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A special issue of Biomolecules (ISSN 2218-273X).

Deadline for manuscript submissions: closed (31 October 2018) | Viewed by 80593

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Prof. Dr. Harald C. Köfeler

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Guest Editor

Center for Medical Research (ZMF), Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
Interests: lipidomics; mass spectrometry
Special Issues, Collections and Topics in MDPI journals

Dr. Gerald N. Rechberger

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Guest Editor

Department of Molecular Biosciences, University of Graz, Graz, Austria
Interests: lipidomics; mass spectrometry; chromatography; method development

Special Issue Information

Dear Colleagues,

Two decades after the genomic life science revolution, which paved the road for elucidation of the genotype, scientists are still trying to get a grip on the phenotype. One highly-vital group of biomolecules that determines the phenotype is the lipidome, sometimes it is even regarded as the most important group because compartmentalization of living organisms from their environment is the physical basis of any and all life. Nevertheless, analysis of the lipidome in its entity is neither simple nor straightforward, although over the last two decades constant technological progress has been made in lipidomics. The underlying key technology to lipidomics is mass spectrometry, often coupled to chromatography. This Special Issue on lipidomics should on one hand emphasize the importance of this ‘omics’ technology, and on the other hand it should also highlight existing methodological bottlenecks and limitations. In this regard we would like to invite review articles which address the above-mentioned issues either from an analytical or a biological perspective. Alternatively, any original research papers contributing significantly to technical progress—be it sample preparation, analytical methods or bioinformatic data analysis—or advancing our understanding of biological processes by innovative interpretation strategies of lipidomic data, are highly welcome.

We look forward to reading your contributions.

Dr. Harald C. Köfeler
Dr. Gerald N. Rechberger
Guest Editors

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Keywords

lipidomics
mass spectrometry
chromatography
data processing
lipid metabolism

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Published Papers (11 papers)

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Research

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22 pages, 3457 KiB

Open AccessCommunication

Mining for Oxysterols in Cyp7b1^−/− Mouse Brain and Plasma: Relevance to Spastic Paraplegia Type 5

by Anna Meljon, Peter J. Crick, Eylan Yutuc, Joyce L. Yau, Jonathan R. Seckl, Spyridon Theofilopoulos, Ernest Arenas, Yuqin Wang and William J. Griffiths

Biomolecules 2019, 9(4), 149; https://doi.org/10.3390/biom9040149 - 13 Apr 2019

Cited by 13 | Viewed by 6150

Abstract

Deficiency in cytochrome P450 (CYP) 7B1, also known as oxysterol 7α-hydroxylase, in humans leads to hereditary spastic paraplegia type 5 (SPG5) and in some cases in infants to liver disease. SPG5 is medically characterized by loss of motor neurons in the corticospinal tract. In an effort to gain a better understanding of the fundamental biochemistry of this disorder, we have extended our previous profiling of the oxysterol content of brain and plasma of Cyp7b1 knockout (-/-) mice to include, amongst other sterols, 25-hydroxylated cholesterol metabolites. Although brain cholesterol levels do not differ between wild-type (wt) and knockout mice, we find, using a charge-tagging methodology in combination with liquid chromatography–mass spectrometry (LC–MS) and multistage fragmentation (MSⁿ), that there is a build-up of the CYP7B1 substrate 25-hydroxycholesterol (25-HC) in Cyp7b1-/- mouse brain and plasma. As reported earlier, levels of (25R)26-hydroxycholesterol (26-HC), 3β-hydroxycholest-5-en-(25R)26-oic acid and 24S,25-epoxycholesterol (24S,25-EC) are similarly elevated in brain and plasma. Side-chain oxysterols including 25-HC, 26-HC and 24S,25-EC are known to bind to INSIG (insulin-induced gene) and inhibit the processing of SREBP-2 (sterol regulatory element-binding protein-2) to its active form as a master regulator of cholesterol biosynthesis. We suggest the concentration of cholesterol in brain of the Cyp7b1-/- mouse is maintained by balancing reduced metabolism, as a consequence of a loss in CYP7B1, with reduced biosynthesis. The Cyp7b1-/- mouse does not show a motor defect; whether the defect in humans is a consequence of less efficient homeostasis of cholesterol in brain has yet to be uncovered. Full article

(This article belongs to the Special Issue Lipidomics)

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13 pages, 2056 KiB

Open AccessEditor’s ChoiceArticle

Quantification of Fecal Short Chain Fatty Acids by Liquid Chromatography Tandem Mass Spectrometry—Investigation of Pre-Analytic Stability

by Gerhard Liebisch, Josef Ecker, Sebastian Roth, Sabine Schweizer, Veronika Öttl, Hans-Frieder Schött, Hongsup Yoon, Dirk Haller, Ernst Holler, Ralph Burkhardt and Silke Matysik

Biomolecules 2019, 9(4), 121; https://doi.org/10.3390/biom9040121 - 28 Mar 2019

Cited by 65 | Viewed by 12547

Abstract

Short chain fatty acids (SCFAs) are generated by the degradation and fermentation of complex carbohydrates, (i.e., dietary fiber) by the gut microbiota relevant for microbe–host communication. Here, we present a method for the quantification of SCFAs in fecal samples by liquid chromatography tandem mass spectrometry (LC-MS/MS) upon derivatization to 3-nitrophenylhydrazones (3NPH). The method includes acetate, propionate, butyrate, and isobutyrate with a run time of 4 min. The reproducible (coefficients of variation (CV) below 10%) quantification of SCFAs in human fecal samples was achieved by the application of stable isotope labelled internal standards. The specificity was demonstrated by the introduction of a quantifier and qualifier ions. The method was applied to investigate the pre-analytic stability of SCFAs in human feces. Concentrations of SCFA may change substantially within hours; the degree and kinetics of these changes revealed huge differences between the donors. The fecal SCFA level could be preserved by the addition of organic solvents like isopropanol. An analysis of the colon content of mice either treated with antibiotics or fed with a diet containing a non-degradable and -fermentable fiber source showed decreased SCFA concentrations. In summary, this fast and reproducible method for the quantification of SCFA in fecal samples provides a valuable tool for both basic research and large-scale studies. Full article

(This article belongs to the Special Issue Lipidomics)

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14 pages, 2579 KiB

Open AccessEditor’s ChoiceArticle

High-Throughput Screening of Lipidomic Adaptations in Cultured Cells

by Aike Jeucken and Jos F. Brouwers

Biomolecules 2019, 9(2), 42; https://doi.org/10.3390/biom9020042 - 24 Jan 2019

Cited by 14 | Viewed by 4916

Abstract

High-throughput screening of biologically active substances in cell cultures remains challenging despite great progress in contemporary lipidomic techniques. These experiments generate large amounts of data that are translated into lipid fingerprints. The subsequent visualization of lipidomic changes is key to meaningful interpretation of experimental results. As a demonstration of a rapid and versatile pipeline for lipidomic analysis, we cultured HeLa cells in 96-well format for four days in the presence or absence of various inhibitors of lipid metabolic pathways. Visualization of the data by principle component analysis revealed a high reproducibility of the method, as well as drug specific changes to the lipidome. Construction of heatmaps and networks revealed the similarities and differences between the effects of different drugs at the lipid species level. Clusters of related lipid species that might represent distinct membrane domains emerged after correlation analysis of the complete dataset. Taken together, we present a lipidomic platform for high-throughput lipidomic analysis of cultured cell lines. Full article

(This article belongs to the Special Issue Lipidomics)

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9 pages, 704 KiB

Open AccessArticle

Cord-Blood Lipidome in Progression to Islet Autoimmunity and Type 1 Diabetes

by Santosh Lamichhane, Linda Ahonen, Thomas Sparholt Dyrlund, Alex M. Dickens, Heli Siljander, Heikki Hyöty, Jorma Ilonen, Jorma Toppari, Riitta Veijola, Tuulia Hyötyläinen, Mikael Knip and Matej Oresic

Biomolecules 2019, 9(1), 33; https://doi.org/10.3390/biom9010033 - 21 Jan 2019

Cited by 22 | Viewed by 5860

Abstract

Previous studies suggest that children who progress to type 1 diabetes (T1D) later in life already have an altered serum lipid molecular profile at birth. Here, we compared cord blood lipidome across the three study groups: children who progressed to T1D (PT1D; n = 30), children who developed at least one islet autoantibody but did not progress to T1D during the follow-up (P1Ab; n = 33), and their age-matched controls (CTR; n = 38). We found that phospholipids, specifically sphingomyelins, were lower in T1D progressors when compared to P1Ab and the CTR. Cholesterol esters remained higher in PT1D when compared to other groups. A signature comprising five lipids was predictive of the risk of progression to T1D, with an area under the receiver operating characteristic curve (AUROC) of 0.83. Our findings provide further evidence that the lipidomic profiles of newborn infants who progress to T1D later in life are different from lipidomic profiles in P1Ab and CTR. Full article

(This article belongs to the Special Issue Lipidomics)

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10 pages, 1290 KiB

Open AccessArticle

UPLC–MS Triglyceride Profiling in Sunflower and Rapeseed Seeds

by Alina Chernova, Rim Gubaev, Pavel Mazin, Svetlana Goryunova, Yakov Demurin, Lyudmila Gorlova, Anna Vanushkina, Waltraud Mair, Nikolai Anikanov, Elena Martynova, Denis Goryunov, Sergei Garkusha, Zhanna Mukhina and Philipp Khaytovich

Biomolecules 2019, 9(1), 9; https://doi.org/10.3390/biom9010009 - 27 Dec 2018

Cited by 12 | Viewed by 6489

Abstract

Sunflower and rapeseed are among the most important sources of vegetable oil for food and industry. The main components of vegetable oil are triglycerides (TAGs) (about 97%). Ultra- performance liquid chromatography coupled with mass spectrometry (UPLC–MS) profiling of TAGs in sunflower and rapeseed has been performed and the TAG profiles obtained for these species have been compared. It has been identified that 34 TAGs are shared by sunflower and rapeseed. It was demonstrated that TAGs 52:2, 52:5, 52:6, 54:3; 54:4, 54:7, 56:3, 56:4, and 56:5 had the highest variability levels between sunflower and rapeseed with the higher presence in rapeseed. TAGs 50:2, 52:3, 52:4, 54:5, and 54:6 also showed high variability, but were the most abundant in sunflower. Moreover, the differences in TAG composition between the winter-type and spring-type rapeseed have been revealed, which may be associated with freezing tolerance. It was shown that winter-type rapeseed seeds contain TAGs with a lower degree of saturation, while in spring-type rapeseed highly saturated lipids are the most abundant. These findings may give new insights into the cold resistance mechanisms in plants the understanding of which is especially important in terms of global climate changes. Full article

(This article belongs to the Special Issue Lipidomics)

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16 pages, 2370 KiB

Open AccessArticle

Total Fatty Acid Analysis of Human Blood Samples in One Minute by High-Resolution Mass Spectrometry

by Sandra F. Gallego, Martin Hermansson, Gerhard Liebisch, Leanne Hodson and Christer S. Ejsing

Biomolecules 2019, 9(1), 7; https://doi.org/10.3390/biom9010007 - 27 Dec 2018

Cited by 27 | Viewed by 8002

Abstract

Total fatty acid analysis is a routine method in many areas, including lipotyping of individuals in personalized medicine, analysis of foodstuffs, and optimization of oil production in biotechnology. This analysis is commonly done by converting fatty acyl (FA) chains of intact lipids into FA methyl esters (FAMEs) and monitoring these by gas-chromatography (GC)-based methods, typically requiring at least 15 min of analysis per sample. Here, we describe a novel method that supports fast, precise and accurate absolute quantification of total FA levels in human plasma and serum samples. The method uses acid-catalyzed transesterification with ¹⁸O-enriched H₂O (i.e., H₂¹⁸O) to convert FA chains into ¹⁸O-labeled free fatty acids. The resulting “mass-tagged” FA analytes can be specifically monitored with improved signal-to-background by 1 min of high resolution Fourier transform mass spectrometry (FTMS) on an Orbitrap-based mass spectrometer. By benchmarking to National Institute of Standards and Technology (NIST) certified standard reference materials we show that the performance of our method is comparable, and at times superior, to that of gold-standard GC-based methods. In addition, we demonstrate that the method supports the accurate quantification of FA differences in samples obtained in dietary intervention studies and also affords specific monitoring of ingested stable isotope-labeled fatty acids (¹³C₁₆-palmitate) in normoinsulinemic and hyperinsulinemic human subjects. Overall, our novel high-throughput method is generic and suitable for many application areas, spanning basic research to personalized medicine, and is particularly useful for laboratories equipped with high resolution mass spectrometers, but lacking access to GC-based instrumentation. Full article

(This article belongs to the Special Issue Lipidomics)

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6 pages, 1108 KiB

Open AccessFeature PaperArticle

Distribution of Glycerophospholipids in the Adult Human Lens

by Jo Ann Seng, Jessica R. Nealon, Stephen J. Blanksby and Todd W. Mitchell

Biomolecules 2018, 8(4), 156; https://doi.org/10.3390/biom8040156 - 22 Nov 2018

Cited by 6 | Viewed by 3477

Abstract

In humans, the age of fibre cells differs across the ocular lens, ranging from those formed before birth in the core of the lens to those formed just prior to death in the outer cortex. The distribution of glycerophospholipids in the adult human lens should reflect this range; however, limited data currently exists to confirm this hypothesis. Accordingly, this study aimed to determine the distribution of glycerophospholipids in adult human lens using mass spectrometry imaging. To achieve this, 20-µm thick slices of two human lenses, aged 51 and 67 were analysed by matrix-assisted laser desorption ionisation imaging mass spectrometry. The data clearly indicate that intact glycerophospholipids such as phosphatidylethanolamine, phosphatidylserine, and phosphatidic acid are mainly present in the outer cortex region, corresponding to the youngest fibre cells, while lyso-phosphatidylethanolamine, likely produced by the degradation of phosphatidylethanolamine, is present in the nucleus (older fibre cells). This study adds further evidence to the relationship between fibre cell age and glycerophospholipid composition. Full article

(This article belongs to the Special Issue Lipidomics)

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14 pages, 1376 KiB

Open AccessArticle

Shotgun Lipidomics Revealed Altered Profiles of Serum Lipids in Systemic Lupus Erythematosus Closely Associated with Disease Activity

by Lu Lu, Changfeng Hu, Yanxia Zhao, Lijiao He, Jia Zhou, Haichang Li, Yu Du, Yonghua Wang, Chengping Wen, Xianlin Han and Yongsheng Fan

Biomolecules 2018, 8(4), 105; https://doi.org/10.3390/biom8040105 - 3 Oct 2018

Cited by 33 | Viewed by 4825

Abstract

The pathogenesis of systemic lupus erythematosus (SLE) remains elusive. It appears that serum lipid metabolism is aberrant in SLE patients. Determination of lipid profiles in the serum of SLE patients may provide insights into the underlying mechanism(s) leading to SLE and may discover potential biomarkers for early diagnosis of SLE. This study aimed to identify and quantify the profile of serum lipids in SLE patients (N = 30) with our powerful multi-dimensional mass spectrometry-based shotgun lipidomics platform. Multivariate analysis in the form of partial least squares-discriminate analysis was performed, and the associations between the changed lipids with cytokines and SLE disease activity index (SLEDAI) were analyzed using a multiple regression method. The results of this study indicated that the composition of lipid species including diacyl phosphatidylethanolamine (dPE) (16:0/18:2, 18:0/18:2, 16:0/22:6, 18:0/20:4, and 18:0/22:6), 18:2 lysoPC (LPC), and ceramide (N22:0 and N24:1) was significantly altered in SLE patients with p < 0.05 and variable importance of the projection (VIP) > 1 in partial least squares-discriminate analysis (PLS-DA). There existed significant associations between IL-10, and both 18:0/18:2 and 16:0/22:6 dPE species with p < 0.0001 and predicting 85.7 and 95.8% of the variability of IL-10 levels, respectively. All the altered lipid species could obviously predict IL-10 levels with F (8, 21) = 3.729, p = 0.007, and R² = 0.766. There was also a significant correlation between the SLEDAI score and 18:0/18:2 dPE (p = 0.031) with explaining 22.6% of the variability of SLEDAI score. Therefore, the panel of changed compositions of dPE and ceramide species may serve as additional biomarkers for early diagnosis and/or prognosis of SLE. Full article

(This article belongs to the Special Issue Lipidomics)

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Review

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16 pages, 298 KiB

Open AccessReview

Quantification of Lipids: Model, Reality, and Compromise

by Spiro Khoury, Cécile Canlet, Marlène Z. Lacroix, Olivier Berdeaux, Juliette Jouhet and Justine Bertrand-Michel

Biomolecules 2018, 8(4), 174; https://doi.org/10.3390/biom8040174 - 14 Dec 2018

Cited by 47 | Viewed by 7424

Abstract

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. Full article

(This article belongs to the Special Issue Lipidomics)

25 pages, 8754 KiB

Open AccessReview

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

by Jenny Leopold, Yulia Popkova, Kathrin M. Engel and Jürgen Schiller

Biomolecules 2018, 8(4), 173; https://doi.org/10.3390/biom8040173 - 13 Dec 2018

Cited by 143 | Viewed by 11428

Abstract

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

(This article belongs to the Special Issue Lipidomics)

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14 pages, 1782 KiB

Open AccessReview

Analytical Considerations of Stable Isotope Labelling in Lipidomics

by Alexander Triebl and Markus R. Wenk

Biomolecules 2018, 8(4), 151; https://doi.org/10.3390/biom8040151 - 16 Nov 2018

Cited by 29 | Viewed by 7988

Abstract

Over the last two decades, lipids have come to be understood as far more than merely components of cellular membranes and forms of energy storage, and are now also being implicated to play important roles in a variety of diseases, with lipid biomarker research one of the most widespread applications of lipidomic techniques both in research and in clinical settings. Stable isotope labelling has become a staple technique in the analysis of small molecule metabolism and dynamics, as it is the only experimental setup by which biosynthesis, remodelling and degradation of biomolecules can be directly measured. Using state-of-the-art analytical technologies such as chromatography-coupled high resolution tandem mass spectrometry, the stable isotope label can be precisely localized and quantified within the biomolecules. The application of stable isotope labelling to lipidomics is however complicated by the diversity of lipids and the complexity of the necessary data analysis. This article discusses key experimental aspects of stable isotope labelling in the field of mass spectrometry-based lipidomics, summarizes current applications and provides an outlook on future developments and potential. Full article

(This article belongs to the Special Issue Lipidomics)

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