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Kopczynski D, Ejsing CS, McDonald JG, Bamba T, Baker ES, Bertrand-Michel J, Brügger B, Coman C, Ellis SR, Garrett TJ, Griffiths WJ, Guan XL, Han X, Höring M, Holčapek M, Hoffmann N, Huynh K, Lehmann R, Jones JW, Kaddurah-Daouk R, Köfeler HC, Meikle PJ, Metz TO, O'Donnell VB, Saigusa D, Schwudke D, Shevchenko A, Torta F, Vizcaíno JA, Welti R, Wenk MR, Wolrab D, Xia Y, Ekroos K, Ahrends R, Liebisch G. The Lipidomics Reporting Checklist A framework for transparency of lipidomic experiments and repurposing resource data. J Lipid Res 2024:100621. [PMID: 39151590 DOI: 10.1016/j.jlr.2024.100621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 07/30/2024] [Accepted: 08/09/2024] [Indexed: 08/19/2024] Open
Abstract
The rapid increase in lipidomic studies has led to a collaborative effort within the community to establish standards and criteria for producing, documenting, and disseminating data. Creating a dynamic easy-to-use checklist that condenses key information about lipidomic experiments into common terminology will enhance the field's consistency, comparability, and repeatability. Here, we describe the structure and rationale of the established Lipidomics Minimal Reporting Checklist to increase transparency in lipidomics research.
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Affiliation(s)
- Dominik Kopczynski
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - 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
| | - Jeffrey G McDonald
- Center for Human Nutrition and Department of Molecular Genetics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Takeshi Bamba
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Erin S Baker
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Justine Bertrand-Michel
- MetaboHUB-Metatoul, National Infrastructure of Metabolomics and Fluxomics, Inserm I2MC, Toulouse, France
| | - Britta Brügger
- Heidelberg University Biochemistry Center (BZH), University of Heidelberg, Heidelberg, Germany
| | - Cristina Coman
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Shane R Ellis
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales, Australia
| | - Timothy J Garrett
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, United States
| | | | - Xue Li Guan
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
| | - Xianlin Han
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Marcus Höring
- Institute of Clinical Chemistry and Laboratory Medicine, University of Regensburg, Regensburg, Germany
| | - Michal Holčapek
- Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czech Republic
| | - Nils Hoffmann
- Institute for Bio- and Geosciences (IBG-5), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Kevin Huynh
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia; Department of Cardiovascular Research Translation and Implementation, La Trobe University, Bundoora, VIC, Australia
| | - Rainer Lehmann
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tuebingen, 72076 Tuebingen, Germany
| | - Jace W Jones
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland, United States
| | - Rima Kaddurah-Daouk
- Department of Psychiatry and Behavioural Sciences, Duke University, Durham, NC, USA; Duke Institute of Brain Sciences, Duke University, Durham, NC, USA; Department of Medicine, Duke University, Durham, NC, USA
| | - Harald C Köfeler
- Core Facility Mass Spectrometry and Lipidomics, ZMF, Medical University of Graz, Graz, Austria
| | - Peter J Meikle
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia; Department of Cardiovascular Research Translation and Implementation, La Trobe University, Bundoora, VIC, Australia
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States
| | - Valerie B O'Donnell
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, UK
| | - Daisuke Saigusa
- Laboratory of Biomedical and Analytical Sciences, Faculty of Pharma-Science, Teikyo University, Tokyo, Japan
| | - Dominik Schwudke
- Division of Bioanalytical Chemistry, Research Center Borstel - Leibniz Lung Center, Borstel, Germany; German Center for Infection Research, Thematic Translational Unit Tuberculosis, Partner Site Hamburg-Lübeck-Borstel-Riems, Germany; German Center for Lung Research (DZL), Airway Research Center North (ARCN), Borstel, Germany
| | - Andrej Shevchenko
- Max-Planck-Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Federico Torta
- Singapore Lipidomics Incubator (SLING), Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore, Singapore
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Ruth Welti
- Kansas Lipidomics Research Center, Division of Biology, Kansas State University, Manhattan, KS, USA
| | - Markus R Wenk
- Singapore Lipidomics Incubator (SLING), Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore, Singapore
| | - Denise Wolrab
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Yu Xia
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Kim Ekroos
- Lipidomics Consulting Ltd., Esbo, Finland.
| | - 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.
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2
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Bishop LM, Fiehn O. Comprehensive lipidomic profiling by plasma separation cards. Anal Bioanal Chem 2023; 415:193-201. [PMID: 36316462 PMCID: PMC10448968 DOI: 10.1007/s00216-022-04399-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/04/2022] [Accepted: 10/21/2022] [Indexed: 01/07/2023]
Abstract
Large-scale lipidomic analyses have been limited by the cost and accessibility of traditional venipuncture sampling. Microsampling techniques offer a less-invasive and more accessible alternative. From a single drop of blood, plasma separation cards (PSC) deliver two volumetric dried plasma samples which are studied here for profiling endogenous blood lipids. Six lots of EDTA-treated human whole blood were used to compare PSC, dried blood spot analyses (DBS), and classic wet plasma extractions. Six replicate extractions were performed for each lot. Nontargeted lipidomics was performed by liquid chromatography-high resolution tandem mass spectrometry. Lipids were annotated by accurate mass/retention time matching and MS/MS spectral library matching using peak intensities for quantitation. Four hundred ninety-eight compounds covering 24 lipid subclasses were annotated. Inter-lot repeatability was evaluated by the percent relative standard deviation (%RSD) for each lot, giving median %RSD values across the lots at 14.6% for PSC, 9.3% for DBS, and 8.6% for wet plasma. Strong correlations of lipid peak intensities between wet plasma and PSCs were observed, but less for DBS. Lipid recovery and stability were comparable between the PSC and DBS samples, with roughly 60% of annotated lipids stable at room temperature after 28 days. Overall, PSCs provide a better alternative for quantitative blood lipidomic analyses compared to dried blood spots. However, problems with lipid stability for samples handled and shipped at room temperature are currently unavoidable outside of a clinical setting. Data transferability and comparability to standard plasma is lipid and lipid class dependent.
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Affiliation(s)
- Lauren M Bishop
- Department of Chemistry, University of California Davis, Davis, CA, USA
- West Coast Metabolomics Center, University of California Davis, Davis, CA, USA
| | - Oliver Fiehn
- Department of Chemistry, University of California Davis, Davis, CA, USA.
- West Coast Metabolomics Center, University of California Davis, Davis, CA, USA.
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3
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da Silva KM, Iturrospe E, Bars C, Knapen D, Van Cruchten S, Covaci A, van Nuijs ALN. Mass Spectrometry-Based Zebrafish Toxicometabolomics: A Review of Analytical and Data Quality Challenges. Metabolites 2021; 11:metabo11090635. [PMID: 34564451 PMCID: PMC8467701 DOI: 10.3390/metabo11090635] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 12/17/2022] Open
Abstract
Metabolomics has achieved great progress over the last 20 years, and it is currently considered a mature research field. As a result, the number of applications in toxicology, biomarker, and drug discovery has also increased. Toxicometabolomics has emerged as a powerful strategy to provide complementary information to study molecular-level toxic effects, which can be combined with a wide range of toxicological assessments and models. The zebrafish model has gained importance in recent decades as a bridging tool between in vitro assays and mammalian in vivo studies in the field of toxicology. Furthermore, as this vertebrate model is a low-cost system and features highly conserved metabolic pathways found in humans and mammalian models, it is a promising tool for toxicometabolomics. This short review aims to introduce zebrafish researchers interested in understanding the effects of chemical exposure using metabolomics to the challenges and possibilities of the field, with a special focus on toxicometabolomics-based mass spectrometry. The overall goal is to provide insights into analytical strategies to generate and identify high-quality metabolomic experiments focusing on quality management systems (QMS) and the importance of data reporting and sharing.
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Affiliation(s)
- Katyeny Manuela da Silva
- Toxicological Center, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, Campus Drie Eiken, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; (E.I.); (A.C.)
- Correspondence: (K.M.d.S.); (A.L.N.v.N.)
| | - Elias Iturrospe
- Toxicological Center, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, Campus Drie Eiken, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; (E.I.); (A.C.)
- Department of In Vitro Toxicology and Dermato-Cosmetology, Faculty of Medicine and Pharmacy, Campus Jette, Free University of Brussels, Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Chloe Bars
- Comparative Perinatal Development, Department of Veterinary Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, Campus Drie Eiken, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; (C.B.); (S.V.C.)
| | - Dries Knapen
- Zebrafishlab, Veterinary Physiology and Biochemistry, Department of Veterinary Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, Campus Drie Eiken, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium;
| | - Steven Van Cruchten
- Comparative Perinatal Development, Department of Veterinary Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, Campus Drie Eiken, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; (C.B.); (S.V.C.)
| | - Adrian Covaci
- Toxicological Center, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, Campus Drie Eiken, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; (E.I.); (A.C.)
| | - Alexander L. N. van Nuijs
- Toxicological Center, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, Campus Drie Eiken, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium; (E.I.); (A.C.)
- Correspondence: (K.M.d.S.); (A.L.N.v.N.)
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Höring M, Krautbauer S, Hiltl L, Babl V, Sigruener A, Burkhardt R, Liebisch G. Accurate Lipid Quantification of Tissue Homogenates Requires Suitable Sample Concentration, Solvent Composition, and Homogenization Procedure-A Case Study in Murine Liver. Metabolites 2021; 11:365. [PMID: 34201055 PMCID: PMC8228350 DOI: 10.3390/metabo11060365] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 05/25/2021] [Accepted: 06/06/2021] [Indexed: 12/03/2022] Open
Abstract
Lipidomics aim to quantify lipid species in all kinds of samples, including tissues. To subject a fixed amount of sample to various workflows, tissue homogenates were frequently prepared at defined concentrations in water or by addition of organic solvents. Here, we investigated this first step of tissue lipidomics by quantitative flow injection analysis coupled to Fourier-Transform mass spectrometry (FTMS). The influence of sample concentration, solvent composition, and homogenization procedure on the recovery of lipids was studied in murine liver. Liver homogenates were prepared either by grinding tissue in liquid nitrogen or by bead-based homogenization. Ground samples were dissolved at different concentrations in water, methanol, and water/methanol = 1/1 (v/v). Here, lipid recovery depends on solvent composition and sample concentration. The recovery of nonpolar lipid classes, including triglycerides and cholesteryl ester, was decreased in methanolic homogenates. In contrast, due to superior dispersion of precipitates, bead-based homogenization resulted in efficient lipid recovery independent of the solvent composition. However, lipid distribution within samples, i.e., lipid content of supernatant and pellet following centrifugation, was altered substantially by solvent composition. In conclusion, accurate lipid quantification of tissue homogenates requires evaluation of solvent composition, sample concentration, as well as the homogenization method to guarantee efficient lipid recovery. Due to a potential loss of lipids, removal of precipitates by centrifugation prior to lipid extraction should be avoided.
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Affiliation(s)
| | | | | | | | | | | | - Gerhard Liebisch
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital of Regensburg, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany; (M.H.); (S.K.); (L.H.); (V.B.); (A.S.); (R.B.)
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5
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Application of Lipid Class Ratios for Sample Stability Monitoring-Evaluation of Murine Tissue Homogenates and SDS as a Stabilizer. Metabolites 2021; 11:metabo11050277. [PMID: 33925735 PMCID: PMC8146515 DOI: 10.3390/metabo11050277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/23/2021] [Accepted: 04/26/2021] [Indexed: 12/17/2022] Open
Abstract
Lipids are a ubiquitous class of structurally complex molecules involved in various biological processes. In the fast-growing field of lipidomics, preanalytical issues are frequently neglected. Here, we investigated the stability of lipid profiles of murine liver, brain, lung, heart, and spleen homogenates by quantitative flow injection analysis using tandem mass spectrometry and high-resolution mass spectrometry. Storage of tissue homogenates at room temperature showed substantial alterations of the lipid profiles reflecting lipolytic action. Therefore, ratios of ceramide to sphingomyelin, lysophosphatidylethanolamine to phosphatidylethanolamine, lysophosphatidylcholine to phosphatidylcholine, and diglyceride to triglyceride were applied to monitor sample stability and the effect of sodium dodecyl sulfate (SDS) as a potential stabilizing agent. The addition of SDS led to a concentration-dependent stabilization of lipid profiles in liver, brain, and heart homogenates, while in lung and spleen homogenates, in particular, the lysophosphatidylethanolamine to phosphatidylethanolamine ratio increased upon addition of SDS. In conclusion, we demonstrated that lipid class ratios reflecting lipolytic activity could be applied to evaluate both the stability of samples and the influence of stabilizers.
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Jain D, Torres R, Celli R, Koelmel J, Charkoftaki G, Vasiliou V. Evolution of the liver biopsy and its future. Transl Gastroenterol Hepatol 2021; 6:20. [PMID: 33824924 PMCID: PMC7829074 DOI: 10.21037/tgh.2020.04.01] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 03/19/2020] [Indexed: 12/12/2022] Open
Abstract
Liver biopsies are commonly used to evaluate a wide variety of medical disorders, including neoplasms and post-transplant complications. However, its use is being impacted by improved clinical diagnosis of disorders, and non-invasive methods for evaluating liver tissue and as a result the indications of a liver biopsy have undergone major changes in the last decade. The evolution of highly effective treatments for some of the common indications for liver biopsy in the last decade (e.g., viral hepatitis B and C) has led to a decline in the number of liver biopsies in recent years. At the same time, the emergence of better technologies for histologic evaluation, tissue content analysis and genomics are among the many new and exciting developments in the field that hold great promise for the future and are going to shape the indications for a liver biopsy in the future. Recent advances in slide scanners now allow creation of "digital/virtual" slides that have image of the entire tissue section present in a slide [whole slide imaging (WSI)]. WSI can now be done very rapidly and at very high resolution, allowing its use in routine clinical practice. In addition, a variety of technologies have been developed in recent years that use different light sources and/or microscopes allowing visualization of tissues in a completely different way. One such technique that is applicable to liver specimens combines multiphoton microscopy (MPM) with advanced clearing and fluorescent stains known as Clearing Histology with MultiPhoton Microscopy (CHiMP). Although it has not yet been extensively validated, the technique has the potential to decrease inefficiency, reduce artifacts, and increase data while being readily integrable into clinical workflows. Another technology that can provide rapid and in-depth characterization of thousands of molecules in a tissue sample, including liver tissues, is matrix assisted laser desorption/ionization (MALDI) mass spectrometry. MALDI has already been applied in a clinical research setting with promising diagnostic and prognostic capabilities, as well as being able to elucidate mechanisms of liver diseases that may be targeted for the development of new therapies. The logical next step in huge data sets obtained from such advanced analysis of liver tissues is the application of machine learning (ML) algorithms and application of artificial intelligence (AI), for automated generation of diagnoses and prognoses. This review discusses the evolving role of liver biopsies in clinical practice over the decades, and describes newer technologies that are likely to have a significant impact on how they will be used in the future.
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Affiliation(s)
- Dhanpat Jain
- Department of Anatomic Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Richard Torres
- Department of Laboratory Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Romulo Celli
- Department of Anatomic Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Jeremy Koelmel
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Georgia Charkoftaki
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, USA
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7
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Fabri JHTM, de Sá NP, Malavazi I, Del Poeta M. The dynamics and role of sphingolipids in eukaryotic organisms upon thermal adaptation. Prog Lipid Res 2020; 80:101063. [PMID: 32888959 DOI: 10.1016/j.plipres.2020.101063] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 08/18/2020] [Accepted: 08/27/2020] [Indexed: 01/09/2023]
Abstract
All living beings have an optimal temperature for growth and survival. With the advancement of global warming, the search for understanding adaptive processes to climate changes has gained prominence. In this context, all living beings monitor the external temperature and develop adaptive responses to thermal variations. These responses ultimately change the functioning of the cell and affect the most diverse structures and processes. One of the first structures to detect thermal variations is the plasma membrane, whose constitution allows triggering of intracellular signals that assist in the response to temperature stress. Although studies on this topic have been conducted, the underlying mechanisms of recognizing thermal changes and modifying cellular functioning to adapt to this condition are not fully understood. Recently, many reports have indicated the participation of sphingolipids (SLs), major components of the plasma membrane, in the regulation of the thermal stress response. SLs can structurally reinforce the membrane or/and send signals intracellularly to control numerous cellular processes, such as apoptosis, cytoskeleton polarization, cell cycle arresting and fungal virulence. In this review, we discuss how SLs synthesis changes during both heat and cold stresses, focusing on fungi, plants, animals and human cells. The role of lysophospholipids is also discussed.
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Affiliation(s)
- João Henrique Tadini Marilhano Fabri
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA; Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Nivea Pereira de Sá
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA
| | - Iran Malavazi
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Maurizio Del Poeta
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, New York, USA; Division of Infectious Diseases, School of Medicine, Stony Brook University, Stony Brook, New York, USA; Veterans Administration Medical Center, Northport, New York, USA.
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8
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Ulmer CZ, Koelmel JP, Jones CM, Garrett TJ, Aristizabal-Henao JJ, Vesper HW, Bowden JA. A Review of Efforts to Improve Lipid Stability during Sample Preparation and Standardization Efforts to Ensure Accuracy in the Reporting of Lipid Measurements. Lipids 2020; 56:3-16. [PMID: 32519378 DOI: 10.1002/lipd.12263] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 05/03/2020] [Accepted: 05/19/2020] [Indexed: 11/07/2022]
Abstract
Lipidomics is a rapidly growing field, fueled by developments in analytical instrumentation and bioinformatics. To date, most researchers and industries have employed their own lipidomics workflows without a consensus on best practices. Without a community-wide consensus on best practices for the prevention of lipid degradation and transformations through sample collection and analysis, it is difficult to assess the quality of lipidomics data and hence trust results. Clinical studies often rely on samples being stored for weeks or months until they are analyzed, but inappropriate sampling techniques, storage temperatures, and analytical protocols can result in the degradation of complex lipids and the generation of oxidized or hydrolyzed metabolite artifacts. While best practices for lipid stability are sample dependent, it is generally recommended that strategies during sample preparation capable of quenching enzymatic activity and preventing oxidation should be considered. In addition, after sample preparation, lipid extracts should be stored in organic solvents with antioxidants at -20 °C or lower in an airtight container without exposure to light or oxygen. This will reduce or eliminate sublimation, and chemically and physically induced molecular transformations such as oxidation, enzymatic transformation, and photon/heat-induced degradation. This review explores the available literature on lipid stability, with a particular focus on human health and/or clinical lipidomic applications. Specifically, this includes a description of known mechanisms of lipid degradation, strategies, and considerations for lipid storage, as well as current efforts for standardization and quality insurance of protocols.
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Affiliation(s)
- Candice Z Ulmer
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Hwy NE, MS F25, Atlanta, GA, 30341, USA
| | - Jeremy P Koelmel
- Department of Environmental Health Sciences, Yale School of Medicine, Yale University, 60 College Street, Room 510, New Haven, CT, 06520, USA
| | - Christina M Jones
- Chemical Sciences Division, Organic Chemical Metrology Group, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899, USA
| | - Timothy J Garrett
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Juan J Aristizabal-Henao
- Center for Environmental and Human Toxicology & Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Hubert W Vesper
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention, 4770 Buford Hwy NE, MS F25, Atlanta, GA, 30341, USA
| | - John A Bowden
- Center for Environmental and Human Toxicology & Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32611, USA
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9
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Koelmel JP, Napolitano MP, Ulmer CZ, Vasiliou V, Garrett TJ, Yost RA, Prasad MNV, Godri Pollitt KJ, Bowden JA. Environmental lipidomics: understanding the response of organisms and ecosystems to a changing world. Metabolomics 2020; 16:56. [PMID: 32307636 DOI: 10.1007/s11306-020-01665-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 03/13/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND Understanding the interaction between organisms and the environment is important for predicting and mitigating the effects of global phenomena such as climate change, and the fate, transport, and health effects of anthropogenic pollutants. By understanding organism and ecosystem responses to environmental stressors at the molecular level, mechanisms of toxicity and adaptation can be determined. This information has important implications in human and environmental health, engineering biotechnologies, and understanding the interaction between anthropogenic induced changes and the biosphere. One class of molecules with unique promise for environmental science are lipids; lipids are highly abundant and ubiquitous across nearly all organisms, and lipid profiles often change drastically in response to external stimuli. These changes allow organisms to maintain essential biological functions, for example, membrane fluidity, as they adapt to a changing climate and chemical environment. Lipidomics can help scientists understand the historical and present biofeedback processes in climate change and the biogeochemical processes affecting nutrient cycles. Lipids can also be used to understand how ecosystems respond to historical environmental changes with lipid signatures dating back to hundreds of millions of years, which can help predict similar changes in the future. In addition, lipids are direct targets of environmental stressors, for example, lipids are easily prone to oxidative damage, which occurs during exposure to most toxins. AIM OF REVIEW This is the first review to summarize the current efforts to comprehensively measure lipids to better understand the interaction between organisms and their environment. This review focuses on lipidomic applications in the arenas of environmental toxicology and exposure assessment, xenobiotic exposures and health (e.g., obesity), global climate change, and nutrient cycles. Moreover, this review summarizes the use of and the potential for lipidomics in engineering biotechnologies for the remediation of persistent compounds and biofuel production. KEY SCIENTIFIC CONCEPT With the preservation of certain lipids across millions of years and our ever-increasing understanding of their diverse biological roles, lipidomic-based approaches provide a unique utility to increase our understanding of the contemporary and historical interactions between organisms, ecosystems, and anthropogenically-induced environmental changes.
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Affiliation(s)
- Jeremy P Koelmel
- Department of Chemistry, University of Florida, 125 Buckman Drive, Gainesville, FL, 32611, USA
- Department of Environmental Health Sciences, School of Public Health, Yale University, New Haven, CT, 06510, USA
| | - Michael P Napolitano
- CSS, Inc., under contract to National Oceanic and Atmospheric Administration, National Centers for Coastal Ocean Science, Hollings Marine Laboratory, 331 Fort Johnson Road, Charleston, SC, 29412, USA
| | - Candice Z Ulmer
- National Institute of Standards and Technology, Hollings Marine Laboratory, 331 Ft. Johnson Road, Charleston, SC, 29412, USA
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, School of Public Health, Yale University, New Haven, CT, 06510, USA
| | - Timothy J Garrett
- Department of Chemistry, University of Florida, 125 Buckman Drive, Gainesville, FL, 32611, USA
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - Richard A Yost
- Department of Chemistry, University of Florida, 125 Buckman Drive, Gainesville, FL, 32611, USA
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, 32610, USA
| | - M N V Prasad
- Department of Plant Sciences, University of Hyderabad, Hyderabad, Telangana, 500046, India
| | - Krystal J Godri Pollitt
- Department of Environmental Health Sciences, School of Public Health, Yale University, New Haven, CT, 06510, USA
| | - John A Bowden
- Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, 1333 Center Drive, Gainesville, FL, 32610, USA.
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Giles C, Takechi R, Lam V, Dhaliwal SS, Mamo JCL. Contemporary lipidomic analytics: opportunities and pitfalls. Prog Lipid Res 2018; 71:86-100. [PMID: 29959947 DOI: 10.1016/j.plipres.2018.06.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 05/18/2018] [Accepted: 06/26/2018] [Indexed: 01/08/2023]
Abstract
Recent advances in analytical techniques have greatly enhanced the depth of coverage, however lipidomic studies are still restricted to analysing only a subset of known lipids. Numerous complementary techniques are used for investigation of cellular lipidomes, including mass spectrometry (MS), nuclear magnetic resonance and vibrational spectroscopy. The development in electrospray ionization (ESI) MS has accelerated lipidomics research in the past two decades and represents one of the most widely used technique. The versatility of ESI-MS systems allows development of methods to detect and quantify a large diversity of lipid species and classes. However, highly targeted and specific approaches can preclude global analysis of many lipid classes. Indeed, experimental procedures are generally optimised for the lipid species, or lipid class of interest. Therefore, careful consideration of experimental procedures is required for characterisation of biological lipidomes. The current review will describe the lipidomic approaches for considering tissue lipid physiology. Discussion of the main sequences in a lipidomics workflow will be presented, including preparation of samples, accurate quantitation of lipid species and statistical modelling.
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Affiliation(s)
- Corey Giles
- Curtin Health Innovation Research Institute, Curtin University, WA, Australia; School of Public Health, Faculty of Health Sciences, Curtin University, WA, Australia
| | - Ryusuke Takechi
- Curtin Health Innovation Research Institute, Curtin University, WA, Australia; School of Public Health, Faculty of Health Sciences, Curtin University, WA, Australia
| | - Virginie Lam
- Curtin Health Innovation Research Institute, Curtin University, WA, Australia; School of Public Health, Faculty of Health Sciences, Curtin University, WA, Australia
| | - Satvinder S Dhaliwal
- Curtin Health Innovation Research Institute, Curtin University, WA, Australia; School of Public Health, Faculty of Health Sciences, Curtin University, WA, Australia
| | - John C L Mamo
- Curtin Health Innovation Research Institute, Curtin University, WA, Australia; School of Public Health, Faculty of Health Sciences, Curtin University, WA, Australia.
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Bioanalytical techniques in lipidomics. Bioanalysis 2018. [DOI: 10.4155/bio-2018-0020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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