Development of a High Coverage Pseudotargeted Lipidomics Method Based on Ultra-High Performance Liquid Chromatography-Mass Spectrometry

Novel insights into the mechanisms of hard exudate in diabetic retinopathy: Findings of serum lipidomic and metabolomics profiling

Objective

Retinal hard exudates (HEs) result from lipoproteins leaking from capillaries into extracellular retinal space, and are related to decreased visual acuity in diabetic retinopathy (DR). This study aims to identify differential serum lipids and metabolites associated with HEs.

Materials and methods

A cross-sectional study was conducted Jul 2017 ∼ Mar 2021. We assessed the amount of HEs using standard ETDRS photographs for comparison. HEs severity was rated as "no or questionable", "moderate" or "severe". Serum samples were processed via high coverage pseudotargeted lipidomics analysis, and untargeted liquid chromatography coupled with time-of-flight mass spectrometry for metabolomics study, respectively. Weighted gene co-expression network analyses, partial least squares-discriminant analysis, and multi-receiver operating characteristic analysis were applied.

Results

A total of 167 patients were included. Discovery group: 116 eyes (116 patients). Validation group: 51 eyes (51 patients). 888 lipids were detected and divided into 18 modules (MEs), ME1 ∼ ME18. Lipids in ME1 significantly increased in patients with HEs in DR (NPDR and PDR combined), NPDR, and PDR, respectively. ME1 enriched to triglycerides (29%), ceramides (17%), and N-acylethanolamines (15%). A combined model of 20 lipids was the best to discriminate HEs, area under curve = 0.804, 95% confidence interval = 0.674-0.916. For metabolomics analysis, 19 metabolites and 13 pathways associated with HEs were identified. Taurine and hypotaurine metabolism, cysteine and methionine metabolism were closely related to HEs (P < 0.01).

Conclusions

The lipids and metabolites identified may serve as prediction biomarkers in the early stage of HEs in DR.

Stepwise solid phase extraction integrated with chemical derivatization for all-in-one injection LC-MS/MS analysis of metabolome and lipidome

The metabolome and lipidome are critical components in illustrating biological processes and pathological mechanisms. Generally, two or more independent methods are required to analyze the two compound panels due to their distinct chemical properties and polarity differences. Here, a novel strategy integrating stepwise solid-phase extraction (SPE) and dansyl chemical derivatization was proposed for all-in-one injection LC-MS/MS analysis of serum metabolome and lipidome. In this workflow, a stepwise elution procedure was firstly optimized to separate the metabolome and lipidome fractions using an Ostro plate. Dansyl chemical derivatization was then applied to label amine/phenol, carboxyl, and carbonyl-containing sub-metabolomes. Our results demonstrated that the dansyl labeling could significantly improve chromatographic separation, enhance the MS response, and overcome the matrix effect of co-eluting lipids. Ultimately, an all-in-one injection LC-MS/MS method measuring 256 lipids (covering 20 subclasses) and 212 metabolites (including amino acids, bile acids, fatty acids, acylcarnitines, indole derivatives, ketones and aldehydes, nucleic acid metabolism, polyamines, etc.) was established. This method was applied to investigate the metabolic changes in cisplatin-induced nephrotoxicity in rats and the results were compared with previous untargeted metabolomics. The presented strategy could predominantly improve the analytical coverage and throughput and can be of great use in discovering reliable potential biomarkers in various applications.

Pseudotargeted Metabolomics Approach Enabling the Classification-Induced Ginsenoside Characterization and Differentiation of Ginseng and Its Compound Formulation Products

The use of diversified ginseng extracts in health-promoting foods is difficult to differentiate, as they share bioactive ginsenosides among different Panax species (e.g., P. ginseng, P. quinquefolius, P. notoginseng, and P. japonicus) and different parts (e.g., root, leaf, and flower). This work was designed to develop a pseudo-targeted metabolomics approach to discover ginsenoside markers facilitating the precise authentication of ginseng and its use in compound formulation products (CFPs). Versatile mass spectrometry experiments on the QTrap mass spectrometer achieved classified characterization of the neutral, malonyl, and oleanolic acid-type ginsenosides, with 567 components characterized. A pseudo-targeted metabolomics approach by multiple reaction monitoring (MRM) of 262 ion pairs could assist to establish key identification points for 12 ginseng species. The simultaneous detection of 14 markers enabled the identification of ginseng from 15 ginseng-containing CFPs. The pseudo-targeted metabolomics strategy enabled better performance in differentiating among multiple ginseng, compared with the full-scan high-resolution mass spectrometry approach.

Lipidomics-Paving the Road towards Better Insight and Precision Medicine in Rare Metabolic Diseases

Even though the application of Next-Generation Sequencing (NGS) has significantly facilitated the identification of disease-associated mutations, the diagnostic rate of rare diseases is still below 50%. This causes a diagnostic odyssey and prevents specific treatment, as well as genetic counseling for further family planning. Increasing the diagnostic rate and reducing the time to diagnosis in children with unclear disease are crucial for a better patient outcome and improvement of quality of life. In many cases, NGS reveals variants of unknown significance (VUS) that need further investigations. The delineation of novel (lipid) biomarkers is not only crucial to prove the pathogenicity of VUS, but provides surrogate parameters for the monitoring of disease progression and therapeutic interventions. Lipids are essential organic compounds in living organisms, serving as building blocks for cellular membranes, energy storage and signaling molecules. Among other disorders, an imbalance in lipid homeostasis can lead to chronic inflammation, vascular dysfunction and neurodegenerative diseases. Therefore, analyzing lipids in biological samples provides great insight into the underlying functional role of lipids in healthy and disease statuses. The method of choice for lipid analysis and/or huge assemblies of lipids (=lipidome) is mass spectrometry due to its high sensitivity and specificity. Due to the inherent chemical complexity of the lipidome and the consequent challenges associated with analyzing it, progress in the field of lipidomics has lagged behind other omics disciplines. However, compared to the previous decade, the output of publications on lipidomics has increased more than 17-fold within the last decade and has, therefore, become one of the fastest-growing research fields. Combining multiple omics approaches will provide a unique and efficient tool for determining pathogenicity of VUS at the functional level, and thereby identifying rare, as well as novel, genetic disorders by molecular techniques and biochemical analyses.

Nutritional lipidomics for the characterization of lipids in food

Lipids represent one out of three major macronutrient classes in the human diet. It is estimated to account for about 15-20% of the total dietary intake. Triacylglycerides comprise the majority of them, estimated 90-95%. Other lipid classes include free fatty acids, phospholipids, cholesterol, and plant sterols as minor components. Various methods are used for the characterization of nutritional lipids, however, lipidomics approaches become increasingly attractive for this purpose due to their wide coverage, comprehensiveness and holistic view on composition. In this chapter, analytical methodologies and workflows utilized for lipidomics profiling of food samples are outlined with focus on mass spectrometry-based assays. The chapter describes common lipid extraction protocols, the distinct instrumental mass-spectrometry based analytical platforms for data acquisition, chromatographic and ion-mobility spectrometry methods for lipid separation, briefly mentions alternative methods such as gas chromatography for fatty acid profiling and mass spectrometry imaging. Critical issues of important steps of lipidomics workflows such as structural annotation and identification, quantification and quality assurance are discussed as well. Applications reported over the period of the last 5years are summarized covering the discovery of new lipids in foodstuff, differential profiling approaches for comparing samples from different origin, species, varieties, cultivars and breeds, and for food processing quality control. Lipidomics as a powerful tool for personalized nutrition and nutritional intervention studies is briefly discussed as well. It is expected that this field is significantly growing in the near future and this chapter gives a short insight into the power of nutritional lipidomics approaches.

Ubiquitin-based pathway acts inside chloroplasts to regulate photosynthesis

Photosynthesis is the energetic basis for most life on Earth, and in plants it operates inside double membrane-bound organelles called chloroplasts. The photosynthetic apparatus comprises numerous proteins encoded by the nuclear and organellar genomes. Maintenance of this apparatus requires the action of internal chloroplast proteases, but a role for the nucleocytosolic ubiquitin-proteasome system (UPS) was not expected, owing to the barrier presented by the double-membrane envelope. Here, we show that photosynthesis proteins (including those encoded internally by chloroplast genes) are ubiquitinated and processed via the CHLORAD pathway: They are degraded by the 26S proteasome following CDC48-dependent retrotranslocation to the cytosol. This demonstrates that the reach of the UPS extends to the interior of endosymbiotically derived chloroplasts, where it acts to regulate photosynthesis, arguably the most fundamental process of life.

Efficacy and mechanism of intermittent fasting in metabolic associated fatty liver disease based on ultraperformance liquid chromatography-tandem mass spectrometry

OBJECTIVES

Drug treatment of metabolic associated fatty liver disease (MAFLD) remains lacking. This study analyzes the efficacy and mechanism underlying intermittent fasting combined with lipidomics.

METHODS

Thirty-two male rats were randomly divided into three groups: Normal group, administered a standard diet; MAFLD group, administered a 60% high-fat diet; time-restricted feeding (TRF) group, administered a 60% high-fat diet. Eating was allowed for 6 h per day (16:00-22:00). After 15 weeks, liver lipidomics and other indicators were compared.

RESULTS

A total of 1,062 metabolites were detected. Compared with the Normal group, the weight, body fat ratio, aspartate aminotransferase, total cholesterol, low-density cholesterol, fasting blood glucose, uric acid, and levels of 317 lipids including triglycerides (TG) (17:0_-18:1_-20:4) were upregulated, whereas the levels of 265 lipids including phosphatidyl ethanolamine (PE) (17:0_-20:5) were downregulated in the MAFLD group (P < 0.05). Compared with the MAFLD group, the weight, body fat ratio, daily food intake, and levels of 253 lipids including TG (17:0_-18:1_-22:5) were lower in the TRF group. Furthermore, the levels of 82 lipids including phosphatidylcholine (PC) (20:4_-22:6) were upregulated in the TRF group (P < 0.05), while serum TG level was increased; however, the increase was not significant (P > 0.05). Enrichment analysis of differential metabolites showed that the pathways associated with the observed changes mainly included metabolic pathways, regulation of lipolysis in adipocytes, and fat digestion and absorption, while reverse-transcription polymerase chain reaction showed that TRF improved the abnormal expression of FAS and PPARα genes in the MAFLD group (P < 0.05).

CONCLUSION

Our results suggest that 6 h of TRF can improve MAFLD via reducing food intake by 13% and improving the expression of genes in the PPARα/FAS pathway, thereby providing insights into the prevention and treatment of MAFLD.

AKR1C3-dependent lipid droplet formation confers hepatocellular carcinoma cell adaptability to targeted therapy

Rationale: Increased lipid droplet (LD) formation has been linked to tumor metastasis, stemness, and chemoresistance in various types of cancer. Here, we revealed that LD formation is critical for the adaptation to sorafenib in hepatocellular carcinoma (HCC) cells. We aim to investigate the LD function and its regulatory mechanisms in HCC. Methods: The key proteins responsible for LD formation were screened by both metabolomics and proteomics in sorafenib-resistant HCC cells and further validated by immunoblotting and immunofluorescence staining. Biological function of AKR1C3 was evaluated by CRISPR/Cas9-based gene editing. Isotopic tracing analysis with deuterium³-labeled palmitate or carbon13-labeled glucose was conducted to investigate fatty acid (FA) and glucose carbon flux. Seahorse analysis was performed to assess the glycolytic flux and mitochondrial function. Selective AKR1C3 inhibitors were used to evaluate the effect of AKR1C3 inhibition on HCC tumor growth and induction of autophagy. Results: We found that long-term sorafenib treatment impairs fatty acid oxidation (FAO), leading to LD accumulation in HCC cells. Using multi-omics analysis in cultured HCC cells, we identified that aldo-keto reductase AKR1C3 is responsible for LD accumulation in HCC. Genetic loss of AKR1C3 fully depletes LD contents, navigating FA flux to phospholipids, sphingolipids, and mitochondria. Furthermore, we found that AKR1C3-dependent LD accumulation is required for mitigating sorafenib-induced mitochondrial lipotoxicity and dysfunction. Pharmacologic inhibition of AKR1C3 activity instantly induces autophagy-dependent LD catabolism, resulting in mitochondrial fission and apoptosis in sorafenib-resistant HCC clones. Notably, manipulation of AKR1C3 expression is sufficient to drive the metabolic switch between FAO and glycolysis. Conclusions: Our findings revealed that AKR1C3-dependent LD formation is critical for the adaptation to sorafenib in HCC through regulating lipid and energy homeostasis. AKR1C3-dependent LD accumulation protects HCC cells from sorafenib-induced mitochondrial lipotoxicity by regulating lipophagy. Targeting AKR1C3 might be a promising therapeutic strategy for HCC tumors.

Plin2-mediated lipid droplet mobilization accelerates exit from pluripotency by lipidomic remodeling and histone acetylation

Metabolic switch is critical for cell fate determination through metabolic functions, epigenetic modifications, and gene expression. However, the mechanisms underlying these alterations and their functional roles remain unclear. Here, we show that Plin2-mediated moderate lipid hydrolysis is critical for pluripotency of embryonic stem cells (ESCs). Upon exit from pluripotency, lipid droplet (LD)-associated protein Plin2 is recognized by Hsc70 and degraded via chaperone-mediated autophagy to facilitate LD mobilization. Enhancing lipid hydrolysis by Plin2 knockout promotes pluripotency exit, which is recovered by ATGL inhibition. Mechanistically, excessive lipid hydrolysis induces a dramatic lipidomic remodeling characterized by decreased cardiolipin and phosphatidylethanolamine, which triggers defects in mitochondrial cristae and fatty acid oxidation, resulting in reduced acetyl-CoA and histone acetylation. Our results reveal how LD mobilization is regulated and its critical role in ESC pluripotency, and indicate the mechanism linking LD homeostasis to mitochondrial remodeling and epigenetic regulation, which might shed light on development and diseases.

Integrated Metabolomics and Lipidomics Approach for the Study of Metabolic Network and Early Diagnosis in Cerebral Infarction

Cerebral infarction (CI) remains a major cause of high mortality and long-term disability worldwide. The exploration of biomarkers and pathogenesis is crucial for the early diagnosis of CI. Although the understanding of metabolic perturbations underlying CI has increased in recent years, the relationship between altered metabolites and disease pathogenesis has only been partially elucidated and requires further investigation. In this study, we performed an integrated metabolomics and lipidomics analysis on 59 healthy subjects and 47 CI patients. Ultimately, 49 metabolite and 68 lipid biomarkers were identified and enriched in 24 disturbed pathways. The metabolic network revealed a significant interaction between altered lipids and other metabolites. Using receiver operating characteristic curve (ROC) analysis, a panel of three polar metabolites and seven lipids was optimized in the training set, which included taurine, oleoylcarnitine, creatinine, PE(22:6/P-18:0), Cer 34:2, GlcCer(d18:0/18:0), DG 44:0, LysoPC(16:0), 22:6-OH/LysoPC, and TAG58:7-FA22:4. Subsequently, a support vector machine (SVM) model was constructed and validated, which showed excellent predictive ability in the validation set. Thereby, the integrated metabolomics and lipidomics approach could contribute to a comprehensive understanding of the metabolic dyshomeostasis associated with the pathogenesis of underlying CI. The present research may promote a deeper understanding and early diagnosis of CI in the clinic. All raw data were deposited in PRIDE (PXD036199).

Downregulation of hepatic ceruloplasmin ameliorates NAFLD via SCO1-AMPK-LKB1 complex

Copper deficiency has emerged to be associated with various lipid metabolism diseases, including non-alcoholic fatty liver disease (NAFLD). However, the mechanisms that dictate the association between copper deficiency and metabolic diseases remain obscure. Here, we reveal that copper restoration caused by hepatic ceruloplasmin (Cp) ablation enhances lipid catabolism by promoting the assembly of copper-load SCO1-LKB1-AMPK complex. Overnutrition-mediated Cp elevation results in hepatic copper loss, whereas Cp ablation restores copper content to the normal level without eliciting detectable hepatotoxicity and ameliorates NAFLD in mice. Mechanistically, SCO1 constitutively interacts with LKB1 even in the absence of copper, and copper-loaded SCO1 directly tethers LKB1 to AMPK, thereby activating AMPK and consequently promoting mitochondrial biogenesis and fatty acid oxidation. Therefore, this study reveals a mechanism by which copper, as a signaling molecule, improves hepatic lipid catabolism, and it indicates that targeting copper-SCO1-AMPK signaling pathway ameliorates NAFLD development by modulating AMPK activity.

Dietary Interventions of Salmon and Silver Carp Phospholipids on Mice with Metabolic Syndrome Based on Lipidomics

The number of metabolic syndromes (MetS) is increasing, and a fish phospholipid diet can reduce the risk of MetS. In this study, the changes in lipid metabolism of colon contents were analyzed by extensive lipidomics in mice with metabolic syndrome by fish phospholipid diet, and mice were randomly divided into experimental groups with different diet types by establishing a MetS model. After 14 weeks, the mice were sacrificed and the serum and colon contents were collected. Ultra-high liquid phase tandem mass spectrometry was used for broadly targeted lipidomic analysis, and the qualitative and quantitative detection of lipid metabolism changes in the colonic contents of mice. Under the intervention of fish phospholipids, MetS mice were significantly inhibited, serum total cholesterol (TC) and triglycerides (TG) decreased, serum high-density lipoprotein (HDL-C) and low-density lipoprotein (LDL-C) levels were improved, fasting blood glucose and insulin levels decreased, and inflammatory factors decreased. Through screening, it was found that thirty-three lipid metabolites may be key metabolites and five have significantly changed metabolic pathways. Modularizing lipid metabolites, it is possible to understand the extent to which different types and concentrations of fish phospholipids affect metabolic syndrome. Therefore, our study may provide new therapeutic clues for improving MetS.

Gut bacteria alleviate smoking-related NASH by degrading gut nicotine

Tobacco smoking is positively correlated with non-alcoholic fatty liver disease (NAFLD)^1-5, but the underlying mechanism for this association is unclear. Here we report that nicotine accumulates in the intestine during tobacco smoking and activates intestinal AMPKα. We identify the gut bacterium Bacteroides xylanisolvens as an effective nicotine degrader. Colonization of B. xylanisolvens reduces intestinal nicotine concentrations in nicotine-exposed mice, and it improves nicotine-exacerbated NAFLD progression. Mechanistically, AMPKα promotes the phosphorylation of sphingomyelin phosphodiesterase 3 (SMPD3), stabilizing the latter and therefore increasing intestinal ceramide formation, which contributes to NAFLD progression to non-alcoholic steatohepatitis (NASH). Our results establish a role for intestinal nicotine accumulation in NAFLD progression and reveal an endogenous bacterium in the human intestine with the ability to metabolize nicotine. These findings suggest a possible route to reduce tobacco smoking-exacerbated NAFLD progression.

The Use of Metabolomics as a Tool to Compare the Regulatory Mechanisms in the Cecum, Ileum, and Jejunum in Healthy Rabbits and with Diarrhea

Simple Summary

The problems caused by antibiotic abuse have swept the world, and the Chinese government has responded to calls for a comprehensive ban on antibiotics. However, not using antibiotics also challenges China’s existing livestock industry. Based on this, we carried out a nontargeted metabolomics analysis of the jejunum, ileum, and cecum of diarrhea rabbits and normal rabbits fed with antibiotic-free diets, respectively, to find out the mechanism of action of each intestinal segment group and between different intestinal segments. The screened differential metabolites were mostly related to intestinal barrier, intestinal inflammation, and autophagy after a KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis. In this paper, we analyzed the metabolic pathways that were significantly different between different intestinal segments and illustrated the mechanism and potential connections of the screened differential metabolites in different intestinal segments in the form of charts.

Abstract

For many years, antibiotics in feed have been an effective and economical means to promote growth and disease resistance in livestock production. However, the rampant abuse of antibiotics has also brought very serious harm to human health and the environment. Therefore, the Chinese government promulgated laws and regulations on 1 July 2020, to prohibit the use of antibiotics in feed. To improve the effect of antibiotic-free feeding on China’s existing rabbit industry, we used the nontargeted metabolomics method to detect the differences between diarrhea rabbits (Dia) and normal rabbits (Con) on an antibiotic-free diet. A total of 1902 different metabolites were identified. A KEGG analysis showed that in the cecum, metabolites were mainly concentrated in bile secretion, antifolate resistance, aldosterone synthesis, and secretion pathways. The ileal metabolites were mainly concentrated in tyrosine metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, steroid hormone biosynthesis, alanine, aspartate, and glutamate metabolism. The metabolites in the jejunum were mainly rich in panquinone and other terpenoid compound quinone biosynthesis, AMPK (adenosine 5′-monophosphate (AMP)-activated protein kinase) signal, inositol phosphate metabolism, and pentose phosphate pathway. After a deep excavation of the discovered differential metabolites and metabolic pathways with large differences between groups, it was found that these metabolic pathways mainly involved intestinal inflammation, intestinal barrier, and autophagy. The results showed that panquinone and other terpenoids could increase AMPK activity to promote cell metabolism and autophagy, thus trying to prevent inflammation and alleviate intestinal disease symptoms. In addition, we discussed the possible reasons for the changes in the levels of seven intestinal endogenous metabolites in rabbits in the diarrhea group. The possibility of improving diarrhea by adding amino acids to feed was discussed. In addition, the intermediate products produced by the pentose phosphate pathway and coenzyme Q had a positive effect on steroid hormone biosynthesis to combat intestinal inflammation.

The Pseudotargeted Metabolomics Study on the Toxicity of Fuzi Using Ultraperformance Liquid Chromatography Tandem Mass Spectrometry

Fuzi is commonly used in traditional Chinese medicine. Clinical Fuzi poisoning cases have frequently been reported. Glycyrrhizae Radix is often used to alleviate Fuzi’s toxicity. However, the poisoning mechanism of Fuzi and the detoxication mechanism of Glycyrrhizae Radix are still not clear. We identified the chemical components of Fuzi at different decoction times (0.5, 1, 2, 4, and 6 h) using ultrahigh performance liquid chromatography quadrupole time-of-flight mass spectrometry. A total of 35 compounds were detected in the Fuzi decoction, including diester alkaloids, monoester alkaloids, amino acids, phenolic acids, organic acids, glycosides, and sugars among others. The content of diester alkaloids (i.e., subaconitine, neoaconitine, and aconitine) in the Fuzi decoction decreased after 2 h of decoction time, while the content of monoester alkaloids (i.e., benzoyl aconitine and benzoyl subaconitine) reached a peak at 2 h. A total of 32 rats were randomly divided into four groups, including 8 cases in the low-dosage Fuzi decoction group A, 8 cases in the high-dosage Fuzi decoction group B, 8 cases in the Fuzi and glycyrrhizae decoction group C, and 8 cases in the control group D. The decoction was administered orally for 7 days. Then, a serum was obtained. The metabolites’ changes were analyzed in serum metabolomics using liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). Statistical analysis and pathway analysis were used to assess the effects of glycyrrhizae on the metabolic changes induced by Fuzi. The behavioral and biochemical characteristics indicated that Fuzi exhibited toxic effects on rats and their metabolic profiles changed. However, the metabolic profiles of the glycyrrhizae group became similar to those of the control group. These profiles showed that glycyrrhizae can effectively improve Fuzi poisoning rats. Our study demonstrated that the established pseudotargeted metabolomics is a powerful approach for investigating the mechanisms of herbal toxicity.

Simultaneous Differentiation of C═C Position Isomerism in Fatty Acids through Ion Mobility and Theoretical Calculations

Fatty acids play a pivotal role in biological processes and have many isomers, particularly at the C═C position, that influence their biological function. Distinguishing between isomers is crucial to investigating their role in health and disease. However, separating the isomers poses a significant analytical challenge. In this study, we developed a simple and rapid strategy combining ion mobility spectrometry and theoretical chemical calculations to differentiate and quantify the C═C positional isomers in 2-/3-butenoic acid (BA), 2-/3-/4-pentenoic acid (PA), and 2-/3-/5-hexenoic acid (HA). C═C positional isomerism was mobility-differentiated by simple complexation with crown ethers (12C4, 15C5, and 18C6) and divalent metal ions (Mg²⁺, Ca²⁺, Mn²⁺, Fe²⁺, Co²⁺, Ni²⁺, Zn²⁺, Sr²⁺, and Ba²⁺), that is, converting C═C positional isomers with small structural differences into complexes with large structural differences through the interaction with metal ions and crown ethers. Metallized isomers were formed but could not be differentiated due to their complex and overlapping extracted ion mobiliograms (EIMs). Binary crown ether-isomer complexes were not observed, indicating that C═C positional isomers could not be separated by simple mixing with crown ethers. However, significant EIM differences were obtained for the formed ternary complexes, allowing baseline separation for the isomers. Notably, all crown ethers and metal ions have a separation effect with the isomers, with a calculated separation resolution (R_p-p) of 0.07-2.44. Theoretical chemical calculations were performed to provide in-depth structural information for the complexes and explain the separation principle. Theoretical conformational space showed that the divalent metal ions act as a bridge connecting the crown ether and the isomer. Additionally, the ternary complex becomes more compact as the distance between C═C and -COOH increases. Theoretical results can reflect the features of mobility experiments, with relative errors between the experiment collision cross-section (CCS) and theoretical CCS of no more than ±8.06%. This method was also evaluated in terms of quantification, accuracy, and precision repeatability. Overall, this study establishes that the crown ether-metal ion pair can function as a robust unit for differentiating C═C positional isomerism.

Revealing the mechanism of Jiegeng decoction attenuates bleomycin-induced pulmonary fibrosis via PI3K/Akt signaling pathway based on lipidomics and transcriptomics

BACKGROUND

Pulmonary fibrosis (PF) is a serious lung disease with unknown etiology and irreversible course. Jiegeng decoction (JGD), a traditional prescription, is widely used to treat lung diseases due to its anti-inflammatory and expectorant effects.

PURPOSE

To explore the effect of JGD on mice with PF and its underlying mechanism. For this purpose, we established a mouse model with PF by bleomycin (BLM) and then administered JGD and pirfenidone at different concentrations.

RESULTS

In vivo, JGD was found to reduce lung inflammation, improve lung function and decrease collagen deposition to alleviate bleomycin-induced PF in mice. The mouse lung tissue was analyzed using lipidomics and transcriptomics. We found phosphatidylinositol was decreased after JGD treatment in lipidomics results, while transcriptomics results showed the critical roles of PI3K/Akt signaling pathway in JGD treatment group. Then, Western Blot and Immunohistochemistry were used to validate that JGD may regulate the expression of Bax, Caspase3, Caspase8, Caspase9 and Bcl-2 apoptosis-related proteins via PI3K/Akt signaling pathway. TUNEL staining revealed that apoptosis mainly occurs on AEC IIs.

CONCLUSION

Our results showed that JGD inhibits apoptosis through the PI3K/Akt signaling pathway, thereby protecting against BLM-induced PF. Hence, JGD is expected to be a potential drug candidate for the treatment of PF.

Rescuing yeast from cell death enables overproduction of fatty acids from sole methanol

Methanol is an ideal feedstock for biomanufacturing that can be beneficial for global carbon neutrality; however, the toxicity of methanol limits the efficiency of methanol metabolism toward biochemical production. We here show that engineering production of free fatty acids from sole methanol results in cell death with decreased cellular levels of phospholipids in the methylotrophic yeast Ogataea polymorpha, and cell growth is restored by adaptive laboratory evolution. Whole-genome sequencing of the adapted strains reveals that inactivation of LPL1 (encoding a putative lipase) and IZH3 (encoding a membrane protein related to zinc metabolism) preserve cell survival by restoring phospholipid metabolism. Engineering the pentose phosphate pathway and gluconeogenesis enables high-level production of free fatty acid (15.9 g l^-1) from sole methanol. Preventing methanol-associated toxicity underscores the link between lipid metabolism and methanol tolerance, which should contribute to enhancing methanol-based biomanufacturing.

Quantitative identification of halo-methyl-benzoquinones as disinfection byproducts in drinking water using a pseudo-targeted LC-MS/MS method

Halobenzoquinones (HBQs) as disinfection byproducts (DBPs) in drinking water is prioritized for research due to their prevalent occurrence and high toxicity. However, only fifteen HBQs can be identified among a high diversity using targeted LC-MS/MS analysis in previous studies due to the lack of chemical standards. In this study, we developed a pseudo-targeted LC-MS/MS method for detecting and quantifying diverse HBQs. Distinct fragment characteristics of HBQs was observed according to the halogen substituent effects, and extended to the development of a multiple-reaction-monitoring (MRM) method for the quantification of the 46 HBQs that were observed in simulated drinking water using non-targeted analysis. The fragmentation mechanism was supported by the changes of Gibbs free energy (ΔG), and a linear relationship between the ΔG and the ionization efficiency of analytes was developed accordingly for quantification of these 46 HBQs, 30 of which were lack of chemical standards. It is noted that 29 of the 30 newly-identified HBQs were halo-methyl-benzoquinones (HMBQs), which were predicted to be carcinogens related with drinking-water bladder cancer risk and be more toxic than non-methyl HBQs. Using the new method, twelve HMBQs were detected in actual drinking water samples with concentrations up to 100.4 ng/L, 3 times higher than that reported previously. The cytotoxicity in CHO cells of HMBQs was over 1-fold higher than that of non-methyl-HBQs. Therefore, HMBQs are an essential, highly toxic group of HBQs in drinking water, which deserve particular monitoring and control.

Intervention of 4% salmon phospholipid on metabolic syndrome in mice based on colonic lipidomics analysis

BACKGROUND

The incidence of metabolic syndrome (MetS) is increasing, and n-3 polyunsaturated fatty acids (PUFAs) in salmon (Oncorhynchus) phospholipids can effectively reduce the risk of MetS.

RESULTS

Under the intervention of 4% salmon phospholipid, the levels of fasting blood glucose (FBG), insulin, monocyte chemoattractant protein-1 (MCP-1), interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α) were significantly reduced in the plasma of MetS mice, whereas adiponectin was significantly increased. By screening, we found that the 18 differential metabolites, consisting of seven triglycerides (TGs), six diglycerides (DGs), one phosphatidylethanolamine (PE), three sphingomyelins (SMs) and one eicosanoid, could be the key differential metabolites, and two metabolic pathways were significantly affected: glycerolipid metabolism and glycerophospholipid metabolism.

CONCLUSION

4% salmon phospholipids could affect MetS by inhibiting insulin resistance, reducing inflammatory factors and promoting the synthesis of PE, yet the mechanism required further study. Our results could help in the treatment of MetS. © 2021 Society of Chemical Industry.

Astilbin from Smilax glabra Roxb. alleviates high-fat diet-induced metabolic dysfunction

Overweight, obesity, and related diseases are currently the major public health problems worldwide. Astilbin, extracted from the rhizome of Smilax glabra Roxb., is known to have significant anti-inflammatory activity and hepatoprotective effect. Studies have shown that it can inhibit adipogenesis in adipocytes in vitro; however, the intervention benefits of astilbin against obesity and related diseases along with its associated mechanisms remain unknown. This study aimed to demonstrate the impact of astilbin consumption on the overall biochemical pattern of high-fat diet (HFD) mice by using a combined multi-omics approach. Our data indicated that astilbin reduced body weight, insulin resistance, and inflammation in mice fed an HFD. Astilbin improved HFD-induced gut microbial dysbiosis by decreasing the Firmicutes-to-Bacteroidetes ratio, by increasing beneficial bacteria such as Alistipes and Muribaculum and decreasing harmful bacteria including Lachnospiraceae FCS020 group, Coriobacteriaceae UCG-002, and Lachnospiraceae UCG-008, resulting in enhanced intestinal carbohydrate and lipid metabolism. Meanwhile, astilbin protected the integrity of the intestinal barrier in HFD mice, increased short-chain fatty acid levels, and reduced metabolic endotoxemia. We further showed that astilbin attenuated hepatic lipid droplet aggregation and triglyceride accumulation in HFD mice, affected glutamate metabolism-related pathways, and enhanced hepatic ATP transduction pathways and attenuated xanthine metabolism pathways in mice, which were positively correlated with the abundance of Alistipes and negatively correlated with Ruminococcaceae UCG-003. The results highlighted that astilbin could be used as a prebiotic for the prevention of "gut-liver axis" damage and metabolic disruption in obese individuals.

Disturbance of serum lipid metabolites and potential biomarkers in the Bleomycin model of pulmonary fibrosis in young mice

Background

Altered metabolic pathways have recently been considered as potential drivers of idiopathic pulmonary fibrosis (IPF) for the study of drug therapeutic targets. However, our understanding of the metabolite profile during IPF formation is lacking.

Methods

To comprehensively characterize the metabolic disorders of IPF, a mouse IPF model was constructed by intratracheal injection of bleomycin into C57BL/6J male mice, and lung tissues from IPF mice at 7 days, 14 days, and controls were analyzed by pathology, immunohistochemistry, and Western Blots. Meanwhile, serum metabolite detections were conducted in IPF mice using LC–ESI–MS/MS, KEGG metabolic pathway analysis was applied to the differential metabolites, and biomarkers were screened using machine learning algorithms.

Results

We analyzed the levels of 1465 metabolites and found that more than one-third of the metabolites were altered during IPF formation. There were 504 and 565 metabolites that differed between M7 and M14 and controls, respectively, while 201 differential metabolites were found between M7 and M14. In IPF mouse sera, about 80% of differential metabolite expression was downregulated. Lipids accounted for more than 80% of the differential metabolite species with down-regulated expression. The KEGG pathway enrichment analysis of differential metabolites was mainly enriched to pathways such as the metabolism of glycerolipids and glycerophospholipids. Eight metabolites were screened by a machine learning random forest model, and receiver operating characteristic curves (ROC) assessed them as ideal diagnostic tools.

Conclusions

In conclusion, we have identified disturbances in serum lipid metabolism associated with the formation of pulmonary fibrosis, contributing to the understanding of the pathogenesis of pulmonary fibrosis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12890-022-01972-6.

Diet composition affects long-term zearalenone exposure on the gut-blood-liver axis metabolic dysfunction in mice

Zearalenone (ZEN), one of the most contaminated Fusarium toxins worldwide, is very common in contaminating wheat, corn oil and other foods. People are more vulnerable to ZEN exposure with more daily caloric intake, yet little is known about the combined effect of different dietary patterns with mycotoxins. This study aimed to compare the effects of long-term ZEN exposure on the overall biochemical landscape of the "gut-blood-liver axis" under normal diet and high-fat diet (HFD) using a combined multi-omics approach. The results indicated that ZEN exposure, possibly via the phenylalanine metabolic pathway, led to dysbiosis of mouse flora, suppression of short-chain fatty acids (SCFAS) metabolism, systemic inflammatory responses, and disturbances in serum and liver metabolism, which were exacerbated in synergy with HFD and ultimately led to a more severe state of lipid metabolism in the liver. We further found that ZEN exposure attenuated the indole-3-propionic acid (IPA) metabolic pathway, enhanced 2-hydroxybutyric acid metabolism in serum, and attenuated β-alanine metabolism in liver which was positively correlated with the abundance of Prevotellaceae UCG-004, Prevotellaceae UCG-001, and Prevotellaceae NK3B31 groups. The results highlighted the damaging effects of ZEN on the gut-blood-liver axis under different dietary patterns, which might serve as a reference for future studies exploring the combined effects of fungal toxins and multiple dietary patterns.

USP22 regulates lipidome accumulation by stabilizing PPARγ in hepatocellular carcinoma

Elevated de novo lipogenesis is considered to be a crucial factor in hepatocellular carcinoma (HCC) development. Herein, we identify ubiquitin-specific protease 22 (USP22) as a key regulator for de novo fatty acid synthesis, which directly interacts with deubiquitinates and stabilizes peroxisome proliferator-activated receptor gamma (PPARγ) through K48-linked deubiquitination, and in turn, this stabilization increases acetyl-CoA carboxylase (ACC) and ATP citrate lyase (ACLY) expressions. In addition, we find that USP22 promotes de novo fatty acid synthesis and contributes to HCC tumorigenesis, however, this tumorigenicity is suppressed by inhibiting the expression of PPARγ, ACLY, or ACC in in vivo tumorigenesis experiments. In HCC, high expression of USP22 positively correlates with PPARγ, ACLY or ACC expression, and associates with a poor prognosis. Taken together, we identify a USP22-regulated lipogenesis mechanism that involves the PPARγ-ACLY/ACC axis in HCC tumorigenesis and provide a rationale for therapeutic targeting of lipogenesis via USP22 inhibition.

Different deubiquitinases are associated to cancer development. Here, the authors show that PPARgamma is stabilized by USP22-mediated deubiquitination leading to lipid accumulation and promoting hepatocellular carcinoma.

Identification of Veratrum Species in Pimacao Based on ITS2 Sequences and Steroidal Alkaloids by a Pseudo-Targeted Metabolomics Method

Pimacao is a traditional Chinese folk medicine and is the main component of the famous Chinese herbal remedy "Yunnan Baiyao" for its significant analgesic activity in the treatment of wounds. Due to increases in consumption, its wild population is now difficult to find, and adulterant from the same genus has occurred. However, this is challenging to distinguish the species of Veratrum in Pimacao using dried roots and rhizomes or medicinal powder. ITS2 sequences and steroidal alkaloids by the non-targeted and pseudo-targeted metabolomics methods were taken advantage of establishing an effective identification method. Based on the ITS2 sequence, metabolite profiling of steroidal alkaloids and morphological characteristics, the classification of two distinct subspecies in V. mengzeanum has been reinforced. In addition, the new subspecies V. mengzeanum subsp. phuwae was collected in China for the first time. The ITS2 sequence could be used in the identification of V. taliense, V. mengtzeanum, V. stenophyllum, and V. nigrum, but is insufficient for intraspecific identification. Simultaneously, 147 variables were labeled by non-targeted analysis accomplished utilizing an ultra-high-performance liquid chromatography electrospray ionization orbitrap tandem mass spectrometry (UPLC-ESI-QE-Orbitrap-MS) system consisting of an Orbitrap QE HF-X. Followed by a pseudo-targeted analysis method developed for the Qtrap 6500-plus mass spectrometry system coupled with an ESI source, 29 labeled steroidal alkaloids detected by the MRM mode could distinguish between four species. Notably, 25 labeled steroidal alkaloids could distinguish between three closely related species. These have the potential to be used as markers for identification. Furthermore, there were several variables with statistical differences between two subspecies of V. mengtzeanum and populations of V. taliense, V. mengtzeanum, and V. stenophyllum.

SWATH-MS2&1: Development and Validation of a Pseudotargeted Lipidomics Method for the Analysis of Glycerol Esters in Milk

Glycerol ester (GE) is a kind of important lipid in milk, which varies greatly depending on many factors. In this study, a novel pseudotargeted lipidomics strategy, named SWATH-MS2&1, was developed for the detection of GEs in milk and the Folch method was selected for the sample preparation. The developed method exhibited a competitive alternative to the acknowledged pseudotargeted strategy, including wider coverage (12 more GEs detected), higher repeatability (12 more GEs, whose coefficient of variation < 0.3), better linearity (5 more GEs, whose R² > 0.8), and similar sensitivity (only 2 GEs less than P-MRM after dilution). SWATH-MS2&1 was applied in the investigation of GEs from different milk samples. The orthogonal partial least-squares difference analysis of 219 GEs identified from SWATH-MS2&1 showed satisfying differentiation of different milk samples, and 76 GEs were screened out as potential markers. Our findings demonstrated that SWATH-MS2&1 could offer an accurate method to measure a wide spectrum of GEs in milk.

Sex-Dependent Environmental Health Risk Analysis of Flupyradifurone

Pesticides are used in agricultural production worldwide, resulting in widespread environmental pollution. Many diseases are closely related to exposure to pesticide residues. In this study, the association between exposure to the pesticide flupyradifurone (FPF), a substitute for neonicotinoids, and sex-dependent thyroid dysfunction was explored for the first time. Exposure using rat models revealed that the FPF metabolism is sex-dependent, with males preferring N-dealkylation and hydrolytic metabolism and females preferring hydroxylation. In particular, novel chloropyridine-site hydroxylation I and II metabolic pathways of FPF were discovered. More importantly, differential metabolic pathways of FPF induced sex-based dysregulation of the hypothalamic-pituitary-thyroid axis, in which females exhibited subclinical hyperthyroidism, while males displayed abnormal hypothyroidism. This may be attributed to the potential agonistic or antagonistic effect of FPF sex-dependent metabolites on liver thyroid hormone receptors. Furthermore, FPF exposure further mediated sex-specific dysregulation of cellular lipid homeostasis, with abnormal fatty acid β-oxidation and excessive energy expenditure in females and the risk of excessive accumulation of triglycerides in males. These results illustrate the potential risk of sex-related thyroid metabolic diseases caused by FPF and provide an important basis and support for further studies of FPF on human health and as an environmental pollutant.

Serum lipidomics profiles reveal potential lipid markers for prediabetes and type 2 diabetes in patients from multiple communities

OBJECTIVE

Dyslipidemia is a hallmark of diabetes mellitus (DM). However, specific lipid molecules closely associated with the initiation and progression of diabetes remain unclear. We used a pseudotargeted lipidomics approach to evaluate the complex lipid changes that occurred long before the diagnosis of type 2 diabetes mellitus (T2DM) and to identify novel lipid markers for screening prediabetes mellitus (PreDM) and T2DM in patients from multiple communities.

METHODS

Four hundred and eighty-one subjects consisting of T2DM, three subtypes of PreDM, and normal controls (NC) were enrolled as discovery cohort. Serum lipidomic profiles of 481 subjects were analyzed using an ultrahigh performance liquid chromatography-triple quadrupole mass spectrometry (UHPLC-QqQ-MS)-based pseudotargeted lipidomics method. The differential lipid molecules were further validated in an independent case-control study consisting of 150 PreDM, 234 T2DM and 94 NC.

RESULTS

Multivariate discriminative analyses show that lipidomics data have considerable potential for identifying lipidome differences among T2DM, subtypes of PreDM and NC. Statistical associations of lipid (sub)species display significant variations in 11 lipid (sub)species levels for T2DM and distinctive differences in 8 lipid (sub)species levels between prediabetic and normoglycemic individuals, with further differences in 8 lipid (sub)species levels among subtypes of PreDM. Adjusted for sex, age and BMI, only two lipid (sub)species of fatty acid (FA) and phosphatidylcholine (PC) were associated at p< 0.05 for PreDM (all) and subtypes of PreDM. The defined lipid markers not only significantly improve the diagnostic accuracy of PreDM and T2DM but also effectively evaluating the risk of developing into each subtype of PreDM and T2DM when addition of age, sex, BMI, and FPG, respectively.

CONCLUSIONS

Our findings improve insights into the lipid metabolic complexity and interindividual variations among subtypes of PreDM and T2DM, beyond the well-known differences in dyslipidemia in clinic.

High Throughput UHPLC-MS-Based Lipidomics Using Vacuum Jacketed Columns

Reversed-phase UHPLC-MS is extensively employed for both the profiling of biological fluids and tissues to characterize lipid dysregulation in disease and toxicological studies. With conventional LC-MS systems the chromatographic performance and throughput are limited due to dispersion from the fluidic connections as well as radial and longitudinal thermal gradients in the LC column. In this study vacuum jacketed columns (VJC), positioned at the source of the mass spectrometer, were applied to the lipidomic analysis of plasma extracts. Compared to conventional UHPLC, the VJC-based methods offered greater resolution, faster analysis, and improved peak intensity. For a 5 min VJC analysis, the peak capacity increased by 66%, peak tailing reduced by up to 34%, and the number of lipids detected increased by 30% compared to conventional UHPLC. The narrower peaks, and thus increased resolution, compared to the conventional system resulted in a 2-fold increase in peak intensity as well a significant improvement in MS and MS/MS spectral quality resulting in a 22% increase in the number of lipids identified. When applied to mouse plasma samples, reproducibility of the lipid intensities in the pooled QC ranged from 1.8-12%, with no related drift in t_R observed.

Fully Automatized Detection of Phosphocholine-Containing Lipids through an Isotopically Labeled Buffer Modification Workflow

High-resolution mass spectrometry is the foremost technique for qualitative and quantitative lipidomics analyses. Glycerophospholipids and sphingolipids, collectively termed polar lipids, are commonly investigated by hyphenated liquid chromatography-mass spectrometry (LC-MS) techniques that reduce aggregation effects and provide a greater dynamic range of detection sensitivity compared to shotgun lipidomics. However, automatic polar lipid identification is hindered by several isobaric and isomer mass overlaps, which cause software programs to often fail to correctly annotate the lipid species. In the present paper, a buffer modification workflow based on the use of labeled and unlabeled acetate ions in the chromatographic buffers was optimized by Box-Behnken design of the experiments and applied to the characterization of phosphocholine-containing lipids in human plasma samples. The contemporary generation of [M + CH₃COO]^-, [M + CD₃COO]^-, and [M - CH₃]^- coupled with a dedicated data processing workflow, which was specifically set up on Compound Discoverer software, allowed us to correctly determine adduct composition, molecular formulas, and grouping, as well as granting a lower false-positive rate and streamlining the manual validation step compared to commonly employed lipidomics platforms. The proposed workflow represents a robust yet easier alternative to the existing approaches for improving lipid annotation, as it does not require extensive sample pretreatment or prior isotopic enrichment or derivatization.

Lipidomic Alterations and PPARα Activation Induced by Resveratrol Lead to Reduction in Lesion Size in Endometriosis Models

Endometriosis is an estrogen-dependent chronic inflammatory disease that affects approximately 10% of women of reproductive age and up to 50% of women with infertility. The heterogeneity of the disease makes accurate diagnosis and treatment a clinical challenge. In this study, we generated two models of endometriosis: the first in rats and the second using human ectopic endometrial stromal cells (HEcESCs) derived from the lesion tissues of endometriosis patients. We then applied resveratrol to assess its therapeutic potential. Resveratrol intervention had significant efficacy to attenuate lesion size and to rectify aberrant lipid profiles of model rats. Lipidomic analysis revealed significant lipidomic alterations, including notable increases of sphingolipids and decreases of both glycerolipids and most phospholipids. Upon resveratrol application, both proliferation capacity and invasiveness parameters decreased, and the early apoptosis proportion increased for HEcESCs. The activation of PPARα was also noted as a factor potentially contributing to recovery from endometriosis in both models. Our study provides valuable insight into the mechanisms of resveratrol in endometriosis and therefore strengthens the potential for optimizing resveratrol treatment for this disease.

Pseudotargeted Lipidomics Strategy Enabling Comprehensive Profiling and Precise Lipid Structural Elucidation of Polyunsaturated Lipid-Rich Echium Oil

Echium oil has great nutritional value as a result of its high content of α-linolenic acid (ALA, 18:3ω-3) and stearidonic acid (SDA, 18:4ω-3). However, the comprehensive lipid profiling and exact structural characterization of bioactive polyunsaturated lipids in echium oil have not yet been obtained. In this study, we developed a novel pseudotargeted lipidomics strategy for comprehensive profiling and lipid structural elucidation of polyunsaturated lipid-rich echium oil. Our approach integrated untargeted lipidomics analysis with a targeted lipidomics strategy based on Paternò-Büchi (PB)-tandem mass spectrometry (MS/MS) using 2-acetylpyridine (2-AP) as the reaction reagent, allowing for high-coverage lipid profiling and simultaneous determination of C═C locations in triacylglycerols (TGs), diacylglycerols (DGs), free fatty acids (FFAs), and sterol esters (SEs) in echium oil. A total of 209 lipid species were profiled, among which 162 unsaturated lipids were identified with C═C location assignment and 42 groups of ω-3 and ω-6 C═C location isomers were discovered. In addition, relative isomer ratios of certain groups of lipid C═C location isomers were revealed. This pseudotargeted lipidomics strategy described in this study is expected to provide new insight into structural characterization of distinctive bioactive lipids in food.

A Workflow to Perform Targeted Metabolomics at the Untargeted Scale on a Triple Quadrupole Mass Spectrometer

The thousands of features commonly observed when performing untargeted metabolomics with quadrupole time-of-flight (QTOF) and Orbitrap mass spectrometers often correspond to only a few hundred unique metabolites of biological origin, which is in the range of what can be assayed in a single targeted metabolomics experiment by using a triple quadrupole (QqQ) mass spectrometer. A major benefit of performing targeted metabolomics with QqQ mass spectrometry is the affordability of the instruments relative to high-resolution QTOF and Orbitrap platforms. Optimizing targeted methods to profile hundreds of metabolites on a QqQ mass spectrometer, however, has historically been limited by the availability of authentic standards, particularly for "unknowns" that have yet to be structurally identified. Here, we report a strategy to develop multiple reaction monitoring (MRM) methods for QqQ instruments on the basis of high-resolution spectra, thereby enabling us to use data from untargeted metabolomics to design targeted experiments without the need for authentic standards. We demonstrate that using high-resolution fragmentation data alone to design MRM methods results in the same quantitative performance as when methods are optimized by measuring authentic standards on QqQ instruments, as is conventionally done. The approach was validated by showing that Orbitrap ID-X data can be used to establish MRM methods on a Thermo TSQ Altis and two Agilent QqQs for hundreds of metabolites, including unknowns, without a dependence on standards. Finally, we highlight an application where metabolite profiling was performed on an ID-X and a QqQ by using the strategy introduced here, with both data sets yielding the same result. The described approach therefore allows us to use QqQ instruments, which are often associated with targeted metabolomics, to profile knowns and unknowns at a comprehensive scale that is typical of untargeted metabolomics.

Untargeted UHPLC-ESI-QTOF-MS/MS analysis with targeted feature extraction at precursor and fragment level for profiling of the platelet lipidome with ex vivo thrombin-activation

Lipids play a major role in platelet signaling and activation. In this study, we analyzed the platelet lipidome in an untargeted manner by reversed-phase UHPLC for lipid species separation coupled to high-resolution QTOF-MS/MS in data-independent acquisition (DIA) mode with sequential window acquisition of all theoretical fragment ion mass spectra (SWATH) for compound detection. Lipid identification and peak picking was supported by the characteristic regular elution pattern of lipids differing in carbon and double bond numbers. It was primarily based on post-acquisition targeted feature extraction from the SWATH data. Multiple extracted ion chromatograms (EICs) from SWATH data of diagnostic ions on MS1 and MS2 level from both positive and negative ion mode allowed to distinguish between poorly resolved isomeric lipids based on their distinct fragment ions, which were used for relative quantification at a molecular lipid species level. It supports assay specificity for relative lipid quantitation via multiple quantifiably ions unlike to data-dependent acquisition methods which rely on precursor ions only. This approach was used to analyze human platelet samples. 457 lipids were annotated. Concentrations of lipids were estimated by stable isotope-labelled lipid class-specific internal standards as surrogate calibrants. Heatmaps of lipid concentrations in dependence on carbon and double bond numbers for the distinct lipid classes revealed a snapshot of the platelet lipidome in the resting state with lipid species distributions within classes supporting some functional interpretations. As expected, activation of the platelets by thrombin has led to significant alterations in the platelet lipidome as proven by univariate (volcano plot) and multivariate (PLS-DA) statistics. Several lipids were significantly up-regulated (lysophosphatidylinositols, oxylipins such as thromboxane B2 (TXB2), hydroxyheptadecatrienoic acid (HHT), hydroxyeicosatetraenoic acid (HETE), hydroxyoctadecadienoic acid (HODE), sphingoid-bases, (very) long chain saturated fatty acids) or down-regulated (lysophosphatidylethanolamines, polyunsaturated fatty acids, phosphatidylinositols). Several of them are well known as biomarkers of platelet activation while others may provide some further insights into pathways of platelet activation and platelet metabolism.

SLIDE-Novel Approach to Apocrine Sweat Sampling for Lipid Profiling in Healthy Individuals

We designed a concept of 3D-printed attachment with porous glass filter disks—SLIDE (Sweat sampLIng DevicE) for easy sampling of apocrine sweat. By applying advanced mass spectrometry coupled with the liquid chromatography technique, the complex lipid profiles were measured to evaluate the reproducibility and robustness of this novel approach. Moreover, our in-depth statistical evaluation of the data provided an insight into the potential use of apocrine sweat as a novel and diagnostically relevant biofluid for clinical analyses. Data transformation using probabilistic quotient normalization (PQN) significantly improved the analytical characteristics and overcame the ‘sample dilution issue’ of the sampling. The lipidomic content of apocrine sweat from healthy subjects was described in terms of identification and quantitation. A total of 240 lipids across 15 classes were identified. The lipid concentrations varied from 10⁻¹⁰ to 10⁻⁴ mol/L. The most numerous class of lipids were ceramides (n = 61), while the free fatty acids were the most abundant ones (average concentrations of 10⁻⁵ mol/L). The main advantages of apocrine sweat microsampling include: (a) the non-invasiveness of the procedure and (b) the unique feature of apocrine sweat, reflecting metabolome and lipidome of the intracellular space and plasmatic membranes. The SLIDE application as a sampling technique of apocrine sweat brings a promising alternative, including various possibilities in modern clinical practice.

Lipid Profiling of 20 Mammalian Cells by Capillary Microsampling Combined with High-Resolution Spectral Stitching Nanoelectrospray Ionization Direct-Infusion Mass Spectrometry

Studies of cellular metabolism can provide profound insights into the underlying molecular mechanisms and metabolic function. To date, the majority of cellular metabolism studies based on chromatography-mass spectrometry (MS) require population cells to obtain informative metabolome. These methods are not only time-consuming but also not suitable for amount-limited cell samples such as circulating tumor cells, stem cells, and neurons. Therefore, it is extremely essential to develop analytical methods enabling to detect metabolome from tens of cells in a high-throughput and high-sensitivity way. In this work, a novel platform for rapid and sensitive detection of lipidome in 20 mammalian cells was proposed using capillary microsampling combined with high-resolution spectral stitching nanoelectrospray ionization direct-infusion MS. It can be used to collect cells rapidly and accurately via the capillary microprobe, extract lipids directly in a 96-well plate using a spray solvent, and detect more than 500 lipids covering 19 lipid subclasses within 3 min. This novel platform was successfully applied to study the lipid features of different cancer cell types and subtypes as well as target cells from tissue samples. This study provides a strategy for determining the lipid species with rich information in tens of cells and demonstrates great potential for clinical applications.

Dynamic recovery after acute single fine particulate matter exposure in male mice: Effect on lipid deregulation and cardiovascular alterations

Many studies have linked airborne fine particulate matter (PM2.5) exposure to cardiovascular diseases. We performed a time-series analysis to investigate whether the disruption of lipid metabolism recovered or lasted after acute PM2.5 exposure in mice. Targeted lipidomic analysis showed that four major plasma membrane phospholipids along with cholesterol esters (CE) were significantly altered on 7th post-exposure day (PED7), and the alteration reached a peak on PED14. On PED21, the phosphatidylcholine (PC) decrease was more marked than on PED14, and its resurgence was indirectly linked to triglyceride (TG) increase. Homocysteine (HCY), lactate dehydrogenase (LDH), and α-hydroxybutyrate dehydrogenase (α-HBDH) levels increased but glucose levels decreased markedly in a dose- and time-dependent manner throughout the experimental period. Network analysis showed that the lasting lipid deregulation on PED21 correlated to myocardial markers and glucose interruption, during which high-density lipoprotein cholesterol (HDL-C) decreased. The present data implied that the constructional membrane lipids were initially interrupted by PM2.5, and the subsequent rehabilitation resulted in the deregulation of storage lipids; the parallel myocardial and glucose effects may be enhanced by the lasting HDL-C lipid deregulation on PED21. These myocardial and lipidomic events were early indicators of cardiovascular risk, resulting from subsequent exposure to and accumulation of PM2.5.

Comprehensive Lipidome and Metabolome Profiling Investigations of Panax quinquefolius and Application in Different Growing Regions Using Liquid Chromatography Coupled with Mass Spectrometry

Panax quinquefolius is one of the most recognized ginseng species. In this study, lipidome and metabolome extraction methods for P. quinquefolius were optimized with methanol/methyl-tert-butyl ether/water (0.3 mg/1 μL/6 μL/8 μL). A total of 497 metabolites were identified, including 365 lipids and 76 ginsenosides. Comprehensive lipidome profiling was first performed for P. quinquefolius, in which 32.6% glycerophospholipids, 39.5% glycerolipids, 9.3% sphingolipids, 3.3% sterol lipids, and 15.3% fatty acyls were identified. Orthogonal partial least squares discrimination analysis (OPLS-DA) showed obvious metabolomic differences in two growing regions of China. In the northern growing region, the ratio of bilayer- to nonbilayer-forming membrane lipids (PCs/PEs, DGDGs/MGDGs), the degree of unsaturation of acyl chains in galactolipids, and the content of membrane glycerophospholipids were increased. In the eastern growing region, the synthesis of storage lipids, ceramides, and fatty acyls was increased, and secondary metabolism was enhanced with 24 differential ginsenosides found. The investigation deepens the understanding of metabolic regulation mechanisms of P. quinquefolius.

Metallothionein Attenuated Arsenic-Induced Cytotoxicity: The Underlying Mechanism Reflected by Metabolomics and Lipidomics

Arsenic ions (As³⁺) have been recognized as a hazard that threatens the health of humans. Metallothionein (MT) rich in cysteine may provide favorable binding sites for chelation of As³⁺. However, the influence of MT on As³⁺-induced toxicity and the underlying mechanism are poorly understood, especially at the metabolic level. Herein, the effects of MT on As³⁺-induced toxicity were evaluated. Cell viability analysis suggested that MT alleviated As³⁺-induced cytotoxicity. The metabolic response of PC12 cells to As³⁺ investigated by lipidomics and metabolomics indicated that the presence of As³⁺ disrupted phospholipids metabolism and induced cell membrane damage. Moreover, energy and amino acid metabolism were perturbed by As³⁺. The perturbation of As³⁺ on metabolism was further illustrated by the decrease of the mitochondrial membrane potential and the rise of cellular reactive oxygen species (ROS). On the contrary, MT rescued As³⁺-induced metabolic disorder and suppressed ROS accumulation. In addition, the binding process between As³⁺ and MT was characterized. The results proved that the As³⁺-MT complex was formed and chelated As³⁺-scavenged ROS, thus alleviating the toxic effects of As³⁺. These results revealed that MT would be a potential agent to reduce As³⁺-induced cytotoxicity.

A Polymer-Based Matrix for Effective SALDI Analysis of Lipids

Surface-assisted laser desorption/ionization (SALDI) has become an attractive branch of matrix-assisted laser desorption/ionization (MALDI) and has been successfully applied for the detection of small molecules due to the lack of the interference of matrix. Herein, the low-cost and highly accessible polyvinylidene fluoride (PVDF) was modified using a facile alkali treatment and investigated as a SALDI matrix. The modified PVDF has a strong optical absorption and can be applied as a dual-mode substrate for both SALDI MS and SALDI imaging analysis. Modified PVDF powder showed superior performance in SALDI MS analysis of lipids, with good reproducibility, high sensitivity, and low background interference, especially for triacylglycerols (TAGs) and fatty acids. Additionally, the lipids in raw and extracted serum were both successfully determined with modified PVDF powder. A modified PVDF membrane (m-PVDF-m) showed excellent ability in lipids imaging in tissues due to its flat surface, mass signal enhancement, and elimination of matrix coating. The distribution of several TAGs and cholesteryl esters on mouse kidney section was presented by SALDI imaging directly on m-PVDF-m. These results demonstrated that modified PVDF materials presented exciting opportunities as matrices for the first time in SALDI MS acquisition and SALDI imaging.

A high coverage pseudotargeted lipidomics method based on three-phase liquid extraction and segment data-dependent acquisition using UHPLC-MS/MS with application to a study of depression rats

Pseudotargeted analysis combines the advantages of untargeted and targeted lipidomics methods based on chromatography-mass spectrometry (MS). This study proposed a comprehensive pseudotargeted lipidomics method based on three-phase liquid extraction (3PLE) and segment data-dependent acquisition (SDDA). We used a 3PLE method to extract the lipids with extensive coverage from biological matrixes. 3PLE was composed of one aqueous and two organic phases. The upper and middle organic phases enriched neutral lipids and glycerophospholipids, respectively, combined and detected together. Besides, the SDDA strategy improved the detection of co-elution ions in the lipidomics analysis. A total of 554 potential lipids were detected by the developed approach in both positive and negative modes using ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS). Compared with the conventional liquid-liquid extraction (LLE) approaches, including methyl tert-butyl ether (MTBE) and Bligh-Dyer (BD) methods, 3PLE combined with SDDA significantly increased the lipid coverage 87.2% and 89.7%, respectively. Also, the proposed pseudotargeted lipidomics approach exhibited higher sensitivity and better repeatability than the untargeted approach. Finally, we applied the established pseudotargeted method to the plasma lipid profiling from the depressed rats and screened 61 differential variables. The results demonstrated that the pseudotargeted method based on 3PLE and SDDA broadened lipid coverage and improved the detection of co-elution ions with excellent sensitivity and precision, indicating significant potential for the lipidomics analysis.

Serum lipid profiling analysis and potential marker discovery for ovarian cancer based on liquid chromatography-Mass spectrometry

Low early diagnosis rate and unclear pathogenesis are the primary reasons for the high mortality of epithelial ovarian cancer (EOC). Lipidomics is a powerful tool for marker discovery and mechanism explanation. Hence, a ultra high-performance liquid chromatography-mass spectrometry based non-targeted lipidomics analysis was performed to acquire lipid profiling of 153 serum samples including healthy control (HC, n = 50), benign ovarian tumor (BOT, n = 41), and EOC (n = 62) to reveal lipid disturbance, then differential lipids were verified in another sample set including 187 sera. Significant lipid disturbance occurred in BOT and EOC, fatty acid, lyso-phosphatidylcholine, and lyso-phosphatidylethanolamine were observed to be increased in BOT and EOC subjects, while phosphatidylcoline, ether phosphatidylcoline (PC-O), ether phosphatidylethanolamine (PE-O), and sphingomyelin significantly decreased. Compared with BOT, PC-Os and PE-Os presented a greater reduction in EOC, and serum ceramide increased only in EOC. Moreover, potential markers consisting of 4 lipids were defined and validated for EOC diagnosis. High areas under the curve (0.854∼0.865 and 0.903∼0.923 for distinguishing EOC and early EOC from non-cancer, respectively) as well as good specificity and sensitivity were obtained. This study not only revealed the characteristics of lipid metabolism in EOC, but also provided a potential marker pattern for aiding EOC diagnosis.

Tracing nitrogenous byproducts during ozonation in the presence of bromide and ammonia using stable isotope labeling and high resolution mass spectrometry

Ammonia has been widely used to inhibit bromate formation during ozonation. However, our recent study found that during ozonation in the presence of bromide and ammonia, toxicity increased under certain conditions that might be attributed to the formation of nitrogenous byproducts. Herein, a typical structural moiety of natural organic matter (NOM), hydroquinone, was evaluated for its potential to form nitrogenous byproducts. During ozonation of the hydroquinone solution containing bromide and ammonia, toxicity of organic byproducts increased significantly. As organic bromine was hardly detected, organic nitrogen was responsible for the increased toxicity. An effective method combining ultra-performance liquid chromatography in tandem with high resolution mass spectrometry (UPLC-HRMS) with an isotope labeling strategy was used to trace nitrogenous byproducts. Four newly formed nitrogenous byproducts were detected, two of which were also detected in Suwannee River natural organic matter (SRNOM) solution treated under the same ozonation condition. Furthermore, the molecular structures and formation pathways of these nitrogenous byproducts were proposed. This study highlights that, despite the widespread use, adding ammonia to inhibit bromate formation during ozonation might increase the toxicity posed by nitrogenous byproducts. During ozonation in the presence of bromide and ammonia, particular attention should be paid to nitrogenous byproducts.

Protein corona formation of human serum albumin with carbon quantum dots from roast salmon

When food-borne nanoparticles enter biological systems, they can interact with various proteins to form protein coronas, which can affect their physicochemical properties and biological identity. In this study, the protein corona formation of carbon quantum dots (CQDs) from roast salmon with human serum albumin (HSA) was explored. Furthermore, the biological identity of the HSA-CQD coronas, in relation to cell apoptosis, energy, glucose and lipid metabolism and acute toxicity in mice, was also investigated. The HSA-CQD coronas were formed between HSA and CQDs via a static binding mechanism, and the binding site of CQDs on HSA was located at both Sudlow's site I and site II. After entering the cytoplasm, the HSA-CQD coronas became localized in the lysosomes and autolysosomes. Importantly, the HSA coronas reduced the cytotoxicity of the CQDs from 18.65% to 9.26%, and the energy metabolism was rectified by changing from glycolytic to aerobic metabolism. The glucose and lipid metabolite profile of cells exposed to the HSA-CQD coronas differed from that of those treated with CQDs, indicating that the HSA-CQD coronas rectified metabolic disturbances caused by CQDs. Histopathological and blood biochemical analysis revealed no statistically significant differences between the treated and control mice after a single CQDs dose of 2000 mg per kg body weight. Overall, the results confirmed the formation of protein coronas between HSA and food-borne fluorescent CQDs, and could be helpful for evaluating the safety of fluorescent CQDs in cooked food items.