Simultaneous Polar Metabolite and N-Glycan Extraction Workflow for Joint-Omics Analysis: A Synergistic Approach for Novel Insights into Diseases.

Bioinformatics and machine learning tools have made it possible to integrate data across different -omics platforms for novel multiomic insights into diseases. To synergistically process -omics data in an integrative manner, analyte extractions for each -omics type need to be done on the same set of clinical samples. Therefore, we introduce a simultaneous dual extraction method for generating both metabolomic (polar metabolites only) and glycomic (protein-derived N-glycans only) profiles from one sample with good extraction efficiency and reproducibility. As proof of the usefulness of the extraction and joint-omics workflow, we applied it on platelet samples obtained from a cohort study comprising 66 coronary heart disease (CHD) patients and 34 matched healthy community-dwelling controls. The metabolomics and N-glycomics data sets were subjected to block partial least-squares-discriminant analysis (block-PLS-DA) based on sparse generalized canonical correlation analysis (CCA) for identifying relevant mechanistic interactions between metabolites and glycans. This joint-omics investigation revealed intermodulative roles that protein-bound carbohydrates or glycoproteins and amino acids have in metabolic pathways and through intermediate protein dysregulations. It also suggested a protective role of the glyco-redox network in CHD, demonstrating proof-of-principle for a joint-omics analysis in providing new insights into disease mechanisms, as enabled by a simultaneous polar metabolite and protein-derived N-glycan extraction workflow.

Evaluation of Anti-Inflammatory Effects of Celery Leaf and Stem Extracts in LPS-Induced RAW 264.7 Cells Using Nitric Oxide Assay and LC-MS Based Metabolomics.

The present work demonstrated and compared the anti-inflammatory effects of celery leaf (CLE) and stem (CSE) extracts. LC-MS-based metabolomics were an effective approach to achieve the biomarker identification and pathway elucidation associated with the reduction in inflammatory responses. The celery extracts suppressed LPS-induced NO production in RAW 264.7 cells, and CLE was five times more effective than CSE. Distinct differences were revealed between the control and celery-treated samples among the 24 characteristic metabolites that were identified. In celery-treated LPS cells, reversals of intracellular (citrulline, proline, creatine) and extracellular (citrulline, lysine) metabolites revealed that the therapeutic outcomes were closely linked to arginine metabolism. Reversals of metabolites when treated with CLE (aspartate, proline) indicated targeted effects on the TCA and urea cycles, while, in the case of CSE (histidine, glucose), the glycolysis and the pentose phosphate pathways were implicated. Subsequently, apigenin and bergapten in CLE were identified as potential biomarkers mediating the anti-inflammatory response.

Effect of glycinebetaine on metabolite profiles of cold-stored strawberry revealed by 1H NMR-based metabolomics.

Glycinebetaine (GB) has long been used as a preservative for refrigerated fruits, but the effect of GB on the global metabolites of cold-stored strawberries is still unclear. In this study, the effects of exogenous application of GB on quality-related metabolites of cold-stored strawberries were investigated by nuclear magnetic resonance (NMR)-based metabolomic analysis. The results showed that the application of GB (especially at the concentration of 10 mM) on cold-stored strawberries effectively stabilized the sugars (d-xylose and d-glucose) and amino acids (tyrosine, leucine, and tryptophan) content, and lowered the acid (acetic acid) content as well. Additionally, the GB content in strawberries also increased. This implies that the appropriate concentration of GB is a natural and safe treatment, which could maintain the quality of cold-stored strawberries by regulating levels of quality-related metabolites, and the ingestion of GB-preserved strawberries may serve as a source of methyl-donor supplementation in our daily diet.

Application of omics beyond the central dogma in coronary heart disease research: A bibliometric study and literature review.

Despite remarkable progress in disease diagnosis and treatment, coronary heart disease (CHD) remains the number one leading cause of death worldwide. Many practical challenges still faced in clinical settings necessitates the pursuit of omics studies to identify alternative/orthogonal biomarkers, as well as to discover novel insights into disease mechanisms. Albeit relatively nascent as compared to the omics frontrunners (genomics, transcriptomics, and proteomics), omics beyond the central dogma (OBCD; e.g., metabolomics, lipidomics, glycomics, and metallomics) have undeniable contributions and prospects in CHD research. In this bibliometric study, we characterised the global trends in publication/citation outputs, collaborations, and research hotspots concerning OBCD-CHD, with a focus on the more prolific fields of metabolomics and lipidomics. As for glycomics and metallomics, there were insufficient publication records on their applications in CHD research for quantitative bibliometrics analysis. Thus, we reviewed their applications in health/disease research in general, discussed and justified their potential in CHD research, and suggested important/promising research avenues. By summarising evidence obtained both quantitatively and qualitatively, this study offers a first and comprehensive picture of OBCD applications in CHD, facilitating the establishment of future research directions.

Optimisation of an Aglycone-Enhanced Celery Extract with Germinated Soy Supplementation Using Response Surface Methodology.

In this study, the extraction conditions of bioactive aglycones from a celery extract supplemented with germinated soy were optimised by a response surface methodology. For subsequent enzymatic hydrolysis to enhance the apigenin content, increased production of its precursor apigetrin was firstly achieved through acidic extraction at optimal conditions, involving water at pH 1, at 75 °C for 2 h. Subsequently, a central composite design was conducted to analyse the pH (3-11) and temperature (25-35 °C) effects on the aglycone levels (apigenin, daidzein and genistein). The optimal extraction conditions were pH 7.02 and 29.99 °C, which resulted in a 40-fold increase in apigenin. The novel and cost-effective application of germinated soy ß-glucosidase for the conversion of aglycones in non-soy foods is demonstrated. The enhanced bioactivities of aglycones may suggest potential applications for similar formulations as functional food ingredients.

Untargeted LC-QTOF-MS/MS based metabolomics approach for revealing bioactive components in probiotic fermented coffee brews.

Amidst trends in non-dairy probiotic foods and functional coffees, we recently developed a fermented coffee brew containing high live counts of the probiotics Lacticaseibacillus rhamnosus GG and Saccharomyces boulardii CNCM-I745. However, probiotic fermentation did not alter levels of principal coffee bioactive components based on targeted analyses. Here, to provide therapeutic justification compared to other non-fermented coffee brews, we aimed to discover postbiotics in coffee brews fermented with L. rhamnosus GG and/or S. boulardii CNCM-I745. By using an untargeted LC-QTOF-MS/MS based metabolomics approach coupled with validated multivariate analyses, 37 differential metabolites between fermentation treatments were putatively annotated. These include the production of postbiotics such as 2-isopropylmalate by S. boulardii CNCM-I745, and aromatic amino acid catabolites (indole-3-lactate, p-hydroxyphenyllactate, 3-phenyllactate), and hydroxydodecanoic acid by L. rhamnosus GG. Overall, LC-QTOF based untargeted metabolomics can be an effective approach to uncover postbiotics, which may substantiate additional potential functionalities of probiotic fermented foods compared to their non-fermented counterparts.

1H NMR-based metabolomics for the discrimination of celery (Apium graveolens L. var. dulce) from different geographical origins.

Celery (Apium graveolens L. var dulce) is a widely cultivated vegetable which is popularly consumed due to its nutrient content and contains bioactive metabolites with positive effects on human physiology. In this study, 1H NMR spectroscopy coupled with multivariate statistical analyses was used to distinguish celery stem and leaf samples from different geographical origins. Principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA) were employed to investigate the differences between celery extracts from three geographical origins: Australia, Taiwan and China. Sugars, amino acids and organic acids were found to contribute significantly to the differentiation between origins, with mannitol identified as an important discriminating metabolite. It was demonstrated that NMR-based metabolomics is an effective approach for establishing reliable metabolomic fingerprints and profiles, enabling the identification of metabolite biomarkers for the possible discrimination of geographical origin.

Improved detection of key odourants in Arabica coffee using gas chromatography-olfactometry in combination with low energy electron ionisation gas chromatography-quadrupole time-of-flight mass spectrometry.

Four Arabica coffees (Brazil, Colombia, Ethiopia, and Guatemala) yield highly variant odours, attesting to the complexities of coffee aroma that command advanced analytical tools. In this study, their volatiles were extracted using solvent-assisted flavour evaporation (SAFE) and headspace solid-phase microextraction (HS-SPME). Due to matrix complexity, some trace odourants were detected in SAFE extracts by aroma extract dilution analysis (AEDA) but remained difficult to quantify by gas chromatography-mass spectrometry (GC-MS). This prompted the application of low energy electron ionisation (EI) coupled with GC-quadrupole time-of-flight (GC-QTOF). Optimal low EI GC-QTOF parameters (EI energy: 15 eV, acquisition rate: 3 Hz) were applied to achieve improved molecular ion signal intensity and reproducibility (relative standard deviation < 10%) across five compounds, which resulted in good linearity (R2 ≥ 0.999) and lowered detection levels (e.g. 0.025 ±â€¯0.005 ng/mL for 4-hydroxy-5-methyl-3(2H)-furanone). Therefore, this method potentially improves the measurement of trace odourants in complex matrices by increasing specificity and sensitivity.

A systematic study of molecular ion intensity and mass accuracy in low energy electron ionisation using gas chromatography-quadrupole time-of-flight mass spectrometry.

Molecular ions, which contain accurate mass information, are valuable for providing elemental composition elucidation. Under the most common electron ionisation (EI) condition (electron energy, 70 eV and temperature, 230 °C), molecular ions are often in relatively low intensities or completely unapparent. In this research, low energy EI source parameters (electron energy and temperature) in a gas chromatography-quadrupole time of flight (GC-QTOF) were systematically studied to evaluate their correlative impact on the intensity and mass accuracy of molecular ions. Lower temperatures were generally associated with higher molecular ion intensities under various EI energies. Apart from compounds with more chemically stable molecular ion structures, the lowest electron energy (12 eV) corresponded to higher intensities. On the other hand, mass accuracy appeared to be mostly constant (≤5 ppm) at different temperatures, while improvement was observed with the use of lower electron energies (12 eV). Moreover, the effect of compound concentration on molecular ion intensity and mass accuracy was studied from 50 to 5000 ppm, and the compound-specific concentration profiles were constructed. Finally, it was found that higher column flow rates corresponded to higher intensities, while the response under 12 eV was higher than that of 70 eV. Mass accuracy remained approximately constant across different flow rates. Therefore, these findings suggest that the use of low energy EI may be a viable approach for the preservation of molecular ions.