1
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Vandenbosch M, Mutuku SM, Mantas MJQ, Patterson NH, Hallmark T, Claesen M, Heeren RMA, Hatcher NG, Verbeeck N, Ekroos K, Ellis SR. Toward Omics-Scale Quantitative Mass Spectrometry Imaging of Lipids in Brain Tissue Using a Multiclass Internal Standard Mixture. Anal Chem 2023; 95:18719-18730. [PMID: 38079536 DOI: 10.1021/acs.analchem.3c02724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Mass spectrometry imaging (MSI) has accelerated our understanding of lipid metabolism and spatial distribution in tissues and cells. However, few MSI studies have approached lipid imaging quantitatively and those that have focused on a single lipid class. We overcome this limitation by using a multiclass internal standard (IS) mixture sprayed homogeneously over the tissue surface with concentrations that reflect those of endogenous lipids. This enabled quantitative MSI (Q-MSI) of 13 lipid classes and subclasses representing almost 200 sum-composition lipid species using both MALDI (negative ion mode) and MALDI-2 (positive ion mode) and pixel-wise normalization of each lipid species in a manner analogous to that widely used in shotgun lipidomics. The Q-MSI approach covered 3 orders of magnitude in dynamic range (lipid concentrations reported in pmol/mm2) and revealed subtle changes in distribution compared to data without normalization. The robustness of the method was evaluated by repeating experiments in two laboratories using both timsTOF and Orbitrap mass spectrometers with an ∼4-fold difference in mass resolution power. There was a strong overall correlation in the Q-MSI results obtained by using the two approaches. Outliers were mostly rationalized by isobaric interferences or the higher sensitivity of one instrument for a particular lipid species. These data provide insight into how the mass resolving power can affect Q-MSI data. This approach opens up the possibility of performing large-scale Q-MSI studies across numerous lipid classes and subclasses and revealing how absolute lipid concentrations vary throughout and between biological tissues.
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Affiliation(s)
- Michiel Vandenbosch
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry, Maastricht University, Maastricht 6229ER, Netherlands
| | - Shadrack M Mutuku
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
| | | | | | | | | | - Ron M A Heeren
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry, Maastricht University, Maastricht 6229ER, Netherlands
| | - Nathan G Hatcher
- Merck & Co., Inc., 770 Sumneytown Pk, West Point, Pennsylvania 19486, United States
| | | | - Kim Ekroos
- Lipidomics Consulting Ltd., Esbo 02230, Finland
| | - Shane R Ellis
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
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2
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Kopczynski D, Hoffmann N, Troppmair N, Coman C, Ekroos K, Kreutz MR, Liebisch G, Schwudke D, Ahrends R. LipidSpace: Simple Exploration, Reanalysis, and Quality Control of Large-Scale Lipidomics Studies. Anal Chem 2023; 95:15236-15244. [PMID: 37792961 PMCID: PMC10585661 DOI: 10.1021/acs.analchem.3c02449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/09/2023] [Indexed: 10/06/2023]
Abstract
Lipid analysis gained significant importance due to the enormous range of lipid functions, e.g., energy storage, signaling, or structural components. Whole lipidomes can be quantitatively studied in-depth thanks to recent analytical advancements. However, the systematic comparison of thousands of distinct lipidomes remains challenging. We introduce LipidSpace, a standalone tool for analyzing lipidomes by assessing their structural and quantitative differences. A graph-based comparison of lipid structures is the basis for calculating structural space models and subsequently computing lipidome similarities. When adding study variables such as body weight or health condition, LipidSpace can determine lipid subsets across all lipidomes that describe these study variables well by utilizing machine-learning approaches. The user-friendly GUI offers four built-in tutorials and interactive visual interfaces with pdf export. Many supported data formats allow an efficient (re)analysis of data sets from different sources. An integrated interactive workflow guides the user through the quality control steps. We used this suite to reanalyze and combine already published data sets (e.g., one with about 2500 samples and 576 lipids in one run) and made additional discoveries to the published conclusions with the potential to fill gaps in the current lipid biology understanding. LipidSpace is available for Windows or Linux (https://lifs-tools.org).
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Affiliation(s)
- Dominik Kopczynski
- Institute
of Analytical Chemistry, University of Vienna, Vienna 1070, Austria
| | - Nils Hoffmann
- Forschungszentrum
Jülich GmbH, Institute for Bio- and Geosciences (IBG-5), Jülich 52428, Germany
| | - Nina Troppmair
- Institute
of Analytical Chemistry, University of Vienna, Vienna 1070, Austria
| | - Cristina Coman
- Institute
of Analytical Chemistry, University of Vienna, Vienna 1070, Austria
| | - Kim Ekroos
- Lipidomics
Consulting Ltd., Esbo 02230, Finland
| | - Michael R. Kreutz
- Leibniz
Group “Dendritic Organelles and Synaptic Function” University
Medical Center Hamburg-Eppendorf, Center
for Molecular Neurobiology, ZMNH, Hamburg 20251, Germany
- RG
Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg 39118, Germany
| | - Gerhard Liebisch
- Institute
of Clinical Chemistry and Laboratory Medicine, University of Regensburg, Regensburg 93053, Germany
| | - Dominik Schwudke
- German
Center for Infection Research (DZIF), Site
Hamburg-Lübeck-Borstel-Riems, Hamburg 22297, Germany
- Airway
Research Center North (ARCN), German Center
for Lung Research (DZL), Grosshansdorf 22927, Germany
- Bioanalytical
Chemistry, Research Center Borstel, Borstel 23845, Germany
| | - Robert Ahrends
- Institute
of Analytical Chemistry, University of Vienna, Vienna 1070, Austria
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3
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Kedia K, Harris R, Ekroos K, Moser KW, DeBord D, Tiberi P, Goracci L, Zhang NR, Wang W, Spellman DS, Bateman K. Investigating Performance of the SLIM-Based High Resolution Ion Mobility Platform for Separation of Isomeric Phosphatidylcholine Species. J Am Soc Mass Spectrom 2023; 34:2176-2186. [PMID: 37703523 DOI: 10.1021/jasms.3c00157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/15/2023]
Abstract
Lipids are structurally diverse molecules that play a pivotal role in a plethora of biological processes. However, deciphering the biological roles of the specific lipids is challenging due to the existence of numerous isomers. This high chemical complexity of the lipidome is one of the major challenges in lipidomics research, as the traditional liquid chromatography-mass spectrometry (LC-MS) based approaches are often not powerful enough to resolve these isomeric and isobaric nuances within complex samples. Thus, lipids are uniquely suited to the benefits provided by multidimensional liquid chromatography-ion mobility-mass spectrometry (LC-IM-MS) analysis. However, many forms of lipid isomerism, including double-bond positional isomers and regioisomers, are structurally similar such that their collision cross section (CCS) differences are unresolvable via conventional IM approaches. Here we evaluate the performance of a high resolution ion mobility (HRIM) system based on structures for lossless ion manipulation (SLIM) technology interfaced to a high resolution quadrupole time-of-flight (QTOF) analyzer to address the noted lipidomic isomerism challenge. SLIM implements the traveling wave ion mobility technique along an ∼13 m ion path, providing longer path lengths to enable improved separation of isomeric features. We demonstrate the power of HRIM-MS to dissect isomeric PC standards differing only in double bond (DB) and stereospecific number (SN) positions. The partial separation of protonated DB isomers is significantly enhanced when they are analyzed as metal adducts. For sodium adducts, we achieve close to baseline separation of three different PC 18:1/18:1 isomers with different cis-double bond locations. Similarly, PC 18:1/18:1 (cis-9) can be resolved from the corresponding PC 18:1/18:1 (trans-9) form. The separation capacity is further enhanced when using silver ion doping, enabling the baseline separation of regioisomers that cannot be resolved when measured as sodium adducts. The sensitivity and reproducibility of the approach were assessed, and the performance for more complex mixtures was benchmarked by identifying PC isomers in total brain and liver lipid extracts.
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Affiliation(s)
- Komal Kedia
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | - Rachel Harris
- MOBILion Systems, Inc., Chadds Ford, Pennsylvania 19317, United States
| | - Kim Ekroos
- Lipidomics Consulting Ltd, Irisviksvägen 31D, 02230 Esbo, Finland
| | - Kelly W Moser
- MOBILion Systems, Inc., Chadds Ford, Pennsylvania 19317, United States
| | - Daniel DeBord
- MOBILion Systems, Inc., Chadds Ford, Pennsylvania 19317, United States
| | - Paolo Tiberi
- Molecular Discovery Ltd., Centennial Park, Borehamwood, Hertfordshire WD6 3FG United Kingdom
| | - Laura Goracci
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy
| | | | - Weixun Wang
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
| | | | - Kevin Bateman
- Merck & Co., Inc., West Point, Pennsylvania 19486, United States
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4
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Wang Q, Hoene M, Hu C, Fritsche L, Ahrends R, Liebisch G, Ekroos K, Fritsche A, Birkenfeld AL, Liu X, Zhao X, Li Q, Su B, Peter A, Xu G, Lehmann R. Ex vivo instability of lipids in whole blood: preanalytical recommendations for clinical lipidomics studies. J Lipid Res 2023; 64:100378. [PMID: 37087100 PMCID: PMC10208886 DOI: 10.1016/j.jlr.2023.100378] [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] [Received: 02/01/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 04/24/2023] Open
Abstract
Reliability, robustness, and interlaboratory comparability of quantitative measurements is critical for clinical lipidomics studies. Lipids' different ex vivo stability in blood bears the risk of misinterpretation of data. Clear recommendations for the process of blood sample collection are required. We studied by UHPLC-high resolution mass spectrometry, as part of the "Preanalytics interest group" of the International Lipidomics Society, the stability of 417 lipid species in EDTA whole blood after exposure to either 4°C, 21°C, or 30°C at six different time points (0.5 h-24 h) to cover common daily routine conditions in clinical settings. In total, >800 samples were analyzed. 325 and 288 robust lipid species resisted 24 h exposure of EDTA whole blood to 21°C or 30°C, respectively. Most significant instabilities were detected for FA, LPE, and LPC. Based on our data, we recommend cooling whole blood at once and permanent. Plasma should be separated within 4 h, unless the focus is solely on robust lipids. Lists are provided to check the ex vivo (in)stability of distinct lipids and potential biomarkers of interest in whole blood. To conclude, our results contribute to the international efforts towards reliable and comparable clinical lipidomics data paving the way to the proper diagnostic application of distinct lipid patterns or lipid profiles in the future.
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Affiliation(s)
- Qingqing Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China; University of Chinese Academy of Sciences, Beijing, China
| | - Miriam Hoene
- Department for Diagnostic Laboratory Medicine, Institute for Clinical Chemistry and Pathobiochemistry, University Hospital Tübingen, Tübingen, Germany
| | - Chunxiu Hu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China
| | - Louise Fritsche
- Institute for Diabetes Research and Metabolic Diseases (IDM) of the Helmholtz Zentrum München at the University of Tuebingen, Tuebingen, Germany; German Center for Diabetes Research (DZD), Tübingen, Germany
| | - Robert Ahrends
- Department of Analytical Chemistry, University of Vienna, Vienna, Austria
| | - Gerhard Liebisch
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | - Kim Ekroos
- Lipidomics Consulting Ltd., Espoo, Finland
| | - Andreas Fritsche
- Institute for Diabetes Research and Metabolic Diseases (IDM) of the Helmholtz Zentrum München at the University of Tuebingen, Tuebingen, Germany; German Center for Diabetes Research (DZD), Tübingen, Germany; Internal Medicine 4, University Hospital Tuebingen, Tuebingen, Germany
| | - Andreas L Birkenfeld
- Institute for Diabetes Research and Metabolic Diseases (IDM) of the Helmholtz Zentrum München at the University of Tuebingen, Tuebingen, Germany; German Center for Diabetes Research (DZD), Tübingen, Germany; Internal Medicine 4, University Hospital Tuebingen, Tuebingen, Germany
| | - Xinyu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China
| | - Xinjie Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China
| | - Qi Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China
| | - Benzhe Su
- School of Computer Science & Technology, Dalian University of Technology, Dalian, China
| | - Andreas Peter
- Department for Diagnostic Laboratory Medicine, Institute for Clinical Chemistry and Pathobiochemistry, University Hospital Tübingen, Tübingen, Germany; Institute for Diabetes Research and Metabolic Diseases (IDM) of the Helmholtz Zentrum München at the University of Tuebingen, Tuebingen, Germany; German Center for Diabetes Research (DZD), Tübingen, Germany
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China.
| | - Rainer Lehmann
- Department for Diagnostic Laboratory Medicine, Institute for Clinical Chemistry and Pathobiochemistry, University Hospital Tübingen, Tübingen, Germany; Institute for Diabetes Research and Metabolic Diseases (IDM) of the Helmholtz Zentrum München at the University of Tuebingen, Tuebingen, Germany; German Center for Diabetes Research (DZD), Tübingen, Germany.
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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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Abstract
A key element of successful lipidomics analysis is a sufficient extraction of lipid molecules typically by two-phase systems such as chloroform-based Bligh and Dyer (B&D). However, numerous metabolomics and lipidomics studies today apply easy to use one-phase extractions. In this work, quantitative flow injection analysis high-resolution mass spectrometry was applied to benchmark the lipid recovery of popular one-phase extraction methods for human plasma samples. The following organic solvents were investigated: methanol (MeOH), ethanol (EtOH), 2-propanol (IPA), 1-butanol (BuOH), acetonitrile (ACN) and the solvent mixtures BuOH/MeOH (3:1) and MeOH/ACN (1:1). The recovery of polar lysophospholipids was sufficient for all tested solvents. However, nonpolar lipid classes such as triglycerides (TG) and cholesteryl esters (CE) revealed extraction efficiencies less than 5% due to precipitation in polar solvents EtOH, MeOH, MeOH/ACN, and ACN. Sample pellets also contained a substantial amount of phospholipids, for example, more than 75% of total phosphatidylcholine and sphingomyelin for ACN. The loss of lipids by precipitation was directly related to the polarity of solvents and lipid classes. Although, lipid recovery increased with the volume of organic solvent, recovery in polar MeOH remains incomplete also for less polar lipid classes such as ceramides. Addition of stable isotope-labeled internal standards prior to lipid extraction could compensate for insufficient lipid recovery for polar lipid classes including lysolipids and phospholipids but not for nonpolar CE and TG. In summary, application of one-phase extractions should be limited to polar lipid classes unless sufficient recovery/solubility of nonpolar lipids has been demonstrated. The presented data reveal that appropriate lipid extraction efficiency is fundamental to achieve accurate lipid quantification.
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Affiliation(s)
- Marcus Höring
- Institute of Clinical Chemistry and Laboratory Medicine, Regensburg University Hospital, D-93042 Regensburg, Germany
| | - Christoph Stieglmeier
- Institute of Clinical Chemistry and Laboratory Medicine, Regensburg University Hospital, D-93042 Regensburg, Germany
| | - Katja Schnabel
- Institute of Clinical Chemistry and Laboratory Medicine, Regensburg University Hospital, D-93042 Regensburg, Germany
| | - Tucker Hallmark
- Avanti Polar Lipids, Alabaster, Alabama 35007, United States
| | - Kim Ekroos
- Lipidomics Consulting Ltd., 02230 Esbo, Finland
| | - Ralph Burkhardt
- Institute of Clinical Chemistry and Laboratory Medicine, Regensburg University Hospital, D-93042 Regensburg, Germany
| | - Gerhard Liebisch
- Institute of Clinical Chemistry and Laboratory Medicine, Regensburg University Hospital, D-93042 Regensburg, Germany
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7
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Vvedenskaya O, Holčapek M, Vogeser M, Ekroos K, Meikle PJ, Bendt AK. Clinical lipidomics – A community-driven roadmap to translate research into clinical applications. J Mass Spectrom Adv Clin Lab 2022; 24:1-4. [PMID: 35199094 PMCID: PMC8844780 DOI: 10.1016/j.jmsacl.2022.02.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [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] [Received: 11/08/2021] [Revised: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 12/29/2022] Open
Abstract
Overview of current state of mass spectrometry based lipidomics. Highlighting ongoing efforts towards harmonization. Invitation to join international community.
Lipid metabolites, beyond triglycerides and cholesterol, have been shown to have vast potential for applications in clinical applications, with substantial societal and economical value. To successfully evolve from the current research-grade methods to assays suitable for routine clinical applications, a harmonization – if not standardization – of these mass spectrometry-based workflows is necessary. Input on clinical needs and technological capabilities must be obtained from all relevant stakeholders, including wet lab scientists, informaticians and data scientists, manufacturers, and medical professionals. In order to build bridges between this diverse group of professionals, the International Lipidomics Society and its Clinical Lipidomics Interest Group were created. This opinion article is intended to provide an overview of international efforts to tackle the issues of workflow harmonization, and to serve as an open invitation for others to join this growing community.
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Affiliation(s)
- Olga Vvedenskaya
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Spectroswiss Sarl, Lausanne, Switzerland
| | - Michal Holčapek
- Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czech Republic
| | - Michael Vogeser
- Institute for Laboratory Medicine in the Munich University Clinic, Munich, Germany
| | - Kim Ekroos
- Lipidomics Consulting Ltd., Esbo, Finland
| | - Peter J. Meikle
- Baker Heart and Diabetes Institute, Melbourne Victoria, Australia
| | - Anne K. Bendt
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore
- Corresponding author.
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8
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Baloni P, Arnold M, Moreno H, Nho K, Kastenmüller G, Suhre K, Buitrago L, Louie G, Kueider‐Paisley A, Saykin AJ, Ekroos K, Meikle PJ, Huynh K, Funk CC, Hood L, Price ND, Baillie R, Han X, Kaddurah‐Daouk RF. Transcriptomics, metabolomics, lipidomics, metabolic flux and mGWAS analyses of sphingolipid pathway highlights novel drugs for Alzheimer’s disease. Alzheimers Dement 2021. [DOI: 10.1002/alz.056152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Matthias Arnold
- Department of Psychiatry and Behavioral Sciences, Duke University Durham NC USA
- Helmholtz Zentrum München, German Research Center for Environmental Health Neuherberg Germany
| | | | - Kwangsik Nho
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine Indianapolis IN USA
| | - Gabi Kastenmüller
- Helmholtz Zentrum München, German Research Center for Environmental Health Neuherberg Germany
- German Center for Diabetes Research (DZD) Neuherberg Germany
| | | | | | - Gregory Louie
- Department of Psychiatry and Behavioral Sciences, Duke University Durham NC USA
| | | | - Andrew J. Saykin
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine Indianapolis IN USA
| | | | | | - Kevin Huynh
- Baker Heart and Diabetes Institute Melbourne VIC Australia
| | | | - Leroy Hood
- Institute for Systems Biology Seattle WA USA
- Providence St. Joseph Health Renton WA USA
| | | | | | - Xianlin Han
- University of Texas Health Sciences Center, San Antonio San Antonio TX USA
| | - Rima F. Kaddurah‐Daouk
- Department of Psychiatry and Behavioral Sciences, Duke University Durham NC USA
- Duke Institute for Brain Sciences, Duke University Durham NC USA
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9
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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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10
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Saigusa D, Hishinuma E, Matsukawa N, Takahashi M, Inoue J, Tadaka S, Motoike IN, Hozawa A, Izumi Y, Bamba T, Kinoshita K, Ekroos K, Koshiba S, Yamamoto M. Comparison of Kit-Based Metabolomics with Other Methodologies in a Large Cohort, towards Establishing Reference Values. Metabolites 2021; 11:652. [PMID: 34677367 PMCID: PMC8538467 DOI: 10.3390/metabo11100652] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 06/28/2021] [Revised: 09/16/2021] [Accepted: 09/17/2021] [Indexed: 12/18/2022] Open
Abstract
Metabolic profiling is an omics approach that can be used to observe phenotypic changes, making it particularly attractive for biomarker discovery. Although several candidate metabolites biomarkers for disease expression have been identified in recent clinical studies, the reference values of healthy subjects have not been established. In particular, the accuracy of concentrations measured by mass spectrometry (MS) is unclear. Therefore, comprehensive metabolic profiling in large-scale cohorts by MS to create a database with reference ranges is essential for evaluating the quality of the discovered biomarkers. In this study, we tested 8700 plasma samples by commercial kit-based metabolomics and separated them into two groups of 6159 and 2541 analyses based on the different ultra-high-performance tandem mass spectrometry (UHPLC-MS/MS) systems. We evaluated the quality of the quantified values of the detected metabolites from the reference materials in the group of 2541 compared with the quantified values from other platforms, such as nuclear magnetic resonance (NMR), supercritical fluid chromatography tandem mass spectrometry (SFC-MS/MS) and UHPLC-Fourier transform mass spectrometry (FTMS). The values of the amino acids were highly correlated with the NMR results, and lipid species such as phosphatidylcholines and ceramides showed good correlation, while the values of triglycerides and cholesterol esters correlated less to the lipidomics analyses performed using SFC-MS/MS and UHPLC-FTMS. The evaluation of the quantified values by MS-based techniques is essential for metabolic profiling in a large-scale cohort.
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Affiliation(s)
- Daisuke Saigusa
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan; (E.H.); (N.M.); (J.I.); (S.T.); (I.N.M.); (K.K.); (S.K.); (M.Y.)
- Medical Biochemistry, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Eiji Hishinuma
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan; (E.H.); (N.M.); (J.I.); (S.T.); (I.N.M.); (K.K.); (S.K.); (M.Y.)
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
| | - Naomi Matsukawa
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan; (E.H.); (N.M.); (J.I.); (S.T.); (I.N.M.); (K.K.); (S.K.); (M.Y.)
- Medical Biochemistry, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Masatomo Takahashi
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan; (M.T.); (Y.I.); (T.B.)
| | - Jin Inoue
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan; (E.H.); (N.M.); (J.I.); (S.T.); (I.N.M.); (K.K.); (S.K.); (M.Y.)
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
| | - Shu Tadaka
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan; (E.H.); (N.M.); (J.I.); (S.T.); (I.N.M.); (K.K.); (S.K.); (M.Y.)
- Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Ikuko N. Motoike
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan; (E.H.); (N.M.); (J.I.); (S.T.); (I.N.M.); (K.K.); (S.K.); (M.Y.)
- Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Atsushi Hozawa
- Department of Preventive Medicine and Epidemiology, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan;
| | - Yoshihiro Izumi
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan; (M.T.); (Y.I.); (T.B.)
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Takeshi Bamba
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan; (M.T.); (Y.I.); (T.B.)
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kengo Kinoshita
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan; (E.H.); (N.M.); (J.I.); (S.T.); (I.N.M.); (K.K.); (S.K.); (M.Y.)
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
- Graduate School of Information Sciences, Tohoku University, 6-3-09, Aramaki Aza-Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Kim Ekroos
- Lipidomics Consulting Ltd., 02230 Espoo, Finland;
| | - Seizo Koshiba
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan; (E.H.); (N.M.); (J.I.); (S.T.); (I.N.M.); (K.K.); (S.K.); (M.Y.)
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku University Tohoku Medical Megabank Organization, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan; (E.H.); (N.M.); (J.I.); (S.T.); (I.N.M.); (K.K.); (S.K.); (M.Y.)
- Medical Biochemistry, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8573, Japan
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11
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Iwama T, Kano K, Saigusa D, Ekroos K, van Echten-Deckert G, Vogt J, Aoki J. Development of an On-Tissue Derivatization Method for MALDI Mass Spectrometry Imaging of Bioactive Lipids Containing Phosphate Monoester Using Phos-tag. Anal Chem 2021; 93:3867-3875. [PMID: 33577289 DOI: 10.1021/acs.analchem.0c04479] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Matrix-assisted laser desorption ionization-mass spectrometry imaging (MALDI-MSI) is an emerging label-free method for mapping the distribution of diverse molecular species in tissue sections. Despite recent progress in MALDI-MSI analyses of lipids, it is still difficult to visualize minor bioactive lipids including lysophosphatidic acid (LPA) and sphingosine-1-phosphate (S1P). Here, we have developed a novel on-tissue derivatization method using Phos-tag, a zinc complex that specifically binds to a phosphate monoester group. MALDI-MSI with Phos-tag derivatization made it possible to image LPA and S1P in the murine brain. Furthermore, we were able to visualize other low-abundance lipids containing phosphate monoester, such as phosphatidic acid and ceramide-1-phosphate. Compared with conventional MALDI-MS, this derivatization produced LPA images with high spatial accuracy discriminating LPA artificially produced during MALDI-MS analysis. In mice with deficiencies in enzymes that degrade LPA and S1P, we observed marked S1P and/or LPA accumulation in specific regions of the brain. Thus, the present study provides a simple and optimal way to reveal the spatial localization of potent bioactive lipid phosphates such as LPA and S1P in tissues.
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Affiliation(s)
- Taiga Iwama
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-8654, Japan.,Laboratory of Molecular and Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai980-8577, Japan
| | - Kuniyuki Kano
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-8654, Japan.,Laboratory of Molecular and Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai980-8577, Japan.,AMED-LEAP, Tokyo100-0004, Japan
| | - Daisuke Saigusa
- AMED-LEAP, Tokyo100-0004, Japan.,Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai980-8577, Japan.,Medical Biochemistry, Tohoku University School of Medicine, Sendai 980-8575, Japan
| | - Kim Ekroos
- Lipidomics Consulting Ltd., 02230 Espoo, Finland
| | | | - Johannes Vogt
- Department of Molecular and Translational Neurosciences, University Medical Hospital, University of Cologne, 50923 Cologne, Germany
| | - Junken Aoki
- Department of Health Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-8654, Japan.,Laboratory of Molecular and Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai980-8577, Japan.,AMED-LEAP, Tokyo100-0004, Japan
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12
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Wormwood Moser KL, Van Aken G, DeBord D, Hatcher NG, Maxon L, Sherman M, Yao L, Ekroos K. High-defined quantitative snapshots of the ganglioside lipidome using high resolution ion mobility SLIM assisted shotgun lipidomics. Anal Chim Acta 2021; 1146:77-87. [DOI: 10.1016/j.aca.2020.12.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 12/03/2020] [Accepted: 12/14/2020] [Indexed: 10/22/2022]
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13
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Lavrynenko O, Titz B, Dijon S, Santos DD, Nury C, Schneider T, Guedj E, Szostak J, Kondylis A, Phillips B, Ekroos K, Martin F, Peitsch MC, Hoeng J, Ivanov NV. Ceramide ratios are affected by cigarette smoke but not heat-not-burn or e-vapor aerosols across four independent mouse studies. Life Sci 2020; 263:118753. [PMID: 33189821 DOI: 10.1016/j.lfs.2020.118753] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 08/20/2020] [Revised: 11/03/2020] [Accepted: 11/10/2020] [Indexed: 11/16/2022]
Abstract
AIMS Smoking is an important risk factor for the development of chronic obstructive pulmonary disease and cardiovascular diseases. This study aimed to further elucidate the role of ceramides, as a key lipid class dysregulated in disease states. MAIN METHODS In this article we developed and validated LC-MS/MS method for ceramides (Cer(d18:1/16:0), Cer(d18:1/18:0), Cer(d18:1/24:0) and Cer(d18:1/24:1(15Z)) for the absolute quantification. We deployed it together with proteomics and transcriptomic analysis to assess the effects of cigarette smoke (CS) from the reference cigarette as well as aerosols from heat-not-burn (HnB) tobacco and e-vapor products in apolipoprotein E-deficient (ApoE-/-) mice over several time points. KEY FINDINGS In the lungs, CS exposure substantially elevated the ratios of Cer(d18:1/24:0) and Cer(d18:1/24:1) to Cer(d18:1/18:0) in two independent ApoE-/- mouse inhalation studies. Data from previous studies, in both ApoE-/- and wild-type mice, further confirmed the reproducibility of this finding. Elevation of these ceramide ratios was also observed in plasma/serum, the liver, and-for the Cer(d18:1/24:1(15Z)) to Cer(d18:1/18:0) ratio-the abdominal aorta. Also, the levels of acid ceramidase (Asah1) and glucocerebrosidase (Gba)-lysosomal enzymes involved in the hydrolysis of glucosylceramides-were consistently elevated in the lungs after CS exposure. In contrast, exposure to HnB tobacco product and e-vapor aerosols did not induce significant changes in the ceramide profiles or associated enzymes. SIGNIFICANCE Our work in mice contributes to the accumulating evidence on the importance of ceramide ratios as biologically relevant markers for respiratory disorders, adding to their already demonstrated role in cardiovascular disease risk assessment in humans.
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Affiliation(s)
- Oksana Lavrynenko
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland.
| | - Bjoern Titz
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Sophie Dijon
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Daniel Dos Santos
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Catherine Nury
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Thomas Schneider
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Emmanuel Guedj
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Justyna Szostak
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Athanasios Kondylis
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Blaine Phillips
- Philip Morris International Research Laboratories Pte. Ltd., Science Park II, 117406, Singapore
| | - Kim Ekroos
- Lipidomics Consulting Ltd., Irisviksvägen 31D, 02230 Esbo, Finland
| | - Florian Martin
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Manuel C Peitsch
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Julia Hoeng
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
| | - Nikolai V Ivanov
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland
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14
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Benke PI, Burla B, Ekroos K, Wenk MR, Torta F. Impact of ion suppression by sample cap liners in lipidomics. Anal Chim Acta 2020; 1137:136-142. [PMID: 33153597 DOI: 10.1016/j.aca.2020.09.055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 07/19/2020] [Revised: 09/14/2020] [Accepted: 09/25/2020] [Indexed: 11/16/2022]
Abstract
Contamination from the polymeric material released by vial caps used for sample introduction in liquid chromatography can significantly affect the signal of the analyte of interest. In particular, repeated injections from the same sample vial can enhance this suppressing effect. Multiple injections of the same sample are often used in metabolomics and lipidomics during routine analyses. Here we demonstrate how the presence of contaminant polymers, originating from the vial closures, significantly influences the estimation of the relative amount of endogenous lipids in human plasma. Furthermore, this can negatively impact other operations in mass spectrometric analysis, such as instrument equilibration and tuning or the common use of technical replicates to improve confidence in data interpretation. Our observations provide critical information on how to improve future analyses through the use of appropriate vial caps, solvents, chromatographic separations and equipment.
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Affiliation(s)
- Peter I Benke
- Singapore Lipidomics Incubator, Department of Biochemistry, Life Sciences Institute and Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Bo Burla
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore
| | - Kim Ekroos
- Lipidomics Consulting Ltd, Irisviksvägen 31D, 02230, Esbo, Finland
| | - Markus R Wenk
- Singapore Lipidomics Incubator, Department of Biochemistry, Life Sciences Institute and Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Federico Torta
- Singapore Lipidomics Incubator, Department of Biochemistry, Life Sciences Institute and Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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15
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Höring M, Ekroos K, Baker PRS, Connell L, Stadler SC, Burkhardt R, Liebisch G. Correction of Isobaric Overlap Resulting from Sodiated Ions in Lipidomics. Anal Chem 2020; 92:10966-10970. [PMID: 32672443 DOI: 10.1021/acs.analchem.0c02408] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Lipidomic analyses aim for absolute quantification of lipid species profiles in biological samples. In past years, mass spectrometry (MS) methods based on high resolution accurate masses (HRAM) have increasingly been applied to identify and quantify lipid species on the MS level. This strategy requires consideration of isobaric overlaps which may also result from various adduct ions. Generally applied solvent additives favor the formation of protonated and ammoniated ions in positive ion mode, yet sodiated ions are also frequently observed. These sodiated ions interfere with protonated ions of the species of the same lipid class with two additional CH2 and three double bonds (Δm/z = 0.0025) and the first isotopic peak overlaps with ammoniated ions of a species with one additional CH2 and four double bonds (Δm/z = 0.0057). In this work, we present an algorithm based on the sodiated to protonated/ammoniated adduct ion ratios of applied internal standards to correct for these interferences. We could demonstrate that these ratios differ significantly between lipid classes but are affected by neither chain length nor number of double bonds within a lipid class. Finally, the algorithm is demonstrated for correcting human serum samples analyzed by Fourier-transform mass spectrometry (FTMS). Here, the application of sodium correction significantly reduced overestimations and misidentifications.
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Affiliation(s)
- Marcus Höring
- Institute of Clinical Chemistry and Laboratory Medicine, Regensburg University Hospital, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
| | - Kim Ekroos
- Lipidomics Consulting Ltd., Irisviksvägen 31D, 02230 Esbo, Finland
| | - Paul R S Baker
- Avanti Polar Lipids, 700 Industrial Park Dr, Alabaster, Alabama 35007, United States
| | - Lisa Connell
- Avanti Polar Lipids, 700 Industrial Park Dr, Alabaster, Alabama 35007, United States
| | - Sonja C Stadler
- Institute of Clinical Chemistry and Laboratory Medicine, Regensburg University Hospital, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
| | - Ralph Burkhardt
- Institute of Clinical Chemistry and Laboratory Medicine, Regensburg University Hospital, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
| | - Gerhard Liebisch
- Institute of Clinical Chemistry and Laboratory Medicine, Regensburg University Hospital, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany
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16
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Ekroos K, Lavrynenko O, Titz B, Pater C, Hoeng J, Ivanov NV. Lipid-based biomarkers for CVD, COPD, and aging - A translational perspective. Prog Lipid Res 2020; 78:101030. [PMID: 32339553 DOI: 10.1016/j.plipres.2020.101030] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [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: 10/29/2019] [Revised: 02/23/2020] [Accepted: 03/16/2020] [Indexed: 12/11/2022]
Abstract
For many diseases, there is an unmet need for new or better biomarkers for improved disease risk assessment and monitoring, as available markers lack sufficient specificity. Lipids are drawing major interest as potential candidates for filling these gaps. This has recently been demonstrated by the identification of selective ceramides for prediction of cardiovascular mortality, enabling improved risk assessment of cardiovascular disease compared with conventional clinical markers. In this review, we discuss current lipid biomarker findings and the possible connection between cardiovascular disease, chronic obstructive pulmonary disease, and aging. Moreover, we discuss how to overcome the current roadblocks facing lipid biomarker research. We stress the need for improved quantification, standardization of methodologies, and establishment of initial reference values to allow for an efficient transfer path of research findings into the clinical landscape, and, ultimately, to put newly identified biomarkers into practical use.
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Affiliation(s)
- Kim Ekroos
- Lipidomics Consulting Ltd., Irisviksvägen 31D, 02230 Esbo, Finland.
| | - Oksana Lavrynenko
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland.
| | - Bjoern Titz
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland.
| | - Calin Pater
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland.
| | - Julia Hoeng
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland.
| | - Nikolai V Ivanov
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchâtel, Switzerland.
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17
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Affiliation(s)
- Michal Holčapek
- Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, 53210, Pardubice, Czech Republic.
| | - Gerhard Liebisch
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, 93053, Regensburg, Germany
| | - Kim Ekroos
- Lipidomics Consulting Ltd., 02230, Espoo, Finland
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18
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O'Donnell VB, Ekroos K, Liebisch G, Wakelam M. Lipidomics: Current state of the art in a fast moving field. Wiley Interdiscip Rev Syst Biol Med 2019; 12:e1466. [PMID: 31646749 DOI: 10.1002/wsbm.1466] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/13/2019] [Accepted: 09/14/2019] [Indexed: 12/15/2022]
Abstract
Lipids are essential for all facets of life. They play three major roles: energy metabolism, structural, and signaling. They are dynamic molecules strongly influenced by endogenous and exogenous factors including genetics, diet, age, lifestyle, drugs, disease and inflammation. As precision medicine starts to become mainstream, there is a huge burgeoning interest in lipids and their potential to act as unique biomarkers or prognostic indicators. Lipids comprise a large component of all metabolites (around one-third), and our expanding knowledge about their dynamic behavior is fueling the hope that mapping their regulatory biochemical pathways on a systems level will revolutionize our ability to prevent, diagnose, and stratify major human diseases. Up to now, clinical lipid measurements have consisted primarily of total cholesterol or triglycerides, as a measure for cardiovascular risk and response to lipid lowering drugs. Nowadays, we are able to measure thousands of individual lipids that make up the lipidome. nuclear magnetic resonance spectrometry (NMR) metabolomics is also being increasingly used in large cohort studies where it can report on total levels of selected lipid classes, and relative levels of fatty acid saturation. To support the application of lipidomics research, LIPID MAPS was established in 2003, and since then has gone on to become the go-to resource for several lipid databases, lipid drawing tools, data deposition, and more recently lipidomics informatics tools, and a lipid biochemistry encyclopedia, LipidWeb. Alongside this, the recently established Lipidomics Standards Initiative plays a key role in standardization of lipidomics methodologies. This article is categorized under: Laboratory Methods and Technologies > Metabolomics Analytical and Computational Methods > Analytical Methods.
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Affiliation(s)
| | - Kim Ekroos
- Lipidomics Consulting Ltd., Esbo, Finland
| | - Gerhard Liebisch
- Institute of Clinical Chemistry and Laboratory Medicine, University of Regensburg, Regensburg, Germany
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19
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Liebisch G, Ahrends R, Arita M, Arita M, Bowden JA, Ejsing CS, Griffiths WJ, Holčapek M, Köfeler H, Mitchell TW, Wenk MR, Ekroos K. Lipidomics needs more standardization. Nat Metab 2019; 1:745-747. [PMID: 32694765 DOI: 10.1038/s42255-019-0094-z] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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20
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Affiliation(s)
- Tiffany Porta Siegel
- Maastricht MultiModal Molecular Imaging (M4I) instituteDivision of Imaging Mass SpectrometryMaastricht University Universiteitssingel 50 6229 ER Maastricht The Netherlands
| | | | - Shane R. Ellis
- Maastricht MultiModal Molecular Imaging (M4I) instituteDivision of Imaging Mass SpectrometryMaastricht University Universiteitssingel 50 6229 ER Maastricht The Netherlands
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21
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Abstract
Lipidomics is a rapidly growing field with numerous examples showing the importance of lipid molecules throughout biology. It has also shed light onto the vast and complex functions performed by many lipids that possess an immense diversity in molecular structures. Mass spectrometry (MS) is the tool of choice for analyzing lipids and has been the key catalyst driving the field forward. However, MS does not yet permit true molecular lipidomics wherein the identification and quantification of lipids having defined molecular structures can be routinely achieved. Here we describe recent advances in MS‐based lipidomics that allow access to higher levels of molecular information in lipidomics experiments. These advances will form a key piece of the puzzle as the field moves towards systems characterization of lipids at the molecular level.
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Affiliation(s)
- Tiffany Porta Siegel
- Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands
| | - Kim Ekroos
- Lipidomics Consulting Ltd., Esbo, Finland
| | - Shane R Ellis
- Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands
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22
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Gajenthra Kumar N, Contaifer D, Baker PRS, Ekroos K, Jefferson KK, Wijesinghe DS. Untargeted lipidomic analysis to broadly characterize the effects of pathogenic and non-pathogenic staphylococci on mammalian lipids. PLoS One 2018; 13:e0206606. [PMID: 30379915 PMCID: PMC6209338 DOI: 10.1371/journal.pone.0206606] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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: 04/09/2018] [Accepted: 10/16/2018] [Indexed: 11/19/2022] Open
Abstract
Modification of the host lipidome via secreted enzymes is an integral, but often overlooked aspect of bacterial pathogenesis. In the current era of prevalent antibiotic resistance, knowledge regarding critical host pathogen lipid interactions has the potential for use in developing novel antibacterial agents. While most studies to date on this matter have focused on specific lipids, or select lipid classes, this provides an incomplete picture. Modern methods of untargeted lipidomics have the capacity to overcome these gaps in knowledge and provide a comprehensive understanding of the role of lipid metabolism in the pathogenesis of infections. In an attempt to determine the role of lipid modifying enzymes produced by staphylococci, we exposed bovine heart lipids, a standardized model for the mammalian lipidome, to spent medium from staphylococcal cultures, and analyzed lipid molecular changes by MS/MSALL shotgun lipidomics. We elucidate distinct effects of different staphylococcal isolates, including 4 clinical isolates of the pathogenic species Staphylococcus aureus, a clinical isolate of the normally commensal species S. epidermidis, and the non-pathogenic species S. carnosus. Two highly virulent strains of S. aureus had a more profound effect on mammalian lipids and modified more lipid classes than the other staphylococcal strains. Our studies demonstrate the utility of the applied untargeted lipidomics methodology to profile lipid changes induced by different bacterial secretomes. Finally, we demonstrate the promise of this lipidomics approach in assessing the specificity of bacterial enzymes for mammalian lipid classes. Our data suggests that there may be a correlation between the bacterial expression of lipid-modifying enzymes and virulence, and could facilitate the guided discovery of lipid pathways required for bacterial infections caused by S. aureus and thereby provide insights into the generation of novel antibacterial agents.
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Affiliation(s)
- Naren Gajenthra Kumar
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Daniel Contaifer
- Department of Pharmacotherapy and Outcomes Sciences, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | | | - Kim Ekroos
- Lipidomics Consulting Ltd., Esbo, Finland
| | - Kimberly K. Jefferson
- Department of Microbiology and Immunology, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Dayanjan S. Wijesinghe
- Department of Pharmacotherapy and Outcomes Sciences, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia, United States of America
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23
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Burla B, Arita M, Arita M, Bendt AK, Cazenave-Gassiot A, Dennis EA, Ekroos K, Han X, Ikeda K, Liebisch G, Lin MK, Loh TP, Meikle PJ, Orešič M, Quehenberger O, Shevchenko A, Torta F, Wakelam MJO, Wheelock CE, Wenk MR. MS-based lipidomics of human blood plasma: a community-initiated position paper to develop accepted guidelines. J Lipid Res 2018; 59:2001-2017. [PMID: 30115755 PMCID: PMC6168311 DOI: 10.1194/jlr.s087163] [Citation(s) in RCA: 192] [Impact Index Per Article: 32.0] [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] [Received: 05/26/2018] [Revised: 08/11/2018] [Indexed: 12/19/2022] Open
Abstract
Human blood is a self-regenerating lipid-rich biological fluid that is routinely collected in hospital settings. The inventory of lipid molecules found in blood plasma (plasma lipidome) offers insights into individual metabolism and physiology in health and disease. Disturbances in the plasma lipidome also occur in conditions that are not directly linked to lipid metabolism; therefore, plasma lipidomics based on MS is an emerging tool in an array of clinical diagnostics and disease management. However, challenges exist in the translation of such lipidomic data to clinical applications. These relate to the reproducibility, accuracy, and precision of lipid quantitation, study design, sample handling, and data sharing. This position paper emerged from a workshop that initiated a community-led process to elaborate and define a set of generally accepted guidelines for quantitative MS-based lipidomics of blood plasma or serum, with harmonization of data acquired on different instrumentation platforms across independent laboratories as an ultimate goal. We hope that other fields may benefit from and follow such a precedent.
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Affiliation(s)
- Bo Burla
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore
| | - Makoto Arita
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Cellular and Molecular Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
- Division of Physiological Chemistry and Metabolism, Keio University Faculty of Pharmacy, Tokyo, Japan
| | - Masanori Arita
- National Institute of Genetics, Shizuoka, Japan and RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Anne K Bendt
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore
| | - Amaury Cazenave-Gassiot
- Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore
| | - Edward A Dennis
- Departments of Pharmacology and Chemistry and Biochemistry, School of Medicine, University of California at San Diego, La Jolla, CA
| | - Kim Ekroos
- Lipidomics Consulting Ltd., Esbo, Finland
| | - Xianlin Han
- Barshop Institute for Longevity and Aging Studies and Department of Medicine-Diabetes, University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - Kazutaka Ikeda
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Cellular and Molecular Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Gerhard Liebisch
- Institute of Clinical Chemistry and Laboratory Medicine, University of Regensburg, Regensburg, Germany
| | - Michelle K Lin
- Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore
| | - Tze Ping Loh
- Department of Laboratory Medicine, National University Hospital, Singapore
| | - Peter J Meikle
- Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Matej Orešič
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland and School of Medical Sciences, Örebro University, Örebro, Sweden
| | - Oswald Quehenberger
- Departments of Pharmacology and Medicine, School of Medicine, University of California at San Diego, La Jolla, CA
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Federico Torta
- Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore
| | | | - Craig E Wheelock
- Division of Physiological Chemistry 2, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Markus R Wenk
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore
- Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore
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24
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Titz B, Gadaleta RM, Lo Sasso G, Elamin A, Ekroos K, Ivanov NV, Peitsch MC, Hoeng J. Proteomics and Lipidomics in Inflammatory Bowel Disease Research: From Mechanistic Insights to Biomarker Identification. Int J Mol Sci 2018; 19:ijms19092775. [PMID: 30223557 PMCID: PMC6163330 DOI: 10.3390/ijms19092775] [Citation(s) in RCA: 24] [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: 08/29/2018] [Revised: 09/11/2018] [Accepted: 09/12/2018] [Indexed: 02/06/2023] Open
Abstract
Inflammatory bowel disease (IBD) represents a group of progressive disorders characterized by recurrent chronic inflammation of the gut. Ulcerative colitis and Crohn's disease are the major manifestations of IBD. While our understanding of IBD has progressed in recent years, its etiology is far from being fully understood, resulting in suboptimal treatment options. Complementing other biological endpoints, bioanalytical "omics" methods that quantify many biomolecules simultaneously have great potential in the dissection of the complex pathogenesis of IBD. In this review, we focus on the rapidly evolving proteomics and lipidomics technologies and their broad applicability to IBD studies; these range from investigations of immune-regulatory mechanisms and biomarker discovery to studies dissecting host⁻microbiome interactions and the role of intestinal epithelial cells. Future studies can leverage recent advances, including improved analytical methodologies, additional relevant sample types, and integrative multi-omics analyses. Proteomics and lipidomics could effectively accelerate the development of novel targeted treatments and the discovery of complementary biomarkers, enabling continuous monitoring of the treatment response of individual patients; this may allow further refinement of treatment and, ultimately, facilitate a personalized medicine approach to IBD.
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Affiliation(s)
- Bjoern Titz
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
| | - Raffaella M Gadaleta
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
| | - Giuseppe Lo Sasso
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
| | - Ashraf Elamin
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
| | - Kim Ekroos
- Lipidomics Consulting Ltd., Irisviksvägen 31D, 02230 Esbo, Finland.
| | - Nikolai V Ivanov
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
| | - Manuel C Peitsch
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
| | - Julia Hoeng
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, CH-2000 Neuchatel, Switzerland.
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25
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Kiamehr M, Alexanova A, Viiri LE, Heiskanen L, Vihervaara T, Kauhanen D, Ekroos K, Laaksonen R, Käkelä R, Aalto-Setälä K. hiPSC-derived hepatocytes closely mimic the lipid profile of primary hepatocytes: A future personalised cell model for studying the lipid metabolism of the liver. J Cell Physiol 2018; 234:3744-3761. [PMID: 30146765 DOI: 10.1002/jcp.27131] [Citation(s) in RCA: 12] [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] [Received: 04/19/2018] [Accepted: 07/09/2018] [Indexed: 12/19/2022]
Abstract
Hepatocyte-like cells (HLCs) differentiated from human-induced pluripotent stem cells offer an alternative platform to primary human hepatocytes (PHHs) for studying the lipid metabolism of the liver. However, despite their great potential, the lipid profile of HLCs has not yet been characterized. Here, we comprehensively studied the lipid profile and fatty acid (FA) metabolism of HLCs and compared them with the current standard hepatocyte models: HepG2 cells and PHHs. We differentiated HLCs by five commonly used methods from three cell lines and thoroughly characterized them by gene and protein expression. HLCs generated by each method were assessed for their functionality and the ability to synthesize, elongate, and desaturate FAs. In addition, lipid and FA profiles of HLCs were investigated by both mass spectrometry and gas chromatography and then compared with the profiles of PHHs and HepG2 cells. HLCs resembled PHHs by expressing hepatic markers: secreting albumin, lipoprotein particles, and urea, and demonstrating similarities in their lipid and FA profile. Unlike HepG2 cells, HLCs contained low levels of lysophospholipids similar to the content of PHHs. Furthermore, HLCs were able to efficiently use the exogenous FAs available in their medium and simultaneously modify simple lipids into more complex ones to fulfill their needs. In addition, we propose that increasing the polyunsaturated FA supply of the culture medium may positively affect the lipid profile and functionality of HLCs. In conclusion, our data showed that HLCs provide a functional and relevant model to investigate human lipid homeostasis at both molecular and cellular levels.
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Affiliation(s)
- Mostafa Kiamehr
- Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Anna Alexanova
- Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Leena E Viiri
- Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | | | | | | | - Kim Ekroos
- Lipidomics Consulting Ltd, Espoo, Finland
| | - Reijo Laaksonen
- Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland.,Zora Biosciences, Espoo, Finland
| | - Reijo Käkelä
- Faculty of Biology and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Katriina Aalto-Setälä
- Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland.,Heart Hospital, Tampere University Hospital, Tampere, Finland
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26
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Abstract
The state-of-art in the lipidomic analysis is summarized here to provide the overview of available sample preparation strategies, mass spectrometry (MS)-based methods for the qualitative analysis of lipids, and the quantitative MS approaches for high-throughput clinical workflows. Major challenges in terms of widely accepted best practices for lipidomic analysis, nomenclature, and standards for data reporting are discussed as well.
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Affiliation(s)
- Michal Holčapek
- Department of Analytical Chemistry, Faculty of Chemical Technology , University of Pardubice , Studentská 573 , 53210 Pardubice , Czech Republic
| | - Gerhard Liebisch
- Institute of Clinical Chemistry and Laboratory Medicine , University Hospital Regensburg , 93053 Regensburg , Germany
| | - Kim Ekroos
- Lipidomics Consulting Ltd. , 02230 Esbo , Finland
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27
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Kavaliauskiene S, Torgersen ML, Lingelem ABD, Klokk TI, Lintonen T, Simolin H, Ekroos K, Skotland T, Sandvig K. Cellular effects of fluorodeoxyglucose: Global changes in the lipidome and alteration in intracellular transport. Oncotarget 2018; 7:79885-79900. [PMID: 27829218 PMCID: PMC5346758 DOI: 10.18632/oncotarget.13089] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 04/25/2016] [Accepted: 10/21/2016] [Indexed: 11/29/2022] Open
Abstract
2-fluoro-2-deoxy-D-glucose (FDG), labeled with 18F radioisotope, is the most common imaging agent used for positron emission tomography (PET) in oncology. However, little is known about the cellular effects of FDG. Another glucose analogue, 2-deoxy-D-glucose (2DG), has been shown to affect many cellular functions, including intracellular transport and lipid metabolism, and has been found to improve the efficacy of cancer chemotherapeutic agents in vivo. Thus, in the present study, we have investigated cellular effects of FDG with the focus on changes in cellular lipids and intracellular transport. By quantifying more than 200 lipids from 17 different lipid classes in HEp-2 cells and by analyzing glycosphingolipids from MCF-7, HT-29 and HBMEC cells, we have discovered that FDG treatment inhibits glucosylceramide synthesis and thus reduces cellular levels of glycosphingolipids. In addition, in HEp-2 cells the levels and/or species composition of other lipid classes, namely diacylglycerols, phosphatidic acids and phosphatidylinositols, were found to change upon treatment with FDG. Furthermore, we show here that FDG inhibits retrograde Shiga toxin transport and is much more efficient in protecting cells against the toxin than 2DG. In summary, our data reveal novel effects of FDG on cellular transport and glycosphingolipid metabolism, which suggest a potential clinical application of FDG as an adjuvant for cancer chemotherapy.
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Affiliation(s)
- Simona Kavaliauskiene
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Center for Cancer Biomedicine, Oslo University Hospital, Oslo, Norway.,Department of Biosciences, University of Oslo, Oslo, Norway
| | - Maria Lyngaas Torgersen
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Center for Cancer Biomedicine, Oslo University Hospital, Oslo, Norway
| | - Anne Berit Dyve Lingelem
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Center for Cancer Biomedicine, Oslo University Hospital, Oslo, Norway
| | - Tove Irene Klokk
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Center for Cancer Biomedicine, Oslo University Hospital, Oslo, Norway
| | | | | | | | - Tore Skotland
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Center for Cancer Biomedicine, Oslo University Hospital, Oslo, Norway
| | - Kirsten Sandvig
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Center for Cancer Biomedicine, Oslo University Hospital, Oslo, Norway.,Department of Biosciences, University of Oslo, Oslo, Norway
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28
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Kiamehr M, Viiri L, Vihervaara T, Koistin K, Hilvo M, Ekroos K, Aalto-Setälä K. Lipidomic profiling of patient-specific ipsc-derived hepatocyte-like cells (HLCs). Atherosclerosis 2017. [DOI: 10.1016/j.atherosclerosis.2017.06.337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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29
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Kiamehr M, Viiri LE, Vihervaara T, Koistinen KM, Hilvo M, Ekroos K, Käkelä R, Aalto-Setälä K. Lipidomic profiling of patient-specific iPSC-derived hepatocyte-like cells. Dis Model Mech 2017; 10:1141-1153. [PMID: 28733363 PMCID: PMC5611970 DOI: 10.1242/dmm.030841] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 07/10/2017] [Indexed: 12/18/2022] Open
Abstract
Hepatocyte-like cells (HLCs) differentiated from human induced pluripotent stem cells (iPSCs) offer an alternative model to primary human hepatocytes to study lipid aberrations. However, the detailed lipid profile of HLCs is yet unknown. In the current study, functional HLCs were differentiated from iPSCs generated from dermal fibroblasts of three individuals by a three-step protocol through the definitive endoderm (DE) stage. In parallel, detailed lipidomic analyses as well as gene expression profiling of a set of lipid-metabolism-related genes were performed during the entire differentiation process from iPSCs to HLCs. Additionally, fatty acid (FA) composition of the cell culture media at different stages was determined. Our results show that major alterations in the molecular species of lipids occurring during DE and early hepatic differentiation stages mainly mirror the quality and quantity of the FAs supplied in culture medium at each stage. Polyunsaturated phospholipids and sphingolipids with a very long FA were produced in the cells at a later stage of differentiation. This work uncovers the previously unknown lipid composition of iPSC-HLCs and its alterations during the differentiation in conjunction with the expression of key lipid-associated genes. Together with biochemical, functional and gene expression measurements, the lipidomic analyses allowed us to improve our understanding of the concerted influence of the exogenous metabolite supply and cellular biosynthesis essential for iPSC-HLC differentiation and function. Importantly, the study describes in detail a cell model that can be applied in exploring, for example, the lipid metabolism involved in the development of fatty liver disease or atherosclerosis.
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Affiliation(s)
- Mostafa Kiamehr
- Faculty of Medicine and Life Sciences, University of Tampere, Tampere, 33520, Finland
| | - Leena E Viiri
- Faculty of Medicine and Life Sciences, University of Tampere, Tampere, 33520, Finland
| | | | | | | | | | - Reijo Käkelä
- Department of Biosciences, University of Helsinki, Helsinki, 00014, Finland
| | - Katriina Aalto-Setälä
- Faculty of Medicine and Life Sciences, University of Tampere, Tampere, 33520, Finland.,Heart Hospital, Tampere University Hospital, Tampere, 33520, Finland
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30
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Busnelli M, Manzini S, Hilvo M, Parolini C, Ganzetti GS, Dellera F, Ekroos K, Jänis M, Escalante-Alcalde D, Sirtori CR, Laaksonen R, Chiesa G. Liver-specific deletion of the Plpp3 gene alters plasma lipid composition and worsens atherosclerosis in apoE -/- mice. Sci Rep 2017; 7:44503. [PMID: 28291223 PMCID: PMC5349609 DOI: 10.1038/srep44503] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [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: 11/09/2016] [Accepted: 02/08/2017] [Indexed: 01/13/2023] Open
Abstract
The PLPP3 gene encodes for a ubiquitous enzyme that dephosphorylates several lipid substrates. Genome-wide association studies identified PLPP3 as a gene that plays a role in coronary artery disease susceptibility. The aim of the study was to investigate the effect of Plpp3 deletion on atherosclerosis development in mice. Because the constitutive deletion of Plpp3 in mice is lethal, conditional Plpp3 hepatocyte-specific null mice were generated by crossing floxed Plpp3 mice with animals expressing Cre recombinase under control of the albumin promoter. The mice were crossed onto the athero-prone apoE-/- background to obtain Plpp3f/fapoE-/-Alb-Cre+ and Plpp3f/fapoE-/-Alb-Cre- offspring, the latter of which were used as controls. The mice were fed chow or a Western diet for 32 or 12 weeks, respectively. On the Western diet, Alb-Cre+ mice developed more atherosclerosis than Alb-Cre- mice, both at the aortic sinus and aorta. Lipidomic analysis showed that hepatic Plpp3 deletion significantly modified the levels of several plasma lipids involved in atherosclerosis, including lactosylceramides, lysophosphatidic acids, and lysophosphatidylinositols. In conclusion, Plpp3 ablation in mice worsened atherosclerosis development. Lipidomic analysis suggested that the hepatic Plpp3 deletion may promote atherosclerosis by increasing plasma levels of several low-abundant pro-atherogenic lipids, thus providing a molecular basis for the observed results.
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Affiliation(s)
- Marco Busnelli
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milano, Italy
| | - Stefano Manzini
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milano, Italy
| | | | - Cinzia Parolini
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milano, Italy
| | - Giulia S Ganzetti
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milano, Italy
| | - Federica Dellera
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milano, Italy
| | | | - Minna Jänis
- Department of Physiology, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Diana Escalante-Alcalde
- Instituto de Fisiología Celular, División de Neurociencias Universidad Nacional Autónoma de México, Cd. Mx. 04510, México
| | - Cesare R Sirtori
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milano, Italy
| | | | - Giulia Chiesa
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milano, Italy
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31
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Liebisch G, Ekroos K, Hermansson M, Ejsing CS. Reporting of lipidomics data should be standardized. Biochim Biophys Acta Mol Cell Biol Lipids 2017; 1862:747-751. [PMID: 28238863 DOI: 10.1016/j.bbalip.2017.02.013] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 02/20/2017] [Accepted: 02/21/2017] [Indexed: 01/03/2023]
Abstract
This article highlights, to our opinion, some of the most pertinent issues related to producing high quality lipidomics data. These issues include pitfalls related to sample collection and storage, lipid extraction, the use of shotgun and LC-MS-based lipidomics approaches, and the identification, annotation and quantification of lipid species. We hope that highlighting these issues will help stimulate efforts to implement reporting standards for dissemination of lipidomics data. This article is part of a Special Issue entitled: BBALIP_Lipidomics Opinion Articles edited by Sepp Kohlwein.
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Affiliation(s)
- Gerhard Liebisch
- Institute of Clinical Chemistry and Laboratory Medicine, University of Regensburg, Germany.
| | - Kim Ekroos
- Lipidomics Consulting Ltd., FI-02230 Esbo, Finland.
| | - Martin Hermansson
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense, Denmark.
| | - Christer S Ejsing
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, DK-5230 Odense, Denmark.
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32
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Havulinna AS, Sysi-Aho M, Hilvo M, Kauhanen D, Hurme R, Ekroos K, Salomaa V, Laaksonen R. Circulating Ceramides Predict Cardiovascular Outcomes in the Population-Based FINRISK 2002 Cohort. Arterioscler Thromb Vasc Biol 2016; 36:2424-2430. [DOI: 10.1161/atvbaha.116.307497] [Citation(s) in RCA: 194] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 10/03/2016] [Indexed: 12/25/2022]
Abstract
Objective—
Ceramides are molecular lipids implicated in apoptosis, inflammation, obesity, and insulin resistance. An earlier study reported that ceramides were associated with fatal outcome among patients with coronary heart disease. Here, we examined whether ceramides are associated with major adverse cardiovascular events (MACEs) among apparently healthy individuals.
Approach and Results—
FINRISK 2002 is a population-based risk factor survey, which recruited men and women aged 25 to 74 years. The cohort was followed up until the end of 2014. We quantified 4 circulating ceramides, Cer(d18:1/16:0), Cer(d18:1/18:0), Cer(d18:1/24:0), and Cer(d18:1/24:1), in 8101 serum samples by a targeted liquid chromatography–tandem mass spectrometry assay. Primary outcome of interest was incident MACE (n=813). Secondary analyses were performed for MACE death (n=116) without previous nonfatal MACE and for recurrent MACE (n=226) among survivors of a previous incident MACE. We used Cox proportional hazard models adjusted for the Framingham covariates to determine the association of ceramides with the outcomes. Of the ceramide species, Cer(d18:1/18:0) had the strongest association with incident MACE and the highest unadjusted hazard ratio of 1.31 (95% confidence interval, 1.21–1.41), which remained significant at 1.21 (95% confidence interval, 1.11–1.33) after Framingham risk factor adjustments. The hazard ratios were generally stronger for recurrent and fatal events than for first events. Clinical net reclassification improvement was 7.5% (
P
=6.9×10
−
5
) for Cer(d18:1/18:0).
Conclusions—
Distinct serum ceramides are associated with the risk of incident MACE in apparently healthy individuals. These results should encourage more detailed analyses of ceramides in cardiovascular pathobiology and suggest new biomarkers of MACE risk.
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Affiliation(s)
- Aki S. Havulinna
- From the Department of Health, National Institute for Health and Welfare, Helsinki, Finland (A.S.H., V.S.); Zora Biosciences Oy, Espoo, Finland (M.S.-A., M.H., D.K., R.H., K.E., R.L.); Medical School, University of Tampere, Finland (R.L.); and Finnish Clinical Biobank, University Hospital of Tampere, Finland (R.L.)
| | - Marko Sysi-Aho
- From the Department of Health, National Institute for Health and Welfare, Helsinki, Finland (A.S.H., V.S.); Zora Biosciences Oy, Espoo, Finland (M.S.-A., M.H., D.K., R.H., K.E., R.L.); Medical School, University of Tampere, Finland (R.L.); and Finnish Clinical Biobank, University Hospital of Tampere, Finland (R.L.)
| | - Mika Hilvo
- From the Department of Health, National Institute for Health and Welfare, Helsinki, Finland (A.S.H., V.S.); Zora Biosciences Oy, Espoo, Finland (M.S.-A., M.H., D.K., R.H., K.E., R.L.); Medical School, University of Tampere, Finland (R.L.); and Finnish Clinical Biobank, University Hospital of Tampere, Finland (R.L.)
| | - Dimple Kauhanen
- From the Department of Health, National Institute for Health and Welfare, Helsinki, Finland (A.S.H., V.S.); Zora Biosciences Oy, Espoo, Finland (M.S.-A., M.H., D.K., R.H., K.E., R.L.); Medical School, University of Tampere, Finland (R.L.); and Finnish Clinical Biobank, University Hospital of Tampere, Finland (R.L.)
| | - Reini Hurme
- From the Department of Health, National Institute for Health and Welfare, Helsinki, Finland (A.S.H., V.S.); Zora Biosciences Oy, Espoo, Finland (M.S.-A., M.H., D.K., R.H., K.E., R.L.); Medical School, University of Tampere, Finland (R.L.); and Finnish Clinical Biobank, University Hospital of Tampere, Finland (R.L.)
| | - Kim Ekroos
- From the Department of Health, National Institute for Health and Welfare, Helsinki, Finland (A.S.H., V.S.); Zora Biosciences Oy, Espoo, Finland (M.S.-A., M.H., D.K., R.H., K.E., R.L.); Medical School, University of Tampere, Finland (R.L.); and Finnish Clinical Biobank, University Hospital of Tampere, Finland (R.L.)
| | - Veikko Salomaa
- From the Department of Health, National Institute for Health and Welfare, Helsinki, Finland (A.S.H., V.S.); Zora Biosciences Oy, Espoo, Finland (M.S.-A., M.H., D.K., R.H., K.E., R.L.); Medical School, University of Tampere, Finland (R.L.); and Finnish Clinical Biobank, University Hospital of Tampere, Finland (R.L.)
| | - Reijo Laaksonen
- From the Department of Health, National Institute for Health and Welfare, Helsinki, Finland (A.S.H., V.S.); Zora Biosciences Oy, Espoo, Finland (M.S.-A., M.H., D.K., R.H., K.E., R.L.); Medical School, University of Tampere, Finland (R.L.); and Finnish Clinical Biobank, University Hospital of Tampere, Finland (R.L.)
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Skotland T, Ekroos K, Kauhanen D, Simolin H, Seierstad T, Berge V, Sandvig K, Llorente A. Molecular lipid species in urinary exosomes as potential prostate cancer biomarkers. Eur J Cancer 2016; 70:122-132. [PMID: 27914242 DOI: 10.1016/j.ejca.2016.10.011] [Citation(s) in RCA: 221] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 10/05/2016] [Accepted: 10/07/2016] [Indexed: 12/21/2022]
Abstract
BACKGROUND Exosomes have recently appeared as a novel source of noninvasive cancer biomarkers, since these nanovesicles contain molecules from cancer cells and can be detected in biofluids. We have here investigated the potential use of lipids in urinary exosomes as prostate cancer biomarkers. METHODS A high-throughput mass spectrometry quantitative lipidomic analysis was performed to reveal the lipid composition of urinary exosomes in prostate cancer patients and healthy controls. RESULTS Control samples were first analysed to characterise the lipidome of urinary exosomes and test the reproducibility of the method. In total, 107 lipid species were quantified in urinary exosomes. Several differences, for example, in cholesterol and phosphatidylcholine, were found between urinary exosomes and exosomes derived from cell lines, thus showing the importance of in vivo studies for biomarker analysis. The 36 most abundant lipid species in urinary exosomes were then quantified in 15 prostate cancer patients and 13 healthy controls. Interestingly, the levels of nine lipids species were found to be significantly different when the two groups were compared. The highest significance was shown for phosphatidylserine (PS) 18:1/18:1 and lactosylceramide (d18:1/16:0), the latter also showed the highest patient-to-control ratio. Furthermore, combinations of these lipid species and PS 18:0-18:2 distinguished the two groups with 93% sensitivity and 100% specificity. Finally, in agreement with the reported dysregulation of sphingolipid metabolism in cancer cells, alteration in specific sphingolipid lipid classes were observed. CONCLUSION This study shows for the first time the potential use of exosomal lipid species in urine as prostate cancer biomarkers.
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Affiliation(s)
- Tore Skotland
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, 0379 Oslo, Norway; Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, 0379 Oslo, Norway
| | - Kim Ekroos
- Zora Biosciences Oy, 02150 Espoo, Finland
| | | | | | - Therese Seierstad
- Division of Radiology and Nuclear Medicine, Oslo University Hospital, 0379 Oslo, Norway
| | - Viktor Berge
- Department of Urology, Oslo University Hospital, 0586 Oslo, Norway
| | - Kirsten Sandvig
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, 0379 Oslo, Norway; Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, 0379 Oslo, Norway; Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Alicia Llorente
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, 0379 Oslo, Norway; Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, 0379 Oslo, Norway.
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Chaudhari A, Håversen L, Mobini R, Andersson L, Ståhlman M, Lu E, Rutberg M, Fogelstrand P, Ekroos K, Mardinoglu A, Levin M, Perkins R, Borén J. ARAP2 promotes GLUT1-mediated basal glucose uptake through regulation of sphingolipid metabolism. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1861:1643-1651. [DOI: 10.1016/j.bbalip.2016.07.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 07/02/2016] [Accepted: 07/25/2016] [Indexed: 11/16/2022]
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Titz B, Luettich K, Leroy P, Boue S, Vuillaume G, Vihervaara T, Ekroos K, Martin F, Peitsch MC, Hoeng J. Alterations in Serum Polyunsaturated Fatty Acids and Eicosanoids in Patients with Mild to Moderate Chronic Obstructive Pulmonary Disease (COPD). Int J Mol Sci 2016; 17:E1583. [PMID: 27657052 PMCID: PMC5037848 DOI: 10.3390/ijms17091583] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [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: 07/14/2016] [Revised: 09/06/2016] [Accepted: 09/13/2016] [Indexed: 01/08/2023] Open
Abstract
Smoking is a major risk factor for several diseases including chronic obstructive pulmonary disease (COPD). To better understand the systemic effects of cigarette smoke exposure and mild to moderate COPD-and to support future biomarker development-we profiled the serum lipidomes of healthy smokers, smokers with mild to moderate COPD (GOLD stages 1 and 2), former smokers, and never-smokers (n = 40 per group) (ClinicalTrials.gov registration: NCT01780298). Serum lipidome profiling was conducted with untargeted and targeted mass spectrometry-based lipidomics. Guided by weighted lipid co-expression network analysis, we identified three main trends comparing smokers, especially those with COPD, with non-smokers: a general increase in glycero(phospho)lipids, including triglycerols; changes in fatty acid desaturation (decrease in ω-3 polyunsaturated fatty acids, and an increase in monounsaturated fatty acids); and an imbalance in eicosanoids (increase in 11,12- and 14,15-DHETs (dihydroxyeicosatrienoic acids), and a decrease in 9- and 13-HODEs (hydroxyoctadecadienoic acids)). The lipidome profiles supported classification of study subjects as smokers or non-smokers, but were not sufficient to distinguish between smokers with and without COPD. Overall, our study yielded further insights into the complex interplay between smoke exposure, lung disease, and systemic alterations in serum lipid profiles.
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Affiliation(s)
- Bjoern Titz
- Philip Morris International Research and Development, Philip Morris Products S.A. (Part of Philip Morris International Group of Companies), Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland.
| | - Karsta Luettich
- Philip Morris International Research and Development, Philip Morris Products S.A. (Part of Philip Morris International Group of Companies), Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland.
| | - Patrice Leroy
- Philip Morris International Research and Development, Philip Morris Products S.A. (Part of Philip Morris International Group of Companies), Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland.
| | - Stephanie Boue
- Philip Morris International Research and Development, Philip Morris Products S.A. (Part of Philip Morris International Group of Companies), Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland.
| | - Gregory Vuillaume
- Philip Morris International Research and Development, Philip Morris Products S.A. (Part of Philip Morris International Group of Companies), Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland.
| | | | - Kim Ekroos
- Zora Biosciences Oy, 02150 Espoo, Finland.
| | - Florian Martin
- Philip Morris International Research and Development, Philip Morris Products S.A. (Part of Philip Morris International Group of Companies), Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland.
| | - Manuel C Peitsch
- Philip Morris International Research and Development, Philip Morris Products S.A. (Part of Philip Morris International Group of Companies), Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland.
| | - Julia Hoeng
- Philip Morris International Research and Development, Philip Morris Products S.A. (Part of Philip Morris International Group of Companies), Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland.
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Busnelli M, Manzini S, Hilvo M, Parolini C, Ganzetti G, Dellera F, Ekroos K, Jänis M, Sirtori C, Laaksonen R, Chiesa G. Hepatocyte-specific PPAP2B ablation increases plasma levels of several minor pro-atherogenic lipid species and worsens atherosclerosis in apoE -/- MICE. Atherosclerosis 2016. [DOI: 10.1016/j.atherosclerosis.2016.07.053] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Chiesa G, Busnelli M, Parolini C, Manzini S, Ganzetti G, Dellera F, Suoniemi M, Hilvo M, Hurme R, Ekroos K, Sirtori C, Laaksonen R. Lipidomics of plasma, liver and aorta of Pcsk9-KO mice. Atherosclerosis 2016. [DOI: 10.1016/j.atherosclerosis.2016.07.581] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Laaksonen R, Ekroos K, Sysi-Aho M, Hilvo M, Vihervaara T, Kauhanen D, Suoniemi M, Hurme R, März W, Scharnagl H, Stojakovic T, Vlachopoulou E, Lokki ML, Nieminen MS, Klingenberg R, Matter CM, Hornemann T, Jüni P, Rodondi N, Räber L, Windecker S, Gencer B, Pedersen ER, Tell GS, Nygård O, Mach F, Sinisalo J, Lüscher TF. Plasma ceramides predict cardiovascular death in patients with stable coronary artery disease and acute coronary syndromes beyond LDL-cholesterol. Eur Heart J 2016; 37:1967-76. [PMID: 27125947 PMCID: PMC4929378 DOI: 10.1093/eurheartj/ehw148] [Citation(s) in RCA: 386] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 03/17/2016] [Indexed: 12/12/2022] Open
Abstract
Aims The aim was to study the prognostic value of plasma ceramides (Cer) as cardiovascular death (CV death) markers in three independent coronary artery disease (CAD) cohorts. Methods and results Corogene study is a prospective Finnish cohort including stable CAD patients (n = 160). Multiple lipid biomarkers and C-reactive protein were measured in addition to plasma Cer(d18:1/16:0), Cer(d18:1/18:0), Cer(d18:1/24:0), and Cer(d18:1/24:1). Subsequently, the association between high-risk ceramides and CV mortality was investigated in the prospective Special Program University Medicine—Inflammation in Acute Coronary Syndromes (SPUM-ACS) cohort (n = 1637), conducted in four Swiss university hospitals. Finally, the results were validated in Bergen Coronary Angiography Cohort (BECAC), a prospective Norwegian cohort study of stable CAD patients. Ceramides, especially when used in ratios, were significantly associated with CV death in all studies, independent of other lipid markers and C-reactive protein. Adjusted odds ratios per standard deviation for the Cer(d18:1/16:0)/Cer(d18:1/24:0) ratio were 4.49 (95% CI, 2.24–8.98), 1.64 (1.29–2.08), and 1.77 (1.41–2.23) in the Corogene, SPUM-ACS, and BECAC studies, respectively. The Cer(d18:1/16:0)/Cer(d18:1/24:0) ratio improved the predictive value of the GRACE score (net reclassification improvement, NRI = 0.17 and ΔAUC = 0.09) in ACS and the predictive value of the Marschner score in stable CAD (NRI = 0.15 and ΔAUC = 0.02). Conclusions Distinct plasma ceramide ratios are significant predictors of CV death both in patients with stable CAD and ACS, over and above currently used lipid markers. This may improve the identification of high-risk patients in need of more aggressive therapeutic interventions.
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Affiliation(s)
- Reijo Laaksonen
- Zora Biosciences, Espoo, Finland Medical School, Tampere University, Tampere, Finland Finnish Clinical Biobank Tampere, University Hospital of Tampere, Tampere, Finland
| | | | | | | | | | | | | | | | - Winfried März
- Medical Clinic V (Nephrology, Hypertensiology, Rheumatology, Endocrinology, Diabetology), Medical Faculty Mannheim, University of Heidelberg, Heidelberg, Germany synlab Academy, synlab Holding Deutschland GmbH, Mannheim and Augsburg, Germany
| | - Hubert Scharnagl
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University Graz, Graz, Austria
| | - Tatjana Stojakovic
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University Graz, Graz, Austria
| | - Efthymia Vlachopoulou
- Transplantation Laboratory, Haartman Institute, University of Helsinki, Helsinki, Finland
| | - Marja-Liisa Lokki
- Transplantation Laboratory, Haartman Institute, University of Helsinki, Helsinki, Finland
| | - Markku S Nieminen
- Transplantation Laboratory, Haartman Institute, University of Helsinki, Helsinki, Finland Heart and Lung Center, Helsinki University Hospital, Helsinki, Finland
| | - Roland Klingenberg
- Department of Cardiology, University Heart Center, University Hospital Zürich and University of Zürich, Zürich, Switzerland
| | - Christian M Matter
- Department of Cardiology, University Heart Center, University Hospital Zürich and University of Zürich, Zürich, Switzerland
| | - Thorsten Hornemann
- Institute of Clinical Chemistry, University Hospital, Zürich, Switzerland
| | - Peter Jüni
- Applied Health Research Centre (AHRC), Li Ka Shing Knowledge Institute of St. Michael's Hospital, and Department of Medicine, University of Toronto, Toronto, Canada
| | - Nicolas Rodondi
- Department of General Internal Medicine, University Hospital Bern, Bern, Switzerland Department of Ambulatory Care and Community Medicine, University of Lausanne, Lausanne, Switzerland
| | - Lorenz Räber
- Cardiovascular Center, Department of Cardiology, University Hospital Bern, Bern, Switzerland
| | - Stephan Windecker
- Cardiovascular Center, Department of Cardiology, University Hospital Bern, Bern, Switzerland
| | - Baris Gencer
- Cardiovascular Center, Department of Cardiology, University Hospital Geneva, Geneva, Switzerland
| | | | - Grethe S Tell
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Ottar Nygård
- Department of Clinical Science, University of Bergen, Bergen, Norway Department of Heart Disease, Haukeland University Hospital, Bergen, Norway
| | - Francois Mach
- Cardiovascular Center, Department of Cardiology, University Hospital Geneva, Geneva, Switzerland
| | - Juha Sinisalo
- Transplantation Laboratory, Haartman Institute, University of Helsinki, Helsinki, Finland Heart and Lung Center, Helsinki University Hospital, Helsinki, Finland
| | - Thomas F Lüscher
- Institute of Clinical Chemistry, University Hospital, Zürich, Switzerland
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Puri P, Xu J, Vihervaara T, Katainen R, Ekroos K, Daita K, Min HK, Joyce A, Mirshahi F, Tsukamoto H, Sanyal AJ. Alcohol produces distinct hepatic lipidome and eicosanoid signature in lean and obese. J Lipid Res 2016; 57:1017-28. [PMID: 27020313 DOI: 10.1194/jlr.m066175] [Citation(s) in RCA: 16] [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] [Received: 12/31/2015] [Indexed: 12/13/2022] Open
Abstract
Alcohol- and obesity-related liver diseases often coexist. The hepatic lipidomics due to alcohol and obesity interaction is unknown. We characterized the hepatic lipidome due to 1) alcohol consumption in lean and obese mice and 2) obesity and alcohol interactions. In the French-Tsukamoto mouse model, intragastric alcohol or isocaloric dextrose were fed with either chow (lean) or high-fat, high-cholesterol diet (obese). Four groups (lean, lean alcohol, obese, and obese alcohol) were studied. MS was performed for hepatic lipidomics, and data were analyzed. Alcohol significantly increased hepatic cholesteryl esters and diacyl-glycerol in lean and obese but was more pronounced in obese. Alcohol produced contrasting changes in hepatic phospholipids with significant enrichment in lean mice versus significant decrease in obese mice, except phosphatidylglycerol, which was increased in both lean and obese alcohol groups. Most lysophospholipids were increased in lean alcohol and obese mice without alcohol use only. Prostaglandin E2; 5-, 8-, and 11-hydroxyeicosatetraenoic acids; and 9- and 13-hydroxyoctadecadienoic acids were considerably increased in obese mice with alcohol use. Alcohol consumption produced distinct changes in lean and obese with profound effects of obesity and alcohol interaction on proinflammatory and oxidative stress-related eicosanoids.
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Affiliation(s)
- Puneet Puri
- Division of Gastroenterology, Hepatology and Nutrition, Department of Internal Medicine, Virginia Commonwealth University School of Medicine, Richmond, VA
| | - Jun Xu
- University of Southern California, Los Angeles, CA
| | | | | | | | - Kalyani Daita
- Division of Gastroenterology, Hepatology and Nutrition, Department of Internal Medicine, Virginia Commonwealth University School of Medicine, Richmond, VA
| | - Hae-Ki Min
- Division of Gastroenterology, Hepatology and Nutrition, Department of Internal Medicine, Virginia Commonwealth University School of Medicine, Richmond, VA
| | | | - Faridoddin Mirshahi
- Division of Gastroenterology, Hepatology and Nutrition, Department of Internal Medicine, Virginia Commonwealth University School of Medicine, Richmond, VA
| | | | - Arun J Sanyal
- Division of Gastroenterology, Hepatology and Nutrition, Department of Internal Medicine, Virginia Commonwealth University School of Medicine, Richmond, VA
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Róg T, Orłowski A, Llorente A, Skotland T, Sylvänne T, Kauhanen D, Ekroos K, Sandvig K, Vattulainen I. Data including GROMACS input files for atomistic molecular dynamics simulations of mixed, asymmetric bilayers including molecular topologies, equilibrated structures, and force field for lipids compatible with OPLS-AA parameters. Data Brief 2016; 7:1171-1174. [PMID: 27761499 PMCID: PMC5063793 DOI: 10.1016/j.dib.2016.03.067] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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: 12/08/2015] [Revised: 03/06/2016] [Accepted: 03/18/2016] [Indexed: 12/01/2022] Open
Abstract
In this Data in Brief article we provide a data package of GROMACS input files for atomistic molecular dynamics simulations of multicomponent, asymmetric lipid bilayers using the OPLS-AA force field. These data include 14 model bilayers composed of 8 different lipid molecules. The lipids present in these models are: cholesterol (CHOL), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylethanolamine (POPE), 1-stearoyl-2-oleoyl-sn-glycero-3-phosphatidyl-ethanolamine (SOPE), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS), 1-stearoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (SOPS), N-palmitoyl-D-erythro-sphingosyl-phosphatidylcholine (SM16), and N-lignoceroyl-D-erythro-sphingosyl-phosphatidylcholine (SM24). The bilayers׳ compositions are based on lipidomic studies of PC-3 prostate cancer cells and exosomes discussed in Llorente et al. (2013) [1], showing an increase in the section of long-tail lipid species (SOPS, SOPE, and SM24) in the exosomes. Former knowledge about lipid asymmetry in cell membranes was accounted for in the models, meaning that the model of the inner leaflet is composed of a mixture of PC, PS, PE, and cholesterol, while the extracellular leaflet is composed of SM, PC and cholesterol discussed in Van Meer et al. (2008) [2]. The provided data include lipids׳ topologies, equilibrated structures of asymmetric bilayers, all force field parameters, and input files with parameters describing simulation conditions (md.mdp). The data is associated with the research article “Interdigitation of Long-Chain Sphingomyelin Induces Coupling of Membrane Leaflets in a Cholesterol Dependent Manner” (Róg et al., 2016) [3].
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Affiliation(s)
- Tomasz Róg
- Department of Physics, Tampere University of Technology, P. O. Box 692, FI-33101 Tampere, Finland; Department of Physics, University of Helsinki, P. O. Box 64, FI-00014, Finland
| | - Adam Orłowski
- Department of Physics, Tampere University of Technology, P. O. Box 692, FI-33101 Tampere, Finland; Department of Physics and Energy, University of Limerick, Limerick, Ireland
| | - Alicia Llorente
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital - The Norwegian Radium Hospital, 0379 Oslo, Norway; Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, 0379 Oslo, Norway
| | - Tore Skotland
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital - The Norwegian Radium Hospital, 0379 Oslo, Norway; Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, 0379 Oslo, Norway
| | | | | | - Kim Ekroos
- Zora Biosciences Oy, 02150 Espoo, Finland
| | - Kirsten Sandvig
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital - The Norwegian Radium Hospital, 0379 Oslo, Norway; Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, 0379 Oslo, Norway; Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, P. O. Box 692, FI-33101 Tampere, Finland; Department of Physics, University of Helsinki, P. O. Box 64, FI-00014, Finland; MEMPHYS - Center for Biomembrane Physics, University of Southern Denmark, Odense, Denmark
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Kauhanen D, Sysi-Aho M, Koistinen KM, Laaksonen R, Sinisalo J, Ekroos K. Development and validation of a high-throughput LC-MS/MS assay for routine measurement of molecular ceramides. Anal Bioanal Chem 2016; 408:3475-83. [PMID: 26922344 DOI: 10.1007/s00216-016-9425-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [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: 12/10/2015] [Revised: 02/09/2016] [Accepted: 02/15/2016] [Indexed: 12/16/2022]
Abstract
Monitoring the levels of the ceramides (Cer) d18:1/16:0, Cer d18:1/18:0, Cer d18:1/24:0, and Cer d18:1/24:1 and ratios thereof in human plasma empowers the prediction of fatal outcome of coronary artery disease (CAD). We describe a validated liquid chromatography-tandem mass spectrometry (LC-MS/MS) methodology for clinical-scaled measurement of the four distinct ceramides. Rapid plasma precipitation was accomplished in 96-well format. Excellent extraction recoveries in the range of 98-109% were achieved for each ceramide. Addition of corresponding D7-labeled ceramide standards facilitated precise quantification of each plasma ceramide species utilizing a novel short 5-min LC-MS/MS method. Neither matrix interference nor carryover was observed. Robust intra- and inter-assay accuracy and precision <15% at five different concentrations were obtained. Linear calibration lines with regressions, R(2) > 0.99, were achieved for all analytes. Short-term bench top, long-term plasma, and extract stability demonstrated that the distinct ceramides were stable in the conditions evaluated. The validity of the methodology was demonstrated by determining the precise ceramide concentrations in a small CAD case-control study. Thus, our LC-MS/MS methodology features simple sample preparation and short analysis time for accurate quantification of Cer d18:1/16:0, Cer d18:1/18:0, Cer d18:1/24:0, and Cer d18:1/24:1, designed for routine analysis.
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Affiliation(s)
| | | | | | | | - Juha Sinisalo
- Heart and Lung Center, Helsinki University Hospital, 00029 HUS, Helsinki, Finland
| | - Kim Ekroos
- Zora Biosciences, Biologinkuja 1, 02150, Espoo, Finland.
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Titz B, Boué S, Phillips B, Talikka M, Vihervaara T, Schneider T, Nury C, Elamin A, Guedj E, Peck MJ, Schlage WK, Cabanski M, Leroy P, Vuillaume G, Martin F, Ivanov NV, Veljkovic E, Ekroos K, Laaksonen R, Vanscheeuwijck P, Peitsch MC, Hoeng J. Effects of Cigarette Smoke, Cessation, and Switching to Two Heat-Not-Burn Tobacco Products on Lung Lipid Metabolism in C57BL/6 and Apoe-/- Mice-An Integrative Systems Toxicology Analysis. Toxicol Sci 2016; 149:441-57. [PMID: 26582801 PMCID: PMC4725611 DOI: 10.1093/toxsci/kfv244] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [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] [Indexed: 12/22/2022] Open
Abstract
The impact of cigarette smoke (CS), a major cause of lung diseases, on the composition and metabolism of lung lipids is incompletely understood. Here, we integrated quantitative lipidomics and proteomics to investigate exposure effects on lung lipid metabolism in a C57BL/6 and an Apolipoprotein E-deficient (Apoe(-/-)) mouse study. In these studies, mice were exposed to high concentrations of 3R4F reference CS, aerosol from potential modified risk tobacco products (MRTPs) or filtered air (Sham) for up to 8 months. The 2 assessed MRTPs, the prototypical MRTP for C57BL/6 mice and the Tobacco Heating System 2.2 for Apoe(-/-) mice, utilize "heat-not-burn" technologies and were each matched in nicotine concentrations to the 3R4F CS. After 2 months of CS exposure, some groups were either switched to the MRTP or underwent cessation. In both mouse strains, CS strongly affected several categories of lung lipids and lipid-related proteins. Candidate surfactant lipids, surfactant proteins, and surfactant metabolizing proteins were increased. Inflammatory eicosanoids, their metabolic enzymes, and several ceramide classes were elevated. Overall, CS induced a coordinated lipid response controlled by transcription regulators such as SREBP proteins and supported by other metabolic adaptations. In contrast, most of these changes were absent in the mice exposed to the potential MRTPs, in the cessation group, and the switching group. Our findings demonstrate the complex biological response of the lungs to CS exposure and support the benefits of cessation or switching to a heat-not-burn product using a design such as those employed in this study.
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Affiliation(s)
- Bjoern Titz
- *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland; *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland;
| | - Stéphanie Boué
- *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Blaine Phillips
- Philip Morris International Research Laboratories, 50 Science Park Road, Singapore, Singapore; and
| | - Marja Talikka
- *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | | | - Thomas Schneider
- *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Catherine Nury
- *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Ashraf Elamin
- *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Emmanuel Guedj
- *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Michael J Peck
- *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Walter K Schlage
- *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Maciej Cabanski
- *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Patrice Leroy
- *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Gregory Vuillaume
- *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Florian Martin
- *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Nikolai V Ivanov
- *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Emilija Veljkovic
- *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Kim Ekroos
- Zora Biosciences Oy, Biologinkuja 1, 02150 Espoo, Finland
| | | | - Patrick Vanscheeuwijck
- *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Manuel C Peitsch
- *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland
| | - Julia Hoeng
- *Philip Morris International Research and Development, Quai Jeanrenaud 5, 2000 Neuchatel, Switzerland;
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Rog T, Orłowski A, Manna M, Llorente A, Skotland T, Sylvänne T, Kauhanen D, Ekroos K, Sandvig K, Vattulainen I. Cholesterol Modulated Interdigitation of Long-Chain Sphingomyelin and Glycolipids. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.3094] [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: 11/26/2022] Open
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Róg T, Orłowski A, Llorente A, Skotland T, Sylvänne T, Kauhanen D, Ekroos K, Sandvig K, Vattulainen I. Interdigitation of long-chain sphingomyelin induces coupling of membrane leaflets in a cholesterol dependent manner. Biochimica et Biophysica Acta (BBA) - Biomembranes 2016; 1858:281-8. [DOI: 10.1016/j.bbamem.2015.12.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Revised: 11/16/2015] [Accepted: 12/01/2015] [Indexed: 12/15/2022]
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Ansari S, Baumer K, Boué S, Dijon S, Dulize R, Ekroos K, Elamin A, Foong C, Guedj E, Hoeng J, Ivanov NV, Krishnan S, Leroy P, Martin F, Merg C, Peck MJ, Peitsch MC, Phillips B, Schlage WK, Schneider T, Talikka M, Titz B, Vanscheeuwijck P, Veljkovic E, Vihervaara T, Vuillaume G, Woon CQ. Comprehensive systems biology analysis of a 7-month cigarette smoke inhalation study in C57BL/6 mice. Sci Data 2016; 3:150077. [PMID: 26731301 PMCID: PMC4700839 DOI: 10.1038/sdata.2015.77] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [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: 12/29/2014] [Accepted: 11/19/2015] [Indexed: 12/12/2022] Open
Abstract
Smoking of combustible cigarettes has a major impact on human health. Using a systems toxicology approach in a model of chronic obstructive pulmonary disease (C57BL/6 mice), we assessed the health consequences in mice of an aerosol derived from a prototype modified risk tobacco product (pMRTP) as compared to conventional cigarettes. We investigated physiological and histological endpoints in parallel with transcriptomics, lipidomics, and proteomics profiles in mice exposed to a reference cigarette (3R4F) smoke or a pMRTP aerosol for up to 7 months. We also included a cessation group and a switching-to-pMRTP group (after 2 months of 3R4F exposure) in addition to the control (fresh air-exposed) group, to understand the potential risk reduction of switching to pMRTP compared with continuous 3R4F exposure and cessation. The present manuscript describes the study design, setup, and implementation, as well as the generation, processing, and quality control analysis of the toxicology and ‘omics’ datasets that are accessible in public repositories for further analyses.
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Affiliation(s)
- Sam Ansari
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Karine Baumer
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Stéphanie Boué
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Sophie Dijon
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Remi Dulize
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Kim Ekroos
- Zora Biosciences Oy, Biologinkuja 1, Espoo 02150, Finland
| | - Ashraf Elamin
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Clement Foong
- Philip Morris International Research Laboratories, 50 Science Park Road, Science Park II, Singapore, Singapore 117406
| | - Emmanuel Guedj
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Julia Hoeng
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Nikolai V Ivanov
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Subash Krishnan
- Philip Morris International Research Laboratories, 50 Science Park Road, Science Park II, Singapore, Singapore 117406
| | - Patrice Leroy
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Florian Martin
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Celine Merg
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Michael J Peck
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Manuel C Peitsch
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Blaine Phillips
- Philip Morris International Research Laboratories, 50 Science Park Road, Science Park II, Singapore, Singapore 117406
| | - Walter K Schlage
- Biology consultant, Max-Baermann-Str. 21, 51429 Bergisch Gladbach, Germany
| | - Thomas Schneider
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Marja Talikka
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Bjoern Titz
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Patrick Vanscheeuwijck
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Emilija Veljkovic
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | | | - Gregory Vuillaume
- Philip Morris International R&D, Philip Morris Products S. A., Quai Jeanrenaud 5, Neuchâtel 2000, Switzerland
| | - Ching Qing Woon
- Philip Morris International Research Laboratories, 50 Science Park Road, Science Park II, Singapore, Singapore 117406
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Affiliation(s)
- Gerhard Liebisch
- Institute of Clinical Chemistry and Laboratory Medicine University of Regensburg Regensburg, Germany
| | - Christer S Ejsing
- Department of Biochemistry and Molecular Biology University of Southern Denmark Odense, Denmark
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Skorve J, Hilvo M, Vihervaara T, Burri L, Bohov P, Tillander V, Bjørndal B, Suoniemi M, Laaksonen R, Ekroos K, Berge RK, Alexson SEH. Fish oil and krill oil differentially modify the liver and brain lipidome when fed to mice. Lipids Health Dis 2015; 14:88. [PMID: 26260413 PMCID: PMC4531896 DOI: 10.1186/s12944-015-0086-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [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: 05/13/2015] [Accepted: 07/24/2015] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Marine food is an important source of omega-3 fatty acids with beneficial health effects. Oils from marine organisms have different fatty acid composition and differ in their molecular composition. Fish oil (FO) has a high content of eicosapentaenoic and docosahexaenoic acids mainly esterified to triacylglycerols, while in krill oil (KO) these fatty acids are mainly esterified to phospholipids. The aim was to study the effects of these oils on the lipid content and fatty acid distribution in the various lipid classes in liver and brain of mice. METHODS Mice were fed either a high-fat diet (HF), a HF diet supplemented with FO or with KO (n = 6). After six weeks of feeding, liver and brain lipid extracts were analysed using a shotgun and TAG lipidomics approach. Student t-test was performed after log-transformation to compare differences between study groups. RESULTS Six weeks of feeding resulted in significant changes in the relative abundance of many lipid classes compared to control mice. In both FO and KO fed mice, the triacylglycerol content in the liver was more than doubled. The fatty acid distribution was affected by the oils in both liver and brain with a decrease in the abundance of 18:2 and 20:4, and an increase in 20:5 and 22:6 in both study groups. 18:2 decreased in all lipid classes in the FO group but with only minor changes in the KO group. Differences between the feeding groups were particularly evident in some of the minor lipid classes that are associated with inflammation and insulin resistance. Ceramides and diacylglycerols were decreased and cholesteryl esters increased in the liver of the KO group, while plasmalogens were decreased in the FO group. In the brain, diacylglycerols were decreased, more by KO than FO, while ceramides and lactosylceramides were increased, more by FO than KO. CONCLUSION The changes in the hepatic sphingolipids and 20:4 fatty acid levels were greater in the KO compared to the FO fed mice, and are consistent with a hypothesis that krill oil will have a stronger anti-inflammatory action and enhances insulin sensitivity more potently than fish oil.
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Affiliation(s)
- Jon Skorve
- Department of Clinical Science, University of Bergen, N-5021, Bergen, Norway.
| | - Mika Hilvo
- Zora Biosciences Oy, Biologinkuja 1, 02150, Espoo, Finland.
| | | | - Lena Burri
- Department of Clinical Science, University of Bergen, N-5021, Bergen, Norway. .,Present address: Aker BioMarine ASA, Fjordalléen 16, NO-0115, Oslo, Norway.
| | - Pavol Bohov
- Department of Clinical Science, University of Bergen, N-5021, Bergen, Norway.
| | - Veronika Tillander
- Division of Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, S-14186, Stockholm, Sweden.
| | - Bodil Bjørndal
- Department of Clinical Science, University of Bergen, N-5021, Bergen, Norway.
| | - Matti Suoniemi
- Zora Biosciences Oy, Biologinkuja 1, 02150, Espoo, Finland.
| | | | - Kim Ekroos
- Zora Biosciences Oy, Biologinkuja 1, 02150, Espoo, Finland.
| | - Rolf K Berge
- Department of Clinical Science, University of Bergen, N-5021, Bergen, Norway. .,Department of Heart Disease, Haukeland University Hospital, N-5021, Bergen, Norway.
| | - Stefan E H Alexson
- Division of Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, S-14186, Stockholm, Sweden.
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Vik R, Tillander V, Skorve J, Vihervaara T, Ekroos K, Alexson SEH, Berge RK, Bjørndal B. Three differently generated salmon protein hydrolysates reveal opposite effects on hepatic lipid metabolism in mice fed a high-fat diet. Food Chem 2015; 183:101-10. [PMID: 25863616 DOI: 10.1016/j.foodchem.2015.03.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [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: 10/17/2014] [Revised: 02/12/2015] [Accepted: 03/03/2015] [Indexed: 01/05/2023]
Abstract
This study investigates the effects of salmon peptide fractions, generated using different enzymatic hydrolyzation methods, on hepatic lipid metabolism. Four groups of mice were fed a high-fat diet with 20% casein (control group) or 15% casein and 5% of peptide fractions (treatment groups E1, E2 and E4) for 6weeks. Weight gain was reduced in mice fed E1 and E4-diets compared to control, despite a similar feed intake. Reduced plasma and liver triacylglycerol levels in E1 and E4-mice were linked to reduced fatty acid synthase (FAS) activity and hepatic expression of lipogenic genes. By contrast, plasma and liver lipids increased in the E2 group, concomitant with increased hepatic FAS activity and Δ9 desaturase gene expression. Shotgun lipidomics showed that MUFAs were significantly reduced in the E1 and E4 groups, whereas PUFAs were increased, and the opposite was observed in the E2 group. In conclusion, bioactive peptides with distinctive properties could potentially be isolated from salmon hydrolysates.
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Affiliation(s)
- Rita Vik
- Department of Clinical Science, University of Bergen, N-5020 Bergen, Norway
| | - Veronika Tillander
- Department of Laboratory Medicine, Division of Clinical Chemistry, Karolinska Institutet, C1-74, Karolinska University Hospital, SE-141 86 Stockholm, Sweden
| | - Jon Skorve
- Department of Clinical Science, University of Bergen, N-5020 Bergen, Norway
| | | | - Kim Ekroos
- Zora Biosciences Oy, Biologinkuja 1, FI-02150 Espoo, Finland
| | - Stefan E H Alexson
- Department of Laboratory Medicine, Division of Clinical Chemistry, Karolinska Institutet, C1-74, Karolinska University Hospital, SE-141 86 Stockholm, Sweden
| | - Rolf K Berge
- Department of Clinical Science, University of Bergen, N-5020 Bergen, Norway; Department of Heart Disease, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Bodil Bjørndal
- Department of Clinical Science, University of Bergen, N-5020 Bergen, Norway.
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Koistinen KM, Suoniemi M, Simolin H, Ekroos K. Quantitative lysophospholipidomics in human plasma and skin by LC–MS/MS. Anal Bioanal Chem 2015; 407:5091-9. [DOI: 10.1007/s00216-014-8453-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Revised: 12/19/2014] [Accepted: 12/23/2014] [Indexed: 11/28/2022]
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50
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Phuyal S, Skotland T, Hessvik NP, Simolin H, Øverbye A, Brech A, Parton RG, Ekroos K, Sandvig K, Llorente A. The ether lipid precursor hexadecylglycerol stimulates the release and changes the composition of exosomes derived from PC-3 cells. J Biol Chem 2014; 290:4225-37. [PMID: 25519911 DOI: 10.1074/jbc.m114.593962] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Exosomes are vesicles released by cells after fusion of multivesicular bodies with the plasma membrane. In this study, we have investigated whether ether lipids affect the release of exosomes in PC-3 cells. To increase the cellular levels of ether lipids, the ether lipid precursor hexadecylglycerol was added to cells. Lipidomic analysis showed that this compound was in fact able to double the cellular levels of ether lipids in these cells. Furthermore, increased levels of ether lipids were also found in exosomes released by cells containing high levels of these lipids. Interestingly, as measured by nanoparticle tracking analysis, cells containing high levels of ether lipids released more exosomes than control cells, and these exosomes were similar in size to control exosomes. Moreover, silver staining and Western blot analyses showed that the protein composition of exosomes released in the presence of hexadecylglycerol was changed; the levels of some proteins were increased, and the levels of others were reduced. In conclusion, this study clearly shows that an increase in cellular ether lipids is associated with changes in the release and composition of exosomes.
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Affiliation(s)
- Santosh Phuyal
- From the Department of Biochemistry, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, 0379 Oslo, Norway, the Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, 0379 Oslo, Norway
| | - Tore Skotland
- From the Department of Biochemistry, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, 0379 Oslo, Norway, the Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, 0379 Oslo, Norway
| | - Nina Pettersen Hessvik
- From the Department of Biochemistry, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, 0379 Oslo, Norway, the Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, 0379 Oslo, Norway
| | | | - Anders Øverbye
- From the Department of Biochemistry, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, 0379 Oslo, Norway, the Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, 0379 Oslo, Norway
| | - Andreas Brech
- From the Department of Biochemistry, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, 0379 Oslo, Norway, the Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, 0379 Oslo, Norway
| | - Robert G Parton
- the Institute for Molecular Bioscience and Centre for Microscopy and Microanalysis, University of Queensland, Brisbane, Queensland 4067, Australia, and
| | - Kim Ekroos
- the Zora Biosciences Oy, 02150 Espoo, Finland
| | - Kirsten Sandvig
- From the Department of Biochemistry, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, 0379 Oslo, Norway, the Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, 0379 Oslo, Norway, the Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Alicia Llorente
- From the Department of Biochemistry, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, 0379 Oslo, Norway, the Centre for Cancer Biomedicine, Faculty of Medicine, University of Oslo, 0379 Oslo, Norway,
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