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Haitzmann T, Schindlmaier K, Frech T, Mondal A, Bubalo V, Konrad B, Bluemel G, Stiegler P, Lackner S, Hrzenjak A, Eichmann T, Köfeler HC, Leithner K. Serine synthesis and catabolism in starved lung cancer and primary bronchial epithelial cells. Cancer Metab 2024; 12:9. [PMID: 38515202 PMCID: PMC10956291 DOI: 10.1186/s40170-024-00337-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 03/13/2024] [Indexed: 03/23/2024] Open
Abstract
Serine and glycine give rise to important building blocks in proliferating cells. Both amino acids are either synthesized de novo or taken up from the extracellular space. In lung cancer, serine synthesis gene expression is variable, yet, expression of the initial enzyme, phosphoglycerate dehydrogenase (PHGDH), was found to be associated with poor prognosis. While the contribution of de novo synthesis to serine pools has been shown to be enhanced by serine starvation, the impact of glucose deprivation, a commonly found condition in solid cancers is poorly understood. Here, we utilized a stable isotopic tracing approach to assess serine and glycine de novo synthesis and uptake in different lung cancer cell lines and normal bronchial epithelial cells in variable serine, glycine, and glucose conditions. Under low glucose supplementation (0.2 mM, 3-5% of normal plasma levels), serine de novo synthesis was maintained or even activated. As previously reported, also gluconeogenesis supplied carbons from glutamine to serine and glycine under these conditions. Unexpectedly, low glucose treatment consistently enhanced serine to glycine conversion, along with an up-regulation of the mitochondrial one-carbon metabolism enzymes, serine hydroxymethyltransferase (SHMT2) and methylenetetrahydrofolate dehydrogenase (MTHFD2). The relative contribution of de novo synthesis greatly increased in low serine/glycine conditions. In bronchial epithelial cells, adaptations occurred in a similar fashion as in cancer cells, but serine synthesis and serine to glycine conversion, as assessed by label enrichments and gene expression levels, were generally lower than in (PHGDH positive) cancer cells. In summary, we found a variable contribution of glucose or non-glucose carbon sources to serine and glycine and a high adaptability of the downstream one-carbon metabolism pathway to variable glucose supply.
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Affiliation(s)
- Theresa Haitzmann
- Division of Pulmonology, Department of Internal Medicine, Medical University of Graz, Auenbruggerplatz 15, 8036, Graz, Austria
| | - Katharina Schindlmaier
- Division of Pulmonology, Department of Internal Medicine, Medical University of Graz, Auenbruggerplatz 15, 8036, Graz, Austria
| | - Tobias Frech
- Division of Pulmonology, Department of Internal Medicine, Medical University of Graz, Auenbruggerplatz 15, 8036, Graz, Austria
| | - Ayusi Mondal
- Division of Pulmonology, Department of Internal Medicine, Medical University of Graz, Auenbruggerplatz 15, 8036, Graz, Austria
- Department of Experimental Oncology, European Institute of Oncology, 20139, Milan, Italy
| | - Visnja Bubalo
- Division of Pulmonology, Department of Internal Medicine, Medical University of Graz, Auenbruggerplatz 15, 8036, Graz, Austria
| | - Barbara Konrad
- Division of Pulmonology, Department of Internal Medicine, Medical University of Graz, Auenbruggerplatz 15, 8036, Graz, Austria
| | - Gabriele Bluemel
- Division of Pulmonology, Department of Internal Medicine, Medical University of Graz, Auenbruggerplatz 15, 8036, Graz, Austria
- Department of Biosciences and Medical Biology, Bioanalytical Research Labs, University of Salzburg, 5020, Salzburg, Austria
| | - Philipp Stiegler
- Division of General, Visceral and Transplant Surgery, Department of Surgery, Medical University of Graz, 8036, Graz, Austria
| | - Stefanie Lackner
- Core Facility Mass Spectrometry and Lipidomics, ZMF, Medical University of Graz, 8036, Graz, Austria
| | - Andelko Hrzenjak
- Division of Pulmonology, Department of Internal Medicine, Medical University of Graz, Auenbruggerplatz 15, 8036, Graz, Austria
- Ludwig Boltzmann Institute for Lung Vascular Research, 8010, Graz, Austria
| | - Thomas Eichmann
- Core Facility Mass Spectrometry and Lipidomics, ZMF, Medical University of Graz, 8036, Graz, Austria
| | - Harald C Köfeler
- Core Facility Mass Spectrometry and Lipidomics, ZMF, Medical University of Graz, 8036, Graz, Austria
| | - Katharina Leithner
- Division of Pulmonology, Department of Internal Medicine, Medical University of Graz, Auenbruggerplatz 15, 8036, Graz, Austria.
- BioTechMed-Graz, 8010, Graz, Austria.
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2
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Schönbacher L, Treichler C, Brandl W, Köfeler HC, Fluhr H, Jantscher‐Krenn E, van Poppel MNM. Prenatal Human Milk Oligosaccharides (HMOs) in the Context of BMI, Gestational Weight Gain, and Lipid Profile-An Association Study in Pregnant Women with Overweight or Obesity. Mol Nutr Food Res 2024; 68:e2300533. [PMID: 38085123 PMCID: PMC10909570 DOI: 10.1002/mnfr.202300533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/26/2023] [Indexed: 02/01/2024]
Abstract
BACKGROUND Human milk oligosaccharides (HMOs) are bioactive glycans first detected in human milk. Their presence in maternal blood during pregnancy suggests systemic functions. Dynamics and associations of the most abundant prenatal HMOs in relation to maternal BMI and serum lipids in a cohort of 87 pregnant women with either overweight or obesity are studied. METHODS Serum HMOs (2'FL, 3'SL, 3'SLN, LDFT), serum lipids (total cholesterol, HDL, LDL, triglycerides), and BMI are measured at 15, 24, and 32 weeks of gestation. RESULTS 2'FL and LDFT are negatively correlated to pre-pregnancy BMI and increase significantly slower between 15 and 24 weeks in highly obese women. Women without detectable increase of serum 2'FL (non-secretors) show a less pronounced gestational weight gain and lower BMI in the third trimester as compared to women phenotype as secretors. Higher early-pregnancy 2'FL is associated with high HDL and low triglycerides in pregnancy. On the other hand, higher 3'SL at 15 weeks is associated with higher triglycerides, LDL, and total cholesterol. CONCLUSIONS Higher early-pregnancy 2'FL is associated with a cardioprotective lipid profile, whereas higher 3'SL is associated with an atherogenic lipid profile. Serum trajectories of 2'FL and LDFT in obese women suggest an obesity mediated delay of α-1,2-fucosylation.
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Affiliation(s)
- Lukas Schönbacher
- Department of Obstetrics and GynecologyMedical University of GrazAuenbruggerplatz 14Graz8036Austria
| | - Carmen Treichler
- Department of Obstetrics and GynecologyMedical University of GrazAuenbruggerplatz 14Graz8036Austria
| | - Waltraud Brandl
- Department of Obstetrics and GynecologyMedical University of GrazAuenbruggerplatz 14Graz8036Austria
| | - Harald C. Köfeler
- BioTechMed‐GrazMozartgasse 12/IIGraz8010Austria
- Center for Medical ResearchMedical University of GrazStiftingtalstraße 24Graz8010Austria
| | - Herbert Fluhr
- Department of Obstetrics and GynecologyMedical University of GrazAuenbruggerplatz 14Graz8036Austria
| | - Evelyn Jantscher‐Krenn
- Department of Obstetrics and GynecologyMedical University of GrazAuenbruggerplatz 14Graz8036Austria
- BioTechMed‐GrazMozartgasse 12/IIGraz8010Austria
| | - Mireille N. M. van Poppel
- BioTechMed‐GrazMozartgasse 12/IIGraz8010Austria
- Institute of Human Movement ScienceSport and HealthUniversity of GrazMozartgasse 14/IGraz8010Austria
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3
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Weiser-Fuchs MT, Maggauer E, van Poppel MNM, Csapo B, Desoye G, Köfeler HC, Groselj-Strele A, Trajanoski S, Fluhr H, Obermayer-Pietsch B, Jantscher-Krenn E. Human Milk Oligosaccharides in Maternal Serum Respond to Oral Glucose Load and Are Associated with Insulin Sensitivity. Nutrients 2023; 15:4042. [PMID: 37764825 PMCID: PMC10534497 DOI: 10.3390/nu15184042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/08/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
(1) Background: Pregnancy presents a challenge to maternal glucose homeostasis; suboptimal adaptations can lead to gestational diabetes mellitus (GDM). Human milk oligosaccharides (HMOs) circulate in maternal blood in pregnancy and are altered with GDM, suggesting influence of glucose homeostasis on HMOs. We thus assessed the HMO response to glucose load during an oral glucose tolerance test (OGTT) and investigated HMO associations with glucose tolerance/insulin sensitivity in healthy pregnant women. (2) Methods: Serum of 99 women, collected at 0 h, 1 h and 2 h during a 75 g OGTT at 24-28 gestational weeks was analyzed for HMOs (2'FL, 3'SLN, LDFT, 3'SL) by HPLC; plasma glucose, insulin and C-peptide were analyzed by standard biochemistry methods. (3) Results: Serum 3'SL concentrations significantly increased from fasting to 1 h after glucose load, while concentrations of the other HMOs were unaltered. Higher 3'SL at all OGTT time points was associated with a generally more diabetogenic profile, with higher hepatic insulin resistance (HOMA-IR), lower insulin sensitivity (Matsuda index) and higher insulin secretion (C-peptide index 1). (4) Conclusions: Rapid increase in serum 3'SL post-oral glucose load (fasted-fed transition) indicates utilization of plasma glucose, potentially for sialylation of lactose. Associations of sialylated HMOs with a more diabetogenic profile suggest sustained adaptations to impaired glucose homeostasis in pregnancy. Underlying mechanisms or potential consequences of observed HMO changes remain to be elucidated.
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Affiliation(s)
- Marie-Therese Weiser-Fuchs
- Department of Obstetrics and Gynecology, Medical University of Graz, 8036 Graz, Austria; (M.-T.W.-F.); (G.D.); (E.J.-K.)
- Research Unit Early Life Determinants (ELiD), Medical University of Graz, 8036 Graz, Austria
| | - Elena Maggauer
- Department of Obstetrics and Gynecology, Medical University of Graz, 8036 Graz, Austria; (M.-T.W.-F.); (G.D.); (E.J.-K.)
| | - Mireille N. M. van Poppel
- Institute of Human Movement Science, Sport and Health, University of Graz, 8010 Graz, Austria;
- BioTechMed, 8010 Graz, Austria;
| | - Bence Csapo
- Department of Obstetrics and Gynecology, Medical University of Graz, 8036 Graz, Austria; (M.-T.W.-F.); (G.D.); (E.J.-K.)
| | - Gernot Desoye
- Department of Obstetrics and Gynecology, Medical University of Graz, 8036 Graz, Austria; (M.-T.W.-F.); (G.D.); (E.J.-K.)
- Research Unit Early Life Determinants (ELiD), Medical University of Graz, 8036 Graz, Austria
| | - Harald C. Köfeler
- BioTechMed, 8010 Graz, Austria;
- Core Facility Mass Spectrometry, Center for Medical Research, Medical University of Graz, 8036 Graz, Austria
| | - Andrea Groselj-Strele
- Core Facility Computational Bioanalytics, Center for Medical Research, Medical University of Graz, 8036 Graz, Austria; (A.G.-S.); (S.T.)
| | - Slave Trajanoski
- Core Facility Computational Bioanalytics, Center for Medical Research, Medical University of Graz, 8036 Graz, Austria; (A.G.-S.); (S.T.)
| | - Herbert Fluhr
- Department of Obstetrics and Gynecology, Medical University of Graz, 8036 Graz, Austria; (M.-T.W.-F.); (G.D.); (E.J.-K.)
- Research Unit Early Life Determinants (ELiD), Medical University of Graz, 8036 Graz, Austria
| | - Barbara Obermayer-Pietsch
- Department of Internal Medicine, Division of Endocrinology and Diabetology, Medical University of Graz, 8036 Graz, Austria;
- Department of Obstetrics and Gynecology, Endocrinology Lab Platform, 8036 Graz, Austria
| | - Evelyn Jantscher-Krenn
- Department of Obstetrics and Gynecology, Medical University of Graz, 8036 Graz, Austria; (M.-T.W.-F.); (G.D.); (E.J.-K.)
- Research Unit Early Life Determinants (ELiD), Medical University of Graz, 8036 Graz, Austria
- BioTechMed, 8010 Graz, Austria;
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4
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Simstich S, Züllig T, D'Aurizio F, Biasotto A, Colao A, Isidori AM, Lenzi A, Fauler G, Köfeler HC, Curcio F, Herrmann M. The impact of different calibration matrices on the determination of insulin-like growth factor 1 by high-resolution-LC-MS in acromegalic and growth hormone deficient patients. Clin Biochem 2023; 114:95-102. [PMID: 36849049 DOI: 10.1016/j.clinbiochem.2023.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 02/01/2023] [Accepted: 02/20/2023] [Indexed: 02/27/2023]
Abstract
OBJECTIVES Calibration is an important source of variability in liquid chromatography mass spectrometry (LC-MS) methods for insulin-like growth factor 1 (IGF-1). This study investigated the impact of different calibrator matrices on IGF-1 measurements by LC-MS. Moreover, the comparability of immunoassays and LC-MS was assessed. DESIGN & METHODS Calibrators from 12.5 to 2009 ng/ml were prepared by spiking WHO international Standard (ID 02/254 NIBSC, UK) into the following matrices: native human plasma, fresh charcoal-treated human plasma (FCTHP), old charcoal-treated human plasma, deionized water, bovine serum albumin (BSA), and rat plasma (RP). A validated in-house LC-MS method was calibrated repeatedly with these calibrators. Then, serum samples from 197 growth hormone excess and deficiency patients were analysed with each calibration. RESULTS The seven calibration curves had different slopes leading to markedly different patient results. The largest differences in IGF-1 concentration from the median (interquartile range) was observed with the calibrator in water and the calibrator in RP (336.4 [279.6-417.0] vs. 112.5 [71.2-171.2], p < 0.001). The smallest difference was observed with calibrators in FCTHP and BSA (141.8 [102.0-198.5] vs. 127.9 [86.9-186.0], p < 0.049). Compared to LC-MS with calibrators in FCTHP, immunoassays showed relevant proportional bias (range: -43% to -68%), constant bias (range: 22.84 to 57.29 ng/ml) and pronounced scatter. Comparing the immunoassays with each other revealed proportional bias of up to 24%. CONCLUSIONS The calibrator matrix is critical for the measurement of IGF-1 by LC-MS. Regardless of the calibrator matrix, LC-MS shows poor agreement with immunoassays. Also, the agreement between different immunoassays is variable.
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Affiliation(s)
- Sebastian Simstich
- Clinical Institute of Medical and Chemical Laboratory Diagnosis, Medical University of Graz, Austria
| | - Thomas Züllig
- Core Facility Mass Spectrometry, Medical University of Graz, Austria; Institute of Molecular Biosciences, University of Graz, Austria
| | - Federica D'Aurizio
- Department of Laboratory Medicine, Institute of Clinical Pathology, Academic Hospital of Udine, Italy
| | | | - Annamaria Colao
- Department of Clinical Medicine and Surgery, Section of Endocrinology, University Federico II, Naples, Italy; UNESCO Chair for Health Education and Sustainable Development, University Federico II, Naples, Italy
| | - Andrea M Isidori
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, Italy
| | - Andrea Lenzi
- Department of Experimental Medicine, Sapienza University of Rome, Italy
| | - Günter Fauler
- Clinical Institute of Medical and Chemical Laboratory Diagnosis, Medical University of Graz, Austria
| | - Harald C Köfeler
- Core Facility Mass Spectrometry, Medical University of Graz, Austria
| | - Francesco Curcio
- Department of Laboratory Medicine, Institute of Clinical Pathology, Academic Hospital of Udine, Italy; Department of Medicine, University of Udine, Italy
| | - Markus Herrmann
- Clinical Institute of Medical and Chemical Laboratory Diagnosis, Medical University of Graz, Austria.
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5
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McDonald JG, Ejsing CS, Kopczynski D, Holčapek M, Aoki J, Arita M, Arita M, Baker ES, Bertrand-Michel J, Bowden JA, Brügger B, Ellis SR, Fedorova M, Griffiths WJ, Han X, Hartler J, Hoffmann N, Koelmel JP, Köfeler HC, Mitchell TW, O'Donnell VB, Saigusa D, Schwudke D, Shevchenko A, Ulmer CZ, Wenk MR, Witting M, Wolrab D, Xia Y, Ahrends R, Liebisch G, Ekroos K. Introducing the Lipidomics Minimal Reporting Checklist. Nat Metab 2022; 4:1086-1088. [PMID: 35934691 DOI: 10.1038/s42255-022-00628-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jeffrey G McDonald
- Center for Human Nutrition and Department of Molecular Genetics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Christer S Ejsing
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Dominik Kopczynski
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Michal Holčapek
- Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czech Republic
| | - Junken Aoki
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
- Graduate School of Pharmaceutical Sciences, University of Tokyo, Tokyo, Japan
| | - Makoto Arita
- RIKEN, Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA
| | - Justine Bertrand-Michel
- MetaboHUB-Metatoul, National Infrastructure of Metabolomics and Fluxomics, Inserm I2MC, Toulouse, France
| | - John A Bowden
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - Britta Brügger
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany
| | - Shane R Ellis
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, Australia
- Illawarra Heath and Medical Research Institute, Wollongong, New South Wales, Australia
| | - Maria Fedorova
- Center for Membrane Biochemistry and Lipid Research, Faculty of Medicine Carl Gustav Carus of TU Dresden, Dresden, Germany
| | | | - Xianlin Han
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
- Department of Medicine - Diabetes, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Jürgen Hartler
- Institute of Pharmaceutical Sciences, University of Graz, Graz, Austria
- Field of Excellence BioHealth - University of Graz, Graz, Austria
| | - Nils Hoffmann
- Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Jeremy P Koelmel
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Harald C Köfeler
- Core Facility Mass Spectrometry and Lipidomics, ZMF, Medical University of Graz, Graz, Austria
| | - Todd W Mitchell
- Illawarra Heath and Medical Research Institute, Wollongong, New South Wales, Australia
| | - Valerie B O'Donnell
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK
| | - Daisuke Saigusa
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Dominik Schwudke
- Research Center Borstel - Leibniz Lung Center, Borstel, Germany
- German Center for Infection Research, Thematic Translational Unit Tuberculosis, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
- German Center for Lung Research (DZL), Airway Research Center North (ARCN), Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Andrej Shevchenko
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Candice Z Ulmer
- Office of Public Health Science, Food Safety and Inspection Service, US Department of Agriculture, Athens, GA, USA
| | - Markus R Wenk
- Singapore Lipidomics Incubator (SLING), Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore, Singapore
| | - Michael Witting
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, Neuherberg, Germany
| | - Denise Wolrab
- Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czech Republic
| | - Yu Xia
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Robert Ahrends
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria.
| | - Gerhard Liebisch
- Institute of Clinical Chemistry and Laboratory Medicine, University of Regensburg, Regensburg, Germany.
| | - Kim Ekroos
- Lipidomics Consulting Ltd., Esbo, Finland.
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6
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Köfeler HC, Ahrends R, Baker ES, Ekroos K, Han X, Hoffmann N, Holčapek M, Wenk MR, Liebisch G. Recommendations for good practice in MS-based lipidomics. J Lipid Res 2021; 62:100138. [PMID: 34662536 PMCID: PMC8585648 DOI: 10.1016/j.jlr.2021.100138] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/29/2021] [Accepted: 10/01/2021] [Indexed: 12/17/2022] Open
Abstract
In the last 2 decades, lipidomics has become one of the fastest expanding scientific disciplines in biomedical research. With an increasing number of new research groups to the field, it is even more important to design guidelines for assuring high standards of data quality. The Lipidomics Standards Initiative is a community-based endeavor for the coordination of development of these best practice guidelines in lipidomics and is embedded within the International Lipidomics Society. It is the intention of this review to highlight the most quality-relevant aspects of the lipidomics workflow, including preanalytics, sample preparation, MS, and lipid species identification and quantitation. Furthermore, this review just does not only highlights examples of best practice but also sheds light on strengths, drawbacks, and pitfalls in the lipidomic analysis workflow. While this review is neither designed to be a step-by-step protocol by itself nor dedicated to a specific application of lipidomics, it should nevertheless provide the interested reader with links and original publications to obtain a comprehensive overview concerning the state-of-the-art practices in the field.
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Affiliation(s)
- Harald C Köfeler
- Core Facility Mass Spectrometry, Medical University of Graz, Graz, Austria.
| | - Robert Ahrends
- Department for Analytical Chemistry, University of Vienna, Vienna, Austria
| | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA
| | - Kim Ekroos
- Lipidomics Consulting Ltd., Esbo, Finland
| | - Xianlin Han
- Barshop Inst Longev & Aging Studies, Univ Texas Hlth Sci Ctr San Antonio, San Antonio, TX, USA
| | - Nils Hoffmann
- Center for Biotechnology, Universität Bielefeld, Bielefeld, Germany
| | - Michal Holčapek
- Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czech Republic
| | - Markus R Wenk
- Singapore Lipidomics Incubator (SLING), Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore, Singapore
| | - Gerhard Liebisch
- Institute of Clinical Chemistry and Laboratory Medicine, Regensburg University Hospital, Regensburg, Germany.
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7
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Vvedenskaya O, Rose TD, Knittelfelder O, Palladini A, Wodke JAH, Schuhmann K, Ackerman JM, Wang Y, Has C, Brosch M, Thangapandi VR, Buch S, Züllig T, Hartler J, Köfeler HC, Röcken C, Coskun Ü, Klipp E, von Schoenfels W, Gross J, Schafmayer C, Hampe J, Pauling JK, Shevchenko A. Nonalcoholic fatty liver disease stratification by liver lipidomics. J Lipid Res 2021; 62:100104. [PMID: 34384788 PMCID: PMC8488246 DOI: 10.1016/j.jlr.2021.100104] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/20/2021] [Accepted: 07/30/2021] [Indexed: 02/06/2023] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a common metabolic dysfunction leading to hepatic steatosis. However, NAFLD's global impact on the liver lipidome is poorly understood. Using high-resolution shotgun mass spectrometry, we quantified the molar abundance of 316 species from 22 major lipid classes in liver biopsies of 365 patients, including nonsteatotic patients with normal or excessive weight, patients diagnosed with NAFL (nonalcoholic fatty liver) or NASH (nonalcoholic steatohepatitis), and patients bearing common mutations of NAFLD-related protein factors. We confirmed the progressive accumulation of di- and triacylglycerols and cholesteryl esters in the liver of NAFL and NASH patients, while the bulk composition of glycerophospho- and sphingolipids remained unchanged. Further stratification by biclustering analysis identified sphingomyelin species comprising n24:2 fatty acid moieties as membrane lipid markers of NAFLD. Normalized relative abundance of sphingomyelins SM 43:3;2 and SM 43:1;2 containing n24:2 and n24:0 fatty acid moieties, respectively, showed opposite trends during NAFLD progression and distinguished NAFL and NASH lipidomes from the lipidome of nonsteatotic livers. Together with several glycerophospholipids containing a C22:6 fatty acid moiety, these lipids serve as markers of early and advanced stages of NAFL.
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Affiliation(s)
- Olga Vvedenskaya
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Tim Daniel Rose
- LipiTUM, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany
| | - Oskar Knittelfelder
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Alessandra Palladini
- Paul Langerhans Institute Dresden of the Helmholtz Zentrum Munich at the University Hospital Carl Gustav Carus, Technische Universität (TU) Dresden, Dresden, Germany; German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | | | - Kai Schuhmann
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Yuting Wang
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Canan Has
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Mario Brosch
- Department of Medicine I, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Germany; Center for Regenerative Therapies Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Veera Raghavan Thangapandi
- Department of Medicine I, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Germany; Center for Regenerative Therapies Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Stephan Buch
- Department of Medicine I, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Germany; Center for Regenerative Therapies Dresden (CRTD), Technische Universität (TU) Dresden, Dresden, Germany
| | - Thomas Züllig
- Core Facility Mass Spectrometry, Medical University of Graz, Graz, Austria
| | - Jürgen Hartler
- Institute of Pharmaceutical Sciences, University of Graz, Graz, Austria; Field of Excellence BioHealth, University of Graz, Graz, Austria
| | - Harald C Köfeler
- Core Facility Mass Spectrometry, Medical University of Graz, Graz, Austria
| | - Christoph Röcken
- Department of Pathology, University Hospital Schleswig Holstein, Kiel, Schleswig-Holstein, Germany
| | - Ünal Coskun
- Paul Langerhans Institute Dresden of the Helmholtz Zentrum Munich at the University Hospital Carl Gustav Carus, Technische Universität (TU) Dresden, Dresden, Germany; German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany; Department of Membrane Biochemistry and Lipid Research, University Hospital Carl Gustav Carus of Technische Universität Dresden, Dresden, Germany
| | - Edda Klipp
- Theoretical Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Witigo von Schoenfels
- Department of Visceral and Thoracic Surgery, University Hospital Schleswig-Holstein, Kiel Campus, Christian-Albrechts-University Kiel, Kiel, Germany; Christian Albrechts University in Kiel Center of Clinical Anatomy Kiel, Schleswig-Holstein, Germany
| | - Justus Gross
- Department of General, Visceral, Vascular and Transplant Surgery, Rostock University Medical Center, Rostock, Germany
| | - Clemens Schafmayer
- Department of General, Visceral, Vascular and Transplant Surgery, Rostock University Medical Center, Rostock, Germany
| | - Jochen Hampe
- Department of Medicine I, University Hospital Dresden, Technische Universität (TU) Dresden, Dresden, Germany
| | - Josch Konstantin Pauling
- LipiTUM, Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, Munich, Germany.
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
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8
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Joshi L, Plastira I, Bernhart E, Reicher H, Triebl A, Köfeler HC, Sattler W. Inhibition of Autotaxin and Lysophosphatidic Acid Receptor 5 Attenuates Neuroinflammation in LPS-Activated BV-2 Microglia and a Mouse Endotoxemia Model. Int J Mol Sci 2021; 22:ijms22168519. [PMID: 34445223 PMCID: PMC8395174 DOI: 10.3390/ijms22168519] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/29/2021] [Accepted: 08/04/2021] [Indexed: 12/22/2022] Open
Abstract
Increasing evidence suggests that systemic inflammation triggers a neuroinflammatory response that involves sustained microglia activation. This response has deleterious consequences on memory and learning capability in experimental animal models and in patients. However, the mechanisms connecting systemic inflammation and microglia activation remain poorly understood. Here, we identify the autotaxin (ATX)/lysophosphatidic acid (LPA)/LPA-receptor axis as a potential pharmacological target to modulate the LPS-mediated neuroinflammatory response in vitro (the murine BV-2 microglia cell line) and in vivo (C57BL/6J mice receiving a single i.p. LPS injection). In LPS-stimulated (20 ng/mL) BV-2 cells, we observed increased phosphorylation of transcription factors (STAT1, p65, and c-Jun) that are known to induce a proinflammatory microglia phenotype. LPS upregulated ATX, TLR4, and COX2 expression, amplified NO production, increased neurotoxicity of microglia conditioned medium, and augmented cyto-/chemokine concentrations in the cellular supernatants. PF8380 (a type I ATX inhibitor, used at 10 and 1 µM) and AS2717638 (an LPA5 antagonist, used at 1 and 0.1 µM) attenuated these proinflammatory responses, at non-toxic concentrations, in BV-2 cells. In vivo, we demonstrate accumulation of PF8380 in the mouse brain and an accompanying decrease in LPA concentrations. In vivo, co-injection of LPS (5 mg/kg body weight) and PF8380 (30 mg/kg body weight), or LPS/AS2717638 (10 mg/kg body weight), significantly attenuated LPS-induced iNOS, TNFα, IL-1β, IL-6, and CXCL2 mRNA expression in the mouse brain. On the protein level, PF8380 and AS2717638 significantly reduced TLR4, Iba1, GFAP and COX2 expression, as compared to LPS-only injected animals. In terms of the communication between systemic inflammation and neuroinflammation, both inhibitors significantly attenuated LPS-mediated systemic TNFα and IL-6 synthesis, while IL-1β was only reduced by PF8380. Inhibition of ATX and LPA5 may thus provide an opportunity to protect the brain from the toxic effects that are provoked by systemic endotoxemia.
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Affiliation(s)
- Lisha Joshi
- Division of Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, 8010 Graz, Austria; (L.J.); (I.P.); (E.B.); (H.R.)
| | - Ioanna Plastira
- Division of Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, 8010 Graz, Austria; (L.J.); (I.P.); (E.B.); (H.R.)
| | - Eva Bernhart
- Division of Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, 8010 Graz, Austria; (L.J.); (I.P.); (E.B.); (H.R.)
| | - Helga Reicher
- Division of Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, 8010 Graz, Austria; (L.J.); (I.P.); (E.B.); (H.R.)
| | - Alexander Triebl
- Core Facility Mass Spectrometry, Medical University of Graz, 8010 Graz, Austria; (A.T.); (H.C.K.)
| | - Harald C. Köfeler
- Core Facility Mass Spectrometry, Medical University of Graz, 8010 Graz, Austria; (A.T.); (H.C.K.)
- BioTechMed Graz, 8010 Graz, Austria
| | - Wolfgang Sattler
- Division of Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, 8010 Graz, Austria; (L.J.); (I.P.); (E.B.); (H.R.)
- BioTechMed Graz, 8010 Graz, Austria
- Correspondence: ; Tel.: +43-316-385-71950
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9
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Geidl-Flueck B, Hochuli M, Németh Á, Eberl A, Derron N, Köfeler HC, Tappy L, Berneis K, Spinas GA, Gerber PA. Fructose- and sucrose- but not glucose-sweetened beverages promote hepatic de novo lipogenesis: A randomized controlled trial. J Hepatol 2021; 75:46-54. [PMID: 33684506 DOI: 10.1016/j.jhep.2021.02.027] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 02/03/2021] [Accepted: 02/18/2021] [Indexed: 01/01/2023]
Abstract
BACKGROUND & AIMS Excessive fructose intake is associated with increased de novo lipogenesis, blood triglycerides, and hepatic insulin resistance. We aimed to determine whether fructose elicits specific effects on lipid metabolism independently of excessive caloric intake. METHODS A total of 94 healthy men were studied in this double-blind, randomized trial. They were assigned to daily consumption of sugar-sweetened beverages (SSBs) containing moderate amounts of fructose, sucrose (fructose-glucose disaccharide) or glucose (80 g/day) in addition to their usual diet or SSB abstinence (control group) for 7 weeks. De novo fatty acid (FA) and triglyceride synthesis, lipolysis and plasma free FA (FFA) oxidation were assessed by tracer methodology. RESULTS Daily intake of beverages sweetened with free fructose and fructose combined with glucose (sucrose) led to a 2-fold increase in basal hepatic fractional secretion rates (FSR) compared to control (median FSR %/day: sucrose 20.8 (p = 0.0015); fructose 19.7 (p = 0.013); control 9.1). Conversely, the same amounts of glucose did not change FSR (median of FSR %/day 11.0 (n.s.)). Fructose intake did not change basal secretion of newly synthesized VLDL-triglyceride, nor did it alter rates of peripheral lipolysis, nor total FA and plasma FFA oxidation. Total energy intake was similar across groups. CONCLUSIONS Regular consumption of both fructose- and sucrose-sweetened beverages in moderate doses - associated with stable caloric intake - increases hepatic FA synthesis even in a basal state; this effect is not observed after glucose consumption. These findings provide evidence of an adaptative response to regular fructose exposure in the liver. LAY SUMMARY This study investigated the metabolic effects of daily sugar-sweetened beverage consumption for several weeks in healthy lean men. It revealed that beverages sweetened with the sugars fructose and sucrose (glucose and fructose combined), but not glucose, increase the ability of the liver to produce lipids. This change may pave the way for further unfavorable effects on metabolic health. CLINICAL TRIAL REGISTRATION NUMBER NCT01733563.
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Affiliation(s)
- Bettina Geidl-Flueck
- Department of Endocrinology, Diabetology and Clinical Nutrition, University Hospital Zurich (USZ) and University of Zurich (UZH), Switzerland.
| | - Michel Hochuli
- Department of Endocrinology, Diabetology and Clinical Nutrition, University Hospital Zurich (USZ) and University of Zurich (UZH), Switzerland; Department of Diabetes, Endocrinology, Nutritional Medicine and Metabolism, Inselspital, Bern University Hospital and University of Bern, Switzerland
| | - Ágota Németh
- Department of Endocrinology, Diabetology and Clinical Nutrition, University Hospital Zurich (USZ) and University of Zurich (UZH), Switzerland
| | - Anita Eberl
- Institute for Biomedicine and Health Sciences, Joanneum Research, Graz, Austria
| | - Nina Derron
- Department of Endocrinology, Diabetology and Clinical Nutrition, University Hospital Zurich (USZ) and University of Zurich (UZH), Switzerland
| | - Harald C Köfeler
- Core Facility Mass Spectrometry, Medical University of Graz, Austria
| | - Luc Tappy
- Department of Physiology, University of Lausanne, Switzerland
| | - Kaspar Berneis
- Department of Endocrinology, Diabetology and Clinical Nutrition, University Hospital Zurich (USZ) and University of Zurich (UZH), Switzerland
| | - Giatgen A Spinas
- Department of Endocrinology, Diabetology and Clinical Nutrition, University Hospital Zurich (USZ) and University of Zurich (UZH), Switzerland
| | - Philipp A Gerber
- Department of Endocrinology, Diabetology and Clinical Nutrition, University Hospital Zurich (USZ) and University of Zurich (UZH), Switzerland
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10
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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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11
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Lesko J, Triebl A, Stacher-Priehse E, Fink-Neuböck N, Lindenmann J, Smolle-Jüttner FM, Köfeler HC, Hrzenjak A, Olschewski H, Leithner K. Phospholipid dynamics in ex vivo lung cancer and normal lung explants. Exp Mol Med 2021; 53:81-90. [PMID: 33408336 PMCID: PMC8080582 DOI: 10.1038/s12276-020-00547-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/22/2020] [Accepted: 11/04/2020] [Indexed: 01/29/2023] Open
Abstract
In cancer cells, metabolic pathways are reprogrammed to promote cell proliferation and growth. While the rewiring of central biosynthetic pathways is being extensively studied, the dynamics of phospholipids in cancer cells are still poorly understood. In our study, we sought to evaluate de novo biosynthesis of glycerophospholipids (GPLs) in ex vivo lung cancer explants and corresponding normal lung tissue from six patients by utilizing a stable isotopic labeling approach. Incorporation of fully 13C-labeled glucose into the backbone of phosphatidylethanolamine (PE), phosphatidylcholine (PC), and phosphatidylinositol (PI) was analyzed by liquid chromatography/mass spectrometry. Lung cancer tissue showed significantly elevated isotopic enrichment within the glycerol backbone of PE, normalized to its incorporation into PI, compared to that in normal lung tissue; however, the size of the PE pool normalized to the size of the PI pool was smaller in tumor tissue. These findings indicate enhanced PE turnover in lung cancer tissue. Elevated biosynthesis of PE in lung cancer tissue was supported by enhanced expression of the PE biosynthesis genes ETNK2 and EPT1 and decreased expression of the PC and PI biosynthesis genes CHPT1 and CDS2, respectively, in different subtypes of lung cancer in publicly available datasets. Our study demonstrates that incorporation of glucose-derived carbons into the glycerol backbone of GPLs can be monitored to study phospholipid dynamics in tumor explants and shows that PE turnover is elevated in lung cancer tissue compared to normal lung tissue.
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Affiliation(s)
- Julia Lesko
- grid.11598.340000 0000 8988 2476Department of Internal Medicine, Division of Pulmonology, Medical University of Graz, 8036 Graz, Austria
| | - Alexander Triebl
- grid.11598.340000 0000 8988 2476Core Facility Mass Spectrometry and Lipidomics, ZMF, Medical University of Graz, Graz, Austria
| | - Elvira Stacher-Priehse
- grid.11598.340000 0000 8988 2476Institute of Pathology, Medical University of Graz, Graz, Austria ,grid.6363.00000 0001 2218 4662Present Address: Institute of Pathology, Asklepios Clinic Munich-Gauting, Munich, Germany
| | - Nicole Fink-Neuböck
- grid.11598.340000 0000 8988 2476Division of Thoracic and Hyperbaric Surgery, Medical University of Graz, Graz, Austria
| | - Jörg Lindenmann
- grid.11598.340000 0000 8988 2476Division of Thoracic and Hyperbaric Surgery, Medical University of Graz, Graz, Austria
| | - Freyja-Maria Smolle-Jüttner
- grid.11598.340000 0000 8988 2476Division of Thoracic and Hyperbaric Surgery, Medical University of Graz, Graz, Austria
| | - Harald C. Köfeler
- grid.11598.340000 0000 8988 2476Core Facility Mass Spectrometry and Lipidomics, ZMF, Medical University of Graz, Graz, Austria
| | - Andelko Hrzenjak
- grid.11598.340000 0000 8988 2476Department of Internal Medicine, Division of Pulmonology, Medical University of Graz, 8036 Graz, Austria ,grid.489038.eLudwig Boltzmann Institute for Lung Vascular Research, Graz, Austria
| | - Horst Olschewski
- grid.11598.340000 0000 8988 2476Department of Internal Medicine, Division of Pulmonology, Medical University of Graz, 8036 Graz, Austria ,grid.489038.eLudwig Boltzmann Institute for Lung Vascular Research, Graz, Austria
| | - Katharina Leithner
- grid.11598.340000 0000 8988 2476Department of Internal Medicine, Division of Pulmonology, Medical University of Graz, 8036 Graz, Austria
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12
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Züllig T, Trötzmüller M, Köfeler HC. Global Lipidomics Profiling by a High Resolution LC-MS Platform. Methods Mol Biol 2021; 2306:39-51. [PMID: 33954938 DOI: 10.1007/978-1-0716-1410-5_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Lipidomics is the determination of big lipid assemblies by mass spectrometry. When using chromatography coupled high resolution mass spectrometry, lipids can be identified by exact mass, fragment spectra, and retention time. This protocol covers lipid extraction, LC-MS data acquisition by Orbitrap mass spectrometry and data processing by Lipid Data Analyzer, a custom developed open source software.
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Affiliation(s)
- Thomas Züllig
- Core Facility Mass Spectrometry, Medical University of Graz, Graz, Austria
| | - Martin Trötzmüller
- Core Facility Mass Spectrometry, Medical University of Graz, Graz, Austria
| | - Harald C Köfeler
- Core Facility Mass Spectrometry, Medical University of Graz, Graz, Austria.
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13
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Hartler J, Armando AM, Trötzmüller M, Dennis EA, Köfeler HC, Quehenberger O. Automated Annotation of Sphingolipids Including Accurate Identification of Hydroxylation Sites Using MS n Data. Anal Chem 2020; 92:14054-14062. [PMID: 33003696 PMCID: PMC7581017 DOI: 10.1021/acs.analchem.0c03016] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Sphingolipids constitute a heterogeneous lipid category that is involved in many key cellular functions. For high-throughput analyses of sphingolipids, tandem mass spectrometry (MS/MS) is the method of choice, offering sufficient sensitivity, structural information, and quantitative precision for detecting hundreds to thousands of species simultaneously. While glycerolipids and phospholipids are predominantly non-hydroxylated, sphingolipids are typically dihydroxylated. However, species containing one or three hydroxylation sites can be detected frequently. This variability in the number of hydroxylation sites on the sphingolipid long-chain base and the fatty acyl moiety produces many more isobaric species and fragments than for other lipid categories. Due to this complexity, the automated annotation of sphingolipid species is challenging, and incorrect annotations are common. In this study, we present an extension of the Lipid Data Analyzer (LDA) "decision rule set" concept that considers the structural characteristics that are specific for this lipid category. To address the challenges inherent to automated annotation of sphingolipid structures from MS/MS data, we first developed decision rule sets using spectra from authentic standards and then tested the applicability on biological samples including murine brain and human plasma. A benchmark test based on the murine brain samples revealed a highly improved annotation quality as measured by sensitivity and reliability. The results of this benchmark test combined with the easy extensibility of the software to other (sphingo)lipid classes and the capability to detect and correctly annotate novel sphingolipid species make LDA broadly applicable to automated sphingolipid analysis, especially in high-throughput settings.
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Affiliation(s)
- Jürgen Hartler
- Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, 92093 California, United States.,Institute of Pharmaceutical Sciences, University of Graz, Universitätsplatz 1/I, 8010 Graz, Austria
| | - Aaron M Armando
- Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, 92093 California, United States
| | - Martin Trötzmüller
- Core Facility for Mass Spectrometry, Medical University of Graz, Stiftingtalstraße 24, 8010 Graz, Austria
| | - Edward A Dennis
- Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, 92093 California, United States
| | - Harald C Köfeler
- Core Facility for Mass Spectrometry, Medical University of Graz, Stiftingtalstraße 24, 8010 Graz, Austria
| | - Oswald Quehenberger
- Department of Pharmacology, University of California San Diego, 9500 Gilman Drive, La Jolla, 92093 California, United States
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14
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Züllig T, Zandl-Lang M, Trötzmüller M, Hartler J, Plecko B, Köfeler HC. A Metabolomics Workflow for Analyzing Complex Biological Samples Using a Combined Method of Untargeted and Target-List Based Approaches. Metabolites 2020; 10:E342. [PMID: 32854199 PMCID: PMC7570008 DOI: 10.3390/metabo10090342] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 08/20/2020] [Accepted: 08/20/2020] [Indexed: 12/22/2022] Open
Abstract
In the highly dynamic field of metabolomics, we have developed a method for the analysis of hydrophilic metabolites in various biological samples. Therefore, we used hydrophilic interaction chromatography (HILIC) for separation, combined with a high-resolution mass spectrometer (MS) with the aim of separating and analyzing a wide range of compounds. We used 41 reference standards with different chemical properties to develop an optimal chromatographic separation. MS analysis was performed with a set of pooled biological samples human cerebrospinal fluid (CSF), and human plasma. The raw data was processed in a first step with Compound Discoverer 3.1 (CD), a software tool for untargeted metabolomics with the aim to create a list of unknown compounds. In a second step, we combined the results obtained with our internally analyzed reference standard list to process the data along with the Lipid Data Analyzer 2.6 (LDA), a software tool for a targeted approach. In order to demonstrate the advantages of this combined target-list based and untargeted approach, we not only compared the relative standard deviation (%RSD) of the technical replicas of pooled plasma samples (n = 5) and pooled CSF samples (n = 3) with the results from CD, but also with XCMS Online, a well-known software tool for untargeted metabolomics studies. As a result of this study we could demonstrate with our HILIC-MS method that all standards could be either separated by chromatography, including isobaric leucine and isoleucine or with MS by different mass. We also showed that this combined approach benefits from improved precision compared to well-known metabolomics software tools such as CD and XCMS online. Within the pooled plasma samples processed by LDA 68% of the detected compounds had a %RSD of less than 25%, compared to CD and XCMS online (57% and 55%). The improvements of precision in the pooled CSF samples were even more pronounced, 83% had a %RSD of less than 25% compared to CD and XCMS online (28% and 8% compounds detected). Particularly for low concentration samples, this method showed a more precise peak area integration with its 3D algorithm and with the benefits of the LDAs graphical user interface for fast and easy manual curation of peak integration. The here-described method has the advantage that manual curation for larger batch measurements remains minimal due to the target list containing the information obtained by an untargeted approach.
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Affiliation(s)
- Thomas Züllig
- Core Facility Mass Spectrometry, Medical University of Graz, 8036 Graz, Austria; (T.Z.); (M.T.)
| | - Martina Zandl-Lang
- Department of Paediatrics and Adolescent Medicine, Division of General Paediatrics, University Childrens’ Hospital Graz, Medical University of Graz, 8036 Graz, Austria; (M.Z.-L.); (B.P.)
| | - Martin Trötzmüller
- Core Facility Mass Spectrometry, Medical University of Graz, 8036 Graz, Austria; (T.Z.); (M.T.)
| | - Jürgen Hartler
- Institute of Pharmaceutical Sciences, University of Graz, 8036 Graz, Austria;
| | - Barbara Plecko
- Department of Paediatrics and Adolescent Medicine, Division of General Paediatrics, University Childrens’ Hospital Graz, Medical University of Graz, 8036 Graz, Austria; (M.Z.-L.); (B.P.)
| | - Harald C. Köfeler
- Core Facility Mass Spectrometry, Medical University of Graz, 8036 Graz, Austria; (T.Z.); (M.T.)
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15
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Wackerlig J, Köfeler HC, Korz V, Hussein AM, Feyissa DD, Höger H, Urban E, Langer T, Lubec G, Lubec J. Differences in Hypothalamic Lipid Profiles of Young and Aged Male Rats With Impaired and Unimpaired Spatial Cognitive Abilities and Memory. Front Aging Neurosci 2020; 12:204. [PMID: 32719597 PMCID: PMC7349000 DOI: 10.3389/fnagi.2020.00204] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/11/2020] [Indexed: 12/11/2022] Open
Abstract
Lipids play a major role for several brain functions, including cognition and memory. There is a series of work on individual lipids showing involvement in memory mechanisms, a concise lipidome was not reported so far. Moreover, there is no evidence for age-related memory decline and there is only work on brain of young vs. aging animals. Aging animals, however, are not a homogeneous group with respect to memory impairments, thus animals with impaired and unimpaired memory can be discriminated. Following recent studies of hippocampal lipid profiles and hypothalamus controlled hormone profiles, the aim of this study was to compare hypothalamic, lipidomic changes in male Sprague-Dawley rats between young (YM), old impaired (OMI) and old unimpaired (OMU) males. Grouping criterions for aged rats were evaluated by testing them in a spatial memory task, the hole-board. YMs were also tested. Subsequently brains were removed, dissected and hypothalami were kept at −80°C until sample preparation and analysis on liquid chromatography / mass spectrometry (LC-MS). Significant differences in the amounts of a series of lipids from several classes could be detected between young and aged and between OMI and OMU. A large number of lipids were increased in OMI and a smaller number in OMU as compared to young rats. Differences of lipid ratios (log2 of ratio) between OMI and OMU consisted of glycerophosphocholines (aPC 36:2 and 36:3; PC 34:0, 36:1, 36:3 and 40:2); Glycerophosphoethanolamines (aPE 34:2, 38:5 and 40:5; LPE 18:1, 20:1, 20:4, 22:4 and 22:6; PE36:1 and 38:4); glycerophosphoserines (PS 36:1, 40:4, and 40:6); triacylglycerol TG 52:4; ceramide Cer 17:2 and sphingomyelin SM 20:0. Thus, hypothalamic lipid profiles across different lipid classes discriminate aged male animals into OMU and OMI. The underlying mechanisms may be related to different functional networks of lipids in memory mechanisms and differences in metabolic processes. The study underlines the importance of lipidomics in the pathophysiology of age-related cognitive decline. The necessity of evaluating the cognitive status of aged subjects by behavioral tests results in more specific detection of critical lipids in memory decline, on which now can be focused in subsequent memory studies in animals and humans.
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Affiliation(s)
- Judith Wackerlig
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Harald C Köfeler
- Center for Medical Research, Medical University of Graz, Graz, Austria
| | - Volker Korz
- Department of Neuroproteomics, Paracelsus Private Medical University, Salzburg, Austria
| | - Ahmed M Hussein
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Daniel D Feyissa
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Harald Höger
- Core Unit of Biomedical Research, Division of Laboratory Animal Science and Genetics, Medical University of Vienna, Vienna, Austria
| | - Ernst Urban
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Thierry Langer
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Gert Lubec
- Neuroscience Laboratory, Paracelsus Medical University, Salzburg, Austria
| | - Jana Lubec
- Neuroscience Laboratory, Paracelsus Medical University, Salzburg, Austria
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16
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Dimas P, Montani L, Pereira JA, Moreno D, Trötzmüller M, Gerber J, Semenkovich CF, Köfeler HC, Suter U. CNS myelination and remyelination depend on fatty acid synthesis by oligodendrocytes. eLife 2019; 8:44702. [PMID: 31063129 PMCID: PMC6504237 DOI: 10.7554/elife.44702] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 04/27/2019] [Indexed: 12/26/2022] Open
Abstract
Oligodendrocytes (OLs) support neurons and signal transmission in the central nervous system (CNS) by enwrapping axons with myelin, a lipid-rich membrane structure. We addressed the significance of fatty acid (FA) synthesis in OLs by depleting FA synthase (FASN) from OL progenitor cells (OPCs) in transgenic mice. While we detected no effects in proliferation and differentiation along the postnatal OL lineage, we found that FASN is essential for accurate myelination, including myelin growth. Increasing dietary lipid intake could partially compensate for the FASN deficiency. Furthermore, FASN contributes to correct myelin lipid composition and stability of myelinated axons. Moreover, we depleted FASN specifically in adult OPCs to examine its relevance for remyelination. Applying lysolecithin-induced focal demyelinating spinal cord lesions, we found that FA synthesis is essential to sustain adult OPC-derived OLs and efficient remyelination. We conclude that FA synthesis in OLs plays key roles in CNS myelination and remyelination.
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Affiliation(s)
- Penelope Dimas
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Zürich, Zürich, Switzerland
| | - Laura Montani
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Zürich, Zürich, Switzerland
| | - Jorge A Pereira
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Zürich, Zürich, Switzerland
| | - Daniel Moreno
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Zürich, Zürich, Switzerland
| | | | - Joanne Gerber
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Zürich, Zürich, Switzerland
| | - Clay F Semenkovich
- Division of Endocrinology, Metabolism and Lipid Research, Washington University Medical School, St. Louis, United States
| | - Harald C Köfeler
- Center for Medical Research, Medical University of Graz, Graz, Austria
| | - Ueli Suter
- Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Zürich, Zürich, Switzerland
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17
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Leithner K, Triebl A, Trötzmüller M, Hinteregger B, Leko P, Wieser BI, Grasmann G, Bertsch AL, Züllig T, Stacher E, Valli A, Prassl R, Olschewski A, Harris AL, Köfeler HC, Olschewski H, Hrzenjak A. The glycerol backbone of phospholipids derives from noncarbohydrate precursors in starved lung cancer cells. Proc Natl Acad Sci U S A 2018; 115:6225-6230. [PMID: 29844165 PMCID: PMC6004450 DOI: 10.1073/pnas.1719871115] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Cancer cells are reprogrammed to consume large amounts of glucose to support anabolic biosynthetic pathways. However, blood perfusion and consequently the supply with glucose are frequently inadequate in solid cancers. PEPCK-M (PCK2), the mitochondrial isoform of phosphoenolpyruvate carboxykinase (PEPCK), has been shown by us and others to be functionally expressed and to mediate gluconeogenesis, the reverse pathway of glycolysis, in different cancer cells. Serine and ribose synthesis have been identified as downstream pathways fed by PEPCK in cancer cells. Here, we report that PEPCK-M-dependent glycerol phosphate formation from noncarbohydrate precursors (glyceroneogenesis) occurs in starved lung cancer cells and supports de novo glycerophospholipid synthesis. Using stable isotope-labeled glutamine and lactate, we show that PEPCK-M generates phosphoenolpyruvate and 3-phosphoglycerate, which are at least partially converted to glycerol phosphate and incorporated into glycerophospholipids (GPL) under glucose and serum starvation. This pathway is required to maintain levels of GPL, especially phosphatidylethanolamine (PE), as shown by stable shRNA-mediated silencing of PEPCK-M in H23 lung cancer cells. PEPCK-M shRNA led to reduced colony formation after starvation, and the effect was partially reversed by the addition of dioleyl-PE. Furthermore, PEPCK-M silencing abrogated cancer growth in a lung cancer cell xenograft model. In conclusion, glycerol phosphate formation for de novo GPL synthesis via glyceroneogenesis is a newly characterized anabolic pathway in cancer cells mediated by PEPCK-M under conditions of severe nutrient deprivation.
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Affiliation(s)
- Katharina Leithner
- Division of Pulmonology, Department of Internal Medicine, Medical University of Graz, A-8036 Graz, Austria;
| | - Alexander Triebl
- Core Facility Mass Spectrometry and Lipidomics, Center for Medical Research (ZMF), Medical University of Graz, A-8010 Graz, Austria
| | - Martin Trötzmüller
- Core Facility Mass Spectrometry and Lipidomics, Center for Medical Research (ZMF), Medical University of Graz, A-8010 Graz, Austria
| | - Barbara Hinteregger
- Core Facility Mass Spectrometry and Lipidomics, Center for Medical Research (ZMF), Medical University of Graz, A-8010 Graz, Austria
| | - Petra Leko
- Division of Pulmonology, Department of Internal Medicine, Medical University of Graz, A-8036 Graz, Austria
| | - Beatrix I Wieser
- Division of Pulmonology, Department of Internal Medicine, Medical University of Graz, A-8036 Graz, Austria
| | - Gabriele Grasmann
- Division of Pulmonology, Department of Internal Medicine, Medical University of Graz, A-8036 Graz, Austria
| | - Alexandra L Bertsch
- Division of Pulmonology, Department of Internal Medicine, Medical University of Graz, A-8036 Graz, Austria
| | - Thomas Züllig
- Core Facility Mass Spectrometry and Lipidomics, Center for Medical Research (ZMF), Medical University of Graz, A-8010 Graz, Austria
| | - Elvira Stacher
- Institute of Pathology, Medical University of Graz, A-8010 Graz, Austria
| | - Alessandro Valli
- Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS Oxford, United Kingdom
| | - Ruth Prassl
- Gottfried Schatz Research Center-Biophysics, Medical University of Graz, A-8010 Graz, Austria
| | - Andrea Olschewski
- Ludwig Boltzmann Institute for Lung Vascular Research, A-8010 Graz, Austria
| | - Adrian L Harris
- Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS Oxford, United Kingdom
| | - Harald C Köfeler
- Core Facility Mass Spectrometry and Lipidomics, Center for Medical Research (ZMF), Medical University of Graz, A-8010 Graz, Austria
| | - Horst Olschewski
- Division of Pulmonology, Department of Internal Medicine, Medical University of Graz, A-8036 Graz, Austria;
| | - Andelko Hrzenjak
- Division of Pulmonology, Department of Internal Medicine, Medical University of Graz, A-8036 Graz, Austria
- Ludwig Boltzmann Institute for Lung Vascular Research, A-8010 Graz, Austria
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18
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Montani L, Pereira JA, Norrmén C, Pohl HBF, Tinelli E, Trötzmüller M, Figlia G, Dimas P, von Niederhäusern B, Schwager R, Jessberger S, Semenkovich CF, Köfeler HC, Suter U. De novo fatty acid synthesis by Schwann cells is essential for peripheral nervous system myelination. J Cell Biol 2018; 217:1353-1368. [PMID: 29434029 PMCID: PMC5881495 DOI: 10.1083/jcb.201706010] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 12/20/2017] [Accepted: 01/22/2018] [Indexed: 01/26/2023] Open
Abstract
Montani et al. reveal that de novo fatty acid synthesis by Schwann cells, mediated by fatty acid synthase, contributes fundamentally to driving myelination in the peripheral nervous system. They identify lipogenic activation of the PPARγ transcriptional network as a putatively involved functional mechanism. Myelination calls for a remarkable surge in cell metabolism to facilitate lipid and membrane production. Endogenous fatty acid (FA) synthesis represents a potentially critical process in myelinating glia. Using genetically modified mice, we show that Schwann cell (SC) intrinsic activity of the enzyme essential for de novo FA synthesis, fatty acid synthase (FASN), is crucial for precise lipid composition of peripheral nerves and fundamental for the correct onset of myelination and proper myelin growth. Upon FASN depletion in SCs, epineurial adipocytes undergo lipolysis, suggestive of a compensatory role. Mechanistically, we found that a lack of FASN in SCs leads to an impairment of the peroxisome proliferator-activated receptor (PPAR) γ–regulated transcriptional program. In agreement, defects in myelination of FASN-deficient SCs could be ameliorated by treatment with the PPARγ agonist rosiglitazone ex vivo and in vivo. Our results reveal that FASN-driven de novo FA synthesis in SCs is mandatory for myelination and identify lipogenic activation of the PPARγ transcriptional network as a putative downstream functional mediator.
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Affiliation(s)
- Laura Montani
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich, Zürich, Switzerland
| | - Jorge A Pereira
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich, Zürich, Switzerland
| | - Camilla Norrmén
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich, Zürich, Switzerland
| | - Hartmut B F Pohl
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich, Zürich, Switzerland
| | - Elisa Tinelli
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich, Zürich, Switzerland
| | - Martin Trötzmüller
- Lipidomics Center for Medical Research, Medical University, Graz, Austria
| | - Gianluca Figlia
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich, Zürich, Switzerland
| | - Penelope Dimas
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich, Zürich, Switzerland
| | - Belinda von Niederhäusern
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich, Zürich, Switzerland
| | - Rachel Schwager
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich, Zürich, Switzerland
| | | | - Clay F Semenkovich
- Division of Endocrinology, Metabolism and Lipid Research, Washington University Medical School, St. Louis, MO
| | - Harald C Köfeler
- Lipidomics Center for Medical Research, Medical University, Graz, Austria
| | - Ueli Suter
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology, ETH Zürich, Zürich, Switzerland
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19
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Hartler J, Triebl A, Ziegl A, Trötzmüller M, Rechberger GN, Zeleznik OA, Zierler KA, Torta F, Cazenave-Gassiot A, Wenk MR, Fauland A, Wheelock CE, Armando AM, Quehenberger O, Zhang Q, Wakelam MJO, Haemmerle G, Spener F, Köfeler HC, Thallinger GG. Deciphering lipid structures based on platform-independent decision rules. Nat Methods 2017; 14:1171-1174. [PMID: 29058722 PMCID: PMC5988032 DOI: 10.1038/nmeth.4470] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Accepted: 09/19/2017] [Indexed: 11/23/2022]
Abstract
We achieve automated and reliable annotation of lipid species and their molecular structures in high-throughput data from chromatography-coupled tandem mass spectrometry using decision rule sets embedded in Lipid Data Analyzer (LDA; http://genome.tugraz.at/lda2). Using various low- and high-resolution mass spectrometry instruments with several collision energies, we proved the method's platform independence. We propose that the software's reliability, flexibility, and ability to identify novel lipid molecular species may now render current state-of-the-art lipid libraries obsolete.
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Affiliation(s)
- Jürgen Hartler
- Institute of Computational Biotechnology, Graz University of Technology, Graz, Austria
- Center for Medical Research, Medical University of Graz, Graz, Austria
- Omics Center Graz, BioTechMed-Graz, Graz, Austria
| | - Alexander Triebl
- Center for Medical Research, Medical University of Graz, Graz, Austria
| | - Andreas Ziegl
- Institute of Computational Biotechnology, Graz University of Technology, Graz, Austria
| | - Martin Trötzmüller
- Center for Medical Research, Medical University of Graz, Graz, Austria
- Omics Center Graz, BioTechMed-Graz, Graz, Austria
| | - Gerald N Rechberger
- Omics Center Graz, BioTechMed-Graz, Graz, Austria
- Department of Molecular Biosciences, University of Graz, Graz, Austria
| | - Oana A Zeleznik
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, U.S.A
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, U.S.A
| | - Kathrin A Zierler
- Department of Molecular Biosciences, University of Graz, Graz, Austria
| | - Federico Torta
- Singapore Lipidomics Incubator, National University of Singapore, Singapore, Singapore
| | | | - Markus R Wenk
- Singapore Lipidomics Incubator, National University of Singapore, Singapore, Singapore
| | - Alexander Fauland
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Craig E Wheelock
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Aaron M Armando
- School of Medicine, University of California San Diego, La Jolla, California, U.S.A
| | - Oswald Quehenberger
- School of Medicine, University of California San Diego, La Jolla, California, U.S.A
| | - Qifeng Zhang
- The Babraham Institute, Babraham Research Campus, Cambridge, U.K
| | | | - Guenter Haemmerle
- Department of Molecular Biosciences, University of Graz, Graz, Austria
| | - Friedrich Spener
- Department of Molecular Biosciences, University of Graz, Graz, Austria
- Department of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Harald C Köfeler
- Center for Medical Research, Medical University of Graz, Graz, Austria
- Omics Center Graz, BioTechMed-Graz, Graz, Austria
| | - Gerhard G Thallinger
- Institute of Computational Biotechnology, Graz University of Technology, Graz, Austria
- Omics Center Graz, BioTechMed-Graz, Graz, Austria
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20
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Bowden JA, Heckert A, Ulmer CZ, Jones CM, Koelmel JP, Abdullah L, Ahonen L, Alnouti Y, Armando AM, Asara JM, Bamba T, Barr JR, Bergquist J, Borchers CH, Brandsma J, Breitkopf SB, Cajka T, Cazenave-Gassiot A, Checa A, Cinel MA, Colas RA, Cremers S, Dennis EA, Evans JE, Fauland A, Fiehn O, Gardner MS, Garrett TJ, Gotlinger KH, Han J, Huang Y, Neo AH, Hyötyläinen T, Izumi Y, Jiang H, Jiang H, Jiang J, Kachman M, Kiyonami R, Klavins K, Klose C, Köfeler HC, Kolmert J, Koal T, Koster G, Kuklenyik Z, Kurland IJ, Leadley M, Lin K, Maddipati KR, McDougall D, Meikle PJ, Mellett NA, Monnin C, Moseley MA, Nandakumar R, Oresic M, Patterson R, Peake D, Pierce JS, Post M, Postle AD, Pugh R, Qiu Y, Quehenberger O, Ramrup P, Rees J, Rembiesa B, Reynaud D, Roth MR, Sales S, Schuhmann K, Schwartzman ML, Serhan CN, Shevchenko A, Somerville SE, St John-Williams L, Surma MA, Takeda H, Thakare R, Thompson JW, Torta F, Triebl A, Trötzmüller M, Ubhayasekera SJK, Vuckovic D, Weir JM, Welti R, Wenk MR, Wheelock CE, Yao L, Yuan M, Zhao XH, Zhou S. Harmonizing lipidomics: NIST interlaboratory comparison exercise for lipidomics using SRM 1950-Metabolites in Frozen Human Plasma. J Lipid Res 2017; 58:2275-2288. [PMID: 28986437 DOI: 10.1194/jlr.m079012] [Citation(s) in RCA: 260] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 10/02/2017] [Indexed: 12/22/2022] Open
Abstract
As the lipidomics field continues to advance, self-evaluation within the community is critical. Here, we performed an interlaboratory comparison exercise for lipidomics using Standard Reference Material (SRM) 1950-Metabolites in Frozen Human Plasma, a commercially available reference material. The interlaboratory study comprised 31 diverse laboratories, with each laboratory using a different lipidomics workflow. A total of 1,527 unique lipids were measured across all laboratories and consensus location estimates and associated uncertainties were determined for 339 of these lipids measured at the sum composition level by five or more participating laboratories. These evaluated lipids detected in SRM 1950 serve as community-wide benchmarks for intra- and interlaboratory quality control and method validation. These analyses were performed using nonstandardized laboratory-independent workflows. The consensus locations were also compared with a previous examination of SRM 1950 by the LIPID MAPS consortium. While the central theme of the interlaboratory study was to provide values to help harmonize lipids, lipid mediators, and precursor measurements across the community, it was also initiated to stimulate a discussion regarding areas in need of improvement.
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Affiliation(s)
- John A Bowden
- Marine Biochemical Sciences Group, Chemical Sciences Division, Hollings Marine Laboratory, National Institute of Standards and Technology, Charleston, SC
| | - Alan Heckert
- Statistical Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD
| | - Candice Z Ulmer
- Marine Biochemical Sciences Group, Chemical Sciences Division, Hollings Marine Laboratory, National Institute of Standards and Technology, Charleston, SC
| | - Christina M Jones
- Marine Biochemical Sciences Group, Chemical Sciences Division, Hollings Marine Laboratory, National Institute of Standards and Technology, Charleston, SC
| | - Jeremy P Koelmel
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL
| | | | - Linda Ahonen
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
| | - Yazen Alnouti
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE
| | - Aaron M Armando
- Departments of Chemistry and Biochemistry and Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA
| | - John M Asara
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA.,Department of Medicine, Harvard Medical School, Boston, MA
| | - Takeshi Bamba
- Division of Metabolomics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - John R Barr
- Division of Laboratory Sciences, Centers for Disease Control and Prevention, National Center for Environmental Health, Atlanta, GA
| | - Jonas Bergquist
- Department of Chemistry-BMC, Analytical Chemistry, Uppsala University, Uppsala, Sweden
| | - Christoph H Borchers
- University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.,Gerald Bronfman Department of Oncology McGill University, Montreal, Quebec, Canada.,Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
| | - Joost Brandsma
- Faculty of Medicine, Academic Unit of Clinical and Experimental Sciences, Southampton General Hospital, University of Southampton, Southampton, United Kingdom
| | - Susanne B Breitkopf
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA
| | - Tomas Cajka
- National Institutes of Health West Coast Metabolomics Center, University of California Davis Genome Center, Davis, CA
| | - Amaury Cazenave-Gassiot
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore and Singapore Lipidomic Incubator (SLING), Life Sciences Institute, Singapore
| | - Antonio Checa
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Michelle A Cinel
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Romain A Colas
- Department of Anesthesiology, Perioperative and Pain Medicine, Center for Experimental Therapeutics and Reperfusion Injury, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Serge Cremers
- Biomarker Core Laboratory, Irving Institute for Clinical and Translational Research, Columbia University Medical Center, New York, NY
| | - Edward A Dennis
- Departments of Chemistry and Biochemistry and Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA
| | | | - Alexander Fauland
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Oliver Fiehn
- National Institutes of Health West Coast Metabolomics Center, University of California Davis Genome Center, Davis, CA.,Biochemistry Department, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Michael S Gardner
- Division of Laboratory Sciences, Centers for Disease Control and Prevention, National Center for Environmental Health, Atlanta, GA
| | - Timothy J Garrett
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL
| | - Katherine H Gotlinger
- Department of Pharmacology, New York Medical College School of Medicine, Valhalla, NY
| | - Jun Han
- University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada
| | | | - Aveline Huipeng Neo
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore and Singapore Lipidomic Incubator (SLING), Life Sciences Institute, Singapore
| | | | - Yoshihiro Izumi
- Division of Metabolomics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - Hongfeng Jiang
- Biomarker Core Laboratory, Irving Institute for Clinical and Translational Research, Columbia University Medical Center, New York, NY
| | - Houli Jiang
- Department of Pharmacology, New York Medical College School of Medicine, Valhalla, NY
| | - Jiang Jiang
- Departments of Chemistry and Biochemistry and Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA
| | - Maureen Kachman
- Metabolomics Core, BRCF, University of Michigan, Ann Arbor, MI
| | | | | | | | - Harald C Köfeler
- Core Facility for Mass Spectrometry, Medical University of Graz, Graz, Austria
| | - Johan Kolmert
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | | | - Grielof Koster
- Faculty of Medicine, Academic Unit of Clinical and Experimental Sciences, Southampton General Hospital, University of Southampton, Southampton, United Kingdom
| | - Zsuzsanna Kuklenyik
- Division of Laboratory Sciences, Centers for Disease Control and Prevention, National Center for Environmental Health, Atlanta, GA
| | - Irwin J Kurland
- Stable Isotope and Metabolomics Core Facility, Diabetes Research Center, Albert Einstein College of Medicine, Bronx, NY
| | - Michael Leadley
- Analytical Facility of Bioactive Molecules, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Karen Lin
- University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada
| | - Krishna Rao Maddipati
- Lipidomics Core Facility and Department of Pathology, Wayne State University, Detroit, MI
| | - Danielle McDougall
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL
| | - Peter J Meikle
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | | | - Cian Monnin
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada
| | - M Arthur Moseley
- Proteomics and Metabolomics Shared Resource, Levine Science Research Center, Duke University School of Medicine, Durham, NC
| | - Renu Nandakumar
- Biomarker Core Laboratory, Irving Institute for Clinical and Translational Research, Columbia University Medical Center, New York, NY
| | - Matej Oresic
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Rainey Patterson
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL
| | | | - Jason S Pierce
- Department of Biochemistry and Molecular Biology Medical University of South Carolina, Charleston, SC
| | - Martin Post
- Analytical Facility of Bioactive Molecules, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Anthony D Postle
- Faculty of Medicine, Academic Unit of Clinical and Experimental Sciences, Southampton General Hospital, University of Southampton, Southampton, United Kingdom
| | - Rebecca Pugh
- Chemical Sciences Division, Environmental Specimen Bank Group, Hollings Marine Laboratory, National Institute of Standards and Technology, Charleston, SC
| | - Yunping Qiu
- Stable Isotope and Metabolomics Core Facility, Diabetes Research Center, Albert Einstein College of Medicine, Bronx, NY
| | - Oswald Quehenberger
- Departments of Medicine and Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA
| | - Parsram Ramrup
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada
| | - Jon Rees
- Division of Laboratory Sciences, Centers for Disease Control and Prevention, National Center for Environmental Health, Atlanta, GA
| | - Barbara Rembiesa
- Department of Biochemistry and Molecular Biology Medical University of South Carolina, Charleston, SC
| | - Denis Reynaud
- Analytical Facility of Bioactive Molecules, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
| | - Mary R Roth
- Division of Biology, Kansas Lipidomics Research Center, Kansas State University, Manhattan, KS
| | - Susanne Sales
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Kai Schuhmann
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Charles N Serhan
- Department of Anesthesiology, Perioperative and Pain Medicine, Center for Experimental Therapeutics and Reperfusion Injury, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Stephen E Somerville
- Hollings Marine Laboratory, Medical University of South Carolina, Charleston, SC
| | - Lisa St John-Williams
- Proteomics and Metabolomics Shared Resource, Levine Science Research Center, Duke University School of Medicine, Durham, NC
| | | | - Hiroaki Takeda
- Division of Metabolomics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka, Japan
| | - Rhishikesh Thakare
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE
| | - J Will Thompson
- Proteomics and Metabolomics Shared Resource, Levine Science Research Center, Duke University School of Medicine, Durham, NC
| | - Federico Torta
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore and Singapore Lipidomic Incubator (SLING), Life Sciences Institute, Singapore
| | - Alexander Triebl
- Core Facility for Mass Spectrometry, Medical University of Graz, Graz, Austria
| | - Martin Trötzmüller
- Core Facility for Mass Spectrometry, Medical University of Graz, Graz, Austria
| | | | - Dajana Vuckovic
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada
| | - Jacquelyn M Weir
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Ruth Welti
- Division of Biology, Kansas Lipidomics Research Center, Kansas State University, Manhattan, KS
| | - Markus R Wenk
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore and Singapore Lipidomic Incubator (SLING), Life Sciences Institute, Singapore
| | - Craig E Wheelock
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Libin Yao
- Division of Biology, Kansas Lipidomics Research Center, Kansas State University, Manhattan, KS
| | - Min Yuan
- Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA
| | - Xueqing Heather Zhao
- Stable Isotope and Metabolomics Core Facility, Diabetes Research Center, Albert Einstein College of Medicine, Bronx, NY
| | - Senlin Zhou
- Lipidomics Core Facility and Department of Pathology, Wayne State University, Detroit, MI
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21
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Šmidák R, Köfeler HC, Hoeger H, Lubec G. Comprehensive identification of age-related lipidome changes in rat amygdala during normal aging. PLoS One 2017; 12:e0180675. [PMID: 28672041 PMCID: PMC5495493 DOI: 10.1371/journal.pone.0180675] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 06/19/2017] [Indexed: 12/28/2022] Open
Abstract
Brain lipids are integral components of brain structure and function. However, only recent advancements of chromatographic techniques together with mass spectrometry allow comprehensive identification of lipid species in complex brain tissue. Lipid composition varies between the individual areas and the majority of previous reports was focusing on individual lipids rather than a lipidome. Herein, a mass spectrometry-based approach was used to evaluate age-related changes in the lipidome of the rat amygdala obtained from young (3 months) and old (20 months) males of the Sprague-Dawley rat strain. A total number of 70 lipid species with significantly changed levels between the two animal groups were identified spanning four main lipid classes, i.e. glycerolipids, glycerophospholipids, sphingolipids and sterol lipids. These included phospholipids with pleiotropic brain function, such as derivatives of phosphatidylcholine, phosphatidylserine, and phosphatidylethanolamine. The analysis also revealed significant level changes of phosphatidic acid, diacylglycerol, sphingomyelin and ceramide that directly represent lipid signaling and affect amygdala neuronal activity. The amygdala is a crucial brain region for cognitive functions and former studies on rats and humans showed that this region changes its activity during normal aging. As the information on amygdala lipidome is very limited the results obtained in the present study represent a significant novelty and may contribute to further studies on the role of lipid molecules in age-associated changes of amygdala function.
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Affiliation(s)
- Roman Šmidák
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Harald C. Köfeler
- Center for Medical Research (ZMF), Medical University Graz, Graz, Austria
| | - Harald Hoeger
- Core Unit of Biomedical Research, Division of Laboratory Animal Science and Genetics, Medical University of Vienna, Himberg, Austria
| | - Gert Lubec
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Neuroproteomics Laboratory, Science Park, Ilkovicova 8, Bratislava, Slovakia
- * E-mail:
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22
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Triebl A, Trötzmüller M, Hartler J, Stojakovic T, Köfeler HC. Lipidomics by ultrahigh performance liquid chromatography-high resolution mass spectrometry and its application to complex biological samples. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1053:72-80. [PMID: 28415015 DOI: 10.1016/j.jchromb.2017.03.027] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 03/08/2017] [Accepted: 03/22/2017] [Indexed: 01/21/2023]
Abstract
An improved approach for selective and sensitive identification and quantitation of lipid molecular species using reversed phase chromatography coupled to high resolution mass spectrometry was developed. The method is applicable to a wide variety of biological matrices using a simple liquid-liquid extraction procedure. Together, this approach combines multiple selectivity criteria: Reversed phase chromatography separates lipids according to their acyl chain length and degree of unsaturation and is capable of resolving positional isomers of lysophospholipids, as well as structural isomers of diacyl phospholipids and glycerolipids. Orbitrap mass spectrometry delivers the elemental composition of both positive and negative ions with high mass accuracy. Finally, automatically generated tandem mass spectra provide structural insight into numerous glycerolipids, phospholipids, and sphingolipids within a single run. Calibration showed linearity ranges of more than four orders of magnitude, good values for accuracy and precision at biologically relevant concentration levels, and limits of quantitation of a few femtomoles on column. Hundreds of lipid molecular species were detected and quantified in three different biological matrices, which cover well the wide variety and complexity of various model organisms in lipidomic research. Together with a software package, this method is a prime choice for global lipidomic analysis of even the most complex biological samples.
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Affiliation(s)
- Alexander Triebl
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Martin Trötzmüller
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria.
| | - Jürgen Hartler
- Institute of Computational Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria
| | - Tatjana Stojakovic
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Auenbruggerplatz 15, 8036 Graz, Austria
| | - Harald C Köfeler
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria; Omics Center Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
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23
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Triebl A, Hartler J, Trötzmüller M, C Köfeler H. Lipidomics: Prospects from a technological perspective. Biochim Biophys Acta Mol Cell Biol Lipids 2017; 1862:740-746. [PMID: 28341148 DOI: 10.1016/j.bbalip.2017.03.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 03/15/2017] [Accepted: 03/16/2017] [Indexed: 12/16/2022]
Abstract
Over the last two decades, lipidomics has evolved into an 'omics' technology pari passu with benchmarking 'omics' technologies, such as genomics or proteomics. The driving force behind this development was a constant advance in mass spectrometry and related technologies. The aim of this opinion article is to give the interested reader a concise but still comprehensive overview about the technological state of the art in lipidomics, current challenges and perspectives for future development. As such, this article guides through the whole workflow of lipidomics, from sampling to data analysis. This article is part of a Special Issue entitled: BBALIP_Lipidomics Opinion Articles edited by Sepp Kohlwein.
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Affiliation(s)
- Alexander Triebl
- Center for Medical Research (ZMF), Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Jürgen Hartler
- Center for Medical Research (ZMF), Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria; Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010 Graz, Austria; Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Martin Trötzmüller
- Center for Medical Research (ZMF), Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Harald C Köfeler
- Center for Medical Research (ZMF), Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria; Omics Center Graz, BioTechMed-Graz, Stiftingtalstrasse 24, 8010 Graz, Austria.
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24
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Meshcheryakova A, Svoboda M, Tahir A, Köfeler HC, Triebl A, Mungenast F, Heinze G, Gerner C, Zimmermann P, Jaritz M, Mechtcheriakova D. Exploring the role of sphingolipid machinery during the epithelial to mesenchymal transition program using an integrative approach. Oncotarget 2016; 7:22295-323. [PMID: 26967245 PMCID: PMC5008362 DOI: 10.18632/oncotarget.7947] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 02/20/2016] [Indexed: 12/30/2022] Open
Abstract
The epithelial to mesenchymal transition (EMT) program is activated in epithelial cancer cells and facilitates their ability to metastasize based on enhanced migratory, proliferative, anti-apoptotic, and pluripotent capacities. Given the fundamental impact of sphingolipid machinery to each individual process, the sphingolipid-related mechanisms might be considered among the most prominent drivers/players of EMT; yet, there is still limited knowledge. Given the complexity of the interconnected sphingolipid system, which includes distinct sphingolipid mediators, their synthesizing enzymes, receptors and transporters, we herein apply an integrative approach for assessment of the sphingolipid-associated mechanisms underlying EMT program. We created the sphingolipid-/EMT-relevant 41-gene/23-gene signatures which were applied to denote transcriptional events in a lung cancer cell-based EMT model. Based on defined 35-gene sphingolipid/EMT-attributed signature of regulated genes, we show close associations between EMT markers, genes comprising the sphingolipid network at multiple levels and encoding sphingosine 1-phosphate (S1P)-/ceramide-metabolizing enzymes, S1P and lysophosphatidic acid (LPA) receptors and S1P transporters, pluripotency genes and inflammation-related molecules, and demonstrate the underlying biological pathways and regulators. Mass spectrometry-based sphingolipid analysis revealed an EMT-attributed shift towards increased S1P and LPA accompanied by reduced ceramide levels. Notably, using transcriptomics data across various cell-based perturbations and neoplastic tissues (24193 arrays), we identified the sphingolipid/EMT signature primarily in lung adenocarcinoma tissues; besides, bladder, colorectal and prostate cancers were among the top-ranked. The findings also highlight novel regulatory associations between influenza virus and the sphingolipid/EMT-associated mechanisms. In sum, data propose the multidimensional contribution of sphingolipid machinery to pathological EMT and may yield new biomarkers and therapeutic targets.
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Affiliation(s)
- Anastasia Meshcheryakova
- Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria
| | - Martin Svoboda
- Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria
| | - Ammar Tahir
- Institute of Analytical Chemistry, University of Vienna, Vienna, Austria
- Mass Spectrometry Center, University of Vienna, Vienna, Austria
| | - Harald C. Köfeler
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, Graz, Austria
| | - Alexander Triebl
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, Graz, Austria
| | - Felicitas Mungenast
- Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria
| | - Georg Heinze
- Section for Clinical Biometrics, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University Vienna, Vienna, Austria
| | - Christopher Gerner
- Institute of Analytical Chemistry, University of Vienna, Vienna, Austria
- Mass Spectrometry Center, University of Vienna, Vienna, Austria
| | | | - Markus Jaritz
- Research Institute of Molecular Pathology, Vienna Biocenter, Vienna, Austria
| | - Diana Mechtcheriakova
- Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna, Austria
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Sala P, Pötz S, Brunner M, Trötzmüller M, Fauland A, Triebl A, Hartler J, Lankmayr E, Köfeler HC. Determination of oxidized phosphatidylcholines by hydrophilic interaction liquid chromatography coupled to Fourier transform mass spectrometry. Int J Mol Sci 2015; 16:8351-63. [PMID: 25874761 PMCID: PMC4425085 DOI: 10.3390/ijms16048351] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 04/02/2015] [Accepted: 04/08/2015] [Indexed: 01/08/2023] Open
Abstract
A novel liquid chromatography-mass spectrometry (LC-MS) approach for analysis of oxidized phosphatidylcholines by an Orbitrap Fourier Transform mass spectrometer in positive electrospray ionization (ESI) coupled to hydrophilic interaction liquid chromatography (HILIC) was developed. This method depends on three selectivity criteria for separation and identification: retention time, exact mass at a resolution of 100,000 and collision induced dissociation (CID) fragment spectra in a linear ion trap. The process of chromatography development showed the best separation properties with a silica-based Kinetex column. This type of chromatography was able to separate all major lipid classes expected in mammalian samples, yielding increased sensitivity of oxidized phosphatidylcholines over reversed phase chromatography. Identification of molecular species was achieved by exact mass on intact molecular ions and CID tandem mass spectra containing characteristic fragments. Due to a lack of commercially available standards, method development was performed with copper induced oxidation products of palmitoyl-arachidonoyl-phosphatidylcholine, which resulted in a plethora of lipid species oxidized at the arachidonoyl moiety. Validation of the method was done with copper oxidized human low-density lipoprotein (LDL) prepared by ultracentrifugation. In these LDL samples we could identify 46 oxidized molecular phosphatidylcholine species out of 99 possible candidates.
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Affiliation(s)
- Pia Sala
- Core Facility for Mass Spectrometry, Medical University of Graz, Stiftingtalstrasse 24, Graz 8010, Austria.
- Institute of Analytical Chemistry and Food Chemistry, Graz University of Technology, Stremayrgasse 9/II, Graz 8010, Austria.
| | - Sandra Pötz
- Core Facility for Mass Spectrometry, Medical University of Graz, Stiftingtalstrasse 24, Graz 8010, Austria.
- Institute of Analytical Chemistry and Food Chemistry, Graz University of Technology, Stremayrgasse 9/II, Graz 8010, Austria.
| | - Martina Brunner
- Core Facility for Mass Spectrometry, Medical University of Graz, Stiftingtalstrasse 24, Graz 8010, Austria.
| | - Martin Trötzmüller
- Core Facility for Mass Spectrometry, Medical University of Graz, Stiftingtalstrasse 24, Graz 8010, Austria.
| | - Alexander Fauland
- Core Facility for Mass Spectrometry, Medical University of Graz, Stiftingtalstrasse 24, Graz 8010, Austria.
- Institute of Analytical Chemistry and Food Chemistry, Graz University of Technology, Stremayrgasse 9/II, Graz 8010, Austria.
| | - Alexander Triebl
- Core Facility for Mass Spectrometry, Medical University of Graz, Stiftingtalstrasse 24, Graz 8010, Austria.
| | - Jürgen Hartler
- Bioinformatics Group, Institute for Knowledge Discovery, Graz University of Technology, Petersgasse 14, Graz 8010, Austria.
- Omics Center Graz, Stiftingtalstrasse 24, Graz 8010, Austria.
| | - Ernst Lankmayr
- Institute of Analytical Chemistry and Food Chemistry, Graz University of Technology, Stremayrgasse 9/II, Graz 8010, Austria.
| | - Harald C Köfeler
- Core Facility for Mass Spectrometry, Medical University of Graz, Stiftingtalstrasse 24, Graz 8010, Austria.
- Omics Center Graz, Stiftingtalstrasse 24, Graz 8010, Austria.
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26
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Walter KM, Schönenberger MJ, Trötzmüller M, Horn M, Elsässer HP, Moser AB, Lucas MS, Schwarz T, Gerber PA, Faust PL, Moch H, Köfeler HC, Krek W, Kovacs WJ. Hif-2α promotes degradation of mammalian peroxisomes by selective autophagy. Cell Metab 2014; 20:882-897. [PMID: 25440060 DOI: 10.1016/j.cmet.2014.09.017] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 08/26/2014] [Accepted: 09/24/2014] [Indexed: 12/21/2022]
Abstract
Peroxisomes play a central role in lipid metabolism, and their function depends on molecular oxygen. Low oxygen tension or von Hippel-Lindau (Vhl) tumor suppressor loss is known to stabilize hypoxia-inducible factors alpha (Hif-1α and Hif-2α) to mediate adaptive responses, but it remains unknown if peroxisome homeostasis and metabolism are interconnected with Hif-α signaling. By studying liver-specific Vhl, Vhl/Hif1α, and Vhl/Hif2α knockout mice, we demonstrate a regulatory function of Hif-2α signaling on peroxisomes. Hif-2α activation augments peroxisome turnover by selective autophagy (pexophagy) and thereby changes lipid composition reminiscent of peroxisomal disorders. The autophagy receptor Nbr1 localizes to peroxisomes and is likewise degraded by Hif-2α-mediated pexophagy. Furthermore, we demonstrate that peroxisome abundance is reduced in VHL-deficient human clear cell renal cell carcinomas with high HIF-2α levels. These results establish Hif-2α as a negative regulator of peroxisome abundance and metabolism and suggest a mechanism by which cells attune peroxisomal function with oxygen availability.
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Affiliation(s)
- Katharina M Walter
- Institute of Molecular Health Sciences, ETH Zurich, CH-8093 Zurich, Switzerland; Competence Center for Systems Physiology and Metabolic Diseases, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Miriam J Schönenberger
- Institute of Molecular Health Sciences, ETH Zurich, CH-8093 Zurich, Switzerland; Competence Center for Systems Physiology and Metabolic Diseases, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Martin Trötzmüller
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, A-8010 Graz, Austria
| | - Michael Horn
- Institute of Molecular Health Sciences, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Hans-Peter Elsässer
- Department of Cytobiology, Philipps-University Marburg, D-35037 Marburg, Germany
| | - Ann B Moser
- Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Miriam S Lucas
- ScopeM - Scientific Center for Optical and Electron Microscopy, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Tobias Schwarz
- ScopeM - Scientific Center for Optical and Electron Microscopy, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Philipp A Gerber
- Division of Endocrinology and Diabetes, University Hospital Zurich, CH-8091 Zurich, Switzerland
| | - Phyllis L Faust
- Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Holger Moch
- Institute of Surgical Pathology, University Hospital Zurich, CH-8091 Zurich, Switzerland
| | - Harald C Köfeler
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, A-8010 Graz, Austria
| | - Wilhelm Krek
- Institute of Molecular Health Sciences, ETH Zurich, CH-8093 Zurich, Switzerland; Competence Center for Systems Physiology and Metabolic Diseases, ETH Zurich, CH-8093 Zurich, Switzerland.
| | - Werner J Kovacs
- Institute of Molecular Health Sciences, ETH Zurich, CH-8093 Zurich, Switzerland; Competence Center for Systems Physiology and Metabolic Diseases, ETH Zurich, CH-8093 Zurich, Switzerland.
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27
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Norrmén C, Figlia G, Lebrun-Julien F, Pereira JA, Trötzmüller M, Köfeler HC, Rantanen V, Wessig C, van Deijk ALF, Smit AB, Verheijen MHG, Rüegg MA, Hall MN, Suter U. mTORC1 controls PNS myelination along the mTORC1-RXRγ-SREBP-lipid biosynthesis axis in Schwann cells. Cell Rep 2014; 9:646-60. [PMID: 25310982 DOI: 10.1016/j.celrep.2014.09.001] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2014] [Revised: 04/05/2014] [Accepted: 08/28/2014] [Indexed: 11/26/2022] Open
Abstract
Myelin formation during peripheral nervous system (PNS) development, and reformation after injury and in disease, requires multiple intrinsic and extrinsic signals. Akt/mTOR signaling has emerged as a major player involved, but the molecular mechanisms and downstream effectors are virtually unknown. Here, we have used Schwann-cell-specific conditional gene ablation of raptor and rictor, which encode essential components of the mTOR complexes 1 (mTORC1) and 2 (mTORC2), respectively, to demonstrate that mTORC1 controls PNS myelination during development. In this process, mTORC1 regulates lipid biosynthesis via sterol regulatory element-binding proteins (SREBPs). This course of action is mediated by the nuclear receptor RXRγ, which transcriptionally regulates SREBP1c downstream of mTORC1. Absence of mTORC1 causes delayed myelination initiation as well as hypomyelination, together with abnormal lipid composition and decreased nerve conduction velocity. Thus, we have identified the mTORC1-RXRγ-SREBP axis controlling lipid biosynthesis as a major contributor to proper peripheral nerve function.
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Affiliation(s)
- Camilla Norrmén
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology Zurich, ETH Zürich, CH-8093 Zurich, Switzerland.
| | - Gianluca Figlia
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology Zurich, ETH Zürich, CH-8093 Zurich, Switzerland
| | - Frédéric Lebrun-Julien
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology Zurich, ETH Zürich, CH-8093 Zurich, Switzerland
| | - Jorge A Pereira
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology Zurich, ETH Zürich, CH-8093 Zurich, Switzerland
| | - Martin Trötzmüller
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, 8010 Graz, Austria
| | - Harald C Köfeler
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, 8010 Graz, Austria
| | - Ville Rantanen
- Research Programs Unit, Genome-Scale Biology, and Institute of Biomedicine, Biochemistry and Developmental Biology, University of Helsinki, 00014 Helsinki, Finland
| | - Carsten Wessig
- Department of Neurology, University of Würzburg, 97080 Würzburg, Germany
| | - Anne-Lieke F van Deijk
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, 1081HV Amsterdam, the Netherlands
| | - August B Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, 1081HV Amsterdam, the Netherlands
| | - Mark H G Verheijen
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, 1081HV Amsterdam, the Netherlands
| | - Markus A Rüegg
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Michael N Hall
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Ueli Suter
- Institute of Molecular Health Sciences, Department of Biology, Swiss Federal Institute of Technology Zurich, ETH Zürich, CH-8093 Zurich, Switzerland.
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28
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Triebl A, Trötzmüller M, Eberl A, Hanel P, Hartler J, Köfeler HC. Quantitation of phosphatidic acid and lysophosphatidic acid molecular species using hydrophilic interaction liquid chromatography coupled to electrospray ionization high resolution mass spectrometry. J Chromatogr A 2014; 1347:104-10. [PMID: 24813932 DOI: 10.1016/j.chroma.2014.04.070] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 03/27/2014] [Accepted: 04/22/2014] [Indexed: 10/25/2022]
Abstract
A method for a highly selective and sensitive identification and quantitation of lysophosphatidic acid (LPA) and phosphatidic acid (PA) molecular species was developed using hydrophilic interaction liquid chromatography (HILIC) followed by negative-ion electrospray ionization high resolution mass spectrometry. Different extraction methods for the polar LPA and PA species were compared and a modified Bligh & Dyer extraction by addition of 0.1M hydrochloric acid resulted in a ≈1.2-fold increase of recovery for the 7 PA and a more than 15-fold increase for the 6 LPA molecular species of a commercially available natural mix compared to conventional Bligh & Dyer extraction. This modified Bligh & Dyer extraction did not show any artifacts resulting from hydrolysis of natural abundant phospholipids. The developed HILIC method is able to separate all PA and LPA species from major polar membrane lipid classes which might have suppressive effects on the minor abundant lipid classes of interest. The elemental compositions of intact lipid species are provided by the high mass resolution of 100,000 and high mass accuracy below 3ppm of the Orbitrap instrument. Additionally, tandem mass spectra were generated in a parallel data dependent acquisition mode in the linear ion trap to provide structural information at molecular level. Limits of quantitation were identified at 45fmol on column and the dynamic range reaches 20pmol on column, covering the range of natural abundance well. By applying the developed method to mouse brain it can be shown that phosphatidic acid contains less unsaturated fatty acids with PA 34:1 and PA 36:1 as the major species. In contrast, for LPA species a high content of polyunsaturated fatty acids (LPA 20:4 and LPA 22:6) was quantified.
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Affiliation(s)
- Alexander Triebl
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Martin Trötzmüller
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria; Omics Center Graz, Stiftingtalstrasse 24, 8010 Graz, Austria.
| | - Anita Eberl
- HEALTH - Institute for Biomedicine and Health Sciences, Joanneum Research Forschungsgesellschaft m.b.H., Graz, Austria
| | - Pia Hanel
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Jürgen Hartler
- Institute for Genomics and Bioinformatics, Graz University of Technology, Graz, Austria; Omics Center Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Harald C Köfeler
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria; Omics Center Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
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29
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Chitraju C, Trötzmüller M, Hartler J, Wolinski H, Thallinger GG, Haemmerle G, Zechner R, Zimmermann R, Köfeler HC, Spener F. The impact of genetic stress by ATGL deficiency on the lipidome of lipid droplets from murine hepatocytes. J Lipid Res 2013; 54:2185-2194. [PMID: 23740967 DOI: 10.1194/jlr.m037952] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We showed earlier that nutritional stress like starvation or high-fat diet resulted in phenotypic changes in the lipidomes of hepatocyte lipid droplets (LDs), representative for the pathophysiological status of the mouse model. Here we extend our former study by adding genetic stress due to knockout (KO) of adipocyte triglyceride lipase (ATGL), the rate limiting enzyme in LD lipolysis. An intervention trial for 6 weeks with male wild-type (WT) and ATGL-KO mice was carried out; both genotypes were fed lab chow or were exposed to short-time starvation. Isolated LDs were analyzed by LC-MS/MS. Triacylglycerol, diacylglycerol, and phosphatidylcholine lipidomes, in that order, provided the best phenotypic signatures characteristic for respective stresses applied to the animals. This was evidenced at lipid species level by principal component analysis, calculation of average values for chain-lengths and numbers of double bonds, and by visualization in heat maps. Structural backgrounds for analyses and metabolic relationships were elaborated at lipid molecular species level. Relating our lipidomic data to nonalcoholic fatty liver diseases of nutritional and genetic etiologies with or without accompanying insulin resistance, phenotypic distinction in hepatocyte LDs dependent on insulin status emerged. Taken together, lipidomes of hepatocyte LDs are sensitive responders to nutritional and genetic stress.
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Affiliation(s)
- Chandramohan Chitraju
- Department of Molecular Biosciences, University of Graz, Lipidomics Research Center, 8010 Graz, Austria
| | - Martin Trötzmüller
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, Lipidomics Research Center, 8010 Graz, Austria; and
| | - Jürgen Hartler
- Institute for Genomics and Bioinformatics, Graz University of Technology, and Core Facility Bioinformatics, Austrian Centre for Industrial Biotechnology, 8010 Graz, Austria
| | - Heimo Wolinski
- Department of Molecular Biosciences, University of Graz, Lipidomics Research Center, 8010 Graz, Austria
| | - Gerhard G Thallinger
- Institute for Genomics and Bioinformatics, Graz University of Technology, and Core Facility Bioinformatics, Austrian Centre for Industrial Biotechnology, 8010 Graz, Austria
| | - Guenter Haemmerle
- Department of Molecular Biosciences, University of Graz, Lipidomics Research Center, 8010 Graz, Austria
| | - Rudolf Zechner
- Department of Molecular Biosciences, University of Graz, Lipidomics Research Center, 8010 Graz, Austria
| | - Robert Zimmermann
- Department of Molecular Biosciences, University of Graz, Lipidomics Research Center, 8010 Graz, Austria
| | - Harald C Köfeler
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, Lipidomics Research Center, 8010 Graz, Austria; and
| | - Friedrich Spener
- Department of Molecular Biosciences, University of Graz, Lipidomics Research Center, 8010 Graz, Austria.
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30
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Chitraju C, Trötzmüller M, Hartler J, Wolinski H, Thallinger GG, Lass A, Zechner R, Zimmermann R, Köfeler HC, Spener F. Lipidomic analysis of lipid droplets from murine hepatocytes reveals distinct signatures for nutritional stress. J Lipid Res 2012; 53:2141-2152. [PMID: 22872753 DOI: 10.1194/jlr.m028902] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Liver steatosis can be induced by fasting or high-fat diet. We investigated by lipidomic analysis whether such metabolic states are reflected in the lipidome of hepatocyte lipid droplets (LDs) from mice fed normal chow diet (FED), fasted (FAS), or fed a high-fat diet (HFD). LC-MS/MS at levels of lipid species profiles and of lipid molecular species uncovered a FAS phenotype of LD enriched in triacylglycerol (TG) molecular species with very long-chain (VLC)-PUFA residues and an HFD phenotype with less unsaturated TG species in addition to characteristic lipid marker species. Nutritional stress did not result in dramatic structural alterations in diacylglycerol (DG) and phospholipid (PL) classes. Moreover, molecular species of bulk TG and of DG indicated concomitant de novo TG synthesis and lipase-catalyzed degradation to be active in LDs. DG species with VLC-PUFA residues would be preferred precursors for phosphatidylcholine (PC) species, the others for TG molecular species. In addition, molecular species of PL classes fitted the hepatocyte Kennedy and phosphatidylethanolamine methyltransferase pathways. We demonstrate that lipidomic analysis of LDs enables phenotyping of nutritional stress. TG species are best suited for such phenotyping, whereas structural analysis of TG, DG, and PL molecular species provides metabolic insights.
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Affiliation(s)
- Chandramohan Chitraju
- Department of Molecular Biosciences, University of Graz, Lipidomics Research Center, 8010 Graz, Austria
| | - Martin Trötzmüller
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, Lipidomics Research Center, 8010 Graz, Austria
| | - Jürgen Hartler
- Institute for Genomics and Bioinformatics, Graz University of Technology, and Core Facility Bioinformatics, Austrian Centre for Industrial Biotechnology, 8010 Graz, Austria
| | - Heimo Wolinski
- Department of Molecular Biosciences, University of Graz, Lipidomics Research Center, 8010 Graz, Austria
| | - Gerhard G Thallinger
- Institute for Genomics and Bioinformatics, Graz University of Technology, and Core Facility Bioinformatics, Austrian Centre for Industrial Biotechnology, 8010 Graz, Austria
| | - Achim Lass
- Department of Molecular Biosciences, University of Graz, Lipidomics Research Center, 8010 Graz, Austria
| | - Rudolf Zechner
- Department of Molecular Biosciences, University of Graz, Lipidomics Research Center, 8010 Graz, Austria
| | - Robert Zimmermann
- Department of Molecular Biosciences, University of Graz, Lipidomics Research Center, 8010 Graz, Austria
| | - Harald C Köfeler
- Core Facility for Mass Spectrometry, Center for Medical Research, Medical University of Graz, Lipidomics Research Center, 8010 Graz, Austria
| | - Friedrich Spener
- Department of Molecular Biosciences, University of Graz, Lipidomics Research Center, 8010 Graz, Austria.
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Hartler J, Tharakan R, Köfeler HC, Graham DR, Thallinger GG. Bioinformatics tools and challenges in structural analysis of lipidomics MS/MS data. Brief Bioinform 2012; 14:375-90. [PMID: 22764120 DOI: 10.1093/bib/bbs030] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Lipidomics, the systematic study of the lipid composition of a cell or tissue, is an invaluable complement to knowledge gained by genomics and proteomics research. Mass spectrometry provides a means to detect hundreds of lipids in parallel, and this includes low abundance species of lipids. Nevertheless, frequently occurring isobaric and isomeric lipid species complicate lipidomics analyses from an analytical and bioinformatics perspective. Various MS/MS strategies have evolved to resolve ambiguous identifications of lipid species, and these strategies have been supported by corresponding bioinformatics analysis tools. This review intends to familiarize readers with available bioinformatics MS/MS analysis tools and databases, the structural information obtainable from these, and their applicability to different MS/MS strategies. Finally, future challenges in detecting double bond positions are investigated from a bioinformatics perspective.
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Hartler J, Trötzmüller M, Chitraju C, Spener F, Köfeler HC, Thallinger GG. Lipid Data Analyzer: unattended identification and quantitation of lipids in LC-MS data. ACTA ACUST UNITED AC 2010; 27:572-7. [PMID: 21169379 DOI: 10.1093/bioinformatics/btq699] [Citation(s) in RCA: 150] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
MOTIVATION The accurate measurement of the lipidome permits insights into physiological and pathological processes. Of the present high-throughput technologies, LC-MS especially bears potential of monitoring quantitative changes in hundreds of lipids simultaneously. In order to extract valuable information from huge amount of mass spectrometry data, the aid of automated, reliable, highly sensitive and specific analysis algorithms is indispensable. RESULTS We present here a novel approach for the quantitation of lipids in LC-MS data. The new algorithm obtains its analytical power by two major innovations: (i) a 3D algorithm that confines the peak borders in m/z and time direction and (ii) the use of the theoretical isotopic distribution of an analyte as selection/exclusion criterion. The algorithm is integrated in the Lipid Data Analyzer (LDA) application which additionally provides standardization, a statistics module for results analysis, a batch mode for unattended analysis of several runs and a 3D viewer for the manual verification. The statistics module offers sample grouping, tests between sample groups and export functionalities, where the results are visualized by heat maps and bar charts. The presented algorithm has been applied to data from a controlled experiment and to biological data, containing analytes distributed over an intensity range of 10(6). Our approach shows improved sensitivity and an extremely high positive predictive value compared with existing methods. Consequently, the novel algorithm, integrated in a user-friendly application, is a valuable improvement in the high-throughput analysis of the lipidome. IMPLEMENTATION AND AVAILABILITY The Java application is freely available for non-commercial users at http://genome.tugraz.at/lda. Raw data associated with this manuscript may be downloaded from ProteomeCommons.org Tranche using the following hash: ZBh3nS5bXk6I/Vn32tB5Vh0qnMpVIW71HByFFQqM0RmdF4/4Hcn H3Wggh9kU2teYVOtM1JWwHIeMHqSS/bc2yYNFmyUAAAAAAACl DQ ==
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Affiliation(s)
- Jürgen Hartler
- Institute for Genomics and Bioinformatics, Graz University of Technology, Graz, Austria
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Köfeler HC, Fauland A, Brunner M, Trötzmüller M. Oxolipidomics: analytical tools for lipidomic analysis of oxidized phospholipids and discovery of possible biomarkers. Chem Phys Lipids 2010. [DOI: 10.1016/j.chemphyslip.2010.05.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Blouin CM, Le Lay S, Eberl A, Köfeler HC, Guerrera IC, Klein C, Le Liepvre X, Lasnier F, Bourron O, Gautier JF, Ferré P, Hajduch E, Dugail I. Lipid droplet analysis in caveolin-deficient adipocytes: alterations in surface phospholipid composition and maturation defects. J Lipid Res 2009; 51:945-56. [PMID: 19965594 PMCID: PMC2853462 DOI: 10.1194/jlr.m001016] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Caveolins form plasmalemnal invaginated caveolae. They also locate around intracellular lipid droplets but their role in this location remains unclear. By studying primary adipocytes that highly express caveolin-1, we characterized the impact of caveolin-1 deficiency on lipid droplet proteome and lipidome. We identified several missing proteins on the lipid droplet surface of caveolin-deficient adipocytes and showed that the caveolin-1 lipid droplet pool is organized as multi-protein complexes containing cavin-1, with similar dynamics as those found in caveolae. On the lipid side, caveolin deficiency did not qualitatively alter neutral lipids in lipid droplet, but significantly reduced the relative abundance of surface phospholipid species: phosphatidylserine and lysophospholipids. Caveolin-deficient adipocytes can form only small lipid droplets, suggesting that the caveolin-lipid droplet pool might be involved in lipid droplet size regulation. Accordingly, we show that caveolin-1 concentration on adipocyte lipid droplets positively correlated with lipid droplet size in obese rodent models and human adipocytes. Moreover, rescue experiments by caveolin- green fluorescent protein in caveolin-deficient cells exposed to fatty acid overload demonstrated that caveolin-coated lipid droplets were able to grow larger than caveolin-devoid lipid droplets. Altogether, these data demonstrate that the lipid droplet-caveolin pool impacts on phospholipid and protein surface composition of lipid droplets and suggest a functional role on lipid droplet expandability.
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Affiliation(s)
- Cédric M Blouin
- Centre de Recherche des Cordeliers, INSERM, U872, Université Pierre et Marie Curie - Paris 6, France
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Blouin CM, Le Lay S, Eberl A, Köfeler HC, Guerrera IC, Bourron O, Hajduch E, Dugail I. Adipocyte caveolin-1 lipid droplet pool is critical for size enlargement by regulating the organelle surface composition. Chem Phys Lipids 2009. [DOI: 10.1016/j.chemphyslip.2009.06.108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Oberacher H, Pavlic M, Libiseller K, Schubert B, Sulyok M, Schuhmacher R, Csaszar E, Köfeler HC. On the inter-instrument and the inter-laboratory transferability of a tandem mass spectral reference library: 2. Optimization and characterization of the search algorithm. J Mass Spectrom 2009; 44:494-502. [PMID: 19152368 DOI: 10.1002/jms.1525] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
A sophisticated matching algorithm developed for highly efficient identity search within tandem mass spectral libraries is presented. For the optimization of the search procedure a collection of 410 tandem mass spectra corresponding to 22 compounds was used. The spectra were acquired in three different laboratories on four different instruments. The following types of tandem mass spectrometric instruments were used: quadrupole-quadrupole-time-of-flight (QqTOF), quadrupole-quadrupole-linear ion trap (QqLIT), quadrupole-quadrupole-quadrupole (QqQ), and linear ion trap-Fourier transform ion cyclotron resonance mass spectrometer (LIT-FTICR). The obtained spectra were matched to an established MS/MS-spectral library that contained 3759 MS/MS-spectra corresponding to 402 different reference compounds. All 22 test compounds were part of the library. A dynamic intensity cut-off, the search for neutral losses, and optimization of the formula used to calculate the match probability were shown to significantly enhance the performance of the presented library search approach. With the aid of these features the average number of correct assignments was increased to 98%. For statistical evaluation of the match reliability the set of fragment ion spectra was extended with 300 spectra corresponding to 100 compounds not included in the reference library. Performance was checked with the aid of receiver operating characteristic (ROC) curves. Using the magnitude of the match probability as well as the precursor ion mass as benchmarks to rate the obtained top hit, overall correct classification of a compound being included or not included in the mass spectrometric library, was obtained in more than 95% of cases clearly indicating a high predictive accuracy of the established matching procedure.
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Affiliation(s)
- Herbert Oberacher
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria.
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Oberacher H, Pavlic M, Libiseller K, Schubert B, Sulyok M, Schuhmacher R, Csaszar E, Köfeler HC. On the inter-instrument and inter-laboratory transferability of a tandem mass spectral reference library: 1. Results of an Austrian multicenter study. J Mass Spectrom 2009; 44:485-493. [PMID: 19165818 DOI: 10.1002/jms.1545] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The inter-instrument and inter-laboratory transferability of a tandem mass spectral reference library originally built on a quadrupole-quadrupole-time-of-flight instrument was examined. The library consisted of 3759 MS/MS spectra collected from 402 reference compounds applying several different collision-energy values for fragmentation. In the course of the multicenter study, 22 test compounds were sent to three different laboratories, where 418 tandem mass spectra were acquired using four different instruments from two manufacturers. The study covered the following types of tandem mass spectrometers: quadrupole-quadrupole-time-of-flight, quadrupole-quadrupole-linear ion trap, quadrupole-quadrupole-quadrupole, and linear ion trap-Fourier transform ion cyclotron resonance mass spectrometer. In each participating laboratory, optimized instrumental parameters were gathered solely from routinely applied workflows. No standardization procedure was applied to increase the inter-instrument comparability of MS/MS spectra. The acquired tandem mass spectra were matched against the established reference library using a sophisticated matching algorithm, which is presented in detail in a companion paper. Correct answers, meaning that the correct compound was retrieved as top hit, were obtained in 98.1% of cases. For the remaining 1.9% of spectra, the correct compound was matched at second rank. The observed high percentage of correct assignments clearly suggests that the developed mass spectral library search approach is to a large extent platform independent.
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Affiliation(s)
- Herbert Oberacher
- Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria.
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Köfeler HC, Gross ML. Correction of accurate mass measurement for target compound verification by quadrupole time-of-flight mass spectrometry. J Am Soc Mass Spectrom 2005; 16:406-408. [PMID: 15734334 DOI: 10.1016/j.jasms.2004.11.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2004] [Revised: 11/16/2004] [Accepted: 11/28/2004] [Indexed: 05/24/2023]
Abstract
The aim of this work is to evaluate quadrupole/time-of-flight (QTOF) mass spectrometry for simultaneous measurement of accurate mass and quantification of a target by using a stable isotopically labeled internal standard. Mixtures of caffeine and (13)C(3)-caffeine (internal standard) at different concentration ratios were analyzed by capillary HPLC/QTOF. A calibration plot for quantification is linear over a factor of 20. Without invoking any correction scheme, the mass accuracy seriously degraded when the ratio of the mass standard to the test compound was not unity. The accuracy could be restored to approximately 2 ppm by using a quadratic function to correct the measured mass as a function of the measured signal ratio of target and internal calibrant.
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Affiliation(s)
- Harald C Köfeler
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, USA
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Köfeler HC, Fauler G, Windischhofer W, Leis HJ. Effect of cytochrome P-450 inhibitors econazole, bifonazole and clotrimazole on prostanoid formation. Br J Pharmacol 2000; 130:1241-6. [PMID: 10903961 PMCID: PMC1572187 DOI: 10.1038/sj.bjp.0703427] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
1. The present study was carried out to clarify the effect of the imidazole antimycotics econazole, bifonazole and clotrimazole on prostanoid biosynthesis. Osteoblast-like MC3T3-E1 cells stimulated by endothelin-1, melittin, ionomycin or arachidonic acid showed diminished prostaglandin E(2) (PGE(2)) production upon pretreatment with econazole. Following pretreatment with bifonazole, stimulation with ionomycin or arachidonic acid also resulted in decreased PGE(2) formation. Clotrimazole inhibited ionomycin but not arachidonic acid stimulated PGE(2) synthesis in MC3T3-E1 cells. 2. The results observed in osteoblast-like UMR-106 cells pretreated with econazole, bifonazole or clotrimazole and stimulated by arachidonic acid were similar with the exception of clotrimazole which was a more effective inhibitor of PGE(2) biosynthesis than in MC3T3-E1 cells. 3. Upon treatment with arachidonic acid thromboxane B(2) (TXB(2)) production in human platelets was abolished completely at concentrations of the three imidazole antimycotics higher than 5 microM (IC(50)<1 microM). 4. These data were confirmed by a direct assay using purified ram seminal vesicle prostaglandin H(2) synthase-1 (PGHS-1), which clearly showed inhibitory properties of econazole (IC(50) 4.7+/-2.3 microM), bifonazole (IC(50) 9.4+/-0.8 microM) and clotrimazole (IC(50) 4.4+/-0.6 microM). 5. Summarizing, these results indicate an inhibitory effect of econazole, bifonazole and clotrimazole on PGHS-1, varying in its potency dependent on the cell system used. In addition TXB(2) formation is affected at doses even lower than those needed to suppress PGE(2) biosynthesis.
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Affiliation(s)
- H C Köfeler
- Department of Biochemical Analysis and Mass Spectrometry, Pediatric Hospital, Graz, Austria.
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