Automated quantitative analysis of complex lipidomes by liquid chromatography/mass spectrometry

Alterations in LDL and HDL after an ischemic stroke associated with carotid atherosclerosis are reversed after 1 year

Approximately, 20% of ischemic strokes are attributed to the presence of atherosclerosis. Lipoproteins play a crucial role in the development of atherosclerosis, with LDL promoting atherogenesis and HDL inhibiting it. Therefore, both their concentrations and their biological properties are decisive factors in atherosclerotic processes. In this study, we examined the qualitative properties of lipoproteins in ischemic stroke patients with carotid atherosclerosis. Lipoproteins were isolated from the blood of healthy controls (n = 27) and patients with carotid atherosclerosis (n = 64) at 7 days and 1 year postischemic stroke. Compared to controls, patients' LDL 7 days poststroke showed increased levels of apoC-III, triacylglycerol, and ceramide, along with decreased cholesterol and phospholipid content. LDL from patients induced more inflammation in macrophages than did LDL from controls. HDL isolated from patients 7 days after stroke showed alterations in the apolipoprotein cargo, with reduced levels of apoA-I and increased levels of apoA-II, and apoC-III compared to controls. Patients' HDL also showed a higher electronegative charge than that of controls and partially lost its ability to counteract the modification of LDL and the inflammatory effects of modified LDL. One year after stroke onset, the composition of patients' LDL and HDL resembled those of the controls. In parallel, LDL and HDL gained positive charge, LDL became less prone to oxidation and aggregation, and HDL regained protective properties. In conclusion, LDL and HDL in ischemic stroke patients with carotid atherosclerosis exhibited alterations in composition and function, which were partially reversed 1 year after stroke.

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.

Direct Regulation of Hyperpolarization-Activated Cyclic-Nucleotide Gated (HCN1) Channels by Cannabinoids

Cannabinoids are a broad class of molecules that act primarily on neurons, affecting pain sensation, appetite, mood, learning, and memory. In addition to interacting with specific cannabinoid receptors (CBRs), cannabinoids can directly modulate the function of various ion channels. Here, we examine whether cannabidiol (CBD) and Δ9-tetrahydrocannabinol (THC), the most prevalent phytocannabinoids in Cannabis sativa, can regulate the function of hyperpolarization-activated cyclic-nucleotide-gated (HCN1) channels independently of CBRs. HCN1 channels were expressed in Xenopus oocytes since they do not express CBRs, and the effects of cannabinoid treatment on HCN1 currents were examined by a two-electrode voltage clamp. We observe opposing effects of CBD and THC on HCN1 current, with CBD acting to stimulate HCN1 function, while THC inhibited current. These effects persist in HCN1 channels lacking the cyclic-nucleotide binding domain (HCN1ΔCNBD). However, changes to membrane fluidity, examined by treating cells with TX-100, inhibited HCN1 current had more pronounced effects on the voltage-dependence and kinetics of activation than THC, suggesting this is not the primary mechanism of HCN1 regulation by cannabinoids. Our findings may contribute to the overall understanding of how cannabinoids may act as promising therapeutic molecules for the treatment of several neurological disorders in which HCN function is disturbed.

Novel Extraction Method for Combined Lipid and Metal Speciation From Caenorhabditis elegans With Focus on Iron Redox Status and Lipid Profiling

Parkinson´s disease progression is linked to iron redox status homeostasis via reactive oxygen species (ROS) formation, and lipids are the primary targets of ROS. The determination of iron redox status in vivo is challenging and requires specific extraction methods, which are so far tedious and very time-consuming. We demonstrated a novel, faster, and less laborious extraction method using the chelator ethylene glycol l-bis(β-aminoethyl ether)-N,N,N′,N′-tetra acetic acid (EGTA) as a stabilizing agent and synthetic quartz beads for homogenization under an argon atmosphere. Additionally, we combined the metal extraction with a well-established lipid extraction protocol using methyl-tert-butyl ether (MTBE) to avoid the problems of lipid precipitation in frozen samples and to determine lipid profiles and metal species from the same batch. The nonextractable matrix, such as the debris, is removed by centrifugation and digested to determine the total metal content of the sample as well. Lipid profiling using RP-LC–MS demonstrated high accordance of the modified extraction method to the reference method, and the organic solvent does not affect the iron redox status equilibrium. Furthermore, rigorous testing demonstrated the stability of the iron redox status equilibrium during the extraction process, secured by complexation, inert atmosphere, fast preparation, and immediately deep frozen extracts.

Metabolomics Data Treatment: Basic Directions of the Full Process

The present chapter describes basic aspects of the main steps for data processing on mass spectrometry-based metabolomics platforms, focusing on the main objectives and important considerations of each step. Initially, an overview of metabolomics and the pivotal techniques applied in the field are presented. Important features of data acquisition and preprocessing such as data compression, noise filtering, and baseline correction are revised focusing on practical aspects. Peak detection, deconvolution, and alignment as well as missing values are also discussed. Special attention is given to chemical and mathematical normalization approaches and the role of the quality control (QC) samples. Methods for uni- and multivariate statistical analysis and data pretreatment that could impact them are reviewed, emphasizing the most widely used multivariate methods, i.e., principal components analysis (PCA), partial least squares-discriminant analysis (PLS-DA), orthogonal partial least square-discriminant analysis (OPLS-DA), and hierarchical cluster analysis (HCA). Criteria for model validation and softwares used in data processing were also approached. The chapter ends with some concerns about the minimal requirements to report metadata in metabolomics.

Polar lipidomic profile shows Chlorococcum amblystomatis as a promising source of value-added lipids

There is a growing trend to explore microalgae as an alternative resource for the food, feed, pharmaceutical, cosmetic and fuel industry. Moreover, the polar lipidome of microalgae is interesting because of the reports of bioactive polar lipids which could foster new applications for microalgae. In this work, we identified for the first time the Chlorococcum amblystomatis lipidome using hydrophilic interaction liquid chromatography-high resolution electrospray ionization- tandem mass spectrometry (HILIC-HR-ESI-MS/MS). The Chlorococcum amblystomatis strain had a lipid content of 20.77% and the fatty acid profile, determined by gas chromatography-mass spectrometry, has shown that this microalga contains high amounts of omega-3 polyunsaturated fatty acids (PUFAs). The lipidome identified included 245 molecular ions and 350 lipid species comprising 15 different classes of glycolipids (6), phospholipids (7) and betaine lipids (2). Of these, 157 lipid species and the main lipid species of each class were esterified with omega-3 PUFAs. The lipid extract has shown antioxidant activity and anti-inflammatory potential. Lipid extracts also had low values of atherogenic (0.54) and thrombogenic index (0.27). In conclusion, the lipid extracts of Chlorococcum amblystomatis have been found to be a source of lipids rich in omega-3 PUFAs for of great value for the food, feed, cosmetic, nutraceutical and pharmaceutical industries.

Application of comprehensive lipidomics to biomarker research on adverse drug reactions

Lipidomics is a relatively new field of omics that focuses on lipids, one of the major categories of metabolites. Owing to their various functions, lipids are considered suitable targets for biomarker development; in addition, lipidomics analysis of adverse drug reactions (ADRs) has been conducted recently. In this review, I have summarized information on comprehensive lipidomics, which involves the analysis of global lipids in a non-targeted manner. Mass spectrometry-based platforms are currently the dominant lipidomics platform owing to their versatile features. I have also summarized the application of lipidomics in biomarker research on ADRs caused by therapeutic drugs in humans and rodents. Additionally, general concerns in and emerging approaches of lipidomics research on ADR have been highlighted. Although biomarkers identified using the lipidomics analysis of ADRs have not been qualified, reported candidates will be evaluated for clinical application. In addition, novel biomarker candidates will be developed via classical and new approaches exemplified in this review.

Seipin Facilitates Triglyceride Flow to Lipid Droplet and Counteracts Droplet Ripening via Endoplasmic Reticulum Contact

Seipin is an oligomeric integral endoplasmic reticulum (ER) protein involved in lipid droplet (LD) biogenesis. To study the role of seipin in LD formation, we relocalized it to the nuclear envelope and found that LDs formed at these new seipin-defined sites. The sites were characterized by uniform seipin-mediated ER-LD necks. At low seipin content, LDs only grew at seipin sites, and tiny, growth-incompetent LDs appeared in a Rab18-dependent manner. When seipin was removed from ER-LD contacts within 1 h, no lipid metabolic defects were observed, but LDs became heterogeneous in size. Studies in seipin-ablated cells and model membranes revealed that this heterogeneity arises via a biophysical ripening process, with triglycerides partitioning from smaller to larger LDs through droplet-bilayer contacts. These results suggest that seipin supports the formation of structurally uniform ER-LD contacts and facilitates the delivery of triglycerides from ER to LDs. This counteracts ripening-induced shrinkage of small LDs.

Quantification of Lipids: Model, Reality, and Compromise

Lipids are key molecules in various biological processes, thus their quantification is a crucial point in a lot of studies and should be taken into account in lipidomics development. This family is complex and presents a very large diversity of structures, so analyzing and quantifying all this diversity is a real challenge. In this review, the different techniques to analyze lipids will be presented: from nuclear magnetic resonance (NMR) to mass spectrometry (with and without chromatography) including universal detectors. First of all, the state of the art of quantification, with the definitions of terms and protocol standardization, will be presented with quantitative lipidomics in mind, and then technical considerations and limitations of analytical chemistry's tools, such as NMR, mass spectrometry and universal detectors, will be discussed, particularly in terms of absolute quantification.

Simultaneous non-polar and polar lipid analysis by on-line combination of HILIC, RP and high resolution MS

Given the chemical diversity of lipids and their biological relevance, suitable methods for lipid profiling and quantification are demanded to reduce sample complexity and analysis times. In this work, we present a novel on-line chromatographic method coupling hydrophilic interaction liquid chromatography (HILIC) dedicated to class-specific separation of polar lipid to reversed-phase chromatography (RP) for non-polar lipid analysis. More specifically, the void volume of the HILIC separation-consisting of non-polar lipids- is transferred to the orthogonal RP column enabling the on-line combination of HILIC with RP without any dilution in the second dimension. In this setup the orthogonal HILIC and RP separations were performed in parallel and the effluents of both columns were combined prior to high-resolution MS detection, offering the full separation space in one analytical run. Rapid separation for both polar and non-polar lipids within only 15 min (including reequilibration time) was enabled using sub-2 μm particles and UHPLC. The method proved to be robust with excellent retention time stability (RSDs < 1%) and LODs in the fmol to pmol (absolute on column) range even in the presence of complex biological matrix such as human plasma. The presented high-resolution LC-MS/MS method leads to class-specific separation of polar lipids and separation of non-polar lipids which is lost in conventional HILIC separations. HILIC-RP-MS is a promising tool for targeted and untargeted lipidomics workflows as three interesting features are combined namely (1) the decreased run time of state of the art shotgun MS methods, (2) the elevated linear dynamic range inherent to chromatographic separation and (3) increased level of identification by separation of polar and non-polar lipid classes.

Supercritical Fluid Chromatography as a Technique to Fractionate High-Valued Compounds from Lipids

Natural products are in high demand these days due to rising awareness among consumers. Healthy diets, especially those in emerging markets, growth in populations with nutritional deficiencies, and supporting government regulations provide high growth opportunities for these compounds. However, extraction of high-valued compounds from natural sources is not an easy task. Natural products are complex matrices, with relevant compounds present in small amounts and often mixed with other compounds of similar structures. Most of the applications are related to the pharmaceutical sector, but interest in food and natural products is growing fast. Lipid and carbohydrate extracts are examples of starting materials employed to purify these relevant compounds. At the same time supercritical fluid chromatography (SFC) is an emerging technique for preparative separation due to (1) use of supercritical fluids, commonly carbon dioxide, giving a large reduction in use of organic solvents; and (2) new hardware has been made commercially available recently that makes SFC a viable option. SFC fulfills high demands with respect to selectivity, versatility and sensibility. Fractionation or purification by SFC of high-valued compounds from natural sources is an interesting option, the relevance of which will increase in the future. This paper is a survey of trends and applications of SFC in the field of natural products purification.

Advances in metabolome information retrieval: turning chemistry into biology. Part II: biological information recovery

This work reports the second part of a review intending to give the state of the art of major metabolic phenotyping strategies. It particularly deals with inherent advantages and limits regarding data analysis issues and biological information retrieval tools along with translational challenges. This Part starts with introducing the main data preprocessing strategies of the different metabolomics data. Then, it describes the main data analysis techniques including univariate and multivariate aspects. It also addresses the challenges related to metabolite annotation and characterization. Finally, functional analysis including pathway and network strategies are discussed. The last section of this review is devoted to practical considerations and current challenges and pathways to bring metabolomics into clinical environments.

Lipidomic Analysis

The state-of-art in the lipidomic analysis is summarized here to provide the overview of available sample preparation strategies, mass spectrometry (MS)-based methods for the qualitative analysis of lipids, and the quantitative MS approaches for high-throughput clinical workflows. Major challenges in terms of widely accepted best practices for lipidomic analysis, nomenclature, and standards for data reporting are discussed as well.

Selection of internal standards for accurate quantification of complex lipid species in biological extracts by electrospray ionization mass spectrometry-What, how and why?

Lipidomics is rapidly expanding because of the great facilitation of recent advances in, and novel applications of, electrospray ionization mass spectrometry techniques. The greatest demands have been for successful quantification of lipid classes, subclasses, and individual molecular species in biological samples at acceptable accuracy. This review addresses the selection of internal standards in different methods for accurate quantification of individual lipid species. The principles of quantification with electrospray ionization mass spectrometry are first discussed to recognize the essentials for quantification. The basics of different lipidomics approaches are overviewed to understand the variables that need to be considered for accurate quantification. The factors that affect accurate quantification are extensively discussed, and the solutions to resolve these factors are proposed-largely through addition of internal standards. Finally, selection of internal standards for different methods is discussed in detail to address the issues of what, how, and why related to internal standards. We believe that thorough discussion of the topics related to internal standards should aid in quantitative analysis of lipid classes, subclasses, and individual molecular species and should have big impacts on advances in lipidomics. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:693-714, 2017.

Lipid profiling of complex biological mixtures by liquid chromatography/mass spectrometry using a novel scanning quadrupole data-independent acquisition strategy

RATIONALE

A novel data-independent acquisition method is detailed that incorporates a scanning quadrupole in front of an orthogonal acceleration time-of-flight (TOF) mass analyser. This approach is described and the attributes are compared and contrasted to other DIA approaches.

METHODS

Specific application of the method to both targeted and untargeted lipidomic identification strategies is discussed, with data from both shotgun and LC separated lipidomics experiments presented.

RESULTS

The benefits of the fast quadrupole scanning technique are highlighted, and include improvements in speed and specificity for complex mixtures providing high quality qualitative and quantitative data.

CONCLUSIONS

In particular the high specificity afforded by the scanning quadrupole improves qualitative information for lipid identification.

Simple and rapid biochemical method to synthesize labeled or unlabeled phosphatidylinositol species

Phosphatidylinositol (PI) is the precursor of many important signaling molecules in eukaryotic cells and, most probably, PI also has important functions in cellular membranes. However, these functions are poorly understood, which is largely due to that i) only few PI species with specific acyl chains are available commercially and ii) there are no simple methods to synthesize such species. Here, we present a simple biochemical protocol to synthesize a variety of labeled or unlabeled PI species from corresponding commercially available phosphatidylcholines. The protocol can be carried out in a single vial in a two-step process which employs three enzymatic reactions mediated by i) commercial phospholipase D from Streptomyces chromofuscus, ii) CDP-diacylglycerol synthase overexpressed in E. coli and iii) PI synthase of Arabidopsis thaliana ectopically expressed in E. coli The PI product is readily purified from the reaction mixture by liquid chromatography since E. coli does not contain endogenous PI or other coeluting lipids. The method allows one to synthesize and purify labeled or unlabeled PI species in 1 or 2 days.Typically, 40-60% of (unsaturated) PC was converted to PI albeit the final yield of PI was less (25-35%) due to losses upon purification.

Enrichment of resolving power improves ion-peak quantification on a lipidomics platform

In this study, we delineated the importance of MS resolving power on the ion-peak quantification of lipids using an Orbitrap Fusion instrument and established a liquid chromatography-based, high-performance lipidomics platform. The ion-peak recognition of several lipids in human plasma, such as LPC(15:0), LPE(22:5), and PC(35:0), was clearly improved by increasing the MS resolving power. In addition, we evaluated the impact of resolving power on the quantitative detection of lipids by automatic ion-peak recognition with calculation of the coefficient of variance (CV). The extracted ions obtained from human plasma were automatically annotated by Compound Discoverer software with manual confirmation of standards or MS²/MS³ fragments (class- and acyl side chain-specific ions and neutral losses). Quantitative evaluation of 499 lipids in human plasma in terms of their CV values clearly demonstrated an improvement in the quantitative performance by enriching the resolving power. Moreover, we evaluated our new lipidomics platform with enriched MS resolving power (setting of 240,000, full width at half maximum at m/z 200). Because automatic annotation by TraceFinder software overlooks several lipid ions, we further manually annotated additional lipid ions, which were confirmed by standards or MS²/MS³ fragments. Eventually, our platform detected 967 lipids encompassing 34 lipid classes, which were confirmed with standards or MS²/MS³ fragments. Of these lipids, 922 scored <20% of the CV values. Taken together, enriching the resolving power improved ion-peak quantification on our novel lipidomics platform, which enabled us to detect broad-spectrum lipids from human plasma.

Reporting of lipidomics data should be standardized

This article highlights, to our opinion, some of the most pertinent issues related to producing high quality lipidomics data. These issues include pitfalls related to sample collection and storage, lipid extraction, the use of shotgun and LC-MS-based lipidomics approaches, and the identification, annotation and quantification of lipid species. We hope that highlighting these issues will help stimulate efforts to implement reporting standards for dissemination of lipidomics data. This article is part of a Special Issue entitled: BBALIP_Lipidomics Opinion Articles edited by Sepp Kohlwein.

Recent advances in expanding the coverage of the lipidome

The lipidome comprises a large array of molecules with diverse physicochemical properties. Lipids are structural components of cells, act as a source of energy, and function as signaling mediators. Alterations in lipid metabolism are involved in the onset and progression of a variety of diseases, including metabolic syndrome and cancer. Because of this, interest in lipidomics, the comprehensive characterization of the lipidome by mass spectrometry, has intensified in recent years. However, obtaining a truly complete overview of all lipids in a sample has remained very challenging due to their enormous structural diversity. Here, we provide an overview of the collection of analytical approaches used to study various lipid classes, emphasizing innovations in sample preparation and liquid chromatography-mass spectrometry (LC-MS). Additionally, we provide practical suggestions for increasing the coverage of the lipidome.

Alterations in Serum Polyunsaturated Fatty Acids and Eicosanoids in Patients with Mild to Moderate Chronic Obstructive Pulmonary Disease (COPD)

Smoking is a major risk factor for several diseases including chronic obstructive pulmonary disease (COPD). To better understand the systemic effects of cigarette smoke exposure and mild to moderate COPD-and to support future biomarker development-we profiled the serum lipidomes of healthy smokers, smokers with mild to moderate COPD (GOLD stages 1 and 2), former smokers, and never-smokers (n = 40 per group) (ClinicalTrials.gov registration: NCT01780298). Serum lipidome profiling was conducted with untargeted and targeted mass spectrometry-based lipidomics. Guided by weighted lipid co-expression network analysis, we identified three main trends comparing smokers, especially those with COPD, with non-smokers: a general increase in glycero(phospho)lipids, including triglycerols; changes in fatty acid desaturation (decrease in ω-3 polyunsaturated fatty acids, and an increase in monounsaturated fatty acids); and an imbalance in eicosanoids (increase in 11,12- and 14,15-DHETs (dihydroxyeicosatrienoic acids), and a decrease in 9- and 13-HODEs (hydroxyoctadecadienoic acids)). The lipidome profiles supported classification of study subjects as smokers or non-smokers, but were not sufficient to distinguish between smokers with and without COPD. Overall, our study yielded further insights into the complex interplay between smoke exposure, lung disease, and systemic alterations in serum lipid profiles.

Lipid Regulation of Sodium Channels

The lipid landscapes of cellular membranes are complex and dynamic, are tissue dependent, and can change with the age and the development of a variety of diseases. Researchers are now gaining new appreciation for the regulation of ion channel proteins by the membrane lipids in which they are embedded. Thus, as membrane lipids change, for example, during the development of disease, it is likely that the ionic currents that conduct through the ion channels embedded in these membranes will also be altered. This chapter provides an overview of the complex regulation of prokaryotic and eukaryotic voltage-dependent sodium (Nav) channels by fatty acids, sterols, glycerophospholipids, sphingolipids, and cannabinoids. The impact of lipid regulation on channel gating kinetics, voltage-dependence, trafficking, toxin binding, and structure are explored for Nav channels that have been examined in heterologous expression systems, native tissue, and reconstituted into artificial membranes. Putative mechanisms for Nav regulation by lipids are also discussed.

Extraction, chromatographic and mass spectrometric methods for lipid analysis

Lipids make up a diverse subset of biomolecules that are responsible for mediating a variety of structural and functional properties as well as modulating cellular functions such as trafficking, regulation of membrane proteins and subcellular compartmentalization. In particular, phospholipids are the main constituents of biological membranes and play major roles in cellular processes like transmembrane signaling and structural dynamics. The chemical and structural variety of lipids makes analysis using a single experimental approach quite challenging. Research in the field relies on the use of multiple techniques to detect and quantify components of cellular lipidomes as well as determine structural features and cellular organization. Understanding these features can allow researchers to elucidate the biochemical mechanisms by which lipid-lipid and/or lipid-protein interactions take place within the conditions of study. Herein, we provide an overview of essential methods for the examination of lipids, including extraction methods, chromatographic techniques and approaches for mass spectrometric analysis.

Phospholipid analysis in sera of horses with allergic dermatitis and in matched healthy controls

Background

Lipids have become an important target for searching new biomarkers typical of different autoimmune and allergic diseases. The most common allergic dermatitis of the horse is related to stings of insects and is known as insect bite hypersensitivity (IBH) or summer eczema, referring to its recurrence during the summer months. This intense pruritus has certain similarities with atopic dermatitis of humans. The treatment of IBH is difficult and therefore new strategies for therapy are needed. Autoserum therapy based on the use of serum phospholipids has recently been introduced for horses. So far, serum lipids relating to these allergic disorders have been poorly determined. The main aim of this study was to analyse phospholipid profiles in the sera of horses with allergic dermatitis and in their healthy controls and to further assess whether these lipid profiles change according to the clinical status after therapy.

Methods

Sera were collected from 10 horses with allergic dermatitis and from 10 matched healthy controls both before and 4 weeks after the therapy of the affected horses. Eczema horses were treated with an autogenous preparation made from a horse’s own serum and used for oral medication. Samples were analysed for their phospholipid content by liquid chromatography coupled to a triple-quadrupole mass spectrometer (LC-MS). Data of phospholipid concentrations between the groups and over the time were analysed by using the Friedman test. Correlations between the change of concentrations and the clinical status were assessed by Spearman’s rank correlation test.

Results

The major phospholipid classes detected were phosphatidylcholine (PC), sphingomyelin (SM), phosphatidylinositol (PI) and phosphatidylethanolamine (PE). Eczema horses had significantly lower total concentrations of PC (p < 0.0001) and SM (p = 0.0115) than their healthy controls. After a 4-week therapy, no significant differences were found between the groups. Changes in SM concentrations correlated significantly with alterations in clinical signs (p = 0.0047).

Conclusions

Horses with allergic dermatitis have an altered phospholipid profile in their sera as compared with healthy horses and these profiles seem to change according to their clinical status. Sphingomyelin seems to have an active role in the course of equine insect bite hypersensitivity.

A2B5+/GFAP+ Cells of Rat Spinal Cord Share a Similar Lipid Profile with Progenitor Cells: A Comparative Lipidomic Study

The central nervous system (CNS) harbors multiple glial fibrillary acidic protein (GFAP) expressing cell types. In addition to the most abundant cell type of the CNS, the astrocytes, various stem cells and progenitor cells also contain GFAP+ populations. Here, in order to distinguish between two types of GFAP expressing cells with or without the expression of the A2B5 antigens, we performed lipidomic analyses on A2B5+/GFAP+ and A2B5-/GFAP+ cells from rat spinal cord. First, A2B5+/GFAP- progenitors were exposed to the leukemia inhibitory factor (LIF) or bone morphogenetic protein (BMP) to induce their differentiation to A2B5+/GFAP+ cells or A2B5-/GFAP+ astrocytes, respectively. The cells were then analyzed for changes in their phospholipid, sphingolipid or acyl chain profiles by mass spectrometry and gas chromatography. Compared to A2B5+/GFAP- progenitors, A2B5-/GFAP+ astrocytes contained higher amounts of ether phospholipids (especially the species containing arachidonic acid) and sphingomyelin, which may indicate characteristics of cellular differentiation and inability for multipotency. In comparison, principal component analyses revealed that the lipid composition of A2B5+/GFAP+ cells retained many of the characteristics of A2B5+/GFAP- progenitors, but their lipid profile was different from that of A2B5-/GFAP+ astrocytes. Thus, our study demonstrated that two GFAP+ cell populations have distinct lipid profiles with the A2B5+/GFAP+ cells sharing a phospholipid profile with progenitors rather than astrocytes. The progenitor cells may require regulated low levels of lipids known to mediate signaling functions in differentiated cells, and the precursor lipid profiles may serve as one measure of the differentiation capacity of a cell population.

Lipidomic analysis can distinguish between two morphologically similar strains of Nannochloropsis oceanica

The two morphologically similar microalgae NMBluh014 and NMBluh-X belong to two different strains of Nannochloropsis oceanica. They possess obviously different feeding effects on bivalves, but are indistinguishable by 18S rRNA and morphological features. In this work, lipidomic analysis followed by principal component analysis and orthogonal projections to latent structures discriminant analysis provided a clear distinction between these strains. Metabolites that definitively contribute to the classification were selected as potential biomarkers. The most important difference in polar lipids were sulfoquinovosyldiacylglycerol (containing 18:1/16:0 and 18:3/16:0) and monogalactosyldiacylglycerol (containing 18:3/16:3 and 20:5/14:0), which were detected only in NMBluh-X. Additionally, an exhaustive qualitative and quantitative profiling of the neutral lipid triacylglycerol (TAG) in the two strains was carried out. The predominant species of TAG containing 16:1/16:1/16:1 acyl groups was detected only in NMBluh-X with a content of ~93.67 ± 11.85 nmol · mg(-1) dry algae at the onset of stationary phase. Meanwhile, TAG containing 16:0/16:0/16:0 was the main TAG in NMBluh014 with a content of 40.25 ± 3.92 nmol · mg(-1) . These results provided the most straightforward evidence for differentiating the two species. The metabolomic profiling indicated that NMBluh-X underwent significant chemical and physiological changes during the growth process, whereas NMBluh014 did not show such noticeable time-dependent metabolite change. This study is the first using Ultra Performance Liquid Chromatography coupled with Electrospray ionization-Quadrupole-Time of Flight Mass Spectrometry (UPLC-Q-TOF-MS) for lipidomic profiling with multivariate statistical analysis to explore lipidomic differences of plesiomorphous microalgae. Our results demonstrate that lipidomic profiling is a valid chemotaxonomic tool in the study of microalgal systematics.

Substrate efflux propensity is the key determinant of Ca2+-independent phospholipase A-β (iPLAβ)-mediated glycerophospholipid hydrolysis

The A-type phospholipases (PLAs) are key players in glycerophospholipid (GPL) homeostasis and in mammalian cells; Ca(2+)-independent PLA-β (iPLAβ) in particular has been implicated in this essential process. However, the regulation of this enzyme, which is necessary to avoid futile competition between synthesis and degradation, is not understood. Recently, we provided evidence that the efflux of the substrate molecules from the bilayer is the rate-limiting step in the hydrolysis of GPLs by some secretory (nonhomeostatic) PLAs. To study whether this is the case with iPLAβ as well, a mass spectrometric assay was employed to determine the rate of hydrolysis of multiple saturated and unsaturated GPL species in parallel using micelles or vesicle bilayers as the macrosubstrate. With micelles, the hydrolysis decreased with increasing acyl chain length independent of unsaturation, and modest discrimination between acyl positional isomers was observed, presumably due to the differences in the structure of the sn-1 and sn-2 acyl-binding sites of the protein. In striking contrast, no significant discrimination between positional isomers was observed with bilayers, and the rate of hydrolysis decreased with the acyl chain length logarithmically and far more than with micelles. These data provide compelling evidence that efflux of the substrate molecule from the bilayer, which also decreases monotonously with acyl chain length, is the rate-determining step in iPLAβ-mediated hydrolysis of GPLs in membranes. This finding is intriguing as it may help to understand how homeostatic PLAs are regulated and how degradation and biosynthesis are coordinated.

Quantitative spatial analysis of the mouse brain lipidome by pressurized liquid extraction surface analysis

Here we describe a novel surface sampling technique termed pressurized liquid extraction surface analysis (PLESA), which in combination with a dedicated high-resolution shotgun lipidomics routine enables both quantification and in-depth structural characterization of molecular lipid species extracted directly from tissue sections. PLESA uses a sealed and pressurized sampling probe that enables the use of chloroform-containing extraction solvents for efficient in situ lipid microextraction with a spatial resolution of 400 μm. Quantification of lipid species is achieved by the inclusion of internal lipid standards in the extraction solvent. The analysis of lipid microextracts by nanoelectrospray ionization provides long-lasting ion spray which in conjunction with a hybrid ion trap-orbitrap mass spectrometer enables identification and quantification of molecular lipid species using a method with successive polarity shifting, high-resolution Fourier transform mass spectrometry (FTMS), and fragmentation analysis. We benchmarked the performance of the PLESA approach for in-depth lipidome analysis by comparing it to conventional lipid extraction of excised tissue homogenates and by mapping the spatial distribution and molar abundance of 170 molecular lipid species across different anatomical mouse brain regions.

Accurate mass searching of individual lipid species candidates from high-resolution mass spectra for shotgun lipidomics

RATIONALE

With the increased mass accuracy and resolution in commercialized mass spectrometers, new developments on shotgun lipidomics could be expected with increased speed, dynamic range, and coverage over lipid species and classes. However, we found that the major issue by using high mass accuracy/resolution instruments to search lipid species is the partial overlap between the two-(13) C-atom-containing isotopologue of a species M (i.e., M+2 isotopologue) and the ion of a species with one less double bond than M (assigned here as L). This partial overlap alone could cause a mass shift of the species L to the lower mass end up to 12 ppm around m/z 750 as well as significant peak broadening.

METHODS

We developed an approach for accurate mass searching by exploring one of the major features of shotgun lipidomics data that lipid species of a class are present in ion clusters where neighboring masses from different species differ by one or a few double bonds. In the approach, a mass-searching window of 18 ppm (from -15 to 3 ppm) was first searched for an entire group of species of a lipid class. Then accurate mass searching of the plus one (13)C isotopologue of individual species was used to eliminate the potential false positive.

RESULTS

The approach was extensively validated through comparing with the species determined by the multi-dimensional MS-based shotgun lipidomics platform. The newly developed strategy of accurate mass searching enables the overlapped L species to be identified and the corresponding peak intensities to be acquired.

CONCLUSIONS

We believe that this novel approach could substantially broaden the applications of high mass accurate/resolution mass spectrometry for shotgun lipidomics.

Development of an automated multi-injection shotgun lipidomics approach using a triple quadrupole mass spectrometer

Shotgun lipidomics is a well-suited approach to monitor lipid alterations due to its ability to scan for varying lipid types on a global, class and individual species level. However, the ability to perform high-throughput shotgun lipidomics has remained challenging due to time-consuming data processing and hardware limitations. To increase the throughput nature of shotgun lipidomics, an automated shotgun lipidomics approach is described utilizing conventional low flow gradient liquid chromatography (LC) analysis (post-injection) coupled with multiple sample injections per sample (on a lipid scan per injection basis). The proposed automated multi-injection approach resulted in a reproducible lipid scanning period of 2.5 min (in a 4.5 min total data acquisition period), thereby providing a sufficient scanning period for performing either mass spectrometric or tandem mass spectrometric analyses. In addition to being simple, robust and reproducible, this approach was also constructed to be cost-effective by using common LC instrumentation and customizable as the data acquisition period can be tailored to perform different scan types, period lengths and scan numbers. Combined with a strategy to create multiple lipid-specific aliquots per sample, the overall approach provides a simple and efficient platform to perform high-throughput lipid profiling.

Choline kinase beta is required for normal endochondral bone formation

BACKGROUND

Choline kinase has three isoforms encoded by the genes Chka and Chkb. Inactivation of Chka in mice results in embryonic lethality, whereas Chkb(-/-) mice display neonatal forelimb bone deformations.

METHODS

To understand the mechanisms underlying the bone deformations, we compared the biology and biochemistry of bone formation from embryonic to young adult wild-type (WT) and Chkb(-/-) mice.

RESULTS

The deformations are specific to the radius and ulna during the late embryonic stage. The radius and ulna of Chkb(-/-) mice display expanded hypertrophic zones, unorganized proliferative columns in their growth plates, and delayed formation of primary ossification centers. The differentiation of chondrocytes of Chkb(-/-) mice was impaired, as was chondrocyte proliferation and expression of matrix metalloproteinases 9 and 13. In chondrocytes from Chkb(-/-) mice, phosphatidylcholine was slightly lower than in WT mice whereas the amount of phosphocholine was decreased by approximately 75%. In addition, the radius and ulna from Chkb(-/-) mice contained fewer osteoclasts along the cartilage/bone interface.

CONCLUSIONS

Chkb has a critical role in the normal embryogenic formation of the radius and ulna in mice.

GENERAL SIGNIFICANCE

Our data indicate that choline kinase beta plays an important role in endochondral bone formation by modulating growth plate physiology.

A versatile ultra-high performance LC-MS method for lipid profiling

A new UPLC-based untargeted lipidomic approach using a qTOF hybrid mass spectrometer is introduced. The applied binary gradient enables separations of lipid species including constitutional isomeric compounds and low abundant lipid classes such as phosphatidic acid (PA). Addition of phosphoric acid to the solvents improves peak shapes for acidic phospholipids. MS(E) scans allow simultaneous acquisition of full scan data and collision induced fragmentation to improve identification of lipid classes and to obtain structural information. The method was used to investigate the lipidome of yeast.

Phosphatidylcholine metabolism and choline kinase in human osteoblasts

There is a paucity of information about phosphatidylcholine (PC) biosynthesis in bone formation. Thus, we characterized PC metabolism in both primary human osteoblasts (HOB) and human osteosarcoma MG-63 cells. Our results show that the CDP-choline pathway is the only de novo route for PC biosynthesis in both HOB and MG-63 cells. Both CK activity and CKα expression in MG-63 cells were significantly higher than those in HOB cells. Silencing of CKα in MG-63 cells had no significant effect on PC concentration but decreased the amount of phosphocholine by approximately 80%. The silencing of CKα also reduced cell proliferation. Moreover, pharmacological inhibition of CK activity impaired the mineralization capacity of MG-63 cells. Our data suggest that CK and its product phosphocholine are required for the normal growth and mineralization of MG-63 cells.

Application of stable isotopes to investigate the metabolism of fatty acids, glycerophospholipid and sphingolipid species

Nature provides an enormous diversity of lipid molecules that originate from various pathways. To gain insight into the metabolism and dynamics of lipid species, the application of stable isotope-labeled tracers combined with mass spectrometric analysis represents a perfect tool. This review provides an overview of strategies to track fatty acid, glycerophospholipid, and sphingolipid metabolism. In particular, the selection of stable isotope-labeled precursors and their mass spectrometric analysis is discussed. Furthermore, examples of metabolic studies that were performed in cell culture, animal and clinical experiments are presented.

Automated label-free quantification of metabolites from liquid chromatography-mass spectrometry data

Liquid chromatography coupled to mass spectrometry (LC-MS) has become a standard technology in metabolomics. In particular, label-free quantification based on LC-MS is easily amenable to large-scale studies and thus well suited to clinical metabolomics. Large-scale studies, however, require automated processing of the large and complex LC-MS datasets.

We present a novel algorithm for the detection of mass traces and their aggregation into features (i.e. all signals caused by the same analyte species) that is computationally efficient and sensitive and that leads to reproducible quantification results. The algorithm is based on a sensitive detection of mass traces, which are then assembled into features based on mass-to-charge spacing, co-elution information, and a support vector machine–based classifier able to identify potential metabolite isotope patterns. The algorithm is not limited to metabolites but is applicable to a wide range of small molecules (e.g. lipidomics, peptidomics), as well as to other separation technologies.

We assessed the algorithm's robustness with regard to varying noise levels on synthetic data and then validated the approach on experimental data investigating human plasma samples. We obtained excellent results in a fully automated data-processing pipeline with respect to both accuracy and reproducibility. Relative to state-of-the art algorithms, ours demonstrated increased precision and recall of the method. The algorithm is available as part of the open-source software package OpenMS and runs on all major operating systems.