Caenorhabditis elegans deep lipidome profiling by using integrative mass spectrometry acquisitions reveals significantly altered lipid networks

Myocardial Lipidomics Revealed Glycerophospholipid and Sphingolipid Metabolism as Therapeutic Targets of Qifu Decoction Against Heart Failure

Qifu decoction (QFD) has shown potential benefits in treating heart failure. However, the potential mechanism of QFD remains unclear. In this study, myocardial lipidomics, based on ultra-high-performance liquid chromatography coupled with an electrospray ionization hybrid quadrupole Orbitrap mass spectrometry (UPLC-ESI-Q-Exactive/MS), was employed to identify potential therapeutic targets of QFD for treating heart failure in a mice model induced by ligating the left anterior descending coronary artery. It was found that 47 lipid metabolites were associated with heart failure, of which 35 showed a significant reversal during QFD treatment. The QFD-reversed lipid metabolites were mainly located on phosphatidylcholine, lysophosphatidylcholine, sphingomyelin, and ceramide, which were involved in glycerophospholipid and sphingolipid metabolism. The results of Western blotting analysis revealed that QFD could effectively alleviate heart failure through increasing the levels of lysophosphatidylcholine acyltransferase 1 (LPCAT1) and sphingomyelin synthase 1 (SMS1) and reducing the levels of acid sphingomyelinase (aSMase) and phospholipase A2 (PLA2) to regulate the metabolic disorders of glycerophospholipid and sphingolipid metabolism. All these results could be concluded that glycerophospholipid and sphingolipid metabolism were the two crucial target pathways for QFD against heart failure, which laid the theoretical groundwork for its clinical application.

Phosphorylated glycosphingolipids are commonly detected in Caenorhabditis elegans lipidomes

INTRODUCTION

The identification of lipids is a cornerstone of lipidomics, and due to the specific characteristics of lipids, it requires dedicated analysis workflows. Identifying novel lipids and lipid species for which no reference spectra are available is tedious and often involves a lot of manual work. Integrating high-resolution mass spectrometry with enhancements from chromatographic and ion mobility separation enables the in-depth investigation of intact lipids.

OBJECTIVES

We investigated phosphorylated glycosphingolipids from the nematode Caenorhabditis elegans, a biomedical model organism, and aimed to identify different species from this class of lipids, which have been described in one particular publication only. We checked if these lipids can be detected in lipid extracts of C. elegans.

METHODS

We used UHPLC-UHR-TOF-MS and UHPLC-TIMS-TOF-MS in combination with dedicated data analysis to check for the presence of phosphorylated glycosphingolipids. Specifically, candidate features were identified in two datasets using Mass Spec Query Language (MassQL) to search fragmentation data. The additional use of retention time (RT) and collisional cross section (CCS) information allowed to filter false positive annotations.

RESULTS

As a result, we detected all previously described phosphorylated glycosphingolipids and novel species as well as their biosynthetic precursors in two different lipidomics datasets. MassQL significantly speeds up the process by saving time that would otherwise be spent on manual data investigations. In total over 20 sphingolipids could be described.

CONCLUSION

MassQL allowed us to search for phosphorylated glycosphingolipids and their potential biosynthetic precursors systematically. Using orthogonal information such as RT and CCS helped filter false positive results. With the detection in two different datasets, we demonstrate that these sphingolipids are a general part of the C. elegans lipidome.

Holistic Comparison of the Lipidomes Simultaneously From 12 Panax Herbal Medicines By Ultra-High-Performance Supercritical Fluid Chromatography Coupled With Ion Mobility-Quadrupole Time-of-Flight Mass Spectrometry

Researches regarding quality control of ginseng focusing on the lipids are rare. Herein, ultra-high-performance supercritical fluid chromatography/ion mobility-quadrupole time-of-flight mass spectrometry (UHPSFC/IM-QTOF-MS) combined with untargeted metabolomic analysis was utilized to holistically characterize and compare the lipidomic difference among 12 Panax-derived herbal medicines. The established UHPSFC/IM-QTOF-MS method, using a Torus 1-AA column with CO2/CH3OH (modifier) as the mobile phase, well resolved the ginseng lipidome within 30 min. The lipid isomers and those easily co-eluted by conventional reversed-phase chromatography got separated, and integrated analyses of the positive-/negative-mode MS data and IM-derived collision cross section (CCS) greatly enhanced lipids identification. By the pattern recognition chemometric analysis of 90 batches of ginseng samples, the root ginseng samples showed significant differences in lipidome composition from those stem/leaf and flower samples. In contrast, red ginseng also contained lipids significantly different from the other root ginseng. Totally 82 potential differential lipids were discovered and identified based on the positive-mode data and 90 ones in the negative mode. Some of these lipid markers might be diagnostic for their authentication. Conclusively, we first report the lipidomic difference among 12 ginseng varieties, and the information obtained can lay foundation for the accurate identification of ginseng from the lipidome level.

Software-aided efficient identification of the components of compound formulae and their metabolites in rats by UHPLC/IM-QTOF-MS and an in-house high-definition MS2 library: Sishen formula as a case

Identifying the compound formulae-related xenobiotics in bio-samples is full of challenges. Conventional strategies always exhibit the insufficiencies in overall coverage, analytical efficiency, and degree of automation, and the results highly rely on the personal knowledge and experience. The goal of this work was to establish a software-aided approach, by integrating ultra-high performance liquid chromatography/ion-mobility quadrupole time-of-flight mass spectrometry (UHPLC/IM-QTOF-MS) and in-house high-definition MS2 library, to enhance the identification of prototypes and metabolites of the compound formulae in vivo, taking Sishen formula (SSF) as a template. Seven different MS2 acquisition methods were compared, which demonstrated the potency of a hybrid scan approach (namely high-definition data-independent/data-dependent acquisition (HDDIDDA)) in the identification precision, MS1 coverage, and MS2 spectra quality. The HDDIDDA data for 55 reference compounds, four component drugs, and SSF, together with the rat bio-samples (e.g., plasma, urine, feces, liver, and kidney), were acquired. Based on the UNIFI™ platform (Waters), the efficient data processing workflows were established by combining mass defect filtering (MDF)-induced classification, diagnostic product ions (DPIs), and neutral loss filtering (NLF)-dominated structural confirmation. The high-definition MS2 spectral libraries, dubbed in vitro-SSF and in vivo-SSF, were elaborated, enabling the efficient and automatic identification of SSF-associated xenobiotics in diverse rat bio-samples. Consequently, 118 prototypes and 206 metabolites of SSF were identified, with the identification rate reaching 80.51% and 79.61%, respectively. The metabolic pathways mainly involved the oxidation, reduction, hydrolysis, sulfation, methylation, demethylation, acetylation, glucuronidation, and the combined reactions. Conclusively, the proposed strategy can drive the identification of compound formulae-related xenobiotics in vivo in an intelligent manner.

Combined matrix-assisted laser desorption/ionisation-mass spectrometry imaging with liquid chromatography-tandem mass spectrometry for observing spatial distribution of lipids in whole Caenorhabditis elegans

RATIONALE

Matrix-assisted laser desorption/ionisation-mass spectrometry imaging (MALDI-MSI) is a powerful label-free technique for biomolecule detection (e.g., lipids), within tissue sections across various biological species. However, despite its utility in many applications, the nematode Caenorhabditis elegans is not routinely used in combination with MALDI-MSI. The lack of studies exploring spatial distribution of biomolecules in nematodes is likely due to challenges with sample preparation.

METHODS

This study developed a sample preparation method for whole intact nematodes, evaluated using cryosectioning of nematodes embedded in a 10% gelatine solution to obtain longitudinal cross sections. The slices were then subjected to MALDI-MSI, using a RapifleX Tissuetyper in positive and negative polarities. Samples were also prepared for liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis using an Exploris 480 coupled to a HPLC Vanquish system to confirm the MALDI-MSI results.

RESULTS

An optimised embedding method was developed for longitudinal cross-sectioning of individual worms. To obtain longitudinal cross sections, nematodes were frozen at -80°C so that all worms were rod shaped. Then, the samples were defrosted and transferred to a 10% gelatine matrix in a cryomold; the worms aligned, and the whole cryomold submerged in liquid nitrogen. Using MALDI-MSI, we were able to observe the distribution of lipids within C. elegans, with clear differences in their spatial distribution at a resolution of 5 μm. To confirm the lipids from MALDI-MSI, age-matched nematodes were subjected to LC-MS/MS. Here, 520 lipids were identified using LC-MS/MS, indicating overlap with MALDI-MSI data.

CONCLUSIONS

This optimised sample preparation technique enabled (un)targeted analysis of spatially distributed lipids within individual nematodes. The possibility to detect other biomolecules using this method thus laid the basis for prospective preclinical and toxicological studies on C. elegans.

Anti-aging activities of neutral and acidic polysaccharides from Polygonum multiflorum Thunb in Caenorhabditis elegans

Polygonum multiflorum Thunb (PM) is used to slow the aging process. Although polysaccharides are a major constituent of PM, their anti-aging properties have not been thoroughly investigated. Therefore, this study aimed to examine the anti-aging effects of polysaccharides extracted from PM using the Caenorhabditis elegans (C. elegans) model. Two types of water-soluble heteropolysaccharides, namely a neutral polysaccharide (RPMP-N) and an acidic polysaccharide (RPMP-A), were obtained from PM. Their structures were elucidated by various methods. The effects of these polysaccharides on the lifespan, levels of antioxidants, and activities of antioxidant-related enzymes in C. elegans were also evaluated. The results showed that RPMP-A had higher GalA content compared with RPMP-N. The average molecular weights of RPMP-N and RPMP-A were 245.30 and 28.45 kDa, respectively. RPMP-N is a α-1,4-linked dextran as the main chain, and contains a small amount of branched dextran with O-6 as the branched linkage site；RPMP-A may be a complex of α-1,4-linked dextran, HG and RG-I. Treatment with RPMP-N and RPMP-A increased the mean lifespan of C. elegans, and significantly regulated oxidative stress. RPMP-A exhibited stronger anti-aging effects compared with RPMP-N. These findings suggest that RPMP-A may be a potent antioxidant and anti-aging component that can be used for developing functional food products and effective dietary supplements.

Development of an Efficient On-Tissue Epoxidation Reaction Mediated by Urea Hydrogen Peroxide for MALDI MS/MS Imaging of Lipid C═C Location Isomers

Unsaturated lipids containing different numbers and locations of C═C bonds are significantly associated with a variety of cellular and metabolic functions. Although matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) has been used to visualize the spatial distribution patterns of various lipids in biological tissues, in situ identification, discrimination, and visualization of lipid C═C location isomers remain challenging. Herein, an efficient and fast on-tissue chemical derivatization (OTCD) approach was developed to pinpoint the locations of C═C bonds in complex lipids in situ via methyltrioxorhenium (MTO)-catalyzed epoxidation of C═C with a urea hydrogen peroxide (UHP)/hexafluoroisopropanol (HFIP) system. The efficiency of OTCD could reach 100% via one-step spray deposition of the solution mixture of MTO/UHP/HFIP at room temperature. The developed OTCD method provided rich structural information on lipid C═C location isomers, and their accurate spatial distribution patterns were resolved in mouse brain tissues. Tissue-specific distributions and changes of lipid C═C location isomers in the liver sections of obese ob/ob and diabetic db/db mice were further investigated, and their correlation in two animal models was revealed. The simplicity and high efficiency of the OTCD method developed for MALDI tandem MSI of lipid C═C location isomers possess great potential for functional spatial lipidomics.

Unveiling potentially convergent key events related to adverse outcome pathways induced by silver nanoparticles via cross-species omics-scale analysis

The adverse effects of silver nanoparticles (AgNPs) have been studied in various models. However, there has been discordance between molecular responses across the literature, attributed to methodological biases and the physicochemical variability of AgNPs. In this study, a gene pathway meta-analysis was conducted to identify convergent and divergent key events (KEs) associated with AgNPs and explore common patterns of these KEs across species. We performed a cross-species analysis of transcriptomic data from multiple studies involving various AgNPs exposure. Pathway enrichment analysis revealed a set of pathways linked to oxidative stress, apoptosis, and metabolite and lipid metabolism, which are considered potentially conserved KEs across species. Subsequently, experiments confirmed that oxidative stress responses could be early KEs in both Caenorhabditis elegans and HepG2 cells. Moreover, AgNPs preferentially impaired the mitochondria, as evidenced by mitochondrial fragmentation and dysfunction. Furthermore, disruption of amino acids, nucleotides, sulfur compounds, glycerolipids, and glycerophospholipids metabolism were in good agreement with gene pathway shreds of evidence. Our findings imply that, although there may be organism-specific responses, potentially conserved events could exist regardless of species and physicochemical factors. These results provide valuable insights into the development of adverse outcome pathways of AgNPs across species and the regulatory toxicity of AgNPs.

Lipid class-dependent alterations of Caenorhabditis elegans under harmane exposure

Altered lipid patterns in Caenorhabditis elegans (C. elegans) resulting from exposure to harmane remain to be explored. In this study, untargeted lipidomics was carried out to elucidate the effects of acute exposure to harmane on the lipidome of C. elegans. Exposure to the compound was evaluated based on the reproduction ability of the worms at 0.1 and 1 μg/mL. No significant effects of harmane were observed at these concentrations. Furthermore, we found that the modulatory effects of harmane on the lipidome of C. elegans at 1 μg/mL were lipid class dependent. In particular, harmane-treated worms were enriched in triglycerides and fatty acids, regardless of the degree of saturation. Glycerophospholipids were generally down-regulated. Furthermore, functional analyses suggested that there was a reduction in lipid membrane bilayer-related terms, and in some related to the mitochondria, and endoplasmic reticulum of C. elegans when treated with harmane. Lipid droplets and storage appeared to be up-regulated. In conclusion, our findings suggest that harmane exposure affects the lipidome of C. elegans in a sophisticated manner. Further investigations are required to elucidate the molecular mechanisms underlying these lipid pattern changes.