![]()
|
|
||||||||
J. Biol. Chem., Vol. 281, Issue 24, 16768-16776, June 16, 2006
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||

12
1








From the
Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan,
Human Metabolome Technologies Inc., Tsuruoka, Yamagata 997-0017, Japan, and the ¶Department of Biochemistry and Integrative Medical Biology, School of Medicine, Keio University, Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
Received for publication, February 27, 2006 , and in revised form, March 29, 2006.
| ABSTRACT |
|---|
|
|
|---|
-glutamylcysteine and glutathione synthetase. Changes in ophthalmate level in mouse serum and liver extracts were closely correlated and ophthalmate levels increased significantly in conjunction with glutathione consumption. Overall, our results provide a broad picture of hepatic metabolite changes following acetaminophen treatment. In addition, we specifically found that serum ophthalmate is a sensitive indicator of hepatic GSH depletion, and may be a new biomarker for oxidative stress. Our method can thus pinpoint specific metabolite changes and provide insights into the perturbation of metabolic pathways on a large scale and serve as a powerful new tool for discovering low molecular weight biomarkers. | INTRODUCTION |
|---|
|
|
|---|
Recent transcriptomic and proteomic studies showed that AAP can cause numerous changes in gene and protein expression levels in pathways related to cellular stress response, mitochondrial function, and metabolism, as well as in cell cycle, structural, signaling, and apoptotic proteins (8, 9). However, little is known about global changes in metabolites. Global information about when and where metabolite levels increase or decrease can reveal connections in biological networks and provide a system level understanding of the cell (1014). However, unlike other functional genomic approaches, metabolome analysis methods are still under development. Current large scale metabolite analysis methods are based on gas chromatography mass spectrometry (15), liquid chromatography mass spectrometry (LC-MS) (16), NMR (17), Fourier transform ion cyclotron resonance mass spectrometry) (18), and capillary electrophoresis mass spectrometry (CE-MS) (19). Whereas these analytical tools allow global metabolite profiling, the exploration and identification of changes in compounds among the enormous amount of data generated are laborious.
Here, we propose a novel strategy to analyze and differentially display metabolic profiles by coupling capillary electrophoresis with electrospray ionization time-of-flight mass spectrometry (CE-TOFMS). Using this profiling system, we determined global changes in metabolite levels in the liver and serum of AAP-treated mice, obtained insights into the perturbation of metabolic pathways related to hepatotoxicity, and identified biomarkers that can reveal acute liver injury.
| MATERIALS AND METHODS |
|---|
|
|
|---|
Metabolite ExtractionFrozen liver tissue (
300 mg) was immediately plunged into methanol (1 ml) containing internal standards (300 µM each of methionine sulfone for cations, MES for anions) and homogenized for 1 min to inactivate enzymes. Then, deionized water (500 µl) was added, 300 µl of the solution were transferred to another tube, and 200 µl of chloroform were added, and the mixture thoroughly mixed. The solution was centrifuged at 12,000 x g for 15 min at 4 °C, and the 300-µl upper aqueous layer was centrifugally filtered through a Millipore 5-kDa cutoff filter to remove proteins. The filtrate was lyophilized and dissolved in 50 µl of Milli-Q water containing reference compounds (200 µM each of 3-aminopyrrolidine and trimesate) prior to CE-TOFMS analysis.
For serum studies, 200-µl samples were plunged into 1.8 ml of methanol containing 55 µM each of methionine sulfone and MES and mixed well. Then 800 µl of deionized water and 2 ml of chloroform were added, and the solution was centrifuged at 2,500 x g for 5 min at 4 °C. The 800-µl upper aqueous layer was centrifugally filtered through a Millipore 5-kDa cutoff filter to remove proteins. Subsequent steps were as for liver samples.
Metabolite StandardsAll chemical standards were obtained from common commercial sources and dissolved in Milli-Q (Millipore, Bedford, MA) water, 0.1 N HCl or 0.1 N NaOH to obtain 10 mM or 100 mM stock solutions. Working standard mixtures were prepared by diluting stock solutions with Milli-Q water just prior to injection into the CE-TOFMS. The chemicals used were of analytical or reagent grade.
InstrumentationAll CE-TOFMS experiments were performed using an Agilent CE capillary electrophoresis system (Agilent Technologies, Waldbronn, Germany), an Agilent G3250AA LC/MSD TOF system (Agilent Technologies, Palo Alto, CA), an Agilent1100 series binary HPLC pump, and the G1603A Agilent CE-MS adapter and G1607A Agilent CE-ESI-MS sprayer kit. For system control and data acquisition we used the G2201AA Agilent ChemStation software for CE and the Analyst QS for Agilent TOFMS software. CE-MS/MS analyses for compound identification were performed on a Q-Star XL Hybrid LC-MS/MS System (Applied Biosystems, Foster City, CA) connected to an Agilent CE instrument.
CE-TOFMS Conditions for Cationic Metabolite AnalysisSeparations were carried out in a fused silica capillary (50 µm inner diameter x 100 cm total length) filled with 1 M formic acid as the electrolyte (21). Approximately 3 nl of sample solution were injected at 50 mbar for 3 s, and 30 kV of voltage was applied. The capillary temperature was maintained at 20 °C, and the sample tray was cooled below 5 °C. Methanol-water (50% v/v) containing 0.5 µM reserpine was delivered as the sheath liquid at 10 µl/min. ESI-TOFMS was operated in the positive ion mode, and the capillary voltage was set at 4,000 V. A flow rate of heated dry nitrogen gas (heater temperature 300 °C) was maintained at 10 psig. In TOFMS, the fragmentor, skimmer, and Oct RFV voltage were set at 75 V, 50 V, and 125 V, respectively. Automatic recalibration of each acquired spectrum was performed using reference masses of reference standards. The methanol adduct ion ([2MeOH + H2O + H]+, m/z 83.0703) and reserpine ([M + H]+, m/z 609.2806) provided the lock mass for exact mass measurements. Exact mass data were acquired at a rate of 10 spectra/s over a 501,000 m/z range.
CE-TOFMS Conditions for Anionic Metabolite AnalysisA cationic polymer-coated SMILE (+) capillary (22) (Nacalai Tesque, Kyoto, Japan) was used as the separation capillary (23). A 50 mM ammonium acetate solution (pH 8.5) was used as electrolyte solution for CE separation. Sample solution (30 nl) was injected at 50 mbar for 30 s and 30 kV of voltage was applied. Ammonium acetate (5 mM) in 50% methanol-water (v/v) containing 20 µM PIPES and 1 µM reserpine was delivered as the sheath liquid at 10 µl/min. ESI-TOFMS was conducted in the negative ion mode; the capillary voltage was set at 3,500 V. For TOFMS, the fragmentor, skimmer, and Oct RFV voltage were set at 100 V, 50 V, and 200 V, respectively. Automatic recalibration of each acquired spectrum was performed using reference masses of standards, i.e. divalent PIPES ([M 2H]2, m/z 150.0230), monovalent PIPES ([M H], m/z 301.0534), and reserpine ([M H], m/z 607.2661). Other conditions were identical to those used in cationic metabolite analysis.
CE-Q-TOFMS Conditions for the Acquisition of MS/MS SpectraMost of the conditions were identical to those in cationic metabolite analysis using CE-TOFMS. Methanol-water (50% v/v) containing 1 µM reserpine was delivered as the sheath liquid at 5 µl/min. ESI-Q-TOFMS was conducted in the positive product ion scan mode; the ion spray voltage was set at 5,500V. Dry air (GS1) was maintained at 10 psi. The declustering potential 1 and 2, and the collision energy voltage were set at 60 V, 15 V, and 20 V, respectively. Recalibration was manually performed with reserpine ([M + H]+, m/z 609.2806) and its fragment ion ([M + H]+, m/z 195.0652).
Data Processing for the Generation of the Metabolome Differential DisplayRaw datasets were preprocessed by binning the data along the m/z axis to 0.02 m/z resolution, subtracting the baseline from each electropherogram by robust nonlinear fitting of the data to a 7th order polynomial and removing the noise from each electropherogram by leveling to 0 all signal intensity values that fell within 5x S.D. of the signal intensities from 1 to 4 min. The resulting data sets were then further binned to 1 m/z unit resolution along the m/z axis. A set of peaks was selected from each dataset using a modified Douglas-Peucker algorithm (24); alignment of datasets along the migration time axis was as described in the text. Annotation tables for both cation and anion modes were generated based on the results of the CE-TOFMS analysis of standard compounds. The annotation labels were aligned to the actual datasets in a similar fashion. Arithmetic operations were applied to whole datasets on a data point-by-data point basis to highlight differences of interest. Averaging the datasets within each group allowed visualization of absolute (difference between the corresponding intensities from the averaged datasets) and relative (absolute difference divided by the larger of the two corresponding intensities) differences. To generate the metabolome differential displays shown in Fig. 1 and supplemental Fig. S1, the product of two results was used so that differences significant in both absolute and relative terms were preferentially visualized. Overlaid electropherograms in the vicinity of the most significant differences from the results of interest were plotted in descending order of significance for visual confirmation. A Mathematica (Wolfram Research Inc.) package for differential analysis of metabolite profiles, a detailed description of which is beyond the scope of this manuscript, will be released separately.
| RESULTS AND DISCUSSION |
|---|
|
|
|---|
|
|
|
To facilitate the analysis and comparison of large and complex data sets produced by CE-MS analysis, visualization tools are desirable. Few available tools exist to do this, especially for CE-MS data where migration time variations between samples are significant. An important issue in the development of a differential displays tool is thus the normalization of the compound migration times. The function derived by Reijenga et al. (26) for electropherogram normalization in CE fit the shifts in migration times between corresponding peaks from different data sets. To align the peaks from two CE-MS data sets, the sum of dynamic programming (DP) scores, serving as a measure of the quality of the alignment, was calculated for all corresponding electropherograms. Partial scores (or gap penalty values) were assigned to the distance between two peaks of a subproblem and the Reijenga function parameters were optimized to achieve the lowest overall DP score (Fig. 4). The time scale of the sample data set was then rescaled to that of the reference and signal intensities were adjusted accordingly to compensate for the compression or expansion of the peaks, thereby conserving their original peak areas.
Differential Display of Liver Metabolites in Acetaminophen-treated MiceTo evaluate the power of our metabolite profiling and differential display methods to pin-point changes in the metabolome in an unbiased manner and identify biomarkers, we determined the changes in murine hepatic metabolite levels after AAP administration. To facilitate the assignment of specific metabolites to peaks, we first analyzed 569 metabolic standards listed in the KEGG LIGAND data base (27) by CE-TOFMS before analyzing tissue-derived samples. Global mass scanning over a 501,000 m/z range was applied in both cation and anion CE modes. Almost all compounds were well resolved and were annotated with numbers referring to the compound list (supplemental Fig. S1, A and B and supplemental Table S2). To study the effects of AAP on liver metabolism, we determined liver metabolite levels two hours (control, supplemental Fig. S1, C and D) after injection with either saline or AAP (point where liver damage is maximum, supplemental Fig. S1, E and F). Our metabolome differential data analysis tool automatically normalized the migration times of all peaks in the samples and matched these with the standard annotation table. This allowed to readily identify the corresponding peaks. A total of 132 metabolites were identified among 1,859 detected peaks (supplemental Table S3).
Among the several changes, differential display of liver metabolites between the controls and AAP treated (2 h) showed extensive depletion of GSH and its oxidized form (GSSG), detected as a divalent ion (Fig. 1). In paired Student's t tests, the level of 13 identifiable metabolites were significantly different (p < 0.01), and most were part of metabolic processes proximal to glutathione biosynthesis such as the transsulfuration pathway, taurine shunt, and remethylation cycles (supplemental Table S3). As seen when plotting results on the glutathione biosynthesis pathways (Fig. 5A), the level of most of these metabolites decreased at 2-h post-AAP treatment. These metabolite changes are likely linked to the GSH depletion by conjugation (oxidation) with NAPQI, and the associated depletion of intermediates for glutathione biosynthesis. On the other hand, the level of methionine, an essential amino acid located upstream in the cysteine synthesis pathway, more than doubled in AAP-treated mice. This alteration could be the result of the AAP-elicited decrease in GSH, which is a necessary cofactor for methionine adenosyltransferase (MAT) (28). Alternately, a possible inhibition of cystathionine
-synthase, the rate-limiting enzyme in the transsulfuration pathway might explain this finding. This can be suggested from the elevation of both methionine and serine levels without a concomitant increase in cystathionine levels at 26 h after AAP exposure (supplemental Fig. S3), although the detailed mechanism requires further examination.
|
Ophthalmate as Major Byproduct after AAP Treatment and Activation of Its BiosynthesisUsing tandem mass spectrometry with a CE-Q-TOFMS system, the precise MS/MS spectra of GSH (Fig. 6A) and the unknown cation (m/z 290.135, 16.5 min) (Fig. 6B) obtained by CE-Q-TOFMS analysis of liver samples were carefully compared. The fragmentation patterns of GSH and the unknown cation were similar, and the mass difference between the four predominant peaks was just around 17.96 Da (indicated by red dashed arrows in Fig. 6). This suggested that the SH (32.980 Da) group in GSH might be replaced by a CH3 (15.023 Da) group (32.98015.023 Da = 17.957 Da) in the unknown compound. To confirm the position of the substitution within the GSH tripeptide (
-Glu-Cys-Gly), we compared the MS/MS fragmentation pattern of both GSH and the unknown cation, the latter based on the structure of ophthalmate (see supplemental Fig. S2). We compared the m/z values of the predominant ions in the resulting compound (blue) with those from the experimentally determined MS/MS fragmentation ions (black) (Fig. 6, A and B) to assess their consistency. The results are consistent with the replacement of the SH group of the cysteine residue of GSH, with a CH3 group to form 2-aminobutyrate (2AB) found in ophthalmate (
-Glu-2AB-Gly). To confirm this, we obtained ophthalmate from commercial sources (Bachem, Bubendorf, Switzerland) and analyzed mouse liver samples spiked with the ophthalmate standard using CE-TOFMS and CE-Q-TOFMS. There was a perfect correspondence with respect to both migration time and MS/MS spectrum between ophthalmate and the unknown compound. This result thus leads us to conclude that the unidentified compound is indeed ophthalmate.
|
|
-glutamylcysteine synthetase (GCS) and glutathione synthetase (GS) (Fig. 5B) (29). Further support for this biosynthetic route comes from previous reports that GCS catalyzes the ligation of glutamine and 2AB (30) and that GS can synthesize ophthalmate from
-Glu-2AB (31). In agreement with this, the level of
-Glu-2AB (m/z 233.113, 15.5 min), a substrate of GS, increased in the liver of AAP-treated mice (Fig. 5B). This finding suggests that GCS, the enzyme that is feedback-inhibited by GSH, and is a rate-limiting step in GSH synthesis (32, 33), was activated during GSH depletion and/or that GS may display lower affinity for
-Glu-2AB compared with
-Glu-Cys.
We further investigated ophthalmate metabolism by lowering the hepatic content of GSH by pretreating mice with BSO or DEM (Fig. 7A). BSO is known to result in significant GCS inhibition (34) and thus cause a reduction of downstream products. On the other hand, DEM leads to the oxidation of the thiol group in GSH (35) and the induction of lipid peroxidation and necrotic cell death (36). Liver and serum samples from control and BSO and DEM treated mice were analyzed in more detail by CE-TOFMS to identify specific changes in the levels of GSH/GSSG and ophthalmate and its precursors. As expected, the levels of GSH as well as
-Glu-2AB and ophthalmate were very low both in the liver and serum of GCS-inhibited mice (Fig. 7, A and B). On the other hand, a marked increase in
-Glu-2AB and ophthalmate levels was seen in DEM-treated mice. We can thus conclude that ophthalmate was synthesized using the same pathway as GSH. The results also suggest that GSH depletion by oxidative compounds such as AAP and DEM resulted in GCS activation, which in turn induced ophthalmate synthesis. However, unlike GSH, ophthalmate was not further metabolized and thus accumulated (Fig. 8).
Ophthalmate as an Oxystress Biomarker Indicating GSH DepletionThe above results in BSO- and DEM-treated mice indicate that a significant portion of these liver metabolites were effluxed to the circulation by the action of ATP-binding cassette (ABC) transporters such as multidrug resistance proteins (37) (Fig. 8). This close correspondence between hepatic and serum levels suggests the possibility that some of the detected compounds could act as biomarkers of GSH level alteration. In addition, the fact that both AAP and DEM result in GSH depletion and an increase in ophthalmate levels suggests that this response is not specific to AAP treatment but possibility reflects a more general cellular response to oxidative stress.
|
|
|
-Glu-2AB, and ophthalmate, together with several metabolic intermediates of glutathione biosynthesis, in both liver and serum of mice at 1, 2, 4, 6, 12, and 24 h after AAP treatment. Most of the monitored metabolites that were detected in liver were also present in serum, but there was no significant difference in their concentration between control and AAP-treated mice (supplemental Fig. S3). On the other hand, significant increases in liver and serum ophthalmate levels were observed with a concurrent hepatic GSH depletion in AAP treated mice (Fig. 9). Despite the high GSH levels in liver, GSH was not detected in serum suggesting that GSH is either not effluxed from liver, or that it is rapidly metabolized or oxidized in serum (40).
Serum ophthalmate increased
5-fold (p = 0.0001) 1 h after AAP treatment, a point at which the liver GSH level dropped dramatically (Fig. 9). The change in hepatic ophthalmate was inversely proportional to the hepatic GSH level. These results thus identify serum ophthalmate level as a potential hepatic GSH biomarker that can reveal liver GSH abnormalities triggered by oxidative stress (Fig. 8).
Whereas hepatic
-Glu-2AB increased 1 h after AAP treatment, serum
-Glu-2AB did not increase significantly (Fig. 9), indicating that hepatic
-Glu-2AB may not readily be exported to the circulation by ABC transporters or that, similarly to GSH, it is rapidly metabolized.
Overall, the time frame of changes in metabolites that we observed agrees very well with a previous report (9) showing a rapid (12 h) induction of multiple hepatic genes and their products following AAP administration in the mouse.
The physiological role of ophthalmate is not clearly established. In this work, it appears to be produced as a byproduct of the GS reaction when GSH, and consequently, cysteine levels are depleted. However, it has been previously suggested that ophthalmate may act as an anticoenzyme (41) that can inhibit enzymes that use GSH as a co-factor. GSH is normally exported in large proportion by the liver into bile and circulation to be used in peripheral tissues (42). Interestingly, ophthalmate was shown to competitively inhibit and trans-stimulate GSH uptake in liver canalicular membranes (43). This may help minimize GSH efflux from liver cells during oxidative stress.
GSH is conjugated to many types of exogenous metabolites such as AAP to increase their solubility and facilitate their excretion. GSH also enhances multidrug resistance protein 1 (MRP1)-mediated transport of the glucoronide conjugate of the tobacco carcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanol (NNAL) and ophthalmate can substitute for this activity (44, 45). Ophthalmate can thus act as a GSH analog for functions that do not require the presence of the thiol group such as activation of transport of exogenous metabolite glucoronides by MRP1. It is thus tempting to speculate that ophthalmate might similarly stimulate the transport of AAP-glucoronide by MRP1 and thus facilitate its elimination. This would provide functional meaning for its synthesis during oxidative stress rather than simply being a consequence or byproduct of cysteine/GSH depletion and the associated activation of GCS.
Because of differences in the analytical methods, our results seem complementary to previous work by Coen et al. (46, 47) who profiled changes in liver metabolites following AAP treatment using NMR. Whereas these authors examined mostly neutral and lipid metabolites, our work using CE-MS and focusing on polar metabolites demonstrates the consequences of GSH depletion and the attempts of the liver to increase its biosynthesis. On the other hand, Coen et al. (46, 47) reported an activation of glycolysis while lipid metabolism was decreased and this may reflect the energy and precursor requirements for GSH and related metabolites biosynthesis as well as mitochondrial damage, respectively. Both studies concur regarding increases in the level of several amino acids, which can be measured by both NMR and CE-TOFMS levels.
We presented a sensitive and high resolution metabolome differential display approach, based on a CE-TOFMS system and data analysis software, that facilitates the global quantification and identification of charged metabolites as well as the visualization of specific changes in complex biological matrices. This approach can be applied to the discovery of biomarkers as we demonstrated by the identification of serum ophthalmate as a biomarker for hepatic GSH depletion following oxidative stress. Ophthalmate measurement can potentially provide valuable information about the hepatic cellular redox state, thereby facilitating the earlier prediction of oxidative damage. This biomarker may thus help to evaluate therapeutic risks, efficacy, and drug actions during the drug development process and potentially facilitate the early detection of several diseases (such as Alzheimers, Parkinsons, and liver disease, AIDS, cancer, cardiac infarction, and diabetes) (48), where oxidative stress is known to play an important role.
| FOOTNOTES |
|---|
The on-line version of this article (available at http://www.jbc.org) contains supplemental data. ![]()
1 These authors contributed equally to this work. ![]()
2 To whom correspondence may be addressed: Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan. Tel.: 81-235-29-0528; Fax: 81-0235-29-0530; E-mail: soga{at}sfc.keio.ac.jp. 3 To whom correspondence may be addressed: Dept. of Biochemistry and Integrative Medical Biology, School of Medicine, Keio University, Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan. E-mail: msuem{at}sc.itc.keio.ac.jp.
4 The abbreviations used are: AAP, acetaminophen; CE-TOFMS, capillary electrophoresis time-of-flight mass spectrometry; 2AB, 2-aminobutyrate; GCS,
-glutamylcysteine synthetase; GS, glutathione synthetase; ip, intraperitoneal; DEM, diethylmaleate; BSO, buthionine sulfoximine; MES, 2-morpholinoethanesulfonate; Oct RFV, octapole radio frequency voltage; ESI-Q-TOFMS, electrospray ionization quadrupole time-of-flight mass spectrometry; PIPES, piperazine-1,4-bis(2-ethansulfonate). ![]()
| ACKNOWLEDGMENTS |
|---|
| REFERENCES |
|---|
|
|
|---|
This article has been cited by other articles:
![]() |
C. Chen, K. W. Krausz, J. R. Idle, and F. J. Gonzalez Identification of Novel Toxicity-associated Metabolites by Metabolomics and Mass Isotopomer Analysis of Acetaminophen Metabolism in Wild-type and Cyp2e1-null Mice J. Biol. Chem., February 22, 2008; 283(8): 4543 - 4559. [Abstract] [Full Text] [PDF] |
||||
![]() |
M. Morohashi, Y. Ohashi, S. Tani, K. Ishii, M. Itaya, H. Nanamiya, F. Kawamura, M. Tomita, and T. Soga Model-based Definition of Population Heterogeneity and Its Effects on Metabolism in Sporulating Bacillus subtilis J. Biochem., August 1, 2007; 142(2): 183 - 191. [Abstract] [Full Text] [PDF] |
||||
![]() |
N. Ishii, K. Nakahigashi, T. Baba, M. Robert, T. Soga, A. Kanai, T. Hirasawa, M. Naba, K. Hirai, A. Hoque, et al. Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations Science, April 27, 2007; 316(5824): 593 - 597. [Abstract] [Full Text] [PDF] |
||||
![]() |
A. Kinoshita, K. Tsukada, T. Soga, T. Hishiki, Y. Ueno, Y. Nakayama, M. Tomita, and M. Suematsu Roles of Hemoglobin Allostery in Hypoxia-induced Metabolic Alterations in Erythrocytes: SIMULATION AND ITS VERIFICATION BY METABOLOME ANALYSIS J. Biol. Chem., April 6, 2007; 282(14): 10731 - 10741. [Abstract] [Full Text] [PDF] |
||||
| |||||||||||||||||||||||||||||||||||||||||||||||||