Lipid profiling of rat peritoneal surface layers by online normal- and reversed-phase 2D LC QToF-MS

An online, two-dimensional (2D) liquid chromatography (LC) quadrupole time-of-flight mass spectrometry (QToF-MS) method was developed for lipid profiling of rat peritoneal surface layers, in which the lipid classes and species could be simultaneously separated in one injection with a significantly increased sensitivity. Different lipid classes were separated on a normal-phase column in the first dimension and lipid molecular species were separated on a reversed-phase column in the second dimension, so that the ion suppression effects were reduced while the detection sensitivity was improved. Identified were 721 endogenous lipid species from 12 lipid classes, in which 415 structures were confirmed using tandem mass spectra, and the other 306 lipid molecular species were identified by accurate masses. The linearity, limit of detection, and repeatability were all satisfactory. The method was applied to the investigation of the lipid changes in rat peritoneal surface layer after peritoneal dialysis, and 32 potential lipid biomarkers were identified, as their concentrations in the dosed group were 2.2–12.5 times of those in the control group. The results revealed that this 2D LC-MS system was a promising tool for lipid profiling of complex biological samples.     

Effects of diet and development on the Drosophila lipidome

Cells produce tens of thousands of different lipid species, but the importance of this complexity in vivo is unclear. Analysis of individual tissues and cell types has revealed differences in abundance of individual lipid species, but there has been no comprehensive study comparing tissue lipidomes within a single developing organism. Here, we used quantitative shotgun profiling by high‐resolution mass spectrometry to determine the absolute (molar) content of 250 species of 14 major lipid classes in 6 tissues of animals at 27 developmental stages raised on 4 different diets. Comparing these lipidomes revealed unexpected insights into lipid metabolism. Surprisingly, the fatty acids present in dietary lipids directly influence tissue phospholipid composition throughout the animal. Furthermore, Drosophila differentially regulates uptake, mobilization and tissue accumulation of specific sterols, and undergoes unsuspected shifts in fat metabolism during larval and pupal development. Finally, we observed striking differences between tissue lipidomes that are conserved between phyla. This study provides a comprehensive, quantitative and expandable resource for further pharmacological and genetic studies of metabolic disorders and molecular mechanisms underlying dietary response.     

Alkaline methanolysis of lipid extracts extends shotgun lipidomics analyses to the low-abundance regime of cellular sphingolipids

Sphingolipids that contain a sphingoid base are composed of hundreds to thousands of distinct compounds, many of which serve as lipid regulators of biological functions. The global analysis of the large number of low-abundance sphingolipid molecular species has been hampered in many cases by the sphingolipid molecular species being overwhelmed by the quantity of other classes of lipid (e.g., glycerophospholipid) molecular species present, thereby imposing severe restrictions on the dynamic range of their measurement using shotgun lipidomics. Herein, we developed a facile approach in which the sphingolipids of cellular extracts were dramatically enriched by direct alkaline methanolysis of lipid extracts followed by extraction to remove the large majority of other endogenous lipid classes. Through direct infusion of the resultant enriched solution, we identified and quantitated a variety of very-low-abundance sphingolipid classes (e.g., sphingosine, psychosine, and lysosphingomyelin) and molecular species (e.g., sphingomyelin) using electrospray ionization mass spectrometry (i.e., shotgun sphingolipidomics). Accordingly, through utilization of these facile enrichment techniques, direct penetrance into the sphingolipidomes has been greatly extended, facilitating new insights into their metabolism and signaling functions in biological systems.     

Validation of a multiplexed and targeted lipidomics assay for accurate quantification of lipidomes

A major challenge of lipidomics is to determine and quantify the precise content of complex lipidomes to the exact lipid molecular species. Often, multiple methods are needed to achieve sufficient lipidomic coverage to make these determinations. Multiplexed targeted assays offer a practical alternative to enable quantitative lipidomics amenable to quality control standards within a scalable platform. Herein, we developed a multiplexed normal phase liquid chromatography-hydrophilic interaction chromatography multiple reaction monitoring method that quantifies lipid molecular species across over 20 lipid classes spanning wide polarities in a single 20-min run. Analytical challenges such as in-source fragmentation, isomer separations, and concentration dynamics were addressed to ensure confidence in selectivity, quantification, and reproducibility. Utilizing multiple MS/MS product ions per lipid species not only improved the confidence of lipid identification but also enabled the determination of relative abundances of positional isomers in samples. Lipid class-based calibration curves were applied to interpolate lipid concentrations and guide sample dilution. Analytical validation was performed following FDA Bioanalytical Method Validation Guidance for Industry. We report repeatable and robust quantitation of 900 lipid species measured in NIST-SRM-1950 plasma, with over 700 lipids achieving inter-assay variability below 25%. To demonstrate proof of concept for biomarker discovery, we analyzed plasma from mice treated with a glucosylceramide synthase inhibitor, benzoxazole 1. We observed expected reductions in glucosylceramide levels in treated animals but, more notably, identified novel lipid biomarker candidates from the plasma lipidome. These data highlight the utility of this qualified lipidomic platform for enabling biological discovery.     

A shotgun lipidomics approach in Sinorhizobium meliloti as a tool in functional genomics

A shotgun lipidomics approach that allowed the analysis of eight lipid classes directly from crude extracts of the soil bacterium Sinorhizobium meliloti is presented. New MS-MS transitions are reported for the analysis of monomethylphosphatidylethanolamines, dimethylphosphatidylethanolamines, and three bacterial non-phosphorus-containing lipid classes [sulfoquinovosyldiacylglycerols, ornithines, and diacylglyceryl-(N,N,N-trimethyl)-homoserines]. Unique MS-MS transitions allowed the analysis of isomeric species from various lipid classes without chromatography. Analyses required small sample amounts and minimal preparation; thus, this methodology has excellent potential to be used as a screening tool for the analysis of large numbers of samples in functional genomics studies. FA distributions within lipid classes of S. meliloti are described for the first time, and the relative positions of fatty acyl substituents (sn-1, sn-2) in phospholipids are presented. FA distributions in diacylglyceryl-(N,N,N-trimethyl)-homoserines were identical to those of phospholipids, indicating a common biosynthetic origin for these lipids. The method was applied to the analysis of mutants deficient in the PhoB regulator protein. Increased lipid cyclopropanation was observed in PhoB-deficient mutants under P_i starvation.     

Temperature-dependent phase behavior of phosphatidylglycerols from chilling-sensitive and chilling-resistant plants

Seven major lipid classes were isolated from leaves of chilling-sensitive and chilling-resistant plants, and the temperature-dependent phase behaviors of their aqueous dispersions were studied by a fluorescence polarization method using trans-parinaric acid and its methyl ester. Phosphatidylglycerols from the chilling-sensitive plants went from the liquid crystalline state into the phase separation state at about 30°C in 100 mm NaCl and at about 40°C in 5 mm MgCl₂. In contrast, phosphatidylglycerols from the chilling-resistant plants went into the phase separation state at a much lower temperature. The other classes of lipids remained in the liquid crystalline state at all temperatures between 5°C and 40°C regardless of the chilling sensitivity of the plants, except sulfoquinovosyl diacylglycerol from sponge cucumber in which phase separation seemed to begin at about 15°C. Compositions and positional distributions of fatty acids of the lipids suggest that the phosphatidylglycerols from the chilling-sensitive plants, but no other lipids, contained large proportions of molecular species which undergo phase transition at room temperature or above. The thermotropic phase behaviors and the fatty acid compositions suggest that, among the major lipid classes from leaves of the chilling-sensitive plants, only phosphatidylglycerol can induce a phase transition. Since a major part of this lipid in leaves originates from the chloroplasts, phase transition probably occurs in the chloroplast membranes.     

Novel advances in shotgun lipidomics for biology and medicine

The field of lipidomics, as coined in 2003, has made profound advances and been rapidly expanded. The mass spectrometry-based strategies of this analytical methodology-oriented research discipline for lipid analysis are largely fallen into three categories: direct infusion-based shotgun lipidomics, liquid chromatography-mass spectrometry-based platforms, and matrix-assisted laser desorption/ionization mass spectrometry-based approaches (particularly in imagining lipid distribution in tissues or cells). This review focuses on shotgun lipidomics. After briefly introducing its fundamentals, the major materials of this article cover its recent advances. These include the novel methods of lipid extraction, novel shotgun lipidomics strategies for identification and quantification of previously hardly accessible lipid classes and molecular species including isomers, and novel tools for processing and interpretation of lipidomics data. Representative applications of advanced shotgun lipidomics for biological and biomedical research are also presented in this review. We believe that with these novel advances in shotgun lipidomics, this approach for lipid analysis should become more comprehensive and high throughput, thereby greatly accelerating the lipidomics field to substantiate the aberrant lipid metabolism, signaling, trafficking, and homeostasis under pathological conditions and their underpinning biochemical mechanisms.     

Analysis of molecular species of plant polar lipids by high-performance and gas liquid chromatography

Total lipid extracts from potato tubers and tobacco leaves are separated into lipid classes by two step HPLC using a silicic column. Elution is first performed for 20 min with a programmed linear gradient of two mixed solvents running from 100% of solution A (isopropanol-hexane, 4:3) to 100% of solution B (isopropanol-hexane-water, 8:6:1.5); the column is then eluted with pure solution B in an isocratic mode for 20 min more. The main polar lipids (MGDG, DGDG, PC, PE, PG) from both plant tissues can be collected and further separated into component molecular species on a simplified HPLC system with a C₁₈ column eluted in an isocratic mode with a polar solvent. Molecular species separations are achieved within 35 min; quantifications are made through GLC analysis of attached fatty acids. Three to five main molecular species are thus clearly identified in each lipid class. In potato tuber, phospholipids (PC, PE) 18:2/18:2 species are predominant. In tobacco leaf, six double bond species (18:3/18:3 and 16:3/18:3) are predominant in galactolipids, whereas PC contains a greater number of molecular species varying by their degree of unsaturation (from 18:3/18:3 to 16:0/18:2). Only certain molecular species of PG contain Δ³-trans-hexadecenoic acid.     

Analysis of cholesteryl esters and diacylglycerols using lithiated adducts and electrospray ionization-tandem mass spectrometry

Cholesteryl ester (CE) and diacylglycerol (DAG) molecular species are important lipid storage and signaling molecules. Mass spectrometric analyses of these lipids are complicated by the presence of isobaric molecular ions shared by these lipid classes and by relatively poor electrospray ionization, which is a consequence of an inherently weak dipole moment in these lipid classes. The current study demonstrates that lithiated adducts of CE and DAG molecular ions have enhanced ionization and lipid class-specific fragmentation in tandem mass spectrometry (MS/MS) scan modes, thereby allowing the implementation of strategies capable of lipid class-specific detection. Using neutral loss (NL) mode for the loss of cholestane from cholesterol esters (NL 368.5) and specific selected reaction monitoring for DAG molecular species, the response of specific molecular species to that of internal standards was determined. CE and DAG molecular species were quantified in human coronary artery endothelial cells (HCAECs) incubated with both palmitic acid and oleic acid. Furthermore, NL 368.5 spectra revealed the oxidation of the aliphatic fatty acid residues of CE molecular species. Taken together, these studies demonstrate a new analytical approach to assessing CE and DAG molecular species that exploits the utility of lithiated adducts in conjunction with MS/MS approaches.     

Characterization of the cardiac phospholipidome of small cetaceans provides adaptational insight and a foundation for indirect population health screening

The maintenance of a tightly regulated heart lipidome is a general hallmark of mammal health. However, in the case of cetaceans, heart tissue lipid composition remains obscure. This work represents a first in-depth state-of-the-art characterization of the lipid content of small cetacean hearts, namely those of Delphinus delphis, Phocoena phocoena, and Stenella coeruleoalba. Phospholipid classes identified were similar to those found in terrestrial mammals. Regarding fatty acid profiles, they revealed a much higher n-3 fatty acid content than that reported for terrestrial counterparts. Phospholipidome characterization allowed identification of 198 lipid species, including phospholipids, lysophospholipids, and sphingomyelins, generally characterized by a high content of species with esterified n-3 fatty acids. The cardiac lipid profile of the three cetacean species is similar in terms of lipid classes, fatty acids, and even molecular lipid species present. However, quantitative differences suggest a divergence of S. coeruleoalba from the other species in terms of fatty acid and phospholipid profile. The identified differences regarding terrestrial counterparts will contribute to better understanding the details of small cetacean cardiac physiology. Moreover, the characterization of cardiac phospholipidome may represent an opportunity to establish lipidomic-based practical tools to reliably and reproducibly assess small cetacean health population status by remote sampling.     

Rice phospholipase A superfamily: organization, phylogenetic and expression analysis during abiotic stresses and development

Background

Phospholipase A (PLA) is an important group of enzymes responsible for phospholipid hydrolysis in lipid signaling. PLAs have been implicated in abiotic stress signaling and developmental events in various plants species. Genome-wide analysis of PLA superfamily has been carried out in dicot plant Arabidopsis. A comprehensive genome-wide analysis of PLAs has not been presented yet in crop plant rice.

Methodology/Principal Findings

A comprehensive bioinformatics analysis identified a total of 31 PLA encoding genes in the rice genome, which are divided into three classes; phospholipase A₁ (PLA₁), patatin like phospholipases (pPLA) and low molecular weight secretory phospholipase A₂ (sPLA₂) based on their sequences and phylogeny. A subset of 10 rice PLAs exhibited chromosomal duplication, emphasizing the role of duplication in the expansion of this gene family in rice. Microarray expression profiling revealed a number of PLA members expressing differentially and significantly under abiotic stresses and reproductive development. Comparative expression analysis with Arabidopsis PLAs revealed a high degree of functional conservation between the orthologs in two plant species, which also indicated the vital role of PLAs in stress signaling and plant development across different plant species. Moreover, sub-cellular localization of a few candidates suggests their differential localization and functional role in the lipid signaling.

Conclusion/Significance

The comprehensive analysis and expression profiling would provide a critical platform for the functional characterization of the candidate PLA genes in crop plants.     

Sphingolipids as modulators of membrane proteins

The diversity of the transmembranome of higher eukaryotes is matched by an enormous diversity of sphingolipid classes and molecular species. The intrinsic properties of sphingolipids are not only suited for orchestrating lateral architectures of biological membranes, but their molecular distinctions also allow for the evolution of protein motifs specifically recognising and interacting with individual lipids. Although various reports suggest a role of sphingolipids in membrane protein function, only a few cases have determined the specificity of these interactions. In this review we discuss examples of specific protein–sphingolipid interactions for which a modulator-like dependency on sphingolipids was assigned to specific proteins. These novel functions of sphingolipids in specific protein–lipid assemblies contribute to the complexity of the sphingolipid classes and other molecular species observed in animal cells. This article is part of a Special Issue entitled New Frontiers in Sphingolipid Biology.     

Identification of Plasma Lipid Biomarkers for Prostate Cancer by Lipidomics and Bioinformatics

Background

Lipids have critical functions in cellular energy storage, structure and signaling. Many individual lipid molecules have been associated with the evolution of prostate cancer; however, none of them has been approved to be used as a biomarker. The aim of this study is to identify lipid molecules from hundreds plasma apparent lipid species as biomarkers for diagnosis of prostate cancer.

Methodology/Principal Findings

Using lipidomics, lipid profiling of 390 individual apparent lipid species was performed on 141 plasma samples from 105 patients with prostate cancer and 36 male controls. High throughput data generated from lipidomics were analyzed using bioinformatic and statistical methods. From 390 apparent lipid species, 35 species were demonstrated to have potential in differentiation of prostate cancer. Within the 35 species, 12 were identified as individual plasma lipid biomarkers for diagnosis of prostate cancer with a sensitivity above 80%, specificity above 50% and accuracy above 80%. Using top 15 of 35 potential biomarkers together increased predictive power dramatically in diagnosis of prostate cancer with a sensitivity of 93.6%, specificity of 90.1% and accuracy of 97.3%. Principal component analysis (PCA) and hierarchical clustering analysis (HCA) demonstrated that patient and control populations were visually separated by identified lipid biomarkers. RandomForest and 10-fold cross validation analyses demonstrated that the identified lipid biomarkers were able to predict unknown populations accurately, and this was not influenced by patient''s age and race. Three out of 13 lipid classes, phosphatidylethanolamine (PE), ether-linked phosphatidylethanolamine (ePE) and ether-linked phosphatidylcholine (ePC) could be considered as biomarkers in diagnosis of prostate cancer.

Conclusions/Significance

Using lipidomics and bioinformatic and statistical methods, we have identified a few out of hundreds plasma apparent lipid molecular species as biomarkers for diagnosis of prostate cancer with a high sensitivity, specificity and accuracy.     

Plant adaptation to frequent alterations between high and low temperatures: remodelling of membrane lipids and maintenance of unsaturation levels

One major strategy by which plants adapt to temperature change is to decrease the degree of unsaturation of membrane lipids under high temperature and increase it under low temperature. We hypothesize that this strategy cannot be adopted by plants in ecosystems and environments with frequent alterations between high and low temperatures, because changes in lipid unsaturation are complex and require large energy inputs. To test this hypothesis, we used a lipidomics approach to profile changes in molecular species of membrane glycerolipids in two plant species sampled from alpine screes and in another two plant species grown in a growth chamber, with the temperature cycling daily between heat and freezing. We found that six classes of phospholipid and two classes of galactolipid showed significant changes, but the degree of unsaturation of total lipids and of three lysophospholipid classes remained unchanged. This pattern of changes in membrane lipids was distinct from that occurring during slow alterations in temperature. We propose two types of model for the adaptation of plants to temperature change: (1) remodelling of membrane lipids but maintenance of the degree of unsaturation are used to adapt to frequent temperature alterations; and (2) both remodelling and changes in the degree of unsaturation to adapt to infrequent temperature alterations.     

Fatty Chains of Different Lipid Classes of Semliki Forest Virus and Host Cell Membranes

Semliki Forest virus was grown in BHK-21 cells. The major classes of phospho-and glycolipids of the virus were analyzed for the compositions of fatty acids, aldehydes, and sphingosine bases, and the major glycerophospholipids were analyzed for the relative proportions of alkenyl-acyl, alkyl-acyl, and diacyl forms. All viral lipid classes proved to be mixtures of several molecular species. Each class contained a characteristic mixture of fatty chains, which was different in all other classes. All viral lipid classes resembled their counterparts of the host plasma membrane and also those of the endoplasmic reticulum. The gangliosides of the virus and the plasma membrane proved to be similar even at the level of individual molecular species. The number of certain lipid molecules in an average virion was less than the number of the protein molecules.     

Differential changes in galactolipid and phospholipid species in soybean leaves and roots under nitrogen deficiency and after nodulation

The availability of nitrogen (N) to plants has a profound impact on carbohydrate and protein metabolism, but little is known about its effect on membrane lipid species. This study examines the changes in galactolipid and phospholipid species in soybean as affected by the availability of N, either supplied to soil or obtained through Bradyrhizobium japonicum nodulation. When N was limited in soil, the content of galactolipids, monogalactosyldiacylglycerol (MGDG) and digalactosyldiacyglycerol (DGDG), decreased drastically in leaves, while a smaller decrease of DGDG was observed in roots. In both leaves and roots, the overall content of different phospholipid classes was largely unchanged by N limitation, although some individual phospholipid molecular species did display significant changes. Nodulation with Bradyrhizobium of soybean grown in N-deficient soil resulted in a large increase in levels of plastidic lipid classes, MGDG, DGDG, and phosphatidylglycerol, along with smaller increases in non-plastidic phospholipids in leaves. Nodulation also led to higher levels of phospholipids in roots without changes in root levels of MGDG and DGDG. Overall, N availability alters lipid content more in leaves than roots and more in galactolipids than phospholipids. Increased N availability leads to increased galactolipid accumulation in leaves, regardless of whether N is supplied from the soil or symbiotic fixation.     

Lipid and Fatty Acid Composition in the Flesh of an Edible Marine Fish: Amadi (Coilia reynaldi)

Amadi is a small sized edible marine fish species (Coilia reynaldi) under the order-Clupeiformes. It is important for principal lipids and in particular for highly unsaturated fatty acids which have potential biomedical benefits. Among the lipid classes, phospholipids were found to be the most predominant constituents than the glycolipid and neutral lipid in Amadi. Twenty six fatty acids were quantified by open tube gas–liquid chromatography. Dominant fatty acids in this fish are Palmitic acid (C_16:0), Stearic acid (C_18:0), Oleic acid (C_18:1n?9), Myristic acid (C_14:0), Palmitoleic acid (C_16:1), Docosahexanoic acid (C_22:6n?3), Pentadecanoic acid (C_15:0), and Eicosatetraenoic acid (C_20:4n?3). Fatty acid deficiency in fish species is indicated by the presence of C_20:3n?9 acid. It is absent in this fish.The content of DHA and EPA are maximum in amount in neutral lipid than other lipid classes.     

Variation in corn (Zea mays L.) for fatty acid compositions of triglycerides and phospholipids

The percentage of linoleic acid in corn germ oil of three crosses, C103D × B73, C103D×B84, and T220×H51, and their reciprocals was investigated. Corn germ oil from F₂, F₃, and backcrossed generations was also examined. More than one gene locus appeared to be involved in conditioning the linoleic acid content in these crosses. Strong maternal effects were exhibited in the F₁'s. Genotype also superimposed variations in fatty acid compositions within the characteristic lipid class patterns of the phospholipids, phosphatidylcholine, phosphatidylethanolamine, and phosphatidylinositol. Fatty acid placements in triglycerides, digalactosyldiglycerides, and phospholipids of one inbred, H51, were determined by lipase and phospholipase hydrolysis. The overall pattern of placement showed that the fatty acids at the 1 position were predominately saturated and those at the 2 position were predominately unsaturated, but the fatty acid distribution was different for each individual lipid class. The molecular species of the phosphatidylcholines and phosphatidylethanolamines were separated by silver nitrate thin-layer chromatography. The major differences in the molecular species were a higher level of the dienoic-dienoic species and a lower level of the monoenoic-monoenoic species in the phosphatidylethanolamines than in the phosphatidylcholines.     

Phospholipid analogues of Porphyromonas gingivalis

Porphyromonas has lipids containing hydroxy acids and C16:0 and iso-C15:0 major monocarboxylic acids among others. Nothing is known of its individual phospholipid molecular species. The aim of this study was to determine molecular weights and putative identities of individual phospholipid molecular species extracted from Porphyromonas gingivalis (seven strains), P. asaccharolytica (one strain) and P. endodontalis (two strains). Cultures on Blood-Fastidious Anaerobe Agar were harvested, washed and freeze-dried. Phospholipids were extracted and separated by fast atom bombardment mass spectrometry (FAB MS) in negative-ion mode. Phospholipid classes were also separated by thin layer chromatography (TLC). The major anions in the range m/z 209-299 were consistent with the presence of the C13: 0, C15: 0, C16: 0 and C18: 3 mono-carboxylate anions. Major polar lipid anion peaks in the range m/z 618-961 were consistent with the presence of molecular species of phosphatidylethanolamine, phosphatidylglycerol and with unidentified lipid analogues. Porphyromonas gingivalis differed from comparison strains of other species by having major anions with m/z 932, 946 and 960. Unusually, a feline strain of P. gingivalis had a major peak of m/z 736. Selected anions were studied by tandem FAB MS which revealed that peaks with m/z 653 and 946 did not correspond to commonly occurring classes of polar lipids. They were however, glycerophosphates. It is concluded that the polar lipid analogue profiles obtained with Porphyromonas are quite different from those of the genera Prevotella and Bacteroides but reveal heterogeneity within P. gingivalis.     

The electrical interplay between proteins and lipids in membranes

All molecular interactions that are relevant to cellular and molecular structures are electrical in nature but manifest in a rich variety of forms that each has its own range and influences on the net effect of how molecular species interact. This article outlines how electrical interactions between the protein and lipid membrane components underlie many of the activities of membrane function. Particular emphasis is placed on spatially localised behaviour in membranes involving modulation of protein activity and microdomain structure.The interactions between membrane lipids and membrane proteins together with their role within cell biology represent an enormous body of work. Broad conclusions are not easy given the complexities of the various systems and even consensus with model membrane systems containing two or three lipid types is difficult. By defining two types of broad lipid–protein interaction, respectively Type I as specific and Type II as more non-specific and focussing on the electrical interactions mostly in the extra-membrane regions it is possible to assemble broad rules or a consensus of the dominant features of the interplay between these two fundamentally important classes of membrane component. This article is part of a special issue entitled: Lipid–protein interactions.