Comprehensive Metabolomic Analysis Research Articles

A comprehensive metabolomics analysis of Torreya grandis nuts with the effective de-astringent treatment during the postharvest ripening stage

Astringency removal is important for the quality of Torreya grandis nut and occurs after harvest. Here, we evaluated the effect of NaHCO3 treatment on astringency removal and compared the differential metabolites of the seed coat and kernel using a UHPLC QQQ-MS-based metabolomics approach. The result revealed the nut astringency was primarily enriched in the seed coat with more soluble tannins. The NaHCO3 treatment greatly shortened the de-astringency process, as indicated by a faster conversion of soluble tannins to insoluble tannins and more acetaldehyde production. Besides, a total of 293 metabolites, including 92 phenolic acids and 37 flavonoids, were tentatively characterized in the seed coat. A further comparative analysis of the metabolomics indicated epigallocatechin, gallocatechin, catechin, procyanidin B1, B2, B3 and C1 to be the major metabolites influenced by the NaHCO3 treatment. This study provides new insights regarding the metabolite differences of Torreya grandis nuts processed with different de-astringent treatments.

Comprehensive transcriptomic and metabolomic profiling reveals the differences between alfalfa sprouts germinated with or without light exposure.

Alfalfa sprouts are among the most nutritionally rich foods, and light exposure is a critical factor in determining their biomass and quality. However, detailed metabolic and molecular differences between yellow and green alfalfa sprouts remain unclear. In this study, comprehensive metabolomic and transcriptomic analyses were integrated to evaluate the nutrient composition of alfalfa sprouts during germination with or without light exposure. Differentially expressed genes and differentially accumulated metabolites in green and yellow alfalfa sprouts were significantly enriched in secondary metabolic pathways, such as the isoflavonoid biosynthesis pathway. Green alfalfa sprouts contained a wide variety of lipids, flavonoids, phenolic acids, and terpenoids, among which the top three upregulated were calycosin, methyl gallate, and epicatechin 3-gallate, whereas yellow alfalfa sprouts contained relatively more isoquercitrin. These results provide new insights into the nutritional value and composition of alfalfa sprouts under different germination regimes.

Therapeutic effect and mechanism of danshensu on coronary heart disease using liquid chromatography combined with mass spectrometry metabolomics

Metabolomics can discover the biomarkers and metabolic pathways, provides the possibility for insights into the pharmacological action and mechanism of natural products. The therapeutic effect and mechanism of danshensu (DSS) on total metabolic pathways has not been well investigated. The aim of this study was to explore the disturbed endogenous biomarkers and metabolic pathways reflecting the pharmacological activity of DSS, and mechanism of action of DSS using comprehensive metabolome analysis based on high-throughput metabolomics technology combined with ultra-high performance liquid chromatography (UPLC) coupled with quadrupole tandem time-of-flight mass spectrometry (Q-TOF-MS) and pattern recognition method. Through the changes of the overall metabolic profile and the related biomarkers, the intervention effect of natural product danshensu (DSS) treatment on CHD model rats was revealed. The results showed that after the model replication was established, the metabolic profile was clearly separated, and a total of 26 potential biomarkers were screened out, and involving 8 metabolic pathways. After different doses of DSS solution were given, a total of 20 biomarkers could be significantly regulated, mainly involving primary bile acid biosynthesis, glycerophospholipid metabolism, and lipid metabolism. It showed UPLC-MS-based metabolomics can be used for discovering potential biomarkers and metabolic pathways of CHD, and to further understand and dissecting pharmacological effects and mechanisms of natural products via metabolomics techniques.

Transcription-associated metabolomic profiling reveals the critical role of frost tolerance in wheat

BackgroundLow temperature is a crucial stress factor of wheat (Triticum aestivum L.) and adversely impacts on plant growth and grain yield. Multi-million tons of grain production are lost annually because crops lack the resistance to survive in winter. Particularlly, winter wheat yields was severely damaged under extreme cold conditions. However, studies about the transcriptional and metabolic mechanisms underlying cold stresses in wheat are limited so far.ResultsIn this study, 14,466 differentially expressed genes (DEGs) were obtained between wild-type and cold-sensitive mutants, of which 5278 DEGs were acquired after cold treatment. 88 differential accumulated metabolites (DAMs) were detected, including P-coumaroyl putrescine of alkaloids, D-proline betaine of mino acids and derivativ, Chlorogenic acid of the Phenolic acids. The comprehensive analysis of metabolomics and transcriptome showed that the cold resistance of wheat was closely related to 13 metabolites and 14 key enzymes in the flavonol biosynthesis pathway. The 7 enhanced energy metabolites and 8 up-regulation key enzymes were also compactly involved in the sucrose and amino acid biosynthesis pathway. Moreover, quantitative real-time PCR (qRT-PCR) revealed that twelve key genes were differentially expressed under cold, indicating that candidate genes POD, Tacr7, UGTs, and GSTU6 which were related to cold resistance of wheat.ConclusionsIn this study, we obtained the differentially expressed genes and differential accumulated metabolites in wheat under cold stress. Using the DEGs and DAMs, we plotted regulatory pathway maps of the flavonol biosynthesis pathway, sucrose and amino acid biosynthesis pathway related to cold resistance of wheat. It was found that candidate genes POD, Tacr7, UGTs and GSTU6 are related to cold resistance of wheat. This study provided valuable molecular information and new genetic engineering clues for the further study on plant resistance to cold stress.

Development of a High-Coverage Quantitative Metabolome Analysis Method Using Four-Channel Chemical Isotope Labeling LC-MS for Analyzing High-Salt Fermented Food.

Metabolome analysis of high-salt fermented food can be an analytical challenge, as the salts can interfere with the sample processing and analysis. In this work, we describe a four-channel chemical isotope labeling (CIL) LC-MS approach for a comprehensive metabolome analysis of high-salt fermented food. The workflow includes metabolite extraction, chemical labeling of metabolites using dansyl chloride, dansylhydrazine, or p-dimethylaminophenacyl bromide reagents to enhance separation and ionization, LC-UV measurement of the total concentration of dansyl-labeled metabolites in each sample for sample normalization, mixing of 13C- and 12C-reagent-labeled samples, high-resolution LC-MS analysis, and data processing. Metabolome analysis of fermented foods, including fermented red pepper (FRP) sauce, soy sauce, and sufu (a fermented soybean food), showed unprecedented high metabolic coverage. Metabolome comparison of FRP, soy sauce, and sufu, as well as soy sauce and sufu, indicated great diversity of metabolite types and abundances in these foods. In addition, we analyzed two groups of samples of the same type, FRP with 10% (w/w) and 15% (w/w) salt contents, and detected large variations in multiple categories of metabolites belonging to a number of different metabolic pathways. We envisage that this CIL LC-MS approach can be generally used for metabolomic studies of high-salt fermented food. CIL LC-MS allows high-coverage identification and quantification that could not be done using other methods.

A Comprehensive Metabolomics Analysis of Fecal Samples from Advanced Adenoma and Colorectal Cancer Patients.

Accurate diagnosis of colorectal cancer (CRC) still relies on invasive colonoscopy. Noninvasive methods are less sensitive in detecting the disease, particularly in the early stage. In the current work, a metabolomics analysis of fecal samples was carried out by ultra-high-performance liquid chromatography–tandem mass spectroscopy (UPLC-MS/MS). A total of 1380 metabolites were analyzed in a cohort of 120 fecal samples from patients with normal colonoscopy, advanced adenoma (AA) and CRC. Multivariate analysis revealed that metabolic profiles of CRC and AA patients were similar and could be clearly separated from control individuals. Among the 25 significant metabolites, sphingomyelins (SM), lactosylceramides (LacCer), secondary bile acids, polypeptides, formiminoglutamate, heme and cytidine-containing pyrimidines were found to be dysregulated in CRC patients. Supervised random forest (RF) and logistic regression algorithms were employed to build a CRC accurate predicted model consisting of the combination of hemoglobin (Hgb) and bilirubin E,E, lactosyl-N-palmitoyl-sphingosine, glycocholenate sulfate and STLVT with an accuracy, sensitivity and specificity of 91.67% (95% Confidence Interval (CI) 0.7753–0.9825), 0.7 and 1, respectively.

Metabolic and Epigenetic Regulation of SMAD7 by STC1 Ameliorates Lung Fibrosis.

As shown in our previous studies, the intratracheal-administration of STC1 (stanniocalcin-1) ameliorates pulmonary fibrosis by reducing oxidative and endoplasmic reticulum stress through the uncoupling of respiration in a bleomycin-treated mouse model. However, the overall effect of STC1 on metabolism was not examined. Therefore, we first conducted a comprehensive metabolomics analysis to screen the overall metabolic changes induced by STC1 in an alveolar epithelial cell line using capillary electrophoresis time-of-flight mass spectrometry. The results were subsequently validated in multiple alveolar epithelial and fibroblast cell lines by performing precise analyses of each substance. STC1 stimulated glycolysis, acetyl-CoA synthesis, and the methionine and cysteine-glutathione pathways, which are closely related to the uncoupling of respiration, modulation of epigenetics, and reduction in oxidative stress. These results are consistent with our previous study. Subsequently, we focused on the inhibitory factor SMAD7, which exerts an antifibrotic effect and is susceptible to epigenetic regulation. STC1 upregulates SMAD7 in an uncoupling protein 2-dependent manner, induces demethylation of the SMAD7 promoter region and acetylation of the SMAD7 protein in human alveolar epithelial and fibroblast cell lines and a bleomycin-treated mouse model, and subsequently attenuates fibrosis. The antifibrotic effects of STC1 may partially depend on the regulation of SMAD7. In the evaluation using lung tissue from patients with idiopathic pulmonary fibrosis, SMAD7 expression and acetylation were high in the alveolar structure-preserving region and low in the fibrotic region. The intratracheal administration of STC1 may prevent the development of pulmonary fibrosis by regulating the metabolism-mediated epigenetic modification of SMAD7 in patients.

Plasma taurine is an axonal excitability-translatable biomarker for amyotrophic lateral sclerosis

Although various body fluid biomarkers for amyotrophic lateral sclerosis (ALS) have been reported, no biomarkers specifically reflecting abnormalities in axonal excitability indices have currently been established. Capillary electrophoresis time-of-flight mass spectrometry and liquid chromatography time-of-flight mass spectrometry were used to perform a comprehensive metabolome analysis of plasma from seven ALS patients and 20 controls, and correlation analysis with disease phenotypes was then performed in 22 other ALS patients. Additionally, electrophysiological studies of motor nerve axonal excitability were performed in all ALS patients. In the ALS and control groups, levels of various metabolites directly associated with skeletal muscle metabolism, such as those involved in fatty acid β-oxidation and the creatine pathway, were detected. Receiver operating characteristic curve analysis of the top four metabolites (ribose-5-phosphate, N6-acetyllysine, dyphylline, 3-methoxytyrosine) showed high diagnostic accuracy (area under the curve = 0.971) in the ALS group compared with the control group. Furthermore, hierarchical cluster analysis revealed that taurine levels were correlated with the strength-duration time constant, an axonal excitability indicator established to predict survival. No significant effects of diabetes mellitus and treatment (Riluzole and Edaravone) on this relationship were detected in the study. Therefore, plasma taurine is a potential novel axonal excitability-translatable biomarker for ALS.

Sera Metabolomics Characterization of Patients at Different Stages in Wuhan Identifies Critical Biomarkers of COVID-19.

We have witnessed the 2-year-long global rampage of COVID-19 caused by the wide spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, knowledge about biomarkers of the entire COVID-19 process is limited. Identification of the systemic features of COVID-19 will lead to critical biomarkers and therapeutic targets for early intervention and clinical disease course prediction. Here, we performed a comprehensive analysis of clinical measurements and serum metabolomics in 199 patients with different stages of COVID-19. In particular, our study is the first serum metabolomic analysis of critical rehabilitation patients and critical death patients. We found many differential metabolites in the comparison of metabolomic results between ordinary, severe, and critical patients and uninfected patients. Through the metabolomic results of COVID-19 patients in various stages, and critical rehabilitation patients and critical death patients, we identified a series of differential metabolites as biomarkers, a separate queue and precise distinction, and predicted COVID-19 verification. These differentially expressed metabolites, included 1,2-di-(9Z,12Z-octadecadienoyl)-sn-glycero-3-phosphate, propylparaben, 20-hydroxyeicosatetraenoic acid, triethanolamine, chavicol, disialosyl galactosyl globoside, 1-arachidonoylglycerophosphoinositol, and alpha-methylstyrene, all of which have been identified for the first time as biomarkers in COVID-19 progression. These biomarkers are involved in many pathological and physiological pathways of COVID-19, for example, immune responses, platelet degranulation, and metabolism which might result in pathogenesis. Our results showed valuable information about metabolites obviously altered in COVID-19 patients with different stages, which could shed light on the pathogenesis as well as serve as potential therapeutic agents of COVID-19.

LC‐MS based urine metabolomic profiling indicate altered gut microbiome and host lipid metabolites in Parkinson’s disease

Evidence indicates that host and gut microbial metabolism are dysregulated prior to the onset of motor symptoms, in the prodromal phase of Parkinson’s disease (PD). There is currently no definitive test for the diagnosis of Parkinson’s disease; this represents an urgent, unmet medical need to enable the effectiveness of current and future therapeutic interventions for PD. The aim of this study was to understand changes in host and microbial metabolism in PD patient biofluids which could reflect a transition from the healthy to diseased state. We performed a comprehensive untargeted metabolomics analysis of urinary lipid metabolites together with altered metabolites associated with the gut microbiota. A total of 64 urine samples consisting of 31 from age matched healthy controls and 33 from PD patients were used in this study. Samples were deproteinized and analysed by reverse phase (RP)/UPLC‐MS/MS methods with positive and negative ion mode electrospray ionization (ESI) and HILIC/UPLC‐MS/MS with negative ion mode ESI. 14 lipid metabolites were significantly altered in PD patients. Five metabolites were associated with bile acid metabolism and nine were from the cholesterol pathway. Changes in secondary bile acid metabolism, particularly secondary bile acids indicative of microbial metabolism changes, were evident in PD patients, with 11 altered metabolites associated with the gut microbiota being significantly altered. Interestingly, several lipid metabolites that were altered in PD patients correlated with specific gut microbiome metabolites. Our results provide new insights into altered lipid metabolism and gut dysbiosis in PD, however, confirmation in a larger cohort would be needed.

Regulation of NAD Metabolism in Diastolic Dysfunction Induced by Metabolic Stress

Patients of heart failure with preserved ejection fraction (HFpEF) have diastolic dysfunction. Intervention targeting mechanisms of diastolic dysfunction is lacking, leading to a growing population of patients with HFpEF. Diabetes and obesity are key risk factors of HFpEF. NAD depletion is associated with heart failure, diabetes and obesity, and is due to NAD redox imbalance, suppressed synthesis and/or activated consumption pathways. Here, we used mouse models manipulating NAD redox balance and hydrolysis to determine their roles in metabolic cardiomyopathy. Cardiac Ndufs4‐KO mice (cKO) have lowered cardiac NAD/NADH ratio, normal baseline function, geometry and energetics. Chronic diabetic stress induced by streptozotocin (STZ) or diet‐induced obesity (DIO) in wild type (WT) mice promoted diastolic dysfunction, which was further exacerbated in cKO mice with latent cardiac NAD redox imbalance. Elevated oxidative stress by SOD2 acetylation and increased TnI‐S150 phosphorylation by energetic deficiency in diabetic cKO hearts led to exacerbated diastolic dysfunction. Elevation of cardiac NAD levels normalized NAD/NADH ratio, ameliorated these pathogenic mechanisms and diastolic dysfunction in metabolically stressed mice. These results supported the causal role of NAD redox imbalance in metabolic cardiomyopathy.Next, we tested whether deficiency of SARM1, an intracellular NAD hydrolase, will ameliorate diastolic dysfunction induced by metabolic stresses. WT and total SARM1‐KO mice were challenged with diabetic stress or DIO. These metabolic stresses led to a decline in diastolic function, which was improved in SARM1‐KO mice. DIO also promoted cardiac hypertrophy that was ameliorated by SARM1 deficiency. To determine that the improvement of diastolic function by SARM1 deficiency was not due to a reversal of systemic metabolic state, a comprehensive plasma metabolomic analyses was performed. Hyperglycemia was similar in diabetic WT and SARM1‐KO plasma. Metabolomic analyses showed significant changes in 58 out of 298 aqueous metabolites and in 26 out of 85 lipid species measured, when comparing non‐diabetic WT to diabetic WT plasma. When comparing the 84 metabolites with diabetic changes from diabetic WT and diabetic SARM1‐KO plasma, only one of the lipid metabolites (PC 16:0/16:0) showed a mild further decrease in SARM1‐KO plasma. The metabolomic data suggest that WT and SARM1‐KO hearts experienced similar metabolic stress, and that the improvement of diastolic dysfunction by SARM1 deficiency was due to the reversal of cardiac pathogenic mechanisms.To determine how SARM1 deficiency affected cardiac NAD metabolism, transcript levels of genes in NAD metabolic pathways were assessed. Expressions of Bst1 and Cd38 NAD hydrolases did not change in SARM1‐KO hearts, suggesting that SARM1 deficiency did not induce compensatory changes in expression of the other NAD hydrolases. SARM1‐KO hearts showed lower expressions in several other NAD consuming genes (e.g. Sirtuins) and NAD synthesis genes (e.g. Nmnats). Cardiac fibrosis, pro‐fibrotic genes (e.g. ctgf) and Nppb expression were induced in diabetic WT hearts and were suppressed by SARM1 deficiency. In summary, our data support the critical roles of NAD redox imbalance and SARM1 in diastolic dysfunction induced by metabolic stress.

Changes in primary metabolites and volatile organic compounds in cotton seedling leaves exposed to silver ions and silver nanoparticles revealed by metabolomic analysis.

In the area of climate change, nanotechnology provides handy tools for improving crop production and assuring sustainability in global agricultural system. Due to excellent physiological and biochemical properties, silver nanoparticles (AgNPs) have been widely studied for potential use in agriculture. However, there are concerns about the mechanism of the toxic effects of the accumulation of AgNPs on crop growth and development. In this study, the impacts of AgNPs on cotton (Gossypium hirsutum) seedlings were evaluated by integrating physiological and comprehensive metabolomic analyses. Potting-soil-grown, two-week-old cotton seedlings were foliar-exposed to 5 mg/plant AgNP or 0.02 mg/plant Ag+ (equivalent to the free Ag+ released from AgNPs). Primary metabolites and volatile organic compounds (VOCs) were identified by gas chromatography–mass spectrometry (GC-MS) and solid-phase microextraction (SPME) GC-MS, respectively. AgNPs inhibited the photosynthetic capacity of the cotton leaves. The metabolic spectrum analysis identified and quantified 73 primary metabolites and 45 VOCs in cotton leaves. Both treatments significantly changed the metabolite profiles of plant leaves. Among the primary metabolites, AgNPs induced marked changes in amino acids, sugars and sugar alcohols. Among the VOCs, 13 volatiles, mainly aldehydes, alkanes and terpenoids, were specifically altered only in response to AgNPs. In summary, our study showed that the comprehensive influence of AgNPs on primary metabolites and VOCs was not merely attributed to the released Ag+ but was caused by AgNP-specific effects on cotton leaves. These results provide important knowledge about the physiological and chemical changes in cotton leaves upon exposure to AgNPs and offer a new insight for supporting the sustainable use of AgNPs in agriculture.

Multi-Omics Reveals That the Rumen Transcriptome, Microbiome, and Its Metabolome Co-regulate Cold Season Adaptability of Tibetan Sheep

Tibetan sheep can maintain a normal life and reproduce in harsh environments under extreme cold and lack of nutrition. However, the molecular and metabolic mechanisms underlying the adaptability of Tibetan sheep during the cold season are still unclear. Hence, we conducted a comprehensive analysis of rumen epithelial morphology, epithelial transcriptomics, microbiology and metabolomics in a Tibetan sheep model. The results showed that morphological structure of rumen epithelium of Tibetan sheep in cold season had adaptive changes. Transcriptomics analysis showed that the differential genes were primarily enriched in the PPAR signaling pathway (ko03320), legionellosis (ko05134), phagosome (ko04145), arginine and proline metabolism (ko00330), and metabolism of xenobiotics by cytochrome P450 (ko00980). Unique differential metabolites were identified in cold season, such as cynaroside A, sanguisorbin B and tryptophyl-valine, which were mainly enriched in arachidonic acid metabolism, arachidonic acid metabolism and linolenic acid metabolism pathways, and had certain correlation with microorganisms. Integrated transcriptome-metabolome-microbiome analysis showed that epithelial gene-GSTM3 expression was upregulated in the metabolism of xenobiotics by the cytochrome P450 pathway during the cold season, leading to the downregulation of some harmful metabolites; TLR5 gene expression was upregulated and CD14 gene expression was downregulated in the legionellosis pathway during the cold season. This study comprehensively described the interaction mechanism between the rumen host and microbes and their metabolites in grazing Tibetan sheep during the cold season. Rumen epithelial genes, microbiota and metabolites act together in some key pathways related to cold season adaptation.

The Integrated Analysis of Transcriptomics and Metabolomics Unveils the Therapeutical Effect of Asiatic Acid on Alcoholic Hepatitis in Rats.

The present study was to investigate the therapeutical effects and mechanisms of Asiatic acid from Potentilla chinensis against alcoholic hepatitis. Rats were intragastrically fed with alcohol for 12weeks to induce alcoholic hepatitis and then treated with various drugs for further 12weeks. The results showed that Asiatic acid significantly alleviated liver injury caused by alcohol in rats, as evidenced by the improved histological changes and the lower levels of AST, ALT, and TBIL. Besides, Asiatic acid significantly enhanced the activity of ADH and ALDH, promoting alcohol metabolism. Asiatic acid suppressed CYP2E1 activity and NADP+/NADPH ratio, resulting in low ROS production. Further study revealed that Asiatic acid markedly reduced hepatocyte apoptosis by regulating the expression levels of apoptosis-related protein. Moreover, Asiatic acid could regulate the Nrf2 and NF-κB signaling pathway, attenuating oxidative stress and inflammation as a result. Interestingly, the comprehensive analysis of transcriptomics and metabolomics indicated that Asiatic acid inhibited the gene expression of Gpat3 and thereby affected the biosynthesis of the metabolites (1-acyl-Sn-glycerol-3-phosphocholine, phosphatidylcholine, phosphatidylethanolamine, and phosphatidylserine), regulating the glycerophospholipid metabolism pathway and ultimately ameliorating hepatocyte damage. In conclusion, this study demonstrates that Asiatic acid can ameliorate alcoholic hepatitis by modulating the NF-κB and Nrf2 signaling pathways and the glycerophospholipid metabolism pathway, which may be developed as a potential medicine for the treatment of alcoholic hepatitis.

ZOOMICS: Comparative Metabolomics of Red Blood Cells From Guinea Pigs, Humans, and Non-human Primates During Refrigerated Storage for Up to 42 Days.

Unlike other rodents, guinea pigs (Cavia porcellus) have evolutionarily lost their capacity to synthesize vitamin C (ascorbate) de novo and, like several non-human primates and humans, rely on dietary intake and glutathione-dependent recycling to cope with oxidant stress. This is particularly relevant in red blood cell physiology, and especially when modeling blood storage, which exacerbates erythrocyte oxidant stress. Herein we provide a comprehensive metabolomics analysis of fresh and stored guinea pig red blood cell concentrates (n = 20), with weekly sampling from storage day 0 through 42. Results were compared to previously published ZOOMICS studies on red blood cells from three additional species with genetic loss of L-gulonolactone oxidase function, including humans (n = 21), olive baboons (n = 20), and rhesus macaques (n = 20). While metabolic trends were comparable across all species, guinea pig red blood cells demonstrated accelerated alterations of the metabolic markers of the storage lesion that are consistent with oxidative stress. Compared to the other species, guinea pig red blood cells showed aberrant glycolysis, pentose phosphate pathway end product metabolites, purine breakdown products, methylation, glutaminolysis, and markers of membrane lipid remodeling. Consistently, guinea pig red blood cells demonstrated higher end storage hemolysis, and scanning electron microscopy confirmed a higher degree of morphological alterations of their red blood cells, as compared to the other species. Despite a genetic inability to produce ascorbate that is common to the species evaluated, guinea pig red blood cells demonstrate accelerated oxidant stress under standard storage conditions. These data may offer relevant insights into the basal and cold storage metabolism of red blood cells from species that cannot synthesize endogenous ascorbate.

Metabolic Footprinting of Microbial Systems Based on Comprehensive In Silico Predictions of MS/MS Relevant Data.

Metabolic footprinting represents a holistic approach to gathering large-scale metabolomic information of a given biological system and is, therefore, a driving force for systems biology and bioprocess development. The ongoing development of automated cultivation platforms increases the need for a comprehensive and rapid profiling tool to cope with the cultivation throughput. In this study, we implemented a workflow to provide and select relevant metabolite information from a genome-scale model to automatically build an organism-specific comprehensive metabolome analysis method. Based on in-house literature and predicted metabolite information, the deduced metabolite set was distributed in stackable methods for a chromatography-free dilute and shoot flow-injection analysis multiple-reaction monitoring profiling approach. The workflow was used to create a method specific for Saccharomyces cerevisiae, covering 252 metabolites with 7 min/sample. The method was validated with a commercially available yeast metabolome standard, identifying up to 74.2% of the listed metabolites. As a first case study, three commercially available yeast extracts were screened with 118 metabolites passing quality control thresholds for statistical analysis, allowing to identify discriminating metabolites. The presented methodology provides metabolite screening in a time-optimised way by scaling analysis time to metabolite coverage and is open to other microbial systems simply starting from genome-scale model information.

Cross-comparative metabolomics reveal sex-age specific metabolic fingerprints and metabolic interactions in acute myocardial infarction

The elucidation of metabolic perturbations and gender-age-specific metabolic characteristics associated with acute myocardial infarction (AMI) is essential for clinical risk stratification and disease management. A comprehensive cross-comparative metabolomics analysis was performed on the sera from 445 healthy controls, 347 AMI patients without cardiovascular disease (CVD), 79 AMI with CVD (AMICVD) patients including 27 deaths. Machine-learning-based integrated biomarker profiling and global network analysis were used to create a multi-biomarker for distinguishing the different AMI outcomes. The changes of most metabolites were dependent on AMI, but gender and age also give additional contributions to the changes of histidine, malonate, O-acetyl-glycoprotein and trimethylamine N-oxide. The altered metabolic pathways included gut dysbiosis, increased amino acid metabolism, glucose metabolism and ketone metabolism, and inactivation of tricarboxylic acid cycle. Enhanced histidine metabolism and microbiota dysbiosis may be one of the key factors during the developing of AMI into AMICVD. For the differential diagnosis of AMI events, three sets of specific multi-biomarkers provided relatively high accuracy with the areas under the curve more than 0.8 and hazard ratio more than 1 in the discovery set, and the results were reproduced and confirmed by the validation set. First use of cross-comparative metabolomics and machine-learning-based integrated biomarker analysis gives great capability to discriminate the different AMI outcomes. Also, the multi-biomarkers seem to be a valid and accurate auxiliary diagnosis biomarker in addition to standard stratification based on clinical parameters.

Clinical Parameters and Metabolomic Biomarkers That Predict Inhospital Outcomes in Patients With ST-Segment Elevated Myocardial Infarctions.

BackgroundPostoperative risk stratification is challenging in patients with ST-segment elevation myocardial infarction (STEMI) who undergo percutaneous coronary intervention. This study aimed to characterize the metabolic fingerprints of patients with STEMI with different inhospital outcomes in the early stage of morbidity and to integrate the clinical baseline characteristics to develop a prognostic prediction model.MethodsPlasma samples were collected retrospectively from two propensity score-matched STEMI cohorts from May 6, 2020 to April 20, 2021. Cohort 1 consisted of 48 survivors and 48 non-survivors. Cohort 2 included 48 patients with unstable angina pectoris, 48 patients with STEMI, and 48 age- and sex-matched healthy controls. Metabolic profiling was generated based on ultra-performance liquid chromatography and a mass spectrometry platform. The comprehensive metabolomic data analysis was performed using MetaboAnalyst version 5.0. The hub metabolite biomarkers integrated into the model were tested using multivariate linear support vector machine (SVM) algorithms and a generalized estimating equation (GEE) model. Their predictive capabilities were evaluated using areas under the curve (AUCs) of receiver operating characteristic curves.ResultsMetabonomic analysis from the two cohorts showed that patients with STEMI with different outcomes had significantly different clusters. Seven differentially expressed metabolites were identified as potential candidates for predicting inhospital outcomes based on the two cohorts, and their joint discriminative capabilities were robust using SVM (AUC = 0.998, 95% CI 0.983–1) and the univariate GEE model (AUC = 0.981, 95% CI 0.969–0.994). After integrating another six clinical variants, the predictive performance of the updated model improved further (AUC = 0.99, 95% CI 0.981–0.998).ConclusionA survival prediction model integrating seven metabolites from non-targeted metabonomics and six clinical indicators may generate a powerful early survival prediction model for patients with STEMI. The validation of internal and external cohorts is required.

Integrated Transcriptomics and Metabolomics Analyses of Stress-Induced Murine Hair Follicle Growth Inhibition.

Psychological stress plays an important role in hair loss, but the underlying mechanisms are not well-understood, and the effective therapies available to regrow hair are rare. In this study, we established a chronic restraint stress (CRS)-induced hair growth inhibition mouse model and performed a comprehensive analysis of metabolomics and transcriptomics. Metabolomics data analysis showed that the primary and secondary metabolic pathways, such as carbohydrate metabolism, amino acid metabolism, and lipid metabolism were significantly altered in skin tissue of CRS group. Transcriptomics analysis also showed significant changes of genes expression profiles involved in regulation of metabolic processes including arachidonic acid metabolism, glutathione metabolism, glycolysis gluconeogenesis, nicotinate and nicotinamide metabolism, purine metabolism, retinol metabolism and cholesterol metabolism. Furthermore, RNA-Seq analyses also found that numerous genes associated with metabolism were significantly changed, such as Hk-1, in CRS-induced hair growth inhibition. Overall, our study supplied new insights into the hair growth inhibition induced by CRS from the perspective of integrated metabolomics and transcriptomics analyses.

Comprehensive analysis of transcriptomics and metabolomics to illustrate the underlying mechanism of helenalin against hepatic fibrosis

This study aimed to investigate the protective mechanisms of helenalin on hepatic fibrosis. In brief, rats were intragastrically administrated with 50% CCl4 for 9 weeks to induce liver fibrosis, followed by treatment with various agents for 6 weeks. The effects of helenalin on hepatic injury were assessed by pathological examinations. The potential targets were predicted by the “Drug-Disease” bioinformatic analysis and then verified by multiple experiments. Moreover, the underlying mechanism was investigated by transcriptomics and metabolomics as a whole. The results showed that helenalin significantly alleviated hepatocyte necrosis and hepatic injury, as proved by the pathological examinations. Also, helenalin markedly attenuated hepatocyte apoptosis by regulating the expression of caspase-3 and Bcl-2 families. Besides, helenalin could significantly reduce collagen accumulation, as evidenced by the decreased contents of collagen, hyaluronic acid and laminin. Moreover, helenalin significantly down-regulated the phosphorylation of PI3K, Akt, FAK, mTOR and P70S6K, and PTEN protein expression, suggesting that helenalin inhibited the PI3K/Akt signaling cascade. Meanwhile, helenalin inhibited the NF-κB signaling pathway by reducing the phosphorylation of IκBα, NF-κB p65 and IKKα/β, alleviating inflammation response. Interestingly, the analysis of transcriptomics and metabolomics indicated that helenalin inhibited the glycerophospholipid metabolism pathway by down-regulating the target genes (CHKA, ETNPPL, LYPLA1, PCYT2, PLD4 and PNPLA6), ultimately ameliorating hepatocyte damage. In conclusion, helenalin ameliorates hepatic fibrosis by regulating the PI3K/Akt and NF-κB signaling pathways and the glycerophospholipid metabolism pathway.