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20 pages, 7024 KiB

Open AccessArticle

Chasing the Major Sphingolipids on Earth: Automated Annotation of Plant Glycosyl Inositol Phospho Ceramides by Glycolipidomics

by Lisa Panzenboeck, Nina Troppmair, Sara Schlachter, Gunda Koellensperger, Jürgen Hartler and Evelyn Rampler

Metabolites 2020, 10(9), 375; https://doi.org/10.3390/metabo10090375 - 19 Sep 2020

Cited by 8 | Viewed by 3657

Abstract

Glycosyl inositol phospho ceramides (GIPCs) are the major sphingolipids on earth, as they account for a considerable fraction of the total lipids in plants and fungi, which in turn represent a large portion of the biomass on earth. Despite their obvious importance, GIPC [...] Read more.

Glycosyl inositol phospho ceramides (GIPCs) are the major sphingolipids on earth, as they account for a considerable fraction of the total lipids in plants and fungi, which in turn represent a large portion of the biomass on earth. Despite their obvious importance, GIPC analysis remains challenging due to the lack of commercial standards and automated annotation software. In this work, we introduce a novel GIPC glycolipidomics workflow based on reversed-phase ultra-high pressure liquid chromatography coupled to high-resolution mass spectrometry. For the first time, automated GIPC assignment was performed using the open-source software Lipid Data Analyzer (LDA), based on platform-independent decision rules. Four different plant samples (salad, spinach, raspberry, and strawberry) were analyzed and the results revealed 64 GIPCs based on accurate mass, characteristic MS2 fragments and matching retention times. Relative quantification using lactosyl ceramide for internal standardization revealed GIPC t18:1/h24:0 as the most abundant species in all plants. Depending on the plant sample, GIPCs contained mainly amine, N-acetylamine or hydroxyl residues. Most GIPCs revealed a Hex-HexA-IPC core and contained a ceramide part with a trihydroxylated t18:0 or a t18:1 long chain base and hydroxylated fatty acid chains ranging from 16 to 26 carbon atoms in length (h16:0–h26:0). Interestingly, four GIPCs containing t18:2 were observed in the raspberry sample, which was not reported so far. The presented workflow supports the characterization of different plant samples by automatic GIPC assignment, potentially leading to the identification of new GIPCs. For the first time, automated high-throughput profiling of these complex glycolipids is possible by liquid chromatography-high-resolution tandem mass spectrometry and subsequent automated glycolipid annotation based on decision rules. Full article

(This article belongs to the Special Issue Advances in Lipidomics: Biomedicine, Nutrients and Methodology)

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15 pages, 3618 KiB

Open AccessArticle

Plasma Lipid Profiling of Three Types of Drug-Induced Liver Injury in Japanese Patients: A Preliminary Study

by Kosuke Saito, Tatehiro Kagawa, Keiji Tsuji, Yuji Kumagai, Ken Sato, Shotaro Sakisaka, Naoya Sakamoto, Mitsuhiko Aiso, Shunji Hirose, Nami Mori, Rieko Tanaka, Toshio Uraoka, Kazuhide Takata, Koji Ogawa, Kazuhiko Mori, Motonobu Sato, Takayoshi Nishiya, Kazuhiko Takamatsu, Noriaki Arakawa, Takashi Izumi, Yasuo Ohno, Yoshiro Saito and Hajime Takikawa Show full author list Hide full author list

Metabolites 2020, 10(9), 355; https://doi.org/10.3390/metabo10090355 - 31 Aug 2020

Cited by 7 | Viewed by 2478

Abstract

Drug-induced liver injury (DILI) is a major adverse event caused by drug treatment, which can be categorized into three types: hepatocellular, mixed, and cholestatic. Although nearly every class of drugs can cause DILI, an overall understanding of lipid profiles in DILI patients is [...] Read more.

Drug-induced liver injury (DILI) is a major adverse event caused by drug treatment, which can be categorized into three types: hepatocellular, mixed, and cholestatic. Although nearly every class of drugs can cause DILI, an overall understanding of lipid profiles in DILI patients is lacking. We used lipidomics to analyze the plasma lipid profiles of patients to understand their hepatic pathophysiology and identify DILI biomarkers. We identified 463 lipids and compared their levels between the acute and recovery phases of the three types of DILI patients. Mixed and cholestatic types demonstrated specific plasma lipid alterations between the phases, but the hepatocellular type did not. Moreover, as specific indicators of mixed-type DILI, levels of several ceramides increased in the acute phase, while those of arachidonic acid-containing ether-linked phosphoglycerolipids decreased. In contrast, as specific indicators of cholestatic-type DILI, levels of palmitic acid-containing saturated or monounsaturated phosphatidylcholines increased in the acute phase, while those of arachidonic acid- or docosahexaenoic acid-containing ether-linked phosphoglycerolipids and phosphatidylinositols decreased. We also identified lipids with a relatively high capacity to discriminate the acute phase from the recovery phase and healthy subjects. These findings may help with understanding the pathophysiology of different DILI types and identify candidate biomarkers. Full article

(This article belongs to the Special Issue Advances in Lipidomics: Biomedicine, Nutrients and Methodology)

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18 pages, 1549 KiB

Open AccessArticle

Lipidomic Profiling of the Epidermis in a Mouse Model of Dermatitis Reveals Sexual Dimorphism and Changes in Lipid Composition before the Onset of Clinical Disease

by Jackeline Franco, Bartek Rajwa, Christina R. Ferreira, John P. Sundberg and Harm HogenEsch

Metabolites 2020, 10(7), 299; https://doi.org/10.3390/metabo10070299 - 21 Jul 2020

Cited by 10 | Viewed by 2492

Abstract

Atopic dermatitis (AD) is a multifactorial disease associated with alterations in lipid composition and organization in the epidermis. Multiple variants of AD exist with different outcomes in response to therapies. The evaluation of disease progression and response to treatment are observational assessments with [...] Read more.

Atopic dermatitis (AD) is a multifactorial disease associated with alterations in lipid composition and organization in the epidermis. Multiple variants of AD exist with different outcomes in response to therapies. The evaluation of disease progression and response to treatment are observational assessments with poor inter-observer agreement highlighting the need for molecular markers. SHARPIN-deficient mice (Sharpin^cpdm) spontaneously develop chronic proliferative dermatitis with features similar to AD in humans. To study the changes in the epidermal lipid-content during disease progression, we tested 72 epidermis samples from three groups (5-, 7-, and 10-weeks old) of cpdm mice and their WT littermates. An agnostic mass-spectrometry strategy for biomarker discovery termed multiple-reaction monitoring (MRM)-profiling was used to detect and monitor 1,030 lipid ions present in the epidermis samples. In order to select the most relevant ions, we utilized a two-tiered filter/wrapper feature-selection strategy. Lipid categories were compressed, and an elastic-net classifier was used to rank and identify the most predictive lipid categories for sex, phenotype, and disease stages of cpdm mice. The model accurately classified the samples based on phospholipids, cholesteryl esters, acylcarnitines, and sphingolipids, demonstrating that disease progression cannot be defined by one single lipid or lipid category. Full article

(This article belongs to the Special Issue Advances in Lipidomics: Biomedicine, Nutrients and Methodology)

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27 pages, 3153 KiB

Open AccessArticle

LC–MS Lipidomics: Exploiting a Simple High-Throughput Method for the Comprehensive Extraction of Lipids in a Ruminant Fat Dose-Response Study

by Benjamin Jenkins, Martin Ronis and Albert Koulman

Metabolites 2020, 10(7), 296; https://doi.org/10.3390/metabo10070296 - 17 Jul 2020

Cited by 20 | Viewed by 4465

Abstract

Typical lipidomics methods incorporate a liquid–liquid extraction with LC–MS quantitation; however, the classic sample extraction methods are not high-throughput and do not perform well at extracting the full range of lipids especially, the relatively polar species (e.g., acyl-carnitines and glycosphingolipids). In this manuscript, [...] Read more.

Typical lipidomics methods incorporate a liquid–liquid extraction with LC–MS quantitation; however, the classic sample extraction methods are not high-throughput and do not perform well at extracting the full range of lipids especially, the relatively polar species (e.g., acyl-carnitines and glycosphingolipids). In this manuscript, we present a novel sample extraction protocol, which produces a single phase supernatant suitable for high-throughput applications that offers greater performance in extracting lipids across the full spectrum of species. We applied this lipidomics pipeline to a ruminant fat dose–response study to initially compare and validate the different extraction protocols but also to investigate complex lipid biomarkers of ruminant fat intake (adjoining onto simple odd chain fatty acid correlations). We have found 100 lipids species with a strong correlation with ruminant fat intake. This novel sample extraction along with the LC–MS pipeline have shown to be sensitive, robust and hugely informative (>450 lipids species semi-quantified): with a sample preparation throughput of over 100 tissue samples per day and an estimated ~1000 biological fluid samples per day. Thus, this work facilitating both the epidemiological involvement of ruminant fat, research into odd chain lipids and also streamlining the field of lipidomics (both by sample preparation methods and data presentation). Full article

(This article belongs to the Special Issue Advances in Lipidomics: Biomedicine, Nutrients and Methodology)

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18 pages, 5925 KiB

Open AccessArticle

Lipid Annotation by Combination of UHPLC-HRMS (MS), Molecular Networking, and Retention Time Prediction: Application to a Lipidomic Study of In Vitro Models of Dry Eye Disease

by Romain Magny, Anne Regazzetti, Karima Kessal, Gregory Genta-Jouve, Christophe Baudouin, Stéphane Mélik-Parsadaniantz, Françoise Brignole-Baudouin, Olivier Laprévote and Nicolas Auzeil

Metabolites 2020, 10(6), 225; https://doi.org/10.3390/metabo10060225 - 29 May 2020

Cited by 18 | Viewed by 3948

Abstract

Annotation of lipids in untargeted lipidomic analysis remains challenging and a systematic approach needs to be developed to organize important datasets with the help of bioinformatic tools. For this purpose, we combined tandem mass spectrometry-based molecular networking with retention time (t_R) [...] Read more.

Annotation of lipids in untargeted lipidomic analysis remains challenging and a systematic approach needs to be developed to organize important datasets with the help of bioinformatic tools. For this purpose, we combined tandem mass spectrometry-based molecular networking with retention time (t_R) prediction to annotate phospholipid and sphingolipid species. Sixty-five standard compounds were used to establish the fragmentation rules of each lipid class studied and to define the parameters governing their chromatographic behavior. Molecular networks (MNs) were generated through the GNPS platform using a lipid standards mixture and applied to lipidomic study of an in vitro model of dry eye disease, i.e., human corneal epithelial (HCE) cells exposed to hyperosmolarity (HO). These MNs led to the annotation of more than 150 unique phospholipid and sphingolipid species in the HCE cells. This annotation was reinforced by comparing theoretical to experimental t_R values. This lipidomic study highlighted changes in 54 lipids following HO exposure of corneal cells, some of them being involved in inflammatory responses. The MN approach coupled to t_R prediction thus appears as a suitable and robust tool for the discovery of lipids involved in relevant biological processes. Full article

(This article belongs to the Special Issue Advances in Lipidomics: Biomedicine, Nutrients and Methodology)

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15 pages, 4548 KiB

Open AccessArticle

Oxylipin Profiles in Plasma of Patients with Wilson’s Disease

by Nadezhda V. Azbukina, Alexander V. Lopachev, Dmitry V. Chistyakov, Sergei V. Goriainov, Alina A. Astakhova, Vsevolod V. Poleshuk, Rogneda B. Kazanskaya, Tatiana N. Fedorova and Marina G. Sergeeva

Metabolites 2020, 10(6), 222; https://doi.org/10.3390/metabo10060222 - 29 May 2020

Cited by 12 | Viewed by 3004

Abstract

Wilson’s disease (WD) is a rare autosomal recessive metabolic disorder resulting from mutations in the copper-transporting, P-type ATPase gene ATP7B gene, but influences of epigenetics, environment, age, and sex-related factors on the WD phenotype complicate diagnosis and clinical manifestations. Oxylipins, derivatives of omega-3, [...] Read more.

Wilson’s disease (WD) is a rare autosomal recessive metabolic disorder resulting from mutations in the copper-transporting, P-type ATPase gene ATP7B gene, but influences of epigenetics, environment, age, and sex-related factors on the WD phenotype complicate diagnosis and clinical manifestations. Oxylipins, derivatives of omega-3, and omega-6 polyunsaturated fatty acids (PUFAs) are signaling mediators that are deeply involved in innate immunity responses; the regulation of inflammatory responses, including acute and chronic inflammation; and other disturbances related to any system diseases. Therefore, oxylipin profile tests are attractive for the diagnosis of WD. With UPLC-MS/MS lipidomics analysis, we detected 43 oxylipins in the plasma profiles of 39 patients with various clinical manifestations of WD compared with 16 healthy controls (HCs). Analyzing the similarity matrix of oxylipin profiles allowed us to cluster patients into three groups. Analysis of the data by VolcanoPlot and partial least square discriminant analysis (PLS-DA) showed that eight oxylipins and lipids stand for the variance between WD and HCs: eicosapentaenoic acid EPA, oleoylethanolamide OEA, octadecadienoic acids 9-HODE, 9-KODE, 12-hydroxyheptadecatrenoic acid 12-HHT, prostaglandins PGD2, PGE2, and 14,15-dihydroxyeicosatrienoic acids 14,15-DHET. The compounds indicate the involvement of oxidative stress damage, inflammatory processes, and peroxisome proliferator-activated receptor (PPAR) signaling pathways in this disease. The data reveal novel possible therapeutic targets and intervention strategies for treating WD. Full article

(This article belongs to the Special Issue Advances in Lipidomics: Biomedicine, Nutrients and Methodology)

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21 pages, 2988 KiB

Open AccessArticle

Lipidomic Phenotyping Reveals Extensive Lipid Remodeling during Adipogenesis in Human Adipocytes

by Florian Miehle, Gabriele Möller, Alexander Cecil, Jutta Lintelmann, Martin Wabitsch, Janina Tokarz, Jerzy Adamski and Mark Haid

Metabolites 2020, 10(6), 217; https://doi.org/10.3390/metabo10060217 - 26 May 2020

Cited by 8 | Viewed by 2987

Abstract

Differentiation of preadipocytes into mature adipocytes is a highly complex cellular process. At lipidome level, the adipogenesis remains poorly characterized. To investigate the lipidomic changes during human adipogenesis, we used the Lipidyzer^TM assay, which quantified 743 lipid species from 11 classes. The [...] Read more.

Differentiation of preadipocytes into mature adipocytes is a highly complex cellular process. At lipidome level, the adipogenesis remains poorly characterized. To investigate the lipidomic changes during human adipogenesis, we used the Lipidyzer^TM assay, which quantified 743 lipid species from 11 classes. The undifferentiated human SGBS cell strain showed a heterogeneous lipid class composition with the most abundant classes, phosphatidylethanolamines (PE), phosphatidylcholines (PC), and sphingomyelins (SM). The differentiation process was accompanied by increased ceramide concentrations. After completion of differentiation around day 4, massive lipid remodeling occurred during maturation, characterized by substantial synthesis of diacylglycerols (DAG), lysophosphatidylethanolamines (LPE), PC, PE, SM, and triacylglycerols (TAG). Lipid species composition became more homogeneous during differentiation to highly concentrated saturated and monounsaturated long-chain fatty acids (LCFA), with the four most abundant being C16:0, C16:1, C18:0, and C18:1. Simultaneously, the amount of polyunsaturated and very long-chain fatty acids (VLCFA) markedly decreased. High negative correlation coefficients between PE and PC species containing VLCFA and TAG species as well as between ceramides and SM imply that PE, PC, and ceramides might have served as additional sources for TAG and SM synthesis, respectively. These results highlight the enormous remodeling at the lipid level over several lipid classes during adipogenesis. Full article

(This article belongs to the Special Issue Advances in Lipidomics: Biomedicine, Nutrients and Methodology)

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11 pages, 1661 KiB

Open AccessArticle

Increased Expression of the Leptin Gene in Adipose Tissue of Patients with Chronic Kidney Disease–The Possible Role of an Abnormal Serum Fatty Acid Profile

by Justyna Korczyńska, Aleksandra Czumaj, Michał Chmielewski, Maciej Śledziński, Adriana Mika and Tomasz Śledziński

Metabolites 2020, 10(3), 98; https://doi.org/10.3390/metabo10030098 - 08 Mar 2020

Cited by 6 | Viewed by 2203

Abstract

Chronic kidney disease (CKD) is associated with an increased level of leptin and an abnormal fatty acid (FA) profile in the serum. However, there are no data on the associations between them, and the reason for increased serum levels in patients with CKD [...] Read more.

Chronic kidney disease (CKD) is associated with an increased level of leptin and an abnormal fatty acid (FA) profile in the serum. However, there are no data on the associations between them, and the reason for increased serum levels in patients with CKD is not well elucidated. Recently, we found that a CKD-related abnormal FA profile caused significant changes in the expression of genes involved in lipid metabolism in hepatocytes. The aim of this study was to examine whether leptin gene expression in subcutaneous adipose tissue (SAT) of patients with CKD may contribute to increased serum levels of this adipokine and whether the abnormal serum FA profile observed in CKD patients has an impact on leptin gene expression in adipocytes. The FA profile was measured in serum samples from patients with CKD and controls by GC–MS. The relative mRNA levels of leptin were measured in SAT by Real-Time PCR. Moreover, the effect of the CKD-related abnormal FA profile on leptin gene expression was studied in in vitro cultured 3T3-L1 adipocytes. Patients with CKD had higher concentrations of serum leptin than controls and higher expression level of the leptin gene in SAT. They also had increased serum monounsaturated FAs and decreased polyunsaturated FAs. The incubation of adipocytes with FAs isolated from CKD patients resulted in an increase of the levels of leptin mRNA. Increased leptin gene expression in SAT may contribute to elevated concentrations of these adipokine in patients with CKD. CKD-related alterations of the FA profile may contribute to elevated serum leptin concentrations in patients with CKD by increasing the gene expression of this adipokine in SAT. Full article

(This article belongs to the Special Issue Advances in Lipidomics: Biomedicine, Nutrients and Methodology)

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Review

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22 pages, 1653 KiB

Open AccessReview

Lipidomics Issues on Human Positive ssRNA Virus Infection: An Update

by David Balgoma, Luis Gil-de-Gómez and Olimpio Montero

Metabolites 2020, 10(9), 356; https://doi.org/10.3390/metabo10090356 - 31 Aug 2020

Cited by 9 | Viewed by 3102

Abstract

The pathogenic mechanisms underlying the Biology and Biochemistry of viral infections are known to depend on the lipid metabolism of infected cells. From a lipidomics viewpoint, there are a variety of mechanisms involving virus infection that encompass virus entry, the disturbance of host [...] Read more.

The pathogenic mechanisms underlying the Biology and Biochemistry of viral infections are known to depend on the lipid metabolism of infected cells. From a lipidomics viewpoint, there are a variety of mechanisms involving virus infection that encompass virus entry, the disturbance of host cell lipid metabolism, and the role played by diverse lipids in regard to the infection effectiveness. All these aspects have currently been tackled separately as independent issues and focused on the function of proteins. Here, we review the role of cholesterol and other lipids in ssRNA+ infection. Full article

(This article belongs to the Special Issue Advances in Lipidomics: Biomedicine, Nutrients and Methodology)

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26 pages, 1743 KiB

Open AccessReview

Fatty Acids and Membrane Lipidomics in Oncology: A Cross-Road of Nutritional, Signaling and Metabolic Pathways

by Carla Ferreri, Anna Sansone, Rosaria Ferreri, Javier Amézaga and Itziar Tueros

Metabolites 2020, 10(9), 345; https://doi.org/10.3390/metabo10090345 - 25 Aug 2020

Cited by 29 | Viewed by 5220

Abstract

Fatty acids are closely involved in lipid synthesis and metabolism in cancer. Their amount and composition are dependent on dietary supply and tumor microenviroment. Research in this subject highlighted the crucial event of membrane formation, which is regulated by the fatty acids’ molecular [...] Read more.

Fatty acids are closely involved in lipid synthesis and metabolism in cancer. Their amount and composition are dependent on dietary supply and tumor microenviroment. Research in this subject highlighted the crucial event of membrane formation, which is regulated by the fatty acids’ molecular properties. The growing understanding of the pathways that create the fatty acid pool needed for cell replication is the result of lipidomics studies, also envisaging novel fatty acid biosynthesis and fatty acid-mediated signaling. Fatty acid-driven mechanisms and biological effects in cancer onset, growth and metastasis have been elucidated, recognizing the importance of polyunsaturated molecules and the balance between omega-6 and omega-3 families. Saturated and monounsaturated fatty acids are biomarkers in several types of cancer, and their characterization in cell membranes and exosomes is under development for diagnostic purposes. Desaturase enzymatic activity with unprecedented de novo polyunsaturated fatty acid (PUFA) synthesis is considered the recent breakthrough in this scenario. Together with the link between obesity and cancer, fatty acids open interesting perspectives for biomarker discovery and nutritional strategies to control cancer, also in combination with therapies. All these subjects are described using an integrated approach taking into account biochemical, biological and analytical aspects, delineating innovations in cancer prevention, diagnostics and treatments. Full article

(This article belongs to the Special Issue Advances in Lipidomics: Biomedicine, Nutrients and Methodology)

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15 pages, 522 KiB

Open AccessReview

Lipidomic-Based Advances in Diagnosis and Modulation of Immune Response to Cancer

by Luis Gil-de-Gómez, David Balgoma and Olimpio Montero

Metabolites 2020, 10(8), 332; https://doi.org/10.3390/metabo10080332 - 14 Aug 2020

Cited by 11 | Viewed by 2629

Abstract

While immunotherapies for diverse types of cancer are effective in many cases, relapse is still a lingering problem. Like tumor cells, activated immune cells have an anabolic metabolic profile, relying on glycolysis and the increased uptake and synthesis of fatty acids. In contrast, [...] Read more.

While immunotherapies for diverse types of cancer are effective in many cases, relapse is still a lingering problem. Like tumor cells, activated immune cells have an anabolic metabolic profile, relying on glycolysis and the increased uptake and synthesis of fatty acids. In contrast, immature antigen-presenting cells, as well as anergic and exhausted T-cells have a catabolic metabolic profile that uses oxidative phosphorylation to provide energy for cellular processes. One goal for enhancing current immunotherapies is to identify metabolic pathways supporting the immune response to tumor antigens. A robust cell expansion and an active modulation via immune checkpoints and cytokine release are required for effective immunity. Lipids, as one of the main components of the cell membrane, are the key regulators of cell signaling and proliferation. Therefore, lipid metabolism reprogramming may impact proliferation and generate dysfunctional immune cells promoting tumor growth. Based on lipid-driven signatures, the discrimination between responsiveness and tolerance to tumor cells will support the development of accurate biomarkers and the identification of potential therapeutic targets. These findings may improve existing immunotherapies and ultimately prevent immune escape in patients for whom existing treatments have failed. Full article

(This article belongs to the Special Issue Advances in Lipidomics: Biomedicine, Nutrients and Methodology)

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19 pages, 6919 KiB

Open AccessReview

The Cardiac Lipidome in Models of Cardiovascular Disease

by Mateusz M. Tomczyk and Vernon W. Dolinsky

Metabolites 2020, 10(6), 254; https://doi.org/10.3390/metabo10060254 - 17 Jun 2020

Cited by 22 | Viewed by 3574

Abstract

Cardiovascular disease (CVD) is the leading cause of death worldwide. There are numerous factors involved in the development of CVD. Among these, lipids have an important role in maintaining the myocardial cell structure as well as cardiac function. Fatty acids (FA) are utilized [...] Read more.

Cardiovascular disease (CVD) is the leading cause of death worldwide. There are numerous factors involved in the development of CVD. Among these, lipids have an important role in maintaining the myocardial cell structure as well as cardiac function. Fatty acids (FA) are utilized for energy, but also contribute to the pathogenesis of CVD and heart failure. Advances in mass spectrometry methods have enabled the comprehensive analysis of a plethora of lipid species from a single sample comprised of a heterogeneous population of lipid molecules. Determining cardiac lipid alterations in different models of CVD identifies novel biomarkers as well as reveals molecular mechanisms that underlie disease development and progression. This information could inform the development of novel therapeutics in the treatment of CVD. Herein, we provide a review of recent studies of cardiac lipid profiles in myocardial infarction, obesity, and diabetic and dilated cardiomyopathy models of CVD by methods of mass spectrometry analysis. Full article

(This article belongs to the Special Issue Advances in Lipidomics: Biomedicine, Nutrients and Methodology)

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