Metabolomics analysis of urine from patients with alcohol-associated liver disease reveals dysregulated caffeine metabolism

Excess alcohol intake causes millions of deaths annually worldwide. Asymptomatic early-stage, alcohol-associated liver disease (ALD) is easily overlooked, and ALD is usually only diagnosed in more advanced stages. We explored the possibility of using polar urine metabolites as biomarkers of ALD for early-stage diagnosis and functional assessment of disease severity by quantifying the abundance of polar metabolites in the urine samples of healthy controls (n = 18), patients with mild or moderate liver injury (n = 21), and patients with severe alcohol-associated hepatitis (n = 25). The polar metabolites in human urine were first analyzed by untargeted metabolomics, showing that 209 urine metabolites are significantly changed in patients, and 17 of these are highly correlated with patients' model for end-stage liver disease (MELD) score. Pathway enrichment analysis reveals that the caffeine metabolic pathway is the most affected in ALD. We then developed a targeted metabolomics method and measured the concentration of caffeine and its metabolites in urine using internal and external standard calibration, respectively. The described method can quantify caffeine and its 14 metabolites in 35 min. The results of targeted metabolomics analysis agree with the results of untargeted metabolomics, showing that 13 caffeine metabolites are significantly decreased in patients. In particular, the concentrations of 1-methylxanthine, paraxanthine, and 5-acetylamino-6-amino-3-methyluracil are markedly decreased with increased disease severity. We suggest that these three metabolites could serve as functional biomarkers for differentiating early-stage ALD from more advanced liver injury.NEW & NOTEWORTHY Our study using both untargeted and targeted metabolomics reveals the caffeine metabolic pathway is dysregulated in ALD. Three caffeine metabolites, 1-methylxanthine, paraxanthine, and 5-acetylamino-6-amino-3-methyluracil, can differentiate the severity of early-stage ALD.

Therapeutic Effect and Mechanism of Si-Miao-Yong-An-Tang on Thromboangiitis Obliterans Based on the Urine Metabolomics Approach

Si-Miao-Yong-An-Tang (SMYAT) is a classic prescription for the treatment of thromboangiitis obliterans (TAO). However, the effect and mechanism are still unclear. This experiment aims to evaluate the therapeutic effect and mechanism of SMYAT on sodium laurate solution induced thromboangiitis obliterans model rats using urine metabolomics. The therapeutic effect of SMYAT was evaluated by histopathology, hemorheology and other indexes. The urine metabolomic method, principal component analysis (PCA) and orthogonal partial least squares discriminant analysis (OPLS-DA) were used for clustering group and discriminant analysis to screen urine differential metabolic biomarkers, and explore new insight into pathophysiological mechanisms of SMYAT in the treatment of TAO. SMYAT has significant antithrombotic and anti-inflammatory effects, according to the results of urine metabolomic analysis, and regulate the metabolic profile of TAO rats, and its return profile is close to the state of control group. Through metabolomics technology, a total of 35 urine biomarkers of TAO model were characterized. Among them, SMYAT treatment can regulate 22 core biomarkers, such as normetanephrine and 4-pyridoxic acid. It is found that the therapeutic effect of SMYAT is closely related to the tyrosine metabolism, vitamin B6 metabolism and cysteine and methionine metabolism. It preliminarily explored the therapeutic mechanism of SMYAT, and provided a scientific basis for the application of SMYAT.

High-Throughput and Untargeted Metabolic Profiling Revealed the Potential Effect and Mechanisms of Paeoniflorin in Young Asthmatic Rats

Paeoniflorin (PF) is a multi-target monoterpenoid glycoside and possesses broad pharmacological functions, e.g., anti-inflammation, anti-depression, antitumor, abirritation, neuroprotection, antioxidant, and enhancing cognitive and learning ability. PF has gained a large amount of attention for its effect on asthma disease as the growth rate of asthma has increased in recent years. However, its mechanism of action on asthma is still unclear. In this study, we have explored the action mechanism of PF on asthma disease. Furthermore, high-throughput untargeted metabolic profiling was performed through ultraperformance liquid chromatography/electrospray ionization quadruple time-of-flight high-definition mass spectrometry (QA) UPLC-Q/TOF-MS combined with pattern recognition approaches and pathway analysis. A total of 20 potential biomarkers were discovered by UPLC/MS and urine metabolic profiling. The key pathways including the citrate cycle (the TCA cycle), pyrimidine metabolism, pentose phosphate pathway, tyrosine metabolism, and tryptophan metabolism were affected by PF. In conclusion, we have discovered metabolite biomarkers and revealed the therapeutic mechanism of PF based on liquid chromatography coupled with mass spectrometry untargeted metabolomics. The untargeted metabolomics combined with UPLC-MS is a useful tool for exploring the therapeutic mechanism and targets of PF in the treatment of asthma. Metabolomics combined with UPLC-MS is an integrated method to explore the metabolic mechanism of PF in the treatment of asthma rats and to reveal the potential targets, providing theoretical support for the study of the treatment of PF.

High-Throughput UHPLC-MS to Screen Metabolites in Feces for Gut Metabolic Health

Feces are the product of our diets and have been linked to diseases of the gut, including Chron’s disease and metabolic diseases such as diabetes. For screening metabolites in heterogeneous samples such as feces, it is necessary to use fast and reproducible analytical methods that maximize metabolite detection. As sample preparation is crucial to obtain high quality data in MS-based clinical metabolomics, we developed a novel, efficient and robust method for preparing fecal samples for analysis with a focus in reducing aliquoting and detecting both polar and non-polar metabolites. Fecal samples (n = 475) from patients with alcohol-related liver disease and healthy controls were prepared according to the proposed method and analyzed in an UHPLC-QQQ targeted platform in order to obtain a quantitative profile of compounds that impact liver-gut axis metabolism. MS analyses of the prepared fecal samples have shown reproducibility and coverage of n = 28 metabolites, mostly comprising bile acids and amino acids. We report metabolite-wise relative standard deviation (RSD) in quality control samples, inter-day repeatability, LOD (limit of detection), LOQ (limit of quantification), range of linearity and method recovery. The average concentrations for 135 healthy participants are reported here for clinical applications. Our high-throughput method provides a novel tool for investigating gut-liver axis metabolism in liver-related diseases using a noninvasive collected sample.

Andrographolide Against Lung Cancer-New Pharmacological Insights Based on High-Throughput Metabolomics Analysis Combined with Network Pharmacology

Andrographolide (Andro) has known to treat various illnesses such as colds, diarrhea, fever and infectious diseases. However, the effect mechanism of Andro is still unclear. Therefore, we used high-throughput metabolomics analysis to discover biomarkers, metabolic profiles and pathways to reveal the pharmacological action and effective mechanism of Andro against lung cancer. The metabolic effects of Andro on lung cancer animal was explored by ultra-performance liquid chromatography-triple-time of flight/mass spectrometry (UPLC-TOF/MS) analysis. Our results showed that Andro exhibited significant protective effects against lung cancer. Compared with control group, a total of 25 metabolites biomarkers was identified in urine of model animals, which 18 of them were regulated toward the normal direction after Andro treatment, and network pharmacology analysis showed that they were related with 570 proteins. Biological pathways analysis showed that the 11 metabolism pathways were regulated by Andro treatment in lung cancer mouse, and amino acid metabolism and arachidonic acid metabolism have great potential as target pathways for Andro against lung cancer. It revealed that high-throughput metabolomics combined with network pharmacology analysis provides deeply insight into the therapeutic mechanisms of natural product for promoting medicine development and disease treatment.

Untargeted metabolomics as a diagnostic tool in NAFLD: discrimination of steatosis, steatohepatitis and cirrhosis

INTRODUCTION

Non-Alcoholic Fatty Liver Disease encompasses a spectrum of diseases ranging from simple steatosis to steatohepatitis (or NASH), up to cirrhosis and hepatocellular carcinoma (HCC). The challenge is to recognize the more severe and/or progressive pathology. A reliable non-invasive method does not exist. Untargeted metabolomics is a novel method to discover biomarkers and give insights on diseases pathophysiology.

OBJECTIVES

We applied metabolomics to understand if simple steatosis, steatohepatitis and cirrhosis in NAFLD patients have peculiar metabolites profiles that can differentiate them among each-others and from controls.

METHODS

Metabolomics signatures were obtained from 307 subjects from two separated enrollments. The first collected samples from 69 controls and 144 patients (78 steatosis, 23 NASH, 15 NASH-cirrhosis, 8 HCV-cirrhosis, 20 cryptogenic cirrhosis). The second, used as validation-set, enrolled 44 controls and 50 patients (34 steatosis, 10 NASH and 6 NASH-cirrhosis).The "Partial-Least-Square Discriminant-Analysis"(PLS-DA) was used to reveal class separation in metabolomics profiles between patients and controls and among each class of patients, and to reveal the metabolites contributing to class differentiation.

RESULTS

Several metabolites were selected as relevant, in particular:Glycocholic acid, Taurocholic acid, Phenylalanine, branched-chain amino-acids increased at the increase of the severity of the disease from steatosis to NASH, NASH-cirrhosis, while glutathione decreased (p < 0.001 for each). Moreover, an ensemble machine learning (EML) model was built (comprehending 10 different mathematical models) to verify diagnostic performance, showing an accuracy > 80% in NAFLD clinical stages prediction.

CONCLUSIONS

Metabolomics profiles of NAFLD patients could be a useful tool to non-invasively diagnose NAFLD and discriminate among the various stages of the disease, giving insights into its pathophysiology.

Targeted Metabolomics Identifies Differential Serum and Liver Amino Acids Biomarkers in Rats with Alcoholic Liver Disease

To investigate changes in serum and hepatic levels of amino acids in ALD and to provide novel evidence and approaches for the prevention and treatment of ALD. Twenty specific pathogen-free SD male rats were devided into two groups, ten for the control group, and ten for the model group. Serum biochemical markers, including alanine aminotransferase, aspartate aminotransferase, laminin and hyaluronidase were measured. Histological analysis of liver tissues was performed. Serum and liver amino acids levels were quantitatively determined by ultra-high-performance liquid chromatography-tandem quadrupole mass spectrometry (UPLC-TQMS)-based targeted metabolomics. Compared with the normal group, ALD rats showed an obvious increase in the levels of β-alanine, alanine, serine, ornithine, tyrosine and the tyrosine ratio, while there was a decrease in arginine levels, the BTR ratio and Fischer's ratio in serum. Additionally, ALD rats exhibited a significant increase in the levels of cysteine and putrescine, while there was a decrease in sarcosine, β-alanine, serine, proline, valine, threonine, ornithine, lysine, histidine, tyrosine, symmetric dimethylarginine, methionine, isoleucine and methionine-sulfoxide levels in liver tissues compared with the normal group. The serum and liver amino acids showed significant changes in ALD rats and can be considered as potential specific diagnostic biomarkers for ALD.

Application of Metabolomics in Diagnosis and Treatment of Chronic Liver Diseases

Chronic liver disease represents stepwise destruction of the liver parenchyma after chronic liver injury, which is often difficult to be diagnosed accurately. Thus, the development of specific biomarkers of chronic liver disease is important. Metabolomics is a powerful tool for biomarker exploration, which enables the exploration of disease pathogenesis or drug action mechanisms at the global metabolic level. The metabolomics workflow generally includes collection, preparation, and analysis of samples, and data processing and bioinformatics. A metabolomics study can simultaneously detect the dysfunctions in the glucose, lipid, amino-acid, and nucleotide metabolisms. Hence, it facilitates the obtaining of a better understanding of the pathogenesis of chronic liver disease and its diagnosis. Many effective drugs could reverse the change of comprehensive biochemical phenotypes induced by chronic liver disease. They can even potentially restore the normal metabolic signatures of patients. Increasingly more researchers have begun to apply metabolomics technologies to diagnose chronic liver disease and investigate the mechanism of action of effective drugs or the variations in drug responses. We are convinced that deepening the understanding of the metabolic alterations could extend their use as powerful biomarkers, promoting the more effective clinical diagnosis and treatment of chronic liver disease in the future.

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.

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.

Study of Fecal and Urinary Metabolite Perturbations Induced by Chronic Ethanol Treatment in Mice by UHPLC-MS/MS Targeted Profiling

Alcoholic liver disease (ALD) as a consequence of ethanol chronic consumption could lead to hepatic cirrhosis that is linked to high morbidity and mortality. Disease diagnosis is still very challenging and usually clear findings are obtained in the later stage of ALD. The profound effect of ethanol on metabolism can be depicted using metabolomics; thus, the discovery of novel biomarkers could shed light on the initiation and the progression of the ALD, serving diagnostic purposes. In the present study, Hydrophilic Interaction Liquid Chromatography tandem Mass Spectrometry HILIC-MS/MS based metabolomics analyisis of urine and fecal samples of C57BL/6 mice of both sexes at two sampling time points was performed, monitoring the effect of eight-week ethanol consumption. The altered hepatic metabolism caused by ethanol consumption induces extensive biochemical perturbations and changes in gut microbiota population on a great scale. Fecal samples were proven to be a suitable specimen for studying ALD since it was more vulnerable to the metabolic changes in comparison to urine samples. The metabolome of male mice was affected on a greater scale than the female metabolome due to ethanol exposure. Precursor small molecules of essential pathways of energy production responded to ethanol exposure. A meaningful correlation between the two studied specimens demonstrated the impact of ethanol in endogenous and symbiome metabolism.

Alcohol, liver disease and the gut microbiota

Alcoholic liver disease, which ranges from mild disease to alcoholic hepatitis and cirrhosis, is a leading cause of morbidity and mortality worldwide. Alcohol intake can lead to changes in gut microbiota composition, even before liver disease development. These alterations worsen with advancing disease and could be complicit in disease progression. Microbial function, especially related to bile acid metabolism, can modulate alcohol-associated injury even in the presence of cirrhosis and alcoholic hepatitis. Microbiota changes might also alter brain function, and the gut-brain axis might be a potential target to reduce alcoholic relapse risk. Gut microbiota manipulation including probiotics, faecal microbial transplant and antibiotics has been studied in alcoholic liver disease with varying success. Further investigation of the modulation of the gut-liver axis is relevant, as most of these patients are not candidates for liver transplantation. This Review focuses on clinical studies involving the gut microbiota in patients with alcoholic liver disease across the spectrum from alcoholic fatty liver to cirrhosis and alcoholic hepatitis. Specific alterations in the gut-liver-brain axis that are complicit in the interactions between the gut microbiota and alcohol addiction are also reviewed.

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.

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.

High-throughput metabolomics enables metabolite biomarkers and metabolic mechanism discovery of fish in response to alkalinity stress

High throughput mass spectrometry (MS)-based metabolomics is a popular platform for small molecule metabolites analyses that are widely used for detecting biomarkers in the research field of environmental assessment. Crucian carp (Carassius carassius, CC) is an economically and ecologically important fish in Asia. It can adapt to extremely high alkalinity, providing us with valuable material to understand the adaptation mechanism for extreme environmental stress. However, the information on the metabolite biomarkers and metabolic mechanisms of CC exposed to alkaline stress is not entirely clear. We applied high-throughput UPLC-Q-TOF/MS combined with chemometrics to identify changes in the metabolome of CC exposed to different concentrations of alkalinity for long term effects. Metabolic differences among alkalinity-treated groups were identified by multivariate statistical analysis. Further, 7 differential metabolites were found after exposure to alkaline conditions. In total, 23 metabolic pathways of these differential metabolites were significantly affected. Alkalinity exposure resulted in widespread change in metabolic profiles in the plasma with disruptions in the phenylalanine metabolism, glycine, serine and threonine metabolism, pyruvate metabolism, tyrosine metabolism, etc. The integrated pathway analysis of the associated metabolites showed that tRNA charging, l-cysteine degradation II, superpathway of methionine degradation, l-serine degradation, tyrosine biosynthesis IV, etc. appear to be the most significantly represented functional categories. Overall, this study demonstrated that metabolic changes in CC played a role in adaptation to the highly alkaline environmental stress.

High throughput mass spectrometry (MS)-based metabolomics is a popular platform for small molecule metabolites analyses that are widely used for detecting biomarkers in the research field of environmental assessment.

Exploration of metabolite signatures using high-throughput mass spectrometry coupled with multivariate data analysis

Disease impacts important metabolic pathways and the alteration of metabolites may serve as a potential biomarker for early-stage diagnosis.

Discovery of serum metabolites for diagnosis of progression of mild cognitive impairment to Alzheimer's disease using an optimized metabolomics method

A nontargeted metabolomics approach was developed to examine metabolic differences in serum samples from the mild cognitive impairment and Alzheimer's disease subjects.

Urine metabolic phenotypes analysis of extrahepatic cholangiocarcinoma disease using ultra-high performance liquid chromatography-mass spectrometry

Extrahepatic cholangiocarcinoma (ECC) is the second most common type of malignant primary tumor with a poor survival rate and an increasing global trend.

High-resolution mass spectrometry for exploring metabolic signatures of sepsis-induced acute kidney injury

Sepsis is a commonly encountered scenario in an intensive care unit (ICU), and the kidney is one of the organs frequently affected.

Urinary UPLC-MS metabolomics dissecting the underlying mechanisms of Huaxian capsule protects against sepsis

Urinary UPLC-MS metabolomics could dissect the underlying mechanisms of HXC protects against SS.

Potential urine biomarkers from a high throughput metabolomics study of severe sepsis in a large Asian cohort

Non-targeted mass spectrometry was used to characterize peripheral biomarkers associated with the urine metabolome in severe sepsis (SS) patients. This is an efficient and convenient tool for diagnosing and screening of SS in a high-risk population.