An Integrated Metabolomic Screening Platform Discovers the Potential Biomarkers of Ischemic Stroke and Reveals the Protective Effect and Mechanism of Folic Acid

Folic acid has a protective effect against ischemic stroke. However, the protective pharmacological mechanism remains unclear. The aim of this study is to explore the protective effect of folic acid on ischemic stroke animals by an integrated metabolomic biomarker screening platform. Based on ultra-performance liquid chromatography-tandem mass spectrometry (UPLC/MS) coupled with multivariate data analysis, the changes in metabolites and pathways were characterized. We found that the metabolic alteration involved a total of 37 metabolites, of which 26 biomarkers such as γ-aminobutyric acid, lysine, glutamate, ribose, and valine can be regulated by folic acid via metabolic pathways of amino acid metabolism, carbohydrate metabolism, fatty acid metabolism, citrate cycle, and pyruvate metabolism, which may be the potential therapeutic targets of folic acid against ischemic stroke. Folic acid as an emerging potential natural anti-fibrosis agent has significant activity in protecting against middle cerebral artery occlusion-induced rat ischemic stroke model by delaying pathological development, reversing the metabolic biomarkers, and mainly regulating the perturbation in amino acid metabolism, carbohydrate metabolism, fatty acid metabolism, citrate cycle, and pyruvate metabolism. It also showed that the integrated metabolic biomarker screening platform could provide a better understanding of the therapeutic effect and mechanism of drugs.

Omics Technologies for High-Throughput-Screening of Cell-Biomaterial Interactions

Recent research effort in biomaterial development has largely focused on engineering bio-instructive materials to stimulate specific cell signaling. Assessing the biological performance of these materials using time-consuming and trial-and-error traditional...

Exploring lipid biomarkers of coronary heart disease for elucidating the biological effects of gelanxinning capsule by lipidomics method based on LC-MS

High-throughput lipidomics technology was used to explore the potential therapeutic targets and mechanism of action of gelanxinning capsule on rat model with coronary heart disease (CHD). This study attempts to provide a novel method to interpret the molecular mechanism of traditional medicine. The lipid markers of CHD were determined by full-scan analysis based on ultra-performance liquid chromatography-high-definition mass spectrometry. Then, the metabolic changes associated with gelanxinning capsule treatment via the modulation of lipid biomarkers and pathway in rats were characterized. After gelanxinning treatment, the metabolic profile tended to recover compared with the model group. A total of 26 potential biomarkers were identified to represent the disorders of lipid metabolism in CHD animal model, of which 19 were regulated by gelanxinning capsule administration, and four metabolic pathways such as glycerophospholipid metabolism, sphingolipid metabolism, glycosylphosphatidylinositol-anchor biosynthesis, and glycerolipid metabolism were involved. From the pathway analysis, it was found that glycerophospholipid metabolism and sphingolipid metabolism with significant differences have the potential to be regarded as new targets for the treatment of CHD. Gelanxinning capsule with its good therapeutic effect protects against CHD by regulating lipid biomarkers and pathway from lipidomics-guided biochemical analysis.

Identification of key lipid metabolites during metabolic dysregulation in the diabetic retinopathy disease mouse model and efficacy of Keluoxin capsule using an UHPLC-MS-based non-targeted lipidomics approach

Diabetic retinopathy (DR) is an important complication of diabetes, and is currently the main cause of blindness among young adults in the world. Previous studies have shown that Keluoxin (KLX) capsules have a significant effect on DR in C57BL/KsJ/db-/- mice (db/db mice), however the unclear mechanism limits its further clinical application and actual value. Further research is urgently needed for the treatment of DR disease. Discovery of key lipid biomarkers and metabolic pathways can reveal and explore the molecular mechanisms related to DR development and discover the effect of Keluoxin (KLX) capsule against DR in db/db mice. Lipidomics has been used for characterizing the pathological conditions via identification of key lipid metabolites and the metabolic pathway. In this study, the high-throughput lipidomics using UHPLC-Q-TOF/MS combined with multivariate statistical analysis, querying multiple network databases and employing ingenuity pathway analysis (IPA) method for molecular target prediction. A total of 30 lipid biomarkers were identified and 7 metabolic pathways including arachidonic acid metabolism and steroid hormone biosynthesis were found. The preventive effect of KLX intervention can regulate 22 biomarkers such as LysoPA(16:0/0:0), prostaglandin D2, cortisol and γ-linolenic acid, etc. IPA platform has predicted that PI3K/MAPK pathway are closely related to DR development. It also showed that high-throughput lipidomics combined with multivariate statistical analysis could deep excavate of the biological significance of the big data, and can provide molecular targets information about the disease treatment.

High-throughput metabolomics discovers metabolite biomarkers and insights the protective mechanism of schisandrin B on myocardial injury rats

Schisandrin B has been proved to possess anti-inflammatory and anti-endoplasmic effects, could improve cardiac function, inhibit apoptosis, and reduce inflammation after ischemic injury. However, the detailed metabolic mechanism and potential pathways of Schisandrin B effects on myocardial injury are unclear. Metabolomics could yield in-depth mechanistic insights and explore the potential therapeutic effect of natural products. In this study, the preparation of doxorubicin-induced myocardial injury rat model for evaluation of Schisandrin B on viral myocarditis sequelae related pathological changes and its mechanism. The metabolite profiling of myocardial injury rats was performed through ultra-high performance liquid chromatography combined with mass spectrometry combined with pattern recognition approaches and pathway analysis. A total of 15 metabolites (nine in positive ion mode and six in negative ion mode) were considered as potential biomarkers of myocardial injury, and these metabolites may correlate with the regulation of Schisandrin B treatment. A total of six metabolic pathways are closely related to Schisandrin B treatment, including glycerophospholipid metabolism, sphingolipid metabolism, purine metabolism, etc. This study revealed the potential biomarkers and metabolic network pathways of myocardial injury, and illuminated the protective mechanism of Schisandrin B on myocardial injury.

Functional Metabolomics Analysis Elucidating the Metabolic Biomarker and Key Pathway Change Associated With the Chronic Glomerulonephritis and Revealing Action Mechanism of Rhein

Chronic glomerulonephritis (CGN) as the culprit of kidney failure can increase the mortality of critically ill patients and seriously threatens people’s health all over the world. This study using metabolomics strategy is to reveal the potential therapeutic mechanism-related targets to evaluate the effects of rhein (RH) on CGN rats. Changes of serum metabolites and pathways were analyzed by non-targeted metabolomic method based on liquid chromatography-mass spectrometry (LC-MS) combined with ingenuity pathway analysis. In addition, the levels of biochemical indicators were also detected. A total of 25 potential biomarkers were identified to express serum metabolic turbulence in CGN animal model, and then 16 biomarkers were regulated by RH trending to the normal states. From metabolite enrichment and pathway analysis, pharmacological activity of RH on CGN were mainly involved in six vital metabolic pathways including phenylalanine, tyrosine and tryptophan biosynthesis, phenylalanine metabolism, arachidonic acid metabolism, tricarboxylic acid cycle (TCA cycle), alanine, aspartate, and glutamate metabolism, arginine and proline metabolism. It suggested CGN treatment with RH, which may be mediated via interference with metabolic pathway such as amino acid metabolism, arachidonic acid metabolism, and TCA cycle to regulating inflammation, oxidation response and immune regulation against CGN. It showed that metabolomics method offer deeply insight into the therapeutic mechanisms of natural product.

Network pharmacology combined with metabolomics approach to investigate the protective role and detoxification mechanism of Yunnan Baiyao formulation

BACKGROUND

Yunnan Baiyao (YNBY) is a traditional Chinese medicine formulae, which has the functions of hemostasis, activating blood circulation and removing blood stasis, anti-inflammation, etc. Although the presence of Caowu (CW, Aconiti Kusnezoffii Radix), the detoxification mechanism of YNBY is still unclear.

PURPOSE

In current study, network pharmacology, toxicological methods and metabolomics technique were applied to explore YNBY in attenuating toxicity of CW.

METHODS

Prediction of targets and pathways of CW were carried out by commonly used network pharmacological method. Simultaneously, SD rats were orally administrated with CW, processed CW (ZCW), YNBY, and YNBY which lack of CW (QCW) for 15 days. Tissue samples were observed with histopathology. Urine samples were analyzed with ultra-performance liquid chromatography-mass spectrometry to screen differential metabolites and related metabolic pathways associated with toxicity of CW. Furthermore, by comparing the changes of the metabolite contents, focused the attenuated metabolic pathway. Finally, the network pharmacological and experimental data were integrated to investigate detoxification mechanism of YNBY.

RESULTS

A total of 44 potential toxicity biomarkers were identified and 14 related pathways were involved in the toxicity of CW. Furthermore, 5 core toxicity biomarkers (2-keto-6-acetamidocaproate, γ-glutamylleucine, prostaglandin E₃, 4-hydroxy-5-(3'-hydroxyphenyl)-valeric acid-3'-O-sulphate, and 3,4-dihydroxy- phenylglycol O-sulfate) were regulated to normal condition in YNBY group. Lysine degradation was locked as the core metabolic pathway of detoxification of YNBY. Integrating the predicted results of network pharmacology, ACHE, SLC6A3, SLC6A4 might be the target of protective role of other herbs in YNBY.

CONCLUSION

Network pharmacology combined with metabolomics exhibited a powerful mean to investigate the herbal toxicity and probed into the detoxification mechanism of formulae, which contributes to its safety evaluation.

High-throughput metabolomic method based on liquid chromatography: high resolution mass spectrometry with chemometrics for metabolic biomarkers and pathway analysis to reveal the protective effects of baicalin on thyroid cancer

Cell metabonomics focuses on discovering metabolic biomarkers and pathway changes in cells from biological systems to obtain the cell properties and functional information under different conditions. Baicalin possesses various pharmacological activities, and plays a vital role in the oncology research field. However, the detailed mechanism of its action is still unclear. In this work, we employed ultra-high performance liquid chromatography-mass spectrometry (UPLC-MS) based non-targeted metabolomics method associated with chemometrics analysis to explore metabolic pathways and biomarkers for investigating the efficacy and pharmacological targets of baicalin against thyroid cancer cells. In addition, morphological observation, parameter calculation of cell proliferation and apoptosis were carried out, which assisted in elucidation of pharmacological activity of baicalin on the human thyroid cancer cells. The results showed that baicalin possesses an intense stimulative apoptosis and inhibits proliferation activity on SW579 human thyroid cancer cells, and partially reversed the cell metabolite abnormalities. A total of nineteen differentiated metabolites in SW579 cells were identified and deemed as potential biomarkers after the baicalin treatment, involving nine metabolic pathways, such as taurine and hypotaurine metabolism, pyrimidine metabolism, fructose and mannose metabolism, steroid hormone biosynthesis and sphingolipid metabolism. High-throughput non-targeted metabolomics provide an insight into specialized mechanism of baicalin against thyroid cancer and contributes to novel drug discovery and thyroid cancer management in clinical practice.

Untargeted lipidomics reveals progression of early Alzheimer's disease in APP/PS1 transgenic mice

Alzheimer's Disease (AD) is closely connected to aberrant lipid metabolism. However, how early AD-like pathology synchronously influences brain and plasma lipidome in AD mice remains unclear. The study of dynamic change of lipidome in early-stage AD mice could be of great interest for the discovery of lipid biomarkers for diagnosis and monitoring of early-stage AD. For the purpose, an untargeted lipidomic strategy was developed for the characterization of lipids (≤ 1,200 Da) perturbation occurring in plasma and brain in early-stage AD mice (2, 3 and 7 months) by ultra-high performance liquid chromatography coupled with quadrupole-time-of-flight mass spectrometry. Significant changes were detected in the levels of several lipid species including lysophospholipids, phosphatidylcholines (PCs), phosphatidylethanolamines (PEs) and Ceramides (Cers), as well as other related lipid compounds such as fatty acids (FAs), diacylglycerols (DGs) and triacylglycerols (TGs) in AD mice. In this sense, disorders of lipid metabolism appear to involve in multiple factors including overactivation of phospholipases and diacylglycerol lipases, decreased anabolism of lysophospholipids in plasma and PEs in plasma and brain, and imbalances in the levels of PCs, FAs and glycerides at different ages. We revealed the changing panels of potential lipid biomarkers with the development of early AD. The study raises the possibility of developing lipid biomarkers for diagnosis of early-stage AD.

High-Throughput Metabolomics Method for Discovering Metabolic Biomarkers and Pathways to Reveal Effects and Molecular Mechanism of Ethanol Extract From Epimedium Against Osteoporosis

Metabolomics is an effective strategy to explore the molecular mechanism of herbal medicine. Epimedium, a traditional Chinese herb from the Epimedium brevicornu Maxim., has a therapeutic effect on osteoporosis (OP), however the molecular mechanism of the anti-OP effect is uncle\ar. Therefore, we investigated the pharmacological effect and action mechanism of ethanol extract of epimedium (Ext-epi) onOP rat model. The serum of OP rats was analyzed utilized UPLC-Q-TOF/MS metabolomics, and the potential biomarkers were screened and identified using multivariate data analysis systems and network databases. To further appraise the influence of Ext-epi on biological markers and metabolic pathways, and reveal the potential mechanism of Ext-epi on OP treatment. The results showed that 46 potential biomarkers were screened out and after intervention with Ext-epi extracts solution, 16 potential biomarkers were significantly recalled. Further pathway experiments showed that key pathway analysis include sarachidonic acid metabolism, glycerolphospholipid metabolism as potential targets which is related with the efficacy of Ext-epi protect against OP. These results explain the correlation between metabolites and molecular mechanisms, which is of great significance for understanding the intervention of Ext-epi on OP. In short, based on UPLC-Q-TOF/MS metabolomics may provide effective strategies for understanding the pathogenesis of diseases and evaluating the intervention effect of natural products.

UPLC-MS metabolomics method provides valuable insights into the effect and underlying mechanisms of Rhizoma Drynariae protecting osteoporosis

Osteoporosis (OP) is a metabolic bone disease in which that volume of bone tissue per unit volume decrease, which is a common disease disturbing the elderly or postmenopausal women. Rhizoma Drynariae (RD) is a kind of herb widely used in thousands of years of clinical practice in China to tonify kidney and prevent osteoporosis, with reliable curative effect. However, the mechanism of its anti-osteoporosis action is still unclear. This study is dedicated to exploration the therapeutic effect of RD on retinoic acid solution-induced OP model rats based on high-throughput metabolomics technology platform, and reveal its influence on metabolomics level, so as to find effective potential biomarkers and therapeutic targets for diagnosing OP. OP model was established by intragastric administration of retinoic acid solution for 21 days, and then the treatment group was treated by intragastric administration of RD solution for 60 days. Blood samples of all groups were collected and analyzed based on UPLC-MS metabolomics and combined with EZinfo 3.0 data analysis, 32 potential biomarkers were identified, including 22 in ESI+ and 10 in ESI-, these biomarkers are related to 9 metabolic pathways. After treatment with RD solution, 21 biomarkers were obviously regulated, these mainly affected linoleic acid metabolic, glycerophospholipid metabolism and arachidonic acid metabolism pathway. The results show that RD can reduce the risk of OP disease, which may be related to the metabolic pathway mentioned above, and provides the foundation for the administer prophylaxis and treatment of OP with natural products.

A high-throughput and untargeted lipidomics approach reveals new mechanistic insight and the effects of salvianolic acid B on the metabolic profiles in coronary heart disease rats using ultra-performance liquid chromatography with mass spectrometry

High-throughput lipidomics provides the possibility for the development of new therapeutic drugs. Accordingly, herein, we reveal the protective role of salvianolic acid B (Sal B) in rats with coronary heart disease (CHD) and propose a new mechanism for its action through a high-throughput and non-targeted lipidomics strategy. A CHD animal model was induced by consecutive high-fat diet feeding with vitamin D3 injection. At the end of the 8th week, the serum sample was analyzed to explore the metabolic biomarker and pathway changes using untargeted lipidomics based on ultra-performance liquid chromatography with mass spectrometry (UPLC/MS). In addition, blood and heart tissue samples were collected and processed for the detection of biochemical indicators and liver histological observation. After salvianolic acid B treatment, the levels of LDH, CK, CK-MB, MYO, CTn1, TG, TC, LDL-c, and Apo(b) were significantly lower than that in the model group, while the levels of HDL-c and Apo(a1) were significantly higher than that in the model group. Furthermore, the histological features of fibrosis and steatosis were also evidently relieved in the model group. A total of twenty-six potential biomarkers were identified to express the lipid metabolic turbulence in the CHD animal models, of which twenty-two were regulated by salvianolic acid B trending to the normal state, including TG(20:0/20:4/o-18:0), PC(20:4/18:1(9Z)), PC(18:3/20:2), PA(18:0/18:2), LysoPE(18:2/0:0), SM(d18:0/22:1), PE(22:6/0:0), LysoPE (20:4/0:0), sphinganine, Cer(d18:0/18:0), PS(14:0/14:1), PC (18:0/16:0), LysoPC(17:0), PE(22:2/20:1), PC(20:3/20:4), PE(20:4/P-16:0), PS(20:3/18:0), cholesterol sulfate, TG(15:0/22:6/18:1), prostaglandin E2, arachidonic acid and sphingosine-1-phosphate. According to the metabolite enrichment and pathway analyses, the pharmacological activity of salvianolic acid B on CHD is mainly involved in three vital metabolic pathways including glycerophospholipid metabolism, sphingolipid metabolism and arachidonic acid metabolism. Thus, based on the lipidomics-guided biochemical analysis of the lipid biomarkers and pathways, Sal B protects against CHD with good therapeutic effect by regulating glycerophospholipid metabolism, sphingolipid metabolism and arachidonic acid metabolism, inhibiting oxidative stress damage and lipid peroxidation.

High-throughput lipidomics provides the possibility for the development of new therapeutic drugs.

Exploring the metabolic biomarkers and pathway changes in crucian under carbonate alkalinity exposure using high-throughput metabolomics analysis based on UPLC-ESI-QTOF-MS

The aims of this study is to explore the metabolomic biomarker and pathway changes in crucian under carbonate alkalinity exposures using high-throughput metabolomics analysis based on ultra-performance liquid chromatography-electrospray ionization-quadrupole time of flight-tandem mass spectrometry (UPLC-ESI-QTOF-MS) for carrying out adaptive evolution of fish in environmental exposures and understanding molecular physiological mechanisms of saline–alkali tolerance in fishes. Under 60 day exposure management, the UPLC-ESI-QTOF-MS technology, coupled with a pattern recognition approach and metabolic pathway analysis, was utilized to give insight into the metabolic biomarker and pathway changes. In addition, biochemical parameters in response to carbonate alkalinity in fish were detected for chronic impairment evaluation. A total of twenty-seven endogenous metabolites were identified to distinguish the biochemical changes in fish in clean water under exposure to different concentrations of carbonate alkalinity (CA); these mainly involved amino acid synthesis and metabolism, arachidonic acid metabolism, glyoxylate and dicarboxylate metabolism, pyruvate metabolism and the citrate cycle (TCA cycle). Compared with the control group, CA exposure increased the level of blood ammonia; TP; ALB; Gln in the liver and gills; GS; urea in blood, the liver and gills; CREA; CPS; Glu and LDH; and decreased the level of weight gain rate, oxygen consumption, discharge rate of ammonia, SOD, CAT, ALT, AST and Na⁺/K⁺-ATPase. At low concentrations, CA can change the normal metabolism of fish in terms of changing the osmotic pressure regulation capacity, antioxidant capacity, ammonia metabolism and liver and kidney function to adapt to the CA exposure environment. As the concentration of CA increases, various metabolic processes in crucian are inhibited, causing chronic damage to the body. The results show that the metabolomic strategy is a potentially powerful tool for identifying the mechanisms in response to different environmental exposomes and offers precious information about the chronic response of fish to CA.

We explore the metabolic biomarker and pathway changes accompanying the adaptive evolution of crucian subjected to carbonate alkalinity exposure, using UPLC-ESI-QTOF-MS, in order to understand the molecular physiological mechanisms of saline–alkali tolerance.

Retracted Article: A high-throughput metabolomics strategy for discovering the influence of differential metabolites and metabolic pathways of huaxian capsules on sepsis-associated Qi deficiency and blood stasis syndrome

High-throughput metabolomics can be used to investigate the therapeutic targets and metabolic mechanisms of traditional Chinese medicine formulae.

High-throughput metabolic profiling, combined with chemometrics and bioinformatic analysis reveals functional alterations in myocardial dysfunction

High-throughput metabolic profiling technology has been used for biomarker discovery and to reveal underlying metabolic mechanisms.

Retracted Article: High performance liquid chromatography coupled with high resolution mass spectrometry-based characterization of lipidomic responses from rats with kidney injuries

Metabolism of lipids is essential for the regulation of a variety of key cellular functions. Recent advances in high performance liquid chromatography coupled with high resolution mass spectrometry have expanded our knowledge of lipid metabolism in diseases. Currently, sepsis is one of the most important public health problems all over the world, which is a serious systemic inflammatory syndrome leading to infection by various agents or trauma and subsequently to a multiple organ dysfunction response. However, little is known about the lipids affected by sepsis and their roles in kidney injuries. In this study, we present targeted and non-targeted lipidomics strategies to discover the lipid metabolism variation in serum in rats with sepsis-induced kidney injuries. Liquid chromatography (LC) coupled with mass spectrometry (MS) and multivariate data analysis were used to obtain the global lipid metabolic profiles. In addition, biochemical parameters and histopathological examination results for the kidney were analyzed to support the pathological changes during sepsis-induced kidney injury. The identification of ten proposed lipids and five relevant pathways will promote a better understanding of lipid profile alterations in kidney injury. The results suggested that lipid metabolism in sepsis-induced kidney injury had changed significantly and contribute by offering potential targets for clinical diagnosis and therapy in the future, which would be worth further studies to broaden the applications of high performance liquid chromatography coupled with high resolution mass spectrometry in the study of lipid metabolism.

In this study, we present targeted and non-targeted lipidomics strategies to discover the lipid metabolism variation in serum in rats with sepsis-induced kidney injuries.

Lipidomic characterisation discovery for coronary heart disease diagnosis based on high-throughput ultra-performance liquid chromatography and mass spectrometry

Although many diagnostic tools have been developed for coronary heart disease (CHD), its diagnosis is still challenging. Lipids play an important role in diseases and a lipidomics approach could offer a platform to clarify the pathogenesis and pathologic changes of this disease. To the best of our knowledge, no lipidomics studies on serum have been attempted to improve the diagnosis and identify the potential biomarkers of CHD. The aim of this study was to investigate the distinctive lipid changes in serum samples of CHD patients and to identify candidate biomarkers for the reliable diagnosis of CHD using this platform. In this study, the serum lipid profiles of CHD patients were measured via ultra-performance liquid chromatography-G2-Si-high definition mass spectrometry combined with multivariate data analysis. A MetaboAnalyst tool was used for the analysis of the receiver operating-characteristic, while the IPA software was applied for the pathway analysis. The obtained results inferred that 33 lipid molecular species involving 6 fatty acids, 21 glycerophospholipids and 6 sphingolipids have significant differences in the serum of CHD patients. Simultaneously, 4 upstream regulatory proteins related to lipid metabolism disorders of CHD were predicted. Ten lipids have high clinical diagnostic significance according to the receiver operating-characteristic curves. This research shows that the in-depth study of lipids in the serum contributes to the clinical diagnosis of CHD and interprets the occurrence and development of CHD.

Although many diagnostic tools have been developed for coronary heart disease (CHD), its diagnosis is still challenging.