Plasma metabolomics in a deep vein thrombosis rat model based on ultra-high performance liquid chromatography-electrostatic field orbitrap high resolution mass spectrometry

Exploring metabolite-mediated links between lipidome and deep vein thrombosis: Insights from Mendelian randomization analysis

The aim was to investigate the causal relationship between the lipidome and deep vein thrombosis (DVT) while identifying and quantifying the role of metabolites as potential mediators. Two-sample Mendelian randomization (MR) analysis of lipid species (n = 7174) and DVT (6767 cases and 330,392 controls) was performed using pooled data from genome-wide association studies. In addition, we quantified the proportion of metabolite-mediated lipidomic effects on DVT using 2-step MR. Phosphatidylcholine (18:0_18:2) levels mined from 179 lipids using MR analysis reduced the risk of DVT (odds ratio [OR]: 0.997; 95% CI: 0.996-0.999; P = 4.25 × 10-4; false discovery rate [FDR] = 0.013). Octadecadienedioate (C18:2-DC) levels increased with the increasing phosphatidylcholine (18:0_18:2) levels (OR: 1.087, 95% confidence interval [CI]: [1.024, 1.154], P = .006). Octadecadienedioate (C18:2-DC) levels mined from 1400 metabolites using MR analysis reduced the DVT risk (OR: 0.997; 95% CI: [0.996, 0.999], P = 6.11 × 10-6; FDR = 8.55 × 10-3). The proportion of the predicted genes for phosphatidylcholine (18:0_18:2) levels mediated by octadecadienedioate (C18:2-DC) levels was 7.8%. This study identified octadecadienedioate (C18:2-DC) levels as a potential mediator of the causal relationship between phosphatidylcholine (18:0_18:2) levels and DVT, which provides direction for the future investigation of DVT; however, further research on other potential mediators is still needed.

[Using metabolomics to explore the effects of epigenetic-modification strategies on the metabolites of Acanthus ilicifolius L. endophytic fungi against ovarian cancer]

Ovarian cancer is a serious threat to women's health and safety. So far, people have discovered more than 130 small molecule compounds of natural origin for anti-tumor, of which approximately 50% are of microbial origin. The Acanthus ilicifolius L. species is primarily distributed in the Guangdong, Hainan, and Guangxi regions of China and grows in tidally accessible coastal areas. Recent studies have revealed that Acanthus ilicifolius L. extracts are endowed with a range of pharmacological properties, including anti-inflammatory, hepatoprotective, antioxidant, and antitumor activities. Endophytic fungi are commonly found in the healthy tissue and organs of medicinal plants. These fungi and the plants they inhabit form mutually beneficial symbiotic relationships. Endophytic fungi produce a series of secondary metabolites, with active substances having shown great economic value and applications prospects in drug research and development as well as for the biological control of plant diseases. Secondary metabolites production by endophytic fungi is regulated by specific gene clusters, and several techniques have been used to stimulate the secondary metabolic processes of fungi, including epigenetic-modification and OSMAC (one strain many compounds) strategies, co-culturing, and gene modification. Among these, epigenetic modification has been shown to be effective; this strategy involves the addition of small-molecule epigenetic modifiers to the culture medium, thereby activating silenced biosynthetic gene clusters without altering the DNA sequences of the fungi. This approach facilitates the expression of silenced genes in endophytic fungi, thereby increasing the number and diversity of secondary metabolites. Furthermore, it assists in overcoming the inhibition of microbial secondary-metabolite synthesis under laboratory conditions, and enhances silenced-gene expressions. The advent of novel analytical techniques and bioinformatics has provided a comprehensive, multifaceted, and holistic understanding of fungal metabolism through the development of metabolomics as a research platform. However, few studies have combined anti-ovarian cancer-activity screening with metabolomic approaches in the search for activity-differentiating metabolites from endophytic fungi under the intervention of epigenetic modifiers. Herein, we investigated the impact of epigenetic modifiers on the secondary metabolites of the endophytic Diaporthe goulteri fungus from Acanthus ilicifolius L. to determine their potential anti-ovarian cancer activities. Crude extracts were obtained by controlling three variables: the number of fermentation days, the type of epigenetic modifier, and its concentration, with activities screened using the CCK-8 (cell counting kit-8) method. Ultra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) was subsequently employed for non-targeted metabolomic analysis. A multivariate statistical analysis model was constructed using principal component analysis and orthogonal partial least squares-discriminant analysis, which combines model and variable importance projection, with qualitative screening performed and significant changes (variable importance in the projection (VIP)≥1; P<0. 05) determined. Fifteen differential metabolites were identified in the fungal and epigenetic modification group, primarily comprising polyketides, amino acids, derivatives, alkaloids, and organic acids, including prenderol, glycine, valine, 2-ethylcaproic acid, rubratoxin B, finasteride, 6-silaspiro[5.5]undecane, 1-(2-nitrophenoxy)octane, heptadecene, 1-pentadecene, 11-ketoetiocholanolone, 3-(1-ethyl-1,3,3-trimethyl-2,3-dihydro-1H-inden-5-yl)butanal, N2-benzoylarginine, tabutrex, (3aR,6S,6aS)-6-(4-hydroxy-2-methoxy-2-butanyl)-4,4-dimethylhexahydro-1(2H)-pentalenone, and 8-aminoquinoline. The expressions of prenderol, 1-(2-nitrophenoxy)octane, 3-(1-ethyl-1,3,3-trimethyl-2,3-dihydro-1H-inden-5-yl)butanal, N2-benzoylarginine, and 8-aminoquinoline were downregulated, whereas the expressions of the remaining 10 substances were upregulated. Polyketides were the main components that exhibited higher expressions. This study showed that latent active differential metabolites can be searched by combining anti-ovarian cancer-activity screening with metabolomics analysis, thereby providing a reference for the further development of Acanthus ilicifolius L. resources and the subsequent targeted isolation of active compounds.

Novel Strategy for Human Deep Vein Thrombosis Diagnosis Based on Metabolomics and Stacking Machine Learning

Deep vein thrombosis (DVT) is a serious health issue that often leads to considerable morbidity and mortality. Diagnosis of DVT in a clinical setting, however, presents considerable challenges. The fusion of metabolomics techniques and machine learning methods has led to high diagnostic and prognostic accuracy for various pathological conditions. This study explored the synergistic potential of dual-platform metabolomics (specifically, gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS)) to expand the detection of metabolites and improve the precision of DVT diagnosis. Sixty-one differential metabolites were identified in serum from DVT patients: 22 from GC-MS and 39 from LC-MS. Among these, five key metabolites were highlighted by SHapley Additive exPlanations (SHAP)-guided feature engineering and then used to develop a stacking diagnostic model. Additionally, a user-friendly interface application system was developed to streamline and automate the application of the diagnostic model, enhancing its practicality and accessibility for clinical use. This work showed that the integration of dual-platform metabolomics with a stacking machine learning model enables faster and more accurate diagnosis of DVT in clinical environments.

Two-sample Mendelian randomization analysis reveals causal relationships between blood lipids and venous thromboembolism

Venous thromboembolism (VTE) is a complex disease that can be classified into two subtypes: deep vein thrombosis (DVT) and pulmonary embolism (PE). Previous observational studies have shown associations between lipids and VTE, but causality remains unclear. Hence, by utilizing 241 lipid-related traits as exposures and data from the FinnGen consortium on VTE, DVT, and PE as outcomes, we conducted two-sample Mendelian randomization (MR) analysis to investigate causal relationships between lipids and VTE, DVT and PE. The MR results identified that fatty acid (FA) unsaturation traits (ratio of bis-allylic bonds to double bonds in lipids, and ratio of bis-allylic bonds to total fatty acids in lipids) were associated with VTE (odds ratio [OR]=1.21, 95% confidence interval [CI]: 1.15-1.27; OR=1.21, 95% CI: 1.13-1.30), DVT (OR=1.24, 95% CI: 1.16-1.33; OR= 1.26, 95% CI: 1.16-1.36) and PE (OR=1.18, 95% CI: 1.08-1.29; OR=1.18, 95% CI: 1.09-1.27). Phosphatidylcholines (PC) exhibit potential causal effects on VTE and PE. PC acyl-alkyl C40:4 (PC ae C40:4) was negatively associated with VTE (OR=0.79, 95% CI: 0.73-0.86), while PC diacyl C42:6 (PC aa C42:6) and PC acyl-alkyl C36:4 (PC ae C36:4) were positively associated with PE (OR=1.44, 95% CI: 1.20-1.72; OR=1.22, 95% CI: 1.10-1.35). Additionally, we found that medium LDL had a protective effect on VTE. Our study indicates that higher FA unsaturation may increase the risk of VTE, DVT, and PE. Different types of PC have either promotive or inhibitory effects on VTE and PE, contributing to a better understanding of the risk factors for VTE.

Exploration on the effect of anserine on the alleviation of DVT and its molecular mechanism

Background

This study aimed to explore the regulatory effect of anserine on HUVEC cell injury and thrombosis in deep venous thrombosis (DVT) rats, and to elucidate the underlying molecular mechanisms.

Methods

Non-targeted metabolomics data analyses were conducted using an ultra-performance liquid chromatography system Vanquish UHPLC and mass spectrometer to detect plasma metabolism profiles. The transcriptome sequencing and gene intervention experiments were performed to verify the regulatory effect. Further in vivo and in vitro experiments were performed. Enzyme-linked immunosorbent assay was used to detect the levels of P-selectin, E-selectin, and vWF, hematoxylin-eosin (HE) staining was performed to observe thrombotic and inflammatory cell infiltration, flow cytometry and TUNEL assays were performed to detect apoptosis, and qPCR and WB assays were conducted to determine the gene and protein expression.

Results

Anserine alleviated HUVECs injury, reduced adhesion molecule expression, and inflammation. It decreased P-selectin, E-selectin, vWF, THBD, TFPI levels, and apoptosis while promoting NOS3, ET-1, and NO release in HUVECs. In DVT rats, anserine reduced P-selectin, E-selectin, vWF, thrombosis, cell infiltration, apoptosis, and promoted NO release. Transcriptome sequencing and gene intervention confirmed anserine's regulation of the PI3K-Akt pathway and coagulation via MYB. CARNMT1, a regulatory enzyme for anserine metabolism, increased anserine content, inhibiting coagulation, thrombosis, cell infiltration, and promoting NO release in rats.

Conclusion

This study confirmed anserine could alleviate DVT by improving the inflammatory response, inhibiting blood agglutination, and promoting vasodilation, providing new potential therapeutic targets, important scientific evidence for the development of DVT management, and new clues for an in-depth understanding of its molecular mechanisms.

Metabolomic profiling of deep vein thrombosis

Deep vein thrombosis (DVT) of the lower extremities is one of the most common peripheral vascular diseases, with significant complications and sequelae. Metabolomics aims to identify small molecules in biological samples. It can serve as a promising method for screening compounds that can be used for early disease detection, diagnosis, treatment response prediction, and prognosis. In addition, high-throughput metabolomics screening can yield significant insights into the pathophysiological pathways of DVT. Currently, the metabolomic profiles of DVT have yielded inconsistent expression patterns. This article examines the recent advancements in metabolomic studies of DVT and analyzes the factors that may influence the results.

ADAMTS13 inhibits H2O2-induced human venous endothelial cell injury to attenuate deep-vein thrombosis by blocking the p38/ERK signaling pathway

Deep vein thrombosis (DVT) is a common complication in hematologic malignancies and immunologic disorders. Endothelial cell injury and dysfunction comprise the critical contributor for the development of DVT. A disintegrin and metalloproteinase with thrombospondin motifs 13 (ADAMTS13), a plasma metalloprotease that cleaves von Willebrand factor, acts as a critical regulator in normal hemostasis. This study was aimed to explore the role of ADAMTS13 in endothelial cell injury during DVT and the possible mechanism. First, human umbilical vein endothelial cells (HUVECs) were exposed to hydrogen peroxide (H2O2). Then, the mRNA and protein expressions of ADAMTS13 were evaluated with the reverse transcription-quantitative polymerase chain reaction and western blot. After treatment with recombinant ADAMTS13 (rADAMTS13; rA13), the viability and apoptosis of H2O2-induced HUVECs were assessed by cell counting kit-8 assay and terminal-deoxynucleoitidyl transferase-mediated nick end labeling staining. In addition, the levels of prostaglandin F1-alpha, endothelin-1, and reactive oxygen species were detected using the enzyme-linked immunosorbent assay and dichloro-dihydro-fluorescein diacetate assay. The expressions of proteins related to p38/extracellular signal-regulated kinase (ERK) signaling pathway were estimated with the western blot. Then, p79350 (p38 agonist) was used to pretreat cells to analyze the regulatory effects of rA13 on p38/ERK signaling in H2O2-induced HUVEC injury. The results revealed that ADAMTS13 expression was significantly downregulated in H2O2-induced HUVECs. The reduced viability and increased apoptosis of HUVECs induced by H2O2 were revived by ADAMTS13. ADAMTS13 also suppressed the oxidative stress in HUVECs after H2O2 treatment. Besides, ADAMTS13 was found to block p38/ERK signaling pathway, and p79350 reversed the impacts of ADAMTS13 on the damage of HUVECs induced by H2O2. To sum up, ADAMTS13 could alleviate H2O2-induced HUVEC injury through the inhibition of p38/ERK signaling pathway.

[Determination of nine organic amine compounds in CO2 absorption liquid by hydrophilic interaction liquid chromatography-electrostatic field orbitrap high resolution mass spectrometry]

Carbon dioxide (CO2) absorption and capture is an effective measure to achieve the "dual carbon" goal of carbon peak and carbon neutrality in China. Organic amine compounds are widely used in the industrial separation and recovery of CO2. Thus, the establishment of analytical methods for organic amine compounds is of great significance for the research and development of carbon capture and storage (CCS) technology and carbon capture, utilization and storage (CCUS) technology. In this study, a method was developed for the determination of nine organic amine compounds in CO2 absorption liquid by hydrophilic interaction liquid chromatography (HILIC)-electrostatic field orbitrap high resolution mass spectrometry. The sample was diluted with water and filtered through a 0.22 μm nylon membrane before sampling and analysis. An Accucore HILIC column (100 mm×2.1 mm, 2.6 μm) was used for separation at 30 ℃. Gradient elution was conducted using 90% acetonitrile aqueous solution containing 5 mmol/L ammonium formate and 0.1% formic acid as mobile phase A and 10% acetonitrile aqueous solution containing 5 mmol/L ammonium formate and 0.1% formic acid as mobile phase B. Determination was performed using an electrospray ion source (ESI) in the positive ion mode. The quantitative analysis was carried out by standard addition method. The chromatographic retention performance of different chromatographic columns and the influence of different mobile phases on the separation of the organic amine compounds were compared, and the method was validated. The results showed that the linear ranges of the nine organic amine compounds were 0.04-25000 ng/mL with the linear correlation coefficients (R2) greater than 0.9910. The limits of detection (LODs) of the method were in the range of 0.0004-0.0080 ng/mL, and the limits of quantification (LOQs) of the method were in the range of 0.0035-0.0400 ng/mL. The average recoveries of the method ranged from 85.30% to 104.26% with relative standard deviations (RSDs) of 0.04%-7.95% at the spiked levels of 1, 1.5 and 3 times sample concentration. The established method was applied to detect the absorption waste liquid of a cement plant, and nine organic amine compounds could be effectively detected. The stability of the actual sample was tested, and the RSDs were 0.10%-6.35% in 48 h at 4 ℃. The method is sensitive, rapid and accurate for the determination of the nine organic amine compounds in industrial waste water. It can provide reference for the detection of organic amine compounds, and provide strong technical support for the research and industrial application of CO2 capture technology.

Study of the Metabolite Changes in Ganoderma lucidum under Pineapple Leaf Residue Stress via LC-MS/MS Coupled with a Non-Targeted Metabolomics Approach

The effects of fermentation metabolites of G. lucidum under different pineapple leaf residue additions were separated and identified using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). The mass spectra showed that the metabolites had good response values only in the positive ion mode, and 3019 metabolites with significant differences, mainly distributed in 95 metabolic pathways, were identified. The multivariate analyses, including the principal component analysis (PCA), orthogonal least squares discriminant analysis (OPLS-DA), and volcano plots (VP), revealed that the G. lucidum metabolites exhibited significant differences (p < 0.05) and were well clustered under various pineapple leaf residue additions, featuring 494–545 upregulated and 998–1043 downregulated metabolites. The differential metabolic pathway analysis proved that two metabolic pathways related to the biosynthesis of amino acids and ABC transporters were particularly significant under the addition of pineapple leaf residue, where amino acids such as histidine and lysine were upregulated in contrast to downregulated tyrosine, valine, L-alanine, and L-asparagine. These study results are considered instrumental in substantiating the application of pineapple leaf residue in the cultivation of G. lucidum and improving its utilization rate and added value.