Contemporary lipidomic analytics: opportunities and pitfalls

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.

Integrated lipidomic and transcriptomics to explore the effects of ethyl acetate extract of Herpetospermum pedunculosum on nonalcoholic fatty liver disease in mice

ETHNOPHARMACOLOGICAL RELEVANCE

Herpetospermum pedunculosum (Ser.) C.B. Clarke (HP), a traditional Tibetan medicine used to treat hepatobiliary diseases, was confirmed that lignans-enriched ethyl acetate extract of HP (EAHP) could alleviate the hepatic injury by modern pharmacological evidence. However, the effects and potential mechanisms of EAHP against nonalcoholic fatty liver disease (NAFLD) are still unknown.

AIM OF THE STUDY

To reveal the effects of EAHP on NAFLD and explore the potential mechanisms from the perspective of lipidomics and transcriptomics.

MATERIALS AND METHODS

UPLC‒Q-TOF‒MS analysis was carried out to investigate the chemical components of EAHP. A Choline-deficient, L-amino acid defined, high fat diet (CDAHFD) was used to establish a NAFLD mouse model. The anti-NAFLD effects of various dosages of EAHP were evaluated by biochemical indexes and histological analysis. Hepatic lipidomic and transcriptomic analysis and multiple bioinformatics methods were used to screen biomarkers and signaling pathways. The levels of the corresponding genes were verified by qPCR.

RESULTS

36 kinds of compounds were identified by UPLC‒Q-TOF‒MS analysis. Oral treatment with EAHP significantly decrease the liver index and the levels of ALT and AST in the serum. The measurements lipid content and Oil Red O staining results suggested that EAHP ameliorated lipid metabolism disorders by reducing the content of TG and LDL-C, increasing HDL-C in the liver. H&E staining and ELISA revealed that EAHP restored hepatic inflammatory infiltration and decrease the levels of IL-1β, IL-6, TNF-α, and increase IL-10 in the serum. Lipidomic analysis showed that EAHP could regulate CDAHFD-induced lipid metabolic disorder. The different lipid metabolites included TG, phosphatidyl choline (PC), diacylglycerol (DG), phosphatidylethanolamine (PE), phosphatidylinositol (PI), ceramide (Cer). Transcriptomic analysis revealed that Bmp8b, Nbl1, Rgma, Sphk1, Thbs1, and Ugt8a were important regulators, which were associated with TGF-β signaling pathway and sphingolipid metabolism. The expressions of above genes detected by were qPCR consistent with transcriptomic data.

CONCLUSIONS

The ameliorative effects of EAHP on NAFLD are potentially attributable to the regulation of sphingolipid metabolism and TGF-β signaling pathway, etc., which results in abnormal hepatic lipid metabolism and inflammatory response.

Serum lipid profiling reveals characteristic lipid signatures associated with stroke in patients with leukoaraiosis

Many lipid biomarkers of stroke have been identified, but the lipid metabolism in elderly patients with leukoaraiosis remains poorly understood. This study aims to explore lipid metabolic processes in stroke among leukoaraiosis patients, which could provide valuable insights for guiding future antithrombotic therapy. In a cohort of 215 individuals undergoing MRI, 13 stroke patients were matched with controls, and 48 stroke patients with leukoaraiosis were matched with 40 leukoaraiosis patients. Serum lipidomics was profiled using UPLC-TOF, and OPLS-DA was applied for metabolite identification. Partial Least Squares Path Model (PLS-PM) assessed pathway weights of novel metabolites in stroke risk, while linear regression explored correlations with clinical outcomes. Lipid profiling identified 168 distinct compounds. From these, 25 lipid molecules were associated with glycerolipid, glycerophospholipid, and sphingolipid metabolism. PLS-PM identified 12 key metabolites, including DG 36:4 (OR = 6.40) as a significant risk factor. Metabolites such as PE 38:5 and FA 16:1;O showed significant correlations with stroke in leukoaraiosis, particularly when the Fazekas score was ≥ 4. Twelve metabolites were identified as key factors in stroke incidence among leukoaraiosis patients. Lipid disturbances in glycerolipids and glycerophospholipids provide valuable insights for further studies on the progression from leukoaraiosis to stroke.

From big data to big insights: statistical and bioinformatic approaches for exploring the lipidome

The goal of lipidomic studies is to provide a broad characterization of cellular lipids present and changing in a sample of interest. Recent lipidomic research has significantly contributed to revealing the multifaceted roles that lipids play in fundamental cellular processes, including signaling, energy storage, and structural support. Furthermore, these findings have shed light on how lipids dynamically respond to various perturbations. Continued advancement in analytical techniques has also led to improved abilities to detect and identify novel lipid species, resulting in increasingly large datasets. Statistical analysis of these datasets can be challenging not only because of their vast size, but also because of the highly correlated data structure that exists due to many lipids belonging to the same metabolic or regulatory pathways. Interpretation of these lipidomic datasets is also hindered by a lack of current biological knowledge for the individual lipids. These limitations can therefore make lipidomic data analysis a daunting task. To address these difficulties and shed light on opportunities and also weaknesses in current tools, we have assembled this review. Here, we illustrate common statistical approaches for finding patterns in lipidomic datasets, including univariate hypothesis testing, unsupervised clustering, supervised classification modeling, and deep learning approaches. We then describe various bioinformatic tools often used to biologically contextualize results of interest. Overall, this review provides a framework for guiding lipidomic data analysis to promote a greater assessment of lipidomic results, while understanding potential advantages and weaknesses along the way.

Comprehensive analysis of phospholipid in milk and their biological roles as nutrients and biomarkers

Phospholipids (PL) have garnered significant attention due to their physiological activities. Milk and other dairy products are important dietary sources for humans and have been extensively used to analyze the presence of PL by various analytical techniques. In this paper, the analysis techniques of PL were reviewed with the eight trigrams of phospholipidomics and a comprehensive fingerprint of 1295 PLs covering 8 subclasses in milk and other dairy products, especially. Technology is the primary productive force. Based on phospholipidomics technology, we further review the relationship between the composition of PL and factors that may be involved in processing and experimental operation, and emphasized the significance of the biological role played by PL in dietary supplements and biomarkers (production, processing and clinical research), and providing the future research directions.

Clinical advances in analytical profiling of signature lipids: implications for severe non-communicable and neurodegenerative diseases

BACKGROUND

Lipids play key roles in numerous biological processes, including energy storage, cell membrane structure, signaling, immune responses, and homeostasis, making lipidomics a vital branch of metabolomics that analyzes and characterizes a wide range of lipid classes. Addressing the complex etiology, age-related risk, progression, inflammation, and research overlap in conditions like Alzheimer's Disease, Parkinson's Disease, Cardiovascular Diseases, and Cancer poses significant challenges in the quest for effective therapeutic targets, improved diagnostic markers, and advanced treatments. Mass spectrometry is an indispensable tool in clinical lipidomics, delivering quantitative and structural lipid data, and its integration with technologies like Liquid Chromatography (LC), Magnetic Resonance Imaging (MRI), and few emerging Matrix-Assisted Laser Desorption Ionization- Imaging Mass Spectrometry (MALDI-IMS) along with its incorporation into Tissue Microarray (TMA) represents current advances. These innovations enhance lipidomics assessment, bolster accuracy, and offer insights into lipid subcellular localization, dynamics, and functional roles in disease contexts.

AIM OF THE REVIEW

The review article summarizes recent advancements in lipidomic methodologies from 2019 to 2023 for diagnosing major neurodegenerative diseases, Alzheimer's and Parkinson's, serious non-communicable cardiovascular diseases and cancer, emphasizing the role of lipid level variations, and highlighting the potential of lipidomics data integration with genomics and proteomics to improve disease understanding and innovative prognostic, diagnostic and therapeutic strategies.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Clinical lipidomic studies are a promising approach to track and analyze lipid profiles, revealing their crucial roles in various diseases. This lipid-focused research provides insights into disease mechanisms, biomarker identification, and potential therapeutic targets, advancing our understanding and management of conditions such as Alzheimer's Disease, Parkinson's Disease, Cardiovascular Diseases, and specific cancers.

Plasma lipidomic profiling reveals six candidate biomarkers for the prediction of incident stroke in patients with hypertension

INTRODUCTION

The burden of stroke in patients with hypertension is very high, and its prediction is critical.

OBJECTIVES

We aimed to use plasma lipidomics profiling to identify lipid biomarkers for predicting incident stroke in patients with hypertension.

METHODS

This was a nested case-control study. Baseline plasma samples were collected from 30 hypertensive patients with newly developed stroke, 30 matched patients with hypertension, 30 matched patients at high risk of stroke, and 30 matched healthy controls. Lipidomics analysis was performed by ultrahigh-performance liquid chromatography-tandem mass spectrometry, and differential lipid metabolites were screened using multivariate and univariate statistical methods. Machine learning methods (least absolute shrinkage and selection operator, random forest) were used to identify candidate biomarkers for predicting stroke in patients with hypertension.

RESULTS

Co-expression network analysis revealed that the key molecular alterations of the lipid network in stroke implicate glycerophospholipid metabolism and choline metabolism. Six lipid metabolites were identified as candidate biomarkers by multivariate statistical and machine learning methods, namely phosphatidyl choline(40:3p)(rep), cholesteryl ester(20:5), monoglyceride(29:5), triglyceride(18:0p/18:1/18:1), triglyceride(18:1/18:2/21:0) and coenzyme(q9). The combination of these six lipid biomarkers exhibited good diagnostic and predictive ability, as it could indicate a risk of stroke at an early stage in patients with hypertension (area under the curve = 0.870; 95% confidence interval: 0.783-0.957).

CONCLUSIONS

We determined lipidomic signatures associated with future stroke development and identified new lipid biomarkers for predicting stroke in patients with hypertension. The biomarkers have translational potential and thus may serve as blood-based biomarkers for predicting hypertensive stroke.

Primary Prevention of Canine Atopic Dermatitis: Breaking the Cycle-A Narrative Review

Canine atopic dermatitis (cAD) is a common and distressing skin condition in dogs, affecting up to 30% of the canine population. It not only impacts their quality of life but also that of their owners. Like human atopic dermatitis (hAD), cAD has a complex pathogenesis, including genetic and environmental factors. Current treatments focus on managing clinical signs, but they can be costly and have limitations. This article emphasizes the importance of preventing cAD from developing in the first place. Understanding the role of the skin's protective barrier is crucial, as its dysfunction plays a vital role in both hAD and cAD. hAD prevention studies have shown promising results in enhancing the skin barrier, but more research is needed to support more robust conclusions. While hAD primary prevention is currently a focal point of intensive investigation in human medicine, research on cAD primary prevention remains under-researched and almost non-existent. Pioneering effective prevention strategies for cAD holds immense potential to enhance the quality of life for both dogs and their owners. Additionally, it bears the promise of a translational impact on human research. Hence, further exploration of this crucial topic is not only relevant but also timely and imperative, warranting support and encouragement.

Lipidomics in pathogenesis, progression and treatment of nonalcoholic steatohepatitis (NASH): Recent advances

Nonalcoholic fatty liver disease (NAFLD) is a chronic liver disease affecting up to 30% of the general adult population. NAFLD encompasses a histological spectrum ranging from pure steatosis to non-alcoholic steatohepatitis (NASH). NASH can progress to cirrhosis and is becoming the most common indication for liver transplantation, as a result of increasing disease prevalence and of the absence of approved treatments. Lipidomic readouts of liver blood and urine samples from experimental models and from NASH patients disclosed an abnormal lipid composition and metabolism. Collectively, these changes impair organelle function and promote cell damage, necro-inflammation and fibrosis, a condition termed lipotoxicity. We will discuss the lipid species and metabolic pathways leading to NASH development and progression to cirrhosis, as well as and those species that can contribute to inflammation resolution and fibrosis regression. We will also focus on emerging lipid-based therapeutic opportunities, including specialized proresolving lipid molecules and macrovesicles contributing to cell-to-cell communication and NASH pathophysiology.

Development and application of lipidomics for food research

Lipidomics is an emerging and promising omics derived from metabolomics to comprehensively analyze all of lipid molecules in biological matrices. The purpose of this chapter is to introduce the development and application of lipidomics for food research. First, three aspects of sample preparation are introduced: food sampling, lipid extraction, and transportation and storage. Second, five types of instruments for data acquisition are summarized: direct infusion-mass spectrometry (MS), chromatographic separation-MS, ion mobility-MS, MS imaging, and nuclear magnetic resonance spectroscopy. Third, data acquisition and analysis software are described for the lipidomics software development. Fourth, the application of lipidomics for food research is discussed such as food origin and adulteration analysis, food processing research, food preservation research, and food nutrition and health research. All the contents suggest that lipidomics is a powerful tool for food research based on its ability of lipid component profile analysis.

Identification of three potential novel biomarkers for early diagnosis of acute ischemic stroke via plasma lipidomics

INTRODUCTION

Acute ischemic stroke (AIS) accounts for the majority of all stroke, globally the second leading cause of death. Due to its rapid development after onset, its early diagnosis is crucial.

OBJECTIVES

We aim to identify potential highly reliable blood-based biomarkers for early diagnosis of AIS using quantitative plasma lipid profiling via a machine learning approach.

METHODS

Lipidomics was used for quantitative plasma lipid profiling, based on ultra-performance liquid chromatography tandem mass spectrometry. Our samples were divided into a discovery and a validation set, each containing 30 AIS patients and 30 health controls (HC). Differentially expressed lipid metabolites were screened based on the criteria VIP > 1, p < 0.05, and fold change > 1.5 or < 0.67. The least absolute shrinkage and selection operator (LASSO) and random forest algorithms in machine learning were used to select differential lipid metabolites as potential biomarkers.

RESULTS

Three key differential lipid metabolites, CarnitineC10:1, CarnitineC10:1-OH and Cer(d18:0/16:0), were identified as potential biomarkers for early diagnosis of AIS. The former two, associated with thermogenesis, were down-regulated, whereas the latter, associated with necroptosis and sphingolipd metabolism, was upregulated. Univariate and multivariate logistic regressions showed that these three lipid metabolites and the resulting diagnostic model exhibited a strong ability in discriminating between AIS patients and HCs in both the discovery and validation sets, with an area under the curve above 0.9.

CONCLUSIONS

Our work provides valuable information on the pathophysiology of AIS and constitutes an important step toward clinical application of blood-based biomarkers for diagnosing AIS.

Integrating metabolomics and lipidomics revealed a decrease in plasma fatty acids but an increase in triglycerides in children with drug-refractory epilepsy

OBJECTIVE

The drug-refractory epilepsy (DRE) in children is commonly observed but the underlying mechanisms remain elusive. We examined whether fatty acids (FAs) and lipids are potentially associated with the pharmacoresistance to valproic acid (VPA) therapy.

METHODS

This single-center, retrospective cohort study was conducted using data from pediatric patients collected between May 2019 and December 2019 at the Children's Hospital of Nanjing Medical University. Ninety plasma samples from 53 responders with VPA monotherapy (RE group) and 37 non-responders with VPA polytherapy (NR group) were collected. Non-targeted metabolomics and lipidomics analysis for those plasma samples were performed to compare the potential differences of small metabolites and lipids between the two groups. Plasma metabolites and lipids passing the threshold of variable importance in projection value >1, fold change >1.2 or <0.8, and p-value <0.05 were regarded as statistically different substances.

RESULTS

A total of 204 small metabolites and 433 lipids comprising 16 different lipid subclasses were identified. The well-established partial least squares-discriminant analysis (PLS-DA) revealed a good separation of the RE from the NR group. The FAs and glycerophospholipids status were significantly decreased in the NR group, but their triglycerides (TG) levels were significantly increased. The trend of TG levels in routine laboratory tests was in line with the lipidomics analysis. Meanwhile, cases from the NR group were characterized by a decreased level of citric acid and L-thyroxine, but with an increased level of glucose and 2-oxoglutarate. The top two enriched metabolic pathways involved in the DRE condition were biosynthesis of unsaturated FAs and linoleic acid metabolism.

SIGNIFICANCE

The results of this study suggested an association between metabolism of FAs and the medically intractable epilepsy. Such novel findings might propose a potential mechanism linked to the energy metabolism. Ketogenic acid and FAs supplementation might therefore be high-priority strategies for DRE management.

The Use of Non-targeted Lipidomics and Histopathology to Characterize the Neurotoxicity of Bifenthrin to Juvenile Rainbow Trout (Oncorhynchus mykiss)

Due to the detection frequencies and measured concentrations in surface water, the type I pyrethroid insecticide, bifenthrin, has been of particular concern within the Sacramento-San Joaquin Delta in California. Concentrations have been detected above levels previously reported to impair neuroendocrine function and induce neurotoxicity to several species of salmonids. Metabolomic and transcriptomic studies indicated impairment of cellular signaling within the brain of exposed animals and potential alteration of lipid metabolism. To better understand the potential impacts of bifenthrin on brain lipids, juvenile rainbow trout (Oncorhynchus mykiss) were exposed to mean bifenthrin concentrations of 28 or 48 ng/L for 14 days, and non-targeted lipidomic profiling in the brain was conducted. Brain tissue sections were also assessed for histopathological insult following bifenthrin treatment. Bifenthrin-exposed trout had a concentration-dependent decrease in the relative abundance of triglycerides (TGs) with levels of phosphatidylcholines (PCs) and phosphatidylethanolamines (PEs) significantly altered following 48 ng/L bifenthrin exposure. An increased incidence of histopathological lesions, such as focal hemorrhages and congestion of blood vessels, was noted in the brains of bifenthrin-treated animals, suggesting an association between altered lipid metabolism and neuronal cell structure and integrity.

New Cardiovascular Risk Assessment Techniques for Primary Prevention: JACC Review Topic of the Week

Risk factor-based models fail to accurately estimate risk in select populations, in particular younger individuals. A sizable number of people are also classified as being at intermediate risk, for whom the optimal preventive strategy could be more precise. Several personalized risk prediction tools, including coronary artery calcium scoring, polygenic risk scores, and metabolic risk scores may be able to improve risk assessment, pending supportive outcome data from clinical trials. Other tools may well emerge in the near future. A multidimensional approach to risk prediction holds the promise of precise risk prediction. This could allow for targeted prevention minimizing unnecessary costs and risks while maximizing benefits. High-risk individuals could also be identified early in life, creating opportunities to arrest the development of nascent coronary atherosclerosis and prevent future clinical events.

Plasma Quantitative Lipid Profiles: Identification of CarnitineC18:1-OH, CarnitineC18:2-OH and FFA (20:1) as Novel Biomarkers for Pre-warning and Prognosis in Acute Myocardial Infarction

This study was aimed to determine the association between potential plasma lipid biomarkers and early screening and prognosis of Acute myocardial infarction (AMI). In the present study, a total of 795 differentially expressed lipid metabolites were detected based on ultra-performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS). Out of these metabolites, 25 lipid metabolites were identified which showed specifical expression in the AMI group compared with the healthy control (HC) group and unstable angina (UA) group. Then, we applied the least absolute shrinkage and selection operator (LASSO) and support vector machine-recursive feature elimination (SVM-RFE) methods to obtain three lipid molecules, including CarnitineC18:1-OH, CarnitineC18:2-OH and FFA (20:1). The three lipid metabolites and the diagnostic model exhibited well predictive ability in discriminating between AMI patients and UA patients in both the discovery and validation sets with an area under the curve (AUC) of 0.9. Univariate and multivariate logistic regression analyses indicated that the three lipid metabolites may serve as potential biomarkers for diagnosing AMI. A subsequent 1-year follow-up analysis indicated that the three lipid biomarkers also had prominent performance in predicting re-admission of patients with AMI due to cardiovascular events. In summary, we used quantitative lipid technology to delineate the characteristics of lipid metabolism in patients with AMI, and identified potential early diagnosis biomarkers of AMI via machine learning approach.

Changes in the Cerebrospinal Fluid and Plasma Lipidome in Patients with Rett Syndrome

Rett syndrome (RTT) is defined as a rare disease caused by mutations of the methyl-CpG binding protein 2 (MECP2). It is one of the most common causes of genetic mental retardation in girls, characterized by normal early psychomotor development, followed by severe neurologic regression. Hitherto, RTT lacks a specific biomarker, but altered lipid homeostasis has been found in RTT model mice as well as in RTT patients. We performed LC-MS/MS lipidomics analysis to investigate the cerebrospinal fluid (CSF) and plasma composition of patients with RTT for biochemical variations compared to healthy controls. In all seven RTT patients, we found decreased CSF cholesterol levels compared to age-matched controls (n = 13), whereas plasma cholesterol levels were within the normal range in all 13 RTT patients compared to 18 controls. Levels of phospholipid (PL) and sphingomyelin (SM) species were decreased in CSF of RTT patients, whereas the lipidomics profile of plasma samples was unaltered in RTT patients compared to healthy controls. This study shows that the CSF lipidomics profile is altered in RTT, which is the basis for future (functional) studies to validate selected lipid species as CSF biomarkers for RTT.

A new update of MALDI-TOF mass spectrometry in lipid research

Matrix-assisted laser desorption and ionization (MALDI) mass spectrometry (MS) is an indispensable tool in modern lipid research since it is fast, sensitive, tolerates sample impurities and provides spectra without major analyte fragmentation. We will discuss some methodological aspects, the related ion-forming processes and the MALDI MS characteristics of the different lipid classes (with the focus on glycerophospholipids) and the progress, which was achieved during the last ten years. Particular attention will be given to quantitative aspects of MALDI MS since this is widely considered as the most serious drawback of the method. Although the detailed role of the matrix is not yet completely understood, it will be explicitly shown that the careful choice of the matrix is crucial (besides the careful evaluation of the positive and negative ion mass spectra) in order to be able to detect all lipid classes of interest. Two developments will be highlighted: spatially resolved Imaging MS is nowadays well established and the distribution of lipids in tissues merits increasing interest because lipids are readily detectable and represent ubiquitous compounds. It will also be shown that a combination of MALDI MS with thin-layer chromatography (TLC) enables a fast spatially resolved screening of an entire TLC plate which makes the method competitive with LC/MS.

Clinical lipidomics: realizing the potential of lipid profiling

Dysregulation of lipid metabolism plays a major role in the etiology and sequelae of inflammatory disorders, cardiometabolic and neurological diseases, and several forms of cancer. Recent advances in lipidomic methodology allow comprehensive lipidomic profiling of clinically relevant biological samples, enabling researchers to associate lipid species and metabolic pathways with disease onset and progression. The resulting data serve not only to advance our fundamental knowledge of the underlying disease process but also to develop risk assessment models to assist in the diagnosis and management of disease. Currently, clinical applications of in-depth lipidomic profiling are largely limited to the use of research-based protocols in the analysis of population or clinical sample sets. However, we foresee the development of purpose-built clinical platforms designed for continuous operation and clinical integration-assisting health care providers with disease risk assessment, diagnosis, and monitoring. Herein, we review the current state of clinical lipidomics, including the use of research-based techniques and platforms in the analysis of clinical samples as well as assays already available to clinicians. With a primary focus on MS-based strategies, we examine instrumentation, analysis techniques, statistical models, prospective design of clinical platforms, and the possible pathways toward implementation of clinical lipidomics.

Recent advances in analytical strategies for mass spectrometry-based lipidomics

Lipids are vital biological molecules and play multiple roles in cellular function of mammalian organisms such as cellular membrane anchoring, signal transduction, material trafficking and energy storage. Driven by the biological significance of lipids, lipidomics has become an emerging science in the field of omics. Lipidome in biological systems consists of hundreds of thousands of individual lipid molecules that possess complex structures, multiple categories, and diverse physicochemical properties assembled by different combinations of polar headgroups and hydrophobic fatty acyl chains. Such structural complexity poses a huge challenge for comprehensive lipidome analysis. Thanks to the great innovations in chromatographic separation techniques and the continuous advances in mass spectrometric detection tools, analytical strategies for lipidomics have been highly diversified so that the depth and breadth of lipidomics have been greatly enhanced. This review will present the current state of mass spectrometry-based analytical strategies including untargeted, targeted and pseudotargeted lipidomics. Recent typical applications of lipidomics in biomarker discovery, pathogenic mechanism and therapeutic strategy are summarized, and the challenges facing to the field of lipidomics are also discussed.

The adaptation of lipid profile of human fibroblasts to alginate 2D films and 3D printed scaffolds

BACKGROUND

The investigation of the interactions between cells and active materials is pivotal in the emerging 3D printing-biomaterial application fields. Here, lipidomics has been used to explore the early impact of alginate (ALG) hydrogel architecture (2D films or 3D printed scaffolds) and the type of gelling agent (CaCl₂ or FeCl₃) on the lipid profile of human fibroblasts.

METHODS

2D and 3D ALG scaffolds were prepared and characterized in terms of water content, swelling, mechanical resistance and morphology before human fibroblast seeding (8 days). Using a liquid chromatography-triple quadrupole-tandem mass spectrometry approach, selected ceramides (CER), lysophosphatidylcholines (LPC), lysophosphatidic acids (LPA) and free fatty acids (FFA) were analyzed.

RESULTS

The results showed a clear alteration in the CER expression profile depending of both the geometry and the gelling agent used to prepare the hydrogels. As for LPCs, the main parameter affecting their distribution is the scaffold architecture with a significant decrease in the relative expression levels of the species with higher chain length (C20 to C22) for 3D scaffolds compared to 2D films. In the case of FFAs and LPAs only slight differences were observed as a function of scaffold geometry or gelling agent.

CONCLUSIONS

Variations in the cell membrane lipid profile were observed for 3D cell cultures compared to 2D and these data are consistent with activation processes occurring through the mutual interactions between fibroblasts and ALG support. These unknown physiologically relevant changes add insights into the discussion about the relationship between biomaterial and the variations of cell biological functions.

Ecotoxico-lipidomics: An emerging concept to understand chemical-metabolic relationships in comparative fish models

Lipids play an essential role in development, homeostatic functions, immune signaling, reproduction, and growth. Although it is evident that changes in lipid biosynthesis and metabolism can affect organismal physiology, few studies have determined how environmental stressors affect lipid pathways, let alone alter global lipid profiles in fish. This is a significant research gap, as a number of environmental contaminants interact with lipid signaling and metabolic pathways. In this review, we highlight the utility of lipidomics as a tool in environmental toxicology, discussing the current state of knowledge regarding chemical-lipidomic perturbations. As with most oviparous animals, the processing and storage of lipids during oocyte development is also particularly important for embryogenesis in fish. Using largemouth bass (Micropterus salmoides) as an example, transcriptomics data suggest that various chemicals alter lipid metabolism and regulation, highlighting the need for more sophisticated investigations into how toxicants impact lipid responses. We also point out the challenges ahead; these include a lack of understanding about lipid processing and signaling in fish, tissue and species-specific lipid composition, and extraneous factors (e.g., nutrition, temperature) that confound interpretation. For example, toxicant exposure can lead to oxidative stress and lipid peroxidation, resulting in complex lipid byproducts that are challenging to measure. With the emergence of lipidomics in systems toxicology, multi-omics approaches are expected to more clearly define effects on physiology, creating stronger linkages between multiple molecular entities (gene-protein-lipid/metabolite). The development and implementation of novel technologies such as ion mobility-mass spectrometry and ozone-induced dissociation support the complete structural elucidation of lipid molecules. This has implications in the adverse outcome pathway framework, which will enhance the application of lipidomics in toxicology by linking these molecular changes to effects at higher levels of biological organization.

Nontargeted lipidomics of novel human plasma reference materials: hypertriglyceridemic, diabetic, and African-American

The unavailability of appropriate quality assurance/quality control materials in many lipidomics applications poses a significant challenge for lipidomics research. It is recommended that samples with certified values and/or consensus estimates, such as NIST SRM 1950-Metabolites in Frozen Human Plasma, be implemented in routine analyses to enable community-wide comparisons of lipidomics results and analytical workflows. Herein, we applied a nontargeted lipidomics method for the analysis of a new human plasma reference material suite developed by NIST (hypertriglyceridemic, diabetic, and African-American plasma pools), in addition to SRM 1950. We identified specific lipidomics fingerprints associated with each sample type, including lauric acid-containing lipids and elevated triacylglycerol levels in hypertriglyceridemic plasma, palmitoleic acid-containing lipids in diabetic plasma, and oxidized fatty acid-containing phospholipids in African-American plasma. This work highlights the importance of developing and profiling application-specific reference materials, while establishing reference data that may be used for system suitability and/or quality control metrics.Graphical abstract.

Mass spectrometry-based lipidomics in food science and nutritional health: A comprehensive review

With the advance in science and technology as well as the improvement of living standards, the function of food is no longer just to meet the needs of survival. Food science and its associated nutritional health issues have been increasingly debated. Lipids, as complex metabolites, play a key role both in food and human health. Taking advantages of mass spectrometry (MS) by combining its high sensitivity and accuracy with extensive selective determination of all lipid classes, MS-based lipidomics has been employed to resolve the conundrum of addressing both qualitative and quantitative aspects of high-abundance and low-abundance lipids in complex food matrices. In this review, we systematically summarize current applications of MS-based lipidomics in food field. First, common MS-based lipidomics procedures are described. Second, the applications of MS-based lipidomics in food science, including lipid composition characterization, adulteration, traceability, and other issues, are discussed. Third, the application of MS-based lipidomics for nutritional health covering the influence of food on health and disease is introduced. Finally, future research trends and challenges are proposed. MS-based lipidomics plays an important role in the field of food science, promoting continuous development of food science and integration of food knowledge with other disciplines. New methods of MS-based lipidomics have been developed to improve accuracy and sensitivity of lipid analysis in food samples. These developments offer the possibility to fully characterize lipids in food samples, identify novel functional lipids, and better understand the role of food in promoting healt.

Administration of Exogenous Melatonin Improves the Diurnal Rhythms of the Gut Microbiota in Mice Fed a High-Fat Diet

The gut microbiota is strongly shaped by a high-fat diet, and obese humans and animals are characterized by low gut microbial diversity and impaired gut microbiota compositions. Comprehensive data on mammalian gut metagenomes shows gut microbiota exhibit circadian rhythms, which is disturbed by a high-fat diet. On the other hand, melatonin is a natural and ubiquitous molecule showing multiple mechanisms of regulating the circadian clock and lipid metabolism, while the role of melatonin in the regulation of the diurnal patterns of gut microbial structure and function in obese animals is not yet known. This study delineates an intricate picture of melatonin-gut microbiota circadian rhythms and may provide insight for obesity intervention.

Melatonin, a circadian hormone, has been reported to improve host lipid metabolism by reprogramming the gut microbiota, which also exhibits rhythmicity in a light/dark cycle. However, the effect of the administration of exogenous melatonin on the diurnal variation in the gut microbiota in mice fed a high-fat diet (HFD) is unclear. Here, we further confirmed the antiobesogenic effect of melatonin on mice fed an HFD for 2 weeks. Samples were collected every 4 h within a 24-h period, and diurnal rhythms of clock gene expression (Clock, Cry1, Cry2, Per1, and Per2) and serum lipid indexes varied with diurnal time. Notably, Clock and triglycerides (TG) showed a marked rhythm in the control in melatonin-treated mice but not in the HFD-fed mice. The rhythmicity of these parameters was similar between the control and melatonin-treated HFD-fed mice compared with that in the HFD group, indicating an improvement caused by melatonin in the diurnal clock of host metabolism in HFD-fed mice. Moreover, 16S rRNA gene sequencing showed that most microbes exhibited daily rhythmicity, and the trends were different for different groups and at different time points. We also identified several specific microbes that correlated with the circadian clock genes and serum lipid indexes, which might indicate the potential mechanism of action of melatonin in HFD-fed mice. In addition, effects of melatonin exposure during daytime or nighttime were compared, but a nonsignificant difference was noticed in response to HFD-induced lipid dysmetabolism. Interestingly, the responses of microbiota-transplanted mice to HFD feeding also varied at different transplantation times (8:00 and 16:00) and with different microbiota donors. In summary, the daily oscillations in the expression of circadian clock genes, serum lipid indexes, and the gut microbiota appeared to be driven by short-term feeding of an HFD, while administration of exogenous melatonin improved the composition and diurnal rhythmicity of some specific gut microbiota in HFD-fed mice.

IMPORTANCE The gut microbiota is strongly shaped by a high-fat diet, and obese humans and animals are characterized by low gut microbial diversity and impaired gut microbiota compositions. Comprehensive data on mammalian gut metagenomes shows gut microbiota exhibit circadian rhythms, which is disturbed by a high-fat diet. On the other hand, melatonin is a natural and ubiquitous molecule showing multiple mechanisms of regulating the circadian clock and lipid metabolism, while the role of melatonin in the regulation of the diurnal patterns of gut microbial structure and function in obese animals is not yet known. This study delineates an intricate picture of melatonin-gut microbiota circadian rhythms and may provide insight for obesity intervention.

Pulsatilla Decoction Can Treat the Dampness-Heat Diarrhea Rat Model by Regulating Glycerinphospholipid Metabolism Based Lipidomics Approach

Ethnopharmacological Relevance

Diarrhea is a major medical problem in clinical practice. According to the theory of traditional Chinese medicine (TCM), different types of diarrhea should be treated with different TCM formulations based on the targeted medical condition. Dampness-heat diarrhea (DHD) is a serious diarrheal disease and Pulsatilla decoction (PD), a TCM, has been found effective against DHD.

Objective

The aim of this study was to clarify the mechanism of action of PD in DHD using an untargeted lipidomics strategy.

Materials and Methods

Wistar rats were randomized to four groups, including the control group, model group, PD groups and self-healing group. The PD groups were given a daily intragastric gavage of PD at doses of 3.76 g/kg. The rat model of DHD established by such complex factors as high-sugar and high-fat diet, improper diet, high temperature and humidity environment, drinking and intraperitoneal injection of Escherichia coli., which imitated the inducing conditions of DHD. Then the clinical symptoms and signs, blood routine, serum inflammatory cytokines levels and the histopathological changes of main organs were detected and observed to evaluate DHD model and therapeutic effect of PD. Lipid biomarkers of DHD were selected by comparing the control and model groups with the colon lipidomics technology and an ultra-high performance liquid chromatography (UHPLC) coupled with Q Exactive plus mass analyzer. Multivariate statistical analysis and pattern recognition were employed to examine different lipids within the colon of PD-treated rats.

Results

The clinical symptoms and signs of the model rats were consistent with the diagnostic criteria of DHD. After treatment with PD, the clinical symptoms and signs of the rats with DHD were improved; the indexes of blood routine and inflammatory cytokines levels tended to be normal. The lipidomics profile of the model group were evidently disordered when compared to the control group. A total of 42 significantly altered lipids between the model-control groups were identified by multivariate statistical analysis. DHD may result from such lipid disorders which are related to glycerophospholipid metabolism, arachidonic acid (AA) metabolism, and sphingolipid metabolism. After PD treatment, the lipidomic profiles of the disorders tended to recover when compared to the model group. Twenty lipid molecules were identified and some glycerophospholipids and AA levels returned close to the normal level.

Conclusion

Glycerophospholipid metabolism may play an important role in the treatment of dampness-heat induced diarrhea using PD.

Platelet lipidome: Dismantling the "Trojan horse" in the bloodstream

The platelet-lipid chapter in the story of atherothrombosis is an old one, recapitulated and revised in many contexts. For decades several stimulating facets have been added to it, both unraveling and increasing the perplexity of platelet-lipid interplay and its pathophysiological consequences. The recent paradigm shift in our perspective has evolved with lipidomic analysis of the intraplatelet compartment and platelet releasate. These investigations have disclosed that platelets are in constant interaction with circulatory lipids, often reflected in their lipid repertoire. In addition, they offer a shielded intracellular space for oxidative lipid metabolism generating "toxic" metabolites that escape degradation by plasma lipases and antioxidant defense, circulate undetected by conventional plasma lipid profile, and deposited at atherosclerotic lesions or thrombus. Lipidomics divulges this silent invader in platelet vehicles, thereby providing potential biomarkers of pathologic manifestations and therapeutic targets to be exploited, which is surmised in this review.

MALDI MS Analysis to Investigate the Lipid Composition of Sperm

Background:

The sperm plasma membrane meets the requirements of sperm transit through the female genital tract and subsequent fertilization. Commonly, the (phospho)lipid composition of sperm is characterized by tremendous amounts of highly unsaturated fatty acyl residues such as docosahexaenoic and docosapentaenoic acid. While human sperm contain almost exclusively diacyl lipids, many animal sperm additionally contain significant amounts of ether lipids such as alkylacyl- and alkenyl-acyl lipids (plasmalogens).

Hypothesis/Objective:

It is suggested that deviations from the typical lipid composition are indicative of pathological changes. Therefore, simple methods to elucidate the sperm lipid composition are essential.

Method:

Matrix-assisted laser desorption and ionization (MALDI) mass spectrometry (MS) is a fast and simple method. Since the selection of the most suitable matrix is a crucial step in MALDI MS, this topic will be highlighted. It will also be shown that MALDI MS can be easily combined with thin-layer chromatography to overcome ion suppression effects.

Results:

The lipid composition of sperm from different species can be elucidated by MALDI MS. However, different matrix compounds have to be used to record positive and negative ion mass spectra. Since some sperm (glyco)lipids are characterized by the presence of sulfate residues which suppress the detection of less acidic lipids in the negative ion mode, previous separation is often necessary. It will be also emphasized that plasmalogens can be easily identified by either enzymatic digestion or treatment with acids.

Conclusion:

MALDI MS is a reliable method to obtain sperm lipid fingerprints in a simple and convenient way.

Recent Developments of Useful MALDI Matrices for the Mass Spectrometric Characterization of Lipids

Matrix-assisted laser desorption/ionization (MALDI) is one of the most successful “soft” ionization methods in the field of mass spectrometry and enables the analysis of a broad range of molecules, including lipids. Although the details of the ionization process are still unknown, the importance of the matrix is commonly accepted. Both, the development of and the search for useful matrices was, and still is, an empirical process, since properties like vacuum stability, high absorption at the laser wavelength, etc. have to be fulfilled by a compound to become a useful matrix. This review provides a survey of successfully used MALDI matrices for the lipid analyses of complex biological samples. The advantages and drawbacks of the established organic matrix molecules (cinnamic or benzoic acid derivatives), liquid crystalline matrices, and mixtures of common matrices will be discussed. Furthermore, we will deal with nanocrystalline matrices, which are most suitable to analyze small molecules, such as free fatty acids. It will be shown that the analysis of mixtures and the quantitative analysis of small molecules can be easily performed if the matrix is carefully selected. Finally, some basic principles of how useful matrix compounds can be “designed” de novo will be introduced.