Early regulation of brain aromatase (cyp19a1b) by estrogen receptors during zebrafish development

Early expression of estrogen receptors (esr) and their role in regulating early expression of cyp19a1b encoding brain aromatase were examined in the brain of zebrafish. Using in toto hybridization and quantitative reverse transcriptase-polymerase chain reaction (RT-PCR), a significant increase in the expression of esr1, esr2a, and esr2b was observed between 24 and 48 hours postfertilization (hpf). In toto hybridization demonstrated that esr2a and esr2b, but not esr1, are found in the hypothalamus. Using real-time RT-PCR, an increase in cyp19a1b mRNAs occurs between 24 and 48 hpf, indicating that expression of cyp19a1b is temporally correlated with that of esr. This increase is blocked by the pure anti-estrogen ICI182,780. Furthermore, E2 treatment of cyp19a1b-GFP (green fluorescent protein) transgenic embryos results in appearance of GFP expression in the brain as early as 25 hpf. These results indicate that basal expression of cyp19a1b expression in the brain of developing zebrafish most likely relies upon expression of esr that are fully functional before 25 hpf.

Combining tissue transcriptomics and urine metabolomics for breast cancer biomarker identification

MOTIVATION

For the early detection of cancer, highly sensitive and specific biomarkers are needed. Particularly, biomarkers in bio-fluids are relatively more useful because those can be used for non-biopsy tests. Although the altered metabolic activities of cancer cells have been observed in many studies, little is known about metabolic biomarkers for cancer screening. In this study, a systematic method is proposed for identifying metabolic biomarkers in urine samples by selecting candidate biomarkers from altered genome-wide gene expression signatures of cancer cells. Biomarkers identified by the present study have increased coherence and robustness because the significances of biomarkers are validated in both gene expression profiles and metabolic profiles.

RESULTS

The proposed method was applied to the gene expression profiles and urine samples of 50 breast cancer patients and 50 normal persons. Nine altered metabolic pathways were identified from the breast cancer gene expression signatures. Among these altered metabolic pathways, four metabolic biomarkers (Homovanillate, 4-hydroxyphenylacetate, 5-hydroxyindoleacetate and urea) were identified to be different in cancer and normal subjects (p <0.05). In the case of the predictive performance, the identified biomarkers achieved area under the ROC curve values of 0.75, 0.79 and 0.79, according to a linear discriminate analysis, a random forest classifier and on a support vector machine, respectively. Finally, biomarkers which showed consistent significance in pathways' gene expression as well as urine samples were identified.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Heat-map visualization of gas chromatography-mass spectrometry based quantitative signatures on steroid metabolism

Abnormalities in steroid hormones are responsible for the development and prevention of endocrine diseases. Due to their biochemical roles in endocrine system, the quantitative evaluation of steroid hormones is needed to elucidate altered expression of steroids. Gas chromatographic-mass spectrometric (GC-MS) profiling of 70 urinary steroids, containing 22 androgens, 18 estrogens, 15 corticoids, 13 progestins, and 2 sterols, were validated and its quantitative data were visualized using hierarchically clustered heat maps to allow "steroid signatures". The devised method provided a good linearity (r(2) > 0.994) with the exception of cholesterol (r(2) = 0.983). Precisions (% CV) and accuracies (% bias) ranged from 0.9% to 11.2% and from 92% to 119%, respectively, for most steroids tested. To evaluate metabolic changes, this method was applied to urine samples obtained from 59 patients with benign prostatic hyperplasia (BPH) versus 41 healthy male subjects. Altered concentrations of urinary steroids found and heat maps produced during this 70-compound study showed also differences between the ratios of steroid precursors and their metabolites (representing enzyme activity). Heat maps showed that oxidoreductases clustered (5alpha-reductase, 3alpha-HSD, 3beta-HSD, and 17beta-HSD, except for 20alpha-HSD). These results support that data transformation is valid, since 5alpha-reductase is a marker of BPH and 17beta-HSD is positively expressed in prostate cells. Multitargeted profiling analysis of steroids generated quantitative results that help to explain correlations between enzyme activities. The data transformation and visualization described may to be found in the integration with the mining biomarkers of hormone-dependent diseases.

Metabolomics study with gas chromatography-mass spectrometry for predicting valproic acid-induced hepatotoxicity and discovery of novel biomarkers in rat urine

Three different doses of valproic acid (20, 100, and 500 mg/kg/d) are administered orally to Sprague-Dawley rats for 5 days, and the feasibility of metabolomics with gas chromatography-mass spectrometry as a predictor of the hepatotoxicity of valproic acid is evaluated. Body weight is found to decrease with the 100-mg/kg/d dose and significantly decrease with the 500-mg/kg/d dose. Mean excreted urine volume is lowest in the 500-mg/kg/d group among all groups. The plasma level of alpha-glutathione-S-transferase, a sensitive and earlier biomarker for hepatotoxicity, increases significantly with administration of 100 and 500 mg/kg/d; however, there is not a significant difference in alpha-glutathione-S-transferase plasma levels between the control and 20-mg/kg/d groups. Clusters in partial least squares discriminant analysis score plots show similar patterns, with changes in physiological conditions and plasma levels of alpha-glutathione-S-transferase; the cluster for the control and 20-mg/kg/d groups does not clearly separate, but the clusters are separate for 100- and 500-mg/kg/d groups. A biomarker of hepatotoxicity, 8-hydroxy-2'-deoxyguanosine and octanoylcarnitine, is identified from nontargeted and targeted metabolic profiling. These results validate that metabolic profiling using gas chromatography-mass spectrometry could be a useful tool for finding novel biomarkers. Thus, a nontargeted metabolic profiling method is established to evaluate the hepatotoxicity of valproic acid and demonstrates proof-of-concept that metabolomic approach with gas chromatography-mass spectrometry has great potential for predicting valproic acid-induced hepatotoxicity and discovering novel biomarkers.

Mass spectrometric profiling of saturated fatty acid esters of steroids separated by high-temperature gas chromatography

An efficient analytical method for simultaneous determination of 12 SFEs in serum is described. The method involves solid-phase extraction to isolate of SFEs from interfering species, especially cholesteryl esters, conversion to trimethylsilyl (TMS) ether derivatives for the direct analysis by gas chromatography-mass spectrometry (GC-MS) using a high temperature MXT-1 (Silcosteel-treated stainless steel) capillary column. All SFEs as their TMS derivatives were well separated with excellent peak shapes within 12 min. Overall recoveries ranged from 88% to 119%, with a detection limits for SFEs ranged from 2 to 30 microg L(-1). The linearity as correlation coefficient was higher than 0.99 except for pregnenolone-3-arachidate (r(2)=0.98) in the concentration range of 5-3000 microg L(-1). Ten serum samples obtained from volunteers were also analyzed and quantitatively determined of DHEA-3-palmitate and pregnenolone-3-stearate in 1.8-1195.8 microg L(-1) concentration. The devised high temperature GC-MS method could be useful for identification of SFEs in biological specimens including serum.

Quantitative metabolic profiling of 21 endogenous corticosteroids in urine by liquid chromatography-triple quadrupole-mass spectrometry

Since corticosteroid metabolism may be affected by disease states, the accurate and precise measurement of endogenous corticosteroids in urine is necessary to understand their biochemical roles. An efficient quantitative profiling of 21 endogenous corticosteroids in urine has been validated by liquid chromatography-tandem mass spectrometry (LC-MS/MS). After enzymatic hydrolysis with beta-glucuronidase, samples were purified using a solid-phase extraction cartridge and then separated through a sub-2 microm particle C18 column (2.1 mm x 50 mm, 1.9 microm) and quantified within 12.1 min using a triple quadrupole MS with electrospray ionization in positive ion mode. All corticosteroids resulted in the base-line separation, which is even achieved for stereo-isomers, such as alpha-/beta-cortol, alpha-/beta-cortolone, and allo-tetrahydrocortisol/tetrahydrocortisol. Overall recoveries ranged from 85% to 106% with limit of quantification ranged from 0.5 to 2.0 ng mL(-1) for the corticosteroids examined. The precision (% CV) and accuracy (% bias) of the assay were 1.7-7.8% and 95.1-105.4%, respectively, in 0.5-200 ng mL(-1) calibration ranges (r(2)>0.9903), for quality-control samples containing 21 endogenous corticosteroids at three different urinary concentrations. Clinical application included quantitative analysis from patients with both prostate cancer and benign prostatic hyperplasia with altered cortisol concentrations. The described LC-MS/MS method eliminates interference from other urine components, has excellent chromatographic resolution achieved by a small particle LC column with a sufficient sensitivity to allow the profiling of both gluco- and mineralo-corticosteroids at a time.

Mass spectrometry based metabolomic approaches in urinary biomarker study of women's cancers

BACKGROUND

The metabolomic approaches for mining biomarkers of women's cancers based on gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry combined with partial least squares-discriminant analysis are described.

METHODS

To identify urinary potential biomarkers, the qualitative and quantitative analyses were introduced with 10 breast, 9 ovarian and 12 cervical cancer patients as well as 22 normal controls, which were considered with their ages and menopausal state.

RESULTS

For comprehensive metabolomic approaches, the non-targeted qualitative profiling was first achieved to get metabolic patterns of collected samples and the targeted quantitative analysis focused on hormonal metabolism was also conducted. Two known biomarkers, i.e., 5-hydroxymethyl-2-deoxyuridine and 8-hydroxy-2-deoxyguanosine, in breast cancer were also confirmed using the present methods. In addition, 3 potential biomarkers for ovarian cancer i.e. 1-methyladenosine, 3-methyluridine, and 4-androstene-3,17-dione, which were categorized in significantly increased level using one way of variance analysis (p<0.05), were identified as quantitatively targeted metabolites with pattern analysis. The cancer markers identified in this study are highly related to metabolites which are responsible for oxidative DNA damage and DNA methylation process.

CONCLUSION

The present metabolomic approaches are not only useful for diagnostic tools and patient stratification, but may be mapped on metabolic network to reflect disease states.

Inclusion complex-based solid-phase extraction of steroidal compounds with entrapped beta-cyclodextrin polymer

Although the hydrophobic interaction-based solid-phase extraction (SPE) has been widely used, the extraction yields of steroids including androgens, estrogens, and corticoids were slightly different along with the physical and chemical properties of each molecule. A new SPE technique based on the formation of an inclusion complex with beta-cyclodextrin (betaCD) has been achieved for comprehensive sample purification in mass spectrometric analysis of 45 endogenous or synthetic androgens, 11 endogenous estrogens, and 21 corticoids. A copolymer of betaCD with epichlorohydrin was prepared by a cross-linking reaction followed by entrapment with 0.3M CaCl(2) to yield an improved SPE sorbent and the hydrolyzed urine samples were applied for purification. Steroidal compounds tested on the entrapped betaCD polymer were extracted with tetrahydrofuran and the overall recoveries ranged from 82% to 112% for 77 steroids in urine. Especially, the hydroxylated estrogens showed an excellent binding capacity (96-116% recovery) to betaCD through hydrogen bonding between their phenolic hydroxyl and exterior hydroxyl groups. A comparison between SPE methods with betaCD and Oasis HLB as a conventional cartridge showed that the extraction efficiency of polar steroids was significantly increased in the betaCD experiment, which has no connection with different polarity of steroid molecules. Due to its multi-functional mechanism derived from molecular inclusion and chemical interactions, this new SPE sorbent resulted in better selectivity and extraction efficiency than that obtained using the conventionally used hydrophobicity-based SPE method.

In vivo and in vitro ethanol exposure in prenatal rat brain: GABA(B) receptor modulation on dopamine D(1) receptor and protein kinase A

We have investigated the effects of prenatal ethanol exposure on GABA(B) receptors (GABA(B)Rs), protein kinase A (PKA), and DA D(1) receptor (DAD(1)R) expressions. GABA(B1)R and GABA(B2)R showed different age-dependent expressions in in vivo fetal rat forebrain from gestational days (GD) 15.5 to 21.5 upon 10% ethanol treatment to mother, with and without baclofen at a dose of 10 mg/kg body weight/day. The protein level changes could not be attributed to changes in the level of transcription since GABA(B)R mRNA presented different expression patterns upon in vivo ethanol treatment. Using in vitro cultivated cortical neurons from GD 17.5 fetuses, we also explored the modulatory effects of ethanol on PKA and DAD(1)R through GABA(B)Rs, under 50 microM baclofen and 100 microM phaclofen administrations, with or without 100 mM of ethanol treatment in the culture media. The results showed that 20 min ethanol treatment without baclofen or phaclofen had increasing effects on both the GABA(B)Rs. Further, baclofen and phaclofen administration significantly affected PKA and GABA(B)R levels upon 20 min and 1 h ethanol treatment. In contrast, DAD(1)R showed increasing effects upon ethanol treatment, which was modulated by GABA(B)R's agonist baclofen and antagonist phaclofen. Therefore the present study suggested that the GABA(B)R activity could modulate ethanol's cellular effects, which possibly including PKA and DAD(1)R activities, and may be an underlying cause of ethanol's effects.

Quantitative determination of progesterones and corticosteroids in human urine using gas chromatography/mass spectrometry: application to pelvic organ prolapse patients

A quantitative analytical method using gas chromatography/mass spectrometry (GC/MS) to determine urinary concentrations of eight progesterones and corticosteroids has been developed. After enzymatic hydrolysis with beta-glucouronidase/arylsulfatase, urine samples were extracted by simple one-step solid-phase extraction. Obtained extracts were derivatized with a mixture of N-methyl-N-(trimethylsilyl)trifluoroacetamide/ammonium iodide/dithiothreitol and determined by GC/MS in selected ion monitoring mode to increase the sensitivity. d(4)-Cortisol and d(9)-progesterone were used as internal standards for two different steroid groups. The linear correlation coefficient was in the range of 0.9913 to 0.9998 and recoveries were over 80% for all compounds. Precision and accuracy were in the range of 0.9-18.1 and 84.1-118.7%, respectively. The limit of quantitation (LOQ) was 10 ng/mL for 11-deoxycorticosterone and 21-deoxycortisol and 5 ng/mL for all other analytes. The developed method was successfully applied on pelvic organ prolapsed patients (n = 10, age: 67.9 +/- 4.9) and post-menopausal (n = 10, age: 63.6 +/- 5.5) control women. Urinary levels of most progesterones and corticosteroids except 11-deoxycorticosterone decreased but only that of 17 alpha-hydroxyprogesterone significantly decreased in patients compared with the control groups. Thus, it is concluded that progesterones could be a factor in the pathogenesis of pelvic organ prolapse, and, among them, 17 alpha-hydroxyprogesterone could be a biomarker for pelvic organ prolapse.

Analysis of polyamines as carbamoyl derivatives in urine and serum by liquid chromatography-tandem mass spectrometry

A quantitative analysis of polyamines in urine and serum by liquid chromatography-tandem mass spectrometry (LC-MS/MS) is described. The polyamines were carbamylated with isobutyl chloroformate, extracted with diethyl ether under pH 9.0, and analyzed by LC-MS/MS with single reaction monitoring mode. The limit of quantification was 1 ng/mL based on a signal-to-noise ratio>3, and the correlation coefficient (r2) for the calibration curves was >0.99 for both urine and serum samples. The present method was applied to urine and serum samples from 30 breast cancer patients and 30 normal female controls. There was no significant difference in the urinary polyamine levels between breast cancer patients and controls. However, 1,3-diaminopropane, putrescine, spermine and N-acetylspermidine levels in serum increased in breast cancer patients. These four serum polyamines may be a good index to study both production and metabolism of polyamines, and a useful tool in assessment of the polyamine status of breast cancer patients.

Quantitative analysis of 17 amino acids in the connective tissue of patients with pelvic organ prolapse using capillary electrophoresis-tandem mass spectrometry

The simultaneous determination of 17 amino acids in connective tissue using capillary electrophoresis is described in this study. Separation was carried out on a fused silica capillary column (80 cm x 50 mm i.d.) with 1M formic acid as the running electrolyte. The detection was conducted on a mass spectrometer by selective reaction monitoring (SRM) mode via an electrospray ionization source. Tissue samples were prepared by reduction and acid hydrolysis to extract amino acids; over 84.3% recovery was seen for all compounds. The method allowed for sensitive, reproducible, and reliable quantification, and all 17 amino acids were separated using this method. Good linearity over the investigated concentration ranges was observed, with values of R higher than 0.993 for all the analytes. Precision and accuracy examined at three concentration levels ranged from 0.2% to 19.5% and 84.1% to 120.0%, respectively. Matrix effects were also tested and ranged from -9.1% to 15.4%. The validated method was applied to the quantitation of 17 amino acids in pelvic connective tissue of pelvic organ prolapsed patients. Methionine, glutamine, and histidine were significantly higher in the experimental patients compared to the controls. This suggests that changes in the amino acid concentrations within the connective tissue could be a factor in the genesis of pelvic organ prolapse. Therefore, this method is potentially applicable for amino acid analysis in tissue, providing a more complete understanding of pelvic organ prolapse.

Ethanol's effect on intracellular signal pathways in prenatal rat cortical neurons is GABAB1 dependent

To confirm the modulation role of GABA(B) on ethanol' effects, we studied the effects of ethanol on the neuronal intracellular signals, protein kinase A (PKA) and cAMP-response element binding protein (CREB), by using a system where GABA(B1) receptors were specifically knocked down in the in vitro cultivated cortical neurons. The results showed that the PKA alpha subunit was increased with ethanol treatment, and could be further increased by administering baclofen and phaclofen. By contrast, baclofen and/or phaclofen could decrease ethanol's up-regulation effects on PKA alpha subunit expression in primary cultured cortical neurons in which the GABA(B1) receptor was specifically knocked down using GABA(B1) receptor RNA interference. Furthermore, these effects could lead to changes of phospho (p)-CREB expression, which showed the same expression pattern as PKA. Finally, we observed changes of GABA(B1), PKA, and p-CREB distribution within the same neuronal cells. These results showed that the GABA(B) receptors are critical to ethanol's cellular effects, which occur via modulating the PKA and CREB transcription pathway, and may be an underlying cause of ethanol's effects.

Caspase-7 mediated cleavage of proteasome subunits during apoptosis

Caspase-3 and caspase-7 are structurally closely related and demonstrate overlapping substrate specificity. However, during apoptosis, they are differentially regulated and show distinct subcellular localizations, implying the presence of specific substrates. In this study, to identify caspase-7 substrates, we treated the lysates derived from caspase-3-deficient MCF-7 cells with purified caspase-7 and analyzed decreased proteins by 2-DE. Intriguingly, several proteasome subunits such as alpha2, alpha6, and Rpt1 are degraded by caspase-7 during apoptosis in vitro and in vivo. Caspase-7 mediated cleavage of proteasome subunits results in the reduction of proteasome activity and thereby increases the accumulation of ubiquitinated proteins in cells. These findings suggest that caspase-7 facilitates the execution of apoptosis through down-regulation of the 26S proteasome, which regulates the turnover of proteins involved in the apoptotic process.

Quantitative analysis of phosphatidylcholine in rat liver tissue by nanoflow liquid chromatography/tandem mass spectrometry

A quantitative method was developed for the determination of phosphatidylcholine (PC) species concentration using nanoflow LC-ESI-MS/MS. In this study, a calibration method is developed to determine the effect of PC carbon chain length on MS peak intensity. Using the multiple standard addition method, a relationship between the peak intensities of different PC species from nanoflow LC-MS and carbon chain length is established first using different injection amounts of PC standards. From this relationship, a calibration curve for each carbon chain length can be obtained for the concentration calculation. It was found that the MS peak area of PC species analyzed by nanoflow LC-MS linearly decreased with increased acyl carbon numbers, and that the effect of the degree of acyl chain unsaturation on MS peak intensity was minimized when the injection amount was maintained at less than 1 pmol. The method was applied for the quantitative calculation of 34 PC species from rat liver, which were identified from data-dependent MS/MS analysis during nanoflow LC separation.