Combined metabolomic and lipidomic analysis uncovers metabolic profile and biomarkers for papillary thyroid carcinoma.

Papillary thyroid carcinoma (PTC) is the most common endocrine malignancy with a rapidly increasing incidence. The pathogenesis of PTC is unclear, but metabolic and lipidomic reprogramming may play a role in tumor growth. We applied ultra-performance liquid chromatography-tandem mass spectrometry to perform widely targeted metabolomics and lipidomics on plasma samples from 94 patients with PTC and 100 healthy controls. We identified 113 differential metabolites and 236 differential lipids, mainly involved in branched-chain amino acid metabolism, glutamate and glutamine metabolism, tricarboxylic acid cycle, and lipid metabolism. We also screened three potential metabolite biomarkers: sebacic acid, L-glutamine, and indole-3-carboxaldehyde. These biomarkers showed excellent diagnostic performance for PTC in both discovery and validation cohorts, with areas under the receiver operating characteristic curves of 0.994 and 0.925, respectively. Our findings reveal distinct metabolic and lipidomic features of PTC and provide novel targets for diagnosis and treatment.

Integration of Metabolomics, Lipidomics, and Proteomics Reveals the Metabolic Characterization of Nonalcoholic Steatohepatitis.

Metabolic dysfunction is associated with nonalcoholic steatohepatitis (NASH) development. However, omics studies investigating metabolic changes in NASH patients are limited. In this study, metabolomics and lipidomics in plasma, as well as proteomics in the liver, were performed to characterize the metabolic profiles of NASH patients. Moreover, the accumulation of bile acids (BAs) in NASH patients prompted us to investigate the protective effect of cholestyramine on NASH. The liver expression of essential proteins involved in FA transport and lipid droplets was significantly elevated in patients with NASH. Furthermore, we observed a distinct lipidomic remodeling in patients with NASH. We also report a novel finding suggesting an increase in the expression of critical proteins responsible for glycolysis and the level of glycolytic output (pyruvic acid) in patients with NASH. Furthermore, the accumulation of branched chain amino acids, aromatic amino acids, purines, and BAs was observed in NASH patients. Similarly, a dramatic metabolic disorder was also observed in a NASH mouse model. Cholestyramine not only significantly alleviated liver steatosis and fibrosis but also reversed NASH-induced accumulation of BAs and steroid hormones. In conclusion, NASH patients were characterized by perturbations in FA uptake, lipid droplet formation, glycolysis, and accumulation of BAs and other metabolites.

An integrated strategy for the systematic chemical characterization of Salvianolate lyophilized injection using four scan modes based on the ultra-high performance liquid chromatography-triple quadrupole-linear ion trap mass spectrometry.

Salvianolate lyophilized injection (SLI), a freeze-dried powder injection derived from aqueous extract of S. miltiorrhiza, is therapeutically used to treat the syndrome of blood stasis and collateral blockage during the recovery period after stroke. To date, it has remained a significant challenge to comprehensively characterize the compounds of SLI, particularly the minor components with potential bioactivities, in one sample injection analysis. Using an integrative four scan modes approach coupled with ultra-high performance liquid chromatography-triple quadrupole-linear ion trap mass spectrometry (UHPLC-QTRAP-MS/MS), we propose a novel, sensitive, and simple strategy for systematic and rapid profiling of the chemical components of SLI. First, an in-house database of constituents from the water-soluble extract of Danshen was created. Second, the fragmentation behaviors of the representative components in SLI were obtained using the untargeted scan mode enhanced MS (EMS)-information dependent acquisition (IDA)-enhanced product ion (EPI). The specific fragments acquired were then utilized to conduct precursor ion (Prec) and neutral loss (NL)-IDA-EPI scans. Following that, a sensitive predictive multiple reaction monitoring (pMRM)-IDA-EPI scan method with 454 transitions was developed based on the prominent fragment ions and plausible predictions. A total of 171 compounds were tentatively identified from SLI. Among them, 27 minor components have not been previously reported. This strategy allows most isomeric compounds at trace levels to be readily distinguished and annotated. Finally, 15 batches of 13 representative components in SLI selected by the qualitative results were accurately quantified. Salvianolic acid A (Sal A), Sal B, Sal D, lithospermic acid (LA), and rosmarinic acid (RA) were proved to be the predominant constituents. Sal B had the highest amount (195.08-350.46 µg·mg-1), followed by LA, Sal A, Sal D, and RA. Moreover, these 15 batches of samples showed good uniformity, and no abnormal batches existed. These results suggest that this novel strategy can accelerate the identification of undiscovered chemical components and serve as an alternative method for in-depth profiling of compounds in other traditional Chinese medicines (TCMs).

High-throughput LC-MS method for the rapid characterisation and comparative analysis of multiple ingredients of four hawthorn leaf extracts.

INTRODUCTION: The comprehensive component characterisation of Chinese herbal medicine is the premise of effectively driving the discovery of pharmacodynamic substances or new drugs in recent years. OBJECTIVE: To use the high-throughput liquid chromatography-mass spectrometry (LC-MS) approach to systematically characterise phytochemical compounds from four hawthorn leaf extracts, along with evaluating their classification. METHODS: In the present study, the compounds from 50% ethanol extract, macro porous resin extract, ethyl acetate extract and standard decoction of hawthorn leaves were completely analysed by ultrahigh-performance liquid chromatography-quadrupole time-of-flight tandem mass spectrometry (UPLC-Q-TOF-MS). RESULTS: Eight-nine compounds were putatively identified by comparison with secondary MS data and available references. Of these compounds identified, 56 compounds were found for the first time in hawthorn leaves, which was somewhat inconsistent with the findings of other studies. It could be inferred that falconoid, organic acids and nitrogenous compounds were the most abundant in 50% ethanol extract and standard decoction extract, which were considered as better choices for extracting hawthorn leaves. CONCLUSIONS: This work developed a simple, accurate and rapid method for the compound identification of hawthorn leaves, which laid the basis for further discovering pharmacodynamic material basis or new drugs from hawthorn leaves.

Pharmacokinetics and metabolism of trans-emodin dianthrones in rats.

ETHNOPHARMACOLOGICAL RELEVANCE: Polygonum multiflorum Thunb. (PM) is a common traditional Chinese medicine with diverse biological activities of resolving toxins, nourishing livers and promoting hairs. Nevertheless, in recent years hepatotoxic adverse reactions caused by the administration of PM have raised worldwide concerns. In our previous study, we found that emodin dianthrones showed hepatotoxicity and may be potential toxicity markers. However, the metabolic transformation and pharmacokinetic behavior of emodin dianthrones in vivo have still not been elucidated. AIM OF THE STUDY: Taking trans-emodin dianthrones (TED) as an example, the present study was conducted to investigate the pharmacokinetics and bioavailability of TED in rats and characterized its metabolic transformation in the plasma, urine and feces of rats. MATERIALS AND METHODS: A rapid and sensitive UPLC-qqq-MS/MS method was developed for accurate quantification of TED in plasma and successfully applied to the pharmacokinetic evaluation of TED in rats after intravenous and oral administration. A reliable UFLC-Q-TOF-MS high resolution mass spectrometry combined with a scientific metabolite identification strategy was used to comprehensively characterize the metabolic transformation of TED in plasma, urine and feces in rats. RESULTS: The established UPLC-qqq-MS/MS method had a linear range of 1-500 ng/mL, and the method was accurate and reliable to meet the quantitative requirements. When 20 mg/kg TED was given by gavage rats, it was rapidly absorbed into the circulatory system and had a long half-life time of 6.44 h and wide tissue distribution in vivo. While intravenous injection of 0.4 mg/kg TED in rats, it was rapidly metabolized and eliminated with a half-life time of 1.82 h. The oral absorption bioavailability of TED was only 2.83%. Furthermore with a sensitive UFLC-Q-TOF-MS technique and metabolite identification strategy, 21 metabolites were successfully identified, including 11 in plasma, 12 in urine and 18 in feces. The main Ⅰ and Ⅱ phase metabolic processes involved glucuronidation, oxidation, carbonylation, (de)methylation, sulfation and hydrogenation. CONCLUSION: TED could be rapidly absorbed into the blood circulation and widely distributed and slowly metabolized in the body and underwent extensive cleavage and metabolic transformation in vivo. The study provided a basis for in-depth elucidation of the toxicology and mechanism research of TED, but also laid the foundation for further research on the material basis of hepatotoxicity of PM.

[Rapid chemome profiling of chemical components of Lonicerae Japonicae Flos using DI-MS/MS~(ALL)].

A new method of MS/MS~(ALL) was designed to sequentially record a MS~2 spectrum at each unit mass window through gas phase fractionation concept, so as to offer an opportunity for universal MS~2 spectral recording with direct infusion(DI). As a proof-of-concept, DI-MS/MS~(ALL) was applied for rapid chemome profiling of a famous herbal medicine named Lonicerae Japonicae Flos. After each MS~2 spectrum was correlated to its precursor ion, the structural annotation was conducted by applying well-defined mass cracking rules, matching the mass spectral data with literatures and referring to those accessible databases. As a result, a total of 54 components were identified from Lonicerae Japonicae Flos extract, including 21 phenolic acids, 13 flavonoids, 12 iridoids, 4 triterpenoids and 4 other compounds. Therefore, DI-MS/MS~(ALL) is a powerful tool for comprehensive, rapid qualitative analysis of chemical profiles of traditional Chinese medicine and other chemical components of complex systems.

Integrated Strategy Drives Direct Infusion-Tandem Mass Spectrometry as an Eligible Tool for Shotgun Pseudo-Targeted Metabolomics of Medicinal Plants.

Direct infusion (DI) has an extraordinary high-throughput advantage. Pseudo-targeted metabolomics (PTM) has been demonstrated integrating the merits of both nontargeted and targeted metabolomics. Herein, we attempted to implant DI into the PTM concept to configure a new strategy allowing shotgun PTM. First, a versatile MS/MSALL program was applied to acquire MS1 and MS2 spectra. Second, online energy-resolved MS (online ER-MS) was conducted to obtain breakdown graph as well as optimal collision energy (OCE) for each ion transition paired by precursor ion and the dominant product ion. Third, selected reaction monitoring (SRM) was responsible to output a quantitative dataset with a constant length. Moreover, breakdown graph also served as orthogonal structural evidence when matching MS2 spectra between DI-MS/MS and an in-house library to strengthen structural annotation confidence. To evaluate and illustrate the utility of the new strategy toward shotgun PTM of medicinal plants, in-depth chemome comparison was conducted within three Cistanche species, all of which are edible medicinal plants and playing essential roles for turning the deserts into the oases. A total of 185 variables participated in the quantitative measurement program. Each diagnostic ion pair was featured with an OCE. Significant species differences occurred, and echinacoside, acteoside, isoacteoside, 2'-acetyl-acteoside, tubuloside B, mannitol, sucrose, betaine, malate, as well as choline were found to be confirmative chemical markers offering primary contributions toward the species discrimination. After cross-validation with LC-MS/MS, DI-MS/MS fortified with the new strategy is an eligible tool for shotgun PTM, beyond Cistanche plants.

Identification of prototypes from Ligustri Lucidi Fructus in rat plasma based on a data-dependent acquisition and multicomponent pharmacokinetic study.

The identification and quantization of traditional Chinese medicine (TCM) are a challenge for researchers and industry. Using untargeted analytical methods, the in vivo detection and identification of TCM compounds are difficult because of the significant interference of endogenous substances. Fortunately, the ongoing development of new analytical technologies, especially Q-Orbitrap-MS, offers some solutions. Our team developed a holistic MS method, combining untargeted data-dependent MS2 (dd-MS2 ) modes to extensively identify TCM prototypes in vivo. The method was successfully applied to the analysis of Ligustri Lucidi Fructus (LLF). LLF is a widely used TCM with a remarkable nourishing effect on the liver and kidney. In the study, we aimed to identify the prototypes in rat plasma after oral administration of LLF extract. Following separation on an HSS T3 column, LLF extract and rat plasma were performed in untargeted dd-MS2 mode. Forty-seven compounds were characterized in rats plasma as prototypes of LLF extract. Furthermore, seven major prototypes were chosen as pharmacokinetic markers to investigate LLF's pharmacokinetic properties. The results provides comprehensive determination of compounds in LLF both in vitro and in vivo, which is important for quality control, pharmacology studies and clinical use of LLF.

Comprehensive profiling of Stephania tetrandra (Fangji) by stepwise DFI and NL-dependent structure annotation algorithm-based UHPLC-Q-TOF-MS and direct authentication by LMJ-HRMS.

Stephania tetrandra S. Moore, a widely used traditional antirheumatic herbal medicine (HM), is a rich source of isoquinoline alkaloids. With the exception of the two recognized isoquinolines, viz. tetrandrine and fangchinoline, the other isoquinoline alkaloids present in S. tetrandra have not been clearly clarified. In addition, due to their similar names and morphological similarities, S. tetrandra is often mistakenly substituted and adulterated with the nephrotoxic Aristolochia fangchi. In this study, ultra-high-performance liquid chromatography-triple time-of-flight mass spectrometry (UHPLC-Q-TOF-MS) was initially employed to comprehensively profile the isoquinolines from S. tetrandra. To overcome the complexities arising due to the similar mass behaviors of the isoquinolines, a stepwise diagnostic fragment ion (DFI) and neutral loss (NL)-dependent structure annotation algorithm was proposed, and this accelerated the identification of 393 isoquinolines distributed over twenty classes. Consequently, liquid microjunction surface sampling-high-resolution mass spectrometry (LMJ-HRMS) was deployed in an attempt to directly authenticate S. tetrandra by the chemical profiling of its crude slice. By matching the 393 isoquinolines, the 87 peaks detected by LMJ-HRMS were assigned to 270 isoquinolines, including the recognized tetrandrine and fangchinoline. The absence of aristolochic acid-related mass signals confirmed the authentication of S. tetrandra. In summary, LMJ-HRMS can be considered a direct, nondestructive, high-throughput, and environment-friendly analytical method for the authentication of HMs. Moreover, the stepwise DFI- and NL-dependent structure annotation algorithm-based UHPLC-Q-TOF-MS method allowed high-coverage detection and high-quality data processing of the inherent structural similarity and complexity of isoquinolines or other phytochemical compounds.

Metabolomics identifies serum and exosomes metabolite markers of pancreatic cancer.

INTRODUCTION: Pancreatic cancer (PC) is one of the most aggressive malignancies, and it's difficult to diagnosis PC at an early stage, which leads to the poor prognosis of PC. OBJECTIVES: To identifiy the possible prognosis or dignosis metabolite biomarkers in the serum exosome of PC patients. METHODS: We employed LC-DDA-MS based untargeted lipidomic analysis to search for potential candidate biomarkers in the serum exosome of PC patients. Then LC-MRM-MS based targeted lipid quantification was used to validate the trends of the candidate biomarkers in larger sample cohorts. RESULTS: About 270 lipids belonging to 20 lipid species were found significantly dysregulated between the serum exosome of PC patients and healthy controls. 61 of them were validated in larger samples size. We further analysis the correlation between these dysregulated lipids and other PC related factors, and results show that LysoPC 22:0, PC (P-14:0/22:2) and PE (16:0/18:1) are all associated with tumor stage, CA19-9, CA242 and tumor diameter. What's more, PE (16:0/18:1) is also found to be significantly correlated with the patient's overall survival. CONCLUSION: These data reveal dysregulated lipids in serum exosome of PC patients, which have potential to be biomarkers for diagnosis, or unveil pathological relationship between exosome and PC progress.

Enhanced identification of the in vivo metabolites of Ecliptae Herba in rat plasma by integrating untargeted data-dependent MS2 and predictive multiple reaction monitoring-information dependent acquisition-enhanced product ion scan.

Detection and identification of the in vivo metabolites of traditional Chinese medicine by untargeted profiling strategies are often confronted with severe interference from complex endogenous substances. Here we developed an integral approach, by combining untargeted data-dependent MS2 (dd-MS2) of Q-Orbitrap mass spectrometry and predictive multiple reaction monitoring-information dependent acquisition-enhanced product ion scan (pMRM-IDA-EPI) of triple quadrupole-linear ion trap (QTRAP) mass spectrometry, aiming to detect and identify more extensive metabolites in bio-samples. Ecliptae Herba (EH) is a widely consumed medicinal herb with the effects of nourishing liver/kidney, but its metabolites in vivo have not been fully elucidated. Firstly, after UHPLC separation on an HSS T3 column, chemical fingerprinting of 70% ethanolic extract of EH was performed by untargeted dd-MS2 in negative ion mode. We could characterize 41 compounds from EH, and 24 were detectable in the plasma of rats (prototypes) after oral administration of EH extract (1 g/kg). Secondly, using echinocystic acid (triterpene), wedelolactone (coumarin), and apigenin (flavonoid) as the different parent templates, an MRM list containing 150 predicted ion-pairs was established to enhance MS2 scan by pMRM-IDA-EPI, which enabled the primary identification of up to 200 metabolites. The biotransformations mainly involve oxidation, hydrogenation, methylation, glucuronidation, sulfonation etc. Thirdly, the rat plasma samples obtained after oral administration of three pure compounds (echinocystic acid, wedelolactone and apigenin) were analyzed to verify the reliability of metabolites identification, and 11, 4, and 10 metabolites were found individually. This is the first comprehensive research on the metabolism of EH in vivo.

Performance of direct anaerobic digestion of dewatered sludge in long-term operation.

Direct anaerobic digestion of dewatered sludge with total solids (TS) content of 15-20% was tested in a horizontal digester for one and half years. The system kept stable with pH 7-8. The concentration of volatile fatty acids was lower than 800 mg/L, free ammonia nitrogen was lower than 200 mg/L, and total alkalinity kept higher than 6000 mg/L. The performance was influenced by organic load rate (OLR) and organic content in feed sludge. When volatile solids (VS) in TS of feed sludge reached 60-65% at OLR 3.50-3.70 g/(L·d), the process exhibited the best performance with organic removal rate of 32.19 ±â€¯7.73% and methane production of 156.86 ±â€¯13.05 ml/g VS added. Microbial analyses indicated that Methanosarcina became predominant and Methanosaeta almost disappeared. Moreover, hydrogenotrophic and methylotrophic methanogens accounted for 18.13-29.40% and 11.58-29.56% of the total, respectively. These provide a new guideline for small-scale or centralized sludge treatment.

Unbiased lipidomic profiling reveals metabolomic changes during the onset and antipsychotics treatment of schizophrenia disease.

INTRODUCTION: Schizophrenia (SCH) is one of the most common psychiatric disorders, which involves impairments in motivation and cognition. The pathological mechanisms underlying SCH are still unknown, and no effective therapies can prevent or treat perfectly the cognitive impairments and deficit symptoms caused by SCH. OBJECTIVES: We aimed to find the lipid expression change in plasma that underlie SCH onset and antipsychotics treatment. METHODS: We performed a data independent acquisition-based untargeted lipidomic approach on a quadrupole-time of flight liquid chromatography coupled to mass spectrometry platform. The plasma lipidomic profiles of SCH patients (n = 20) pre- and post-antipsychotics treatment were acquired as well as healthy controls (n = 29). Grouped or paired t-test were used to analyze the data. RESULTS: Over 1000 features were detected by our lipidomic analysis, of which 445 lipids belonging to 17 lipid species were reliably identified by tandem mass spectrometry. After statistical analysis, 47 lipids belonging to 9 lipid species were found to be dysregulated between naive SCH patients and healthy controls, and 50 lipids belonging to 9 lipid species were found to be dysregulated after antipsychotics treatment. These findings include several new SCH-relevant lipid species such as sphingomyelin, acylcarnitine and ceramide. Four types of lipid expression regulative patterns can be concluded from the above mentioned findings, revealing information about mechanism, side-effect and potential target of antipsychotics. CONCLUSIONS: The work presented here have revealed several new lipid species which are significantly dysregulated in SCH disease development or antipsychotics treatment. These lipids provide new evidence for the pathological studies of SCH and new antipsychotics development, or can be considered as potentially candidate biomarkers for further validation.

Workflow development for targeted lipidomic quantification using parallel reaction monitoring on a quadrupole-time of flight mass spectrometry.

Advances in high-resolution mass spectrometers with faster scanning capabilities and higher sensitivities have expanded these instruments' functionality beyond traditional data-dependent acquisition in targeted metabolomics. Apart from the traditional multiple reaction monitoring strategy, the parallel reaction monitoring (PRM) strategy is also used for targeted metabolomics quantification. The high resolution and mass accuracy of full-scan (MS1) and tandem mass spectrometry (MS/MS) scan result in sufficient selectivity by monitoring all MS/MS fragment ions for each target precursor and simultaneously providing flexibility in assay method construction and post-acquisition data analysis. In this study, using an orthogonal quadrupole-time of flight liquid chromatography-mass spectrometry system (QTOF LC-MS), we investigated the applicability of a large-scale targeted lipidomic assay using scheduled PRM. This method monitored 222 lipids belonging to 15 lipid species in serum. Robustness, reproducibility, and quantitative performance were assessed using chemical standards and serum samples. Finally, we demonstrated the application of this PRM-based targeted metabolomic workflow to systemic lupus erythematosus, a severe autoimmunological disease. Results showed that 63 lipids belonging to 11 lipid species were significantly changed. In summary, at the first time, a robust targeted lipidomic workflow was established using PRM acquisition strategy on a Q-TOF platform, providing another powerful tool for targeted metabolomic analysis.

Evolution of microbial community along with increasing solid concentration during high-solids anaerobic digestion of sewage sludge.

High-solids anaerobic digestion (HSAD), a promising method with smaller reactor and less heating energy consumption, showed relatively lower digestion efficiency sometimes and higher tolerance to some inhibitors. To investigate the phenomena, the archaeal and bacterial communities in four anaerobic digesters treating sewage sludge with total solids (TS) of 10-19% were investigated. Although acetoclastic methanogenesis conducted mainly by genus Methanosarcina was still the main pathway producing methane, the total ratio of acetoclastic methanogens decreased along with the increased TS. In contrary, the relative abundance of hydrogenotrophic methanogens increased from 6.8% at TS 10% to 22.3% at TS 19%, and methylotrophic methanogens from 10.4% to 20.9%. The bacterial community was dominated by five phyla. Acidogenic and acetogenic bacteria affiliated to Firmicutes decreased following the increase of TS; while the proteolysis phylum Bacteroidetes increased, with a tolerant family ST-12K33 notably existing in the digesters at TS 17% and 19%.

Determination and pharmacokinetics of isoferulic acid in rat plasma by high-performance liquid chromatography after oral administration of isoferulic acid and Rhizoma Cimicifugae extract.

A simple and specific high-performance liquid chromatographic (HPLC) method with ultraviolet (UV) absorbance detection has been developed for the determination of isoferulic acid in rat plasma. The plasma samples were deproteinized with methanol after the addition of internal standard (IS) tinidazole. The analysis was performed on a Kromasil C18 column (250 mm x 4.6 mm i.d., 5 microm particle size) with acetonitrile-0.05% phosphoric acid (25:75, v/v) as mobile phase. The linear range was 0.0206-5.15 microg ml(-1) and the lower limit of quantification (LLOQ) was 0.0206 microg ml(-1). The intra- and inter-day relative standard deviations (R.S.D.s%) were less than 11.4 and 12.3%, respectively, and accuracy as relative error (R.E.%) between -6.7 and -1.1%. Mean extraction recovery was above 80%. The validated method was successfully applied to the pharmacokinetic study of isoferulic acid in rat plasma after oral administration of isoferulic acid and Rhizoma Cimicifugae extract.