Two-dimensional analysis of phospholipids by capillary liquid chromatography/electrospray ionization mass spectrometry

Identification of oxygenated triacylglycerols in pistachio nuts' lipids by reverse-phase high-resolution-liquid chromatography-ESI mass spectrometry

Hydroxy- and peroxy-triacylglycerols are common products of lipid peroxidation formed during oil storage or heating or as enzymatic oxidation product of arachidonic acid as signaling molecules in mammals. In this study, oxygenated triacylglycerides (TAG) were identified in pistachio oil based on reverse phase(RP), high-performance liquid chromatography coupled with electrospray ionization and mass spectrometry (HPLC- ESI -MS). 20 novel lipid plant metabolites, classified based on their fragment spectra into a hydroxy (TAG-OH), an epoxy (TAG-O), and hydroperoxide (TAG-OOH) groups. We believe that this class of compounds has been for the first time observed as genuine secondary plant metabolites in a natural source in this case pistachio lipids of dietary relevance.

Investigating the Potential of Lipids for Use as Biomarkers for Glioblastoma via an Untargeted Lipidomics Approach

OBJECTIVE

The types and functions of lipids involved in glioblastoma (GB) are not well known. Lipidomics is a new field that examines cellular lipids on a large scale and novel aplication of lipidomics in the biomedical sciences have emerged. This study aimed to investigate the potential of blood lipids for use as biomarkers for the diagnosis of GB via untargated lipidomic approach. Gaining a deeper understanding of lipid metabolism in patients with GB can contribute to the early diagnosis with GB patiens and also development of novel and better therapeutic options.

METHODS

This study was performed using blood samples collected from 14 patients (eight females and six males) and 14 controls (eight females and six males). Lipids were extracted from blood samples and quantified using phosphorus assay. Lipid profiles of between patients with GB and controls were compared via an untargeted lipidomics approach using 6530 Accurate-Mass Q-TOF LC/MS mass spectrometer.

RESULTS

According to the results obtained using the untargeted lipidomics approach, differentially regulated lipid species, including fatty acid (FA), glycerolipid (GL), glycerophospholipid (PG), saccharolipid (SL), sphingolipid (SP), and sterol lipid (ST) were identified between in patients with GB and controls.

CONCLUSION

Differentially regulated lipids were identified in patients with GB, and these lipid species were predicted as potential biomarkers for diagnosis of GB.

Optimisation of high-speed lipidome analysis by nanoflow ultrahigh-performance liquid chromatography-tandem mass spectrometry: Application to identify candidate biomarkers for four different cancers

Lipid analysis is a powerful tool that can elucidate the pathogenic roles of lipids in metabolic diseases, and facilitate the development of potential biomarkers. Lipid analysis by large-scale lipidomics requires a high-speed and high-throughput analytical platform. In the present study, a high-speed analytical method for lipid analysis using nanoflow ultrahigh-performance liquid chromatography-electrospray ionisation-tandem mass spectrometry (nUHPLC-ESI-MS/MS) was optimised by investigating the effects of column flow rate, pump flow rate, dwell time, initial binary mobile phase composition, and gradient duration on the separation efficiency of standard lipid mixtures. The minimum gradient time for high-speed lipid separation was determined by examining the time-based separation efficiency and spectral overlap of isobaric lipid species during selected reaction monitoring-based quantification of sphingomyelin and a second isotope of phosphatidylcholine, which differ in molecular weight by only 1 Da. Finally, the optimised nUHPLC-ESI-MS/MS method was applied to analyse 200 plasma samples from patients with liver, gastric, lung, and colorectal cancer to evaluate its performance by measuring previously identified candidate lipid biomarkers. About 73% of the reported marker candidates (6 out of 7 in liver, 5/9 in gastric, 4/6 in lung, and 6/7 in colorectal cancer) could be assigned using the optimised method, supporting its use for high-throughput lipid analysis.

High-coverage lipidomics for functional lipid and pathway analyses

Rapid advances in front-end separation approaches and analytical technologies have accelerated the development of lipidomics, particularly in terms of increasing analytical coverage to encompass an expanding repertoire of lipids within a single analytical approach. Developments in lipid pathway analysis, however, have somewhat lingered behind, primarily due to (1) the lack of coherent alignment between lipid identifiers in common databases versus that generated from experiments, owing to the differing structural resolution of lipids at molecular level that is specific to the analytical approaches adopted by various laboratories; (2) the immense complexity of lipid metabolic relationships that may entail head group changes, fatty acyls modifications of various forms (e.g. elongation, desaturation, oxidation), as well as active remodeling that demands a multidimensional, panoramic view to take into account all possibilities in lipid pathway analyses. Herein, we discuss current efforts undertaken to address these challenges, as well as alternative form of "pathway analyses" that may be particularly useful for uncovering functional lipid interactions under different biological contexts. Consolidating lipid pathway analyses will be indispensable in facilitating the transition of lipidomics from its prior role of phenotype validation to a hypothesis-generating tool that uncovers novel molecular targets to drive downstream mechanistic pursuits under biomedical settings.

Lipid alterations in the skeletal muscle tissues of mice after weight regain by feeding a high-fat diet using nanoflow ultrahigh performance liquid chromatography-tandem mass spectrometry

This study investigated lipid alterations in muscle tissues [gastrocnemius (Gas) and soleus (Sol)] of mice under different diet programs (weight gain, weight maintenance, weight regain, and controls) by nanoflow ultrahigh pressure liquid chromatography-electrospray ionization-tandem mass spectrometry. Since overloaded lipids in the skeletal muscle tissues by excessive fat accumulation are related to insulin resistance leading to type II diabetes mellitus, analysis of lipid alteration in muscle tissues with respect to high-fat diet (HFD) is important to understand obesity related diseases. A total of 345 individual lipid species were identified with their molecular structures, and 184 lipids were quantified by selected reaction monitoring method. Most triacylglycerol (TG) and phosphatidylethanolamine (PE) species displayed a significant (>2-fold, p < 0.01) increase in both the Gas and Sol and to a larger degree in the Gas. However, lipid classes involved in insulin resistance and anti-inflammatory response, including lysophosphatidylcholine (18:0), diacylglycerol (16:0_18:1, 16:0_18:2, and 18:1_18:1), ceramide (d18:1/24:0 and d18:1/24:1), and phosphatidylinositol (18:0/20:4), showed a significant accumulation in the Sol exclusively after HFD treatment. In addition, the lipid profiles were not significantly altered in mice that were fed HFD only for the last 4 weeks (weight gain group), suggesting that consuming HFD in the younger age period can be more effective in the Gas. This study reveals that lipid classes related to insulin resistance accumulated more in the Sol than in the Gas following HFD treatment and the weight regain program perturbed lipid profiles of the Sol to a greater extent than that by the other diet programs, confirming that the Sol tissue is more influenced by HFD than Gas.

Protocols for Enzymatic Fluorometric Assays to Quantify Phospholipid Classes

Phospholipids, consisting of a hydrophilic head group and two hydrophobic acyl chains, are essential for the structures of cell membranes, plasma lipoproteins, biliary mixed micelles, pulmonary surfactants, and extracellular vesicles. Beyond their structural roles, phospholipids have important roles in numerous biological processes. Thus, abnormalities in the metabolism and transport of phospholipids are involved in many diseases, including dyslipidemia, atherosclerosis, cholestasis, drug-induced liver injury, neurological diseases, autoimmune diseases, respiratory diseases, myopathies, and cancers. To further clarify the physiological, pathological, and molecular mechanisms and to identify disease biomarkers, we have recently developed enzymatic fluorometric assays for quantifying all major phospholipid classes, phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, phosphatidic acid, phosphatidylinositol, phosphatidylglycerol + cardiolipin, and sphingomyelin. These assays are specific, sensitive, simple, and high-throughput, and will be applicable to cells, intracellular organelles, tissues, fluids, lipoproteins, and extracellular vesicles. In this review, we present the detailed protocols for the enzymatic fluorometric measurements of phospholipid classes in cultured cells.

A new approach for characterization of phosphatidylcholines and lysophosphatidylcholine in human plasma

Aim: Characterization of phosphatidylcholines (PCs) and lysophosphatidylcholine in human plasma using LC-IT-MSⁿ. The characterization approach was based on trapping the eluted positive ions and applying low voltage for fragmentation to MS² and further fragmentation of the most abundant two peaks to obtain MS³. This approach allowed linking the MS³ data to MS² and precursor ion. Methodology: The fatty acid part, at sn-1 and sn-2 of the glycerol backbone, could be identified based on the favored cleavage pathway. Conclusion: The dysregulated PCs and lysophosphatidylcholines in human plasma obtained from acute coronary syndrome cases, and Type 2 diabetes patients suffering no coronary syndromes were estimated and matched versus healthy volunteers. An epoxide form of 16:0-18:2 PC was confirmed, m/z 774.6.

Aging-related lipidomic changes in mouse serum, kidney, and heart by nanoflow ultrahigh-performance liquid chromatography-tandem mass spectrometry

Aging refers to the intracellular accumulation of reactive oxygen species that damages proteins, DNA, and lipids. As alterations in lipid metabolism may trigger metabolic disorders and the onset of metabolic diseases, changes in lipid profiles can be closely related to aging. In this study, a comprehensive lipidomic comparison between 4- and 25-month-old mice was performed to investigate age-induced changes in the lipid profiles of mouse serum, kidney, and heart using nanoflow ultrahigh-performance liquid chromatography-electrospray ionization-tandem mass spectrometry. Quantitative analysis of 279 of the 542 identified lipids revealed significant changes upon aging, mainly showing decreased levels in the three types of samples. Exceptionally, most triacylglycerols showed significant increases in heart tissue. The kidney was influenced more by aging than the serum and heart. The highly abundant lipids in each lipid class with significant decreases (> 2-fold, p < 0.01) were lysophosphatidic acid 18:1, lysophosphatidylinositol 20:4, and ceramide d:18:1/24:0 in serum; lysophosphatidylglycerol 16:0 in heart tissue; and eight phosphatidylethanolamines (20:4, 22:6, 36:2, 36:3, 38:4, 38:5, 38:6, 40:6, and 40:7), two cardiolipins (72:7 and 72:8), and lysophosphatidylcholine 18:0 in kidney tissue. The findings indicate the potential of lipidomic analysis to study characteristic age-related lipid changes.

Nano-LC/NSI MS Refines Lipidomics by Enhancing Lipid Coverage, Measurement Sensitivity, and Linear Dynamic Range

Nano-liquid chromatography (nLC)-nanoelectrospray (NSI) is one of the cornerstones of mass-spectrometry-based bioanalytics. Nevertheless, the application of nLC is not yet prevalent in lipid analyses. In this study, we established a reproducible nLC separation for global lipidomics and describe the merits of using such a miniaturized system for lipid analyses. In order to enable comprehensive lipid analyses that is not restricted to specific lipid classes, we particularly optimized sample preparation conditions and reversed-phase separation parameters. We further benchmarked the developed nLC system to a commonly used high flow HPLC/ESI MS system in terms of lipidome coverage and sensitivity. The comparison revealed an intensity gain between 2 and 3 orders of magnitude for individual lipid classes and an increase in the linear dynamic range of up to 2 orders of magnitude. Furthermore, the analysis of the yeast lipidome using nLC/NSI resulted in more than a 3-fold gain in lipid identifications. All in all, we identified 447 lipids from the core phospholipid lipid classes (PA, PE, PC, PS, PG, and PI) in Saccharomyces cerevisiae.

High-fat diet-induced lipidome perturbations in the cortex, hippocampus, hypothalamus, and olfactory bulb of mice

Given their important role in neuronal function, there has been an increasing focus on altered lipid levels in brain disorders. The effect of a high-fat (HF) diet on the lipid profiles of the cortex, hippocampus, hypothalamus, and olfactory bulb of the mouse brain was investigated using nanoflow ultrahigh pressure liquid chromatography-electrospray ionization-tandem mass spectrometry in the current study. For 8 weeks, two groups of 5-week-old mice were fed either an HF or normal diet (6 mice from each group analyzed as the F and N groups, respectively). The remaining mice in both groups then received a 4-week normal diet. Each group was then subdivided into two groups for another 4-week HF or normal diet. Quantitative analysis of 270 of the 359 lipids identified from brain tissue revealed that an HF diet significantly affected the brain lipidome in all brain regions that were analyzed. The HF diet significantly increased diacylglycerols, which play a role in insulin resistance in all regions that were analyzed. Although the HF diet increased most lipid species, the majority of phosphatidylserine species were decreased, while lysophosphatidylserine species, with the same acyl chain, were substantially increased. This result can be attributed to increased oxidative stress due to the HF diet. Further, weight-cycling (yo-yo effect) was found more critical for the perturbation of brain lipid profiles than weight gain without a preliminary experience of an HF diet. The present study reveals systematic alterations in brain lipid levels upon HF diet analyzed either by lipid class and molecular levels.

Ruthenium photoredox-triggered phospholipid membrane formation

As more methodologies for generating and manipulating biomimetic cellular systems are developed, opportunities arise for combining different methods to create more complex synthetic biological constructs. This necessitates an increasing need for tools to selectively trigger individual methodologies. Here we demonstrate ruthenium tris-bipyridine mediated photoredox triggering of the copper catalyzed alkyne azide cycloaddition reaction (CuAAC), resulting in the synthesis of biomimetic phospholipids in situ, and subsequent membrane assembly. The use of a ruthenium-copper electron transport chain to trigger phospholipid assembly opens up future opportunities for spatiotemporal synthesis of membranes.

Effects of high-fat diet and age on the blood lipidome and circulating endocannabinoids of female C57BL/6 mice

Alterations in lipid metabolism play a significant role in the pathogenesis of obesity-associated disorders, and dysregulation of the lipidome across multiple diseases has prompted research to identify novel lipids indicative of disease progression. To address the significant gap in knowledge regarding the effect of age and diet on the blood lipidome, we used shotgun lipidomics with electrospray ionization-mass spectrometry (ESI-MS). We analyzed blood lipid profiles of female C57BL/6 mice following high-fat diet (HFD) and low-fat diet (LFD) consumption for short (6weeks), long (22weeks), and prolonged (36weeks) periods. We examined endocannabinoid levels, plasma esterase activity, liver homeostasis, and indices of glucose tolerance and insulin sensitivity to compare lipid alterations with metabolic dysregulation. Multivariate analysis indicated differences in dietary blood lipid profiles with the most notable differences after 6weeks along with robust alterations due to age. HFD altered phospholipids, fatty acyls, and glycerolipids. Endocannabinoid levels were affected in an age-dependent manner, while HFD increased plasma esterase activity at all time points, with the most pronounced effect at 6weeks. HFD-consumption also altered liver mRNA levels of PPARα, PPARγ, and CD36. These findings indicate an interaction between dietary fat consumption and aging with widespread effects on the lipidome, which may provide a basis for identification of female-specific obesity- and age-related lipid biomarkers.

Analytical approaches for lipidomics and its potential applications in neuropsychiatric disorders

OBJECTIVES

In this review, the authors discuss an overview of lipidomics followed by in-depth discussion of its application to the study of human diseases, including extraction methods of lipids, analytical techniques and clinical research in neuropsychiatric disorders.

METHODS

Lipidomics is a lipid-targeted metabolomics approach aiming at the comprehensive analysis of lipids in biological systems. Recent technological advancements in mass spectrometry and chromatography have greatly enhanced the development and applications of metabolic profiling of diverse lipids in complex biological samples.

RESULTS

An effective evaluation of the clinical course of diseases requires the application of very precise diagnostic and assessment approaches as early as possible. In order to achieve this, "omics" strategies offer new opportunities for biomarker identification and/or discovery in complex diseases and may provide pathological pathways understanding for diseases beyond traditional methodologies.

CONCLUSIONS

This review highlights the importance of lipidomics for the future perspectives as a tool for biomarker identification and discovery and its clinical application.

Lipidomic analysis of skeletal muscle tissues of p53 knockout mice by nUPLC-ESI-MS/MS

Tumour suppressor p53 is known to be associated with the maintenance of mitochondrial functional properties in the skeletal muscles. As deactivation or mutation of p53 can affect the synthesis of lipids, investigating the relationship between p53-related energy generation metabolism and perturbation of lipid profile is critical. In this study, 329 lipid species (among 412 identified species) in two different skeletal muscle tissues (the gastrocnemius and soleus) from p53 knockout (KO) mice were quantitatively analysed using nanoflow ultrahigh performance liquid chromatography tandem mass spectrometry (nUPLC-MS/MS). Overall, lipids from the soleus tissues were more affected by p53 KO than those from the gastrocnemius in most lipid profiles. In p53 KO, lysophosphatidylcholine (LPC), lysophosphatidylserine (LPS), phosphatidic acid (PA), sphingomyelin (SM), and triacylglycerol (TAG), including 6 TAG (44:2, 46:0, 58:5, 58:8, 58:9, and 50:0), were significantly increased (p < 0.05) by 1.4–2-fold only in the soleus tissue. Overall monohexosylceramide (MHC) levels, including those of 3 MHC species (d18:0/24:0, d18:1/22:0, and d18:1/24:0), were significantly increased (p < 0.05) by 2–4 fold, only in the gastrocnemius tissue. The results suggest that lipid profiles are significantly altered by the lack of p53 in muscle tissues.

Relative Quantification of Phospholipids Based on Isotope-Labeled Methylation by Nanoflow Ultrahigh Performance Liquid Chromatography-Tandem Mass Spectrometry: Enhancement in Cardiolipin Profiling

In this study, lipid analysis based on isotope-labeled methlylation (ILM) was performed by nanoflow ultrahigh performance liquid chromatography-eletrospray ionization-tandem mass spectrometry (nUPLC-ESI-MS/MS) for enhanced detection and quantification of targeted phospholipids. ILM depends on methylation of phosphate groups by (trimethylsilyl)diazomethane, and the ILM based quantitation with reversed phase nUPLC-ESI-MS/MS provides advantages in PL profiling such as enhanced detectability of methylated PLs owing to increased hydrophobicity and substantial increase in resolution due to the increase of retention. Efficacy of ILM in nUPLC-ESI-MS/MS analysis was evaluated in the selected reaction monitoring (SRM) method by varying the mixing ratio of H-/D-methylated PL standards, which resulted in the successful quantification of 24 species, including phosphatidic acid (PA), phosphatidylserine (PS), phosphatidylglycerol (PG), ceramide-1-phosphate (Cer1P), phosphoinositides, and cardiolipin (CL), with ∼6.6% variation in the calculated ratio of H-/D-methylated PLs. The method was applied to the lipid extracts from a DU145 cell line after D-allose treatment, resulting in the quantification of 83 PLs of which results were not statistically different from those obtained by conventional quantification methods. Morever, detection and quantification of CLs and PAs were evidenced to be highly effective when used with the ILM method as 43 CLs and 20 PAs from cellular lipid extracts were analyzed while only 18 CLs and 12 PAs were identified when conventional methods were carried out. This proves the ILM combined with LC-MS to be a promising method for analysis of the aforementioned classes of lipids. Overall, the study highlighted the applicability of targeted quantification by the ILM method in lipidomic analysis and demonstrated an improvement in the detection of less abundant anionic PLs.

Evaluation of treadmill exercise effect on muscular lipid profiles of diabetic fatty rats by nanoflow liquid chromatography-tandem mass spectrometry

We compare comprehensive quantitative profiling of lipids at the molecular level from skeletal muscle tissues (gastrocnemius and soleus) of Zucker diabetic fatty rats and Zucker lean control rats during treadmill exercise by nanoflow liquid chromatography-tandem mass spectrometry. Because type II diabetes is caused by decreased insulin sensitivity due to excess lipids accumulated in skeletal muscle tissue, lipidomic analysis of muscle tissues under treadmill exercise can help unveil the mechanism of lipid-associated insulin resistance. In total, 314 lipid species, including phospholipids, sphingolipids, ceramides, diacylglycerols (DAGs), and triacylglycerols (TAGs), were analyzed to examine diabetes-related lipid species and responses to treadmill exercise. Most lysophospholipid levels increased with diabetes. While DAG levels (10 from the gastrocnemius and 13 from the soleus) were >3-fold higher in diabetic rats, levels of most of these decreased after exercise in soleus but not in gastrocnemius. Levels of 5 highly abundant TAGs (52:1 and 54:3 in the gastrocnemius and 48:2, 50:2, and 52:4 in the soleus) displaying 2-fold increases in diabetic rats decreased after exercise in the soleus but not in the gastrocnemius in most cases. Thus, aerobic exercise has a stronger influence on lipid levels in the soleus than in the gastrocnemius in type 2 diabetic rats.

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.

Variations in plasma and urinary lipids in response to enzyme replacement therapy for Fabry disease patients by nanoflow UPLC-ESI-MS/MS

A deficiency of α-galactosidase A causes Fabry disease (FD) by disrupting lipid metabolism, especially trihexosylceramide (THC). Enzyme replacement therapy (ERT) is clinically offered to FD patients in an attempt to lower the accumulated lipids. Studies on specific types of lipids that are directly or indirectly altered by FD are very scarce, even though they are crucial in understanding the biological process linked to the pathogenesis of FD. We performed a comprehensive lipid profiling of plasma and urinary lipids from FD patients with nanoflow liquid chromatography electrospray-ionization tandem mass spectrometry (nLC-ESI-MS/MS) and identified 129 plasma and 111 urinary lipids. Among these, lipids that exhibited alternations (>twofold) in patients were selected as targets for selected reaction monitoring (SRM)-based high-speed quantitation using nanoflow ultra-performance LC-ESI-MS/MS (nUPLC-ESI-MS/MS) and 31 plasma and 26 urinary lipids showed significant elevation among FD patients. Higher percentages of sphingolipids (SLs; 48% for plasma and 42% for urine) were highly elevated in patients; whereas, a smaller percentage of phospholipids (PLs; 15% for plasma and 13% for urine) were significantly affected. Even though α-galactosidase A is reported to affect THC only, the results show that other classes of lipids (especially SLs) are changed as well, indicating that FD not only alters metabolism of THC but various classes of lipids too. Most lipids showing significant increases in relative amounts before ERT decreased after ERT, but overall, ERT influenced plasma lipids more than urinary lipids.

Phospholipidomic identification of potential serum biomarkers in dengue fever, hepatitis B and hepatitis C using liquid chromatography-electrospray ionization-tandem mass spectrometry

The serum phospholipid (PL) profiles of healthy volunteers (HE) and patients with recently diagnosed dengue fever (DF), hepatitis B (HBV), and hepatitis C (HCV) were investigated using liquid chromatography-ion trap-mass spectrometry (LC-IT-MS) and liquid chromatography-triple quad-mass spectrometry (LC-TQ-MS). Major PLs, including lyso-phosphatidylcholins (LPCs), phosphatidylcholins (PCs), phosphatidylinositols (PIs), phosphatidylethanolamines (PEs) and phosphatidylserines (PSs), were characterized in human serum using LC-IT-MS. Thirty-five PLs were quantified using seven non-endogenous odd-carbon PL standards. An MS search protocol for the identification of PLs is described. The analytical method was optimized to achieve maximum recovery and detection. PLs were detected with minimal ionization suppression. The PLs species were characterized on the basis of (i) MS(2) peaks due to polar head, (ii) precursor ion or neutral loss scans, (iii) identification of fatty acid, (iv) identification of sn-1 and sn-2 fatty acid. The quantitation data were subjected to principal component analysis (PCA), and a significant difference was observed between the PL profiles of the investigated diseases and those of HE subjects. The significance of the changes in each lipid among the four groups was statistically assessed using one-way analysis of variance (ANOVA) followed by Bonferroni post hoc multiple comparison. The serum profiles of 28 PLs were determined to be significantly different and enabled the discrimination between HE individuals and the studied patients. Potentially dysregulated PLs were considered as differentiating biomarkers to diagnose DF, HBV, and HCV.

Lipidomics applications for disease biomarker discovery in mammal models

Lipidomics is a lipid-targeted metabolomics approach focusing on comprehensive analysis of all lipids with which they interact in biology systems. Recent technological advances in MS and chromatography have greatly enhanced the developments and applications of metabolic profiling of diverse lipids in complex biological samples. Lipidomics will not only provide insights into the specific functions of lipid species in health and disease, but will also identify potential biomarkers for establishing preventive or therapeutic programs for human disease. In this review, recent applications of lipidomics to understand animal models of disease such as metabolic syndromes, neurodegenerative diseases, cancer and infectious diseases are considered. We also discuss the lipidomics for the future perspectives and their potential problems.

Differential effects of cocaine exposure on the abundance of phospholipid species in rat brain and blood

BACKGROUND

Lipid profiles in the blood are altered in human cocaine users, suggesting that cocaine exposure can induce lipid remodeling.

METHODS

Lipid changes in the brain tissues of rats sensitized to cocaine were determined through shotgun lipidomics using electrospray ionization-mass spectrometry (ESI-MS). We also performed pairwise principal component analysis (PCA) to assess cocaine-induced changes in blood lipid profiles. Alterations in the abundance of phospholipid species were correlated with behavioral changes in the magnitude of either the initial response to the drug or locomotor sensitization.

RESULTS

Behavioral sensitization altered the relative abundance of several phospholipid species in the hippocampus and cerebellum, measured one week following the final exposure to cocaine. In contrast, relatively few effects on phospholipids in either the dorsal or the ventral striatum were observed. PCA analysis demonstrated that cocaine altered the relative abundance of several glycerophospholipid species as compared to saline-injected controls in blood. Subsequent MS/MS analysis identified some of these lipids as phosphatidylethanolamines, phosphatidylserines and phosphatidylcholines. The relative abundance of some of these phospholipid species were well-correlated (R(2) of 0.7 or higher) with either the initial response to cocaine or locomotor sensitization.

CONCLUSION

Taken together, these data demonstrate that a cocaine-induced sensitization assay results in the remodeling of specific phospholipids in rat brain tissue in a region-specific manner and also alters the intensities of certain types of phospholipid species in rat blood. These results further suggest that such changes may serve as biomarkers to assess the neuroadaptations occurring following repeated exposure to cocaine.

Preferential incorporation of shorter and less unsaturated acyl phospholipids into high density lipoprotein-like particles in the ABCA1- and ABCA7-mediated biogenesis with apoA-I

Molecular species of phosphatidylcholine (PC) and sphingomyelin (SPM) were globally analyzed for lipidomics in the nascent high-density lipoprotein (HDL)-like particles generated with human apolipoprotein A-I (apoA-I) form HEK293 cells where either human ATP binding cassette transporter (ABC) A1 or ABCA7 was transfected and overexpressed. SPM/PC ratio was higher in the ABCA1-mediated HDL than ABCA7-mediated HDL likely being related to their cholesterol content, while it was less than the ratio in the cell membrane in either case. Molecular species composition of hydrocarbon chain moiety in each phospholipid in the HDL largely reflected that in the cells the lipoprotein originated in, without remarkable difference between ABCA1 and ABCA7. Further analysis, however, revealed apparent preference for the molecules with shorter hydrocarbon chain length for both PC and SPM in their relative incorporation into HDL by ABCA1 and ABCA7. Likewise, it was in favor for less-unsaturated hydrocarbon chains of PC while this preference was not apparent for SPM. The results are consistent with the view that assembly of HDL particles with extracellular apoA-I is primarily with the cellular phospholipid molecules being regulated in part by their physicochemical nature.

Lipidomic profiling of plasma and urine from patients with Gaucher disease during enzyme replacement therapy by nanoflow liquid chromatography-tandem mass spectrometry

Gaucher disease (GD) is a rare genetic disorder that arises from lipid species, especially monohexosylceramide (MHC), accumulating in different organs. GD results from a β-glucocerebrosidase deficiency, causing metabolic or neurologic complications. This study comprehensively profiled lipids from patients and healthy controls to discover active lipid species related to GD. Most studies have evaluated lipids from one type of biological sample, such as plasma, urine, or spinal fluid, which are the main sources of lipids in human bodies. The purpose of this study, however, was to collect and assess both plasma and urine samples from a group of individuals, explore the lipids, and select characteristic species that show significant differences between controls and patients from the two sources. Also, the response of lipids to enzyme replacement therapy (ERT), which is targeted to reduce excessive lipid accumulation within lysosomes, was investigated by obtaining plasma and urine from patients after receiving the therapy. Most lipid species were found in both plasma and urine but their concentrations differed, and some species were found in either plasma or urine only. Out of 125 plasma and 105 urinary lipids that were identified by nLC-ESI-MS/MS, 20 plasma and 10 urinary lipids were selected as characteristic species for having average concentrations that were significantly increased or decreased in patients by greater than 2-fold. Moreover, the concentrations of most lipids that showed greater than 2-fold of difference in patients decreased after ERT indicating that these species were directly or indirectly affected by the therapy.

Separation and identification of phosphatidylcholine regioisomers by combining liquid chromatography with a fusion of collision-and ozone-induced dissociation

The differentiation of closely related lipid isomers is increasingly important to our evolving understanding of lipid biochemistry but it is equally challenging to contemporary chromatographic and mass spectral analyses. Recently, we described a novel ion-activation approach based on combining collision- with ozone-induced dissociation (CID/OzID) for the identification of the relative acyl chain substitution positions in glycerophospholipids. Here we demonstrate, for the first time, that CID/OzID can be effectively combined with reversed-phase chromatography to enable the separation and unambiguous identification of regioisomeric pairs of phosphatidylcholines that differ only in the arrangement of acyl chains on the glycerol backbone.

Rapid identification of glycerophospholipids from RAW264.7 cells by UPLC/ESI -QTOF-MS

The study aims to develop a rapid, sensitive ultra-performance liquid chromatography coupled with an electrospray ionization quadruple time-of-flight tandem mass spectrometry (UPLC/Q-TOF-MS) analytical method for identifying glycerophospholipids (GPLs) from RAW264.7 cells. A total of 78 GPLs including 22 phosphatidylethanolamines (PEs), 49 phosphatidylcholines (PCs), four phosphatidylglycerols, one phosphatidylinositol and two unknown GPLs were identified. PC (14:0/16:1), PC (14:0/16:0), PE (0:0/20:3), PE (22:5/0:0) and PE (22:3/0:0) were identified for the first time. The UPLC/Q-TOF-MS method is suitable for targeting analysis of GPLs from RAW264.7 cells, which allows us to find out new GPLs compositions related to inflammatory diseases and to explain their pharmacological roles in inflammatory process.

Impact of inhaled nitric oxide on the sulfatide profile of neonatal rat brain studied by TOF-SIMS imaging

Despite advances in neonatal intensive care leading to an increased survival rate in preterm infants, brain lesions and subsequent neurological handicaps following preterm birth remain a critical issue. To prevent brain injury and/or enhance repair, one of the most promising therapies investigated in preclinical models is inhaled nitric oxide (iNO). We have assessed the effect of this therapy on brain lipid content in air- and iNO-exposed rat pups by mass spectrometry imaging using a time-of-flight secondary ion mass spectrometry (TOF-SIMS) method. This technique was used to map the variations in lipid composition of the rat brain and, particularly, of the white matter. Triplicate analysis showed a significant increase of sulfatides (25%–50%) in the white matter on Day 10 of life in iNO-exposed animals from Day 0–7 of life. These robust, repeatable and semi-quantitative data demonstrate a potent effect of iNO at the molecular level.

Targeted lipidomics - advances in profiling lysophosphocholine and platelet-activating factor second messengers

Glycerophosphocholines are the major building blocks of biological membranes. They are also precursors of low-molecular-weight second messengers with mass to charge ratios of 450-600. These messengers include lysophosphatidylcholines (LPCs) and lyso-platelet activating factors (PAFs) that may be further processed into PAFs. Often considered as a single species, LPCs, PAFs and lyso-PAFs are, in fact, families of glycerophosphocholine-derived lipids distinguished by the linkage of their sn-1 carbon chains to the phosphoglyceride backbone (ester or ether), their sn-1 carbon chain length and degree of unsaturation, and the identity of their sn-2 constituents (a hydroxyl or acetyl group). Each LPC and PAF species exhibits a different affinity for its cognate G-protein-coupled receptors, and each species elicits receptor-independent actions that play critical signalling roles. Targeted mass spectrometry-based lipidomic approaches are enabling the molecular identification and quantification of these low-abundance second messengers. Variations between datasets map the temporal landscape of second messengers available for signalling, and provide snapshots of the state of structural membrane compositional remodelling at the time of extraction. Here, we review a number of advances in lipidomic methodologies used to identify LPCs, lyso-PAFs and PAFs, and highlight how these targeted approaches are providing valuable insight into the roles played by the cellular lipidome in cell function and disease susceptibility.

Mass spectrometry based phospholipidomics of mammalian thymus and leukemia patients: implication for function of iNKT cells

In previous studies phospholipids have been proved to be involved in biochemical, physiological, and pathological processes. As a special class of phospholipids, peroxisome-derived lipids (PDLs) have been proved to be potential ligands of invariant natural killer T (iNKT) cells in recent studies. Here, on the basis of phospholipidomics, we focused on the relative quantity of PDLs extracted from mammalian thymus or bone marrow using electrospray ionization mass spectrometry (MS). In phospholipid analysis, we identified 12 classes of phospholipids and accounted for their relative quantities by comparing their relative abundances in the MS(1) map. Our results show that PDLs are present in mammalian thymus as well as mouse spleen and liver. Interestingly, the relative quantity of PDLs extracted from human acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL) bone marrows is higher than that extracted from bone marrow of healthy donors. Our results may help to explain the close correlation between PDLs and iNKT cell function in thymus, spleen, liver, and especially in leukemia patients. We think that our phospholipidomics work may reveal a function of iNKT cells.

Computational approach to structural identification of phospholipids using raw mass spectra from nanoflow liquid chromatography-electrospray ionization-tandem mass spectrometry

A qualitative analysis tool (LiPilot) for identifying phospholipids (PLs), including lysophospholipids (LPLs), from biological mixtures is introduced. The developed algorithm utilizes raw data obtained from nanoflow liquid chromatography-electrospray ionization-tandem mass spectrometry experiments of lipid mixture samples including retention time and m/z values of precursor and fragment ions from data-dependent, collision-induced dissociation. Library files based on typical fragmentation patterns of PLs generated with an LTQ-Velos ion trap mass spectrometer are used to identify PL or LPL species by comparing experimental fragment ions with typical fragment ions in the library file. Identification is aided by calculating a confidence score developed in our laboratory to maximize identification efficiency. Analysis includes the influence of total ion intensities of matched and unmatched fragment ions, the difference in m/z values between observed and theoretical fragment ions, and a weighting factor used to differentiate regioisomers through data filtration. The present study focused on targeted identification of particular PL classes. The identification software was evaluated using a mixture of 24 PL and LPL standards. The software was further tested with a human urinary PL mixture sample, with 93 PLs and 22 LPLs identified.

Bioinformatics tools and challenges in structural analysis of lipidomics MS/MS data

Lipidomics, the systematic study of the lipid composition of a cell or tissue, is an invaluable complement to knowledge gained by genomics and proteomics research. Mass spectrometry provides a means to detect hundreds of lipids in parallel, and this includes low abundance species of lipids. Nevertheless, frequently occurring isobaric and isomeric lipid species complicate lipidomics analyses from an analytical and bioinformatics perspective. Various MS/MS strategies have evolved to resolve ambiguous identifications of lipid species, and these strategies have been supported by corresponding bioinformatics analysis tools. This review intends to familiarize readers with available bioinformatics MS/MS analysis tools and databases, the structural information obtainable from these, and their applicability to different MS/MS strategies. Finally, future challenges in detecting double bond positions are investigated from a bioinformatics perspective.

Profiling changes triggered during maturation of dendritic cells: a lipidomic approach

Lipids are important in several biological processes because they act as signalling and regulating molecules, or, locally, as membrane components that modulate protein function. This paper reports the pattern of lipid composition of dendritic cells (DCs), a cell type of critical importance in inflammatory and immune responses. After activation by antigens, DCs undergo drastic phenotypical and functional transformations, in a process known as maturation. To better characterize this process, changes of lipid profile were evaluated by use of a lipidomic approach. As an experimental model of DCs, we used a foetal skin-derived dendritic cell line (FSDC) induced to mature by treatment with lipopolysaccharide (LPS). The results showed that LPS treatment increased ceramide (Cer) and phosphatidylcholine (PC) levels and reduced sphingomyelin (SM) and phosphatidylinositol (PI) content. Mass spectrometric analysis of a total lipid extract and of each class of lipids revealed that maturation promoted clear changes in ceramide profile. Quantitative analysis enabled identification of an increase in the total ceramide content and enhanced Cer at m/z 646.6, identified as Cer(d18:1/24:1), and at m/z 648.6, identified as Cer(d18:1/24:0). The pattern of change of these lipids give an extremely rich source of data for evaluating modulation of specific lipid species triggered during DC maturation.

Multi-dimensional mass spectrometry-based shotgun lipidomics and novel strategies for lipidomic analyses

Since our last comprehensive review on multi-dimensional mass spectrometry-based shotgun lipidomics (Mass Spectrom. Rev. 24 (2005), 367), many new developments in the field of lipidomics have occurred. These developments include new strategies and refinements for shotgun lipidomic approaches that use direct infusion, including novel fragmentation strategies, identification of multiple new informative dimensions for mass spectrometric interrogation, and the development of new bioinformatic approaches for enhanced identification and quantitation of the individual molecular constituents that comprise each cell's lipidome. Concurrently, advances in liquid chromatography-based platforms and novel strategies for quantitative matrix-assisted laser desorption/ionization mass spectrometry for lipidomic analyses have been developed. Through the synergistic use of this repertoire of new mass spectrometric approaches, the power and scope of lipidomics has been greatly expanded to accelerate progress toward the comprehensive understanding of the pleiotropic roles of lipids in biological systems.

Optimized extraction of phospholipids and lysophospholipids for nanoflow liquid chromatography-electrospray ionization-tandem mass spectrometry

The efficiencies of four different methods for the extraction of phospholipids (PLs) and lysophospholipids (LPLs) from human plasma samples were examined by comparing extraction recovery values using nanoflow liquid chromatography-electrospray ionization-mass spectrometry (nLC-ESI-MS). For recovery measurements, six PL and six LPL standards of different head groups were spiked into a human plasma sample, and the peak areas of each individual species after extraction were measured from the chromatograms of the nLC-ESI-MS runs. Recovery was calculated by comparing the peak area of an extracted standard species with that of the same species' spike after extraction of the same plasma sample. For lipid extraction, four different extraction methods were examined: three based on the Folch method with different organic solvents such as CHCl(3), methyl-tert-butyl ether (MTBE), and MTBE/CH(3)OH, and one relatively fast method involving CH(3)OH only. Evaluations of recovery showed that the modified Folch method with MTBE/CH(3)OH proposed in this study was effective for extracting most PL and LPL standards. Then, the four extraction methods were compared with the identified numbers of plasma PLs and LPLs, of which molecular structures can be confirmed by data-dependent, collision-induced dissociation experiments during nLC-ESI-MS-MS. These results demonstrated that the proposed method yielded the identification of 54 LPLs and 66 PLs from a plasma sample, which was the highest identification rate among the four methods.

Quantitative analysis of glycerophospholipids by LC-MS: acquisition, data handling, and interpretation

As technology expands what it is possible to accurately measure, so too the challenges faced by modern mass spectrometry applications expand. A high level of accuracy in lipid quantitation across thousands of chemical species simultaneously is demanded. While relative changes in lipid amounts with varying conditions may provide initial insights or point to novel targets, there are many questions that require determination of lipid analyte absolute quantitation. Glycerophospholipids present a significant challenge in this regard, given the headgroup diversity, large number of possible acyl chain combinations, and vast range of ionization efficiency of species. Lipidomic output is being used more often not just for profiling of the masses of species, but also for highly-targeted flux-based measurements which put additional burdens on the quantitation pipeline. These first two challenges bring into sharp focus the need for a robust lipidomics workflow including deisotoping, differentiation from background noise, use of multiple internal standards per lipid class, and the use of a scriptable environment in order to create maximum user flexibility and maintain metadata on the parameters of the data analysis as it occurs. As lipidomics technology develops and delivers more output on a larger number of analytes, so must the sophistication of statistical post-processing also continue to advance. High-dimensional data analysis methods involving clustering, lipid pathway analysis, and false discovery rate limitation are becoming standard practices in a maturing field.

Lipidomics era: accomplishments and challenges

Lipid mediators participate in signal transduction pathways, proliferation, apoptosis, and membrane trafficking in the cell. Lipids are highly complex and diverse owing to the various combinations of polar headgroups, fatty acyl chains, and backbone structures. This structural diversity continues to pose a challenge for lipid analysis. Here we review the current state of the art in lipidomics research and discuss the challenges facing this field. The latest technological developments in mass spectrometry, the role of bioinformatics, and the applications of lipidomics in lipid metabolism and cellular physiology and pathology are also discussed.