1 expression, measured as a positive control, was found associated with current smoking but not with DLCs. We conclude that DLCs do probably not facilitate the growth of endometriotic lesions by up-regulating the local expression of aromatase.

Invasive aspergillosis in association with criminal arsenic poisoning.

A 26-year-old man suffered acute arsenic poisoning after a poisoning attempt. He developed multiple organ failure including encephalopathy, bleeding disorders, pancreatitis, renal and hepatocellular impairment. Generalized erythroderma also developed within one week after admission. The developed acute respiratory distress syndrome and Aspergillus fumigatus was isolated from the endotracheal aspirate. Despite intensive care support, antidote administration and various epuration techniques, the patient died on day 26 from subarachnoid bleeding. An autopsy was obtained and the concentration of arsenic was determined in different tissues. Multiple abscesses due to Aspergillus fumigatus were seen in the lungs, myocardium and kidneys. This uncommon complication in a previously immunocompetent patient could be related to impaired immunity directly caused by arsenic poisoning.

Increased serum polychlorobiphenyl levels in Belgian women with adenomyotic nodules of the rectovaginal septum.

The sum of bulk polychlorobiphenyl levels was significantly higher in women with rectovaginal adenomyosis than in women with endometriosis and controls.

Assessment of cadmium impregnation in women suffering from endometriosis: a preliminary study.

Environmental chemicals with oestrogen-like activity are suspected aetiological factors of endometriosis. In animal experiments, cadmium was recently shown to possess oestrogen-like properties. In the frame of a case-control study designed to investigate environmental risk factors for endometriosis, we compared cadmium urinary excretion (CdU) and blood concentration in 59 patients with peritoneal endometriosis, deep endometriotic (adenomyotic) nodules of the recto-vaginal septum and controls. After standardisation for age (30 years) and smoking status, the mean levels of cadmium in urine were (geometric mean [geometric S.D.]) 0.25 [1.50], 0.29 [1.76] and 0.26 [1.46] microg/g creatinine, respectively. Cadmium concentrations in blood did not differ among the three groups. These data, therefore, do not support a role for cadmium in the onset or the growth of endometriosis or deep endometriotic (adenomyotic) nodules of the recto-vaginal septum.

Applications of liquid chromatography coupled to mass spectrometry-based metabolomics in clinical chemistry and toxicology: A review.

The metabolome is the set of small molecular mass organic compounds found in a given biological media. It includes all organic substances naturally occurring from the metabolism of the studied living organism, except biological polymers, but also xenobiotics and their biotransformation products. The metabolic fingerprints of biofluids obtained by mass spectrometry (MS) or nuclear magnetic resonance (NMR)-based methods contain a few hundreds to thousands of signals related to both genetic and environmental contributions. Metabolomics, which refers to the untargeted quantitative or semi-quantitative analysis of the metabolome, is a promising tool for biomarker discovery. Although proof-of-concept studies by metabolomics-based approaches in the field of toxicology and clinical chemistry have initially been performed using NMR, the use of liquid chromatography hyphenated to mass spectrometry (LC/MS) has increased over the recent years, providing complementary results to those obtained with other approaches. This paper reviews and comments the input of LC/MS in this field. We describe here the overall process of analysis, review some seminal papers in the field and discuss the perspectives of metabolomics for the biomonitoring of exposure and diagnosis of diseases.

Mass spectrometry-based methods for the determination of sulfur and related metabolite concentrations in cell extracts.

The sulfur metabolic pathway plays a central role in cell metabolism. It provides the sulfur amino acids methionine and cysteine, which are essential for protein synthesis, homocysteine, which lies at a critical juncture of this pathway, S-adenosylmethionine, the universal methyl donor in the cell, and glutathione (GSH), which has many crucial functions including protection against oxidative stress and xenobiotics. The intracellular level of these metabolites, which are closely connected with other cellular metabolic pathways, is of major importance for cell physiology and health. Three mass spectrometry-based methods for the determination of sulfur metabolites and also related compounds linked to the glutathione biosynthesis pathway are presented and discussed. The first one enables absolute quantification of these metabolites in cell extracts. It is based on liquid chromatography-electrospray triple quadrupole mass spectrometry coupled to (15)N uniform metabolic labeling of the yeast Saccharomyces cerevisiae. The two other methods are global approaches to metabolite detection involving a high-resolution mass spectrometer, the LTQ-Orbitrap. Ions related to metabolites of interest are picked up from complex and information-rich metabolic fingerprints. By these means, it is possible to detect analytical information outside the initial scope of investigation.

Electron paramagnetic resonance as a tool to evaluate human ovarian tissue reoxygenation after xenografting.

OBJECTIVE: To develop electron paramagnetic resonance (EPR) oximetry as a tool to characterize the oxygen environment in human ovarian xenografts in the early postgrafting period. DESIGN: Prospective experimental study. SETTING: Gynecology research unit in a university hospital. PATIENT(S): Biopsies were obtained from 6 women aged 22-35 years. INTERVENTION(S): Frozen-thawed human ovarian tissue fragments were grafted to an intraperitoneal site in nude mice. Before grafting, lithium phthalocyanine, an oxygen reporter, was implanted inside the fragments. MAIN OUTCOME MEASURE(S): To monitor partial pressure of oxygen (pO(2)) by EPR on postgrafting days 3, 5, 7, 10, 14, 17, and 21 and validate the technique by histologic assessment. RESULT(S): A period of hypoxia was identified before day 5, followed by gradual but significant oxygenation over the next 5 days, suggesting an active process of graft revascularization. Reoxygenation kinetics in human ovarian xenotransplants were quantified. CONCLUSION(S): Our data validated the EPR oximetry technique as a tool to monitor pO(2) in ovarian grafting. The critical early period of hypoxia was identified, and the first steps of reoxygenation were characterized. In the future, our model may be used to evaluate new freezing and grafting protocols with the aim of reducing potential cryoinjury and initial ischemia-reperfusion damage.

Environmental and host-associated risk factors in endometriosis and deep endometriotic nodules: a matched case-control study.

Peritoneal endometriosis (PE) and deep endometriotic nodules (DEN) are gynecological diseases recently shown to be associated with elevated serum concentrations of organochlorines. The objective of the present study was to compare risk factors associated with both forms of the disease, with a particular attention to potential sources of organochlorine exposure. This matched case-control study with prospective recruitment included 88 triads (PE-DEN-control). All women were face-to-face interviewed with a standardized questionnaire, and serum dioxin and polychlorinated biphenyl measurements were available for 58 of them. Alcohol consumption (odds ratio (OR): 5.82 [confidence interval at 95% (95%CI) 1.20-28.3]) in DEN and low physical activity at work for DEN (OR: 4.58 [95%CI 1.80-11.62]) and PE (OR: 5.61 [95%CI 1.90-16.60]) were traced as significant risk factors. Organochlorine-related factors (use of tampons, occupational or environmental exposure) were not related to the disease. The current consumption of foodstuffs that were more likely to contribute to organochlorine body burden did not differ among the groups. Only some of these fatty foodstuffs (marine fish, pig meat) were traced by multiple regression analysis as significant determinants of organochlorine body burden, explaining only a small fraction (20%) of the interindividual variation of organochlorine body burden. We conclude that PE and DEN share similar patterns of risk or protective factors.

Expression of aromatase (P450 aromatase/CYP19) in peritoneal and ovarian endometriotic tissues and deep endometriotic (adenomyotic) nodules of the rectovaginal septum.

We found, by reverse transcription--real time--polymerase chain reaction, that the expression of aromatase (CYP19) in ovarian, peritoneal endometriosis, and deep endometriotic nodules is significantly different, which strengthens the theory of three distinct clinical entities. Compared with peritoneal endometriosis, ovarian endometriosis exhibits an 8-fold higher expression of aromatase, which suggests that aromatase inhibitors may be particularly active in this form of endometriosis.