Update on LIPID MAPS classification, nomenclature, and shorthand notation for MS-derived lipid structures

Determining β-Monosaccharide Head Group Composition with High-Resolution Cyclic Ion Mobility Separations Coupled to Tandem Mass Spectrometry as a First Step for Unknown Cerebroside Analysis

Cerebrosides, a class of biologically important lipids, are comprised of a monosaccharide head group along with their ceramide tail. However, their accurate characterization is challenging because of the isomerism in both the tail, from potential double bond positioning, or in the head from monosaccharide composition and αβ anomericity. In this work, we focused on tackling the identification of the β-monosaccharide head group, as either glucose or galactose, in various cerebroside isomers as well as demonstrating how our methodology could be applied to unknowns found in a porcine extract. To achieve this, we performed collision-induced dissociation prior to cyclic ion mobility separations to generate monosaccharide fragment ions from the starting cerebroside precursor ions. With this pre-cIMS CID approach, we observed that the cIMS separations of the fragment ions were diagnostic of the β-monosaccharide head group composition (i.e., glucose versus galactose), regardless of the ceramide tail length. From there, we demonstrated an example of how this methodology could also be applied to cerebrosides found in a porcine extract and a framework for how this approach could be added to existing workflows in developing collision cross section databases. Overall, we envision that our developed pre-cIMS CID-based approach will be a complementary and orthogonal tool to existing ones in glycolipidomics workflows.

Comprehensive analysis of oxidized arachidonoyl-containing glycerophosphocholines using ion mobility spectrometry-mass spectrometry

The biological significance of oxidized arachidonoyl-containing glycerophosphocholines, exemplified by the oxidation products of 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (oxPAPC), in pathological processes is well-established. However, despite their widespread use in redox lipidomics research, the precise chemical composition of the heterogeneous mixtures of oxPAPC generated in vitro -including the high prevalence of isomers and the oxidation mechanisms involved- remain inadequately understood. To address these knowledge gaps, we developed a multidimensional in-house database from a commercial oxPAPC preparation -employing Liquid Chromatography coupled to Quadrupole Time-of-Flight Mass Spectrometry (LC-QTOF-MS) and Ion Mobility Spectrometry-Mass Spectrometry (IMS-MS). This database includes lipid names, retention times, accurate mass values (m/z), adduct profiles, MS/MS information, as well as collision cross-section (CCS) values. Our investigation elucidated 34 compounds belonging to distinct subsets of oxPAPC products, encompassing truncated, full-length, and cyclized variants. The integration of IMS-MS crucially facilitated: (i) structural insights among regioisomers, exemplified by the 5,6-PEIPC and 11,12-PEIPC epoxy-isoprostane derivatives, (ii) novel Collision Cross Section (CCS) values, and (iii) cleaner MS/MS spectra for elucidating the fragmentation mechanisms involved to yield specific fragment ions. These diagnostic ions were employed to successfully characterize full-length isomers present in human plasma samples from patients with mucormycosis. This comprehensive oxPAPC characterization not only advances the understanding of lipid peroxidation products but also enhances analytical capabilities for in vitro-generated oxidized mixtures. The implementation of this robust database, containing multiple orthogonal (i.e., independent) pieces of information, will serve as a comprehensive resource for the field.

Lipidomics and cardiovascular disease

Cardiovascular diseases (CVDs) remain the leading cause of mortality worldwide, necessitating innovative approaches for early detection and personalized interventions. Lipidomics, leveraging advanced mass spectrometry techniques, has become instrumental in deciphering lipid-mediated mechanisms in CVDs. This review explores the application of lipidomics in identifying biomarkers for myocardial infarction, heart failure, stroke, and calcific aortic valve stenosis (CAVS). This review examines the technological advancements in shotgun lipidomics and LC/MS, which provide unparalleled insights into lipid composition and function. Key lipid biomarkers, including ceramides and lysophospholipids, have been linked to disease progression and therapeutic outcomes. Integrating lipidomics with genomic and proteomic data reveals the molecular underpinnings of CVDs, enhancing risk prediction and intervention strategies. This review positions lipidomics as a transformative tool in reshaping cardiovascular research and clinical practice.

Imaging and spatially resolved mass spectrometry applications in nephrology

The application of spatially resolved mass spectrometry (MS) and MS imaging approaches for studying biomolecular processes in the kidney is rapidly growing. These powerful methods, which enable label-free and multiplexed detection of many molecular classes across omics domains (including metabolites, drugs, proteins and protein post-translational modifications), are beginning to reveal new molecular insights related to kidney health and disease. The complexity of the kidney often necessitates multiple scales of analysis for interrogating biofluids, whole organs, functional tissue units, single cells and subcellular compartments. Various MS methods can generate omics data across these spatial domains and facilitate both basic science and pathological assessment of the kidney. Optimal processes related to sample preparation and handling for different MS applications are rapidly evolving. Emerging technology and methods, improvement of spatial resolution, broader molecular characterization, multimodal and multiomics approaches and the use of machine learning and artificial intelligence approaches promise to make these applications even more valuable in the field of nephology. Overall, spatially resolved MS and MS imaging methods have the potential to fill much of the omics gap in systems biology analysis of the kidney and provide functional outputs that cannot be obtained using genomics and transcriptomic methods.

Three-Layer Electrospray Constructing Charged Microdroplets for Online Derivatization and Position Identification of Lipid C═C Bonds

Numerous studies have demonstrated that charged microdroplets can significantly accelerate chemical reactions. In this work, we developed a novel three-layer electrospray ionization source (TL-ESI). This source generated charged microdroplets capable of facilitating the rapid epoxidation of unsaturated lipid C═C bonds with the derivatization reagent 3-chloroperbenzoic acid (m-CPBA) in an online process, achieving a conversion rate of up to 92.8%─a performance not achievable with conventional electrospray ionization source (ESI). Compared to conventional ESI, the TL-ESI effectively compartmentalized reactants, enabled precise control over the reaction process, and supported rapid online derivatization of lipid C═C bonds with m-CPBA. When integrated with tandem mass spectrometry (MS/MS), this source further enabled the localization of lipid C═C bond positions. The TL-ESI is characterized by its simplicity in design, ease of operation, and seamless integration with mass spectrometry (MS). These advantages make it an efficient and practical tool for locating C═C bond positions in unsaturated lipids, even within complex sample matrices. Additionally, this work highlights the potential of the TL-ESI as an innovative platform for accelerating chemical reactions via charged microdroplets, offering a valuable addition to the toolbox of modern analytical chemistry.

Extended coverage of human serum glycosphingolipidome by 4D-RP-LC TIMS-PASEF unravels association with Parkinson's disease

Glycosphingolipids (GSLs) are important targets in immune, infectious, lysosomal storage diseases, cancer, and neurodegenerative diseases. Circulatory GSLs profiling in clinical samples is restricted by the lack of mid- and high-throughput analytical methods and deep coverage of long-chain sialylated glycosphingolipidome. We present a 4-dimensional (4D)-glycosphingolipidomics platform for routine glycosphingolipidome profiling encompassing: extraction and fractionation of sialylated GSLs with 3 to 15 monosaccharides, neutral GSLs and sulfatides; µL-flow reversed-phase LC-TIMS-PASEF MS analysis; semi-quantification strategy adapted for fractionated glycosphingolipidome, and referential CCS, RT, and m/z values for GSLs annotation. 4D-glycosphingolipidomics of human serum reveals a high structural heterogeneity, amounting to 376 GSLs: 159 GSLs of ganglio- and neolacto-series, 145 neutral GSLs and 72 sulfatides. Here we demonstrate the platform's utility for clinical profiling of Parkinson's disease (PD) sera. 41 neolacto- and ganglio-species discriminate PD patients from controls and 14 GSLs differentiate sex subgroups, laying the foundation for further functional GSL studies with PD.

Dried blood spot microsampling: A semi-quantitative 4D-lipidomics approach using ultrahigh-performance liquid chromatography - high-resolution mass spectrometry (UHPLC - HRMS)

Dried blood spot (DBS) sample collections can offer a minimally invasive, cost-effective alternative to traditional venepuncture for remote sampling and high-frequency metabolic profiling. We present an optimized protocol for DBS-based extraction and comprehensive untargeted 4D lipid profiling using ultrahigh-performance liquid chromatography coupled with high-resolution mass spectrometry (trapped ion mobility - mass spectrometry), designed to support large-scale applications in population-wide lipidomics research. Inclusion of stable isotopically labelled internal standards allowed for semi-quantitative subclass-level correction for 10 μL DBS samples, enhancing the number of reproducible lipids within our curated target list (focussed on 432 unique rule-based lipid annotations out of 6845 features) across positive and negative heated electrospray ionization modes. The reproducibility of unique lipid features detected in replicate DBS (n = 6) was assessed on both peak areas (351 lipids <25 % CV) and calculated concentrations relative to internal standards (432 lipids <25 % CV), underscoring the benefit of internal standard addition. Storage conditions for DBS were also evaluated to determine short-term lipid stability at different temperatures (-20 °C, 4 °C, room temperature, and 45 °C). The majority of lipid subclasses, excluding a minority of glycerophospholipids and oxylipins, were stable up to 1 week at -20 °C and 4 °C (log2-fold change <30 % difference), which supports the short-term storage capacity for DBS in field and clinical settings. Similar stability was observed within a week at room temperature, excluding phosphatidylethanolamines and phosphatidylglycerols (log2-fold change >30 % difference). Application of the optimized workflow to a microsampling device (n = 6) identified 432 unique lipid features (CV < 25 %) with three repeated samplings over an hour showing minimal impact on lipid profiles by principal component analysis, showing promise for high-frequency, longitudinal DBS monitoring in population health. This work represents a significant advance, highlighting the potential for reliable lipid analysis from DBS samples with short-term stability under various storage conditions, an important logistical benefit for remote or resource-limited settings.

Benchmarking of Trapped Ion Mobility Spectrometry in Differentiating Plasmalogens from Other Ether Lipids in Lipidomics Experiments

Trapped Ion Mobility Spectrometry (TIMS) has demonstrated promising potential as a powerful discriminating method when coupled with mass spectrometry, enhancing the precision of feature annotation. Such a technique is particularly valuable for lipids, where a large number of isobaric but structurally distinct molecular species often coexist within the same sample matrix. In this study, we explored the potential of ion mobility for ether lipid isomer differentiation. Mammalian ether phospholipids are characterized by a fatty alcohol residue at the sn-1 position of their glycerol backbone. They can make up to 20% of the total phospholipid mass and are present in a broad range of tissues. There they are, for example, crucial for nervous system function, membrane homeostasis, and inter- as well as intracellular signaling. Molecular ether lipid species are difficult to distinguish analytically, as they occur as 1-O-alkyl and 1-O-alkenyl subclasses, with the latter being also known as plasmalogens. Isomeric ether lipid pairs can be separated with reversed-phase chromatography. However, their precise identification remains challenging due to the lack of clear internal reference points, inherent to the nature of lipid profiles and the lack of sufficient commercially available standard substances. Here, we demonstrate─with focus on phosphatidylethanolamines─that ion mobility measurements allow to discriminate between the ether lipid subclasses through distinct differences in their gas phase geometries. This approach offers significant advantages as it does not depend on potential retention time differences between different chromatographic systems. However, the current resolution in the ion mobility dimension is not sufficient to baseline separate 1-O-alkyl and 1-O-alkenyl isobars, and the observed differences are not yet accurately represented in existing collision cross section databases. Despite these challenges, the predictable properties of the ion mobility behavior of ether lipid species can significantly support their accurate annotation and hold promise for future advancements in lipid research.

Dual fragmentation via collision-induced and oxygen attachment dissociations using water and its radicals for C=C position-resolved lipidomics

Oxygen attachment dissociation (OAD) is a tandem mass spectrometry (MS/MS) technique for annotating the positions of double bonds (C=C) in complex lipids. Although OAD has been used for untargeted lipidomics, its availability has been limited to the positive ion mode, requiring the independent use of a collision-induced dissociation (CID) method. In this study, we demonstrated the OAD MS/MS technique in the negative-ion mode for profiling phosphatidylserines, phosphatidylglycerols, phosphatidylinositols, and sulfatides, where the fragmentation mechanism remained consistent with that in the positive ion mode. Furthermore, we proposed optimal conditions for the simultaneous acquisition of CID- and OAD-specific fragment ions, termed OAciD, where oxygen atoms and hydroxy radicals facilitate C=C position-specific fragmentation, while residual water vapor induces cleavage of low-energy covalent bonds as observed in CID. Finally, theoretical fragment ions were implemented in MS-DIAL 5 to accelerate C=C position-resolved untargeted lipidomics. The OAciD methodology was used to illuminate brain region-specific marmoset lipidomes with C=C positional information, including the estimation of C=C positional isomer ratios. We also characterized the profiles of polyunsaturated fatty acid-containing lipids, finding that lipids containing omega-3 fatty acids were enriched in the cerebellum, whereas those containing omega-6 fatty acids were more abundant in the hippocampus and frontal lobe.

Enthalpies and Entropies of Activation for sn-1/sn-2 Acyl Chain Loss in Glycerophospholipid Anions via Dipolar DC Kinetics

Glycerophospholipids (GPs) have been observed to prefer losing a particular fatty acyl chain over the other, with the preference for the chain in either the sn-1 or sn-2 position being different between various GP classes. It has been assumed that the sn preference results from the entropic favorability of the transition state conformation; however, this has not been measured previously. Here, we demonstrate the application of our previously established collision-based activation method to GP fragmentation. The method utilizes a dipolar direct current (DDC) potential across a pair of opposing rods to force ions out of the center of the ion trap, causing them to undergo radio frequency (RF) heating by absorbing power from the trapping RF field. We confirmed that the previous assumption holds for some species studied here, wherein the ΔH‡ values were nearly identical and the ΔS‡ values showed greater differences between the sn positions. However, some species and ion types seem to be more driven by ΔH‡. Additionally, the loss of the fatty acyl chains as neutrals rather than ions should also be considered if one is to thoroughly weigh which chain is indeed the preferred loss, as including all forms of acyl chain loss results in an overall favorability for the acyl chain in the sn-2 position to be lost. The driving force behind these different losses seems to be a mixture of entropic and enthalpic reasons, with the identity and presence of the headgroup playing an important role in the observed fragmentation and the measured activation parameters.

Do circulating sphingolipid species correlate with age? A study in a normoglycemic biracial population

Sphingolipids (SPLs) are essential membrane lipids with significant bioactive roles involved in various cellular processes, and their alterations have been found to be linked to many diseases, including age-related diseases. However, comprehensive studies on the association of plasma sphingolipids with aging in large, diverse cohorts remain limited. The objective of this study was to investigate the relationship between plasma sphingolipid levels and aging in a cohort of 240 normoglycemic, biracial individuals (Black and White), aged 19-65 years. Using a targeted lipidomics approach, we measured 76 sphingolipid species using liquid chromatography-tandem mass spectrometry (LC-MS/MS) in picomole/mL and determined changes in their levels with age and their correlations with aging. We found significant age-related changes in several sphingolipid species, including ceramide C18:1 and several very long-chain sphingomyelins (VLC SMs), such as C28:1 and C30:1, increases with age, showing a positive correlation. On the other hand, glycosphingolipids (monohexosylceramide, MHC; lactosylceramide, LacCer) and sphingosine (So) showed strong negative correlations with aging. A significant correlation was also observed between the ratios of saturate/monosaturated sphingolipid species with aging. In conclusion, our findings provide novel insights into the dynamic changes of circulating sphingolipids with aging. Specific sphingolipid species, such as Ceramide C18:1 and SM, accumulate with age, while others, including MHC, LacCer, and So decrease. These results suggest that the plasma SPL profile may provide valuable information about healthy aging and age-associated disease conditions.

Xingxiao pills suppresses lung adenocarcinoma progression by modulating lipid metabolism and inhibiting the PLA2G4A-GLI1-SOX2 Axis

BACKGROUND

Lung adenocarcinoma (LUAD) remains a leading cause of cancer mortality due to resistance, metastasis, and recurrence. Unlike conventional cytotoxic therapies, Xingxiao Pills (XXP), a classic traditional Chinese medicine formula, offers a complementary approach to treating LUAD, while its non-cytotoxic anti-cancer mechanisms remain unclear.

PURPOSE

To investigate the effect and mechanism of XXP on LUAD progression and stemness via lipid metabolism regulation.

METHOD

UHPLC-MS/MS was used to analyze the chemical constituents of XXP. The effects of XXP on LUAD cell proliferation, migration, invasion, and stemness were evaluated using CCK-8, Transwell, and tumor sphere assays. A LUAD xenograft model confirmed XXP's anti-tumor effects. Transcriptomics, metabolomics, ELISA, qRT-PCR, and Western blot were used to investigate the underlying mechanisms. Kaplan-Meier (KM) survival analysis and stemness index scores were performed for LUAD patients based on the TCGA dataset. Statistical analyses were performed using Student's t-test, ANOVA, and KM survival analysis (p< 0.05 considered significant).

RESULTS

XXP inhibits LUAD progression in mouse and cell models by targeting lipid metabolism reprogramming. It suppresses FA synthesis, elongation, oxidation, and glycerophospholipid (GPL) metabolism while upregulating arachidonic acid (AA) metabolism. Mechanistic studies revealed that XXP attenuates tumor stemness by inhibiting PLA2G4A (cPLA2), lowering AA release, and disrupting SMO/GLI1/SOX2 signaling, an effect also observed with the cPLA2 inhibitor AACOCF3. KM analysis showed that higher PLA2G4A expression correlated with a worse 5-year prognosis in LUAD (p = 0.0047). The low GPL/high AA group (consistent with XXP's metabolic pattern) had better survival (p = 0.0028) and a lower stemness index (p< 0.0001) than the high GPL/low AA unrelated group.

CONCLUSION

Xingxiao Pill modulates GPL and AA metabolism and downregulates the PLA2G4A (cPLA2)-AA/SMO/GLI1/SOX2 axis. Through this mechanism, XXP effectively inhibits tumor growth and stemness by targeting lipid metabolism.

Advanced profiling and structural analysis of anencephaly gangliosides by ion mobility tandem mass spectrometry

Anencephaly, the most severe type of neural tube defects (NTDs) in humans, occurs between the third and fourth gestational weeks (GW), involves the cranial part of the NT and results in the absence of the forebrain and skull. Exposed to amniotic fluid toxicity, neural tissue is degraded and prevented from development. Currently, little is known about the molecular bases of the disease and the possible involvement of glycans. In this context, considering the role played by gangliosides (GGs) in fetal brain development and the previous achievements of ion mobility separation (IMS) mass spectrometry (MS) in biomarker discovery, we report here on the introduction of this advanced analytical technique in NTD research, and its optimization for a comprehensive determination of anencephaly gangliosidome. Three native GG extracts from residual brains of anencephalic fetuses in 28, 35 and 37 GW were comparatively profiled by IMS MS, structurally analyzed by IMS MS/MS, and finally assessed against a native GG mixture from normal fetal brain. IMS MS provided data on 343 anencephaly gangliosides vs. only 157 known before and revealed for the first time the incidence of the entire penta-to octasialylated series. The comparative assay disclosed variations in GG expression with fetal age and a correlation of the pattern with the developmental stage. In contrast to the normal fetal brain, the neural tissue in anencephaly was found to contain an elevated number of polysialogangliosides and a lower expression of O-Ac- and GalNAc-modified glycoforms. These species worth further detailed investigation as new potential anencephaly markers.

Uncovering mechanisms of thiazolidinediones on osteogenesis and adipogenesis using spatial fluxomics

OBJECTIVE

Insulin-sensitizing drugs, despite their broad use against type 2 diabetes, can adversely affect bone health, and the mechanisms underlying these side effects remain largely unclear. Here, we investigated the different metabolic effects of a series of thiazolidinediones, including rosiglitazone, pioglitazone, and the second-generation compound MSDC-0602K, on human mesenchymal stem cells (MSCs).

METHODS

We developed 13C subcellular metabolomic tracer analysis measuring separate mitochondrial and cytosolic metabolite pools, lipidomic network-based isotopologue models, and bioorthogonal click chemistry, to demonstrate that MSDC-0602K differentially affected bone marrow-derived MSCs (BM-MSCs) and adipose tissue-derived MSCs (AT-MSCs). In BM-MSCs, MSDC-0602K promoted osteoblastic differentiation and suppressed adipogenesis. This effect was clearly distinct from that of the earlier drugs and that on AT-MSCs.

RESULTS

Fluxomic data reveal unexpected differences between this drug's effect on MSCs and provide mechanistic insight into the pharmacologic inhibition of mitochondrial pyruvate carrier 1 (MPC). Our study demonstrates that MSDC-0602K retains the capacity to inhibit MPC, akin to rosiglitazone but unlike pioglitazone, enabling the utilization of alternative metabolic pathways. Notably, MSDC-0602K exhibits a limited lipogenic potential compared to both rosiglitazone and pioglitazone, each of which employs a distinct lipogenic strategy.

CONCLUSIONS

These findings indicate that the new-generation drugs do not compromise bone structure, offering a safer alternative for treating insulin resistance. Moreover, these results highlight the ability of cell compartment-specific metabolite labeling by click reactions and tracer metabolomics analysis of complex lipids to discover molecular mechanisms within the intersection of carbohydrate and lipid metabolism.

Platelet lipidomics indicates enhanced thrombocyte activation in patients with antiphospholipid syndrome in vivo

BACKGROUND

Antiphospholipid syndrome (APS) is an autoimmune disorder characterized by the presence of antiphospholipid antibodies in patients with thromboembolic/thromboinflammatory events and/or obstetric complications.

OBJECTIVES

The aim of this study was to examine whether there are alterations in the platelet lipidome of APS patients in comparison with patients affected by thromboembolism without APS (control) and healthy volunteers.

METHODS

We applied quantitative mass spectrometry-based lipidomics to investigate the platelet lipidome of isolated resting and thrombin-stimulated platelets as well as platelet release in patients with APS, controls, and healthy volunteers.

RESULTS

Lipidomic data revealed an increase in lysophospholipids (LPLs) in platelets from APS patients, specifically in lysophosphatidylcholine and lysophosphatidylethanolamine species. As LPLs are cleavage products generated by phospholipase A (PLA) from the corresponding phospholipid precursor, LPL/phospholipid ratios may be employed as surrogates for PLA1 and PLA2 activities. The surrogate ratios for PLA2, which participates in the release of arachidonic acid during platelet activation, were significantly increased in APS in both resting platelets and upon thrombin-induced activation for phosphatidylcholine and phosphatidylethanolamine. The phosphatidylcholine-PLA2 surrogate ratio was found to correlate with serum levels of anti-β2-glycoprotein I and anticardiolipin immunoglobulin G. Finally, receiver operator characteristic analysis demonstrated excellent discrimination of patients with APS from controls and healthy volunteers.

CONCLUSION

These findings provide substantial evidence that platelet activation is enhanced in APS in vivo, involving the activation of PLA2.

Lipidome plasticity in medium- and long-chain fatty acid oxidation disorders: Insights from dried blood spot lipidomics

Fatty acid (FA) oxidation disorders (FAOD) are characterized by accumulation of specific acylcarnitines (CAR) and FA and can lead to potentially severe complications. In this study, dried blood spots (DBS) combined with LC-MS lipidomics analysis were used to assess lipidome plasticity in medium-chain acyl-CoA dehydrogenase deficiency (MCADD), long-chain hydroxyacyl-CoA dehydrogenase deficiency (LCHADD), and very long-chain acyl-CoA dehydrogenase deficiency (VLCADD), compared to control (CT) individuals, for screening potential prognostic biomarkers. Statistically significant variations were found in CAR, biomarkers for FAOD diagnosis, but other lipid species showed variations depending on the FAOD. Common changes in all FAOD included a few phosphatidylcholine (PC) lipid species, notably an up-regulation of LPC 16:1, possibly associated with a higher risk of cardiovascular disease (CVD). In LCHADD and VLCADD, an up-regulation of odd-chain PC (PC 33:0, PC 35:4 and PC 37:4) was observed. VLCADD exhibited higher levels of odd-chain TG, while LCHADD showed an up-regulation of ceramide (Cer 41:2;O2). The increase in the Cer class has been found to be associated with neurodegeneration and may contribute to the risk of developing this condition in LCHADD. An upregulation of ether-linked PC lipid species, including plasmenyl (known as endogenous antioxidants), was observed in MCADD, possibly as a response to increased oxidative stress reported in this disorder. Overall, DBS combined with lipidomics effectively pinpoints the lipid plasticity in FAOD, highlighting potential specific biomarkers for disease prognosis that warrant further validation for their association with the development of FAOD comorbidities.

Introduction of a Lipidomics Scoring System for data quality assessment

The scientific field of lipidomics has shown a constantly growing publication number in recent years, which is accompanied by an increasing need for quality standards. While the official shorthand nomenclature of lipids is a first and important step towards a reporting quality tool, an additional point score would reflect the quality of reported data at an even more detailed granularity. Thus, we propose a lipidomics scoring scheme that considers all the different layers of analytical information to be obtained by mass spectrometry, chromatography, and ion mobility spectrometry and awards scoring points for each of them. Furthermore, the scoring scheme is integrated with the annotation levels as proposed by the official shorthand nomenclature, with a point score, which roughly correlates with the annotated compound details. The merit of such a scoring system is the fact that it abstracts evidence for structural information into a number, which gives even the non-lipidomics expert an idea about the reporting, and by extension, data quality at first glance. Additionally, it could serve as an aid for internal quality control and for data quality assessment in the peer review process.

Skylite: Skyline-Based Lipid Isomer Retention Time Evaluation for Lipidomics in Metabolic Dysfunction-Associated Steatohepatitis

Metabolic dysfunction-associated steatotic liver disease (MASLD) is the most prevalent liver disorder worldwide and can progress to steatohepatitis. Elevated de novo lipogenesis (DNL) is a key contributor to hepatic steatosis. Fatty acid (FA) desaturation produces several unsaturated lipid isomers that are structurally very similar but have diverse biological functions. However, due to their structural similarity, many conventional mass spectrometry approaches cannot detect such metabolic alterations. Thus, we introduce the Skylite (Skyline-based lipid isomer retention time evaluation) workflow using conventional liquid chromatography-mass spectrometry (LC-MS) to identify important isomer features. Retention times of isomeric phosphatidylcholines are compared with the well-characterized human plasma reference standard NIST 1950. Retention time trends correlate well with fixed-charge derivatized FA in liquid chromatography and ozone-induced dissociation mass spectrometry data. The interpretation is supported by double bond diagnostic fragments in LC-MS/MS experiments of epoxidized hydrolyzed fatty acids. We investigate hepatic lipid profiles, focusing on esterified fatty acids in two mouse models of metabolic dysfunction-associated steatohepatitis (MASH). Out of 37 phosphatidylcholine sum compositions, the workflow identifies 123 lipid features. Importantly, CCl4-induced and melanocortin-4 receptor knockout mice on a western diet (WD) have significantly higher levels of mead acid, branched-chain fatty acid, and n-7 PUFA incorporated into phosphatidylcholines. While the MASH mouse liver tissues contain notable amounts of n-7 PUFA, no n-10 PUFA were detected, potentially indicating a unique desaturation pattern. The screening for altered lipid isomer profiles bridges the gap between high-throughput analyses and specialized structure-resolved techniques.

Lipid metabolism alterations in peripheral neuropathies

Alterations in lipid metabolism are increasingly recognized as central pathological hallmarks of inherited and acquired peripheral neuropathies. Correct lipid balance is critical for cellular homeostasis. However, the mechanisms linking lipid disturbances to cellular dysfunction and whether these changes are primary drivers or secondary effects of disease remain unresolved. This is particularly relevant in the peripheral nervous system, where the lipid-rich myelin integrity is critical for axonal function, and even subtle perturbations can cause widespread effects. This review explores the role of lipids as structural components as well as signaling molecules, emphasizing their metabolic role in peripheral neurons and Schwann cells. Additionally, we explore the genetic and environmental connections in both inherited and acquired peripheral neuropathies, respectively, which are known to affect lipid metabolism in peripheral neurons or Schwann cells. Overall, we highlight how understanding lipid-centric mechanisms could advance biomarker discovery and therapeutic interventions for peripheral nerve disorders.

Lipid droplets play versatile roles in ovarian development of the razor clam Sinonovacula constricta: Insights from proteomic and lipidomic analyses

Lipid droplet (LD) deposition is a common phenomenon during ovarian development across marine mollusks; however, studies on the protein and lipid composition of their ovarian LDs remain limited. Here, we purified LDs from the ovaries of Sinonovacula constricta and isolated proteins and lipids from these purified LDs for proteomic and lipidomic analyses. Our proteomic analysis identified 3243 proteins, with PLIN2 being the most abundant (37.03 ± 13.56 %). We subsequently conducted a functional analysis of the top 500 most abundant LD-associated proteins, categorizing them into 15 groups, including those involved in lipid metabolism, sterol biosynthesis, tricarboxylic acid cycle, carbohydrate metabolism, G protein superfamily, protein chaperones, transport proteins, nucleotide-catabolic process, protein processing and degradation, cytoskeletal proteins, oxidative stress and immunity, and ribosome-associated proteins. In our lipidomic analysis, we identified 1158 molecules across 52 lipid classes, with phosphatidylcholine (PC) exhibiting the greatest diversity at 209 varieties, followed by EtherPC with 177 varieties and triglyceride (TG) with 149 varieties. The fatty acid (FA) analysis of LDs revealed that 16:0 was the most abundant (30.01 ± 0.42 %). Additionally, LDs were found rich in long-chain polyunsaturated FAs (35.63 ± 4.36 %), particularly EPA and DHA. Moreover, we analyzed the FA composition of TGs, PCs, and EtherPCs derived from ovarian LDs. In PCs and TGs, the predominant FAs were 16:0, 16:1, and 18:3, while 16:0, 22:6, and 18:4 constituted the major FA species in EtherPCs. Together, our results suggest that ovarian LDs in S. constricta not only participate in lipid metabolism but also interact with other organelles and metabolic processes, thereby facilitating ovarian development.

The Bioactive Sphingolipid Playbook. A Primer for the Uninitiated as well as Sphingolipidologists

Sphingolipids and glycosphingolipids are among the most structurally diverse and complex compounds in the mammalian metabolome. They are well known to play important roles in biological architecture, cell-cell communication and cellular regulation, and for many biological processes, multiple sphingolipids are involved. Thus, it is not surprising that untargeted genetic/transcriptomic/pharmacologic/metabolomic screens have uncovered changes in sphingolipids and sphingolipid genes/proteins while studying physiological and pathological processes. Consequently, with increasing frequency, both targeted and untargeted mass spectrometry methodologies are being used to conduct sphingolipidomic analyses. Interpretation of such large data sets and design of follow-up experiments can be daunting for investigators with limited expertise with sphingolipids (and sometimes even for someone well-versed in sphingolipidology). Therefore, this review gives an overview of essential elements of sphingolipid structure and analysis, metabolism, functions, and roles in disease, and discusses some of the items to consider when interpreting lipidomics data and designing follow-up investigations.

Novel Charge-Switch Derivatization Method Using 3-(Chlorosulfonyl)benzoic Acid for Sensitive RP-UHPLC/MS/MS Analysis of Acylglycerols, Sterols, and Prenols

Chemical derivatization involves the reaction of an analyte with a derivatization agent to modify its structure, improving the peak shape, chromatographic performance, structural analysis, ionization efficiency, and sensitivity. A novel derivatization method using 3-(chlorosulfonyl)benzoic acid is developed for the determination of monoacylglycerols, diacylglycerols, free sterols, and tocopherols using the reversed-phase ultra-high-performance liquid chromatography-tandem mass spectrometry (RP-UHPLC/MS/MS) method in the negative ion mode. The chromatographic and mass spectrometric properties of derivatized lipids are investigated by using 29 lipid standards spanning four lipid classes. The derivatization process is optimized using pooled plasma spiked by 9 internal standards, achieving an optimal yield with a reaction time of 40 min at 60 °C. The stability of the derivatives is confirmed, with short-term stability maintained for 10 h at 4 °C and long-term stability preserved for 5 days at -80 °C. The repeatability and reproducibility are verified by one/two operator(s), which underscores the simplicity and robustness of the method, and calibration curves with high linear regression coefficients illustrate the accuracy of the method. The derivatization approach, which combines RP-UHPLC/MS/MS and the use of specific fragmentation patterns, significantly reduces limits of detection, reaching 15-25 pmol/mL for free sterols in plasma. The optimized method is applied to the analysis of human plasma, leading to the identification of 92 lipid species in the targeted lipid classes. This represents a substantial improvement in sensitivity and detection capabilities compared to those of previously reported methods.

Coral incorporating microplastics leads to a health-risking immunometabolic shift

Microplastic pollution has been associated with coral susceptibility to disease, yet the underlying mechanism is unclear. An untargeted lipidomic profiling was therefore performed to gain an insight into the effect of microplastics on a vulnerable coral (Turbinaria mesenterina) of actively reacting to suspended particles. Expending storage lipids on actions such as increasing 20:4-possessing ether membrane lipids and mitochondrial β-oxidation for immunoactivation was observed in coral hosts. A molecular realignment of symbiotic communication was correspondingly observed from symbiotic algae activating anti-inflammatory actions, which employed the 22:6-deriving effects that expended storage lipids as well, by, for example, increasing 22:6-possessing membrane lipids. Symbiotic algae reacting against the heightened host immunity also led to a metabolic compromise that lowered photoprotective capacity. Worryingly, increasing these polyunsaturated membrane lipids potentially sensitize the cells to oxidative stress-induced cell death that was simultaneously indicated by a sphingolipid profile as lipid peroxidation preliminarily increased in coral. Microplastic accumulation thus potentially increase coral susceptibility to environmental factors being able to elevating the oxidative stress, such as light-heat stress. In this manner, microplastic pollution in the ocean would chronically impair coral health, being highlighted by this study.

Hepatic stellate cells control liver zonation, size and functions via R-spondin 3

Hepatic stellate cells (HSCs) have a central pathogenetic role in the development of liver fibrosis. However, their fibrosis-independent and homeostatic functions remain poorly understood1-5. Here we demonstrate that genetic depletion of HSCs changes WNT activity and zonation of hepatocytes, leading to marked alterations in liver regeneration, cytochrome P450 metabolism and injury. We identify R-spondin 3 (RSPO3), an HSC-enriched modulator of WNT signalling, as responsible for these hepatocyte-regulatory effects of HSCs. HSC-selective deletion of Rspo3 phenocopies the effects of HSC depletion on hepatocyte gene expression, zonation, liver size, regeneration and cytochrome P450-mediated detoxification, and exacerbates alcohol-associated and metabolic dysfunction-associated steatotic liver disease. RSPO3 expression decreases with HSC activation and is inversely associated with outcomes in patients with alcohol-associated and metabolic dysfunction-associated steatotic liver disease. These protective and hepatocyte-regulating functions of HSCs via RSPO3 resemble the R-spondin-expressing stromal niche in other organs and should be integrated into current therapeutic concepts.

Lipidome visualisation, comparison, and analysis in a vector space

A shallow neural network was used to embed lipid structures in a 2- or 3-dimensional space with the goal that structurally similar species have similar vectors. Tests on complete lipid databanks show that the method automatically produces distributions which follow conventional lipid classifications. The embedding is accompanied by the web-based software, Lipidome Projector. This displays user lipidomes as 2D or 3D scatterplots for quick exploratory analysis, quantitative comparison and interpretation at a structural level. Examples of published data sets were used for a qualitative comparison with literature interpretation.

Phosphatidylcholine synthesis and remodeling in brain endothelial cells

Mammalian cells synthesize hundreds of different variants of their prominent membrane lipid phosphatidylcholine (PC), all differing in the side chain composition. This batch is constantly remodeled by the Lands cycle, a metabolic pathway replacing one chain at a time. Using the alkyne lipid lyso-phosphatidylpropargylcholine (LpPC), a precursor and intermediate in PC synthesis and remodeling, we study both processes in brain endothelial bEND3 cells. A novel method for multiplexed sample analysis by mass spectrometry is developed that offers high throughput and molecular species resolution of the propargyl-labeled PC lipids. Their time-resolved profiles and kinetic parameters of metabolism demonstrate the plasticity of the PC pool and the acute handling of lipid influx in endothelial cells differs from that in hepatocytes. Side chain remodeling as a form of lipid cycling adapts the PC pool to the cell's need and maintains lipid homeostasis. We estimate that endothelial cells possess the theoretical capacity to remodel up to 99% of their PC pool within 3.5 h using the Lands cycle. However, PC species are not subjected stochastically to this remodeling pathway as different species containing duplets of saturated, omega-3, and omega-6 side chains show different decay kinetics. Our findings emphasize the essential function of Lands cycling for monitoring and adapting the side chain composition of PC in endothelial cells.

Serum phospholipids and sphingolipids are linked to early-stage osteoarthritis by lipidomic profiling

BACKGROUND

Osteoarthritis (OA) is associated with abnormal lipid metabolism, wherein elevated levels of phospholipids (PLs) and sphingolipids (SLs) in human and canine synovial fluid (SF) have been observed. The aim of this lipidomic study was to evaluate how closely blood lipid levels reflect changes in SF, building on previous findings.

METHODS

Lipids were extracted from knee SF and serum of 44 joint-healthy donors and 58 early (eOA) or late OA (lOA) patients. By electrospray ionization tandem mass spectrometry (ESI-MS/MS), we quantified the extracted lipids and conducted comprehensive statistical analyses.

RESULTS

Human SF and serum had similar PL and SL compositions. Quantifying 91 lipid species from 6 major classes revealed OA-related changes in serum, with the lowest levels in healthy controls and elevated levels already in the eOA cohort. Generally, serum PL and SL levels were 3-12 times higher than in SF. Specific PL species were elevated in both SF and serum of eOA and lOA patients compared to healthy controls, while nearly 10% of the PL species measured were higher exclusively in the serum of OA patients.

CONCLUSIONS

The significant lipidomic alterations that were detected at an average Outerbridge score of less than 2 suggest that certain serum PLs may serve as indicators for monitoring the early stages of OA even before radiologic detection is possible. With 10% of PL species elevated only in OA serum, our data implicate the existence of a systemic response that parallels the local lipid metabolic response to OA.

Fast and comprehensive lipidomic analysis using supercritical fluid chromatography coupled with low and high resolution mass spectrometry

Despite advances in the last few years, the use of supercritical fluid chromatography (SFC) in combination with mass spectrometry (MS) for lipidomic analysis has not reached the popularity of LC-MS. However, SFC presents clear advantages that can be exploited, such as fast, reproducible and class-based separations including nonpolar lipid classes, such as cholesterol esters, triacylglycerols, diacylglycerols, monoacylglycerols and cholesterol. In this study we show how SFC can be used for comprehensive lipidomic analyses after optimization of parameters such as back-pressure regulator (BPR), column temperature or overfeed volume of injection. We also compare the performances of triple quadrupole (QqQ) and quadrupole time-of-flight (QTOF) mass spectrometers coupled to SFC in terms of qualitative and quantitative analyses.

Fermenting shea nuts using the traditional pit method yields better physicochemical properties with potential environmental benefits

Shea oil, a globally consumed commodity, is intricately linked to the labor of women in Sub-Saharan Africa. This study examines local perceptions and adoption of a traditional shea nut fermentation method using subterranean pits in rural West African communities, and the chemical profiles of the kernels processed through different traditional methods. Key findings are that 1) local processors prefer the pit method due to its convenience and efficiency, and 2) lipid analyses indicate that fermenting shea nuts for three to six months results in an optimal chemical profile, characterized by lower free fatty acid (more than threefold) and polar lipid (more than 15-fold) content compared to boiled kernels. This enhances quality and mechanical processability, both criteria desirable for industrial applications. This study fills an important gap by chemically characterizing a traditional shea processing practice that has received little scientific attention. The results imply that the pit method holds potential for industrial shea oil extraction and for reducing firewood and water use in producing communities. However, this potential depends on fair benefit-sharing, local communities' willingness to adopt the new practice, and overcoming the challenges for scaling up.

Clinical lipidomics reveals high individuality and sex specificity of circulatory lipid signatures: a prospective healthy population study

Lipid metabolism and circulatory lipid levels are tightly associated with the (cardio)metabolic health. Consequently, MS-based lipidomics has emerged as a powerful phenotyping tool in epidemiological, human population, and in clinical intervention studies. However, ensuring high-throughput and reproducible measurement of a wide panel of circulatory lipid species in large-scale studies poses a significant challenge. Here, we applied a recently developed quantitative LC-MS/MS lipidomics approach to a subset of 1,086 fasted plasma samples belonging to apparently healthy participants from prospective Lausanne population study. This high-coverage and high-throughput hydrophilic interaction liquid chromatography-based methodology allowed for the robust measurement of 782 circulatory lipid species spanning 22 lipid classes and six orders of magnitude-wide concentration range. This was achieved by combining semiautomated sample preparation using a stable isotope dilution approach and the alternate analysis of National Institute of Standards and Technology plasma reference material, as a quality control. Based on National Institute of Standards and Technology quality control analysis, median between-batch reproducibility was 8.5%, over the course of analysis of 13 independent batches comprising 1,086 samples collected from 364 individuals at three time points. Importantly, the biological variability, per lipid species, was significantly higher than the batch-to-batch analytical variability. Furthermore, the significantly lower between-subject (than within-subject) variability and unsupervised sample clustering demonstrated the high individuality and sex specificity of circulatory lipidome. The most prominent sex differences were reported for sphingomyelins and ether-linked phospholipids present in significantly higher concentrations in female plasma. The high individuality and sex specificity of circulatory lipidome constitute important pre-requisites for the application of lipidomics in next-generation metabolic health monitoring.

Lipidomics reveals cell specific changes during pluripotent differentiation to neural and mesodermal lineages

Due to their self-renewal and differentiation capabilities, pluripotent stem cells hold immense potential for advancing our understanding of human disease and developing cell-based or pharmacological interventions. Realizing this potential, however, requires a thorough understanding of the basal cellular mechanisms which occur during differentiation. Lipids are critical molecules that define the morphological, biochemical, and functional role of cells. This, combined with emerging evidence linking lipids to neurodegeneration, cardiovascular health, and other diseases, makes lipids a critical class of analytes to assess normal and abnormal cellular processes. While previous work has examined the lipid composition of stem cells, uncertainties remain about which changes are conserved and which are unique across distinct cell types. In this study, we investigated lipid alterations of induced pluripotent stem cells (iPSCs) at critical stages of differentiation toward neural or mesodermal fates. Lipidomic analyses of distinct differentiation stages were completed using a platform coupling liquid chromatography, ion mobility spectrometry, and mass spectrometry (LC-IMS-MS) separations. Results illustrated a shared triacylglyceride and free fatty acid accumulation in early iPSCs that were utilized at different stages of differentiation. Unique fluctuations through differentiation were also observed for certain phospholipid classes, sphingomyelins, and ceramides. These insights into lipid fluctuations across iPSC differentiation enhance our fundamental understanding of lipid metabolism within pluripotent stem cells and during differentiation, while also paving the way for a more precise and effective application of pluripotent stem cells in human disease interventions.

LC-MS analysis of serum lipidomic and metabolomic signatures in pediatric patients with acute lymphoblastic leukemia

BACKGROUND

Acute lymphoblastic leukemia (ALL) is a prevalent hematologic malignancy that primarily affects children. The diagnosis and treatment of pediatric ALL remain challenging. This study aimed to identify differential lipids and metabolites that may hold potential for improving ALL treatment.

METHODS

In this retrospective case-control study, serum samples obtained from children with ALL and healthy controls were analyzed. Serum lipidome and metabolome alterations of ALL were analyzed by comparing pediatric patients with ALL with healthy controls based on liquid chromatography high-resolution mass spectrometry analysis of serum lipidomic and metabolomic signatures.

RESULTS

We identified 2,298 lipid features in the serum. Among them, 72 (3.13%) differed significantly in pediatric patients with ALL compared to healthy controls. Notably, sphingolipids (ceramide and sphingomyelin) and phospholipids exhibited the most pronounced changes. Targeted analysis of ceramides revealed significantly elevated levels of Cer 18:0 and Cer 20:0 in the serum of pediatric patients with ALL. Additionally, gut microbial-related lipids (such as sulfonolipids and fatty acid esters of hydroxy fatty acids) showed significant alterations. Metabolomic analysis identified 15 differential metabolites, indicating disrupted nucleotide and amino acid metabolism. Furthermore, the dysregulated lipids and metabolites correlated with various blood indicators, with ceramide and nucleosides positively associated with white blood cell count but negatively correlated with hemoglobin and platelet.

CONCLUSION

These findings shed light on abnormal molecular signatures contributing to pediatric ALL and may serve as potential biomarker panel for therapy of ALL.

The Lipid Composition of the Exo-Metabolome from Haemonchus contortus

Background/Objectives: Metabolomic studies of different parasite-derived biomolecules, such as lipids, are needed to broaden the discovery of novel targets and overcome anthelmintic resistance. Lipids are involved in diverse functions in biological systems, including parasitic helminths, but little is known about their role in the biology of these organisms and their impact on host-parasite interactions. This study aimed to characterize the lipid profile secreted by Haemonchus contortus, the major parasitic nematodes of farm ruminants. Methods: H. contortus adult worms were recovered from infected sheep and cultured ex vivo. Parasite medium was collected at different time points and samples were subjected to an untargeted global lipidomic analysis. Lipids were extracted and subjected to Liquid Chromatography-Mass Spectrometry (LC-MS/MS). Annotated lipids were normalized and subjected to statistical analysis. Lipid clusters' fold change (FC) and individual lipid features were compared at different time points. Lipids were also analyzed by structural composition and saturation bonding. Results: A total of 1057 H. contortus lipid features were annotated, including glycerophospholipids, fatty acyls, sphingolipids, glycerolipids, and sterols. Most of these compounds were unsaturated lipids. We found significant FC differences in the lipid profile in a time-dependent manner. Conclusions: We predict that many lipids found in our study act as signaling molecules for nematodes' physiological functions, such as adaptation to nutrient changes, life span and mating, and as modulators on the host immune responses.

Microflow Liquid Chromatography Coupled to Multinozzle Electrospray Ionization for Improved Lipidomics Coverage of 3D Clear Cell Renal Cell Carcinoma

In most bioanalytical laboratories, high-resolution mass spectrometry (HRMS) systems with electrospray ionization (ESI) are hyphenated to liquid chromatography platforms. The latter typically operate under analytical flow (AF; 0.2-1 mL/min) regimes. Hence, AF/ESI-HRMS methods prioritize the detection of analytes of higher abundances or ionizability and tend to suffer from matrix effects or ion suppression. A far higher sensitivity can be obtained with electrospray at nanoflow (10-1000 nL/min) thanks to a better ionization efficiency and significant decrease in matrix effects. Both advantages are crucial to reliably accessing low-abundance compounds or weakly ionizable analytes. This work presents a microflow (μF) chromatographic setup coupled to a novel microfabricated multinozzle electrospray (mnESI) emitter with five nozzles spraying at 600 nL/min per nozzle for untargeted HRMS lipidomic profiling. With a runtime of 19 min, similar to our established analytical flow (AF/ESI) lipidomics platform, μF/mnESI produced a 16-fold median increase across 69 deuterated lipid standards. The performance of this new configuration was also evaluated in the context of the profiling of a 3D clear cell renal cell carcinoma (ccRCC) model exposed to a multidrug combination therapy. The processing of the acquired data resulted in 1270 (μF/mnESI) vs 752 (AF/ESI) MS2-annotated lipids. Among those, 762 achieved <10% variation on pooled QC samples for μF/mnESI compared to only 361 for the AF method. In addition, the measurements of ccRCC samples confirmed the improvements in ionization efficiency and adduct patterns observed with standards, enabling to annotate 79 oxidized triglycerides, 38 cholesterol esters (only five and four detected in AF/ESI, respectively), and 12 sitosterol esters, not yet reported in mammalian cell cultures.

Interactions of Fatty Acid and Cholesterol Metabolism with Cellular Stress Response Pathways in Cancer

Lipids have essential functions as structural components of cellular membranes, as efficient energy storage molecules, and as precursors of signaling mediators. While deregulated glucose and amino acid metabolism in cancer have received substantial attention, the roles of lipids in the metabolic reprogramming of cancer cells are less well understood. However, since the first description of de novo fatty acid biosynthesis in cancer tissues almost 70 years ago, numerous studies have investigated the complex functions of altered lipid metabolism in cancer. Here, we will summarize the mechanisms by which oncogenic signaling pathways regulate fatty acid and cholesterol metabolism to drive rapid proliferation and protect cancer cells from environmental stress. The review also discusses the role of fatty acid metabolism in metabolic plasticity required for the adaptation to changing microenvironments during cancer progression and the connections between fatty acid and cholesterol metabolism and ferroptosis.

CAMKIIδ Reinforces Lipid Metabolism and Promotes the Development of B Cell Lymphoma

The most prevalent types of lymphomas are B cell lymphomas (BCL). Newer therapies for BCL have improved the prognosis for many patients. However, approximately 30% with aggressive BCL either remain refractory or ultimately relapse. These patients urgently need other options. This study shows how calcium/calmodulin-dependent protein kinase II delta (CAMKIIδ) is pivotal for BCL development. In BCL cells, ablation of CAMKIIδ inhibits both lipolysis from lipid droplets and oxidative phosphorylation (OXPHOS). With lipolysis blocked, BCL progression is markedly suppressed in two distinct BCL mouse models: MYC-driven EµMyc mice and Myc/Bcl2 double-expressed mice. When CAMKIIδ is present, it destabilizes transcription factor Forkhead Box O3A (FOXO3A) by phosphorylating it at Ser7 and Ser12. This then permits transcription of downstream gene IRF4 - a master transcription factor of lipid metabolism. The CAMKIIδ/FOXO3A axis bolsters lipid metabolism, mitochondrial respiration, and tumor fitness in BCL under metabolic stress. This study also evaluates Tetrandrine (TET), a small molecule compound, as a potent CAMKIIδ inhibitor. TET attenuates metabolic fitness and elicits therapeutic responses both in vitro and in vivo. Collectively, this study highlights how CAMKIIδ is critical in BCL progression. The results also pave the way for innovative therapeutic strategies for treating aggressive BCL.

Glial Biologist's Guide to Mass Spectrometry-Based Lipidomics: A Tutorial From Sample Preparation to Data Analysis

Neurological diseases are associated with disruptions in the brain lipidome that are becoming central to disease pathogenesis. Traditionally perceived as static structural support in membranes, lipids are now known to be actively involved in cellular signaling, energy metabolism, and other cellular activities involving membrane curvature, fluidity, fusion or fission. Glia are critical in the development, health, and function of the brain, and glial regulation plays a major role in disease. The major pathways of glial dysregulation related to function are associated with downstream products of metabolism including lipids. Taking advantage of significant innovations and technical advancements in instrumentation, lipidomics has emerged as a popular omics discipline, serving as the prevailing approach to comprehensively define metabolic alterations associated with organismal development, damage or disease. A key technological platform for lipidomics studies is mass spectrometry (MS), as it affords large-scale profiling of complex biological samples. However, as MS-based techniques are often refined and advanced, the relative comfort level among biologists with this instrumentation has not followed suit. In this review, we aim to highlight the importance of the study of glial lipids and to provide a concise record of best practices and steps for MS-based lipidomics. Specifically, we outline procedures for glia lipidomics workflows ranging from sample collection and extraction to mass spectrometric analysis to data interpretation. To ensure these approaches are more accessible, this tutorial aims to familiarize glia biologists with sample handling and analysis techniques for MS-based lipidomics, and to guide non-experts toward generating high quality lipidomics data.

Cerebellar lipid dysregulation in SCA3: A comparative study in patients and mice

Spinocerebellar ataxia type 3 (SCA3) is the most common dominantly inherited ataxia and belongs to the family of nine diseases caused by a polyglutamine expansion in the disease-causing protein. In SCA3, a polyglutamine expansion in ATXN3 causes neuron loss in disease-vulnerable brain regions, resulting in progressive loss of coordination and ultimately death. There are no disease-modifying or preventative treatments for this uniformly fatal disorder. Recent studies demonstrate prominent white matter atrophy and microstructural alterations in disease-vulnerable brain regions of SCA3 patients and mouse models. However, the major constituent of white matter - lipids - remains understudied in SCA3. In this study, we conducted the first unbiased investigation of brain lipids in SCA3, focusing on the disease-vulnerable cerebellum of SCA3 postmortem patients and mouse models. Liquid chromatography-mass spectrometry uncovered widespread lipid reductions in patients with SCA3. Lipid downregulation was recapitulated in early- to mid-stage mouse models of SCA3, including transgenic YACQ84 and Knock-in Q300 mice. End-stage Knock-in Q300 mice displayed a progressive reduction in lipid content, highlighting targets that could benefit from early therapeutic intervention. In contrast, Atxn3-Knock-out mice showed mild lipid upregulation, emphasizing a toxic gain-of-function mechanism underlying lipid downregulation in SCA3. We conclude that lipids are significantly altered in SCA3 and establish a platform for continued exploration of lipids in disease through interactive data visualization websites. Pronounced reductions in myelin-enriched lipids suggest that lipid dysregulation could underlie white matter atrophy in SCA3. This study establishes the basis for future work elucidating the mechanistic, biomarker, and therapeutic potential of lipids in SCA3.

A guide to reverse metabolomics-a framework for big data discovery strategy

Untargeted metabolomics is evolving into a field of big data science. There is a growing interest within the metabolomics community in mining tandem mass spectrometry (MS/MS)-based data from public repositories. In traditional untargeted metabolomics, samples to address a predefined question are collected and liquid chromatography with MS/MS data are generated. We then identify metabolites associated with a phenotype (for example, disease versus healthy) and elucidate or validate their structural details (for example, molecular formula, structural classification, substructure or complete structural annotation or identification). In reverse metabolomics, we start with MS/MS spectra for known or unknown molecules. These spectra are used as search terms to search public data repositories to discover phenotype-relevant information such as organ/biofluid distribution, disease condition, intervention status (for example, pre- and postintervention), organisms (for example, mammals versus others), geography and any other biologically relevant associations. Here we guide the reader through a four-part process: (1) obtaining the MS/MS spectra of interest (Universal Spectrum Identifier) and (2) Mass Spectrometry Search Tool searches to find the files associated with the MS/MS that are in available databases, (3) using the Reanalysis Data User Interface framework to link the files with their metadata and (4) validating the observations. Parts 1-3 could take from hours to days depending on the method used for collecting MS/MS spectra. For example, we use MS/MS spectra from three small molecules: phenylalanine-cholic acid (a microbially conjugated bile acid), phenylalanine-C4:0 and histidine-C4:0 (two N-acyl amides). We leverage the Global Natural Products Social Molecular Networking-based framework to explore the microbial producers of these molecules and their associations with health conditions and organ distributions in humans and rodents.

Evaluation of Novel Pyridine-Based Compounds Integrating Bioactive Amide and Hydrazide Groups as a Potential Fungicide Agent

A series of novel pyridine-based compounds integrating bioactive amide and hydrazide groups were designed and synthesized through an active group splicing strategy. The fungicidal bioassays indicated that several compounds showed remarkable and broad-spectrum inhibitory activity. Notably, compound A5 displayed satisfactory in vitro fungicidal activity against Fusarium graminearum, Magnaporthe oryzae, Rhizoctonia solani, Colletotrichum gloeosporioides, Botrytis cinerea, Sclerotinia sclerotiorum, Alternaria sp., and Physalospora piricola, with EC50 values of 2.53, 2.84, 1.64, 7.59, 4.67, 5.50, and 2.84 μg mL-1, respectively. Additionally, A5 also showed promising in vivo preventive efficiency against F. graminearum and R. solani at 100 μg mL-1. Preliminary investigation of the fungicidal mechanism demonstrated that the differentially expressed genes and differential metabolites in R. solani treated with A5 at 10 μg mL-1 exhibited notable enrichment in pathways associated with lipid metabolism, potentially linking to the plasma membrane contraction observed by TEM. Furthermore, to assess the environmental compatibility of compound A5, its toxicity to zebrafish, hydrolysis rates in different pH buffers, and effects on the growth of wheat seedlings were evaluated. These findings will provide substantial theoretical guidance for the development of new environmentally friendly fungicides.

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.

Association of Plasma Lipid Patterns and LDL Cholesterol Levels with Breslow Thickness and Ulceration in Melanoma Patients

Recent evidence has highlighted the critical role of lipids in tumor biology. In this study, we analyzed the plasma lipid profiles of 151 melanoma patients (University of Debrecen, Department of Dermatology, Hungary) to examine the associations between specific lipid species and commonly used LDL-C lipid parameters, as well as the Breslow thickness and ulceration of primary tumors. Our analysis included patients who underwent primary tumor resection, comprising 83 individuals without metastases and 68 with metastases at the time of blood sampling. Lipid profiling was performed using the Lipidyzer™ platform, which targets over 1100 lipid species. Following quality control filtering, 802 lipids were included in the subsequent analyses. Ten lipids were found to have decreased plasma levels, while one lipid exhibited elevated plasma levels, both associated with an increased risk of higher Breslow thickness. Additionally, patients with thicker tumors (≥2 mm) demonstrated significantly higher LDL-C levels after adjusting for age, sex, therapy, and tumor presence (p = 0.032). Using forward stepwise regression, we identified a combination of four lipids-(CE(20:5), LCER(24:1), PE(P18:1/18:1), and LPE(18:2))-that demonstrated the strongest correlation with Breslow depth (AUC = 0.779, as determined by ROC analysis). Additionally, we identified 11 lipids significantly associated with tumor ulceration. Stepwise regression analysis further revealed two lipids (FFA(16:0) and PC(15:0/18:1)) capable of predicting tumor ulceration with an AUC score of 0.740. These findings suggest that individual lipid metabolism may influence tumor thickness and ulceration during the development and progression of primary melanoma.

Untargeted lipidomics reveals unique lipid signatures of extracellular vesicles from porcine colostrum and milk

Extracellular vesicles (EV) are membranous vesicles considered as significant players in cell-to-cell communication. Milk provides adequate nutrition, transfers immunity, and promotes neonatal development, and milk EV are suggested to play a crucial role in these processes. Milk samples were obtained on days 0, 7, and 14 after parturition from sows receiving either a standard diet (ω-6:ω-3 = 13:1) or a test diet enriched in ω-3 (ω-6:ω-3 = 4:1). EV were isolated using ultracentrifugation coupled with size exclusion chromatography, and characterized by nanoparticle tracking analysis, transmission electron microscopy, and assessment of EV markers via Western blotting. The lipidome was determined following a liquid chromatography-quadrupole time-of-flight mass spectrometry approach. Here, we show that different stages of lactation (colostrum vs mature milk) have a distinct extracellular vesicle lipidomic profile. The distinct lipid content can be further explored to understand and regulate milk EV functionalities and primordial for enabling their diagnostic and therapeutic potential.

iSODA: A Comprehensive Tool for Integrative Omics Data Analysis in Single- and Multi-Omics Experiments

Thanks to the plummeting costs of continuously evolving omics analytical platforms, research centers collect multiomics data more routinely. They are, however, confronted with the lack of a versatile software solution to harmoniously analyze single-omics and interpret multiomics data. We have developed iSODA, a web-based application for the analysis of single- and multiomics data. The tool emphasizes intuitive interactive visualizations designed for user-driven data exploration. Researchers can access a variety of functions ranging from simple visualization like volcano plots and PCA to advanced functional analyses like enrichment analysis and lipid saturation analysis. For integrated multiomics, iSODA incorporates multi-omics factor analysis and similarity network fusion. The ability to adapt the data on-the-fly allows for tasks, such as the removal of outlier samples or failed features, imputation, or normalization. All results are presented through interactive plots, the modular design supports extensions, and tooltips and tutorials provide comprehensive guidance for users. iSODA is accessible under http://isoda.online/.

Effect of rhGH treatment on lipidome and brown fat activity in prepuberal small for gestational age children: a pilot study

Recombinant human growth hormone (rhGH) therapy is the primary treatment for children born small for gestational age (SGA) who fail to show spontaneous catch-up growth by two or four years. While its effects on white adipose tissue are well-documented, this pilot study aimed to investigate its impact on the lipidome and the thermogenic and endocrine activities of brown adipose tissue (BAT) in SGA children following rhGH treatment. The study involved 11 SGA children divided into two groups: (a) SGA children who were not treated with rhGH (n = 4) and (b) SGA children who received rhGH treatment with Saizen® (n = 7). This second group of seven SGA children was followed for 12 months after initiating rhGH treatment. Interventions included 12-hour fasting blood extraction and infrared thermography at baseline and 3 and 12 months post-treatment. Five appropriate-for-gestational-age (AGA) children served as controls. Exclusion criteria included endocrinological, genetic, or chronic diseases. Untargeted lipidomics analysis was performed using liquid chromatography-mass spectrometry (LC-MS), and serum biomarker levels were measured using ELISA assays. Serum lipidomic analysis revealed that free fatty acids (FFAs) increased to levels close to those of the AGA group after three months of rhGH administration, including polyunsaturated fatty acids, correlating with reduced leptin levels. Elevated levels of 1a,1b-dihomo-PGJ2 and adrenic acid suggested potential aging markers. rhGH treatment also significantly reduced meteorin-like (METRNL) and monocyte chemoattractant protein-1 (MCP1) serum levels to control levels. rhGH influences the serum lipidome, promoting changes in maturation and metabolism. Further research is required to clarify the direct effects of rhGH on specific lipid species and batokines, potentially addressing metabolic disturbances linked to obesity and aging.

Phospholipids and Sphingolipids in Osteoarthritis

Many studies now emphasize the intricate relationship between lipid metabolism and osteoarthritis (OA), a leading cause of disability. This narrative review examines alterations in the levels of phospholipids (PLs) and sphingolipids (SLs) in synovial fluid (SF), plasma, serum, and articular tissues; discusses their role in joint lubrication, inflammation, and cartilage degradation; and describes their potential as diagnostic markers and therapeutic targets. Key findings include stage-dependent elevated levels of specific PLs and SLs in the SF, blood, and tissue of OA patients, implicating them as possible biomarkers of disease severity and progression. Studies suggest that beyond the involvement of these lipids in joint lubrication, individual species, such as lysophosphatidylcholine (LPC) 16:0, lysophosphatidic acid (LPA), ceramide-1-phosphate (C1P), and sphingosine-1-phosphate (S1P), contribute to pain, inflammation, and degradation of joints through various signaling pathways. Cross-species comparisons suggest that dogs and mice experience similar lipidomic changes during OA as humans, rendering them valuable models for studying lipid-related mechanisms. PLs and SLs in SF appear to originate primarily from the synovial blood capillaries through diffusion. In addition, lipids that are produced locally by fibroblast-like synoviocytes (FLSs) are influenced by cytokines and growth factors that regulate the biosynthesis of PLs for joint lubrication. Emerging research has identified genes such as UGCG and ESYT1 as regulators of lipid metabolism in OA. Further, we examine the suitability of lipids as biomarkers of OA and the potential of targeting the PL and SL pathways to treat OA, emphasizing the need for further research to translate these findings into clinical applications.

Analysis of triacylglycerol regioisomers in plant oils using direct inlet negative ion chemical ionization tandem mass spectrometry

Triacylglycerols (TGs) are the primary lipids of plant oils and the positional distribution of fatty acids (FAs) is essential to physicochemical, functional, and nutritional qualities of oils. Most studies have reported TG species in plant oils. In some studies, FA combinations in each TG species have been reported still neglecting the regioisomer composition of TGs. In this study, a fast direct inlet negative ion chemical ionization tandem mass spectrometric (NICI-MS/MS) method and optimization algorithm were applied to study the regioisomerism of TGs in 18 different plant oils. According to FA composition results, oleic, FA 18:1(9); linoleic, FA 18:2(9,12); palmitic, FA 16:0 and stearic acid, FA 18:0 were the most abundant FAs, composing mainly TG species having acyl carbon numbers 50, 52 and 54 and 1-4 double bonds. Based on 35 detected TG species, oils were classified into five groups using clustering analysis. Each group had a different dominant TG species of which the most abundant were triunsaturated ones. In regioisomeric pairs or triplets, FA 16:0, FA 16:1(9), FA 18:0, and FA 18:2(9,12) were more commonly in the sn-1/3 position, while FA 18:1 slightly preferred sn-2. The most abundant TG regioisomers were: TG 16:0_18:1(sn-2)_18:1 (52:2, mainly 18:1 in sn-2) especially in avocado, macadamia nut, olive, and palm oils; TG 18:2_18:2(sn-2)_18:1 and TG 18:2_18:1(sn-2)_18:2 (TG 54:5, mainly 18:2 in sn-2) in corn, pumpkin seed, sesame, and sunflower oils. The use of high-throughput NICI-MS/MS method to study regioisomers in commercial plant oils contributes to further studies on profiling lipid structure and developing products with specific TG compositions to meet dietary needs. The regiospecific information of TGs in edible oils is crucial for understanding their health benefits and functional properties, which are in turn needed in selecting oils for various applications.

Assessment of the effects of cadmium, samarium and gadolinium on the blue mussel (Mytilus edulis): A biochemical, transcriptomic and metabolomic approach

Improving the understanding of how chemicals affect on organisms and assessing the associated environmental risks is of major interest in environmental studies. This can be achieved by using complementary approaches based on the study of the molecular responses of organisms. Because of the known chemical pressures on the environment, regulations on the content of some chemicals, such as cadmium, have been mostly completed. In contrast, the environmental toxicity of rare earth elements (REEs), which are widely used in industry, has only recently begun to receive attention. Here, we investigated the effects of cadmium, and two REEs, samarium and gadolinium, on marine mussels under laboratory exposures. We found that after an 8-day exposure at 500 µg/L, the metals were bioaccumulated by the mussels. Furthermore, samarium and gadolinium affected two oxidative stress biomarkers, GST and SOD. Lipidomic analysis showed that lipid content was modulated by the REEs, but not by cadmium. Interestingly, several compounds belonging to the phosphoinositide metabolism were more abundant, suggesting a pro-mitotic or cell survival response, while a higher abundance of cardiolipins after samarium exposure suggested an alteration of mitochondrial activity. Moreover, depending on the tissue and the metal considered, transcriptional analyses revealed an effect on metallothionein, hsp70/90, energy metabolism enzymes, as well as pro-mitotic transcript accumulation. Thus, this study sheds a new light on metal toxicity and in particularl REEs by highlighting the accumulation and toxicity of cadmium, samarium and gadolinium at 500 µg/L at different molecular levels, from gene expression to the lipidome of blue mussels.

Temperature adaptation of yeast phospholipid molecular species at the acyl chain positional level

Yeast is a poikilothermic organism and adapts its lipid composition to the environmental temperature to maintain membrane physical properties. Studies addressing temperature-dependent adaptation of the lipidome have described changes in the phospholipid composition at the level of sum composition (e.g. PC 32:1) and molecular composition (e.g. PC 16:0_16:1). However, there is little information at the level of positional isomers (e.g. PC 16:0/16:1 versus PC 16:1/16:0). Here, we used collision- and ozone-induced dissociation (CID/OzID) mass spectrometry to investigate homeoviscous adaptation of PC, PE and PS to determine the phospholipid acyl chains at the sn-1 and sn-2 position. Our data establish the sn-molecular species composition of PC, PE and PS in the lipidome of yeast cultured at different temperatures.