Exploring urinary modified nucleosides as biomarkers for diabetic retinopathy: Development and validation of a ultra performance liquid chromatography-tandem mass spectrometry method

The dynamic modification of RNA plays a crucial role in biological regulation and is strongly linked to human disease development and progression. Notably, modified nucleosides in urine have shown promising potential as early diagnostic biomarkers for various conditions. In this study, we developed and validated a rapid, sensitive, and accurate UPLC-MS/MS method for quantifying eight types of modified nucleosides (N1-methyladenosine (m1A), N6-methyladenosine (m6A), 5-methyluridine (m5U), 5-taurinomethyl-2-thiouridine (τm5s2U), 5-methylcytidine (m5C), 2'-O-methylcytidine (Cm), N1-methylguanosine (m1G), and N7-methylguanosine (m7G) in human urine. Using the method, we measured the urinary concentrations of m1A, m6A, m5U, τm5s2U, m5C, Cm, m1G, and m7G in a total of 21 control individuals and 23 patients diagnosed with diabetic retinopathy (DR). Cm levels showed promise as a diagnostic marker for diabetic retinopathy (DR), with a significant value (P < 0.01) and an AUC of 0.735. Other modified nucleosides also exhibited significant differences within specific subpopulations. As non-proliferative diabetic retinopathy (NPDR) signifies the latent early stage of diabetic retinopathy, we developed a multivariate linear model that integrates patients' sex, age, height, and urinary concentration of modified nucleosides which aims to predict and differentiate between healthy individuals, NPDR patients, and proliferative diabetic retinopathy (PDR) patients. Encouragingly, the model achieved satisfactory accuracy rates: healthy (81%), NPDR (75%), and PDR (80%). Our findings provide valuable insights into the development of an early, cost-effective, and noninvasive diagnostic approach for diabetic retinopathy.

Simultaneous Quantification of Nucleosides and Nucleotides from Biological Samples

We report a reverse phase chromatography mass spectrometry (LC-MS) method for simultaneous quantification of nucleosides and nucleotides from biological samples, where compound identification was achieved by a tier-wise approach and compound quantification was achieved via external calibration. A total of 65 authentic standards of nucleosides and nucleotides were used for the platform development. The limit of detection (LOD) of those compounds ranged from 0.05 nmol/L to 1.25 μmol/L, and their limit of quantification (LOQ) ranged from 0.10 nmol/L to 2.50 μmol/L. Using the developed method, nucleosides and nucleotides from human plasma, human urine, and rat liver were quantified. Seventy-nine nucleosides and nucleotides were identified from human urine and 28 of them were quantified with concentrations of 13.0 nmol/L-151 μmol/L. Fifty-five nucleosides and nucleotides were identified from human plasma and 22 of them were quantified with concentrations of 1.21 nmol/L-8.54 μmol/L. Fifty-one nucleosides and nucleotides were identified from rat liver and 23 were quantified with concentrations of 1.03 nmol/L-31.7 μmol/L. These results demonstrate that the developed method can be used to investigate the concentration change of nucleosides and nucleotides in biological samples for the purposes of biomarker discovery or elucidation of disease mechanisms.

Evaluation of bisphenol A exposure induced oxidative RNA damage by liquid chromatography-mass spectrometry

Highlighted evidence suggests the possible implication of bisphenol A (BPA) exposure on a variety of biological functions, such as DNA damage. Similar to DNA, exposed to BPA may also have potential risks to RNA damage due to its induction of reactive oxygen species. However, there are no related research reports about such health risks of BPA. Therefore, this work tried to investigate the BPA exposure induced oxidative RNA damage by detecting urinary nucleosides, the end-products of RNA metabolism. An ultra-high performance liquid chromatography-Orbitrap mass spectrometry method was applied to selectively and sensitively determine urinary nucleosides. As a result, 66 nucleosides were identified and the effects of BPA exposure on these nucleosides in rat urine samples were evaluated. The nucleosides showed different changing tendency along with different exposure dose of BPA. The strongest effect was observed in high does-exposure rats, indicating dose-response relationship between BPA-treatment and urinary nucleosides. Significant change of some nucleosides, including 8-oxoguanosine, was observed in the high-dose exposure group, suggesting obvious RNA damage to rats. To the best of our knowledge, it is the first study about the RNA damage induced by BPA exposure. The results provided a new perspective on the toxic effects of BPA exposure.

Modified nucleosides as biomarkers for early cancer diagnose in exposed populations

There is increasing worldwide interest in developing of markers for tumor diagnosis and identification of individuals who are at high cancer risk. Cancer, like other diseases accompanied by metabolic disorders, causes characteristic effects on cell turnover rate, activity of modifying enzymes, and RNA/DNA modifications. This results in an increased excretion of modified nucleosides in cancer patients. Therefore, for many years modified nucleosides have been suggested as tumor markers. The aim of the study was to elucidate further the usefulness of urinary nucleosides as possible markers at early detection of cancer in persons which are exposed against tumor promoting influences during their working life. Uranium miners are exposed to many kinds of pollutants that can cause health damage even lead to carcinogenesis. We analyzed modified nucleosides in urine samples from 92 miners who are at high risk for lung cancer to assess the levels of nucleosides by a multilayer perceptron (MLP) classifier - a neural network model. Eighteen nucleosides/metabolites were detected with reversed-phase high-pressure liquid chromatography (RP-HPLC). A valid set of urinary metabolites were selected and multivariate statistical technique of multilayer perceptron neural network were applied. In a previous study, MLP shows a sensitivity and specificity of 97 and 85%, respectively. MLP classification including the most relevant markers/nucleosides clearly demonstrates the elevation of RNA metabolism in miners, which is associated with possible malignant disease. We found that there were 30 subjects with early health disorders among 92 uranium workers based on MLP technique using modified nucleosides. The combination of RP-HPLC analysis of modified nucleosides and subsequent MLP analyses represents a promising tool for the development of a non-invasive prediction system and may assist in developing management and surveillance procedures.

Urinary modified nucleosides as novel biomarkers for diagnosis and prognostic monitoring of urothelial bladder cancer

AIMS AND BACKGROUND

To ascertain the value of the detection of urinary modified nucleosides in the early diagnosis and prognostic monitoring of urothelial bladder cancer.

METHODS

One hundred seventeen patients with urothelial bladder carcinoma and 66 healthy volunteers were included in the study. High-performance liquid chromatography/electrospray ionization quadrupole time-of-flight mass spectrometry (HPLC/ESI-Q-TOF-MS) was used to measure the levels of urinary modified nucleosides in the bladder cancer and control groups. Postoperative monitoring was done every 3 months in patients with noninvasive carcinoma; 85 patients attended the 1-year follow-up visit.

RESULTS

The levels of m1A, ac4C, O6-MeG and 1-MeI were significantly higher in cases than controls (P < 0.05). The highest sensitivity (92.45%) and specificity (87.50%) were obtained when 1-MeI detection was combined with m1A detection. The m1A and 1-MeI levels 3 months after operation in both patient groups were significantly lower than the preoperative levels (P < 0.01). The no-recurrence group subsequently maintained low levels, but in the recurrence group the levels rose again almost to preoperative values. At 6, 9 and 12 months after operation, the m1A and 1-MeI levels of the recurrence group were higher than those of the no-recurrence group and the control group (P < 0.01).

CONCLUSIONS

Urinary modified nucleosides might become novel tumor markers that will facilitate the clinical management and will be helpful in the diagnosis and follow-up of urothelial bladder cancer. m1A and 1-MeI appear to be most promising for clinical use and be worthy of further study in the near future.

Analysis of urinary methylated nucleosides of patients with coronary artery disease by high-performance liquid chromatography/electrospray ionization tandem mass spectrometry

RATIONALE

In recent years, methylated nucleosides have been considered to be potential biomarkers to human diseases. The early diagnosis of coronary artery disease (CAD) is an unsolved problem in clinical cardiology. The aim of our study is to evaluate whether urinary methylated nucleosides can serve as useful biomarkers for CAD.

METHODS

A solid-phase extraction (SPE) column was used for extraction and purification of methylated nucleosides in urine, and high-performance liquid chromatography/electrospray ionization tandem mass spectrometry (HPLC/ESI-MS/MS) was employed for specific, sensitive and rapid determination of the urinary methylated nucleosides from patients with cardiac events.

RESULTS

We have analyzed six methylated nucleosides (N(3)-methylcytidine, N(1)-methyladenosine, N(6)-methyladenosine, N(2)-methylguanosine, N(1)-methylguanosine and N(2),N(2)-dimethylguanosine) in urine from 51 patients with CAD and 25 non-CAD controls by HPLC/ESI-MS/MS using selective reaction monitoring (SRM). Our results have shown that there were significant differences in the N(6)-methyladenosine levels from the patients and the non-CAD controls in the urine analyzed.

CONCLUSIONS

The results have indicated that HPLC/ESI-MS/MS is a highly specific and sensitive tool to measure urinary methylated nucleosides for analysis of CAD. Our result has revealed that the evaluation of urinary methylated nucleosides might be helpful in the analysis of CAD by liquid chromatography/mass spectrometry. Therefore, this N(6)-methyladenosine is worthy of further studies in the near future.

Mass spectrometry analysis of nucleosides and nucleotides

Mass spectrometry has been widely utilised in the study of nucleobases, nucleosides and nucleotides as components of nucleic acids and as bioactive metabolites in their own right. In this review, the application of mass spectrometry to such analysis is overviewed in relation to various aspects regarding the analytical mass spectrometric and chromatographic techniques applied and also the various applications of such analysis.

Urinary nucleosides as biomarkers of breast, colon, lung, and gastric cancer in Taiwanese

Urinary nucleosides are associated with many types of cancer. In this study, six targeted urinary nucleosides, namely adenosine, cytidine, 3-methylcytidine, 1-methyladenosine, inosine, and 2-deoxyguanosine, were chosen to evaluate their role as biomarkers of four different types of cancer: lung cancer, gastric cancer, colon cancer, and breast cancer. Urine samples were purified using solid-phase extraction (SPE) and then analyzed using high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). The Mann-Whitney U test and Principal Component Analysis (PCA) were used to compare differences in urinary nucleosides between patients with one of four types of cancer and healthy controls. The diagnostic sensitivity of single nucleosides for different types of cancer ranged from 14% to 69%. In contrast, the diagnostic sensitivity of a set of six nucleosides ranged from 37% to 69%. The false-positive identification rate associated with the set of six nucleosides in urine was less than 2% compared with that of less than 5% for a single nucleoside. Furthermore, combining the set of six urinary nucleosides with carcinoembryonic antigen improved the diagnostic sensitivity for colon cancer. In summary, the study show that a set of six targeted nucleosides is a good diagnostic marker for breast and colon cancers but not for lung and gastric cancers.

Borated titania, a new option for the selective enrichment of cis-diol biomolecules

As low abundance cis-diol biomolecules are of great significance in biological organisms, preparation of materials for the selective enrichment of such compounds is highly favorable for the development of the related proteomics and metabolomics. To this end, we have prepared monolithic borated titania by a non-aqueous sol-gel strategy as a new inorganic affinity material for the specific capture of nucleosides, glycopeptides and glycoproteins. Benefiting from the inorganic framework, this material prevented the hydrophobic interference, which was somewhat inevitable for the mainstream organic-based boronate affinity materials. The prepared material was carefully characterized by scanning electron microscope (SEM), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS) and nitrogen-sorption experiments to investigate the morphology and elemental composition. The excellent performance of borated titania on enrichment of cis-diol biomolecules was demonstrated by extracting the glycopeptides from horseradish peroxidase (HRP) digestion, standard glycoproteins, and nucleosides from a human-urine matrix. This kind of inorganic affinity material offers a new option for selective enrichment or separation of cis-diol biomolecules.

Analysis of urinary nucleosides as helper tumor markers in hepatocellular carcinoma diagnosis

Hepatocellular carcinoma (HCC) is a common neoplasm in Taiwan, for which early diagnosis is difficult and the prognosis is usually poor. HCC is usually diagnosed by abdominal sonography and serum alpha-fetoprotein (AFP) detection. Modified nucleosides, regarded as indicators for the whole-body turnover of RNAs, are excreted in abnormal amounts in the urine of patients with malignancies and can serve as tumor markers. We analyzed the excretion patterns of urinary nucleosides from 25 HCC patients and 20 healthy volunteers by high-performance liquid chromatography/electrospray ionization tandem mass spectrometry (HPLC/ESI-MS/MS) under optimized conditions. The HPLC/ESI-MS/MS approach with selective reaction monitoring (SRM) allowed for the sensitive determination of nucleosides in human urine samples. The mean levels of the urinary nucleosides adenosine, cytidine, and inosine were significantly higher in HCC patients than healthy volunteers (average of 1.78-, 2.26-, and 1.47-fold, respectively). However, the mean levels of urinary 1-methyladenosine, 3-methylcytidine, uridine, and 2'-deoxyguanosine were not significantly different. Combined with the determination of serum AFP levels, the higher levels of urinary adenosine, cytidine, and inosine may be additional diagnosis markers for HCC in Taiwanese patients.

Analysis of modified nucleosides in the urine of patients with malignant cancer by liquid chromatography/electrospray ionization mass spectrometry

As modified nucleosides reflect altered tRNA turnover which seems to be impaired in the body of cancer patients, they have been evaluated as potential tumor markers. High-performance liquid chromatography/electrosprary ionization quadrupole time-of-flight mass spectrometry (HPLC/ESI-Q-TOFMS) was used to identify nucleosides purified from urine in positive ionization mode. Potential nucleosides were assessed by their evident UV absorbance in HPLC and then further examined by mass spectrometric techniques. In this manner, 21 nucleosides were detected in the urine of a patient with lymphoid cancer including three modified nucleosides 5'-dehydro-2-deoxyinosine, N1,N2,N7-trimethylguanosine and N1-methyl-N2-ethylguanosine, which had never been reported previously.

Identification of urinary modified nucleosides and ribosylated metabolites in humans via combined ESI-FTICR MS and ESI-IT MS analysis

The physiological response of the human body to several diseases can be reflected by the metabolite pattern in biological fluids. Cancer, like other diseases accompanied by metabolic disorders, causes characteristic effects on cell turnover rate, activity of modifying enzymes, and RNA/DNA modifications. This results in an altered excretion of modified nucleosides and biochemically related compounds. In the course of our metabolic profiling project, we screened 24-h urine of patients suffering from lung, rectal, or head and neck cancer for previously unknown ribosylated metabolites. Therefore, we developed a sample preparation procedure based on boronate affinity chromatography followed by additional prepurification with preparative TLC. The isolated metabolites were analyzed by ion trap mass spectrometry (IT MS) and Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS). IT MS was applied for LC-auto MS(3) screening runs and MS(n(n=4-6)) syringe pump infusion experiments, yielding characteristic fragmentation patterns. FTICR MS measurements enabled the calculation of corresponding molecular formulae based on accurate mass determination (mass accuracy: 1-5 ppm for external and sub-ppm values for internal calibration). We were able to identify 22 metabolites deriving from cellular RNA metabolism and related metabolic pathways like histidine metabolism, purine biosynthesis, methionine/polyamine cycle, and nicotinate/nicotinamide metabolism. The compounds 1-ribosyl-3-hydroxypyridinium, 1-ribosyl-pyridinium, and 3-ribosyl-1-methyl-l-histidinium as well as a series of ribosylated histamines, conjugated to carboxylic acids at the N(omega)-position were found as novel urinary constituents. The occurrence of the modified nucleosides 2-methylthio-N(6)-(cis-hydroxyisopentenyl)-adenosine, 5-methoxycarbonylmethyl-2-thiouridine, N(6)-methyl-N(6)-threonylcarbamoyladenosine, and 2-methylthio-N(6)-threonylcarbamoyladenosine in human urine is verified for the first time.

[Lung cancer diagnosis based on urinary modified nucleoside metabolic profiling]

OBJECTIVE

To study the feasibility of modified urinary nucleosides metabolic profiling on lung cancer diagnoses.

METHODS

The modified urinary nucleosides metabolic profiling from 42 normal adults and 80 patients with lung cancer were determined by a coupled-column high performance liquid chromatography system. Partial least squares-discriminant analysis (PLS-DA) models were used to class differentiation between the lung cancer patients and controls and to discover potential biomarkers.

RESULT

The PLS-DA model results showed that there was a clear differentiation between normal adults and lung cancers patients, with the value of prediction (Q2) equals to 0.744.

CONCLUSION

Modified urinary nucleosides metabolic profiling method is useful for lung cancer diagnoses.

Development and validation of urinary nucleosides and creatinine assay by capillary electrophoresis with solid phase extraction

For the analysis of metabolite nucleoside profiles, capillary electrophoretic (CE) methods preceded by appropriate solid phase extraction procedures have been developed. The approach has been proposed for the determination of 13 nucleosides and creatinine in human urine. A background solution composed of 100 mM borate-72 mM phosphate-160 mM SDS and a fused silica capillary of 70 cm length to detector and 50 microm i.d. were used. The methods developed were statistically validated for their linearity, trueness, precision and selectivity. Stability of the analyzed nucleoside profiles in urine during storage was checked. Validation parameters of solid phase extraction procedures for urinary nucleosides were evaluated. The developed analytical methods were employed for the analysis of 22 urine samples from healthy patients and cancer patients from the urological ward. Nucleoside profiles were compared among the subjects. It was proved that the methods proposed were suitable for a fast and reliable determination of urinary creatinine and modified nucleoside profiles, which can be further submitted for the metabonomic analysis of cancer patients.

Urinary nucleosides based potential biomarker selection by support vector machine for bladder cancer recognition

BACKGROUND

Urinary nucleosides are potential biomarkers for many kinds of cancers. But up to now, it has been little focused in bladder cancer recognition. The aim of present study is try to validate the potential of urinary nucleoside as biomarker for bladder cancer diagnosis by finding out some urinary nucleosides with good discriminative performance for bladder cancer recognition in urinary nucleoside profile.

METHODS

20 urinary samples for cancer and the same number for control are collected and treated by capillary electrophoresis-mass spectrometry experiments to achieve urinary nucleoside profile, in which 44 peaks were integrated and the ratios of the relative peak area to the concentration of urinary creatinine were used as features to describe all samples. Support vector machine based recursive feature elimination (SVM-RFE) and a new feature selection method called support vector machine based partial exhaustive search algorithm (SVM-PESA) were used for biomarker identification and seeking optimal feature subsets for bladder cancer recognition.

RESULTS

Based on the urinary nucleoside profile, 22 optimal feature subsets consist of 3-4 features were found with 95% 5-fold cross validation accuracy, 100% sensitivity and 90% specificity by SVM-PESA, whose performance were much better than that of optimal feature subset selected by SVM-RFE. By analyzing the statistical histogram of features' appearance frequency in several best feature subsets, urinary nucleosides with m/z 317, 290 and 304 were thought as potential biomarkers for bladder cancer recognition.

CONCLUSIONS

These results indicated urinary nucleosides may be useful as tumor biomarkers for bladder cancer, and the new method for biomarker selection is effective.

Evaluation of different warping methods for the analysis of CE profiles of urinary nucleosides

Nowadays, numerous metabolite concentrations can readily be determined in a given biological sample by high-throughput analytical methods. However, such raw analytical data comprise noninformative components due to many disturbances normally occurring in the analyses of biological material. To eliminate those unwanted original analytical data components, advanced chemometric data preprocessing methods might be of help. Here, such methods are applied to electrophoretic nucleoside profiles in urine samples of cancer patients and healthy volunteers. In this study, three warping methods: dynamic time warping (DTW), correlation optimized warping (COW), and parametric time warping (PTW) were examined on two sets of electrophoretic data by means of quality of peaks alignment, time of preprocessing, and way of customization. The application of warping methods helped to limit shifting of peaks and enabled differentiation between whole electropherograms of healthy and cancer patients objectively by a principal component analysis (PCA). The evaluation of preprocessed data and raw data by PC analysis confirms differences between the applied warping tools and proves their suitability in metabonomic data interpretation.

Multilayer perceptron tumour diagnosis based on chromatography analysis of urinary nucleosides

Nucleosides in human urine are of interest as a biochemical marker for cancer, acquired immune deficiency syndrome (AIDS) and the whole-body turnover of RNAs. A reversed-phase high-performance liquid chromatography (RP-HPLC) method with photodiode-array detection was used to quantitatively analyze urinary normal and modified nucleosides. 55 persons with malignant tumors of various types, 13 persons with benign tumors and 41 healthy controls were investigated within a clinical intervention study. Artificial neural networks (ANN) have been used as a practical pattern recognition tool to distinguish cancer patients from healthy persons. Using a multilayer perceptron (MPL), a specificity of 85%, and a sensitivity of 97% in differentiation between tumor patients and healthy persons was achieved. The differentiation between benign and malignant tumors had a sensitivity of 60% and a specificity of 84%. These results verify the usefulness of ANN and the RP-HPLC method for tumor recognition in agreement with existing studies.

Novel approach for developing urinary nucleosides profile by capillary electrophoresis–mass spectrometry

A simple, rapid and efficient capillary electrophoresis-mass spectrometry (CE-MS) method was developed to analyze urinary nucleosides for the first time. The composition of CE buffer and MS parameters were systematically optimized. The optimum buffer was 150 mM acetic acid containing 15% methanol and 15% ethanol. The optimum MS parameters were: methanol containing 0.5% acetic acid was selected as the sheath liquid and the flow rate was 5 microL/min; the flow rate and temperature of drying gas were 6L/min and 150 degrees C, respectively; the pressure of nebulizing gas was 2 psig; and the fragmentor and ESI voltage were 100 V and 4000 V, respectively. Under the optimum CE-MS conditions, the urinary nucleosides were separated within 18 min. The linearity between the relative peak areas and the corresponding concentration of nine nucleosides markers were excellent. The limits of detection (S/N=3) of markers were 0.00862-3.82 nmol/mL. The optimum CE-MS method was applied to analyze urine from 20 bladder cancer patients and 20 healthy volunteers. Considering the standards of many nucleosides cannot be obtained, it is not the ratios of the concentrations of nucleosides to that of creatinine in the literatures, but the ratios of the relative peak area of nucleosides to the concentration of creatinine that used for pattern recognition. And, the statistical analysis result indicated this method was feasible.

Increased urinary level of oxidized nucleosides in patients with mild-to-moderate Alzheimer's disease

OBJECTIVE

Oxidative stress may play an important role in the pathogenesis of Alzheimer's disease (AD).

DESIGN AND METHODS

To investigate the possible role of oxidative DNA damage in the pathogenesis of AD, we measured the metabolite concentrations of oxidized nucleosides (pseudouridine, 1-methyladenosine, 5-methylcytidine, 5-methyl-2'-deoxycytidine, 3-methyluridine, N(2), N(2)-dimethylguanosine, 8-hydroxy-2'-deoxyguanosine, 5-deoxyadenosine and 2-deoxyguanosine) in urine between AD (n=36) and control subjects (n=34) using liquid chromatography-mass spectrometry (LC-MS) without urine preparation.

RESULTS

In AD, the 3-methyluridine, 1-methyladenosine, 8-hydroxy-2'-deoxyguanosine (p<0.05, respectively), 2-deoxyguanosine (p<0.01) and pseudouridine, N(2), N(2)-dimethylguanosine (p<0.001, respectively) were significantly increased when compared with the control subjects.

CONCLUSION

The results indicate that oxidized urinary nucleosides may be useful as biomarkers for AD in early stages.

Increasing conclusiveness of metabonomic studies by chem-informatic preprocessing of capillary electrophoretic data on urinary nucleoside profiles

Nowadays, bioinformatics offers advanced tools and procedures of data mining aimed at finding consistent patterns or systematic relationships between variables. Numerous metabolites concentrations can readily be determined in a given biological system by high-throughput analytical methods. However, such row analytical data comprise noninformative components due to many disturbances normally occurring in analysis of biological samples. To eliminate those unwanted original analytical data components advanced chemometric data preprocessing methods might be of help. Here, such methods are applied to electrophoretic nucleoside profiles in urine samples of cancer patients and healthy volunteers. The electrophoretic nucleoside profiles were obtained under following conditions: 100 mM borate, 72.5 mM phosphate, 160 mM SDS, pH 6.7; 25 kV voltage, 30 degrees C temperature; untreated fused silica capillary 70 cm effective length, 50 microm I.D. Different most advanced preprocessing tools were applied for baseline correction, denoising and alignment of electrophoretic data. That approach was compared to standard procedure of electrophoretic peak integration. The best results of preprocessing were obtained after application of the so-called correlation optimized warping (COW) to align the data. The principal component analysis (PCA) of preprocessed data provides a clearly better consistency of the nucleoside electrophoretic profiles with health status of subjects than PCA of peak areas of original data (without preprocessing).

Modified nucleosides: an accurate tumour marker for clinical diagnosis of cancer, early detection and therapy control

Modified nucleosides, regarded as indicators for the whole-body turnover of RNAs, are excreted in abnormal amounts in the urine of patients with malignancies. To test their usefulness as tumour markers and to compare them with the conventional tumour markers, fractionated urine samples were analysed using chromatography. The excretion patterns of nucleosides of 68 cancer patients with malignant and benign tumours and 41 healthy controls have been studied. Significant elevations in the total sum and the concentrations of at least three (or four) of indicator nucleosides cytidine, pseudouridine, 2-pyridone-5-carboxamide-N1-ribofuranoside, N2,N2-dimethylguanine, 1-methylguanosine, 2-methylguanosine and 1-methyladenosine indicate a tumour with a sensitivity of 54% (77%) and a specificity of 86% (98%). Using an artificial neural network analysis, a sensitivity of 97% and a specificity of 85% were achieved in differentiating between tumour and control volunteers. The comparison with carcinoembryonic antigen, cancer antigen 15-3 und tissue polypeptide antigen indicates that urinary nucleosides may be useful tumour markers. This study suggests that the simultaneous determination of modified nucleosides and creatinine in urine samples of patients with cancer leads to an advantage to current methods and is a useful method to detect cancer early and to control the success of therapy.

Direct determination of nucleosides in the urine of patients with breast cancer using column-switching liquid chromatography–tandem mass spectrometry

We developed an analytical method for a simple, sensitive and simultaneous determination of oxidized nucleosides in urine using column-switching liquid chromatography-electrospray/tandem mass spectrometry (LC-ESI/MS/MS). We connected two columns through a six-way switching valve and effectively separated nucleosides in the urine from the interference by column-switching liquid chromatography. We monitored separated nucleosides using positive ionization tandem mass spectrometry in selective reaction monitoring (SRM) mode. The calibration ranges of nucleosides were 0.2-100 nmol/mL. The linearity of the method was 0.994-0.999, and the limits-of-detection (LOD) at a signal-to-noise (S/N) ratio of 3 were 0.1-0.2 nmol/mL. The coefficients of variation were in the range 2.28-11.74% for within-day variation and 4.36-11.15% for day-to-day variation, respectively. To explore the relationship between breast cancer and the nucleosides level in human urine, we measured the concentrations of nucleosides in female patients with breast cancer (n = 30) and in normal female subjects (n = 30). The concentration of nucleosides was significantly increased in patients with breast cancer when compared with the normal controls (1-methyladenosine; p < 0.005, N(2),N(2)-dimethylguanosine; p < 0.01, 5-hydroxymethyl-2'-deoxyuridine; p < 0.001, 8-hydroxy-2-deoxyguanosine; p < 0.001). Therefore, the elevated levels of nucleosides could be used as an important biomarker for breast-cancer research.

Normal and modified urinary nucleosides represent novel biomarkers for colorectal cancer diagnosis and surgery monitoring

BACKGROUND

Up to now, there is still no ideal tumor marker in early diagnosis and effective monitoring, especially for surgical resection of colorectal cancer (CRC). The aim of the present study was to evaluate the application of urinary normal and modified nucleosides in diagnosis and surgery monitoring of CRC.

METHODS

Between October 2002 and July 2003, 52 consecutive patients with pathological confirmed CRC were enrolled. Spontaneous urine samples were collected 1 day before surgery and on day 8 postoperatively, and 14 urinary nucleosides were determined by reverse-phase high-performance liquid chromatography (RP-HPLC). Another 62 healthy people were also studied as control. The clinical routine tumor markers, serum carcinoembryonic antigen (CEA), carbohydrate antigen (CA)199, CA125, and alpha-fetoprotein (AFP) of CRC patients, were correspondingly evaluated by electrochemiluminescent immunoassay.

RESULTS

The levels of 11 out of 14 of the determined urinary nucleosides in the CRC group were much higher than those of normal controls. Through the principal component analysis of these 14 nucleosides, 76.9% of CRC patients were correctly classified. The sensitivity of this analysis was much higher than that of CEA (38.5%), CA199 (40.4%), CA125 (15.4%), and AFP (17.3%; P < 0.01). Receiver operating characteristic (ROC) curve analysis of 1-methylguanosine (m1G) and pseudouridine (Pseu) showed good sensitivity-specificity profiles of the diagnosis of CRC. The elevated levels of the nine nucleosides significantly decreased after curative resection of 40 CRC cases. The data also showed that the preoperative levels of some nucleosides were positively related with tumor size and Dukes staging of CRC.

CONCLUSION

The evaluation of normal and modified urinary nucleosides might become novel tumor markers, which will be facilitated in the clinical setting and helpful in the diagnosis, management and follow up of CRC. Pseu and m1G may be more promising for clinical use and be worthy of further studies in the near future.

Urinary nucleosides as biological markers for patients with colorectal cancer

AIM: Fourteen urinary nucleosides, primary degradation products of tRNA, were evaluated to know the potential as biological markers for patients with colorectal cancer.

METHODS: The concentrations of 14 kinds of urinary nucleosides from 52 patients with colorectal cancer, 10 patients with intestinal villous adenoma and 60 healthy adults were determined by column switching high performance liquid chromatography method.

RESULTS: The mean levels of 12 kinds of urinary nucleosides (except uridine and guanosine) in the patients with colorectal cancer were significantly higher than those in patients with intestinal villous adenoma or the healthy adults. Using the levels of 14 kinds of urinary nucleosides as the data vectors for principal component analysis, 71% (37/52) patients with colorectal cancer were correctly classified from healthy adults, in which the identification rate was much higher than that of CEA method (29%). Only 10% (1/10) of patients with intestinal villous adenoma were indistinguishable from patients with colorectal cancer. The levels of m1G, Pseu and m1A were positively related with tumor size and Duke’s stages of colorectal cancer. When monitoring the changes in urinary nucleoside concentrations of patients with colorectal cancer associated with surgery, it was found that the overall correlations with clinical assessment were 84% (27/32) and 91% (10/11) in response group and progressive group, respectively.

CONCLUSION: These findings indicate that urinary nucleosides determined by column switching high performance liquid chromatography method may be useful as biological markers for colorectal cancer.

MALDI-TOF MS analysis of urinary nucleosides

As RNA turnover seems to be impaired in cancer patients, modified nucleosides have been evaluated as potential tumor markers. Modified nucleosides are mainly formed post-transcriptionally in tRNA, set free during RNA metabolism, and excreted in urine. Especially methylated nucleosides play an important role, as their levels are higher in urine from cancer patients. For structural elucidation of known and unknown nucleosides from urine samples of cancer patients, MALDI-TOF MS and MALDI-PSD were used for the first time. This technique generally ensures high sensitivity, mass resolution, and accuracy. In our analytical approach we prepurified nucleosides from urine by affinity chromatography and subsequently separated them by semipreparative high performance liquid chromatography. The different fractions were collected separately and analyzed by MALDI-TOF MS and PSD-MALDI using a mixture of six low molecular weight calibrants for internal or external calibration. The molecular totals formulas based on a mass accuracy of 10 ppm and below were calculated and a systematic data base search was performed. The inherent problem of the MALDI-technique, the reduced sensitivity for low molecular weight substances caused by matrix suppression effects, was reduced by our technique. We identified several nucleosides in urine, which were previously identified via retention times and UV spectra of standards after HPLC analysis. Eight further nucleosides were observed. This work demonstrates for the first time the potential of MALDI-TOF and PSD-MALDI in combination with semipreparative HPLC for assignment of nucleosides in urine. The particularly high mass accuracy of this mass spectrometric method provides opportunities for identifying unknown compounds.

Determination of urinary nucleosides by direct injection and coupled-column high-performance liquid chromatography

A coupled-column liquid chromatographic method for the direct analysis of 14 urinary nucleosides is described. Efficient on-line clean-up and concentration of 14 nucleosides from urine samples were obtained by using a boronic acid-substituted silica column (40 mm x 4.0 mm I.D.) as the first column (Col-1) and a Hypersil ODS2 column (250 mm x 4.6 mm I.D.) as the second column (Col-2). The mobile phases applied consisted of 0.25 mol/L ammonium acetate (pH 8.5) on Col-1, and of 25 mmol/L potassium dihydrogen phosphate (pH 4.5) on Col-2, respectively. Determination of urinary nucleosides was performed on Col-2 column by using a linear gradient elution comprising 25 mmol/L potassium dihydrogen phosphate (pH 4.5) and methanol-water (60:40, v/v) with UV detection at 260 nm. Urinary nucleosides analysis can be carried out by this procedure in 50 min requiring only pH adjustment and the protein precipitation by centrifugation of urine samples. Calibration plots of 14 standard nucleosides showed excellent linearity (r > 0.995) and the limits of detection were at micromolar levels. Both of intra- and inter-day precisions of the method were better than 6.6% for direct determination of 14 nucleosides. The validated method was applied to quantify 14 nucleosides in 20 normal urines to establish reference ranges.

[Application of urinary nucleosides in the diagnosis and surgical monitoring of colorectal cancer]

OBJECTIVE

To evaluate the value of urinary normal and modified nucleosides in diagnosis and surgical monitoring of colorectal cancer (CRC).

METHODS

Between October 2002 and July 2003, 52 consecutive patients with pathological confirmed CRC were included in this study. Spontaneous urine samples were collected 1 d before and 8 d after surgery and 14 kinds of urinary nucleosides in the samples were determined by reversed-phase high-performance liquid chromatography (RP-HPLC) method. Another 62 healthy volunteers were also enrolled as controls. The routine clinical tumor markers, including serum CEA, CA199, CA125 and AFP levels of CRC patients were evaluated by electrochemical-luminescence immunoassay simultaneously.

RESULTS

The mean levels of pseudouridine (Pseu), adenosine (A), cytidine (C), 1-methyladenosine (m1A), 1-methylinosine (m1I), 3-methyluridine + 5-methyluridine (mU), 2,2-methylguanosine (m22G), inosine (I), 1-methylguanosine (m1G), N4-acetylcytidine (ac4C), N6-methyladenosine (m6A) among 14 kinds of determined urinary nucleosides in CRC group were much higher than those of controls (P < 0.05). Based on principal component analysis, 76.9% of CRC patients were correctly identified, which was much higher than that of CEA (38.5%), CA199 (40.4%), CA125 (15.4%), and AFP (17.3%) (P < 0.01). ROC curve analysis of m1G, and Pseu showed good sensitivity-specificity profiles to CRC. Two classification equations, Y(normal) = -3.009 + 0.0272 x Pseu + 4.918 x m1G and Y(CRC) = -8.057 + 0.0667 x Pseu + 8.258 x m1G, were established by Bayes stepwise discriminate analysis for predicting carcinogenesis of CRC. The elevated levels of Pseu, C, U (uridine), m1A, m1I, m1G, ac4C, A, m22G dramatically decreased after curative resection of 40 cases of CRC. And our data also showed that the preoperative levels of Pseu, m1G, m1A and m22G were positively related with tumor size and the preoperative levels of m1A, m22G and ac4C were positively related with Duke's staging of CRC (P < 0.05).

CONCLUSIONS

Normal and modified urinary nucleosides may become additional tumor markers which are feasible in the clinical setting and will prove helpful in the diagnosis, management and follow-up of CRC, and Pseu and m1G may be more promising for clinical application.

Chromatographic, capillary electrophoretic and matrix-assisted laser desorption ionization time-of-flight mass spectrometry analysis of urinary modified nucleosides as tumor markers

Modified nucleosides are formed posttranscriptionally in RNA. During RNA turnover free modified nucleosides are formed which circulate in the blood stream and are excreted in the urine. Their levels are increased in a number of malignant diseases, and they can be used in clinical chemistry as tumor markers. The analysis includes the isolation of the nucleosides from urine with phenylboronate gel and their separation and quantitation by HPLC on C18 columns or by capillary electrophoresis on uncoated columns applying a sodium dodecyl sulfate-borate-phosphate buffer. Identification of the nucleosides is performed with matrix-assisted laser desorption ionization time-of-flight mass spectrometry including post source decay spectra. In two clinical studies the diagnostic value of urinary modified nucleosides is investigated, in a study on children with leukemia and other malignant diseases and a study on women with breast cancer. Candidate markers are pseudouridine, 1-methylguanosine, N2-methylguanosine, 3-methyluridine and 1-methyl-inosine.

Age-dependence of urinary normal and modified nucleosides in childhood as determined by reversed-phase high-performance liquid chromatography

Modified nucleosides have been characterized as tumor markers for a number of malignant diseases. In order to use these markers in children, the age-dependence of the nucleoside levels in healthy children has to be established and taken into account in diagnostic decisions. In this study, the levels of 12 normal and modified nucleosides in urine of 166 healthy children and adolescents with an age between 1 day and 19 years are determined by reversed-phase HPLC, and age-dependent reference ranges are defined. The urinary nucleoside concentrations are related to the creatinine concentrations, which allows the use of randomly collected urine samples. All nucleoside levels in urine of children decrease with age, most pronounced during the first 4 years of life, and the age-dependence of the reference values of the individual nucleosides can be approximated by a mathematical function y = b(0) + b(1) (1/x) with the regression coefficients b(0) and b(1,) the nucleoside levels y and the age x between 1 year and 19 years. In the very young children, the shifts in the nucleoside concentrations are more differentiated. Starting with low levels on the first day of life, the concentrations of all studied nucleosides rise up to an age of 1-2 months, when they reach their absolute maximum for all age periods, and then decrease.

Clinical significance and prognostic value of urinary nucleosides in breast cancer patients

OBJECTIVE

Thirteen urinary nucleosides, primarily degradation products of tRNA, were evaluated as potential tumor markers for breast cancer patients.

DESIGN AND METHODS

The micellar electrokinetic chromatography (MEKC) method has been used to analyze the urinary nucleosides in 41 healthy controls, 20 patients with benign breast tumors, and 26 breast cancer patients.

RESULTS

Urinary nucleoside concentrations of breast cancer patients were found to increase significantly compared to those of patients with benign breast tumors and healthy controls. By using 13 nucleoside concentrations as data vectors for principal component analysis (PCA), 73% (19/26) of breast cancer patients were correctly identified from healthy controls, while only 20% (4/20) of patients with benign breast tumors were indistinguishable from breast cancer patients. The mean level of all forms of urinary nucleosides in patients with metastatic breast cancer was higher than that in patients with primary breast cancer. The levels of modified nucleosides tended to decrease and return to normal after surgery.

CONCLUSION

The results indicate that urinary nucleosides may be useful as tumor markers for breast cancer.

[Development of high performance liquid chromatographic method using monolithic column for the determination of urinary nucleosides]

Modified nucleosides excreted in urine have been studied as possible bio-markers for malignant tumors. Reversed-phase high performance liquid chromatography (RP-HPLC) is one of the most popular analytical tools. However, its analysis time is longer than desired. The analytical method for urinary nucleosides has been developed using a monolithic column and a linear gradient elution of 25 mmol/L KH2PO4 solution (pH 4.55) and 60% methanol in water with UV detection at 260 nm. Twelve urinary nucleosides were completely separated. The monolithic column presented similar analytical characteristics to reversed-phase column. The time of the analysis is only 23 min, in general much shorter than the methods using a packed RP-HPLC. The method developed is sensitive, reliable and suitable for clinical applications.

Recent developments in the determination of urinary cancer biomarkers by capillary electrophoresis

Investigation of effective biomarkers for cancers is currently a popular area of study in clinical and cancer researches, because it can potentially lead to pre-cancer screening or pre-cancer diagnosis and may provide useful information on cancer type and the disease's stage of progression. More and more biochemical or chemical fluid components of the human body such as urine, blood, and cerebrospinal fluid have been considered to contain biomarkers, which are useful in cancer researches, pre-cancer diagnosis, and cancer follow-ups during or after cancer treatment. Several modern analytical techniques, such as gas chromatography (GC), high-performance liquid chromatography (HPLC), capillary electrophoresis (CE), and other separation techniques as well as hyphenated techniques, have been extensively used in study of cancer biomarkers. Among these techniques, CE is considered to be a highly efficient and practical analytical technique because of the small sample volume requirement and its wide separation versatility, ranging from small inorganic molecules to large biomolecules. This review discusses the latest developments involving biomarkers and their analysis by CE, including a discussion of instrumental conditions, method developments, and data analysis.

A rapid and sensitive method for quantitation of nucleosides in human urine using liquid chromatography/mass spectrometry with direct urine injection

Oxidized nucleosides are biochemical markers for tumors, aging, and neurodegenerative diseases. However, during the last decade, the analytical methods for nucleosides by gas chromatography/mass spectrometry (GC/MS) and high-performance liquid chromatography (HPLC) with single-parameter detectors like electron-capture detection (ECD) have not been sufficiently rapid or reliable to detect nucleosides in urine and to analyze clinical samples. It has been reported (Dudley et al., Rapid Commun Mass Spectrom. 2000; 14: 1200) that liquid chromatography with electrospray mass spectrometry (LC/ESI-MS) is more specific and sensitive for analysis of nucleosides than HPLC with conventional detectors; however, this method required complex extraction steps. In the present work a direct LC/ESI-MS method for nucleosides without extraction of urine samples has been developed. Analysis of nucleosides using positive-ion mode with selected reaction monitoring effectively eliminated potential interferences from endogenous constituents of the urine. This highly selective and sensitive method made it possible to analyze urinary nucleosides with a lower limit of quantitation of 0.2 nmol/mL. The method has been validated, with both excellent linearity and reproducibility, in the calibration range from 0.2-400 nmol/mL. The correlation coefficients of the calibration curves were higher than 0.987. The coefficients of variation were in the range 0.03-14.92% (inter-day) and 0.54-14.39% (intra-day), respectively.

Urinary modified nucleosides as tumor markers

Extracts of urinary nucleosides have been sequentially purified and examined by mass spectrometric analysis. Seventeen modified nucleosides have been unequivocally identified and a further five provisionally identified. While several nucleosides were found only in a small number of extracts, the occurrence and levels of others were found to correlate with the tumour type and stage.

Urinary nucleosides as potential tumor markers evaluated by learning vector quantization

Modified nucleosides were recently presented as potential tumor markers for breast cancer. The patterns of the levels of urinary nucleosides are different for tumor bearing individuals and for healthy individuals. Thus, a powerful pattern recognition method is needed. Although backpropagation (BP) neural networks are becoming increasingly common in medical literature for pattern recognition, it has been shown that often-superior methods exist like learning vector quantization (LVQ) and support vector machines (SVM). The aim of this feasibility study is to get an indication of the performance of urinary nucleoside levels evaluated by LVQ in contrast to the evaluation the popular BP and SVM networks. Urine samples were collected from female breast cancer patients and from healthy females. Twelve different ribonucleosides were isolated and quantified by a high performance liquid chromatography (HPLC) procedure. LVQ, SVM and BP networks were trained and the performance was evaluated by the classification of the test sets into the categories "cancer" and "healthy". All methods showed a good classification with a sensitivity ranging from 58.8 to 70.6% at a specificity of 88.4-94.2% for the test patterns. Although the classification performance of all methods is comparable, the LVQ implementations are superior in terms of more qualitative features: the results of LVQ networks are more reproducible, as the initialization is deterministic. The LVQ networks can be trained by unbalanced sizes of the different classes. LVQ networks are fast during training, need only few parameters adjusted for training and can be retrained by patterns of "local individuals". As at least some of these features play an important role in an implementation into a medical decision support system, it is recommended to use LVQ for an extended study.

[Significance of urinary nucleosides in diagnosis of gastric carcinoma]

BACKGROUND & OBJECTIVE

It was reported that urinary modified nucleosides with abnormally high amounts were found in many cancer patients. This study was designed to investigate the usefulness of urinary nucleosides in the diagnosis of gastric carcinoma.

METHODS

The concentrations of 15 kinds of urinary nucleosides from 50 healthy persons and 48 patients with gastric carcinoma were determined by high-performance liquid chromatography (HPLC). Of 48 patients with gastric carcinoma, 25 underwent serum CEA examination.

RESULTS

The average levels of 14 kinds of urinary nucleosides, m5U excepted, from patients with gastric carcinoma were higher than those from health persons (P< 0.05). Pseu 22.91+/-4.90, 34.87+/-21.41; U 0.34+/-0.32, 0.62+/-0.82; A 0.58+/-0.16, 0.96+/-0.75; C 0.17+/-0.15,0.24+/-0.19; m5U 0.03+/-0.07,0.07+/-0.06; I 0.26+/-0.10, 0.43+/-0.36; m1I 1.34+/-0.34, 2.44+/-1.39; ac4C 0.75+/-0.24, 1.08+/-0.72; G 0.09+/-0.04, 0.14+/-0.10; X 1.20+/-0.42, 1.90+/-1.09; m2G 0.61+/-0.16, 1.00+/-0.69; m6A 0.04+/-1.13, 0.07+/-0.08; m1A 2.26+/-0.56, 3.71+/-2.21; m22G 1.34+/-0.27, 2.25+/-1.39; m1G 0.80+/-0.25, 1.41+/-0.86. The level of nucleoside I was positively correlated with the tumor size (P< 0.05). The level of nucleoside X was positively correlated with lymph node metastasis (P< 0.05). Using the concentrations of 15 nucleosides as the data vectors, principal component analysis was applied to classify gastric cancer patients and normal adults, 63%(30/48) of cancer patients were correctly classified, in which the identification rate was higher than that of CEA method (12%).

CONCLUSION

Urinary modified nucleoside increased in the patients with gastric carcinoma, and it may be helpful in the diagnosis of gastric carcinoma.

Study of urinary nucleosides as biological marker in cancer patients analyzed by micellar electrokinetic capillary chromatography

Thirteen normal and modified nucleosides, primarily degradation products of transfer ribonucleic acid (tRNA), were evaluated as potential tumor markers for cancer patients. Their urinary concentrations were determined by means of micellar electrokinetic capillary chromatography (MEKC) in the urine from 54 healthy adults and 70 cancer patients, then quantitatively expressed as a function of creatinine excretion. It was found that urinary nucleosides for cancer patients were on the average significantly higher than those for healthy controls, however, no significant differences were found between male and female or between different ages. Based on 13 urinary nucleoside concentrations, principal component analysis (PCA) could be used to classify 72% of cancer patients from the healthy controls. The present study shows that the precise measurement of urinary nucleosides by MEKC in combining with PCA technique may provide a clinically useful approach for diagnosis of cancer.

Artificial neural network classification based on high-performance liquid chromatography of urinary and serum nucleosides for the clinical diagnosis of cancer

Nucleosides in human urine and serum have frequently been studied as a possible biomedical marker for cancer, acquired immune deficiency syndrome (AIDS) and the whole-body turnover of RNAs. Fifteen normal and modified nucleosides were determined in 69 urine and 42 serum samples using high-performance liquid chromatography (HPLC). Artificial neural networks have been used as a powerful pattern recognition tool to distinguish cancer patients from healthy persons. The recognition rate for the training set reached 100%. In the validating set, 95.8 and 92.9% of people were correctly classified into cancer patients and healthy persons when urine and serum were used as the sample for measuring the nucleosides. The results show that the artificial neural network technique is better than principal component analysis for the classification of healthy persons and cancer patients based on nucleoside data.

[Investigation of urinary nucleosides excretion of intestinal cancer patients by reversed-phase high performance liquid chromatography]

A method for the determination of urinary nucleosides with reversed-phase high performance liquid chromatography is described. After nucleosides were extracted from urine on phenyl boronic acid affinity chromatography, the analysis was performed on a column (4.6 mm i.d. x 250 mm, 5 microns) at 22 degrees C using a linear gradient elution comprising 25 mmol/L KH2PO4 solution (pH 4.55) and 60% methanol in water with UV detection at 260 nm. This method was used for the determination of 15 urinary nucleosides of 41 intestinal cancer patients and 52 normal adults. The results showed that the average concentrations of 12 urinary nucleosides from intestinal cancer patients were much higher than those of normal adults with P < 0.001. Using the concentrations of 15 nucleosides as the data vectors, principal component analysis was applied to classify intestinal cancer patients and normal adults and 76% (31/41) of the cancer patients were correctly classified. It is concluded that the method is sensitive, reliable and suitable for basic research and clinical applications to malignant tumours.

Quantification of 8-oxo-guanine and guanine as the nucleobase, nucleoside and deoxynucleoside forms in human urine by high-performance liquid chromatography-electrospray tandem mass spectrometry

Oxidative DNA damage, linked pathogenically to a variety of diseases such as cancer and ageing, can be investigated by measuring specific DNA repair products in urine. Within the last decade, since it was established that such products were excreted into urine, progress in their analysis in urine has been limited. Guanine is the DNA base most prone to oxidation. We present a method for determination of the urinary 8-hydroxylated species of guanine, based on direct injection of urine onto a high-performance liquid chromatography (HPLC)-tandem mass spectrometry system. The analysis covers the 8-hydroxylated base, ribonucleoside and deoxynucleoside, and the corresponding non-oxidised species. Without pre-treatment of urine the detection limits for the nucleobases are approximately 2 nM (50 fmol injected) and for the nucleosides approximately 0.5 nM (12.5 fmol injected). Previously, liquid chromatography of the nucleobases has been problematic but is made possible by low-temperature reverse-phase C18 chromatography, a method that increases retention on the column. In the case of the nucleosides, retention was almost total and provides a means for on-column concentration of larger urine samples and controlled high peak gradient elution. The total excretion of 8-hydroxylated guanine species was 212 nmol/24 h. The oxidised base accounted for 64%, the ribonucleoside for 23% and the deoxynucleoside for 13%, indicating substantial oxidation of RNA in humans. In rat urine, excretion of the oxidised base was more dominant, the percentages of the oxidised base, ribonucleoside and deoxynucleosides being 89, 8 and 3%. This finding is at odds with previous reports using immunoaffinity pre-purification and HPLC-electrochemical detection analysis. The developed method now makes it possible to measure oxidative nucleic acid stress to both RNA and DNA in epidemiological and intervention settings, and our findings indicate a substantial RNA oxidation in addition to DNA oxidation. The small volume needed also makes the method applicable to small experimental animals.

Capillary electrophoretic profiling and pattern recognition analysis of urinary nucleosides from uterine myoma and cervical cancer patients

Capillary electrophoretic (CE) profiling analysis combined with pattern recognition methods is described for the correlation between urinary nucleoside profiles and uterine cervical cancer. Nucleosides were extracted from urine specimens by solid-phase extraction in affinity mode using phenylboronic acid gel. CE separation was carried out with an uncoated fused-silica capillary (570 mm x 50 microm I.D.) maintained at 20 degrees C, using 25 mM borate-42.5 mM phosphate buffer (pH 6.7) containing 200 mM sodium dodecyl sulfate as the run buffer under the applied voltage of 20 kV. A total of 15 nucleosides were positively identified in urine samples (2 ml) from eight uterine myoma (benign tumor group), 10 uterine cervical cancer (malignant tumor group) patients and 10 healthy females (normal group) studied. The star symbol plots drawn based on each mean concentration of nucleosides normalized to that in normal group enabled one to discriminate malignant and benign groups from normal group. In addition, canonical discriminant analysis performed on the nucleoside data of 28 individual urine specimens correctly classified into three separate clusters according to groups in the canonical plot.

Analysis of urinary nucleosides. II. Comparison of mass spectrometric methods for the analysis of urinary nucleosides

Qualitative and quantitative analyses of urinary nucleosides have diagnostic potential as tumour markers. We have developed separation techniques linked to mass spectrometric detection in order to overcome the problems associated with past identification and quantitation methods. The three methods of analysis utilised were: gas chromatography/mass spectrometry (GC/MS), high-performance liquid chromatography/ion-trap mass spectrometry (HPLC/ITMS) and capillary liquid chromatography/triple quadrupole mass spectrometry (CapLC/TQMS). Here we compare the relative effectiveness of each of the techniques for subsequent application in the systematic study of urinary nucleoside profiles in cancer patients. All three methods proved to be valuable techniques for such urinary nucleoside analyses, and a combination rather than one single choice is concluded as the ideal.

Excretion pattern investigation of urinary normal and modified nucleosides of breast cancer patients by RP-HPLC and factor analysis method

Modified nucleosides, formed post-transcriptionally in RNA by a number of modification enzymes, are excreted in abnormal levels in the urine of patients with malignant tumors. To test their usefulness as tumor markers, and to compare them with the conventional tumor markers, a reversed-phase high-performance liquid chromatographic (RP-HPLC) method and a factor analysis method have been used to study the excretion pattern of nucleosides of breast cancer patients. A clear cut differentiation of the breast cancer group and the healthy individuals in two clusters without overlapping was obtained.

Detection and characterization of modified nucleosides in serum and urine of uremic patients using capillary liquid chromatography-frit-fast atom bombardment mass spectrometry

To determine RNA metabolism in uremia, capillary liquid chromatography-frit-fast atom bombardment mass spectrometry was employed for the characterization of ribonucleosides in serum and urine of uremic patients, and the profiles were compared with those of healthy subjects. We have characterized 20 nucleosides in serum and 23 nucleosides in urine from both healthy subjects and uremic patients; most of them were modified nucleosides derived from tRNA breakdown products. Four metabolites derived from allopurinol were detected as exogenous nucleosides in patients receiving allopurinol; these include allopurinol-1-riboside, oxipurinol-1-riboside, oxipurinol-7-riboside and a unknown oxipurinol riboside. The endogenous and exogenous ribonucleosides were retained at higher levels in uremic serum, and may play a contributory role as toxins responsible for clinical symptoms of uremia.

Application of capillary electrophoresis in clinical chemistry: the clinical value of urinary modified nucleosides

Urinary modified nucleosides were determined by capillary electrophoresis using a 300 mM SDS-25 mM sodium tetraborate-50 mM sodium dihydrogenphosphate buffer. The nucleosides were extracted from urine by phenylboronate affinity gel chromatography. In cancer patients the levels of the modified nucleosides are generally elevated. By an artificial neural network method breast cancer patients were differentiated from normal individuals, which indicates that the modified nucleosides could be of clinical value as tumor markers.

Development of a purification procedure for the isolation of nucleosides from urine prior to mass spectrometric analysis

A chromatographic separation of nucleosides from urine has been developed in order to facilitate their mass spectrometric analysis for clinical diagnosis. A number of chromatographic resins were studied in order to develop an effective and efficient purification procedure. The optimized sequential protocol comprises a centrifugation, acidification and neutralization step, followed by application of an affinity chromatographic column and finally further separation on an acidic cation exchange column and a basic anion exchanger. This scheme shows effective clean-up of a standard radiolabelled nucleoside with a recovery of 92.5%, and recovery of nucleosides added to urine samples before extraction showed recoveries of 72-82%.

Analysis of urinary nucleosides. I. Optimisation of high performance liquid chromatography/electrospray mass spectrometry

In order to optimise the analysis of urinary nucleosides by high performance liquid chromatography/mass spectrometry (HPLC/MS), the HPLC separation of these compounds was performed at different 'flow rates' and 0.2mL/min was found to give both a better separation and ionisation. The ionisation conditions were optimised to give the best intensity of the molecules quasi-molecular ions. The ion distribution profile and ionisation in both positive and negative mode were examined and the detection of the protonated molecule in positive mode chosen for further analysis. The limits of detection of the method developed are reported and representative LC/MS and LC/MS/MS spectra shown. Typical urinary nucleoside chromatograms are presented.