Metabolite profiling and pathway analysis of acute hepatitis rats by UPLC-ESI MS combined with pattern recognition methods

Use of high-resolution metabolomics to assess the biological perturbations associated with maternal exposure to Bisphenol A and Bisphenol F among pregnant African American women

BACKGROUND

Human and animal exposure to bisphenol A (BPA) has been associated with adverse developmental and reproductive effects. The molecular mechanisms by which BPA exposure exerts its effects are not well-understood, even less known about its analogues bisphenol F (BPF). To address these knowledge gaps, we conducted an untargeted metabolome-wide association study (MWAS) to identify metabolic perturbations associated with BPA/BPF exposures in a pregnant African American cohort.

METHODS

From a subset of study participants enrolled in the Atlanta African American Maternal-Child cohort, we collected both urine samples, for targeted exposure assessment of BPA (N = 230) and BPF (N = 48), and serum samples, for high-resolution metabolomics (HRM) profiling (N = 230), during early pregnancy (8-14 weeks' gestation). Using an established untargeted HRM workflow consisting of MWAS modeling, pathway enrichment analysis, and chemical annotation and confirmation, we investigated the potential metabolic pathways and features associated with BPA/BPF exposures.

RESULTS

The geometric mean creatinine-adjusted concentrations of urinary BPA and BPF were 0.85 ± 2.58 and 0.70 ± 4.71 µg/g creatinine, respectively. After false positive discovery rate correction at 20 % level, 264 and 733 unique metabolic features were significantly associated with urinary BPA and BPF concentrations, representing 10 and 12 metabolic pathways, respectively. Three metabolic pathways, including steroid hormones biosynthesis, lysine and lipoate metabolism, were significantly associated with both BPA and BPF exposure. Using chemical standards, we have confirmed the chemical identity of 16 metabolites significantly associated with BPA or BPF exposure.

CONCLUSIONS

Our findings support that exposure to BPA and BPF in pregnant women is associated with the perturbation of aromatic amino acid metabolism, xenobiotics metabolism, steroid biosynthesis, and other amino acid metabolism closely linked to stress responses, inflammation, neural development, reproduction, and weight regulation.

Liver and urine metabolomics reveal the protective effect of Gandou decoction in copper-laden Hepatolenticular degeneration model rats

Hepatolenticular degeneration (HLD) is an inherited disorder associated with human copper metabolism. Gandou decoction (GDD), a traditional Chinese medicinal formula, has been used as a therapeutic agent for the treatment of HLD in China for decades. Recent pharmacological evaluation in our laboratory has demonstrated that GDD exerts positive and beneficial effects on HLD model rats. However, its underlying therapeutic mechanisms are not yet well understood. To explore the potential therapeutic effects of GDD against HLD, liver and urine metabolomics approach combined with histopathological examination were performed to reveal the underlying mechanisms. Changes in metabolic profiles were estimated by ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) coupled with multivariate statistical analyses. The results indicated that GDD could significantly improve liver pathological variations. Moreover, 19 and 11 significantly altered metabolites were found in the liver and urine between the normal and model groups, respectively. After GDD treatment, the levels of all these disordered metabolites showed different degrees of improvement compared with the model group, including lysoPC(18:2), lysoPE(20:2/0:0), PC(18:1/14:1), alpha-linolenic acid, sphinganine, taurochenodesoxycholic acid, tetracosahexaenoic acid, 13-OxoODE, and 13-L-hydroperoxyl inoleic acid. Metabolic pathway enrichment suggested that lipid and oxidative stress metabolism were the two main pathways that participated in copper-laden rat models with GDD administration. This work indicates that GDD could achieve a therapeutic effect on HLD by ameliorating the associated metabolic disturbances.

Clinical Application of Metabolomics in Pancreatic Diseases: A Mini-Review

Metabolomics is a powerful new analytical method to describe the set of metabolites within cellular tissue and bodily fluids. Metabolomics can uncover detailed information about metabolic changes in organisms. The morphology of these metabolites represents the metabolic processes that occur in cells, such as anabolism, catabolism, inhomogeneous natural absorption and metabolism, detoxification, and metabolism of biomass energy. Because the metabolites of different diseases are different, the specificity of the changes can be found by metabolomics testing, which provides a new source of biomarkers for the early identification of diseases and the difference between benign and malignant states. Metabolomics has a wide application potential in pancreatic diseases, including early detection, diagnosis, and identification of pancreatic diseases. However, there are few studies on metabolomics in pancreatic diseases in the literature. This article reviews the application of metabolomics in the diagnosis, prognosis, treatment, and evaluation of pancreatic diseases.

Optimization of extraction parameters of Pleurotus eryngii polysaccharides and evaluation of the hypolipidemic effect

The hot water extraction of polysaccharides from the fruiting body of Pleurotus eryngii was studied. In this paper, according to single-factor experiments, a response surface methodology and the Box–Behnken design were applied to optimize the extraction parameters of Pleurotus eryngii polysaccharides (PEP). The optimal extraction conditions were as follows: a temperature of 79 °C, a time of 3.11 h, a ratio of water to fruiting bodies of 52.6 mL g⁻¹. Under these parameters, the yield of PEP was 7.53%. When mice with hyperlipidemia were administered low, medium or high doses of PEP, their body weight was reduced compared with the model group, and the degree of weight loss was proportional to the dose. At the 16th week of PEP treatment, blood lipid biochemical parameters such as total cholesterol, triglycerides, low-density lipoprotein-cholesterol, aspartate aminotransferase, and alanine aminotransferase levels were all decreased. However, high-density lipoprotein-cholesterol levels increased after PEP treatment. Histopathological examination of the liver showed that low, medium and high doses of PEP had a certain liver protective effect. High-dose PEP treatment had the best effect in regard to lipid-lowering and liver protection. In addition, the metabolome of the mice was analyzed by LC-MS, and the results indicated that C16 sphinganine can be used as a potential biomarker, which displayed significant differences among the six groups. In conclusion, the possible metabolic mechanism of the PEP on lipid-lowering was closely related to sphingolipid metabolism.

The hot water extraction of polysaccharides from the fruiting body of Pleurotus eryngii was studied.

Serum and urine metabolomics reveal potential biomarkers of T2DM patients with nephropathy

Background

Diabetes is a metabolic disease and is often accompanied by severe microvascular and macrovascular complications. A comprehensive understanding of its complex mechanisms can help prevent type 2 diabetes mellitus (T2DM) complications, such as diabetic nephropathy (DN).

Methods

To reveal the systemic metabolic changes related to renal injury, clinical information of T2DM patients with or without nephropathy was collected, and it was found that serum urea levels of DN patients were significantly higher in T2DM patients without nephropathy. Further along the disease progression, the serum urea levels also gradually increased. We used gas chromatograph coupled with time-of-flight mass spectrometry (GC-TOFMS) metabolomics to analyze the serum and urine metabolites of T2DM patients with or without nephropathy to study the metabolic changes associated with the disease.

Results

Finally, we identified 61 serum metabolites and 46 urine metabolites as potential biomarkers related to DN (P<0.05, VIP >1). In order to determine which metabolic pathways were major altered in DN, we summarized pathway analysis based on P values from their impact values and enrichment. There were 9 serum metabolic pathways and 12 urine metabolic pathways with significant differences in serum and urine metabolism, respectively.

Conclusions

This study emphasizes that GC-TOFMS-based metabolomics provides insight into the potential pathways in the pathogenesis and progression of DN.

High-Throughput Metabolomics for Identification of Metabolic Pathways and Deciphering the Effect Mechanism of Dioscin on Rectal Cancer From Cell Metabolic Profiles Coupled With Chemometrics Analysis

High-throughput liquid chromatography-mass spectrometry (LC-MS)-based metabolomics can provide the holistic analysis of the low molecular weight endogenous metabolites in cells and reflect the changes of cellular regulation and metabolic pathways. Our study designed to reveal the potentially pharmacological effects of dioscin on SW480 rectal cancer cells using nontargeted metabolomics method to probe into small molecular metabolites and pathway changes. After the cell assay of proliferation, apoptosis, migration, and invasion, the dioscin-treated cell samples were prepared for nontargeted metabolomics analysis based on LC-MS tool to describe the metabolic profiles. Dioscin has prevented cell proliferation and accelerated cell apoptosis, and it also inhibited the SW480 rectal cancer cells' migration and invasion. A total of 22 metabolites were selected as promising biomarkers of pharmacological reaction of dioscin to rectal cancer, and eight highly correlated pathways including D-glutamine and D-glutamate metabolism, pyruvate metabolism, arachidonic acid metabolism, phenylalanine metabolism, tryptophan metabolism, glycolysis or gluconeogenesis, citrate cycle (TCA cycle), and butanoate metabolism were identified. It showed that strategies based on cell metabolomics are helpful tools to discover the small molecular metabolites to elucidate the action mechanism of drug.

Comparative metabolomics unveils molecular changes and metabolic networks of syringin against hepatitis B mice by untargeted mass spectrometry

Untargeted metabolomics technology was used to discover the metabolic pathways and biomarkers for revealing the potential biological mechanism of syringin on hepatitis B virus. Serum samples were analyzed by ultra-performance liquid chromatography-mass spectrometry (UPLC-MS)-based comparative metabolomics coupled with pattern recognition methods and network pathway. In addition, the histopathology, HBV DNA detection of liver tissue, and biochemical indicators of liver function change were also explored for investigating the antiviral effect of syringin. In comparison to the model group, the metabolic profiles of the turbulence in transgenic mice tended to recover to the same as the control group after syringin therapy. A total of 33 potential biomarkers were determined to explore the metabolic disorders in the hepatitis B animal model, of which 25 were regulated by syringin, and 8 metabolic pathways, such as phenylalanine, tyrosine and tryptophan biosynthesis, phenylalanine metabolism, arachidonic acid metabolism, glyoxylate and dicarboxylate metabolism, were involved. Syringin markedly reduced the liver pathology change, inhibited HBV DNA replication, and improved liver function. Amino acid metabolism is a potential target for the treatment of hepatitis B. The hepatoprotective effect of syringin may contribute to ameliorating oxidative stress and preventing protein and DNA replication. Comparative metabolomics is a promising tool for discovering metabolic pathways and biomarkers of the hepatitis B animal model as targets to reveal the effects and mechanism of syringin, which benefits the development of natural products and advances the treatment of diseases.

Untargeted metabolomics technology was used to discover the metabolic pathways and biomarkers for revealing the potential biological mechanism of syringin on hepatitis B virus.

High-throughput liquid chromatography mass-spectrometry-driven lipidomics discover metabolic biomarkers and pathways as promising targets to reveal the therapeutic effects of the Shenqi pill

Lipidomics, a branch of metabonomics, could provide a powerful technique for discovery of lipid molecules to reveal disease status and drug efficacy.

Using high-throughput metabolomics to discover perturbed metabolic pathways and biomarkers of allergic rhinitis as potential targets to reveal the effects and mechanism of geniposide

In this study, we probed the molecular mechanisms of metabolic biomarkers and pathways affected by the bioactive ingredient geniposide (GP), which was shown to protect against experimental allergic rhinitis in mice. The methods used here involved a metabolomics strategy based on ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-TOF/MS). Using the metabolomics strategy, serum samples of mice in control, model and GP groups were used to explore the differential production of metabolites and pathways related to defense activity of GP towards allergic rhinitis. Allergic symptom, inflammatory factors, and cell populations in the mice spleens were reversed by GP treatment. Seventeen potential biomarkers were discovered in experimental allergic rhinitis mice. GP was shown to have a regulatory effect on 12 of them, which were associated with 8 key metabolic pathways. The ingenuity pathway analysis platform was used to further understand the relationship between metabolic changes and pharmacological activity of GP. The pathways which affected by GP involved cellular growth and proliferation, organismal development, and free radical scavenging. This metabolomics study produced valuable information about potential biomarkers and pathways affected by GP during its effective prevention and therapeutic targeting of allergic rhinitis.

In this study, we probed the molecular mechanisms of metabolic biomarkers and pathways affected by the bioactive ingredient geniposide (GP), which was shown to protect against experimental allergic rhinitis in mice.

High-Throughput Metabolomics Evaluate the Efficacy of Total Lignans From Acanthophanax Senticosus Stem Against Ovariectomized Osteoporosis Rat

Postmenopausal osteoporosis (PMOP) is a common clinical illness in postmenopausal women, but there is no effective drug at present. Metabolomics approach was used to explore the potential biomarkers of PMOP and evaluate the efficacy and therapeutic targets of total lignans in the stem of Acanthophanax senticosus (ASSL) on the ovariectomized osteoporosis model rats. UPLC/MS and pattern recognition methods were used for serum metabolites discovery to illustrate the pathological mechanism of PMOP model rats, and then revealing the intervention effect of ASSL. The pattern recognition result showed that serum metabolic profiles of the sham operation group and the model group were clustered clearly, and 16 potential biomarkers were finally identified (7 in positive ion mode and 9 in negative ion mode), and they are involved in 15 related metabolic pathways. After oral administration of ASSL, 10 biomarkers were found to be significantly up-regulated and mainly regulated metabolic pathways include unsaturated fatty acid biosynthesis, linoleic acid metabolism, and arachidonic acid metabolism, primary bile acid synthesis, tyrosine metabolism, etc. Our study demonstrated that the ASSL could affect the endogenous metabolites related metabolic mechanism, provides a pharmacological basis of the ASSL for PMOP treatment.

High-throughput metabolomics and ingenuity pathway approach reveals the pharmacological effect and targets of Ginsenoside Rg1 in Alzheimer's disease mice

Ginsenoside Rg1, a natural triterpenoid saponins compound isolated from the Panax species, has been found to possess neuroprotective properties in neurodegenerative diseases such as Alzheimer's disease (AD). However, its pharmacological mechanism on AD has not been studied. In this study, an ultra-performance liquid chromatography combined with quadrupole time of-flight mass spectrometry (UPLC-Q/TOF-MS) based non-targeted metabolomics strategy was performed to explore the mechanism of Ginsenoside Rg1 protecting against AD mice by characterizing metabolic biomarkers and regulation pathways changes. A total of nineteen potential metabolites in serum were discovered and identified to manifest the difference between wild-type mice and triple transgenic mice in control and model group, respectively. Fourteen potential metabolites involved in ten metabolic pathways such as linoleic acid metabolism, arachidonic acid metabolism, tryptophan metabolism and sphingolipid metabolism were affected by Rg1. From the ingenuity pathway analysis (IPA) platform, the relationship between gene, protein, metabolites alteration and protective activity of ginsenoside Rg1 in AD mice are deeply resolved, which refers to increased level of albumin, amino acid metabolism and molecular transport. In addition, quantitative analysis of key enzymes in the disturbed pathways by proteomics parallel reaction was employed to verify changed metabolic pathway under Ginsenoside Rg1. The UPLC-Q/TOF-MS based serum metabolomics method brings about new insights into the pharmacodynamic studies of Ginsenoside Rg1 on AD mice.

Discovery of potential therapeutic targets for non-small cell lung cancer using high-throughput metabolomics analysis based on liquid chromatography coupled with tandem mass spectrometry

Lung cancer is a severe health problem and threatens a patient's quality of life. The metabolites present in biological systems are expected to be key mediators and the changes in these metabolites play an important role in promoting health. Metabolomics can unravel the global metabolic changes and identify significant biological pathways involved in disease development. However, the role of metabolites in lung cancer is still largely unknown. In the present study, we developed a liquid chromatography coupled with tandem mass spectrometry method for biomarker discovery and identification of non-small cell lung cancer (NSCLC) from metabolomics data sets and aimed to investigate the metabolic profiles of NSCLC samples to identify potential disease biomarkers and to reveal the pathological mechanism. After cell metabolite extraction, the metabolic changes in NSCLC cells were characterized and targeted metabolite analysis was adopted to offer a novel opportunity to probe into the relationship between differentially regulated cell metabolites and NSCLC. Quantitative analysis of key enzymes in the disturbed pathways by proteomics was employed to verify metabolomic pathway changes. A total of 13 specific biomarkers were identified in NSCLC cells related with metabolic disturbance of NSCLC morbidity, which were involved in 4 vital pathways, namely glycine, serine and threonine metabolism, aminoacyl-tRNA biosynthesis, tyrosine metabolism and sphingolipid metabolism. The proteomics analysis illustrated the obvious fluctuation of the expression of the key enzymes in these pathways, including the downregulation of 3-phosphoglycerate dehydrogenase, phosphoserine phosphatase, tyrosinase and argininosuccinic acid catenase. NSCLC occurrence is mainly related to amino acid and fatty acid metabolic alteration. These findings highlight that the metabolome can provide information on the molecular profiles of cells, which can aid in investigating the metabolite changes to reveal the pathological mechanism.

Untargeted Metabolomics Differentiates l-Carnitine Treated Septic Shock 1-Year Survivors and Nonsurvivors

l-Carnitine is a candidate therapeutic for the treatment of septic shock, a condition that carries a ≥40% mortality. Responsiveness to l-carnitine may hinge on unique metabolic profiles that are not evident from the clinical phenotype. To define these profiles, we performed an untargeted metabolomic analysis of serum from 21 male sepsis patients enrolled in a placebo-controlled l-carnitine clinical trial. Although treatment with l-carnitine is known to induce changes in the sepsis metabolome, we found a distinct set of metabolites that differentiated 1-year survivors from nonsurvivors. Following feature alignment, we employed a new and innovative data reduction strategy followed by false discovery correction, and identified 63 metabolites that differentiated carnitine-treated 1-year survivors versus nonsurvivors. Following identification by MS/MS and database search, several metabolite markers of vascular inflammation were determined to be prominently elevated in the carnitine-treated nonsurvivor cohort, including fibrinopeptide A, allysine, and histamine. While preliminary, these results corroborate that metabolic profiles may be useful to differentiate l-carnitine treatment responsiveness. Furthermore, these data show that the metabolic signature of l-carnitine-treated nonsurvivors is associated with a severity of illness (e.g., vascular inflammation) that is not routinely clinically detected.

Exploring metabolic biomarkers and regulation pathways of acute pancreatitis using ultra-performance liquid chromatography combined with a mass spectrometry-based metabolomics strategy

Acute pancreatitis (AP), as a common kind of pancreas-based inflammatory disease, is accompanied by a serious and abnormal metabolism. However, the specific metabolic process of AP is still unclear. Novel and effective drugs against acute pancreatitis are urgently required. To explore the metabolic biomarkers and regulation pathways of acute pancreatitis, ultra-performance liquid chromatography (UPLC) combined with a mass spectrometry (MS)-based metabolomics strategy was used. Sixteen male adult Sprague-Dawley rats were divided into two groups: a sham operation group (SO) and an AP model group. The AP animal model was induced via the retrograde ductal infusion of 3.5% sodium taurocholate, and rats in the SO group were infused with 0.9% saline. After serum sample collection and sacrifice, a metabolomics strategy based on UPLC-MS was used to detect serum metabolites and metabolic pathways by comparing the SO and AP model groups through full-scan analysis. A total of 19 metabolites were detected in the serum for highlighting the differences between the two groups: l-arabitol, citric acid, isocitric acid, l-phenylalanine, l-tyrosine, dihydroxyacetone, l-valine, succinic acid, 3-hydroxybutyric acid, uric acid, acetylglycine, palmitic amide, homocysteine, d-glutamine, l-arginine, arachidonic acid, N-acetylserotonin, (R)-3-hydroxy-hexadecanoic acid, and d-mannose. Six crucial metabolic pathways, phenylalanine, tyrosine and tryptophan biosynthesis, arachidonic acid metabolism, glyoxylate and dicarboxylate metabolism and the citrate cycle, were involved; these have potential to become novel targets for the treatment of AP. The ingenuity pathway analysis (IPA) platform is used to gain insights into the metabolic targets in the system, referring to development disorders, cell-to-cell signaling and interactions, cellular assembly and organization, cell compromise, cell growth and proliferation, carbohydrate metabolism and others. It is suggested that UPLC-MS-based metabolomics is capable of accurately depicting the pathological mechanisms of acute pancreatitis, which can drive new drug development.

Acute pancreatitis (AP), as a common kind of pancreas-based inflammatory disease, is accompanied by a serious and abnormal metabolism.

Exploring potential biomarkers of coronary heart disease treated by Jing Zhi Guan Xin Pian using high-throughput metabolomics

Coronary heart disease (CHD) is a relatively complex disease characterized by narrowing of the arterial lumen and reduction of blood flow to the heart. There is no effective early diagnosis and prevention method. Jing Zhi Guan Xin Pian (JZGXP) is a new preparation prepared from the effective extract of Guanxin II. It is made of five components of traditional Chinese medicine and functions by promoting blood circulation and removing blood stasis and is used for the treatment of CHD and angina pectoris. In our study, a CHD rat model was prepared using a high-fat diet combined with intraperitoneal injection of vitamin D3. Clinical biochemical indexes (TG, CHO and HDL-C), histopathology (coronary and myocardial tissue), electrocardiogram and cardiac indexes were used to evaluate the efficacy of JZGXP in the treatment of CHD model rats. UPLC-HDMS-based metabolomics techniques were used to find metabolic profiles, biomarkers and related metabolic pathways in CHD models and to evaluate the effects of JZGXP on them. At the same time, the targets of JZGXP for the treatment of CHD were analyzed. Our study ultimately identified 25 biomarkers associated with CHD models. Further studies found that these 25 biomarkers involved 9 metabolic pathways in the body and found that JZGXP can recall 21 biomarkers in the urine of model rats and these biomarkers involve nine metabolic pathways. Finally, the targets of JZGXP for the treatment of CHD were β-alanine metabolism and tyrosine metabolism, i.e. amino acids metabolism. This study showed that metabolomics technology is effective for exploring potential biomarkers associated with syndromes or diseases and the therapeutic mechanisms of a traditional Chinese medicine formulation.

Coronary heart disease (CHD) is a relatively complex disease characterized by narrowing of the arterial lumen and reduction of blood flow to the heart.

Applications and potential mechanisms of herbal medicines for rheumatoid arthritis treatment: a systematic review

In this review, we systematically discuss the role of traditional Chinese medicine (TCM) in rheumatoid arthritis (RA) disease treatment. TCM classifies the subtypes of RA through its own theoretical method, which is beneficial for more accurate diagnosis and treatment with Chinese herbal medicines (CHMs) that are more suitable for different syndromes. TCM mainly uses a flexible combination of CHMs to play an important role in RA treatment. The main components of these extracts can be subdivided into alkaloids, flavonoids, triterpenes, saponins and other compounds. Using a platform of transgenic and induced arthritis models, we explore the potential mechanisms of TCM against RA with the help of omics analysis techniques and methods. These mechanisms are mainly CHM and its extracts can inhibit RA patients and experimental animal models, including synovitis, vascular proliferation and bone injury; this involves many biological signal exchange targets and pathways. In conclusion, the role of TCM in RA treatment mainly involves reducing the expression and secretion of pro-inflammatory factors, thus decreasing the degree of abnormal immune response.

In this review, we systematically discuss the role of traditional Chinese medicine (TCM) in rheumatoid arthritis (RA) disease treatment.

Metabolic profiling of copper-laden hepatolenticular degeneration model rats and the interventional effects of Gandou decoction using UPLC-Q-TOF/MS

The direct cause of hepatolenticular degeneration (HLD) is copper metabolic disorder caused by autosomal recessive inheritance. Gandou decoction (GDD), a classical traditional Chinese medicine formula, exhibits unambiguous therapeutic effect on HLD in China for decades. However, the mechanism of effect on HLD is not clear. With this purpose, the effects of copper content and histopathology inspection on the HLD rat model were investigated. Then, metabolomics study based on ultra-performance liquid chromatography quadrupole-time-of-flight mass spectrometry (UPLC-Q-TOF/MS^E) analysis and multivariate statistical analysis was adopted to further reveal the mechanism of action of GDD against HLD. The results showed that the characteristics of liver tissues after GDD treatment were significantly reversed, close to the control group, suggesting that GDD has a therapeutic effect on HLD. Furthermore, HLD interferes with 2 metabolites of the metabolic pathway in rats. Among them, up-regulation of Lactic acid, Tryptophan, Phenylalanine, Triacylglycerol and down-regulation of Linoleic acid, Alpha Linolenic acid, Phosphatidylcholine, Taurine is particularly significant. Analysis of metabolic pathways by a unique pathway analysis revealed significant changes in several pathways including lipid metabolism, amino metabolism and glucose metabolism in HLD. This study showed that GDD could provide satisfactory therapeutic effects on HLD and metabolomics study can be utilized to further understand the molecular mechanisms.

Mass spectrometry-driven drug discovery for development of herbal medicine

Herbal medicine (HM) has made a major contribution to the drug discovery process with regard to identifying products compounds. Currently, more attention has been focused on drug discovery from natural compounds of HM. Despite the rapid advancement of modern analytical techniques, drug discovery is still a difficult and lengthy process. Fortunately, mass spectrometry (MS) can provide us with useful structural information for drug discovery, has been recognized as a sensitive, rapid, and high-throughput technology for advancing drug discovery from HM in the post-genomic era. It is essential to develop an efficient, high-quality, high-throughput screening method integrated with an MS platform for early screening of candidate drug molecules from natural products. We have developed a new chinmedomics strategy reliant on MS that is capable of capturing the candidate molecules, facilitating their identification of novel chemical structures in the early phase; chinmedomics-guided natural product discovery based on MS may provide an effective tool that addresses challenges in early screening of effective constituents of herbs against disease. This critical review covers the use of MS with related techniques and methodologies for natural product discovery, biomarker identification, and determination of mechanisms of action. It also highlights high-throughput chinmedomics screening methods suitable for lead compound discovery illustrated by recent successes.

Dissect new mechanistic insights for geniposide efficacy on the hepatoprotection using multiomics approach

A multi-omics approach could yield in-depth mechanistic insights. Here, we performed an integrated analysis of miRNAome, proteome and metabolome, aimed to investigate the underlying mechanism of active product geniposide in ethanol-induced apoptosis. We found that integrative meta-analysis identified 28 miRNAs, 20 proteins and 7 metabolites significantly differentially expressed, respectively. Further analysis identified geniposide extensively regulated multiple metabolism pathways and the most important related pathway was citrate cycle (TCA cycle). In addition, geniposide can improve energy metabolism benefits using the Extracellular Flux Analyzer. Of particular significance, miR-144-5p exhibits a high positive correlation with oxoglutaric acid, isocitrate dehydrogenase (IDH) 1 and 2 that involved in the TCA cycle. Furthermore,we discovered that miR-144-5p regulates TCA cycle metabolism through IDH1 and IDH2. Collectively, we describe for the first time the hepatoprotective effect of geniposide decreased miR-144-5p level, capable of regulating TCA cycle by directly targeting IDH1 and IDH2 and promoting functional consequences in cells. Integrating metabolomics, miRNAomics and proteomics approach and thereby analyzing microRNAs and proteins as well as metabolites can give valuable information about the functional regulation pattern and action mechanism of natural products.

Serum Metabonomics of Mild Acute Pancreatitis

BACKGROUND

Mild acute pancreatitis (MAP) is a common acute abdominal disease, and exhibits rising incidence in recent decades. As an important component of systemic biology, metabonomics is a new discipline developed following genomics and proteomics. In this study, the objective was to analyze the serum metabonomics of patients with MAP, aiming to screen metabolic markers with potential diagnostic values.

METHODS

An analysis platform with ultra performance liquid chromatography-high-resolution mass spectrometry was used to screen the difference metabolites related to MAP diagnosis and disease course monitoring.

RESULTS

A total of 432 endogenous metabolites were screened out from 122 serum samples, and 49 difference metabolites were verified, among which 12 difference metabolites were identified by nonparametric test. After material identification, eight metabolites exhibited reliable results, and their levels in MAP serum were higher than those in healthy serum. Four metabolites exhibited gradual downward trend with treatment process going on, and the differences were statistically significant (P < 0.05).

CONCLUSION

Metabonomic analysis has revealed eight metabolites with potential diagnostic values toward MAP, among which four metabolites can be used to monitor the disease course.

Advanced mass spectrometry-based multi-omics technologies for exploring the pathogenesis of hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is one of the primary hepatic malignancies and is the third most common cause of cancer related death worldwide. Although a wealth of knowledge has been gained concerning the initiation and progression of HCC over the last half century, efforts to improve our understanding of its pathogenesis at a molecular level are still greatly needed, to enable clinicians to enhance the standards of the current diagnosis and treatment of HCC. In the post-genome era, advanced mass spectrometry driven multi-omics technologies (e.g., profiling of DNA damage adducts, RNA modification profiling, proteomics, and metabolomics) stand at the interface between chemistry and biology, and have yielded valuable outcomes from the study of a diversity of complicated diseases. Particularly, these technologies are being broadly used to dissect various biological aspects of HCC with the purpose of biomarker discovery, interrogating pathogenesis as well as for therapeutic discovery. This proof of knowledge-based critical review aims at exploring the selected applications of those defined omics technologies in the HCC niche with an emphasis on translational applications driven by advanced mass spectrometry, toward the specific clinical use for HCC patients. This approach will enable the biomedical community, through both basic research and the clinical sciences, to enhance the applicability of mass spectrometry-based omics technologies in dissecting the pathogenesis of HCC and could lead to novel therapeutic discoveries for HCC.

Metabolic fingerprinting to understand therapeutic effects and mechanisms of silybin on acute liver damage in rat

BACKGROUND

Metabolic fingerprinting is a rapid and noninvasive analysis, representing a powerful approach for the characterization of phenotypes and the distinction of specific metabolic states due to environmental alterations. It has become a valuable analytical approach for the characterization of phenotypes and is the rapidly evolving field of the comprehensive measurement of ideally all endogenous metabolites in bio-samples. Silybin has displayed bright prospects in the prevention and therapy of liver injury, and we had conducted a preliminary exploration on the molecular mechanism of the hepatoprotective effects of silybin. Because the knowledge on the metabolic responses of an acute liver damage rat to the silybin is still scarce, metabolic fingerprinting can provide relevant information on the intrinsic metabolic adjustments.

MATERIALS AND METHODS

Here, the physiological and metabolic changes in the acute liver damage rat were investigated by performing a metabolic analysis. The phenotypic response was assessed by liquid chromatography/mass spectrometry (LC/MS) combined with pattern recognition approaches such as principal components analysis and partial least squares projection to supervised latent structures and discriminant analysis. Multivariate analysis of the data showed trends in scores plots that were related to the concentration of the silybin.

RESULTS

Results indicate 10 ions (7 upregulated and 3 downregulated) as differentiating metabolites. Key observations include perturbations of metabolic pathways linked to glutathione metabolism, tryptophan metabolism, cysteine and methionine metabolism, etc., Overall, this investigation illustrates the power of the LC/MS combined with the pattern recognition methods that can engender new insights into silybin affecting on metabolism pathways of an acute liver damage rat.

CONCLUSION

The present study demonstrates that the combination of metabolic fingerprinting with appropriate chemometric analysis is a valuable approach for studying cellular responses to silybin drug and can provide additional insight into the mechanisms.

Metabolomics approach to identify therapeutically potential biomarkers of the Zhi-Zi-Da-Huang decoction effect on the hepatoprotective mechanism

A NMR-based metabolomics approach was applied to find potential plasma and liver biomarkers responsible for the hepatoprotective effects of Zhi-Zi-Da-Huang decoction (ZZDHD).

UPLC-Q-TOF/MS based metabolomic profiling of serum and urine of hyperlipidemic rats induced by high fat diet

Hyperlipidemia is considered to be a high lipid level in blood, can induce metabolic disorders and dysfunctions of the body, and results in some severe complications. Therefore, hunting for some metabolite markers and clarifying the metabolic pathways in vivo will be an important strategy in the treatment and prevention of hyperlipidemia. In this study, a rat model of hyperlipidemia was constructed according to histopathological data and biochemical parameters, and the metabolites of serum and urine were analyzed by UPLC-Q-TOF/MS. Combining pattern recognition and statistical analysis, 19 candidate biomarkers were screened and identified. These changed metabolites indicated that during the development and progression of hyperlipidemia, energy metabolism, lipid metabolism, amino acid metabolism and nucleotide metabolism were mainly disturbed, which are reported to be closely related to diabetes, cardiovascular diseases, etc. This study demonstrated that a UPLC-Q-TOF/MS based metabolomic approach is useful to profile the alternation of endogenous metabolites of hyperlipidemia.