Bipartite network analysis reveals metabolic gene expression profiles that are highly associated with the clinical outcomes of acute myeloid leukemia

Dysregulated and reprogrammed metabolism are one of the most important characteristics of cancer, and exploiting cancer cell metabolism can aid in understanding the diverse clinical outcomes for patients. To investigate the differences in metabolic pathways among patients with acute myeloid leukemia (AML) and differential survival outcomes, we systematically conducted microarray data analysis of the metabolic gene expression profiles from 384 patients available from the Gene Expression Omnibus and Cancer Genome Atlas databases. Pathway enrichment analysis of differentially expressed genes (DEGs) showed that the metabolic differences between low-risk and high-risk patients mainly existed in two pathways: biosynthesis of unsaturated fatty acids and oxidative phosphorylation. Using the gene-pathway bipartite network, 62 metabolic genes were identified from 272 DEGs involved in 88 metabolic pathways. Based on the expression patterns of the 62 genes, patients with shorter overall survival (OS) durations in the training set (hazard ratio (HR) = 1.58, p = 0.038) and in two test sets (HR = 1.69 and 1.56 and p = 0.089 and 0.029, respectively) were well discriminated by hierarchical clustering analysis. Notably, the expression profiles of ALAS2, BCAT1, BLVRB, and HK3 showed distinct differences between the low-risk and high-risk patients. In addition, models for predicting the OS outcome of AML from the 62 gene signatures achieved improved performance compared with previous studies. In conclusion, our findings reveal significant differences in metabolic processes of patients with AML with diverse survival durations and provide valuable information for clinical translation.     

Chemometrics‐assisted chromatographic fingerprinting: An illicit methamphetamine case study

The volatile chemical constituents in complex mixtures can be analyzed using gas chromatography with mass spectrometry. This analysis allows the tentative identification of diverse impurities of an illicit methamphetamine sample. The acquired two‐dimensional data of liquid–liquid extraction was resolved by multivariate curve resolution alternating curve resolution to elucidate the embedded peaks effectively. This is the first report on the application of a curve resolution approach for chromatogram fingerprinting to identify particularly the embedded impurities of a drug of abuse. Indeed, the strong and broad peak of methamphetamine makes identifying the underlying peaks problematic and even impossible. Mathematical separation instead of conventional chromatographic approaches was performed in a way that trace components embedded in methamphetamine peak were successfully resolved. Comprehensive analysis of the chromatogram, using multivariate curve resolution, resulted in elution profiles and mass spectra for each pure compound. Impurities such as benzaldehyde, benzyl alcohol, benzene, propenyl methyl ketone, benzyl methyl ketone, amphetamine, N‐benzyl‐2‐methylaziridine, phenethylamine, N ,N ,α‐trimethylamine, phenethylamine, N ,α,α‐trimethylmethamphetamine, N‐acetylmethamphetamine, N‐formylmethamphetamine, and other chemicals were identified. A route‐specific impurity, N‐benzyl‐2‐methylaziridine, indicating a synthesis route based on ephedrine/pseudoephedrine was identified. Moreover, this is the first report on the detection of impurities such as phenethylamine, N ,α,α‐trimethylamine (a structurally related impurity), and clonitazene (as an adulterant) in an illicit methamphetamine sample.     

Metabolic mapping of Schisandra sphenanthera extract and its active lignans using a metabolomic approach based on ultra high performance liquid chromatography with high‐resolution mass spectrometry

Schisandra sphenanthera , the dried ripe fruit of Schisandra sphenanthera Rehd. et Wils , is widely used as a restorative, tonic and nutrition in many countries. Wuzhi tablet, an ethanol extract preparation of Schisandra sphenanthera , is a well‐known herbal medicine widely used in China. Our previous studies show that Wuzhi tablet and its active lignans significantly protect liver injury. However, its metabolic profile remains unknown in vivo and in vitro . In this study, ultra high performance liquid chromatography coupled with electrospray ionization high‐resolution mass spectrometry based metabolomics was employed to decipher the metabolic map of Wuzhi tablet and its active lignans. Serum (2 h) and urine (24 h) samples after a 700 mg/kg single oral dose of Wuzhi tablet, and mice liver microsome samples after incubation with its active lignans were collected and analyzed. The data were further analyzed using metabolomics and metabolite identification software. In total, 33 metabolites in vivo and 34 metabolites in vitro were identified, and six among them were new metabolites. The major metabolic reactions encompassed demethylation, hydroxylation, dehydrogenation, and epoxidation. Taken together, in vitro and in vivo studies revealed the metabolic profile of Wuzhi tablet and its active lignans and demethylation and hydroxylation were their major metabolic pathways.     

Plastic surface strain mapping of bent sheets by image correlation

A technique using a single CCD camera, a precision rotation/translation stage, a telecentric zoom lens, and digital image correlation software is described for measuring surface profiles and surface plastic strain distributions of a bent thin sheet. The measurement principles, based on both parallel and pinhole perspective projections, are outlined and the relevant mathematical equations for computing the profiles and displacement fields on a curved surface are presented. The typical optical setup as well as the experimental measurement and digital image correlation analysis procedure are described. The maximum errors in the in-plane and out-of-plane coordinates or displacements are about ±5 and ±25 μm, respectively, and the maximum errors in surface strain mapping are about 0.1% or less based on a series of evaluation tests on flat and curved sample surfaces over a physical field of view of 15.2 × 11.4 mm². As an application example, the shape and surface plastic strain distribution example, the shape and surface plastic strain distributions around a bent apex of a flat 2 mm thick automotive aluminum AA5182-O sheet, which underwent a 90° bend with three bend ratios of 2t, 1t, and 0.6t, are determined using the proposed technique.     

Towards the reduction of matrix effects in inductively coupled plasma mass spectrometry without compromising detection limits: The use of argon-nitrogen mixed-gas plasma

The multivariate optimization of a mixed-gas plasma was conducted in an attempt to find conditions minimizing matrix effects without sacrificing the detection limits that are observed with an all argon plasma optimized for maximum sensitivity in inductively coupled plasma mass spectrometry. Compared to the latter, where 49.1 ± 7.1% (n = 17) analyte signal suppression resulted in the presence of 0.1 M Na, 3.8 ± 3.2% suppression (and 2.8 ± 2.1% enhancement in some cases) was observed in the optimized mixed-gas plasma with 0.13% v/v N₂ in the plasma gas and 0.11% in the central channel as a sheath gas around the nebulizer gas flow. Furthermore, improved detection limits were observed for Al, Co, Pd, and V with the optimized mixed-gas plasma compared to an argon plasma at maximum sensitivity. The robustness of this mixed-gas plasma was further demonstrated through the accurate determination of U and Mo in NASS-5 seawater certified reference material using a simple external calibration, without matrix-matching or internal standardization. Indeed, the result obtained for Mo (9.1 ± 1.9 μg/L) was within the 95% confidence interval of the certified value of 9.6 ± 1.0 μg/L, while that obtained for U (3.0 ± 0.2 μg/L) was close to the information value of 2.6 μg/L. Spatial profiling results suggest better energy transfer between the toroidal zone and the central channel in the mixed-gas plasma.     

Determination of metabolites in Uncaria sinensis by HPLC and GC-MS after green solvent microwave-assisted extraction

Uncaria sinensis (Oliv.) Havil (Rubiaceae) has been used as an important Traditional Chinese Medicine (TCM) herb for the treatment of fevers and various nervous disorders. The major bioactive secondary metabolites from different classes of chemical compounds, i.e. organic acid, flavonoid and alkaloid, present in this TCM herb, namely catechin, caffeic acid, epicatechin and rhynchophylline, were extracted by microwave-assisted extraction (MAE) method with ultra-pure water as the extraction solvent. The optimal extraction conditions for this green solvent MAE method were found to be 100 °C for 20 min. The recoveries of the compounds were found to be comparable to that of heating under reflux using ultra-pure water for 60 min. The method precision (RSD, n = 6) was found to vary from 0.19% to 5.60% for the proposed method on different days for the secondary metabolites. Simultaneously, the key primary metabolites such as sucrose and phenylalanine for the biosynthesis of bioactive secondary metabolites were successfully characterized by GC-MS. Furthermore, an approach using the combination of primary and secondary metabolite profiling based on their chemical fingerprints with Principal Component Analysis (PCA) was successfully developed to evaluate the quality of U. sinensis obtained from different sources. This approach was shown to be feasible in discriminating U. sinensis from different origins and thus a potential application for the quality control of other medicinal herbs.     

Metabolic Profiling of Human Colorectal Cancer Using High Resolution 1H Nuclear Magnetic Resonance Spectroscopy

Colorectal cancer (CRC) is the third commonest malignancy cancer worldwide. Clear understandings of global metabolic profiling of the normal mucosa and cancer tissues are vitally important to aid optimizing the clinical management strategy and understanding CRC biology. We studied metabolic characteristics of 20 CRC and 20 distant normal mucosa tissues extracts from 20 patients using high resolution ¹H NMR spectroscopy in conjunction with multivariate analyses, such as principal component analysis (PCA). Compared with distant normal mucosa tissues, lactate, taurine, ornithine and polyamine were present at significantly higher levels in CRC tissue extracts whereas myo‐inositol was present at significantly lower level. Two metabolites ratios such as myo‐inositol/taurine and myo‐inositol/(ornithine+polyamine) appear to be the most valuable biomarkers for the differentiation CRC from normal mucosa tissues. Our data suggested that HR ¹H NMR spectroscopy combined with multivariate analyses is a potentially useful technology for detecting malignant changes in the normal mucosa tissues, the technique may be further exploited for future CRC biomarker research or identification of targets for therapeutic manipulations.     

Separation strategies for untargeted metabolomics

Metabolomics has rapidly become a profiling technique of choice for biomarker elucidation and molecular diagnostics in addition to studies focused on understanding disease pathogenesis. Key to the success of metabolomics in these areas has been the techniques to separate and analyze the chemically diverse group of compounds comprising the metabolome by using global and untargeted approaches. Untargeted metabolomic efforts have the goal of examining as many metabolites as possible simultaneously and most frequently use an LC/MS-based approach. Here, the importance of LC in an untargeted metabolomic workflow is outlined and separation strategies for optimization are reviewed within the context of these criteria.     

Liquid chromatography/mass spectrometry-based metabolic profiling to elucidate chemical differences of tobacco leaves between Zimbabwe and China

An approach was developed for extracting and analyzing the chemical components of tobacco leaves based on solvent extraction and rapid & resolution liquid chromatography/quadrupole time-of-flight mass spectrometry analysis. Two solvents with different polarities were used to extract hydrophilic components and hydrophobic components, respectively, the combined analytical data can provide a "global" view of metabolites. Based on the evaluation of parallel samples, it was found that this approach provided good repeatability, accurate and reliable profiling data, and is suitable for the metabolomics study of tobacco leaves. In order to find the chemical component differences of tobacco leaves, 56 samples from Zimbabwe and China were analyzed using the developed method. The metabolite data were processed by multivariate statistic technique; an obvious group classification between Zimbabwe and China was observed, 14 significantly changed compounds were found, and 9 of them were identified.     

Gas chromatography-mass spectrometric method for metabolic profiling of tobacco leaves

A gas chromatography-mass spectrometric method was developed for profiling of tobacco leaves. The differentiation among tobacco leaves planted in two different regions was investigated. Prior to analysis, the extraction solvent formulation was optimized and a combination of water, methanol and acetonitrile with a volume ratio of 3:1:1 was found to be optimal. The reproducibility of the method was satisfactory. Kendall tau-b rank correlation coefficients were equal to 1 (p<0.05) for 82% of the resolved peaks (up to 95% of the overall peak areas), indicating the good response correlation. Forty-four compounds including 9 saccharides, 9 alcohols, 9 amino acids, 16 organic acids and phosphoric acid were identified based on standard compounds. The method was successfully applied for profiling of tobacco leaves from Zimbabwe and Yunnan of China. Our result revealed that levels of saccharides and their derivatives including xylose, ribose, fructose, glucose, turanose, xylitol and glyceric acid were more abundant while sucrose, glucitol and D-gluconic acid were less abundant in tobacco leaves from Yunnan as compared to those from Zimbabwe. Amino acids such as L-alanine, L-tyrosine and L-threonine were found to be richer in Zimbabwe tobacco than in Yunnan tobacco.