1
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Jiang H, Milanov M, Jüngert G, Angebauer L, Flender C, Smudde E, Gather F, Vogel T, Jessen HJ, Koch HG. Control of a chemical chaperone by a universally conserved ATPase. iScience 2024; 27:110215. [PMID: 38993675 PMCID: PMC11237923 DOI: 10.1016/j.isci.2024.110215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 05/16/2024] [Accepted: 06/05/2024] [Indexed: 07/13/2024] Open
Abstract
The universally conserved YchF/Ola1 ATPases regulate stress response pathways in prokaryotes and eukaryotes. Deletion of YchF/Ola1 leads to increased resistance against environmental stressors, such as reactive oxygen species, while their upregulation is associated with tumorigenesis in humans. The current study shows that in E. coli, the absence of YchF stimulates the synthesis of the alternative sigma factor RpoS by a transcription-independent mechanism. Elevated levels of RpoS then enhance the transcription of major stress-responsive genes. In addition, the deletion of ychF increases the levels of polyphosphate kinase, which in turn boosts the production of the evolutionary conserved and ancient chemical chaperone polyphosphate. This potentially provides a unifying concept for the increased stress resistance in bacteria and eukaryotes upon YchF/Ola1 deletion. Intriguingly, the simultaneous deletion of ychF and the polyphosphate-degrading enzyme exopolyphosphatase causes synthetic lethality in E. coli, demonstrating that polyphosphate production needs to be fine-tuned to prevent toxicity.
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Affiliation(s)
- Hong Jiang
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, Albert-Ludwigs University Freiburg, 79104 Freiburg, Germany
| | - Martin Milanov
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, Albert-Ludwigs University Freiburg, 79104 Freiburg, Germany
| | - Gabriela Jüngert
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Larissa Angebauer
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Clara Flender
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Eva Smudde
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Fabian Gather
- Institute for Anatomy and Cell Biology, Department of Molecular Embryology, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Tanja Vogel
- Institute for Anatomy and Cell Biology, Department of Molecular Embryology, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Henning J. Jessen
- Institute for Organic Chemistry, Faculty of Chemistry and Pharmacy, University Freiburg 79104 Freiburg, Germany
| | - Hans-Georg Koch
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
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2
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Hussain AA, Bilgin M, Carlsson J, Foged MM, Mortensen EL, Bulik CM, Støving RK, Sjögren JM. Elevated lipid class concentrations in females with anorexia nervosa before and after intensive weight restoration treatment-A lipidomics study. Int J Eat Disord 2023; 56:2260-2272. [PMID: 37715358 DOI: 10.1002/eat.24063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/17/2023]
Abstract
OBJECTIVE To study the plasma lipidome of patients with anorexia nervosa (AN) before and after weight restoration treatment and report associations with AN subtypes and oral contraceptive pill (OCP) usage. METHODS Quantitative shotgun lipidomics analysis was used to study plasma lipids of 50 female patients with AN before and after weight restoration treatment and 50 healthy female controls (HC). The AN group was assessed with blood samples and questionnaires before and after weight restoration. RESULTS In total we quantified 260 lipid species representing 26 lipid classes of which 13 lipid class concentrations were elevated in patients with AN at admission compared with HC. Lipid classes remained elevated after weight restoration treatment of 84 days (median; interquartile range 28), and only the concentration of the ceramide lipid class increased between pre- and post-treatment (p = .03), whereas lysophosphatidylcholine (LPC, p = .02), ether-linked Phosphatidylcholine (LPCO, p = .02), and lysophosphatidylethanolamine (LPE, p = .009) decreased. CONCLUSION In AN, 13 out of 26 lipid class concentrations were elevated at admission and remained elevated post-treatment. Ceramides increased further between pre- and post-weight restoration treatment, which could be related to the rapid weight gain during re-nutrition. Further research is needed to elucidate the effects of weight restoration treatment on short- and long-term lipid profiles in individuals with AN. PUBLIC SIGNIFICANCE STATEMENT Lipidomics research can increase the understanding of AN, a complex and potentially life-threatening eating disorder. By analyzing lipids, or fats, in the body, we can identify biological markers that may inform diagnosis and develop more effective treatments. This research can also shed light on the underlying mechanisms of the disorder, leading to a better understanding of the processes involved in eating behavior.
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Affiliation(s)
- Alia Arif Hussain
- Eating Disorder Research Unit, Mental Health Center, Ballerup, Copenhagen University Hospital-Mental Health Services CPH, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Mesut Bilgin
- Lipidomics Core Facility, Danish Cancer Institute, Copenhagen, Denmark
| | - Jessica Carlsson
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Competence Centre for Transcultural Psychiatry, Mental Health Centre Ballerup, Mental Health Services of the Capital Region of Denmark, Copenhagen, Denmark
| | - Mads Møller Foged
- Lipidomics Core Facility, Danish Cancer Institute, Copenhagen, Denmark
| | - Erik Lykke Mortensen
- Unit of Medical Psychology, Section of Environmental Health, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
- Center for Healthy Aging, University of Copenhagen, Copenhagen, Denmark
| | - Cynthia M Bulik
- Department of Psychiatry, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - René Klinkby Støving
- Center for Eating Disorders, Odense University Hospital, Odense, Denmark
- Research Unit for Medical Endocrinology, Odense University Hospital, Odense, Denmark
- Research Unit, Child and Adolescent Psychiatry, Mental Health Services in the Region of Southern Denmark, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Jan Magnus Sjögren
- Eating Disorder Research Unit, Mental Health Center, Ballerup, Copenhagen University Hospital-Mental Health Services CPH, Copenhagen, Denmark
- Institute of Clinical Science, Department of Psychiatry, Umeå University, Umeå, Sweden
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3
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Yeo J, Kang J, Kim H, Moon C. A Critical Overview of HPLC-MS-Based Lipidomics in Determining Triacylglycerol and Phospholipid in Foods. Foods 2023; 12:3177. [PMID: 37685110 PMCID: PMC10486615 DOI: 10.3390/foods12173177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 09/10/2023] Open
Abstract
With the current advancement in mass spectrometry (MS)-based lipidomics, the knowledge of lipidomes and their diverse roles has greatly increased, enabling a deeper understanding of the action of bioactive lipid molecules in plant- and animal-based foods. This review provides in-depth information on the practical use of MS techniques in lipidomics, including lipid extraction, adduct formation, MS analysis, data processing, statistical analysis, and bioinformatics. Moreover, this contribution demonstrates the effectiveness of MS-based lipidomics for identifying and quantifying diverse lipid species, especially triacylglycerols and phospholipids, in foods. Further, it summarizes the wide applications of MS-based lipidomics in food science, such as for assessing food processing methods, detecting food adulteration, and measuring lipid oxidation in foods. Thus, MS-based lipidomics may be a useful method for identifying the action of individual lipid species in foods.
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Affiliation(s)
- JuDong Yeo
- Department of Food Science and Biotechnology of Animal Resources, Konkuk University, Seoul 05029, Republic of Korea; (J.K.); (H.K.); (C.M.)
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4
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Menzel JP, Young RSE, Benfield AH, Scott JS, Wongsomboon P, Cudlman L, Cvačka J, Butler LM, Henriques ST, Poad BLJ, Blanksby SJ. Ozone-enabled fatty acid discovery reveals unexpected diversity in the human lipidome. Nat Commun 2023; 14:3940. [PMID: 37402773 DOI: 10.1038/s41467-023-39617-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 06/15/2023] [Indexed: 07/06/2023] Open
Abstract
Fatty acid isomers are responsible for an under-reported lipidome diversity across all kingdoms of life. Isomers of unsaturated fatty acids are often masked in contemporary analysis by incomplete separation and the absence of sufficiently diagnostic methods for structure elucidation. Here, we introduce a comprehensive workflow, to discover unsaturated fatty acids through coupling liquid chromatography and mass spectrometry with gas-phase ozonolysis of double bonds. The workflow encompasses semi-automated data analysis and enables de novo identification in complex media including human plasma, cancer cell lines and vernix caseosa. The targeted analysis including ozonolysis enables structural assignment over a dynamic range of five orders of magnitude, even in instances of incomplete chromatographic separation. Thereby we expand the number of identified plasma fatty acids two-fold, including non-methylene-interrupted fatty acids. Detection, without prior knowledge, allows discovery of non-canonical double bond positions. Changes in relative isomer abundances reflect underlying perturbations in lipid metabolism.
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Affiliation(s)
- Jan Philipp Menzel
- School of Chemistry and Physics, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Centre for Materials Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Centre for Data Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Institute of Clinical Chemistry, Inselspital, Bern University Hospital, 3010, Bern, Switzerland
| | - Reuben S E Young
- School of Chemistry and Physics, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Centre for Materials Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Faculty of Science, Medicine and Health, School of Chemistry and Molecular Bioscience, Wollongong, NSW, Australia
| | - Aurélie H Benfield
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Translational Research Institute, Brisbane, QLD, 4102, Australia
| | - Julia S Scott
- South Australian Immunogenomics Cancer Institute and Freemasons Centre for Male Health and Wellbeing, University of Adelaide, Adelaide, SA, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Puttandon Wongsomboon
- School of Chemistry and Physics, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Centre for Materials Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Lukáš Cudlman
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 542/2, 16600, Prague, Czech Republic
- Department of Analytical Chemistry, Faculty of Science, Charles University, Prague 2, Czech Republic
| | - Josef Cvačka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 542/2, 16600, Prague, Czech Republic
- Department of Analytical Chemistry, Faculty of Science, Charles University, Prague 2, Czech Republic
| | - Lisa M Butler
- South Australian Immunogenomics Cancer Institute and Freemasons Centre for Male Health and Wellbeing, University of Adelaide, Adelaide, SA, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Sónia T Henriques
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Translational Research Institute, Brisbane, QLD, 4102, Australia
| | - Berwyck L J Poad
- School of Chemistry and Physics, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Centre for Materials Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Stephen J Blanksby
- School of Chemistry and Physics, Queensland University of Technology, Brisbane, QLD, 4000, Australia.
- Centre for Materials Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia.
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5
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Mønsted MØ, Bilgin M, Kuzma M, Pelantová H, Pedersen K, Tomášová P, Nazmutdinova A, Šedivá B, Funda D, Castro-Mejía JL, Holm LJ, Nielsen DS, Haupt-Jorgensen M. Reduced phosphatidylcholine level in the intestinal mucus layer of prediabetic NOD mice. APMIS 2023; 131:237-248. [PMID: 36811202 DOI: 10.1111/apm.13302] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023]
Abstract
Type 1 diabetes (T1D) is an autoimmune disease with rising incidence. Pre- and manifest T1D is associated with intestinal barrier dysfunction, skewed microbiota composition, and serum dyslipidemia. The intestinal mucus layer protects against pathogens and its structure and phosphatidylcholine (PC) lipid composition may be compromised in T1D, potentially contributing to barrier dysfunction. This study compared prediabetic Non-Obese Diabetic (NOD) mice to healthy C57BL/6 mice by analyzing the intestinal mucus PC profile by shotgun lipidomics, plasma metabolomics by mass spectrometry and nuclear magnetic resonance, intestinal mucus production by histology, and cecal microbiota composition by 16 S rRNA sequencing. Jejunal mucus PC class levels were decreased in early prediabetic NOD vs C57BL/6 mice. In colonic mucus of NOD mice, the level of several PC species was reduced throughout prediabetes. In plasma, similar reductions of PC species were observed in early prediabetic NOD mice, where also increased beta-oxidation was prominent. No histological alterations were found in jejunal nor colonic mucus between the mouse strains. However, the β-diversity of the cecal microbiota composition differed between prediabetic NOD and C57BL/6 mice, and the bacterial species driving this difference were related to decreased short-chain fatty acid (SCFA)-production in the NOD mice. This study reports reduced levels of PCs in the intestinal mucus layer and plasma of prediabetic NOD mice as well as reduced proportions of SCFA-producing bacteria in cecal content at early prediabetes, possibly contributing to intestinal barrier dysfunction and T1D.
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Affiliation(s)
- Mia Øgaard Mønsted
- Department of Pathology, Rigshospitalet, The Bartholin Institute, Copenhagen, Denmark
| | - Mesut Bilgin
- Lipidomics Core Facility, Cell Death and Metabolism Unit, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Marek Kuzma
- Institute of Microbiology, Czech Academy of Sciences, Prague, The Czech Republic
| | - Helena Pelantová
- Institute of Microbiology, Czech Academy of Sciences, Prague, The Czech Republic
| | - Kristina Pedersen
- Department of Pathology, Rigshospitalet, The Bartholin Institute, Copenhagen, Denmark
| | - Petra Tomášová
- Institute of Microbiology, Czech Academy of Sciences, Prague, The Czech Republic
| | | | - Blanka Šedivá
- Faculty of Applied Sciences, University of West Bohemia, Plzeň, The Czech Republic
| | - David Funda
- Institute of Microbiology, Czech Academy of Sciences, Prague, The Czech Republic
| | | | - Laurits Juulskov Holm
- Department of Pathology, Rigshospitalet, The Bartholin Institute, Copenhagen, Denmark
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6
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Kale D, Kikul F, Phapale P, Beedgen L, Thiel C, Brügger B. Quantification of Dolichyl Phosphates Using Phosphate Methylation and Reverse-Phase Liquid Chromatography-High Resolution Mass Spectrometry. Anal Chem 2023; 95:3210-3217. [PMID: 36716239 PMCID: PMC9933046 DOI: 10.1021/acs.analchem.2c03623] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Dolichyl monophosphates (DolPs) are essential lipids in glycosylation pathways that are highly conserved across almost all domains of life. The availability of DolP is critical for all glycosylation processes, as these lipids serve as membrane-anchored building blocks used by various types of glycosyltransferases to generate complex post-translational modifications of proteins and lipids. The analysis of DolP species by reverse-phase liquid chromatography-mass spectrometry (RPLC-MS) remains a challenge due to their very low abundance and wide range of lipophilicities. Until now, a method for the simultaneous qualitative and quantitative assessment of DolP species from biological membranes has been lacking. Here, we describe a novel approach based on simple sample preparation, rapid and efficient trimethylsilyl diazomethane-dependent phosphate methylation, and RPLC-MS analysis for quantification of DolP species with different isoprene chain lengths. We used this workflow to selectively quantify DolP species from lipid extracts derived of Saccharomyces cerevisiae, HeLa, and human skin fibroblasts from steroid 5-α-reductase 3- congenital disorders of glycosylation (SRD5A3-CDG) patients and healthy controls. Integration of this workflow with global lipidomics analyses will be a powerful tool to expand our understanding of the role of DolPs in pathophysiological alterations of metabolic pathways downstream of HMG-CoA reductase, associated with CDGs, hypercholesterolemia, neurodegeneration, and cancer.
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Affiliation(s)
- Dipali Kale
- Heidelberg
University Biochemistry Center (BZH), 69120Heidelberg, Germany,Leibniz-Institut
für Analytische Wissenschaften-ISAS-e.V., 44139Dortmund, Germany,
| | - Frauke Kikul
- Heidelberg
University Biochemistry Center (BZH), 69120Heidelberg, Germany
| | - Prasad Phapale
- Leibniz-Institut
für Analytische Wissenschaften-ISAS-e.V., 44139Dortmund, Germany
| | - Lars Beedgen
- Centre
for Child and Adolescent Medicine, University
Hospital Heidelberg, 69120Heidelberg, Germany
| | - Christian Thiel
- Centre
for Child and Adolescent Medicine, University
Hospital Heidelberg, 69120Heidelberg, Germany
| | - Britta Brügger
- Heidelberg
University Biochemistry Center (BZH), 69120Heidelberg, Germany,
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7
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Pärn A, Olsen D, Tuvikene J, Kaas M, Borisova E, Bilgin M, Elhauge M, Vilstrup J, Madsen P, Ambrozkiewicz MC, Goz RU, Timmusk T, Tarabykin V, Gustafsen C, Glerup S. PCSK9 deficiency alters brain lipid composition without affecting brain development and function. Front Mol Neurosci 2023; 15:1084633. [PMID: 36733269 PMCID: PMC9887304 DOI: 10.3389/fnmol.2022.1084633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 12/16/2022] [Indexed: 01/18/2023] Open
Abstract
PCSK9 induces lysosomal degradation of the low-density lipoprotein (LDL) receptor (LDLR) in the liver, hereby preventing removal of LDL cholesterol from the circulation. Accordingly, PCSK9 inhibitory antibodies and siRNA potently reduce LDL cholesterol to unprecedented low levels and are approved for treatment of hypercholesterolemia. In addition, PCSK9 inactivation alters the levels of several other circulating lipid classes and species. Brain function is critically influenced by cholesterol and lipid composition. However, it remains unclear how the brain is affected long-term by the reduction in circulating lipids as achieved with potent lipid lowering therapeutics such as PCSK9 inhibitors. Furthermore, it is unknown if locally expressed PCSK9 affects neuronal circuits through regulation of receptor levels. We have studied the effect of lifelong low peripheral cholesterol levels on brain lipid composition and behavior in adult PCSK9 KO mice. In addition, we studied the effect of PCSK9 on neurons in culture and in vivo in the developing cerebral cortex. We found that PCSK9 reduced LDLR and neurite complexity in cultured neurons, but neither PCSK9 KO nor overexpression affected cortical development in vivo. Interestingly, PCSK9 deficiency resulted in changes of several lipid classes in the adult cortex and cerebellum. Despite the observed changes, PCSK9 KO mice had unchanged behavior compared to WT controls. In conclusion, our findings demonstrate that altered PCSK9 levels do not compromise brain development or function in mice, and are in line with clinical trials showing that PCSK9 inhibitors have no adverse effects on cognitive function.
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Affiliation(s)
- Angela Pärn
- Department of Biomedicine, Aarhus University, Aarhus, Denmark,*Correspondence: Angela Pärn, ✉
| | - Ditte Olsen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Jürgen Tuvikene
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia,Protobios LLC, Tallinn, Estonia
| | - Mathias Kaas
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Ekaterina Borisova
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, Berlin, Germany,Tomsk National Research Medical Center of the Russian Academy of Sciences, Research Institute of Medical Genetics, Tomsk, Russia
| | - Mesut Bilgin
- Danish Cancer Society Research Center, Lipidomics Core Facility, Copenhagen, Denmark
| | - Mie Elhauge
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Joachim Vilstrup
- Department of Biomedicine, Aarhus University, Aarhus, Denmark,Draupnir Bio ApS, INCUBA Skejby, Aarhus, Denmark
| | - Peder Madsen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark,Draupnir Bio ApS, INCUBA Skejby, Aarhus, Denmark
| | - Mateusz C. Ambrozkiewicz
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Roman U. Goz
- Department of Neurobiology, University of Pittsburgh Medical School, Pittsburgh, PA, United States
| | - Tõnis Timmusk
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia,Protobios LLC, Tallinn, Estonia
| | - Victor Tarabykin
- Institute of Cell Biology and Neurobiology, Charité - Universitätsmedizin Berlin, Berlin, Germany,Tomsk National Research Medical Center of the Russian Academy of Sciences, Research Institute of Medical Genetics, Tomsk, Russia
| | - Camilla Gustafsen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark,Draupnir Bio ApS, INCUBA Skejby, Aarhus, Denmark,Camilla Gustafsen, ✉
| | - Simon Glerup
- Department of Biomedicine, Aarhus University, Aarhus, Denmark,Draupnir Bio ApS, INCUBA Skejby, Aarhus, Denmark,Simon Glerup, ✉
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8
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Stahl-Meyer K, Bilgin M, Holland LKK, Stahl-Meyer J, Kirkegaard T, Petersen NHT, Maeda K, Jäättelä M. Galactosyl- and glucosylsphingosine induce lysosomal membrane permeabilization and cell death in cancer cells. PLoS One 2022; 17:e0277058. [PMID: 36409725 PMCID: PMC9678304 DOI: 10.1371/journal.pone.0277058] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 10/18/2022] [Indexed: 11/22/2022] Open
Abstract
Isomeric lysosphingolipids, galactosylsphingosine (GalSph) and glucosylsphingosine (GlcSph), are present in only minute levels in healthy cells. Due to defects in their lysosomal hydrolysis, they accumulate at high levels and cause cytotoxicity in patients with Krabbe and Gaucher diseases, respectively. Here, we show that GalSph and GlcSph induce lysosomal membrane permeabilization, a hallmark of lysosome-dependent cell death, in human breast cancer cells (MCF7) and primary fibroblasts. Supporting lysosomal leakage as a causative event in lysosphingolipid-induced cytotoxicity, treatment of MCF7 cells with lysosome-stabilizing cholesterol prevented GalSph- and GlcSph-induced cell death almost completely. In line with this, fibroblasts from a patient with Niemann-Pick type C disease, which is caused by defective lysosomal cholesterol efflux, were significantly less sensitive to lysosphingolipid-induced lysosomal leakage and cell death. Prompted by the data showing that MCF7 cells with acquired resistance to lysosome-destabilizing cationic amphiphilic drugs (CADs) were partially resistant to the cell death induced by GalSph and GlcSph, we compared these cell death pathways with each other. Like CADs, GalSph and GlcSph activated the cyclic AMP (cAMP) signalling pathway, and cAMP-inducing forskolin sensitized cells to cell death induced by low concentrations of lysosphingolipids. Contrary to CADs, lysosphingolipid-induced cell death was independent of lysosomal Ca2+ efflux through P2X purinerigic receptor 4. These data reveal GalSph and GlcSph as lysosome-destabilizing lipids, whose putative use in cancer therapy should be further investigated. Furthermore, the data supports the development of lysosome stabilizing drugs for the treatment of Krabbe and Gaucher diseases and possibly other sphingolipidoses.
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Affiliation(s)
- Kamilla Stahl-Meyer
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
- Orphazyme A/S, Copenhagen, Denmark
| | - Mesut Bilgin
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Lya K. K. Holland
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Jonathan Stahl-Meyer
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
| | | | | | - Kenji Maeda
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
- * E-mail: (MJ); (KM)
| | - Marja Jäättelä
- Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
- Department of Cellular and molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- * E-mail: (MJ); (KM)
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9
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Dannenberger D, Eggert A, Kalbe C, Woitalla A, Schwudke D. Are n-3 PUFAs from Microalgae Incorporated into Membrane and Storage Lipids in Pig Muscle Tissues?-A Lipidomic Approach. ACS OMEGA 2022; 7:24785-24794. [PMID: 35874219 PMCID: PMC9301695 DOI: 10.1021/acsomega.2c02476] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
For the study of molecular mechanisms of to lipid transport and storage in relation to dietary effects, lipidomics has been rarely used in farm animal research. A feeding study with pigs (German Landrace sows) and supplementation of microalgae (Schizochytrium sp.) was conducted. The animals were allocated to the control group (n = 15) and the microalgae group (n = 16). Shotgun lipidomics was applied. This study enabled us to identify and quantify 336 lipid species from 15 different lipid classes in pig skeletal muscle tissues. The distribution of the lipid classes was significantly altered by microalgae supplementation, and ether lipids of phosphatidylcholine (PC), phosphatidylethanolamine (PE), and phosphatidic acid (PA) were significantly decreased. The total concentration of triacylglycerides (TAGs) was not affected. TAGs with high degree of unsaturation (TAG 56:7, TAG 56:6, TAG 54:6) were increased in the microalgae group, and major abundant species like TAG 52:2 and TAG 52:1 were not affected by the diet. Our results confirmed that dietary DHA and EPA are incorporated into storage and membrane lipids of pig muscles, which further led to systemic changes in the lipidome composition.
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Affiliation(s)
- Dirk Dannenberger
- Lipid
Metabolism and Muscular Adaptation Workgroup, Research Institute for Farm Animal Biology, Institute of Muscle Biology
and Growth, 18196 Dummerstorf, Germany
| | - Anja Eggert
- Institute
of Genetics and Biometry, Research Institute
for Farm Animal Biology, 18196 Dummerstorf, Germany
| | - Claudia Kalbe
- Lipid
Metabolism and Muscular Adaptation Workgroup, Research Institute for Farm Animal Biology, Institute of Muscle Biology
and Growth, 18196 Dummerstorf, Germany
| | - Anna Woitalla
- Division
of Bioanalytical Chemistry, Research Center
Borstel—Leibniz Lung Center, 23845 Borstel, Germany
| | - Dominik Schwudke
- Division
of Bioanalytical Chemistry, Research Center
Borstel—Leibniz Lung Center, 23845 Borstel, Germany
- German
Center for Lung Research (DZL), Airway Research Center North (ARCN), Research Center Borstel—Leibniz Lung Center, 23845 Borstel, Germany
- German
Center for Infection Research, Thematic Translational Unit Tuberculosis, Research Center Borstel—Leibniz Lung Center, 23845 Borstel, Germany
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10
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Hoffmann N, Mayer G, Has C, Kopczynski D, Al Machot F, Schwudke D, Ahrends R, Marcus K, Eisenacher M, Turewicz M. A Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics. Metabolites 2022; 12:metabo12070584. [PMID: 35888710 PMCID: PMC9319858 DOI: 10.3390/metabo12070584] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/17/2022] [Accepted: 06/19/2022] [Indexed: 12/13/2022] Open
Abstract
Mass spectrometry is a widely used technology to identify and quantify biomolecules such as lipids, metabolites and proteins necessary for biomedical research. In this study, we catalogued freely available software tools, libraries, databases, repositories and resources that support lipidomics data analysis and determined the scope of currently used analytical technologies. Because of the tremendous importance of data interoperability, we assessed the support of standardized data formats in mass spectrometric (MS)-based lipidomics workflows. We included tools in our comparison that support targeted as well as untargeted analysis using direct infusion/shotgun (DI-MS), liquid chromatography−mass spectrometry, ion mobility or MS imaging approaches on MS1 and potentially higher MS levels. As a result, we determined that the Human Proteome Organization-Proteomics Standards Initiative standard data formats, mzML and mzTab-M, are already supported by a substantial number of recent software tools. We further discuss how mzTab-M can serve as a bridge between data acquisition and lipid bioinformatics tools for interpretation, capturing their output and transmitting rich annotated data for downstream processing. However, we identified several challenges of currently available tools and standards. Potential areas for improvement were: adaptation of common nomenclature and standardized reporting to enable high throughput lipidomics and improve its data handling. Finally, we suggest specific areas where tools and repositories need to improve to become FAIRer.
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Affiliation(s)
- Nils Hoffmann
- Forschungszentrum Jülich GmbH, Institute for Bio- and Geosciences (IBG-5), 52425 Jülich, Germany
- Correspondence: (N.H.); (M.T.); Tel.: +49-(0)521-106-86780 (N.H.)
| | - Gerhard Mayer
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Germany;
| | - Canan Has
- Biological Mass Spectrometry, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany;
- University Hospital Carl Gustav Carus, 01307 Dresden, Germany
- CENTOGENE GmbH, 18055 Rostock, Germany
| | - Dominik Kopczynski
- Department of Analytical Chemistry, University of Vienna, 1090 Vienna, Austria; (D.K.); (R.A.)
| | - Fadi Al Machot
- Faculty of Science and Technology, Norwegian University for Life Science (NMBU), 1433 Ås, Norway;
| | - Dominik Schwudke
- Bioanalytical Chemistry, Forschungszentrum Borstel, Leibniz Lung Center, 23845 Borstel, Germany;
- Airway Research Center North, German Center for Lung Research (DZL), 23845 Borstel, Germany
- German Center for Infection Research (DZIF), TTU Tuberculosis, 23845 Borstel, Germany
| | - Robert Ahrends
- Department of Analytical Chemistry, University of Vienna, 1090 Vienna, Austria; (D.K.); (R.A.)
| | - Katrin Marcus
- Center for Protein Diagnostics (ProDi), Medical Proteome Analysis, Ruhr University Bochum, 44801 Bochum, Germany; (K.M.); (M.E.)
| | - Martin Eisenacher
- Center for Protein Diagnostics (ProDi), Medical Proteome Analysis, Ruhr University Bochum, 44801 Bochum, Germany; (K.M.); (M.E.)
- Faculty of Medicine, Medizinisches Proteom-Center, Ruhr University Bochum, 44801 Bochum, Germany
| | - Michael Turewicz
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Düsseldorf, 85764 Neuherberg, Germany
- Correspondence: (N.H.); (M.T.); Tel.: +49-(0)521-106-86780 (N.H.)
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11
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A set of gene knockouts as a resource for global lipidomic changes. Sci Rep 2022; 12:10533. [PMID: 35732804 PMCID: PMC9218125 DOI: 10.1038/s41598-022-14690-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 06/10/2022] [Indexed: 11/14/2022] Open
Abstract
Enzyme specificity in lipid metabolic pathways often remains unresolved at the lipid species level, which is needed to link lipidomic molecular phenotypes with their protein counterparts to construct functional pathway maps. We created lipidomic profiles of 23 gene knockouts in a proof-of-concept study based on a CRISPR/Cas9 knockout screen in mammalian cells. This results in a lipidomic resource across 24 lipid classes. We highlight lipid species phenotypes of multiple knockout cell lines compared to a control, created by targeting the human safe-harbor locus AAVS1 using up to 1228 lipid species and subspecies, charting lipid metabolism at the molecular level. Lipid species changes are found in all knockout cell lines, however, some are most apparent on the lipid class level (e.g., SGMS1 and CEPT1), while others are most apparent on the fatty acid level (e.g., DECR2 and ACOT7). We find lipidomic phenotypes to be reproducible across different clones of the same knockout and we observed similar phenotypes when two enzymes that catalyze subsequent steps of the long-chain fatty acid elongation cycle were targeted.
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12
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Lauber C, Gerl MJ, Klose C, Ottosson F, Melander O, Simons K. Lipidomic risk scores are independent of polygenic risk scores and can predict incidence of diabetes and cardiovascular disease in a large population cohort. PLoS Biol 2022; 20:e3001561. [PMID: 35239643 PMCID: PMC8893343 DOI: 10.1371/journal.pbio.3001561] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 01/31/2022] [Indexed: 12/22/2022] Open
Abstract
Type 2 diabetes (T2D) and cardiovascular disease (CVD) represent significant disease burdens for most societies and susceptibility to these diseases is strongly influenced by diet and lifestyle. Physiological changes associated with T2D or CVD, such has high blood pressure and cholesterol and glucose levels in the blood, are often apparent prior to disease incidence. Here we integrated genetics, lipidomics, and standard clinical diagnostics to assess future T2D and CVD risk for 4,067 participants from a large prospective population-based cohort, the Malmö Diet and Cancer-Cardiovascular Cohort. By training Ridge regression-based machine learning models on the measurements obtained at baseline when the individuals were healthy, we computed several risk scores for T2D and CVD incidence during up to 23 years of follow-up. We used these scores to stratify the participants into risk groups and found that a lipidomics risk score based on the quantification of 184 plasma lipid concentrations resulted in a 168% and 84% increase of the incidence rate in the highest risk group and a 77% and 53% decrease of the incidence rate in lowest risk group for T2D and CVD, respectively, compared to the average case rates of 13.8% and 22.0%. Notably, lipidomic risk correlated only marginally with polygenic risk, indicating that the lipidome and genetic variants may constitute largely independent risk factors for T2D and CVD. Risk stratification was further improved by adding standard clinical variables to the model, resulting in a case rate of 51.0% and 53.3% in the highest risk group for T2D and CVD, respectively. The participants in the highest risk group showed significantly altered lipidome compositions affecting 167 and 157 lipid species for T2D and CVD, respectively. Our results demonstrated that a subset of individuals at high risk for developing T2D or CVD can be identified years before disease incidence. The lipidomic risk, which is derived from only one single mass spectrometric measurement that is cheap and fast, is informative and could extend traditional risk assessment based on clinical assays.
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Affiliation(s)
- Chris Lauber
- Lipotype GmbH, Dresden, Germany
- TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Hanover Medical School and the Helmholtz Centre for Infection Research, Institute for Experimental Virology, Hanover, Germany
| | | | | | - Filip Ottosson
- Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Olle Melander
- Department of Clinical Sciences, Lund University, Malmö, Sweden
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13
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Ziziphus joazeiro Stem Bark Extract as a Green Corrosion Inhibitor for Mild Steel in Acid Medium. Processes (Basel) 2021. [DOI: 10.3390/pr9081323] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The aqueous extract of Joazeiro stem bark (EJSB) and its high molecular weight fraction (HMWF) were examined as potential corrosion inhibitors of mild steel in 1 mol L−1 hydrochloric acid media, using weight-loss measurements, potentiodynamic polarization curves and an electrochemical impedance spectroscopy (EIS).Varying the concentration of the inhibitors from 100 to 800 mg L−1, the results show an increase in anticorrosive efficiency from 85.4 to 89.8 and 89.8 to 93.0% for EJSB and its HMWF, respectively, using the data of the gravimetric essay, and from 84.5 to 94.5 and 89.9 to 94.7% for EJSB and its HMWF, respectively, from the impedance data. The composition of the crude extract was chemically characterized by liquid chromatography-high resolution mass spectrometry. Additionally, scanning electron microscopy (SEM) and X-ray photoelectron spectroscopy (XPS) were used, respectively, to morphologically and chemically characterize the surface. Considering that the saponin molecules, the main constituent from juá, are responsible for its inhibitory action, quantum chemical calculations showed that the C67, C69 and O144 atoms likely have an important role in the process of electron-donation of saponin to metal, due to the higher values of ƒk+ and %HOMO observed on these atoms.
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14
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Lipinska P, Sell-Kubiak E, Pawlak P, Madeja ZE, Warzych E. Response of Bovine Cumulus-Oocytes Complexes to Energy Pathway Inhibition during In Vitro Maturation. Genes (Basel) 2021; 12:genes12060838. [PMID: 34072406 PMCID: PMC8228821 DOI: 10.3390/genes12060838] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/13/2021] [Accepted: 05/25/2021] [Indexed: 12/25/2022] Open
Abstract
Glucose or fatty acids (FAs) metabolisms may alter the ovarian follicle environment and thus determine oocyte and the nascent embryo quality. The aim of the experiment was to investigate the effect of selective inhibition of glucose (iodoacetate + DHEA) or FA (etomoxir) metabolism on in vitro maturation (IVM) of bovine COCs (cumulus-oocyte complexes) to investigate oocyte's development, quality, and energy metabolism. After in vitro fertilization, embryos were cultured to the blastocyst stage. Lipid droplets, metabolome, and lipidome were analyzed in oocytes and cumulus cells. mRNA expression of the selected genes was measured in the cumulus cells. ATP and glutathione relative levels were measured in oocytes. Changes in FA content in the maturation medium were evaluated by mass spectrometry. Our results indicate that only glucose metabolism is substantial to the oocyte during IVM since only glucose inhibition decreased embryo culture efficiency. The most noteworthy differences in the reaction to the applied inhibition systems were observed in cumulus cells. The upregulation of ketone body metabolism in the cumulus cells of the glucose inhibition group suggest possibly failed attempts of cells to switch into lipid consumption. On the contrary, etomoxir treatment of the oocytes did not affect embryo development, probably due to undisturbed metabolism in cumulus cells. Therefore, we suggest that the energy pathways analyzed in this experiment are not interchangeable alternatives in bovine COCs.
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15
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Züllig T, Köfeler HC. HIGH RESOLUTION MASS SPECTROMETRY IN LIPIDOMICS. MASS SPECTROMETRY REVIEWS 2021; 40:162-176. [PMID: 32233039 PMCID: PMC8049033 DOI: 10.1002/mas.21627] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 03/06/2020] [Indexed: 05/04/2023]
Abstract
The boost of research output in lipidomics during the last decade is tightly linked to improved instrumentation in mass spectrometry. Associated with this trend is the shift from low resolution-toward high-resolution lipidomics platforms. This review article summarizes the state of the art in the lipidomics field with a particular focus on the merits of high mass resolution. Following some theoretical considerations on the benefits of high mass resolution in lipidomics, it starts with a historical perspective on lipid analysis by sector instruments and moves further to today's instrumental approaches, including shotgun lipidomics, liquid chromatography-mass spectrometry, matrix-assisted laser desorption ionization-time-of-flight, and imaging lipidomics. Subsequently, several data processing and data analysis software packages are critically evaluated with all their pros and cons. Finally, this article emphasizes the importance and necessity of quality standards as the field evolves from its pioneering phase into a mature and robust omics technology and lists various initiatives for improving the applicability of lipidomics. © 2020 The Authors. Mass Spectrometry Reviews published by John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Thomas Züllig
- Core Facility Mass SpectrometryMedical University of Graz, ZMFGrazAustria
| | - Harald C. Köfeler
- Core Facility Mass SpectrometryMedical University of Graz, ZMFGrazAustria
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16
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A normalized signal calibration with a long-term reference improves the robustness of RPLC-MRM/MS lipidomics in plasma. Anal Bioanal Chem 2021; 413:4077-4090. [PMID: 33907864 DOI: 10.1007/s00216-021-03364-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 04/19/2021] [Indexed: 10/21/2022]
Abstract
Improving the reliability of quantification in lipidomic analyses is crucial for its successful application in the discovery of new biomarkers or in clinical practice. In this study, we propose a workflow to improve the accuracy and precision of lipidomic results issued by the laboratory. Lipid species from 11 classes were analyzed by a targeted RPLC-MRM/MS method. The peak areas of species were used to estimate concentrations by an internal standard calibration approach (IS-calibration) and by an alternative normalization signal calibration schema (NS-calibration). The latter uses a long-term reference plasma material as a matrix-matched external calibrator whose accuracy was compared to the NIST SRM-1950 mean consensus values reported by the Interlaboratory Lipidomics Comparison Exercise. The bias of lipid concentrations showed a good accuracy for 69 of 89 quantified lipids. The quantitation of species by the NS-calibration schema improved the within- and between-batch reproducibility in quality control samples, in comparison to the usual IS-calibration approach. Moreover, the NS-calibration workflow improved the robustness of the lipidomics measurements reducing the between-batch variability (relative standard deviation <10% for 95% of lipid species) in real conditions tested throughout the analysis of 120 plasma samples. In addition, we provide a free access web tool to obtain the concentration of lipid species by the two previously mentioned quantitative approaches, providing an easy follow-up of quality control tasks related to lipidomics.
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17
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Ravandeh M, Kahlert H, Jablonowski H, Lackmann JW, Striesow J, Agmo Hernández V, Wende K. A combination of electrochemistry and mass spectrometry to monitor the interaction of reactive species with supported lipid bilayers. Sci Rep 2020; 10:18683. [PMID: 33122650 PMCID: PMC7596530 DOI: 10.1038/s41598-020-75514-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 10/15/2020] [Indexed: 01/21/2023] Open
Abstract
Reactive oxygen and nitrogen species (RONS), e.g. generated by cold physical plasma (CPP) or photodynamic therapy, interfere with redox signaling pathways of mammalian cells, inducing downstream consequences spanning from migratory impairment to apoptotic cell death. However, the more austere impact of RONS on cancer cells remains yet to be clarified. In the present study, a combination of electrochemistry and high-resolution mass spectrometry was developed to investigate the resilience of solid-supported lipid bilayers towards plasma-derived reactive species in dependence of their composition. A 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayer was undisturbed by 200 µM H2O2 (control) but showed full permeability after CPP treatment and space-occupying oxidation products such as PoxnoPC, PAzePC, and POPC hydroperoxide were found. Electron paramagnetic resonance spectroscopy demonstrated the presence of hydroxyl radicals and superoxide anion/hydroperoxyl radicals during the treatment. In contrast, small amounts of the intramembrane antioxidant coenzyme Q10 protected the bilayer to 50% and LysoPC was the only POPC derivative found, confirming the membrane protective effect of Q10. Such, the lipid membrane composition including the presence of antioxidants determines the impact of pro-oxidant signals. Given the differences in membrane composition of cancer and healthy cells, this supports the application of cold physical plasma for cancer treatment. In addition, the developed model using the combination of electrochemistry and mass spectrometry could be a promising method to study the effect of reactive species or mixes thereof generated by chemical or physical sources.
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Affiliation(s)
- M Ravandeh
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
- Leibniz-Institute for Plasma Science and Technology, ZIK Plasmatis, Felix-Hausdorff-Str. 2, 17489, Greifswald, Germany
| | - H Kahlert
- Institute of Biochemistry, University of Greifswald, Felix-Hausdorff-Str. 4, 17489, Greifswald, Germany
| | - H Jablonowski
- Leibniz-Institute for Plasma Science and Technology, ZIK Plasmatis, Felix-Hausdorff-Str. 2, 17489, Greifswald, Germany
| | - J-W Lackmann
- Leibniz-Institute for Plasma Science and Technology, ZIK Plasmatis, Felix-Hausdorff-Str. 2, 17489, Greifswald, Germany
| | - J Striesow
- Leibniz-Institute for Plasma Science and Technology, ZIK Plasmatis, Felix-Hausdorff-Str. 2, 17489, Greifswald, Germany
| | - V Agmo Hernández
- Department of Chemistry-BMC, Uppsala University, Husargatan 3, 75123, Uppsala, Sweden
- Department of Pharmacy, Uppsala University, Husargatan 3, 75123, Uppsala, Sweden
| | - K Wende
- Leibniz-Institute for Plasma Science and Technology, ZIK Plasmatis, Felix-Hausdorff-Str. 2, 17489, Greifswald, Germany.
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18
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Nielsen IØ, Vidas Olsen A, Dicroce-Giacobini J, Papaleo E, Andersen KK, Jäättelä M, Maeda K, Bilgin M. Comprehensive Evaluation of a Quantitative Shotgun Lipidomics Platform for Mammalian Sample Analysis on a High-Resolution Mass Spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:894-907. [PMID: 32129994 DOI: 10.1021/jasms.9b00136] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Shotgun lipidomics is a powerful tool that enables simultaneous and fast quantification of diverse lipid classes through mass spectrometry based analyses of directly infused crude lipid extracts. We present here a shotgun lipidomics platform established to quantify 38 lipid classes belonging to four lipid categories present in mammalian samples and show the fine-tuning and comprehensive evaluation of its experimental parameters and performance. We first determined for all the targeted lipid classes the collision energy levels optimal for the recording of their lipid class- and species-specific fragment ions and fine-tuned the energy levels applied in the platform. We then performed a series of titrations to define the boundaries of linear signal response for the targeted lipid classes, and demonstrated that the dynamic quantification range spanned more than 3 orders of magnitude and reached sub picomole levels for 35 lipid classes. The platform identified 273, 261, and 287 lipid species in brain, plasma, and cultured fibroblast samples, respectively, at the respective optimal working sample amounts. The platform properly quantified the majority of these identified lipid species, while lipid species measured to be below the limit of quantification were efficiently removed from the data sets by the use of statistical analyses of data reproducibility or a cutoff threshold. Finally, we demonstrated that a series of parameters of cell culture conditions influence lipidomics outcomes, including confluency, medium supplements, and use of transfection reagents. The present study provides a guideline for setting up and using a simple and efficient platform for quantitatively exploring the mammalian lipidome.
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Affiliation(s)
- Inger Ødum Nielsen
- Unit for Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen DK-2100, Denmark
| | - André Vidas Olsen
- Computational Biology Laboratory, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen DK-2100, Denmark
| | - Jano Dicroce-Giacobini
- Unit for Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen DK-2100, Denmark
| | - Elena Papaleo
- Computational Biology Laboratory, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen DK-2100, Denmark
- Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Klaus Kaae Andersen
- Unit for Statistics and Epidemiology, Danish Cancer Society Research Center, Copenhagen DK-2100, Denmark
| | - Marja Jäättelä
- Unit for Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen DK-2100, Denmark
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Kenji Maeda
- Unit for Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen DK-2100, Denmark
| | - Mesut Bilgin
- Unit for Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen DK-2100, Denmark
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19
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Lipidomics from sample preparation to data analysis: a primer. Anal Bioanal Chem 2019; 412:2191-2209. [PMID: 31820027 PMCID: PMC7118050 DOI: 10.1007/s00216-019-02241-y] [Citation(s) in RCA: 169] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/09/2019] [Accepted: 10/25/2019] [Indexed: 12/26/2022]
Abstract
Lipids are amongst the most important organic compounds in living organisms, where they serve as building blocks for cellular membranes as well as energy storage and signaling molecules. Lipidomics is the science of the large-scale determination of individual lipid species, and the underlying analytical technology that is used to identify and quantify the lipidome is generally mass spectrometry (MS). This review article provides an overview of the crucial steps in MS-based lipidomics workflows, including sample preparation, either liquid–liquid or solid-phase extraction, derivatization, chromatography, ion-mobility spectrometry, MS, and data processing by various software packages. The associated concepts are discussed from a technical perspective as well as in terms of their application. Furthermore, this article sheds light on recent advances in the technology used in this field and its current limitations. Particular emphasis is placed on data quality assurance and adequate data reporting; some of the most common pitfalls in lipidomics are discussed, along with how to circumvent them.
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20
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Wibberg D, Batut B, Belmann P, Blom J, Glöckner FO, Grüning B, Hoffmann N, Kleinbölting N, Rahn R, Rey M, Scholz U, Sharan M, Tauch A, Trojahn U, Usadel B, Kohlbacher O. The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR. F1000Res 2019; 8. [PMID: 33163154 PMCID: PMC7607484 DOI: 10.12688/f1000research.20244.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/04/2020] [Indexed: 12/25/2022] Open
Abstract
The German Network for Bioinformatics Infrastructure (de.NBI) is a national and academic infrastructure funded by the German Federal Ministry of Education and Research (BMBF). The de.NBI provides (i) service, (ii) training, and (iii) cloud computing to users in life sciences research and biomedicine in Germany and Europe and (iv) fosters the cooperation of the German bioinformatics community with international network structures. The de.NBI members also run the German node (ELIXIR-DE) within the European ELIXIR infrastructure. The de.NBI / ELIXIR-DE training platform, also known as special interest group 3 (SIG 3) ‘Training & Education’, coordinates the bioinformatics training of de.NBI and the German ELIXIR node. The network provides a high-quality, coherent, timely, and impactful training program across its eight service centers. Life scientists learn how to handle and analyze biological big data more effectively by applying tools, standards and compute services provided by de.NBI. Since 2015, more than 300 training courses were carried out with about 6,000 participants and these courses received recommendation rates of almost 90% (status as of July 2020). In addition to face-to-face training courses, online training was introduced on the de.NBI website in 2016 and guidelines for the preparation of e-learning material were established in 2018. In 2016, ELIXIR-DE joined the ELIXIR training platform. Here, the de.NBI / ELIXIR-DE training platform collaborates with ELIXIR in training activities, advertising training courses via TeSS and discussions on the exchange of data for training events essential for quality assessment on both the technical and administrative levels. The de.NBI training program trained thousands of scientists from Germany and beyond in many different areas of bioinformatics.
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Affiliation(s)
- Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, 33501, Germany
| | - Bérénice Batut
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, 79110, Germany
| | - Peter Belmann
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, 33501, Germany
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, 35392, Germany
| | - Frank Oliver Glöckner
- Alfred-Wegener-Institut - Helmholtz Zentrum für Polar- und Meeresforschung and Jacobs University Bremen, Campus Ring 1, Bremen, 28759, Germany
| | - Björn Grüning
- Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Freiburg, 79110, Germany
| | - Nils Hoffmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, 44227, Germany
| | - Nils Kleinbölting
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, 33501, Germany
| | - René Rahn
- Algorithmic Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, Takustraße 9, Berlin, 14195, Germany
| | - Maja Rey
- Scientific Databases and Visualization Group, Heidelberg Institute for Theoretical Studies (HITS) gGmbH, Schloss-Wolfsbrunnenweg 35, Heidelberg, 69118, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, 06466, Germany
| | - Malvika Sharan
- The Heidelberg Center for Human Bioinformatics (HD-HuB), European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, 69117, Germany
| | - Andreas Tauch
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, 33501, Germany
| | - Ulrike Trojahn
- The Heidelberg Center for Human Bioinformatics (HD-HuB), European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, 69117, Germany
| | - Björn Usadel
- IBG-2 Plant Sciences, Forschungszentrum Jülich, Jülich, 52428, Germany
| | - Oliver Kohlbacher
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, 72076, Germany.,Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, 72076, Germany.,Translational Bioinformatics, University Hospital Tubingen, Tübingen, 72076, Germany.,Biomolecular Interactions, Max Planck Institute for Development Biology, Tübingen, 72076, Germany
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21
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Schuhmann K, Moon H, Thomas H, Ackerman JM, Groessl M, Wagner N, Kellmann M, Henry I, Nadler A, Shevchenko A. Quantitative Fragmentation Model for Bottom-Up Shotgun Lipidomics. Anal Chem 2019; 91:12085-12093. [PMID: 31441640 PMCID: PMC6751524 DOI: 10.1021/acs.analchem.9b03270] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 08/23/2019] [Indexed: 01/01/2023]
Abstract
Quantitative bottom-up shotgun lipidomics relies on molecular species-specific "signature" fragments consistently detectable in tandem mass spectra of analytes and standards. Molecular species of glycerophospholipids are typically quantified using carboxylate fragments of their fatty acid moieties produced by higher-energy collisional dissociation of their molecular anions. However, employing standards whose fatty acids moieties are similar, yet not identical, to the target lipids could severely compromise their quantification. We developed a generic and portable fragmentation model implemented in the open-source LipidXte software that harmonizes the abundances of carboxylate anion fragments originating from fatty acid moieties having different sn-1/2 positions at the glycerol backbone, length of the hydrocarbon chain, and number and location of double bonds. The postacquisition adjustment enables unbiased absolute (molar) quantification of glycerophospholipid species independent of instrument settings, collision energy, and employed internal standards.
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Affiliation(s)
- Kai Schuhmann
- Max
Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - HongKee Moon
- Max
Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Henrik Thomas
- Max
Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Jacobo Miranda Ackerman
- Max
Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Michael Groessl
- Department
of Nephrology and Hypertension, Inselspital,
Bern University Hospital, Freiburgstr. 15, 3010 Bern, Switzerland
- Department
for BioMedical Research, University of Bern, Murtenstr. 35, 3010 Bern, Switzerland
| | - Nicolai Wagner
- Max
Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Markus Kellmann
- Thermo
Fisher Scientific, Hanna-Kunath-Str.
11, 28199 Bremen, Germany
| | - Ian Henry
- Max
Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - André Nadler
- Max
Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Andrej Shevchenko
- Max
Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
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22
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Fernández-López M, Gil-de-la-Fuente A, Godzien J, Rupérez FJ, Barbas C, Otero A. LAS: A Lipid Annotation Service Capable of Explaining the Annotations It Generates. Comput Struct Biotechnol J 2019; 17:1113-1122. [PMID: 31462967 PMCID: PMC6709375 DOI: 10.1016/j.csbj.2019.07.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 07/19/2019] [Accepted: 07/26/2019] [Indexed: 01/30/2023] Open
Abstract
The Lipid Annotation Service (LAS) is a representational state transfer (REST) application programming interface (API) service designed to aid researchers performing lipid annotation. It assigns certainty levels (very unlikely, unlikely, likely, and very likely) to the putative annotations received as input and explains the rationale of such assignments. Its rules, obtained from the Centre for Metabolomics and Bioanalysis (CEMBIO) and from a literature review, enable LAS to extract evidence to support or refute the annotations automatically by checking the inter-rule relationships. LAS is the first metabolite annotation tool capable of explaining in natural language (English) the evidence that supports or refutes the annotations. This facilitates the understanding of the results by the user and, thus, increases the user's confidence in the results. Concerning its performance, in an evaluation of blood plasma samples whose compounds had previously been identified using well-established standards, LAS yielded an F-measure higher than 80%.
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Key Words
- API, Application Programming Interface
- CEMBIO, Centre for Metabolomics and Bioanalysis
- CER, Ceramide
- CMM, Ceu Mass Mediator
- CMM-ES, CMM Expert System
- CS, Composite Spectrum
- DG, Diradylglycerols
- EM, Experimental Mass
- Explanations in natural language
- FA, Fatty Acid
- HMDB, Human Metabolome Database
- InChI, IUPAC International Chemical Identifier
- Knowledge based system
- LAS, Lipid Identification System
- LPC, Lysoglycerophosphocholine
- LPE, Lysoglycerophosphoethanolamine
- LPG, Lysoglycerophosphoglycerol
- LPS, Lysoglycerophosphoserine
- Lipid annotation
- MB, MassBank
- MG, Monoradylglycerols
- MZ, MZedDB
- PA, Glycerophosphate
- PC, Glycerophosphocholine
- PE, Glycerophosphoethanolamine
- PG, Glycerophosphoglycerol
- PI, Glycerophosphoinositol
- PS, Glycerophosphoserine
- REST API service
- REST, REpresentational State Transfer
- RT, Retention Time
- SM, Phosphosphingolipid
- ST, Sterol (Cholesterol ester)
- TG, Triradylglycerols
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Affiliation(s)
- Mariano Fernández-López
- Department of Information Technology, Escuela Politécnica Superior, Universidad CEU-San Pablo, Campus Montepríncipe, Boadilla del Monte, Madrid 28668, Spain
- Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad CEU-San Pablo, Campus Montepríncipe, Boadilla del Monte, Madrid, 28668, Spain
- Corresponding author at: Department of Information Technology, Escuela Politécnica Superior, Universidad CEU-San Pablo, Campus Montepríncipe, Boadilla del Monte, Madrid 28668, Spain.
| | - Alberto Gil-de-la-Fuente
- Department of Information Technology, Escuela Politécnica Superior, Universidad CEU-San Pablo, Campus Montepríncipe, Boadilla del Monte, Madrid 28668, Spain
- Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad CEU-San Pablo, Campus Montepríncipe, Boadilla del Monte, Madrid, 28668, Spain
| | - Joanna Godzien
- Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad CEU-San Pablo, Campus Montepríncipe, Boadilla del Monte, Madrid, 28668, Spain
- Clinical Research Centre, Medical University of Bialystok, Poland
| | - Francisco J. Rupérez
- Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad CEU-San Pablo, Campus Montepríncipe, Boadilla del Monte, Madrid, 28668, Spain
| | - Coral Barbas
- Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad CEU-San Pablo, Campus Montepríncipe, Boadilla del Monte, Madrid, 28668, Spain
| | - Abraham Otero
- Department of Information Technology, Escuela Politécnica Superior, Universidad CEU-San Pablo, Campus Montepríncipe, Boadilla del Monte, Madrid 28668, Spain
- Centre for Metabolomics and Bioanalysis (CEMBIO), Facultad de Farmacia, Universidad CEU-San Pablo, Campus Montepríncipe, Boadilla del Monte, Madrid, 28668, Spain
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23
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Hoejholt KL, Mužić T, Jensen SD, Dalgaard LT, Bilgin M, Nylandsted J, Heimburg T, Frandsen SK, Gehl J. Calcium electroporation and electrochemotherapy for cancer treatment: Importance of cell membrane composition investigated by lipidomics, calorimetry and in vitro efficacy. Sci Rep 2019; 9:4758. [PMID: 30894594 PMCID: PMC6427041 DOI: 10.1038/s41598-019-41188-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 02/20/2019] [Indexed: 12/21/2022] Open
Abstract
Calcium electroporation is a novel anti-cancer treatment investigated in clinical trials. We explored cell sensitivity to calcium electroporation and electroporation with bleomycin, using viability assays at different time and temperature points, as well as heat calorimetry, lipidomics, and flow cytometry. Three cell lines: HT29 (colon cancer), MDA-MB231 (breast cancer), and HDF-n (normal fibroblasts) were investigated for; (a) cell survival dependent on time of addition of drug relative to electroporation (1.2 kV/cm, 8 pulses, 99 µs, 1 Hz), at different temperatures (37 °C, 27 °C, 17 °C); (b) heat capacity profiles obtained by differential scanning calorimetry without added calcium; (c) lipid composition by mass spectrometry; (d) phosphatidylserine in the plasma membrane outer leaflet using flow cytometry. Temperature as well as time of drug administration affected treatment efficacy in HT29 and HDF-n cells, but not MDA-MB231 cells. Interestingly the HT29 cell line displayed a higher phase transition temperature (approximately 20 °C) versus 14 °C (HDF-n) and 15 °C (MDA-MB231). Furthermore the HT29 cell membranes had a higher ratio of ethers to esters, and a higher expression of phosphatidylserine in the outer leaflet. In conclusion, lipid composition and heat capacity of the membrane might influence permeabilisation of cells and thereby the effect of calcium electroporation and electrochemotherapy.
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Affiliation(s)
- K L Hoejholt
- Center for Experimental Drug and Gene Electrotransfer, Department of Oncology, Copenhagen University Hospital Herlev, Herlev, Denmark
| | - T Mužić
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - S D Jensen
- Center for Experimental Drug and Gene Electrotransfer, Department of Oncology, Copenhagen University Hospital Herlev, Herlev, Denmark
| | - L T Dalgaard
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - M Bilgin
- Danish Cancer Society Research Center (DCRC), Copenhagen, Denmark
| | - J Nylandsted
- Danish Cancer Society Research Center (DCRC), Copenhagen, Denmark
| | - T Heimburg
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - S K Frandsen
- Center for Experimental Drug and Gene Electrotransfer, Department of Oncology, Copenhagen University Hospital Herlev, Herlev, Denmark.
- Center for Experimental Drug and Gene Electrotransfer, Department of Clinical Oncology and Palliative Care, Zealand University Hospital, Roskilde, Denmark.
| | - J Gehl
- Center for Experimental Drug and Gene Electrotransfer, Department of Oncology, Copenhagen University Hospital Herlev, Herlev, Denmark.
- Center for Experimental Drug and Gene Electrotransfer, Department of Clinical Oncology and Palliative Care, Zealand University Hospital, Roskilde, Denmark.
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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24
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Müller C, Hardt M, Schwudke D, Neuman BW, Pleschka S, Ziebuhr J. Inhibition of Cytosolic Phospholipase A 2α Impairs an Early Step of Coronavirus Replication in Cell Culture. J Virol 2018; 92:e01463-17. [PMID: 29167338 PMCID: PMC5790932 DOI: 10.1128/jvi.01463-17] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 11/14/2017] [Indexed: 12/15/2022] Open
Abstract
Coronavirus replication is associated with intracellular membrane rearrangements in infected cells, resulting in the formation of double-membrane vesicles (DMVs) and other membranous structures that are referred to as replicative organelles (ROs). The latter provide a structural scaffold for viral replication/transcription complexes (RTCs) and help to sequester RTC components from recognition by cellular factors involved in antiviral host responses. There is increasing evidence that plus-strand RNA (+RNA) virus replication, including RO formation and virion morphogenesis, affects cellular lipid metabolism and critically depends on enzymes involved in lipid synthesis and processing. Here, we investigated the role of cytosolic phospholipase A2α (cPLA2α) in coronavirus replication using a low-molecular-weight nonpeptidic inhibitor, pyrrolidine-2 (Py-2). The inhibition of cPLA2α activity, which produces lysophospholipids (LPLs) by cleaving at the sn-2 position of phospholipids, had profound effects on viral RNA and protein accumulation in human coronavirus 229E-infected Huh-7 cells. Transmission electron microscopy revealed that DMV formation in infected cells was significantly reduced in the presence of the inhibitor. Furthermore, we found that (i) viral RTCs colocalized with LPL-containing membranes, (ii) cellular LPL concentrations were increased in coronavirus-infected cells, and (iii) this increase was diminished in the presence of the cPLA2α inhibitor Py-2. Py-2 also displayed antiviral activities against other viruses representing the Coronaviridae and Togaviridae families, while members of the Picornaviridae were not affected. Taken together, the study provides evidence that cPLA2α activity is critically involved in the replication of various +RNA virus families and may thus represent a candidate target for broad-spectrum antiviral drug development.IMPORTANCE Examples of highly conserved RNA virus proteins that qualify as drug targets for broad-spectrum antivirals remain scarce, resulting in increased efforts to identify and specifically inhibit cellular functions that are essential for the replication of RNA viruses belonging to different genera and families. The present study supports and extends previous conclusions that enzymes involved in cellular lipid metabolism may be tractable targets for broad-spectrum antivirals. We obtained evidence to show that a cellular phospholipase, cPLA2α, which releases fatty acid from the sn-2 position of membrane-associated glycerophospholipids, is critically involved in coronavirus replication, most likely by producing lysophospholipids that are required to form the specialized membrane compartments in which viral RNA synthesis takes place. The importance of this enzyme in coronavirus replication and DMV formation is supported by several lines of evidence, including confocal and electron microscopy, viral replication, and lipidomics studies of coronavirus-infected cells treated with a highly specific cPLA2α inhibitor.
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Affiliation(s)
- Christin Müller
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
| | - Martin Hardt
- Imaging Unit, Biomedical Research Center, Justus Liebig University Giessen, Giessen, Germany
| | - Dominik Schwudke
- Division of Bioanalytical Chemistry, Priority Area Infection, Research Center Borstel, Leibniz Center for Medicine and Bioscience, Borstel, Germany
| | | | - Stephan Pleschka
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
| | - John Ziebuhr
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany
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25
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Abstract
Shotgun lipidomics offers fast and reproducible identification and quantification of lipids in clinical samples. Lipid extraction procedures based on the methyl tert-butyl protocol are well established for performing shotgun lipidomics in biomedical research. Here, we describe a shotgun lipidomics workflow that is well suited for the analysis of clinical samples such as tissue samples, blood plasma, and peripheral blood mononuclear cells.
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Affiliation(s)
- Lars F Eggers
- Division of Bioanalytical Chemistry, Research Center Borstel, Borstel, 23845, Germany
| | - Dominik Schwudke
- Division of Bioanalytical Chemistry, Research Center Borstel, Borstel, 23845, Germany.
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26
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Schuhmann K, Srzentić K, Nagornov KO, Thomas H, Gutmann T, Coskun Ü, Tsybin YO, Shevchenko A. Monitoring Membrane Lipidome Turnover by Metabolic 15N Labeling and Shotgun Ultra-High-Resolution Orbitrap Fourier Transform Mass Spectrometry. Anal Chem 2017; 89:12857-12865. [PMID: 29111682 DOI: 10.1021/acs.analchem.7b03437] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Lipidomes undergo permanent extensive remodeling, but how the turnover rate differs between lipid classes and molecular species is poorly understood. We employed metabolic 15N labeling and shotgun ultra-high-resolution mass spectrometry (sUHR) to quantify the absolute (molar) abundance and determine the turnover rate of glycerophospholipids and sphingolipids by direct analysis of total lipid extracts. sUHR performed on a commercial Orbitrap Elite instrument at the mass resolution of 1.35 × 106 (m/z 200) baseline resolved peaks of 13C isotopes of unlabeled and monoisotopic peaks of 15N labeled lipids (Δm = 0.0063 Da). Therefore, the rate of metabolic 15N labeling of individual lipid species could be determined without compromising the scope, accuracy, and dynamic range of full-lipidome quantitative shotgun profiling. As a proof of concept, we employed sUHR to determine the lipidome composition and fluxes of 62 nitrogen-containing membrane lipids in human hepatoma HepG2 cells.
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Affiliation(s)
- Kai Schuhmann
- Max Planck Institute of Molecular Cell Biology and Genetics , Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Kristina Srzentić
- Ecole Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
| | | | - Henrik Thomas
- Max Planck Institute of Molecular Cell Biology and Genetics , Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Theresia Gutmann
- Paul Langerhans Institute Dresden of the Helmholtz Zentrum München at the University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden , Fetscher Strasse 74, 01307 Dresden, Germany.,German Center for Diabetes Research , Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Ünal Coskun
- Paul Langerhans Institute Dresden of the Helmholtz Zentrum München at the University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden , Fetscher Strasse 74, 01307 Dresden, Germany.,German Center for Diabetes Research , Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Yury O Tsybin
- Spectroswiss , EPFL Innovation Park, Building I, 1015 Lausanne, Switzerland
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics , Pfotenhauerstrasse 108, 01307 Dresden, Germany
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27
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Schwudke D, Shevchenko A, Hoffmann N, Ahrends R. Lipidomics informatics for life-science. J Biotechnol 2017; 261:131-136. [PMID: 28822794 DOI: 10.1016/j.jbiotec.2017.08.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 08/07/2017] [Accepted: 08/09/2017] [Indexed: 12/27/2022]
Abstract
Lipidomics encompasses analytical approaches that aim to identify and quantify the complete set of lipids, defined as lipidome in a given cell, tissue or organism as well as their interactions with other molecules. The majority of lipidomics workflows is based on mass spectrometry and has been proven as a powerful tool in system biology in concert with other Omics disciplines. Unfortunately, bioinformatics infrastructures for this relatively young discipline are limited only to some specialists. Search engines, quantification algorithms, visualization tools and databases developed by the 'Lipidomics Informatics for Life-Science' (LIFS) partners will be restructured and standardized to provide broad access to these specialized bioinformatics pipelines. There are many medical challenges related to lipid metabolic alterations that will be fostered by capacity building suggested by LIFS. LIFS as member of the 'German Network for Bioinformatics' (de.NBI) node for 'Bioinformatics for Proteomics' (BioInfra.Prot) and will provide access to the described software as well as to tutorials and consulting services via a unified web-portal.
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Affiliation(s)
- D Schwudke
- Research Center Borstel, Leibniz Center for Medicine and Biosciences, Borstel, Germany
| | - A Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - N Hoffmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany
| | - R Ahrends
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany.
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28
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29
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Schuhmann K, Thomas H, Ackerman JM, Nagornov KO, Tsybin YO, Shevchenko A. Intensity-Independent Noise Filtering in FT MS and FT MS/MS Spectra for Shotgun Lipidomics. Anal Chem 2017; 89:7046-7052. [PMID: 28570056 DOI: 10.1021/acs.analchem.7b00794] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Shotgun lipidomics relies on the direct infusion of total lipid extracts into a high resolution tandem mass spectrometer. A single shotgun analysis produces several hundred of densely populated FT MS and FT MS/MS spectra, each of which might comprise thousands of peaks although a very small percentage of those belong to lipids. Eliminating noise by adjusting a minimal peak intensity threshold is biased and inefficient since lipid species and classes vary in their natural abundance and ionization capacity. We developed a method of peak intensity-independent noise filtering in shotgun FT MS and FT MS/MS spectra that capitalizes on a stable composition of the infused analyte leading to consistent time-independent detection of its bona fide components. Repetition rate filtering relies on a single quantitative measure of peaks detection reproducibility irrespectively of their absolute intensities, masses, or assumed elemental compositions. In comparative experiments, it removed more than 95% of signals detectable in shotgun spectra without compromising the accuracy and scope of lipid identification and quantification. It also accelerated spectra processing by 15-fold and increased the number of simultaneously processed spectra by ∼500-fold hence eliminating the major bottleneck in high-throughput bottom-up shotgun lipidomics.
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Affiliation(s)
- Kai Schuhmann
- MPI of Molecular Cell Biology and Genetics , 01307 Dresden, Germany
| | - Henrik Thomas
- MPI of Molecular Cell Biology and Genetics , 01307 Dresden, Germany
| | | | | | - Yury O Tsybin
- Spectroswiss , EPFL Innovation Park, 1015 Lausanne, Switzerland
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30
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Sellin J, Schulze H, Paradis M, Gosejacob D, Papan C, Shevchenko A, Psathaki OE, Paululat A, Thielisch M, Sandhoff K, Hoch M. Characterization of Drosophila Saposin-related mutants as a model for lysosomal sphingolipid storage diseases. Dis Model Mech 2017; 10:737-750. [PMID: 28389479 PMCID: PMC5483003 DOI: 10.1242/dmm.027953] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 04/04/2017] [Indexed: 11/20/2022] Open
Abstract
Sphingolipidoses are inherited diseases belonging to the class of lysosomal storage diseases (LSDs), which are characterized by the accumulation of indigestible material in the lysosome caused by specific defects in the lysosomal degradation machinery. While some LSDs can be efficiently treated by enzyme replacement therapy (ERT), this is not possible if the nervous system is affected due to the presence of the blood-brain barrier. Sphingolipidoses in particular often present as severe, untreatable forms of LSDs with massive sphingolipid and membrane accumulation in lysosomes, neurodegeneration and very short life expectancy. The digestion of intralumenal membranes within lysosomes is facilitated by lysosomal sphingolipid activator proteins (saposins), which are cleaved from a prosaposin precursor. Prosaposin mutations cause some of the severest forms of sphingolipidoses, and are associated with perinatal lethality in mice, hampering studies on disease progression. We identify the Drosophila prosaposin orthologue Saposin-related (Sap-r) as a key regulator of lysosomal lipid homeostasis in the fly. Its mutation leads to a typical spingolipidosis phenotype with an enlarged endolysosomal compartment and sphingolipid accumulation as shown by mass spectrometry and thin layer chromatography. Sap-r mutants show reduced viability with ∼50% survival to adulthood, allowing us to study progressive neurodegeneration and analyze their lipid profile in young and aged flies. Additionally, we observe a defect in sterol homeostasis with local sterol depletion at the plasma membrane. Furthermore, we find that autophagy is increased, resulting in the accumulation of mitochondria in lysosomes, concomitant with increased oxidative stress. Together, we establish Drosophila Sap-r mutants as a lysosomal storage disease model suitable for studying the age-dependent progression of lysosomal dysfunction associated with lipid accumulation and the resulting pathological signaling events.
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Affiliation(s)
- Julia Sellin
- LIMES-Institute, Program Unit Development & Genetics, Laboratory for Molecular Developmental Biology, University of Bonn, Carl-Troll-Strasse 31, 53115 Bonn, Germany
| | - Heike Schulze
- LIMES-Institute, Program Unit Membrane Biology & Lipid Biochemistry, c/o Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
| | - Marie Paradis
- LIMES-Institute, Program Unit Development & Genetics, Laboratory for Molecular Developmental Biology, University of Bonn, Carl-Troll-Strasse 31, 53115 Bonn, Germany
| | - Dominic Gosejacob
- LIMES-Institute, Program Unit Development & Genetics, Laboratory for Molecular Developmental Biology, University of Bonn, Carl-Troll-Strasse 31, 53115 Bonn, Germany
| | - Cyrus Papan
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Andrej Shevchenko
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Olympia Ekaterina Psathaki
- University of Osnabrück, Department of Zoology and Developmental Biology, Barbarastraße 11, 49076 Osnabrueck, Germany
| | - Achim Paululat
- University of Osnabrück, Biology, EM unit, Barbarastraße 11, 49076 Osnabrueck, Germany
| | - Melanie Thielisch
- LIMES-Institute, Program Unit Development & Genetics, Laboratory for Molecular Developmental Biology, University of Bonn, Carl-Troll-Strasse 31, 53115 Bonn, Germany
| | - Konrad Sandhoff
- LIMES-Institute, Program Unit Membrane Biology & Lipid Biochemistry, c/o Kekulé Institute of Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121 Bonn, Germany
| | - Michael Hoch
- LIMES-Institute, Program Unit Development & Genetics, Laboratory for Molecular Developmental Biology, University of Bonn, Carl-Troll-Strasse 31, 53115 Bonn, Germany
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31
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32
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Sales S, Knittelfelder O, Shevchenko A. Lipidomics of Human Blood Plasma by High-Resolution Shotgun Mass Spectrometry. Methods Mol Biol 2017; 1619:203-212. [PMID: 28674888 DOI: 10.1007/978-1-4939-7057-5_16] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Clinical lipidomics is an emerging biomarker discovery approach that compares lipid profiles under pathologically and physiologically normal conditions. Here we describe a method for the absolute (molar) quantification of more than 200 molecules from 14 major lipid classes from 5 μL of human blood plasma using high-resolution top-down shotgun mass spectrometry. Because of its technical simplicity and robustness, the protocol lends itself for high-throughput clinical lipidomics screens.
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Affiliation(s)
- Susanne Sales
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307, Dresden, Germany
| | - Oskar Knittelfelder
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307, Dresden, Germany
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307, Dresden, Germany.
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33
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Bilgin M, Born P, Fezza F, Heimes M, Mastrangelo N, Wagner N, Schultz C, Maccarrone M, Eaton S, Nadler A, Wilm M, Shevchenko A. Lipid Discovery by Combinatorial Screening and Untargeted LC-MS/MS. Sci Rep 2016; 6:27920. [PMID: 27312775 PMCID: PMC4911551 DOI: 10.1038/srep27920] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 05/26/2016] [Indexed: 11/29/2022] Open
Abstract
We present a method for the systematic identification of picogram quantities of new lipids in total extracts of tissues and fluids. It relies on the modularity of lipid structures and applies all-ions fragmentation LC-MS/MS and Arcadiate software to recognize individual modules originating from the same lipid precursor of known or assumed structure. In this way it alleviates the need to recognize and fragment very low abundant precursors of novel molecules in complex lipid extracts. In a single analysis of rat kidney extract the method identified 58 known and discovered 74 novel endogenous endocannabinoids and endocannabinoid-related molecules, including a novel class of N-acylaspartates that inhibit Hedgehog signaling while having no impact on endocannabinoid receptors.
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Affiliation(s)
- Mesut Bilgin
- Max Planck Institute for Cell Biology and Genetics, Pfotenhauerstraβe 108, 01307 Dresden, Germany
| | - Petra Born
- Max Planck Institute for Cell Biology and Genetics, Pfotenhauerstraβe 108, 01307 Dresden, Germany
| | - Filomena Fezza
- Department of Experimental Medicine and Surgery, Tor Vergata University of Rome, via Montpellier 1, 00133, Rome, Italy.,European Center for Brain Research/Fondazione Santa Lucia, via del Fosso di Fiorano 65, 00143 Rome, Italy
| | - Michael Heimes
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Nicolina Mastrangelo
- Department of Medicine, Campus Bio-Medico University of Rome, Via Alvaro del Portillo 21, 00128 Rome
| | - Nicolai Wagner
- Max Planck Institute for Cell Biology and Genetics, Pfotenhauerstraβe 108, 01307 Dresden, Germany
| | - Carsten Schultz
- European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Mauro Maccarrone
- European Center for Brain Research/Fondazione Santa Lucia, via del Fosso di Fiorano 65, 00143 Rome, Italy.,Department of Medicine, Campus Bio-Medico University of Rome, Via Alvaro del Portillo 21, 00128 Rome
| | - Suzanne Eaton
- Max Planck Institute for Cell Biology and Genetics, Pfotenhauerstraβe 108, 01307 Dresden, Germany
| | - André Nadler
- Max Planck Institute for Cell Biology and Genetics, Pfotenhauerstraβe 108, 01307 Dresden, Germany.,European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Matthias Wilm
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, 4 Dublin, Ireland
| | - Andrej Shevchenko
- Max Planck Institute for Cell Biology and Genetics, Pfotenhauerstraβe 108, 01307 Dresden, Germany
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34
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Ghaste M, Mistrik R, Shulaev V. Applications of Fourier Transform Ion Cyclotron Resonance (FT-ICR) and Orbitrap Based High Resolution Mass Spectrometry in Metabolomics and Lipidomics. Int J Mol Sci 2016; 17:ijms17060816. [PMID: 27231903 PMCID: PMC4926350 DOI: 10.3390/ijms17060816] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/14/2016] [Accepted: 05/17/2016] [Indexed: 02/02/2023] Open
Abstract
Metabolomics, along with other "omics" approaches, is rapidly becoming one of the major approaches aimed at understanding the organization and dynamics of metabolic networks. Mass spectrometry is often a technique of choice for metabolomics studies due to its high sensitivity, reproducibility and wide dynamic range. High resolution mass spectrometry (HRMS) is a widely practiced technique in analytical and bioanalytical sciences. It offers exceptionally high resolution and the highest degree of structural confirmation. Many metabolomics studies have been conducted using HRMS over the past decade. In this review, we will explore the latest developments in Fourier transform mass spectrometry (FTMS) and Orbitrap based metabolomics technology, its advantages and drawbacks for using in metabolomics and lipidomics studies, and development of novel approaches for processing HRMS data.
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Affiliation(s)
- Manoj Ghaste
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, Denton, TX 76203, USA.
| | | | - Vladimir Shulaev
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, Denton, TX 76203, USA.
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35
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Ma Y, Kind T, Yang D, Leon C, Fiehn O. MS2Analyzer: A software for small molecule substructure annotations from accurate tandem mass spectra. Anal Chem 2014; 86:10724-31. [PMID: 25263576 PMCID: PMC4222628 DOI: 10.1021/ac502818e] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 09/27/2014] [Indexed: 01/08/2023]
Abstract
Systematic analysis and interpretation of the large number of tandem mass spectra (MS/MS) obtained in metabolomics experiments is a bottleneck in discovery-driven research. MS/MS mass spectral libraries are small compared to all known small molecule structures and are often not freely available. MS2Analyzer was therefore developed to enable user-defined searches of thousands of spectra for mass spectral features such as neutral losses, m/z differences, and product and precursor ions from MS/MS spectra in MSP/MGF files. The software is freely available at http://fiehnlab.ucdavis.edu/projects/MS2Analyzer/ . As the reference query set, 147 literature-reported neutral losses and their corresponding substructures were collected. This set was tested for accuracy of linking neutral loss analysis to substructure annotations using 19 329 accurate mass tandem mass spectra of structurally known compounds from the NIST11 MS/MS library. Validation studies showed that 92.1 ± 6.4% of 13 typical neutral losses such as acetylations, cysteine conjugates, or glycosylations are correct annotating the associated substructures, while the absence of mass spectra features does not necessarily imply the absence of such substructures. Use of this tool has been successfully demonstrated for complex lipids in microalgae.
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Affiliation(s)
- Yan Ma
- UC
Davis Genome Center−Metabolomics, University of California, Davis, California 95616, United States
| | - Tobias Kind
- UC
Davis Genome Center−Metabolomics, University of California, Davis, California 95616, United States
| | - Dawei Yang
- UC
Davis Genome Center−Metabolomics, University of California, Davis, California 95616, United States
- SPKLOMHNM
and Central Laboratory, Zhong Yuan Academy of Biological Medicine, Liaocheng University, Liaocheng People’s Hospital, Liaocheng, Shandong 252000, P. R. China
| | - Carlos Leon
- UC
Davis Genome Center−Metabolomics, University of California, Davis, California 95616, United States
- Biomedical
Engineering School, Carlos III University, Avda Universidad 30, 28911, Leganes, Madrid, Spain
| | - Oliver Fiehn
- UC
Davis Genome Center−Metabolomics, University of California, Davis, California 95616, United States
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36
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Papan C, Penkov S, Herzog R, Thiele C, Kurzchalia T, Shevchenko A. Systematic screening for novel lipids by shotgun lipidomics. Anal Chem 2014; 86:2703-10. [PMID: 24471557 DOI: 10.1021/ac404083u] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
A commonly accepted LIPID MAPS classification recognizes eight major lipid categories and over 550 classes, while new lipid classes are still being discovered by targeted biochemical approaches. Despite their compositional diversity, complex lipids such as glycerolipids, glycerophospholipids, saccharolipids, etc. are constructed from unique structural moieties, e.g., glycerol, fatty acids, choline, phosphate, and trehalose, that are linked by amide, ether, ester, or glycosidic bonds. This modular organization is also reflected in their MS/MS fragmentation pathways, such that common building blocks in different lipid classes tend to generate common fragments. We take advantage of this stereotyped fragmentation to systematically screen for new lipids sharing distant structural similarity to known lipid classes and have developed a discovery approach based on the computational querying of shotgun mass spectra by LipidXplorer software. We applied this concept for screening lipid extracts of C. elegans larvae at the dauer and L3 stages that represent alternative developmental programs executed in response to environmental challenges. The search, covering more than 1.5 million putative chemical compositions, identified a novel class of lyso-maradolipids specifically enriched in dauer larvae.
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Affiliation(s)
- Cyrus Papan
- Max Planck Institute for Cell Biology and Genetics , Pfotenhauerstraße 108, 01307 Dresden, Germany
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