Noninvasive detection of colorectal cancer by analysis of exhaled breath

There has been growing interest in exhaled breath analysis for cancer screening and disease monitoring; however, limited breath biomarker information exists regarding colorectal cancer (CRC). The objective of this study was to screen for breath biomarkers of CRC. Exhaled breath was collected from 20 CRC patients and 20 healthy controls; subsequently, solid-phase microextraction–gas chromatography/mass spectrometry (SPME-GC/MS) was used to assess the exhaled volatile organic compounds (VOCs) of the study participants. The statistical methods of principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) were performed to process the final data. The VOCs in the exhalations of CRC patients exhibited significant differences from the VOCs in the exhalations of healthy controls; in particular, relative to the latter exhalations, the former exhalations contain significantly higher levels of cyclohexanone, 2,2-dimethyldecane, dodecane, 4-ethyl-1-octyn-3-ol, ethylaniline, cyclooctylmethanol, trans-2-dodecen-1-ol, and 3-hydroxy-2,4,4-trimethylpentyl 2-methylpropanoate but significantly lower levels of 6-t-butyl-2,2,9,9-tetramethyl-3,5-decadien-7-yne (P?<?0.05). Analyses of breath VOCs provide a related model of CRC exhalation that could represent an effective and convenient screening method for this disease.

肠癌患者尿中核苷排放的高效液相法研究

 用反相高效液相法测定尿中核苷。通过苯基硼酸亲和法提取尿中核苷,在柱(4 6mmi d ×250mm,5μm)上以25mmol/L磷酸二氢钾溶液(pH4 55)和60%的甲醇水溶液作为流动相进行二元梯度淋洗,于22℃下进行反相分离,260nm处紫外检测。用该法测定了41例肠癌患者和52例正常人尿中15种核苷的含量(用核苷与肌酐的摩尔比表示,下同),结果表明肠癌患者中有12种核苷的含量比正常人显著性增高(P<0 001)。以15种核苷的含量作为参量,结合主成分分析区分正常人和肠癌患者,对癌症病人的识别率达76%(31/41)。     

Targeted serum metabolite profiling of nucleosides in esophageal adenocarcinoma

Nucleosides are indicators of the whole‐body turnover of transfer RNA. Based on the activity of cancer cells these molecules could potentially be used as cancer biomarkers, and several studies have determined that the metabolic levels of nucleosides are significantly altered in cancer patients compared to control groups. Here we report a targeted metabolite investigation of serum nucleosides in esophageal adenocarcinoma specimens. We quantified eight nucleosides using high‐performance liquid chromatography/triple quadrupole mass spectrometry (HPLC/TQMS) and determined that the metabolic levels of 1‐methyladenosine (p <2.14 × 10^?7), N²,N²‐dimethylguanosine (p <2.78 × 10^?7), N²‐methylguanosine (p <2.48 × 10^?6) and cytidine (p <6.98 × 10^?4) were significantly elevated while the concentration of uridine (p <3.74 × 10^?3) was significantly lowered in serum samples from cancer patients compared to those of control group. Our results suggest that nucleosides could potentially serve as useful biomarkers to identify esophageal adenocarcinoma. Copyright © 2010 John Wiley & Sons, Ltd.     

Synthesis, structure, and biological evaluation of C-2 sulfonamido pyrimidine nucleosides

The C-2 sulfonamido pyrimidine nucleosides were prepared by opening the 2,2′- or 2,3′-bond in anhydronucleosides under nucleophilic attack of sulfonamide anions. Reaction of the sodium salt of p-toluenesulfonamide or 2-(aminosulfonyl)-N,N-dimethylnicotinamide with 2,2′-anhydro-1-(β-d-arabinofuranosyl)cytosine gave the C-2 sulfonamido derivatives in excellent yields. Ring opening of the less reactive 2,2′-anhydrouridine and 2,3′-anhydrothymidine could be accomplished with DBU/CH₃CN activation of p-toluenesulfonamide, giving moderate yields for C-2 sulfonamido derivatives. The action of acetic acid or ZnBr₂/CH₂Cl₂ on 5-methyl-N²-tosyl-1-(2-deoxy-5-O-trityl-β-d-threo-pentofuranosyl)isocytosine led to the cleavage of both the protection group and the nucleoside bond, yielding 5-methyl-N²-tosylisocytosine as the major product. Structures of the prepared C-2 sulfonamido nucleosides were confirmed by the 1D and 2D NMR experiments, and X-ray structural analysis of 4-imino-N²-tosylamino-1-(β-d-arabinofuranosyl)pyrimidine. Both methods confirmed β-configuration and anti-conformation of the 2-sulfonamido nucleosides. The investigated compounds displayed moderate inhibition of tumor cell growth in vitro, as determined by the MTT assay using six different human tumor cell lines.     

Replacement of Canonical DNA Nucleobases by Benzotriazole and 1,2,3‐Triazolo[4,5‐d]pyrimidine: Synthesis,Fluorescence, and Ambiguous Base Pairing

The syntheses and the fluorescence properties of 7H‐3,6‐dihydro‐1,2,3‐triazolo[4,5‐d]pyrimidin‐7‐one 2′‐deoxy‐β‐D ‐ribonucleosides (=2′‐deoxy‐8‐azainosine) 3 (N³), 15 (N²), and 16 (N¹) as well as of 1,2,3‐benzotriazole 2′‐O‐methyl‐β‐ or ‐α‐D ‐ribofuranosides 6 (N¹) and 24 (N¹) are described. Also the fluorescence properties of 1,2,3‐benzotriazole 2′‐deoxy‐β‐D ‐ribofuranosides 4 (N¹) and 5 (N²) are evaluated. From the nucleosides 3 – 6 , the phosphoramidites 19, 26a, 26b , and 28 are prepared and employed in solid‐phase oligonucleotide synthesis. In 12‐mer DNA duplexes, compound 3 shows similar ambiguous base‐pairing properties as 2′‐deoxyinosine ( 1 ), while the nucleosides 4 – 6 show strong pairing with each other and discriminate very little the four canonical DNA constituents.     

Determination of the Polar Compounds in Vegetable Oil by Ultra-Performance Liquid Chromatography–Quadrupole-Time-of-Flight-Mass Spectrometry with Chemometrics

High-throughput ultra-performance liquid chromatography–quadrupole time-of-flight mass spectrometry was combined with chemometric tools for the rapid determination of polar components in camellia oil, rapeseed oil, and waste cooking oil. The results were analyzed by two unsupervised methods: principal component analysis (one-way ANOVA, p<.05) and volcano plot analysis (p<.05, fold change ≥2) and supervised method: partial least squares discriminant analysis. The results showed that the oils were correctly classified based on their polar components. The first three principal components reflected most detail with a cumulative contribution rate of 84.67% using principal component analysis. The prediction accuracy was close to 100% using partial least squares discriminant analysis. Nineteen components were screened by principal component analysis; twelve were preliminary identified as palmitamide, phytosphingosine, eicosasphinganine, 1-monopalmitin, glyceryl monooleate, glyceryl monostearate, 1α-hydroxyvitamin D2, 1-linoleoyl glycerol, oleamide, sphinganine, stearamide, and linoleic acid. The proposed method may be applied to effectively and accurately authenticate edible oils.     

4‐Nitroindazole: Its Ambiguous Nature in Oligonucleotide Base Pairing and the Influence of the Glycosylation Position on the Duplex Stability

Oligonucleotides incorporating the regioisomeric 4‐nitroindazole N¹‐ and N²‐(2′‐deoxy‐β‐D ‐ribofuranosides) 7 and 8 were synthesized and their base‐pairing properties investigated. For solid‐phase synthesis, the phosphoramidites 11 and 12 were prepared. Oligonucleotides containing the building block 7 or 8 show ambiguous base pairing. Duplexes have similar T_m values when the modified bases are positioned opposite to the four canonical DNA constituents. The glycosylation position of the regioisomeric 4‐nitroindazole nucleosides has very little influence on the duplex stability.     

Elemental Chemometrics as Tools to Depict Stalked Barnacle (Pollicipes pollicipes) Harvest Locations and Food Safety

The stalked barnacle Pollicipes pollicipes is an abundant species on the very exposed rocky shore habitats of the Spanish and Portuguese coasts, constituting also an important economical resource, as a seafood item with high commercial value. Twenty-four elements were measured by untargeted total reflection X-ray fluorescence spectroscopy (TXRF) in the edible peduncle of stalked barnacles sampled in six sites along the Portuguese western coast, comprising a total of 90 individuals. The elemental profile of 90 individuals originated from several geographical sites (N = 15 per site), were analysed using several chemometric multivariate approaches (variable in importance partial least square discriminant analysis (VIP-PLS-DA), stepwise linear discriminant analysis (S-LDA), linear discriminant analysis (LDA), random forests (RF) and canonical analysis of principal components (CAP)), to evaluate the ability of each approach to trace the geographical origin of the animals collected. As a suspension feeder, this species introduces a high degree of background noise, leading to a comparatively lower classification of the chemometric approaches based on the complete elemental profile of the peduncle (canonical analysis of principal components and linear discriminant analysis). The application of variable selection approaches such as the VIP-PLS-DA and S-LDA significantly increased the classification accuracy (77.8% and 84.4%, respectively) of the samples according to their harvesting area, while reducing the number of elements needed for this classification, and thus the background noise. Moreover, the selected elements are similar to those selected by other random and non-random approaches, reinforcing the reliability of this selection. This untargeted analytical procedure also allowed to depict the degree of risk, in terms of human consumption of these animals, highlighting the geographical areas where these delicacies presented lower values for critical elements compared to the standard thresholds for human consumption.     

Distinguishing Ontario ginseng landraces and ginseng species using NMR-based metabolomics

The use of ¹H-NMR-based metabolomics to distinguish and identify unique markers of five Ontario ginseng (Panax quinquefolius L.) landraces and two ginseng species (P. quinquefolius and P. ginseng) was evaluated. Three landraces (2, 3, and 5) were distinguished from one another in the principal component analysis (PCA) scores plot. Further analysis was conducted and specific discriminating metabolites from the PCA loadings were determined. Landraces 3 and 5 were distinguishable on the basis of a decreased NMR intensity in the methyl ginsenoside region, indicating decreased overall ginsenoside levels. In addition, landrace 5 was separated by an increased amount of sucrose relative to the rest of the landraces. Landrace 2 was separated from the rest of the landraces by the increased level of ginsenoside R_b1. The Ontario P. quinquefolius was also compared with Asian P. ginseng by PCA, and clear separation between the two groups was detected in the PCA scores plot. The PCA loadings plot and a t-test NMR difference plot were able to identify an increased level of maltose and a decreased level of sucrose in the Asian ginseng compared with the Ontario ginseng. An overall decrease of ginsenoside content, especially ginsenoside R_b1, was also detected in the Asian ginseng’s metabolic profile. This study demonstrates the potential of NMR-based metabolomics as a powerful high-throughput technique in distinguishing various closely related ginseng landraces and its ability to identify metabolic differences from Ontario and Asian ginseng. The results from this study will allow better understanding for quality assessment, species authentication, and the potential for developing a fully automated method for quality control.

Metabolomic Profilings of Urine and Serum from High Fat-Fed Rats via 1H NMR Spectroscopy and Pattern Recognition

¹H NMR spectroscopy in combination with multivariate statistical analysis was applied to explore the metabolic variability in urine and serum of high fat-fed rats relative to normal chow-fed ones. Metabolites contributing to intergroup discrimination identified by partial least squares discriminant analysis include 3-hydroxybutyrate, glutamate, glutamine, citrate, choline, hippurate, alanine, lactate, creatinine, taurine, acetate, etc. The aging effect along with long-term feeding was delineated with metabolic trajectory in principal component analysis score plot and age-related differences on metabolic profiling under different dietary intervention were recognised. The identified metabolites responsible for obesity were all imported into a web tool for network-based interpretation of compound lists to interpret their functional context, molecular mechanisms and disturbed signalling pathway globally and systematically. The results are useful for interpreting the pathology of obesity and further probing into the relationship between dietary-induced obesity and type 2 diabetes mellitus.     

Mass spectrometry profiling analysis enables the identification of new modifications in ribosomal RNA

Ribosomal RNAs (rRNAs) provide the structural framework of ribosomes and play critical roles in protein translation. In ribosome biogenesis, rRNAs acquire various modifications that can influence the structure and catalytic activity of ribosomes. However, rRNA modifications in plants have yet to be fully defined. Herein, we proposed a method to purify rRNAs by a successive isolation with different strategies, including polyA-based mRNA depletion and agarose gel electrophoresis-based purification, with which highly pure rRNAs could be obtained. In addition, we developed a liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) method to systematically profile and characterize modifications from the isolated highly pure plant 18S rRNA and 25S rRNA. LC-ESI-MS/MS analysis showed that 10 and 12 kinds of modifications were present in plant 18S rRNA and 25S rRNA, respectively. Notably, among these identified modifications, 2 kinds of modifications of N²,N²-dimethylguanosine (m^2,2G) and N⁶,N⁶-dimethyladenosine (m^6,6A) in 18S rRNA, and 4 kinds of modifications of m^2,2G, m^6,6A, N7-methylguanosine (m⁷G) and 3-methyluridin (m³U) in 25S rRNA, were first reported to be present in plants. Moreover, exposure of Arabidopsis thaliana to cadmium (Cd) led to significant changes of modifications in both 18S rRNA and 25S rRNA of plants, indicating that rRNA modifications play important roles in response to environmental stress. The discovery of new modifications in plant rRNAs improves the spectra of plant rRNA modifications and may promote the investigation of the functional roles of plant ribosomes in regulating gene expression.     

Analysis of urinary nucleosides. IV. Identification of urinary purine nucleosides by liquid chromatography/electrospray mass spectrometry

Modified urinary nucleosides are potentially invaluable in cancer diagnosis. High-performance liquid chromatography (HPLC) was combined with full scan mass spectrometry (MS), tandem mass spectrometry and MSn analysis in order to identify purine nucleosides purified from urine. UV peaks evident in the chromatogram were examined by the various mass spectrometric techniques and adenosine, 1-methyladenosine, xanthosine, N1-methylguanosine, N2-methylguanosine, N2,N2-dimethylguanosine, N2,N2,N7-trimethylguanosine, inosine, and 1-methylinosine were each identified in the urine samples from cancer patients. The benefits of the use of LC/MS compared with HPLC alone are discussed.     

In and ex vivo breast disease study by Raman spectroscopy

In this work, Raman spectra in the 900?C1,800?cm^?1 wavenumber region of in vivo and ex vivo breast tissues of both healthy mice (normal) and mice with induced mammary gland tumors (abnormal) were measured. In the case of the in vivo tissues, the Raman spectra were collected for both transcutaneous (with skin) and skin-removed tissues. To identify the spectral differences between normal and cancer breast tissue, the paired t-test was carried out for each wavenumber using the whole spectral range from both groups. Quadratic discriminate analysis based on principal component analysis (PCA) was also used to determine and evaluate differences in the Raman spectra for the various samples as a basis for diagnostic purposes. The differences in the Raman spectra of the samples were due to biochemical changes at the molecular, cellular and tissue levels. The sensitivity and specificity of the classification scheme based on the differences in the Raman spectra obtained by PCA were evaluated using the receiver operating characteristic (ROC) curve. The in vivo transcutaneous normal and abnormal tissues were correctly classified based on their measured Raman spectra with a discriminant proportion of 73%, while the in vivo skin-removed normal and abnormal tissues were correctly classified again based on their measured Raman spectra with a discriminant proportion of 86%. This result reveals a strong influence due to the skin of the breast, which decreased the specificity by 11%. Finally, the results from ex vivo measurements gave the highest specificity and sensitivity: 96 and 97%, respectively, as well as a largest percentage for correct discrimination: 94%. Now that the important bands have been experimentally determined in this and other works, what remains is for first principles molecular-level simulations to determine whether the changes are simply due to conformational changes, due to aggregation, due to changes in the environment, or complex interactions of all of the above.     

A convenient approach towards boron cluster modifications with adenosine and 2′-deoxyadenosine

New 2′-deoxyadenosine and adenosoine modifications: 8-[(2-dimethylaminoethyl)amino]-2′-deoxyadenosine and 8-[(2-dimethylaminoethyl)amino]adenosine were prepared and their reactivity towards cyclic oxonium adducts of closo-dodecaborate and cobalt-bis-dicarbollide was studied. The cleavage reactions of clusters oxonium rings by N,N-dimethylanio group of modified nucleosides led to the first [B₁₂H₁₂]²⁻ and new [Co(C₂B₉H₁₁)₂]⁻ conjugates with adenosine and 2′-deoxyadenosine respectively. The proposed methodology provides a convenient route for the synthesis of libraries of boron cluster modified adenosine and 2′-deoxyadenosine derivatives for biological screening.     

Polymer coated sensor array based on quartz crystal microbalance for chemical agent analysis

Quartz crystal microbalance (QCM) gas sensors based on polymeric material were fabricated and their gas response characteristics were examined for four simulant gases of chemical agents, which were dimethyl methyl phosphonate (DMMP), N,N-dimethylacetamide (DMA), 1,5-dichloropentane (DCP) and dichloroethane (DCE). For the selection of appropriate coating materials, both principal component analysis (PCA) and hierarchical cluster methods were applied to a data set collected from 15 QCM sensors for 12 analytes. Four appropriate coating materials were selected after optimizing the correlation between the 15 coating materials and the first four principal component (PC) factors. The four chosen polymers were used as sensitive component for a sensor array, and then PCA is adapted to classify four simulant gases. The results show that the QCM sensor array has high sensitivity and selectivity to four chemical agents.     

New nucleoside analogues and their 5′-triphosphates: Synthesis and biological properties

Bicyclic furano-and pyrrolo[2,3-d]pyrimidine nucleosides and purine nucleosides modified at the N¹ atom and/or the 6-position have been synthesized. Among the tested nontoxic bicyclic nucleosides and N⁶-carboxyalkyladenosines, only furo[2,3-d]pyrimidine with the C₁₀H₂₁ substituent and N⁶-carboxymethyladenosine exhibit moderate anti-HCV activity in the virus replicon system and N¹-hydroxyinosine exhibits high anti-HCV activity and significant cytotoxicity. The corresponding 5′-triphosphates have been synthesized and studied as substrates/inhibitors of HCV enzymes: NS5B protein (RNA-dependent RNA polymerase) and NS3 protein (NTP-dependent RNA helicase).     

Structural Biochemistry 14. Permethylation of Nucleosides

Prominent molecular ions are generally observed in the field ionization (FI) mass spectra of unprotected nucleosides.² In the one exception so far observed, that of guanosine, we found the simple methyl derivative, N²,N²-dimethylguanosine, to afford an easily detectible molecular ion. The electron impact (EI) mass spectrum of N²,N²-dimethylguanosine also displayed a molecular ion and suggested that nucleoside methyl derivatives might be more easily studied by EI methods. For this purpose and the more important objective of developing methods for sequencing small nucleic acid units by computer assisted³ FI-EI mass spectrometry, a program was initiated (1967) to explore permethylation of nucleosides. We believe protection by permethylation to be superior to pertrimethylsilylation and acetylation principally for reasons involving molecular weight and stability. Concurrently it was anticipated that such nucleoside methylation studies would afford routes to partially mathylated nucleosides of value in characterizing such components of virus and cellular DNA and RNA⁴. Subsequently, using variations of the methanol-DCCI,⁵ diazomethane with various Lewis acids,⁶ methyl iodide in, for example, dimethylsulfoxide,⁷ methyl iodide-sodium hydride in dimethylformamide,⁸ methyl iodide-silver oxides⁹ and methyl iodidemethylsulfinyl carbanion in dimethylsulfoxide,¹⁰ techniques were evaluated but none was found to provide permethyl nucleosides in high yield.¹¹ The latter two methods have, however, been applied to methylating nucleosides for EI mass spectral investigations.¹²     

CE Profiling of Organic Acids in Distilled Alcohol Beverages Using Pattern Recognition Analysis

The objective of this work has been to assess the potential of capillary isotachophoretic organic acids profiling using multivariate statistical methods to classify brandy samples and wine distillate samples. The leading electrolyte was 10 mmol L⁻¹ hydrochloric acid including 0.1% methylhydroxylethylcellulose adjusted with β-alanine to pH 2.9. The terminating electrolyte was 5 mmol L⁻¹ acetic acid. Principal component analysis, cluster analysis, and linear discriminant analysis were used for the classification of beverages. The results show that for the 12 acids analysed, 98.57% of the total variance is extracted by the six principal components (PC). After performing backward linear discriminant analysis, a classification function was obtained containing four variables: formic (PC2-loadings: 0.989), lactic (PC1-loadings: 0.886), malic (PC1-loadings: 0.989) and oxalic (PC2-loadings: 0.777) acids, which provide 100.0% correct classification of brandies and wine distillates.

     

Substituent Reactivity and Tautomerism of Isoguanosine and Related Nucleosides

The substituent reactivity and tautomerism of isoguanine nucleosides is studied. Benzoylation or tosylation of isoguanine nucleosides (pyridine, room temperature) yields the 2-benzoyl derivatives 7c, 11 , and 12 or the 2-tosyl compounds 13 and 14 . The isobutyrylation of the 6-amino group which did not occur under these conditions was induced in the presence of Me₃SiCl. In the absence of Me₃SiCl, the reactivity of isoguanine substituents decreases in the order from 2-oxo → 5′-OH → 3′-OH → 6-NH₂. From isoguanine nucleosides, the N¹-( 2b ), N³-( 17 ), N⁶-( 15a,b ), and 2-O-alkylated ( 3b ) derivatives were prepared. Their pK_a values were determined and the UV and ¹³C-NMR spectra compared with regard to the alkylation position. Also the tautomeric forms of isoguanine nucleosides were determined UV-spectrophotometrically in aqueous and nonaqueous solution. Isoguanosine ( 1a ), its 2′-deoxy analogue 1b as well as the N⁶-methyl- and 8-substituted derivatives form lactam tautomers in aqueous solution, whereas the lactim form is present in dioxane.