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Hao M, Yi L, Cheng W, Zhu J, Zhao S. Lipidomics analysis reveals new insights into crisp grass carp associated with meat texture. Heliyon 2024; 10:e32179. [PMID: 38868033 PMCID: PMC11168433 DOI: 10.1016/j.heliyon.2024.e32179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 05/22/2024] [Accepted: 05/29/2024] [Indexed: 06/14/2024] Open
Abstract
Feeding faba beans to grass carp could crisp its muscle texture to avoid softening, the relationship between texture formation throughout the crisping process and the critical lipids regulating the fish quality has not yet been clarified. Herein, an 60-day nutritional trial and untargeted lipidomic analysis was used to study the changes of lipids in crisp grass carp dorsal muscle. A total of 1036 lipids were remarkably different between ordinary and crisp grass carp. The concentrations of the LPC, LPE, PG, Cer, Hex2Cer, SM, MG and MGMG were positively correlated with hardness and springiness, and the CL, TG, PMe, WE, dMePE and AcCa were negative correlation. High content of lipids involved in storage in ordinary grass carp, such as glycerophospholipids, polyunsaturated and saturated fatty acid content. In contrast, high content of membrane components in crisp grass carp, such as monounsaturated fatty acid, sphingolipid and glycerolipids content, and the distribution of PUFA in lipid molecules was related to lipid biosynthesis. This study might provide some insights into improved knowledge of the association between meat texture and lipid molecules in fish fed with faba bean.
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Affiliation(s)
- Meilin Hao
- College of Biology and Agriculture (College of Food Science and Technology), Zunyi Normal College, Zunyi, 563006, China
| | - Lanlan Yi
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Wenjie Cheng
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Junhong Zhu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Sumei Zhao
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
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2
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Solosky AM, Kirkwood-Donelson KI, Odenkirk MT, Baker ES. Recent additions and access to a multidimensional lipidomic database containing liquid chromatography, ion mobility spectrometry, and tandem mass spectrometry information. Anal Bioanal Chem 2024:10.1007/s00216-024-05351-4. [PMID: 38814344 DOI: 10.1007/s00216-024-05351-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 05/14/2024] [Accepted: 05/16/2024] [Indexed: 05/31/2024]
Abstract
The importance of lipids in biology continues to grow with their recent linkages to more diseases and conditions, microbiome fluctuations, and environmental exposures. These associations have motivated researchers to evaluate lipidomic changes in numerous matrices and studies. Lipidomic analyses, however, present numerous challenges as lipid species have broad chemistries that require different extraction methods and instrumental analyses to evaluate and separate their many isomers and isobars. Increasing knowledge about different lipid characteristics is therefore crucial for improving their separation and identification. Here, we present a multidimensional database for lipids analyzed on a platform combining reversed-phase liquid chromatography, drift tube ion mobility spectrometry, collision-induced dissociation, and mass spectrometry (RPLC-DTIMS-CID-MS). This platform and the different separation characteristics it provides enables more confident lipid annotations when compared to traditional tandem mass spectrometry platforms, especially when analyzing highly isomeric molecules such as lipids. This database expands on our previous publication containing only human plasma and bronchoalveolar lavage fluid lipids and provides experimental RPLC retention times, IMS collision cross section (CCS) values, and m/z information for 877 unique lipids from additional biofluids and tissues. Specifically, the database contains 1504 precursor [M + H]+, [M + NH4]+, [M + Na]+, [M-H]-, [M-2H]2-, [M + HCOO]-, and [M + CH3COO]- ion species and their associated CID fragments which are commonly targeted in clinical and environmental studies, in addition to being present in the chloroform layer of Folch extractions. Furthermore, this multidimensional RPLC-DTIMS-CID-MS database spans 5 lipid categories (fatty acids, sterols, sphingolipids, glycerolipids, and glycerophospholipids) and 24 lipid classes. We have also created a webpage (tarheels.live/bakerlab/databases/) to enhance the accessibility of this resource which will be populated regularly with new lipids as we identify additional species and integrate novel standards.
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Affiliation(s)
- Amie M Solosky
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kaylie I Kirkwood-Donelson
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, Durham, NC, USA
| | - Melanie T Odenkirk
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO, USA
| | - Erin S Baker
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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3
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Anderson BJ, Brademan DR, He Y, Overmyer KA, Coon JJ. LipiDex 2 Integrates MS n Tree-Based Fragmentation Methods and Quality Control Modules to Improve Discovery Lipidomics. Anal Chem 2024; 96:6715-6723. [PMID: 38640432 DOI: 10.1021/acs.analchem.4c00359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2024]
Abstract
As lipidomics experiments increase in scale and complexity, data processing tools must support workflows for new liquid chromatography-mass spectrometry (LC-MS) methods while simultaneously supporting quality controls to maximize the confidence in lipid identifications. LipiDex 2 improves lipidomics data processing algorithms from LipiDex 1 and introduces new tools for spectral matching and peak annotation functions, with improvements in speed and user-friendliness. In silico spectral library generation now supports tandem mass spectral (MSn) tree-based fragmentation methods, and the LipiDex 2 workflow fully integrates the fragmentation logic into the data processing steps to enable lipid identification at the appropriate level of structural resolution. Finally, LipiDex 2 features new modules for automated quality control checks that also allow users to visualize data quality in a data dashboard user interface.
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Affiliation(s)
- Benton J Anderson
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Dain R Brademan
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Yuchen He
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Katherine A Overmyer
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Joshua J Coon
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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4
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Witting M, Malik A, Leach A, Bridge A, Aimo L, Conroy MJ, O'Donnell VB, Hoffmann N, Kopczynski D, Giacomoni F, Paulhe N, Gassiot AC, Poupin N, Jourdan F, Bertrand-Michel J. Challenges and perspectives for naming lipids in the context of lipidomics. Metabolomics 2024; 20:15. [PMID: 38267595 PMCID: PMC10808356 DOI: 10.1007/s11306-023-02075-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/01/2023] [Indexed: 01/26/2024]
Abstract
INTRODUCTION Lipids are key compounds in the study of metabolism and are increasingly studied in biology projects. It is a very broad family that encompasses many compounds, and the name of the same compound may vary depending on the community where they are studied. OBJECTIVES In addition, their structures are varied and complex, which complicates their analysis. Indeed, the structural resolution does not always allow a complete level of annotation so the actual compound analysed will vary from study to study and should be clearly stated. For all these reasons the identification and naming of lipids is complicated and very variable from one study to another, it needs to be harmonized. METHODS & RESULTS In this position paper we will present and discuss the different way to name lipids (with chemoinformatic and semantic identifiers) and their importance to share lipidomic results. CONCLUSION Homogenising this identification and adopting the same rules is essential to be able to share data within the community and to map data on functional networks.
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Affiliation(s)
- Michael Witting
- Metabolomics and Proteomics Core, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
- Chair of Analytical Food Chemistry, TUM School of Life Sciences, Technical University of Munich, Maximus-von-Imhof-Forum 2, 85354, Freising-Weihenstephan, Germany
| | - Adnan Malik
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Andrew Leach
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Alan Bridge
- SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1211, Geneva 4, Switzerland
| | - Lucila Aimo
- SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1211, Geneva 4, Switzerland
| | - Matthew J Conroy
- Division of Infection and Immunity, Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Valerie B O'Donnell
- Division of Infection and Immunity, Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Nils Hoffmann
- Institute for Bio- and Geosciences (IBG-5), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Dominik Kopczynski
- Institute for Analytical Chemistry, Universität Wien, Währingerstrasse 38, 1090, Vienna, Austria
| | - Franck Giacomoni
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
- MetaboHUB, National Infrastructure of Metabolomics and Fluxomics ANR-11-INBS-0010, 31077, Toulouse, France
| | - Nils Paulhe
- Université Clermont Auvergne, INRAE, UNH, Plateforme d'Exploration du Métabolisme, MetaboHUB Clermont, Clermont-Ferrand, France
- MetaboHUB, National Infrastructure of Metabolomics and Fluxomics ANR-11-INBS-0010, 31077, Toulouse, France
| | - Amaury Cazenave Gassiot
- Singapore Lipidomics Incubator, Life Sciences Institute, and Precision Medicine TRP, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Nathalie Poupin
- UMR1331 Toxalim, Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Fabien Jourdan
- MetaboHUB, National Infrastructure of Metabolomics and Fluxomics ANR-11-INBS-0010, 31077, Toulouse, France
- UMR1331 Toxalim, Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, Toulouse, France
| | - Justine Bertrand-Michel
- MetaboHUB, National Infrastructure of Metabolomics and Fluxomics ANR-11-INBS-0010, 31077, Toulouse, France.
- I2MC, Inserm U1297, Université de Toulouse, Toulouse, France.
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5
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Kale D, Fatangare A, Phapale P, Sickmann A. Blood-Derived Lipid and Metabolite Biomarkers in Cardiovascular Research from Clinical Studies: A Recent Update. Cells 2023; 12:2796. [PMID: 38132115 PMCID: PMC10741540 DOI: 10.3390/cells12242796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/24/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023] Open
Abstract
The primary prevention, early detection, and treatment of cardiovascular disease (CVD) have been long-standing scientific research goals worldwide. In the past decades, traditional blood lipid profiles have been routinely used in clinical practice to estimate the risk of CVDs such as atherosclerotic cardiovascular disease (ASCVD) and as treatment targets for the primary prevention of adverse cardiac events. These blood lipid panel tests often fail to fully predict all CVD risks and thus need to be improved. A comprehensive analysis of molecular species of lipids and metabolites (defined as lipidomics and metabolomics, respectively) can provide molecular insights into the pathophysiology of the disease and could serve as diagnostic and prognostic indicators of disease. Mass spectrometry (MS) and nuclear magnetic resonance (NMR)-based lipidomics and metabolomics analysis have been increasingly used to study the metabolic changes that occur during CVD pathogenesis. In this review, we provide an overview of various MS-based platforms and approaches that are commonly used in lipidomics and metabolomics workflows. This review summarizes the lipids and metabolites in human plasma/serum that have recently (from 2018 to December 2022) been identified as promising CVD biomarkers. In addition, this review describes the potential pathophysiological mechanisms associated with candidate CVD biomarkers. Future studies focused on these potential biomarkers and pathways will provide mechanistic clues of CVD pathogenesis and thus help with the risk assessment, diagnosis, and treatment of CVD.
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Affiliation(s)
- Dipali Kale
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44139 Dortmund, Germany; (A.F.); (P.P.)
| | | | | | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., 44139 Dortmund, Germany; (A.F.); (P.P.)
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6
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Shing K, Sapp E, Boudi A, Liu S, Seeley C, Marchionini D, DiFiglia M, Kegel-Gleason KB. Early whole-body mutant huntingtin lowering averts changes in proteins and lipids important for synapse function and white matter maintenance in the LacQ140 mouse model. Neurobiol Dis 2023; 187:106313. [PMID: 37777020 PMCID: PMC10731584 DOI: 10.1016/j.nbd.2023.106313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/02/2023] Open
Abstract
Expansion of a triplet repeat tract in exon 1 of the HTT gene causes Huntington's disease (HD). The mutant HTT protein (mHTT) has numerous aberrant interactions with diverse, pleiomorphic effects. Lowering mHTT is a promising approach to treat HD, but it is unclear when lowering should be initiated, how much is necessary, and what duration should occur to achieve benefits. Furthermore, the effects of mHTT lowering on brain lipids have not been assessed. Using a mHtt-inducible mouse model, we analyzed mHtt lowering initiated at different ages and sustained for different time-periods. mHTT protein in cytoplasmic and synaptic compartments of the striatum was reduced 38-52%; however, there was minimal lowering of mHTT in nuclear and perinuclear regions where aggregates formed at 12 months of age. Total striatal lipids were reduced in 9-month-old LacQ140 mice and preserved by mHtt lowering. Subclasses important for white matter structure and function including ceramide (Cer), sphingomyelin (SM), and monogalactosyldiacylglycerol (MGDG), contributed to the reduction in total lipids. Phosphatidylinositol (PI), phosphatidylserine (PS), and bismethyl phosphatidic acid (BisMePA) were also changed in LacQ140 mice. Levels of all subclasses except ceramide were preserved by mHtt lowering. mRNA expression profiling indicated that a transcriptional mechanism contributes to changes in myelin lipids, and some but not all changes can be prevented by mHtt lowering. Our findings suggest that early and sustained reduction in mHtt can prevent changes in levels of select striatal proteins and most lipids, but a misfolded, degradation-resistant form of mHTT hampers some benefits in the long term.
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Affiliation(s)
- Kai Shing
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Ellen Sapp
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Adel Boudi
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Sophia Liu
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | - Connor Seeley
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA
| | | | - Marian DiFiglia
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA 02129, USA
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7
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Menzel JP, Young RSE, Benfield AH, Scott JS, Wongsomboon P, Cudlman L, Cvačka J, Butler LM, Henriques ST, Poad BLJ, Blanksby SJ. Ozone-enabled fatty acid discovery reveals unexpected diversity in the human lipidome. Nat Commun 2023; 14:3940. [PMID: 37402773 DOI: 10.1038/s41467-023-39617-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 06/15/2023] [Indexed: 07/06/2023] Open
Abstract
Fatty acid isomers are responsible for an under-reported lipidome diversity across all kingdoms of life. Isomers of unsaturated fatty acids are often masked in contemporary analysis by incomplete separation and the absence of sufficiently diagnostic methods for structure elucidation. Here, we introduce a comprehensive workflow, to discover unsaturated fatty acids through coupling liquid chromatography and mass spectrometry with gas-phase ozonolysis of double bonds. The workflow encompasses semi-automated data analysis and enables de novo identification in complex media including human plasma, cancer cell lines and vernix caseosa. The targeted analysis including ozonolysis enables structural assignment over a dynamic range of five orders of magnitude, even in instances of incomplete chromatographic separation. Thereby we expand the number of identified plasma fatty acids two-fold, including non-methylene-interrupted fatty acids. Detection, without prior knowledge, allows discovery of non-canonical double bond positions. Changes in relative isomer abundances reflect underlying perturbations in lipid metabolism.
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Affiliation(s)
- Jan Philipp Menzel
- School of Chemistry and Physics, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Centre for Materials Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Centre for Data Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Institute of Clinical Chemistry, Inselspital, Bern University Hospital, 3010, Bern, Switzerland
| | - Reuben S E Young
- School of Chemistry and Physics, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Centre for Materials Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Faculty of Science, Medicine and Health, School of Chemistry and Molecular Bioscience, Wollongong, NSW, Australia
| | - Aurélie H Benfield
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Translational Research Institute, Brisbane, QLD, 4102, Australia
| | - Julia S Scott
- South Australian Immunogenomics Cancer Institute and Freemasons Centre for Male Health and Wellbeing, University of Adelaide, Adelaide, SA, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Puttandon Wongsomboon
- School of Chemistry and Physics, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Centre for Materials Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Lukáš Cudlman
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 542/2, 16600, Prague, Czech Republic
- Department of Analytical Chemistry, Faculty of Science, Charles University, Prague 2, Czech Republic
| | - Josef Cvačka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 542/2, 16600, Prague, Czech Republic
- Department of Analytical Chemistry, Faculty of Science, Charles University, Prague 2, Czech Republic
| | - Lisa M Butler
- South Australian Immunogenomics Cancer Institute and Freemasons Centre for Male Health and Wellbeing, University of Adelaide, Adelaide, SA, Australia
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
| | - Sónia T Henriques
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Translational Research Institute, Brisbane, QLD, 4102, Australia
| | - Berwyck L J Poad
- School of Chemistry and Physics, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Centre for Materials Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Stephen J Blanksby
- School of Chemistry and Physics, Queensland University of Technology, Brisbane, QLD, 4000, Australia.
- Centre for Materials Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia.
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8
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Manz KE, Feerick A, Braun JM, Feng YL, Hall A, Koelmel J, Manzano C, Newton SR, Pennell KD, Place BJ, Godri Pollitt KJ, Prasse C, Young JA. Non-targeted analysis (NTA) and suspect screening analysis (SSA): a review of examining the chemical exposome. JOURNAL OF EXPOSURE SCIENCE & ENVIRONMENTAL EPIDEMIOLOGY 2023; 33:524-536. [PMID: 37380877 PMCID: PMC10403360 DOI: 10.1038/s41370-023-00574-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/30/2023]
Abstract
Non-targeted analysis (NTA) and suspect screening analysis (SSA) are powerful techniques that rely on high-resolution mass spectrometry (HRMS) and computational tools to detect and identify unknown or suspected chemicals in the exposome. Fully understanding the chemical exposome requires characterization of both environmental media and human specimens. As such, we conducted a review to examine the use of different NTA and SSA methods in various exposure media and human samples, including the results and chemicals detected. The literature review was conducted by searching literature databases, such as PubMed and Web of Science, for keywords, such as "non-targeted analysis", "suspect screening analysis" and the exposure media. Sources of human exposure to environmental chemicals discussed in this review include water, air, soil/sediment, dust, and food and consumer products. The use of NTA for exposure discovery in human biospecimen is also reviewed. The chemical space that has been captured using NTA varies by media analyzed and analytical platform. In each media the chemicals that were frequently detected using NTA were: per- and polyfluoroalkyl substances (PFAS) and pharmaceuticals in water, pesticides and polyaromatic hydrocarbons (PAHs) in soil and sediment, volatile and semi-volatile organic compounds in air, flame retardants in dust, plasticizers in consumer products, and plasticizers, pesticides, and halogenated compounds in human samples. Some studies reviewed herein used both liquid chromatography (LC) and gas chromatography (GC) HRMS to increase the detected chemical space (16%); however, the majority (51%) only used LC-HRMS and fewer used GC-HRMS (32%). Finally, we identify knowledge and technology gaps that must be overcome to fully assess potential chemical exposures using NTA. Understanding the chemical space is essential to identifying and prioritizing gaps in our understanding of exposure sources and prior exposures. IMPACT STATEMENT: This review examines the results and chemicals detected by analyzing exposure media and human samples using high-resolution mass spectrometry based non-targeted analysis (NTA) and suspect screening analysis (SSA).
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Affiliation(s)
- Katherine E Manz
- School of Engineering, Brown University, Providence, RI, 02912, USA.
| | - Anna Feerick
- Agricultural & Environmental Chemistry Graduate Group, University of California, Davis, Davis, CA, 95616, USA
| | - Joseph M Braun
- Department of Epidemiology, Brown University, Providence, RI, 02912, USA
| | - Yong-Lai Feng
- Exposure and Biomonitoring Division, Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, Canada
| | - Amber Hall
- Department of Epidemiology, Brown University, Providence, RI, 02912, USA
| | - Jeremy Koelmel
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, 06520, USA
| | - Carlos Manzano
- Department of Chemistry, Faculty of Science, University of Chile, Santiago, RM, Chile
- School of Public Health, San Diego State University, San Diego, CA, USA
| | - Seth R Newton
- Office of Research and Development, U.S. Environmental Protection Agency, Washington, DC, USA
| | - Kurt D Pennell
- School of Engineering, Brown University, Providence, RI, 02912, USA
| | - Benjamin J Place
- National Institute of Standards and Technology, 100 Bureau Dr, Gaithersburg, MD, 20899, USA
| | - Krystal J Godri Pollitt
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT, 06520, USA
| | - Carsten Prasse
- Department of Environmental Health & Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA
- Risk Sciences and Public Policy Institute, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Joshua A Young
- Division of Biology, Chemistry and Materials Science, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, Food and Drug Administration, Silver Spring, MD, 20993, USA
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9
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Wang W, Rong Z, Wang G, Hou Y, Yang F, Qiu M. Cancer metabolites: promising biomarkers for cancer liquid biopsy. Biomark Res 2023; 11:66. [PMID: 37391812 DOI: 10.1186/s40364-023-00507-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/27/2023] [Indexed: 07/02/2023] Open
Abstract
Cancer exerts a multitude of effects on metabolism, including the reprogramming of cellular metabolic pathways and alterations in metabolites that facilitate inappropriate proliferation of cancer cells and adaptation to the tumor microenvironment. There is a growing body of evidence suggesting that aberrant metabolites play pivotal roles in tumorigenesis and metastasis, and have the potential to serve as biomarkers for personalized cancer therapy. Importantly, high-throughput metabolomics detection techniques and machine learning approaches offer tremendous potential for clinical oncology by enabling the identification of cancer-specific metabolites. Emerging research indicates that circulating metabolites have great promise as noninvasive biomarkers for cancer detection. Therefore, this review summarizes reported abnormal cancer-related metabolites in the last decade and highlights the application of metabolomics in liquid biopsy, including detection specimens, technologies, methods, and challenges. The review provides insights into cancer metabolites as a promising tool for clinical applications.
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Affiliation(s)
- Wenxiang Wang
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China
- Peking University People's Hospital Thoracic Oncology Institute, Beijing, 100044, China
| | - Zhiwei Rong
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University Health Science Center, Beijing, 100191, China
| | - Guangxi Wang
- Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yan Hou
- Department of Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
- Clinical Research Center, Peking University, Beijing, 100191, China
| | - Fan Yang
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China.
- Peking University People's Hospital Thoracic Oncology Institute, Beijing, 100044, China.
| | - Mantang Qiu
- Department of Thoracic Surgery, Peking University People's Hospital, Beijing, 100044, China.
- Peking University People's Hospital Thoracic Oncology Institute, Beijing, 100044, China.
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10
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Munjoma N, Isaac G, Muazzam A, Cexus O, Azhar F, Pandha H, Whetton AD, Townsend PA, Wilson ID, Gethings LA, Plumb RS. High Throughput LC-MS Platform for Large Scale Screening of Bioactive Polar Lipids in Human Plasma and Serum. J Proteome Res 2022; 21:2596-2608. [PMID: 36264332 DOI: 10.1021/acs.jproteome.2c00297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lipids play a key role in many biological processes, and their accurate measurement is critical to unraveling the biology of diseases and human health. A high throughput HILIC-based (LC-MS) method for the semiquantitative screening of over 2000 lipids, based on over 4000 MRM transitions, was devised to produce an accessible and robust lipidomic screen for phospholipids in human plasma/serum. This methodology integrates many of the advantages of global lipid analysis with those of targeted approaches. Having used the method as an initial "wide class" screen, it can then be easily adapted for a more targeted analysis and quantification of key, dysregulated lipids. Robustness was assessed using 1550 continuous injections of plasma extracts onto a single column and via the evaluation of columns from 5 different batches of stationary phase. Initial screens in positive (239 lipids, 431 MRM transitions) and negative electrospray ionization (ESI) mode (232 lipids, 446 MRM transitions) were assessed for reproducibility, sensitivity, and dynamic range using analysis times of 8 min. The total number of lipids monitored using these screening methods was 433 with an overlap of 38 lipids in both modes. A polarity switching method for accurate quantification, using the same LC conditions, was assessed for intra- and interday reproducibility, accuracy, dynamic range, stability, carryover, dilution integrity, and matrix interferences and found to be acceptable. This polarity switching method was then applied to lipids important in the stratification of human prostate cancer samples.
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Affiliation(s)
- Nyasha Munjoma
- Scientific Operations, Waters Corporation, Wilmslow, SK9 4AX, United Kingdom
| | - Giorgis Isaac
- Scientific Operations, Waters Corporation, Milford, Massachusetts 01757, United States
| | - Ammara Muazzam
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, Manchester Cancer Research Centre, University of Manchester, Manchester, M13 9NT, United Kingdom.,Stoller Biomarker Discovery Centre, Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, United Kingdom
| | - Olivier Cexus
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, GU2 7YH, United Kingdom
| | - Fowz Azhar
- Salford Royal NHS Foundation Trust, Salford Royal Hospital, Salford, Manchester, M6 8HD, United Kingdom
| | - Hardev Pandha
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, GU2 7YH, United Kingdom
| | - Anthony D Whetton
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, Manchester Cancer Research Centre, University of Manchester, Manchester, M13 9NT, United Kingdom.,Stoller Biomarker Discovery Centre, Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, United Kingdom
| | - Paul A Townsend
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, Manchester Cancer Research Centre, University of Manchester, Manchester, M13 9NT, United Kingdom.,Stoller Biomarker Discovery Centre, Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, United Kingdom.,Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, GU2 7YH, United Kingdom
| | - Ian D Wilson
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College, Du Cane Road, London, W12 0NN, United Kingdom
| | - Lee A Gethings
- Scientific Operations, Waters Corporation, Wilmslow, SK9 4AX, United Kingdom.,Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, GU2 7YH, United Kingdom
| | - Robert S Plumb
- Scientific Operations, Waters Corporation, Milford, Massachusetts 01757, United States
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11
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Breeur M, Ferrari P, Dossus L, Jenab M, Johansson M, Rinaldi S, Travis RC, His M, Key TJ, Schmidt JA, Overvad K, Tjønneland A, Kyrø C, Rothwell JA, Laouali N, Severi G, Kaaks R, Katzke V, Schulze MB, Eichelmann F, Palli D, Grioni S, Panico S, Tumino R, Sacerdote C, Bueno-de-Mesquita B, Olsen KS, Sandanger TM, Nøst TH, Quirós JR, Bonet C, Barranco MR, Chirlaque MD, Ardanaz E, Sandsveden M, Manjer J, Vidman L, Rentoft M, Muller D, Tsilidis K, Heath AK, Keun H, Adamski J, Keski-Rahkonen P, Scalbert A, Gunter MJ, Viallon V. Pan-cancer analysis of pre-diagnostic blood metabolite concentrations in the European Prospective Investigation into Cancer and Nutrition. BMC Med 2022; 20:351. [PMID: 36258205 PMCID: PMC9580145 DOI: 10.1186/s12916-022-02553-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 09/05/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Epidemiological studies of associations between metabolites and cancer risk have typically focused on specific cancer types separately. Here, we designed a multivariate pan-cancer analysis to identify metabolites potentially associated with multiple cancer types, while also allowing the investigation of cancer type-specific associations. METHODS We analysed targeted metabolomics data available for 5828 matched case-control pairs from cancer-specific case-control studies on breast, colorectal, endometrial, gallbladder, kidney, localized and advanced prostate cancer, and hepatocellular carcinoma nested within the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort. From pre-diagnostic blood levels of an initial set of 117 metabolites, 33 cluster representatives of strongly correlated metabolites and 17 single metabolites were derived by hierarchical clustering. The mutually adjusted associations of the resulting 50 metabolites with cancer risk were examined in penalized conditional logistic regression models adjusted for body mass index, using the data-shared lasso penalty. RESULTS Out of the 50 studied metabolites, (i) six were inversely associated with the risk of most cancer types: glutamine, butyrylcarnitine, lysophosphatidylcholine a C18:2, and three clusters of phosphatidylcholines (PCs); (ii) three were positively associated with most cancer types: proline, decanoylcarnitine, and one cluster of PCs; and (iii) 10 were specifically associated with particular cancer types, including histidine that was inversely associated with colorectal cancer risk and one cluster of sphingomyelins that was inversely associated with risk of hepatocellular carcinoma and positively with endometrial cancer risk. CONCLUSIONS These results could provide novel insights for the identification of pathways for cancer development, in particular those shared across different cancer types.
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Affiliation(s)
- Marie Breeur
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, NME Branch, 69372 CEDEX 08, Lyon, France
| | - Pietro Ferrari
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, NME Branch, 69372 CEDEX 08, Lyon, France
| | - Laure Dossus
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, NME Branch, 69372 CEDEX 08, Lyon, France
| | - Mazda Jenab
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, NME Branch, 69372 CEDEX 08, Lyon, France
| | - Mattias Johansson
- Genetics Branch, International Agency for Research on Cancer, 69372 CEDEX 08, Lyon, France
| | - Sabina Rinaldi
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, NME Branch, 69372 CEDEX 08, Lyon, France
| | - Ruth C Travis
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, OX3 7LF, UK
| | - Mathilde His
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, NME Branch, 69372 CEDEX 08, Lyon, France
| | - Tim J Key
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, OX3 7LF, UK
| | - Julie A Schmidt
- Cancer Epidemiology Unit, Nuffield Department of Population Health, University of Oxford, Oxford, OX3 7LF, UK
- Department of Clinical Epidemiology, Department of Clinical Medicine, Aarhus University Hospital and Aarhus University, DK-8200, Aarhus N, Denmark
| | - Kim Overvad
- Department of Public Health, Aarhus University, DK-8000, Aarhus C, Denmark
| | - Anne Tjønneland
- Danish Cancer Society Research Center Diet, Genes and Environment Nutrition and Biomarkers, DK-2100, Copenhagen, Denmark
| | - Cecilie Kyrø
- Danish Cancer Society Research Center Diet, Genes and Environment Nutrition and Biomarkers, DK-2100, Copenhagen, Denmark
| | - Joseph A Rothwell
- Université Paris-Saclay, UVSQ, Inserm, CESP U1018, "Exposome and Heredity" team, Gustave Roussy, 94800, Villejuif, France
| | - Nasser Laouali
- Université Paris-Saclay, UVSQ, Inserm, CESP U1018, "Exposome and Heredity" team, Gustave Roussy, 94800, Villejuif, France
| | - Gianluca Severi
- Université Paris-Saclay, UVSQ, Inserm, CESP U1018, "Exposome and Heredity" team, Gustave Roussy, 94800, Villejuif, France
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Verena Katzke
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
| | - Matthias B Schulze
- Department of Molecular Epidemiology, German Institute of Human Nutrition, 14558, Nuthetal, Germany
| | - Fabian Eichelmann
- Department of Molecular Epidemiology, German Institute of Human Nutrition, 14558, Nuthetal, Germany
- German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany
| | - Domenico Palli
- Institute of Cancer Research, Prevention and Clinical Network (ISPRO), 50139, Florence, Italy
| | - Sara Grioni
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, 20133, Milan, Italy
| | - Salvatore Panico
- Dipartimento di Medicina Clinica e Chirurgia, Federico II University, 80131, Naples, Italy
| | - Rosario Tumino
- Hyblean Association for Epidemiological Research, AIRE-ONLUS, 97100, Ragusa, Italy
| | - Carlotta Sacerdote
- Unit of Cancer Epidemiology Città della Salute e della Scienza University-Hospital, 10126, Turin, Italy
| | - Bas Bueno-de-Mesquita
- Centre for Nutrition, Prevention and Health Services, National Institute for Public Health and the Environment (RIVM), PO Box 1, 3720, BA, Bilthoven, The Netherlands
| | - Karina Standahl Olsen
- Department of Community Medicine, UiT The Arctic University of Norway, N-9037, Tromsø, Norway
| | | | - Therese Haugdahl Nøst
- Department of Community Medicine, UiT The Arctic University of Norway, N-9037, Tromsø, Norway
| | - J Ramón Quirós
- Public Health Directorate, 33006, Oviedo, Asturias, Spain
| | - Catalina Bonet
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Spain
| | - Miguel Rodríguez Barranco
- Escuela Andaluza de Salud Pública (EASP), 18011, Granada, Spain
- Instituto de Investigación Biosanitaria ibs. GRANADA, 18012, Granada, Spain
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), 28029, Madrid, Spain
| | - María-Dolores Chirlaque
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), 28029, Madrid, Spain
- Department of Epidemiology, Regional Health Council, IMIB-Arrixaca, Murcia University, 30003, Murcia, Spain
| | - Eva Ardanaz
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), 28029, Madrid, Spain
- Navarra Public Health Institute, 31003, Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, 31008, Pamplona, Spain
| | - Malte Sandsveden
- Department of Clinical Sciences Malmö Lund University, SE-214 28, Malmö, Sweden
| | - Jonas Manjer
- Departement of Surgery, Skåne University Hospital Malmö, Lund University, SE-214 28, Malmö, Sweden
| | - Linda Vidman
- Department of Radiation Sciences, Oncology Umeå University, SE-901 87, Umeå, Sweden
| | - Matilda Rentoft
- Department of Radiation Sciences, Oncology Umeå University, SE-901 87, Umeå, Sweden
| | - David Muller
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK
| | - Kostas Tsilidis
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK
| | - Alicia K Heath
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, W2 1PG, UK
| | - Hector Keun
- Department of Surgery and Cancer, Cancer Metabolism and Systems Toxicology Group, Division of Cancer, Imperial College London, London, SW7 2AZ, UK
| | - Jerzy Adamski
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
- Institute of Biochemistry, Faculty of Medicine, University of Ljubljana, 1000, Ljubljana, Slovenia
| | - Pekka Keski-Rahkonen
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, NME Branch, 69372 CEDEX 08, Lyon, France
| | - Augustin Scalbert
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, NME Branch, 69372 CEDEX 08, Lyon, France
| | - Marc J Gunter
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, NME Branch, 69372 CEDEX 08, Lyon, France
| | - Vivian Viallon
- Nutrition and Metabolism Branch, International Agency for Research on Cancer, NME Branch, 69372 CEDEX 08, Lyon, France.
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12
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Hertzog A, Selvanathan A, Devanapalli B, Ho G, Bhattacharya K, Tolun AA. A narrative review of metabolomics in the era of "-omics": integration into clinical practice for inborn errors of metabolism. Transl Pediatr 2022; 11:1704-1716. [PMID: 36345452 PMCID: PMC9636448 DOI: 10.21037/tp-22-105] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 08/23/2022] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND AND OBJECTIVE Traditional targeted metabolomic investigations identify a pre-defined list of analytes in samples and have been widely used for decades in the diagnosis and monitoring of inborn errors of metabolism (IEMs). Recent technological advances have resulted in the development and maturation of untargeted metabolomics: a holistic, unbiased, analytical approach to detecting metabolic disturbances in human disease. We aim to provide a summary of untargeted metabolomics [focusing on tandem mass spectrometry (MS-MS)] and its application in the field of IEMs. METHODS Data for this review was identified through a literature search using PubMed, Google Scholar, and personal repositories of articles collected by the authors. Findings are presented within several sections describing the metabolome, the current use of targeted metabolomics in the diagnostic pathway of patients with IEMs, the more recent integration of untargeted metabolomics into clinical care, and the limitations of this newly employed analytical technique. KEY CONTENT AND FINDINGS Untargeted metabolomic investigations are increasingly utilized in screening for rare disorders, improving understanding of cellular and subcellular physiology, discovering novel biomarkers, monitoring therapy, and functionally validating genomic variants. Although the untargeted metabolomic approach has some limitations, this "next generation metabolic screening" platform is becoming increasingly affordable and accessible. CONCLUSIONS When used in conjunction with genomics and the other promising "-omic" technologies, untargeted metabolomics has the potential to revolutionize the diagnostics of IEMs (and other rare disorders), improving both clinical and health economic outcomes.
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Affiliation(s)
- Ashley Hertzog
- NSW Biochemical Genetics Service, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Arthavan Selvanathan
- Genetic Metabolic Disorders Service, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Beena Devanapalli
- NSW Biochemical Genetics Service, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Gladys Ho
- Sydney Genome Diagnostics, The Children's Hospital at Westmead, Westmead, NSW, Australia.,Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Kaustuv Bhattacharya
- Genetic Metabolic Disorders Service, The Children's Hospital at Westmead, Westmead, NSW, Australia.,Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Adviye Ayper Tolun
- NSW Biochemical Genetics Service, The Children's Hospital at Westmead, Westmead, NSW, Australia.,Specialty of Genomic Medicine, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
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13
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Witchey SK, Doyle MG, Fredenburg JD, St Armour G, Horman B, Odenkirk MT, Aylor DL, Baker ES, Patisaul HB. Impacts of Gestational FireMaster 550 Exposure on the Neonatal Cortex Are Sex Specific and Largely Attributable to the Organophosphate Esters. Neuroendocrinology 2022; 113:1262-1282. [PMID: 36075192 PMCID: PMC9992460 DOI: 10.1159/000526959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/24/2022] [Indexed: 11/19/2022]
Abstract
INTRODUCTION Flame retardants (FRs) are common bodily and environmental pollutants, creating concern about their potential toxicity. We and others have found that the commercial mixture FireMaster® 550 (FM 550) or its individual brominated (BFR) and organophosphate ester (OPFR) components are potential developmental neurotoxicants. Using Wistar rats, we previously reported that developmental exposure to FM 550 or its component classes produced sex- and compound-specific effects on adult socioemotional behaviors. The underlying mechanisms driving the behavioral phenotypes are unknown. METHODS To further mechanistic understanding, here we conducted transcriptomics in parallel with a novel lipidomics approach using cortical tissues from newborn siblings of the rats in the published behavioral study. Inclusion of lipid composition is significant because it is rarely examined in developmental neurotoxicity studies. Pups were gestationally exposed via oral dosing to the dam to FM 550 or the BFR or OPFR components at environmentally relevant doses. RESULTS The neonatal cortex was highly sexually dimorphic in lipid and transcriptome composition, and males were more significantly impacted by FR exposure. Multiple adverse modes of action for the BFRs and OPFRs on neurodevelopment were identified, with the OPFRs being more disruptive than the BFRs via multiple mechanisms including dysregulation of mitochondrial function and disruption of cholinergic and glutamatergic systems. Disrupted mitochondrial function by environmental factors has been linked to a higher risk of autism spectrum disorders and neurodegenerative disorders. Impacted lipid classes included ceramides, sphingomyelins, and triacylglycerides. Robust ceramide upregulation in the OPFR females could suggest a heightened risk of brain metabolic disease. CONCLUSIONS This study reveals multiple mechanisms by which the components of a common FR mixture are developmentally neurotoxic and that the OPFRs may be the compounds of greatest concern.
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Affiliation(s)
- Shannah K Witchey
- Department of Biological Sciences, NC State University, Raleigh, North Carolina, USA
| | - Michael G Doyle
- Department of Chemistry, NC State University, Raleigh, North Carolina, USA
| | - Jacob D Fredenburg
- Department of Biological Sciences, NC State University, Raleigh, North Carolina, USA
| | - Genevieve St Armour
- Department of Biological Sciences, NC State University, Raleigh, North Carolina, USA
| | - Brian Horman
- Department of Biological Sciences, NC State University, Raleigh, North Carolina, USA
| | - Melanie T Odenkirk
- Department of Chemistry, NC State University, Raleigh, North Carolina, USA
| | - David L Aylor
- Department of Biological Sciences, NC State University, Raleigh, North Carolina, USA
- Center for Human Health and the Environment, NC State University, Raleigh, North Carolina, USA
| | - Erin S Baker
- Department of Chemistry, NC State University, Raleigh, North Carolina, USA
| | - Heather B Patisaul
- Center for Human Health and the Environment, NC State University, Raleigh, North Carolina, USA
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14
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Kirkwood KI, Pratt BS, Shulman N, Tamura K, MacCoss MJ, MacLean BX, Baker ES. Utilizing Skyline to analyze lipidomics data containing liquid chromatography, ion mobility spectrometry and mass spectrometry dimensions. Nat Protoc 2022; 17:2415-2430. [PMID: 35831612 DOI: 10.1038/s41596-022-00714-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 04/21/2022] [Indexed: 12/26/2022]
Abstract
Lipidomics studies suffer from analytical and annotation challenges because of the great structural similarity of many of the lipid species. To improve lipid characterization and annotation capabilities beyond those afforded by traditional mass spectrometry (MS)-based methods, multidimensional separation methods such as those integrating liquid chromatography, ion mobility spectrometry, collision-induced dissociation and MS (LC-IMS-CID-MS) may be used. Although LC-IMS-CID-MS and other multidimensional methods offer valuable hydrophobicity, structural and mass information, the files are also complex and difficult to assess. Thus, the development of software tools to rapidly process and facilitate confident lipid annotations is essential. In this Protocol Extension, we use the freely available, vendor-neutral and open-source software Skyline to process and annotate multidimensional lipidomic data. Although Skyline ( https://skyline.ms/skyline.url ) was established for targeted processing of LC-MS-based proteomics data, it has since been extended such that it can be used to analyze small-molecule data as well as data containing the IMS dimension. This protocol uses Skyline's recently expanded capabilities, including small-molecule spectral libraries, indexed retention time and ion mobility filtering, and provides a step-by-step description for importing data, predicting retention times, validating lipid annotations, exporting results and editing our manually validated 500+ lipid library. Although the time required to complete the steps outlined here varies on the basis of multiple factors such as dataset size and familiarity with Skyline, this protocol takes ~5.5 h to complete when annotations are rigorously verified for maximum confidence.
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Affiliation(s)
- Kaylie I Kirkwood
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA
| | - Brian S Pratt
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Nicholas Shulman
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Kaipo Tamura
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Brendan X MacLean
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA. .,Comparative Medicine Institute, North Carolina State University, Raleigh, NC, USA.
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15
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Odenkirk M, Horman BM, Dodds JN, Patisaul HB, Baker ES. Combining Micropunch Histology and Multidimensional Lipidomic Measurements for In-Depth Tissue Mapping. ACS MEASUREMENT SCIENCE AU 2022; 2:67-75. [PMID: 35647605 PMCID: PMC9139744 DOI: 10.1021/acsmeasuresciau.1c00035] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
While decades of technical and analytical advancements have been utilized to discover novel lipid species, increase speciation, and evaluate localized lipid dysregulation at subtissue, cellular, and subcellular levels, many challenges still exist. One limitation is that the acquisition of both in-depth spatial information and comprehensive lipid speciation is extremely difficult, especially when biological material is limited or lipids are at low abundance. In neuroscience, for example, it is often desired to focus on only one brain region or subregion, which can be well under a square millimeter for rodents. Herein, we evaluate a micropunch histology method where cortical brain tissue at 2.0, 1.25, 1.0, 0.75, 0.5, and 0.25 mm diameter sizes and 1 mm depth was collected and analyzed with multidimensional liquid chromatography, ion mobility spectrometry, collision induced dissociation, and mass spectrometry (LC-IMS-CID-MS) measurements. Lipid extraction was optimized for the small sample sizes, and assessment of lipidome coverage for the 2.0 to 0.25 mm diameter sizes showed a decline from 304 to 198 lipid identifications as validated by all 4 analysis dimensions (~35% loss in coverage for ~88% less tissue). While losses were observed, the ~200 lipids and estimated 4630 neurons contained within the 0.25 punch still provided in-depth characterization of the small tissue region. Furthermore, while localization routinely achieved by mass spectrometry imaging (MSI) and single cell analyses is greater, this diameter is sufficiently small to isolate subcortical, hypothalamic, and other brain regions in adult rats, thereby increasing the coverage of lipids within relevant spatial windows without sacrificing speciation. Therefore, micropunch histology enables in-depth, region-specific lipid evaluations, an approach that will prove beneficial to a variety of lipidomic applications.
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Affiliation(s)
- Melanie
T. Odenkirk
- Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Brian M. Horman
- Department
of Biological Sciences, North Carolina State
University, Raleigh, North Carolina 27695, United States
| | - James N. Dodds
- Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Heather B. Patisaul
- Department
of Biological Sciences, North Carolina State
University, Raleigh, North Carolina 27695, United States
- Center
for Human Health and the Environment, North
Carolina State University, Raleigh, North Carolina 27695, United States
| | - Erin S. Baker
- Department
of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
- Comparative
Medicine Institute, North Carolina State
University, Raleigh, North Carolina 27695, United States
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16
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Bai F, Wang X, Niu X, Shen G, Ye J. Lipidomic Profiling Reveals the Reducing Lipid Accumulation Effect of Dietary Taurine in Groupers ( Epinephelus coioides). Front Mol Biosci 2022; 8:814318. [PMID: 35004860 PMCID: PMC8740052 DOI: 10.3389/fmolb.2021.814318] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 11/29/2021] [Indexed: 11/13/2022] Open
Abstract
A lipidomic analysis was conducted to provide the first detailed overview of lipid molecule profiles in response to dietary lipid and taurine and associations of liver lipid-lowering effects of dietary taurine with lipid molecular species and the positional distributions of fatty acids in the liver of juvenile orange-spotted groupers (Epinephelus coioides). The results indicated that the liver was more sensitive to varied dietary lipid and taurine contents than the muscle with regard to lipid molecules. A total of 131 differential lipid molecules (DLMs) were observed in the liver of groupers when dietary taurine was increased from 0 to 1% at 15% lipid, among which all the up and down-regulated DLMs are phospholipids (PLs) and triglycerides (TGs), respectively. The liver content of TGs containing 18:2n-6 attached at the sn-2 and sn-3 positions on the glycerol backbone increased with increasing dietary lipid from 10 to 15% but decreased with increasing dietary taurine from 0 to 1%. Therefore, dietary taurine can not only reduce lipid accumulation through decreasing the contents of TGs containing 18:2n-6 at the sn-2 and sn-3 positions but also enhance the anti-inflammatory capacity and health status of groupers. This study will also provide a new insight into the function of taurine in farmed fish.
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Affiliation(s)
- Fakai Bai
- Xiamen Key Laboratory for Feed Quality Testing and Safety Evaluation, Fisheries College of Jimei University, Xiamen, China
| | - Xuexi Wang
- Key Laboratory of Marine Biotechnology of Fujian Province, Institute of Oceanology, Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xingjian Niu
- Xiamen Key Laboratory for Feed Quality Testing and Safety Evaluation, Fisheries College of Jimei University, Xiamen, China
| | - Guiping Shen
- Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance, Department of Electronic Science, Xiamen University, Xiamen, China
| | - Jidan Ye
- Xiamen Key Laboratory for Feed Quality Testing and Safety Evaluation, Fisheries College of Jimei University, Xiamen, China
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17
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Koelmel JP, Xie H, Price EJ, Lin EZ, Manz KE, Stelben P, Paige MK, Papazian S, Okeme J, Jones DP, Barupal D, Bowden JA, Rostkowski P, Pennell KD, Nikiforov V, Wang T, Hu X, Lai Y, Miller GW, Walker DI, Martin JW, Godri Pollitt KJ. An actionable annotation scoring framework for gas chromatography-high-resolution mass spectrometry. EXPOSOME 2022; 2:osac007. [PMID: 36483216 PMCID: PMC9719826 DOI: 10.1093/exposome/osac007] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/28/2022] [Accepted: 08/03/2022] [Indexed: 04/16/2023]
Abstract
Omics-based technologies have enabled comprehensive characterization of our exposure to environmental chemicals (chemical exposome) as well as assessment of the corresponding biological responses at the molecular level (eg, metabolome, lipidome, proteome, and genome). By systematically measuring personal exposures and linking these stimuli to biological perturbations, researchers can determine specific chemical exposures of concern, identify mechanisms and biomarkers of toxicity, and design interventions to reduce exposures. However, further advancement of metabolomics and exposomics approaches is limited by a lack of standardization and approaches for assigning confidence to chemical annotations. While a wealth of chemical data is generated by gas chromatography high-resolution mass spectrometry (GC-HRMS), incorporating GC-HRMS data into an annotation framework and communicating confidence in these assignments is challenging. It is essential to be able to compare chemical data for exposomics studies across platforms to build upon prior knowledge and advance the technology. Here, we discuss the major pieces of evidence provided by common GC-HRMS workflows, including retention time and retention index, electron ionization, positive chemical ionization, electron capture negative ionization, and atmospheric pressure chemical ionization spectral matching, molecular ion, accurate mass, isotopic patterns, database occurrence, and occurrence in blanks. We then provide a qualitative framework for incorporating these various lines of evidence for communicating confidence in GC-HRMS data by adapting the Schymanski scoring schema developed for reporting confidence levels by liquid chromatography HRMS (LC-HRMS). Validation of our framework is presented using standards spiked in plasma, and confident annotations in outdoor and indoor air samples, showing a false-positive rate of 12% for suspect screening for chemical identifications assigned as Level 2 (when structurally similar isomers are not considered false positives). This framework is easily adaptable to various workflows and provides a concise means to communicate confidence in annotations. Further validation, refinements, and adoption of this framework will ideally lead to harmonization across the field, helping to improve the quality and interpretability of compound annotations obtained in GC-HRMS.
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Affiliation(s)
- Jeremy P Koelmel
- Department of Environmental Health Science, Yale School of Public Health, New Haven, CT, USA
| | - Hongyu Xie
- Department of Environmental Science, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Elliott J Price
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic
| | - Elizabeth Z Lin
- Department of Environmental Health Science, Yale School of Public Health, New Haven, CT, USA
| | | | - Paul Stelben
- Department of Environmental Health Science, Yale School of Public Health, New Haven, CT, USA
| | - Matthew K Paige
- Department of Environmental Health Science, Yale School of Public Health, New Haven, CT, USA
| | - Stefano Papazian
- Department of Environmental Science, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
- National Facility for Exposomics, Metabolomics Platform, Science for Life Laboratory, Stockholm University, Solna 171 65, Sweden
| | - Joseph Okeme
- Department of Environmental Health Science, Yale School of Public Health, New Haven, CT, USA
| | - Dean P Jones
- School of Medicine, Department of Medicine, Emory University, Atlanta, GA, USA
| | - Dinesh Barupal
- Icahn School of Medicine at Mount Sinai, Department of Environmental Medicine and Public Health, New York, NY, USA
| | - John A Bowden
- Department of Physiological Sciences, Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, USA
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | | | - Kurt D Pennell
- School of Engineering, Brown University, Providence, RI, USA
| | | | - Thanh Wang
- MTM Research Centre, Örebro University, Örebro, Sweden
| | - Xin Hu
- School of Medicine, Department of Medicine, Emory University, Atlanta, GA, USA
| | - Yunjia Lai
- Mailman School of Public Health, Department of Environmental Health Sciences, Columbia University, New York, NY, USA
| | - Gary W Miller
- Mailman School of Public Health, Department of Environmental Health Sciences, Columbia University, New York, NY, USA
| | | | - Jonathan W Martin
- Department of Environmental Science, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
- National Facility for Exposomics, Metabolomics Platform, Science for Life Laboratory, Stockholm University, Solna 171 65, Sweden
| | - Krystal J Godri Pollitt
- To whom correspondence should be addressed: (Krystal J. Godri Pollitt) and (Douglas I. Walker)
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da Silva KM, Iturrospe E, Heyrman J, Koelmel JP, Cuykx M, Vanhaecke T, Covaci A, van Nuijs ALN. Optimization of a liquid chromatography-ion mobility-high resolution mass spectrometry platform for untargeted lipidomics and application to HepaRG cell extracts. Talanta 2021; 235:122808. [PMID: 34517665 DOI: 10.1016/j.talanta.2021.122808] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 12/26/2022]
Abstract
Analytical methods to evaluate the lipidome of biological samples need to provide high data quality to ensure comprehensive profiling and reliable structural elucidation. In this perspective, liquid chromatography-high resolution mass spectrometry (LC-HRMS) is the state-of-the-art technique for lipidomic analysis of biological samples. There are thousands of lipids in most biological samples, and therefore separation methods before introduction to the mass spectrometer is key for relative quantitation and identification. Chromatographic methods differ across laboratories, without any consensus on the best methodologies. Therefore, we designed an experiment to determine the optimal LC methodology, and assessed the value of ion mobility for an additional dimension of separation. To apply an untargeted method for hypothesis generation focused on lipidomics, LC-HRMS parameters were optimized based on the measurement of 50 panel lipids covering key human metabolic pathways. Reversed-phase liquid chromatography columns were compared based on a quality scoring system considering the signal-to-noise ratio, peak shape, and retention factor. Furthermore, drift tube ion mobility spectrometry (DTIMS) was implemented to increase peak capacity and confidence during annotation by providing collision cross section (CCS) values for the analytes under investigation. However, hyphenating DTIMS to LC-HRMS may result in a reduced sensitivity due to impaired duty cycles. To increase the signal intensity, a Box-Behnken design (BBD) was used to optimize four key factors, i.e. drift entrance voltage, drift exit voltage, rear funnel entrance, and rear funnel exit voltages. Application of a maximized desirability function provided voltages for the above-mentioned parameters resulting in higher signal intensity compared to each combination of parameters used during the BBD. In addition, the influence of single pulse and Hadamard 4-bit multiplexed modes on signal intensity was explored and different trap filling and release times of ions were evaluated. The optimized LC-DTIM-HRMS platform was applied to extracts from HepaRG cells and resulted in 3912 high-quality features (<30% median relative standard deviation; n = 6, t = 24 h). From these features, 436 lipid species could be annotated (i.e., matching based on accurate mass <5 ppm, isotopic pattern, in-silico MS/MS fragmentation, and in-silico CCS database matching <3%). The application of LC-DTIM-HRMS for untargeted analysis workflows is growing and the platform optimization, as described here, can be used to guide the method development and CCS database comparison for high confidence lipid annotation.
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Affiliation(s)
| | - Elias Iturrospe
- University of Antwerp, Toxicological Centre, Universiteitsplein 1, 2610, Antwerp, Belgium; Vrije Universiteit Brussel, Department of In Vitro Toxicology and Dermato-cosmetology, Laarbeeklaan 103, 1090, Jette, Belgium
| | - Joris Heyrman
- University of Antwerp, Toxicological Centre, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Jeremy P Koelmel
- Yale University, School of Public Health, New Haven, CT, 06520, United States
| | - Matthias Cuykx
- Antwerp University Hospital, Laboratory of Clinical Medicine, Drie Eikenstraat 655, 2650, Edegem, Belgium
| | - Tamara Vanhaecke
- Vrije Universiteit Brussel, Department of In Vitro Toxicology and Dermato-cosmetology, Laarbeeklaan 103, 1090, Jette, Belgium
| | - Adrian Covaci
- University of Antwerp, Toxicological Centre, Universiteitsplein 1, 2610, Antwerp, Belgium
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19
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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: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [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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20
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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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21
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Lichtenberg S, Trifonova OP, Maslov DL, Balashova EE, Lokhov PG. Metabolomic Laboratory-Developed Tests: Current Status and Perspectives. Metabolites 2021; 11:423. [PMID: 34206934 PMCID: PMC8305461 DOI: 10.3390/metabo11070423] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/11/2021] [Accepted: 06/25/2021] [Indexed: 12/18/2022] Open
Abstract
Laboratory-developed tests (LDTs) are a subset of in vitro diagnostic devices, which the US Food and Drug Administration defines as "tests that are manufactured by and used within a single laboratory". The review describes the emergence and history of LDTs. The current state and development prospects of LDTs based on metabolomics are analyzed. By comparing LDTs with the scientific metabolomics study of human bio samples, the characteristic features of metabolomic LDT are shown, revealing its essence, strengths, and limitations. The possibilities for further developments and scaling of metabolomic LDTs and their potential significance for healthcare are discussed. The legal aspects of LDT regulation in the United States, European Union, and Singapore, demonstrating different approaches to this issue, are also provided. Based on the data presented in the review, recommendations were made on the feasibility and ways of further introducing metabolomic LDTs into practice.
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Affiliation(s)
- Steven Lichtenberg
- Metabometrics, Inc., 651 N Broad St, Suite 205 #1370, Middletown, DE 19709, USA
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (D.L.M.); (E.E.B.)
| | - Oxana P. Trifonova
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (D.L.M.); (E.E.B.)
| | - Dmitry L. Maslov
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (D.L.M.); (E.E.B.)
| | - Elena E. Balashova
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (D.L.M.); (E.E.B.)
| | - Petr G. Lokhov
- Institute of Biomedical Chemistry, 10 Building 8, Pogodinskaya Street, 119121 Moscow, Russia; (O.P.T.); (D.L.M.); (E.E.B.)
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22
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Zhen H, Teng Q, Mosley JD, Collette TW, Yue Y, Bradley PM, Ekman DR. Untargeted Lipidomics for Determining Cellular and Subcellular Responses in Zebrafish ( Danio rerio) Liver Cells Following Exposure to Complex Mixtures in U.S. Streams. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:8180-8190. [PMID: 34096267 PMCID: PMC8453666 DOI: 10.1021/acs.est.1c01132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Surface waters often contain a variety of chemical contaminants potentially capable of producing adverse outcomes in both humans and wildlife due to impacts from industrial, urban, and agricultural activity. Here, we report the results of a zebrafish liver (ZFL) cell-based lipidomics approach to assess the potential ecotoxicological effects of complex contaminant mixtures using water collected from eight impacted streams across the United States mainland and Puerto Rico. We initially characterized the ZFL lipidome using high resolution mass spectrometry, resulting in the annotation of 508 lipid species covering 27 classes. We then identified lipid changes induced by all streamwater samples (nonspecific stress indicators) as well as those unique to water samples taken from specific streams. Subcellular impacts were classified based on organelle-specific lipid changes, including increased lipid saturation (endoplasmic reticulum stress), elevated bis(monoacylglycero)phosphate (lysosomal overload), decreased ubiquinone (mitochondrial dysfunction), and elevated ether lipids (peroxisomal stress). Finally, we demonstrate how these results can uniquely inform environmental monitoring and risk assessments of surface waters.
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Affiliation(s)
- Huajun Zhen
- U.S. Environmental Protection Agency, Center for Environmental Measurement and Modeling, Athens, Georgia 30605, United States
| | - Quincy Teng
- U.S. Environmental Protection Agency, Center for Environmental Measurement and Modeling, Athens, Georgia 30605, United States
| | - Jonathan D Mosley
- U.S. Environmental Protection Agency, Center for Environmental Measurement and Modeling, Athens, Georgia 30605, United States
| | - Timothy W Collette
- U.S. Environmental Protection Agency, Center for Environmental Measurement and Modeling, Athens, Georgia 30605, United States
| | - Yang Yue
- U.S. Environmental Protection Agency, Center for Environmental Measurement and Modeling, Athens, Georgia 30605, United States
| | - Paul M Bradley
- U.S. Geological Survey, South Atlantic Water Science Center, Columbia, South Carolina 29210, United States
| | - Drew R Ekman
- U.S. Environmental Protection Agency, Center for Environmental Measurement and Modeling, Athens, Georgia 30605, United States
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23
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Untargeted lipidomics reveals metabolic responses to different dietary n-3 PUFA in juvenile swimming crab (Portunus trituberculatus). Food Chem 2021; 354:129570. [PMID: 33761340 DOI: 10.1016/j.foodchem.2021.129570] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 02/21/2021] [Accepted: 03/06/2021] [Indexed: 11/21/2022]
Abstract
While tissue fatty acid compositions reflect that of the dietary lipid source, little information is available on how dietary oils modify lipid class and molecular species profiles in hepatopancreas of crustacean. Herein, an 8-week nutritional trial and untargeted lipidomic analysis were used to investigate the impacts of dietary n-3 PUFA lipid sources including fish oil, krill oil and linseed oil on the lipidomic characteristics of hepatopancreas of swimming crab (Portunus trituberculatus). Dietary krill oil significantly increased distribution of 20:5n-3 and 22:6n-3 at sn-2 in phosphatidylcholine and phosphatidylethanolamine compared to fish oil. Fish oil intake promoted the deposition of 20:5n-3 and 22:6n-3 at sn-1,2,3 in triglyceride compared to linseed oil, which significantly increased the specific accumulation of 18:3n-3 at sn-1,3 in triglyceride and sn-2 in phosphatidylcholine and phosphatidylethanolamine. The study revealed metabolic responses to different dietary n-3 PUFA in swimming crab, which provided novel insight into the lipid nutrition of crustacean.
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24
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Borrego SL, Fahrmann J, Hou J, Lin DW, Tromberg BJ, Fiehn O, Kaiser P. Lipid remodeling in response to methionine stress in MDA-MBA-468 triple-negative breast cancer cells. J Lipid Res 2021; 62:100056. [PMID: 33647277 PMCID: PMC8042402 DOI: 10.1016/j.jlr.2021.100056] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 02/12/2021] [Accepted: 02/19/2021] [Indexed: 02/08/2023] Open
Abstract
Methionine (Met) is an essential amino acid and critical precursor to the cellular methyl donor S-adenosylmethionine. Unlike nontransformed cells, cancer cells have a unique metabolic requirement for Met and are unable to proliferate in growth media where Met is replaced with its metabolic precursor, homocysteine. This metabolic vulnerability is common among cancer cells regardless of tissue origin and is known as "methionine dependence", "methionine stress sensitivity", or the Hoffman effect. The response of lipids to Met stress, however, is not well-understood. Using mass spectroscopy, label-free vibrational microscopy, and next-generation sequencing, we characterize the response of lipids to Met stress in the triple-negative breast cancer cell line MDA-MB-468 and its Met stress insensitive derivative, MDA-MB-468res-R8. Lipidome analysis identified an immediate, global decrease in lipid abundances with the exception of triglycerides and an increase in lipid droplets in response to Met stress specifically in MDA-MB-468 cells. Furthermore, specific gene expression changes were observed as a secondary response to Met stress in MDA-MB-468, resulting in a downregulation of fatty acid metabolic genes and an upregulation of genes in the unfolded protein response pathway. We conclude that the extensive changes in lipid abundance during Met stress is a direct consequence of the modified metabolic profile previously described in Met stress-sensitive cells. The changes in lipid abundance likely results in changes in membrane composition inducing the unfolded protein response we observe.
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Affiliation(s)
- Stacey L Borrego
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA
| | - Johannes Fahrmann
- West Coast Metabolomics Center, University of California, Davis, Davis, CA, USA; Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jue Hou
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, USA
| | - Da-Wei Lin
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA
| | - Bruce J Tromberg
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA, USA; National Institute of Biomedical Imaging and Bioengineering, Bethesda, MD, USA
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California, Davis, Davis, CA, USA
| | - Peter Kaiser
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, USA.
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25
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Wörheide MA, Krumsiek J, Kastenmüller G, Arnold M. Multi-omics integration in biomedical research - A metabolomics-centric review. Anal Chim Acta 2021; 1141:144-162. [PMID: 33248648 PMCID: PMC7701361 DOI: 10.1016/j.aca.2020.10.038] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/09/2020] [Accepted: 10/19/2020] [Indexed: 02/07/2023]
Abstract
Recent advances in high-throughput technologies have enabled the profiling of multiple layers of a biological system, including DNA sequence data (genomics), RNA expression levels (transcriptomics), and metabolite levels (metabolomics). This has led to the generation of vast amounts of biological data that can be integrated in so-called multi-omics studies to examine the complex molecular underpinnings of health and disease. Integrative analysis of such datasets is not straightforward and is particularly complicated by the high dimensionality and heterogeneity of the data and by the lack of universal analysis protocols. Previous reviews have discussed various strategies to address the challenges of data integration, elaborating on specific aspects, such as network inference or feature selection techniques. Thereby, the main focus has been on the integration of two omics layers in their relation to a phenotype of interest. In this review we provide an overview over a typical multi-omics workflow, focusing on integration methods that have the potential to combine metabolomics data with two or more omics. We discuss multiple integration concepts including data-driven, knowledge-based, simultaneous and step-wise approaches. We highlight the application of these methods in recent multi-omics studies, including large-scale integration efforts aiming at a global depiction of the complex relationships within and between different biological layers without focusing on a particular phenotype.
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Affiliation(s)
- Maria A Wörheide
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Jan Krumsiek
- Institute for Computational Biomedicine, Englander Institute for Precision Medicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Gabi Kastenmüller
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; German Center for Diabetes Research (DZD), Neuherberg, Germany
| | - Matthias Arnold
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany; Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA.
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26
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Rose BS, Leaptrot KL, Harris RA, Sherrod SD, May JC, McLean JA. High Confidence Shotgun Lipidomics Using Structurally Selective Ion Mobility-Mass Spectrometry. Methods Mol Biol 2021; 2306:11-37. [PMID: 33954937 PMCID: PMC10127451 DOI: 10.1007/978-1-0716-1410-5_2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ion mobility (IM) is a gas phase separation strategy that can either supplement or serve as a high-throughput alternative to liquid chromatography (LC) in shotgun lipidomics. Incorporating the IM dimension in untargeted lipidomics workflows can help resolve isomeric lipids, and the collision cross section (CCS) values obtained from the IM measurements can provide an additional molecular descriptor to increase lipid identification confidence. This chapter provides a broad overview of an untargeted ion mobility-mass spectrometry (IM-MS) workflow using a commercial drift tube ion mobility-quadrupole-time-of-flight mass spectrometer (IM-QTOF) for high confidence lipidomics.
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Affiliation(s)
- Bailey S Rose
- Center for Innovative Technology, Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - Katrina L Leaptrot
- Center for Innovative Technology, Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - Rachel A Harris
- Center for Innovative Technology, Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - Stacy D Sherrod
- Center for Innovative Technology, Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - Jody C May
- Center for Innovative Technology, Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - John A McLean
- Center for Innovative Technology, Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA.
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
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27
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From Prevention to Disease Perturbations: A Multi-Omic Assessment of Exercise and Myocardial Infarctions. Biomolecules 2020; 11:biom11010040. [PMID: 33396843 PMCID: PMC7824308 DOI: 10.3390/biom11010040] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/20/2020] [Accepted: 12/24/2020] [Indexed: 12/15/2022] Open
Abstract
While a molecular assessment of the perturbations and injury arising from diseases is essential in their diagnosis and treatment, understanding changes due to preventative strategies is also imperative. Currently, complex diseases such as cardiovascular disease (CVD), the leading cause of death worldwide, suffer from a limited understanding of how the molecular mechanisms taking place following preventive measures (e.g., exercise) differ from changes occurring due to the injuries caused from the disease (e.g., myocardial infarction (MI)). Therefore, this manuscript assesses lipidomic changes before and one hour after exercise treadmill testing (ETT) and before and one hour after a planned myocardial infarction (PMI) in two separate patient cohorts. Strikingly, unique lipidomic perturbations were observed for these events, as could be expected from their vastly different stresses on the body. The lipidomic results were then combined with previously published metabolomic characterizations of the same patients. This integration provides complementary insights into the exercise and PMI events, thereby giving a more holistic understanding of the molecular changes associated with each.
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28
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Manzi M, Palazzo M, Knott ME, Beauseroy P, Yankilevich P, Giménez MI, Monge ME. Coupled Mass-Spectrometry-Based Lipidomics Machine Learning Approach for Early Detection of Clear Cell Renal Cell Carcinoma. J Proteome Res 2020; 20:841-857. [PMID: 33207877 DOI: 10.1021/acs.jproteome.0c00663] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A discovery-based lipid profiling study of serum samples from a cohort that included patients with clear cell renal cell carcinoma (ccRCC) stages I, II, III, and IV (n = 112) and controls (n = 52) was performed using ultraperformance liquid chromatography coupled to quadrupole-time-of-flight mass spectrometry and machine learning techniques. Multivariate models based on support vector machines and the LASSO variable selection method yielded two discriminant lipid panels for ccRCC detection and early diagnosis. A 16-lipid panel allowed discriminating ccRCC patients from controls with 95.7% accuracy in a training set under cross-validation and 77.1% accuracy in an independent test set. A second model trained to discriminate early (I and II) from late (III and IV) stage ccRCC yielded a panel of 26 compounds that classified stage I patients from an independent test set with 82.1% accuracy. Thirteen species, including cholic acid, undecylenic acid, lauric acid, LPC(16:0/0:0), and PC(18:2/18:2), identified with level 1 exhibited significantly lower levels in samples from ccRCC patients compared to controls. Moreover, 3α-hydroxy-5α-androstan-17-one 3-sulfate, cis-5-dodecenoic acid, arachidonic acid, cis-13-docosenoic acid, PI(16:0/18:1), PC(16:0/18:2), and PC(O-16:0/20:4) contributed to discriminate early from late ccRCC stage patients. The results are auspicious for early ccRCC diagnosis after validation of the panels in larger and different cohorts.
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Affiliation(s)
- Malena Manzi
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD CABA, Argentina.,Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires. Junín 956, C1113AAD Buenos Aires, Argentina
| | - Martín Palazzo
- LM2S, Université de Technologie de Troyes, 12 rue Marie-Curie, CS42060 Troyes, France.,Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET, Instituto Partner de la Sociedad Max Planck, Godoy Cruz 2390, C1425FQD CABA, Argentina
| | - María Elena Knott
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD CABA, Argentina
| | - Pierre Beauseroy
- LM2S, Université de Technologie de Troyes, 12 rue Marie-Curie, CS42060 Troyes, France
| | - Patricio Yankilevich
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA), CONICET, Instituto Partner de la Sociedad Max Planck, Godoy Cruz 2390, C1425FQD CABA, Argentina
| | - María Isabel Giménez
- Departamento de Diagnóstico y Tratamiento, Hospital Italiano de Buenos Aires, Tte. Gral. Juan Domingo Perón 4190, C1199ABB CABA, Argentina
| | - María Eugenia Monge
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Godoy Cruz 2390, C1425FQD CABA, Argentina
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Horta D, Moreno-Torres M, Ramírez-Lázaro MJ, Lario S, Kuligowski J, Sanjuan-Herráez JD, Quintas G, Villoria A, Calvet X. Analysis of the Association between Fatigue and the Plasma Lipidomic Profile of Inflammatory Bowel Disease Patients. J Proteome Res 2020; 20:381-392. [PMID: 32969224 DOI: 10.1021/acs.jproteome.0c00462] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Inflammatory bowel disease (IBD) is a chronic, relapsing noninfectious inflammatory condition of the intestinal tract with two main phenotypes, ulcerative colitis (UC) and Crohn's disease (CD), and globally increasing incidence and prevalence. Nearly 80% of the IBD patients with active disease and 50% of those with inactive disease suffer fatigue with significant impairment of their quality of life. Fatigue has been associated with multiple factors in IBD patients but, in most cases, no direct cause can be identified, and risk factors in clinically quiescent IBD are contradictory. Furthermore, as the assessment of fatigue is subjective, there is an unmet clinical need for fatigue biomarkers. In this explorative study, we analyzed the plasma lipidomic profiles of 47 quiescent UC and CD patients (23 fatigued, 24 nonfatigued) using ultraperformance liquid chromatography-time-of-flight mass spectrometry (UPLC-TOFMS). The results showed changes in lipids associated with fatigue and IBD. Significantly decreased levels of phosphatidylcholines, plasmanyls, sphingomyelins, lysophosphatidylcholines, phosphatidylethanolamines, phosphatidylinositols, phosphatidylserines, and eicosanoids were observed in patients with fatigue. Network and metabolic pathway analysis indicated a dysregulation of the arachidonic acid and glycerophospholipid metabolisms and the sphingolipid pathway. The protein-metabolite interaction network showed interactions between functionally related metabolites and proteins, displaying 40 disease-associated hidden proteins including ABDH4, GLTP, and LCAT.
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Affiliation(s)
- Diana Horta
- Digestive Diseases Service, Hospital Universitari Parc Taulí, Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, 08208 Spain.,Departament de Medicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Spain
| | - Marta Moreno-Torres
- Unidad de Hepatología Experimental, Health Research Institute La Fe, Valencia, 46026 Spain
| | - María José Ramírez-Lázaro
- Digestive Diseases Service, Hospital Universitari Parc Taulí, Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, 08208 Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas CIBERehd, Instituto de Salud Carlos III, Madrid, 28029 Spain
| | - Sergio Lario
- Digestive Diseases Service, Hospital Universitari Parc Taulí, Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, 08208 Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas CIBERehd, Instituto de Salud Carlos III, Madrid, 28029 Spain
| | - Julia Kuligowski
- Neonatal Research Group, Health Research Institute La Fe, Valencia, 46026 Spain
| | | | - Guillermo Quintas
- Health and Biomedicine, LEITAT Technological Center, Barcelona, 08028 Spain.,Unidad Analítica, Health Research Institute Hospital La Fe, Valencia, 46026 Spain
| | - Albert Villoria
- Digestive Diseases Service, Hospital Universitari Parc Taulí, Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, 08208 Spain.,Departament de Medicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas CIBERehd, Instituto de Salud Carlos III, Madrid, 28029 Spain
| | - Xavier Calvet
- Digestive Diseases Service, Hospital Universitari Parc Taulí, Institut d'Investigació i Innovació Parc Taulí I3PT, Universitat Autònoma de Barcelona, Sabadell, 08208 Spain.,Departament de Medicina, Universitat Autònoma de Barcelona, Bellaterra, 08193 Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas CIBERehd, Instituto de Salud Carlos III, Madrid, 28029 Spain
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30
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Advances in Liquid Chromatography–Mass Spectrometry-Based Lipidomics: A Look Ahead. JOURNAL OF ANALYSIS AND TESTING 2020. [DOI: 10.1007/s41664-020-00135-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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31
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Eicher T, Kinnebrew G, Patt A, Spencer K, Ying K, Ma Q, Machiraju R, Mathé EA. Metabolomics and Multi-Omics Integration: A Survey of Computational Methods and Resources. Metabolites 2020; 10:E202. [PMID: 32429287 PMCID: PMC7281435 DOI: 10.3390/metabo10050202] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/07/2020] [Accepted: 05/13/2020] [Indexed: 02/06/2023] Open
Abstract
As researchers are increasingly able to collect data on a large scale from multiple clinical and omics modalities, multi-omics integration is becoming a critical component of metabolomics research. This introduces a need for increased understanding by the metabolomics researcher of computational and statistical analysis methods relevant to multi-omics studies. In this review, we discuss common types of analyses performed in multi-omics studies and the computational and statistical methods that can be used for each type of analysis. We pinpoint the caveats and considerations for analysis methods, including required parameters, sample size and data distribution requirements, sources of a priori knowledge, and techniques for the evaluation of model accuracy. Finally, for the types of analyses discussed, we provide examples of the applications of corresponding methods to clinical and basic research. We intend that our review may be used as a guide for metabolomics researchers to choose effective techniques for multi-omics analyses relevant to their field of study.
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Affiliation(s)
- Tara Eicher
- Biomedical Informatics Department, The Ohio State University College of Medicine, Columbus, OH 43210, USA; (T.E.); (G.K.); (K.S.); (Q.M.); (R.M.)
- Computer Science and Engineering Department, The Ohio State University College of Engineering, Columbus, OH 43210, USA
| | - Garrett Kinnebrew
- Biomedical Informatics Department, The Ohio State University College of Medicine, Columbus, OH 43210, USA; (T.E.); (G.K.); (K.S.); (Q.M.); (R.M.)
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH 43210, USA;
- Bioinformatics Shared Resource Group, The Ohio State University, Columbus, OH 43210, USA
| | - Andrew Patt
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, 9800 Medical Center Dr., Rockville, MD, 20892, USA;
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH 43210, USA
| | - Kyle Spencer
- Biomedical Informatics Department, The Ohio State University College of Medicine, Columbus, OH 43210, USA; (T.E.); (G.K.); (K.S.); (Q.M.); (R.M.)
- Biomedical Sciences Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- Nationwide Children’s Research Hospital, Columbus, OH 43210, USA
| | - Kevin Ying
- Comprehensive Cancer Center, The Ohio State University and James Cancer Hospital, Columbus, OH 43210, USA;
- Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, OH 43210, USA
| | - Qin Ma
- Biomedical Informatics Department, The Ohio State University College of Medicine, Columbus, OH 43210, USA; (T.E.); (G.K.); (K.S.); (Q.M.); (R.M.)
| | - Raghu Machiraju
- Biomedical Informatics Department, The Ohio State University College of Medicine, Columbus, OH 43210, USA; (T.E.); (G.K.); (K.S.); (Q.M.); (R.M.)
- Computer Science and Engineering Department, The Ohio State University College of Engineering, Columbus, OH 43210, USA
- Department of Pathology, Wexner Medical Center, The Ohio State University, Columbus, OH 43210, USA
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH 43210, USA
| | - Ewy A. Mathé
- Biomedical Informatics Department, The Ohio State University College of Medicine, Columbus, OH 43210, USA; (T.E.); (G.K.); (K.S.); (Q.M.); (R.M.)
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, NIH, 9800 Medical Center Dr., Rockville, MD, 20892, USA;
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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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Eiriksson FF, Nøhr MK, Costa M, Bödvarsdottir SK, Ögmundsdottir HM, Thorsteinsdottir M. Lipidomic study of cell lines reveals differences between breast cancer subtypes. PLoS One 2020; 15:e0231289. [PMID: 32287294 PMCID: PMC7156077 DOI: 10.1371/journal.pone.0231289] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 03/19/2020] [Indexed: 12/24/2022] Open
Abstract
Breast cancer (BC) is the most prevalent type of cancer in women in western countries. BC mortality has not declined despite early detection by screening, indicating the need for better informed treatment decisions. Therefore, a novel noninvasive diagnostic tool for BC would give the opportunity of subtype-specific treatment and improved prospects for the patients. Heterogeneity of BC tumor subtypes is reflected in the expression levels of enzymes in lipid metabolism. The aim of the study was to investigate whether the subtype defined by the transcriptome is reflected in the lipidome of BC cell lines. A liquid chromatography mass spectrometry (LC-MS) platform was applied to analyze the lipidome of six cell lines derived from human BC cell lines representing different BC subtypes. We identified an increased abundance of triacylglycerols (TG) ≥ C-48 with moderate or multiple unsaturation in fatty acyl chains and down-regulated ether-phosphatidylethanolamines (PE) (C-34 to C-38) in cell lines representing estrogen receptor and progesterone receptor positive tumor subtypes. In a cell line representing HER2-overexpressing tumor subtype an elevated expression of TG (≤ C-46), phosphatidylcholines (PC) and PE containing short-chained (≤ C-16) saturated or monounsaturated fatty acids were observed. Increased abundance of PC ≥ C-40 was found in cell lines of triple negative BC subtype. In addition, differences were detected in lipidomes within these previously defined subtypes. We conclude that subtypes defined by the transcriptome are indeed reflected in differences in the lipidome and, furthermore, potentially biologically relevant differences may exist within these defined subtypes.
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Affiliation(s)
- Finnur Freyr Eiriksson
- Faculty of Pharmaceutical Sciences, University of Iceland, Reykjavík, Iceland
- Faculty of Medicine, University of Iceland, Reykjavík, Iceland
- ArcticMass, Reykjavík, Iceland
| | - Martha Kampp Nøhr
- Faculty of Pharmaceutical Sciences, University of Iceland, Reykjavík, Iceland
- Biomedical Center, University of Iceland, Reykjavík, Iceland
| | - Margarida Costa
- Faculty of Pharmaceutical Sciences, University of Iceland, Reykjavík, Iceland
- ArcticMass, Reykjavík, Iceland
| | - Sigridur Klara Bödvarsdottir
- Faculty of Medicine, University of Iceland, Reykjavík, Iceland
- Biomedical Center, University of Iceland, Reykjavík, Iceland
| | - Helga Margret Ögmundsdottir
- Faculty of Medicine, University of Iceland, Reykjavík, Iceland
- Biomedical Center, University of Iceland, Reykjavík, Iceland
| | - Margret Thorsteinsdottir
- Faculty of Pharmaceutical Sciences, University of Iceland, Reykjavík, Iceland
- ArcticMass, Reykjavík, Iceland
- Biomedical Center, University of Iceland, Reykjavík, Iceland
- * E-mail:
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Koelmel JP, Li X, Stow SM, Sartain MJ, Murali A, Kemperman R, Tsugawa H, Takahashi M, Vasiliou V, Bowden JA, Yost RA, Garrett TJ, Kitagawa N. Lipid Annotator: Towards Accurate Annotation in Non-Targeted Liquid Chromatography High-Resolution Tandem Mass Spectrometry (LC-HRMS/MS) Lipidomics Using A Rapid and User-Friendly Software. Metabolites 2020; 10:E101. [PMID: 32178227 PMCID: PMC7142889 DOI: 10.3390/metabo10030101] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 02/28/2020] [Accepted: 03/06/2020] [Indexed: 01/01/2023] Open
Abstract
Lipidomics has great promise in various applications; however, a major bottleneck in lipidomics is the accurate and comprehensive annotation of high-resolution tandem mass spectral data. While the number of available lipidomics software has drastically increased over the past five years, the reduction of false positives and the realization of obtaining structurally accurate annotations remains a significant challenge. We introduce Lipid Annotator, which is a user-friendly software for lipidomic analysis of data collected by liquid chromatography high-resolution tandem mass spectrometry (LC-HRMS/MS). We validate annotation accuracy against lipid standards and other lipidomics software. Lipid Annotator was integrated into a workflow applying an iterative exclusion MS/MS acquisition strategy to National Institute of Standards and Technology (NIST) SRM 1950 Metabolites in Frozen Human Plasma using reverse phase LC-HRMS/MS. Lipid Annotator, LipidMatch, and MS-DIAL produced consensus annotations at the level of lipid class for 98% and 96% of features detected in positive and negative mode, respectively. Lipid Annotator provides percentages of fatty acyl constituent species and employs scoring algorithms based on probability theory, which is less subjective than the tolerance and weighted match scores commonly used by available software. Lipid Annotator enables analysis of large sample cohorts and improves data-processing throughput as compared to previous lipidomics software.
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Affiliation(s)
- Jeremy P. Koelmel
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA; (R.A.Y.); (T.J.G.)
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT 06520, USA;
| | - Xiangdong Li
- Agilent Technologies, Santa Clara, CA 95051, USA; (X.L.); (S.M.S.); (M.J.S.); (A.M.); (N.K.)
| | - Sarah M. Stow
- Agilent Technologies, Santa Clara, CA 95051, USA; (X.L.); (S.M.S.); (M.J.S.); (A.M.); (N.K.)
| | - Mark J. Sartain
- Agilent Technologies, Santa Clara, CA 95051, USA; (X.L.); (S.M.S.); (M.J.S.); (A.M.); (N.K.)
| | - Adithya Murali
- Agilent Technologies, Santa Clara, CA 95051, USA; (X.L.); (S.M.S.); (M.J.S.); (A.M.); (N.K.)
| | - Robin Kemperman
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA; (R.K.); (J.A.B.)
| | - Hiroshi Tsugawa
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; (H.T.); (M.T.)
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Mikiko Takahashi
- RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan; (H.T.); (M.T.)
| | - Vasilis Vasiliou
- Department of Environmental Health Sciences, Yale School of Public Health, New Haven, CT 06520, USA;
| | - John A. Bowden
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA; (R.K.); (J.A.B.)
- Center for Environmental and Human Toxicology & Department of Physiological Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Richard A. Yost
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA; (R.A.Y.); (T.J.G.)
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA; (R.K.); (J.A.B.)
| | - Timothy J. Garrett
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA; (R.A.Y.); (T.J.G.)
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA; (R.K.); (J.A.B.)
| | - Norton Kitagawa
- Agilent Technologies, Santa Clara, CA 95051, USA; (X.L.); (S.M.S.); (M.J.S.); (A.M.); (N.K.)
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Laudicella VA, Beveridge C, Carboni S, Franco SC, Doherty MK, Long N, Mitchell E, Stanley MS, Whitfield PD, Hughes AD. Lipidomics analysis of juveniles' blue mussels (Mytilus edulis L. 1758), a key economic and ecological species. PLoS One 2020; 15:e0223031. [PMID: 32084137 PMCID: PMC7034892 DOI: 10.1371/journal.pone.0223031] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 01/28/2020] [Indexed: 02/07/2023] Open
Abstract
Blue mussels (Mytilus edulis L. 1758) are important components of coastal ecosystems and in the economy of rural and coastal areas. The understanding of their physiological processes at key life stages is important both within food production systems and in the management of wild populations. Lipids are crucial molecules for bivalve growth, but their diversity and roles have not been fully characterised. In this study, traditional lipid profiling techniques, such as fatty acid (FA) and lipid class analysis, are combined to untargeted lipidomics to elucidate the lipid metabolism in newly settled spat fed on a range of diets. The evaluated diets included single strains treatments (Cylindrotheca fusiformis CCAP 1017/2 -CYL, Isochrysis galbana CCAP 927/1- ISO, Monodopsis subterranean CCAP 848/1 -MONO, Nannochloropsis oceanica CCAP 849/10- NANNO) and a commercial algae paste (SP). Spat growth was influenced by the diets, which, according to their efficacy were ranked as follows: ISO>NANNO/CYL>SP>MONO. A higher triacylglycerols (TG) content, ranging from 4.23±0.82 μg mgashfree Dry weight (DW)-1 at the beginning of the trial (T0) to 51±15.3 μg mgashfreeDW-1 in ISO, characterised significant growth in the spat, whereas, a reduction of TG (0.3±0.08 μg mgashfreeDW-1 in MONO), mono unsaturated FA-MUFA (from 8.52±1.02 μg mgFAashfreeDW-1 at T0 to 2.81±1.02 μg mgFAashfreeDW-1 in MONO) and polyunsaturated FA-PUFA (from 17.57±2.24 μg mgFAashfreeDW-1 at T0 to 6.19±2.49 μg mgFAashfreeDW-1 in MONO) content characterised poor performing groups. Untargeted lipidomics evidenced how the availability of dietary essential PUFA did not influence only neutral lipids but also the membrane lipids, with changes in lipid molecular species in relation to the essential PUFA provided via the diet. Such changes have the potential to affect spat production cycle and their ability to respond to the surrounding environment. This study evidenced the advantages of coupling different lipid analysis techniques, as each technique disclosed relevant information on nutritional requirements of M. edulis juveniles, expanding the existing knowledge on the physiology of this important species.
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Affiliation(s)
| | - Christine Beveridge
- Scottish Association for Marine Sciences, Dunstaffnage Marine Laboratory, Oban, United Kingdom
| | - Stefano Carboni
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
| | - Sofia C. Franco
- Scottish Association for Marine Sciences, Dunstaffnage Marine Laboratory, Oban, United Kingdom
| | - Mary K. Doherty
- Division of Biomedical Sciences, University of the Highlands and Islands, Centre for Health Sciences, Inverness, United Kingdom
| | - Nina Long
- Scottish Association for Marine Sciences, Dunstaffnage Marine Laboratory, Oban, United Kingdom
| | - Elaine Mitchell
- Scottish Association for Marine Sciences, Dunstaffnage Marine Laboratory, Oban, United Kingdom
| | - Michele S. Stanley
- Scottish Association for Marine Sciences, Dunstaffnage Marine Laboratory, Oban, United Kingdom
| | - Phillip D. Whitfield
- Division of Biomedical Sciences, University of the Highlands and Islands, Centre for Health Sciences, Inverness, United Kingdom
| | - Adam D. Hughes
- Scottish Association for Marine Sciences, Dunstaffnage Marine Laboratory, Oban, United Kingdom
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Maddox SW, Fraser Caris RH, Baker KL, Burkus-Matesevac A, Peverati R, Chouinard CD. Ozone-Induced Cleavage of Endocyclic C═C Double Bonds within Steroid Epimers Produces Unique Gas-Phase Conformations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:411-417. [PMID: 32031388 DOI: 10.1021/jasms.9b00058] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Herein we demonstrate the first application of ozone-induced cleavage of endocyclic C═C double bonds for improved steroid isomer separation using ion mobility-mass spectrometry. Steroids represent a challenging biomolecular class for ion mobility (IM) separations due to their structural rigidity and subtle stereochemical differences. In this work, we compare the effects of ozonolysis on the relative mobilities of a model stereoisomer pair, testosterone and epitestosterone. A solution-phase ozonolysis approach is used due to its simplicity, relatively low cost, and potential for rapid, online analysis. Despite the presence of solvent-based addition products, we observe that these steroids undergo an ozone-based cleavage resulting in unique, stable gas-phase conformations. The resulting resolution between testosterone and epitestosterone, with collision cross section values of 176.6 and 193.3 Å2, respectively, demonstrates a significant improvement in comparison with previous IM-based approaches. The significantly smaller conformation observed for epitestosterone is stabilized by a three-point interaction between the oxygen-containing functional groups and a sodium ion; this same conformation cannot be sterically achieved by testosterone. Identification of this specific structural difference is strengthened by experimental results showing the disappearance of this conformation following in-source water loss, which eliminates the potential for that three-point interaction. Computational modeling of the lowest energy gas-phase structures for these ozone products corroborates the experimental results. In conclusion, this approach provides tremendous potential as a rapid IM separation method for steroid isomers and other endocyclic C═C double bond containing molecules.
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Affiliation(s)
- Samuel W Maddox
- Chemistry Program, Department of Biomedical and Chemical Engineering and Sciences , Florida Institute of Technology , Melbourne , Florida 32901 , United States
| | - Robert H Fraser Caris
- Chemistry Program, Department of Biomedical and Chemical Engineering and Sciences , Florida Institute of Technology , Melbourne , Florida 32901 , United States
| | - Kristie L Baker
- Chemistry Program, Department of Biomedical and Chemical Engineering and Sciences , Florida Institute of Technology , Melbourne , Florida 32901 , United States
| | - Aurora Burkus-Matesevac
- Chemistry Program, Department of Biomedical and Chemical Engineering and Sciences , Florida Institute of Technology , Melbourne , Florida 32901 , United States
| | - Roberto Peverati
- Chemistry Program, Department of Biomedical and Chemical Engineering and Sciences , Florida Institute of Technology , Melbourne , Florida 32901 , United States
| | - Christopher D Chouinard
- Chemistry Program, Department of Biomedical and Chemical Engineering and Sciences , Florida Institute of Technology , Melbourne , Florida 32901 , United States
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Wu Z, Bagarolo GI, Thoröe-Boveleth S, Jankowski J. "Lipidomics": Mass spectrometric and chemometric analyses of lipids. Adv Drug Deliv Rev 2020; 159:294-307. [PMID: 32553782 DOI: 10.1016/j.addr.2020.06.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 06/03/2020] [Accepted: 06/06/2020] [Indexed: 01/01/2023]
Abstract
Lipids are ubiquitous in the human organism and play essential roles as components of cell membranes and hormones, for energy storage or as mediators of cell signaling pathways. As crucial mediators of the human metabolism, lipids are also involved in metabolic diseases, cardiovascular and renal diseases, cancer and/or hepatological and neurological disorders. With rapidly growing evidence supporting the impact of lipids on both the genesis and progression of these diseases as well as patient wellbeing, the characterization of the human lipidome has gained high interest and importance in life sciences and clinical diagnostics within the last 15 years. This is mostly due to technically advanced molecular identification and quantification methods, mainly based on mass spectrometry. Mass spectrometry has become one of the most powerful tools for the identification of lipids. New lipidic mediators or biomarkers of diseases can be analysed by state-of-the art mass spectrometry techniques supported by sophisticated bioinformatics and biostatistics. The lipidomic approach has developed dramatically in the realm of life sciences and clinical diagnostics due to the available mass spectrometric methods and in particular due to the adaptation of biostatistical methods in recent years. Therefore, the current knowledge of lipid extraction methods, mass-spectrometric approaches, biostatistical data analysis, including workflows for the interpretation of lipidomic high-throughput data, are reviewed in this manuscript.
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Affiliation(s)
- Zhuojun Wu
- Institute for Molecular Cardiovascular Research, University Hospital RWTH Aachen, Aachen, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Giulia Ilaria Bagarolo
- Institute for Molecular Cardiovascular Research, University Hospital RWTH Aachen, Aachen, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Sven Thoröe-Boveleth
- Institute for Molecular Cardiovascular Research, University Hospital RWTH Aachen, Aachen, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Joachim Jankowski
- Institute for Molecular Cardiovascular Research, University Hospital RWTH Aachen, Aachen, Pauwelsstraße 30, 52074 Aachen, Germany; School for Cardiovascular Diseases, Maastricht University, Universiteitssingel 50, Maastricht, The Netherlands.
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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 INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2019; 12:e1466. [PMID: 31646749 DOI: 10.1002/wsbm.1466] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [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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Kappler L, Lehmann R. Mass-spectrometric multi-omics linked to function – State-of-the-art investigations of mitochondria in systems medicine. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.115635] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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40
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Marshall DL, Criscuolo A, Young RSE, Poad BLJ, Zeller M, Reid GE, Mitchell TW, Blanksby SJ. Mapping Unsaturation in Human Plasma Lipids by Data-Independent Ozone-Induced Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1621-1630. [PMID: 31222675 DOI: 10.1007/s13361-019-02261-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/27/2019] [Accepted: 05/27/2019] [Indexed: 06/09/2023]
Abstract
Over 1500 different lipids have been reported in human plasma at the sum composition level. Yet the number of unique lipids present is surely higher, once isomeric contributions from double bond location(s) and fatty acyl regiochemistry are considered. In order to resolve this ambiguity, herein, we describe the incorporation of ozone-induced dissociation (OzID) into data-independent shotgun lipidomics workflows on a high-resolution hybrid quadrupole-Orbitrap platform. In this configuration, [M + Na]+ ions generated by electrospray ionization of a plasma lipid extract were transmitted through the quadrupole in 1 Da segments. Reaction of mass-selected lipid ions with ozone in the octopole collision cell yielded diagnostic ions for each double bond position. The increased ozone concentration in this region significantly improved ozonolysis efficiency compared with prior implementations on linear ion-trap devices. This advancement translates into increased lipidome coverage and improvements in duty cycle for data-independent MS/MS analysis using shotgun workflows. Grouping all precursor ions with a common OzID neutral loss enables straightforward classification of the lipidome by unsaturation position (with respect to the methyl terminus). Two-dimensional maps obtained from this analysis provide a powerful visualization of structurally related lipids and lipid isomer families within plasma. Global profiling of lipid unsaturation in plasma extracts reveals that most unsaturated lipids are present as isomeric mixtures. These new insights provide a unique picture of underlying metabolism that could in the future provide novel indicators of health and disease.
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Affiliation(s)
- David L Marshall
- Central Analytical Research Facility, Institute for Future Environments, Queensland University of Technology, Brisbane, QLD, 4000, Australia.
| | - Angela Criscuolo
- Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, Leipzig, Germany
- Center for Biotechnology and Biomedicine, Universität Leipzig, Leipzig, Germany
- Thermo Fisher Scientific (Bremen) GmbH, Hanna-Kunath Str. 11, 28199, Bremen, Germany
| | - Reuben S E Young
- School of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology, Brisbane, Australia
| | - Berwyck L J Poad
- Central Analytical Research Facility, Institute for Future Environments, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Martin Zeller
- Thermo Fisher Scientific (Bremen) GmbH, Hanna-Kunath Str. 11, 28199, Bremen, Germany
| | - Gavin E Reid
- School of Chemistry, Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Australia
| | - Todd W Mitchell
- School of Medicine and Molecular Horizons, University of Wollongong, Wollongong, Australia
- Illawarra Health and Medical Research Institute, Wollongong, Australia
| | - Stephen J Blanksby
- Central Analytical Research Facility, Institute for Future Environments, Queensland University of Technology, Brisbane, QLD, 4000, Australia.
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Wang XD, Lin P, Li YX, Chen G, Yang H, He Y, Li Q, Liu RC. Identification of potential agents for thymoma by integrated analyses of differentially expressed tumour-associated genes and molecular docking experiments. Exp Ther Med 2019; 18:2001-2014. [PMID: 31452699 PMCID: PMC6704584 DOI: 10.3892/etm.2019.7817] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 06/20/2019] [Indexed: 12/12/2022] Open
Abstract
Thymoma, derived from the epithelial cells of the thymus, is a rare malignant tumour type. Following diagnosis with thymoma, patients generally undergo surgical treatment. However, patients with advanced-stage disease are only candidates for chemotherapy and have poor survival. Therefore, it is urgently required to explore effective chemotherapeutic agents for the treatment of thymoma. In the present study, a Bioinformatics analysis was performed to identify novel drugs for thymoma. Differentially expressed genes (DEGs) in thymoma were obtained by Gene Expression Profiling Interactive Analysis. Subsequently, these genes were processed by Connectivity Map analysis to identify suitable compounds. In addition, Metascape software was used to verify drug and target binding. Molecular docking technology was used to verify drug and target binding. Finally, absorption, distribution, metabolism and excretion parameters in the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform database were used for drug screening and for evaluation of the potential clinical value. In total, 2,447 DEGs, including 2,204 upregulated and 243 downregulated genes, were identified from 118 thymoma patients and 339 normal samples. The top 10 drugs displaying the most significant negative correlations were fulvestrant, hesperetin, zidovudine, hydrocortisone, rolitetracycline, ellipticine, sirolimus, quinisocaine, oestradiol (estradiol) and harmine. The predicted targets of these drugs were then confirmed. The score for the association between estrogen receptor 1 (ESR1) and fulvestrant was 0.99. According to the molecular docking analysis, the total scores for the interaction between ESR1 were 10.26, and those for the interaction between tamoxifen and ESR1 were 6.60. The oral bioavailability (%), drug-likeness and drug half-life for hesperetin were 70.31, 0.27 and 15.78, respectively; those for oestradiol were 53.56, 0.32 and 3.50, respectively; and those for harmine were 56.80, 0.13 and 5.04, respectively. In conclusion, several potential therapeutic drugs for thymoma were identified in the present study. The results suggested that the compounds, including fulvestrant, estradiol, hesperetin and ellipticine, represent the most likely drugs for the treatment of thymoma. Future studies should focus on testing these novel compounds in vitro and in vivo.
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Affiliation(s)
- Xiao-Dong Wang
- Department of Medical Ultrasonics, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Peng Lin
- Department of Medical Ultrasonics, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Yu-Xin Li
- Department of Medical Ultrasonics, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Hong Yang
- Department of Medical Ultrasonics, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Yun He
- Department of Medical Ultrasonics, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Qing Li
- Department of Medical Ultrasonics, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Ruo-Chuan Liu
- Department of Medical Ultrasonics, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
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Monge ME, Dodds JN, Baker ES, Edison AS, Fernández FM. Challenges in Identifying the Dark Molecules of Life. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2019; 12:177-199. [PMID: 30883183 PMCID: PMC6716371 DOI: 10.1146/annurev-anchem-061318-114959] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Metabolomics is the study of the metabolome, the collection of small molecules in living organisms, cells, tissues, and biofluids. Technological advances in mass spectrometry, liquid- and gas-phase separations, nuclear magnetic resonance spectroscopy, and big data analytics have now made it possible to study metabolism at an omics or systems level. The significance of this burgeoning scientific field cannot be overstated: It impacts disciplines ranging from biomedicine to plant science. Despite these advances, the central bottleneck in metabolomics remains the identification of key metabolites that play a class-discriminant role. Because metabolites do not follow a molecular alphabet as proteins and nucleic acids do, their identification is much more time consuming, with a high failure rate. In this review, we critically discuss the state-of-the-art in metabolite identification with specific applications in metabolomics and how technologies such as mass spectrometry, ion mobility, chromatography, and nuclear magnetic resonance currently contribute to this challenging task.
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Affiliation(s)
- María Eugenia Monge
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1425FQD, Ciudad de Buenos Aires, Argentina
| | - James N Dodds
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Arthur S Edison
- Department of Genetics, Department of Biochemistry and Molecular Biology, and Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, USA
| | - Facundo M Fernández
- School of Chemistry and Biochemistry, Georgia Institute of Technology and Petit Institute for Biochemistry and Bioscience, Atlanta, Georgia 30332, USA;
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Increased throughput and ultra-high mass resolution in DESI FT-ICR MS imaging through new-generation external data acquisition system and advanced data processing approaches. Sci Rep 2019; 9:8. [PMID: 30626890 PMCID: PMC6327097 DOI: 10.1038/s41598-018-36957-1] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Accepted: 11/28/2018] [Indexed: 12/20/2022] Open
Abstract
Desorption electrospray ionisation-mass spectrometry imaging (DESI-MSI) is a powerful imaging technique for the analysis of complex surfaces. However, the often highly complex nature of biological samples is particularly challenging for MSI approaches, as options to appropriately address molecular complexity are limited. Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) offers superior mass accuracy and mass resolving power, but its moderate throughput inhibits broader application. Here we demonstrate the dramatic gains in mass resolution and/or throughput of DESI-MSI on an FT-ICR MS by developing and implementing a sophisticated data acquisition and data processing pipeline. The presented pipeline integrates, for the first time, parallel ion accumulation and detection, post-processing absorption mode Fourier transform and pixel-by-pixel internal re-calibration. To achieve that, first, we developed and coupled an external high-performance data acquisition system to an FT-ICR MS instrument to record the time-domain signals (transients) in parallel with the instrument’s built-in electronics. The recorded transients were then processed by the in-house developed computationally-efficient data processing and data analysis software. Importantly, the described pipeline is shown to be applicable even to extremely large, up to 1 TB, imaging datasets. Overall, this approach provides improved analytical figures of merits such as: (i) enhanced mass resolution at no cost in experimental time; and (ii) up to 4-fold higher throughput while maintaining a constant mass resolution. Using this approach, we not only demonstrate the record 1 million mass resolution for lipid imaging from brain tissue, but explicitly show such mass resolution is required to resolve the complexity of the lipidome.
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Yang Q, Zhang AH, Miao JH, Sun H, Han Y, Yan GL, Wu FF, Wang XJ. Metabolomics biotechnology, applications, and future trends: a systematic review. RSC Adv 2019; 9:37245-37257. [PMID: 35542267 PMCID: PMC9075731 DOI: 10.1039/c9ra06697g] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Accepted: 11/03/2019] [Indexed: 12/12/2022] Open
Abstract
Given the highly increased incidence of human diseases, a better understanding of the related mechanisms regarding endogenous metabolism is urgently needed. Mass spectrometry-based metabolomics has been used in a variety of disease research areas. However, the deep research of metabolites remains a difficult and lengthy process. Fortunately, mass spectrometry is considered to be a universal tool with high specificity and sensitivity and is widely used around the world. Mass spectrometry technology has been applied to various basic disciplines, providing technical support for the discovery and identification of endogenous substances in living organisms. The combination of metabolomics and mass spectrometry is of great significance for the discovery and identification of metabolite biomarkers. The mass spectrometry tool could further improve and develop the exploratory research of the life sciences. This mini review discusses metabolomics biotechnology with a focus on recent applications of metabolomics as a powerful tool to elucidate metabolic disturbances and the related mechanisms of diseases. Given the highly increased incidence of human diseases, a better understanding of the related mechanisms regarding endogenous metabolism is urgently needed.![]()
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Affiliation(s)
- Qiang Yang
- Department of Pharmaceutical Analysis
- National Engineering Laboratory for the Development of Southwestern Endangered Medicinal Materials
- Guangxi Botanical Garden of Medicinal Plant
- National Chinmedomics Research Center
- Sino-America Chinmedomics Technology Collaboration Center
| | - Ai-hua Zhang
- Department of Pharmaceutical Analysis
- National Engineering Laboratory for the Development of Southwestern Endangered Medicinal Materials
- Guangxi Botanical Garden of Medicinal Plant
- National Chinmedomics Research Center
- Sino-America Chinmedomics Technology Collaboration Center
| | - Jian-hua Miao
- Department of Pharmaceutical Analysis
- National Engineering Laboratory for the Development of Southwestern Endangered Medicinal Materials
- Guangxi Botanical Garden of Medicinal Plant
- National Chinmedomics Research Center
- Sino-America Chinmedomics Technology Collaboration Center
| | - Hui Sun
- Department of Pharmaceutical Analysis
- National Engineering Laboratory for the Development of Southwestern Endangered Medicinal Materials
- Guangxi Botanical Garden of Medicinal Plant
- National Chinmedomics Research Center
- Sino-America Chinmedomics Technology Collaboration Center
| | - Ying Han
- Department of Pharmaceutical Analysis
- National Engineering Laboratory for the Development of Southwestern Endangered Medicinal Materials
- Guangxi Botanical Garden of Medicinal Plant
- National Chinmedomics Research Center
- Sino-America Chinmedomics Technology Collaboration Center
| | - Guang-li Yan
- Department of Pharmaceutical Analysis
- National Engineering Laboratory for the Development of Southwestern Endangered Medicinal Materials
- Guangxi Botanical Garden of Medicinal Plant
- National Chinmedomics Research Center
- Sino-America Chinmedomics Technology Collaboration Center
| | - Fang-fang Wu
- Department of Pharmaceutical Analysis
- National Engineering Laboratory for the Development of Southwestern Endangered Medicinal Materials
- Guangxi Botanical Garden of Medicinal Plant
- National Chinmedomics Research Center
- Sino-America Chinmedomics Technology Collaboration Center
| | - Xi-jun Wang
- Department of Pharmaceutical Analysis
- National Engineering Laboratory for the Development of Southwestern Endangered Medicinal Materials
- Guangxi Botanical Garden of Medicinal Plant
- National Chinmedomics Research Center
- Sino-America Chinmedomics Technology Collaboration Center
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Gathungu RM, Larrea P, Sniatynski MJ, Marur VR, Bowden JA, Koelmel JP, Starke-Reed P, Hubbard VS, Kristal BS. Optimization of Electrospray Ionization Source Parameters for Lipidomics To Reduce Misannotation of In-Source Fragments as Precursor Ions. Anal Chem 2018; 90:13523-13532. [PMID: 30265528 PMCID: PMC6297073 DOI: 10.1021/acs.analchem.8b03436] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Lipidomics requires the accurate annotation of lipids in complex samples to enable determination of their biological relevance. We demonstrate that unintentional in-source fragmentation (ISF, common in lipidomics) generates ions that have identical masses to other lipids. Lysophosphatidylcholines (LPC), for example, generate in-source fragments with the same mass as free fatty acids and lysophosphatidylethanolamines (LPE). The misannotation of in-source fragments as true lipids is particularly insidious in complex matrixes since most masses are initially unannotated and comprehensive lipid standards are unavailable. Indeed, we show such LPE/LPC misannotations are incorporated in the data submitted to the National Institute of Standards and Technology (NIST) interlaboratory comparison exercise. Computer simulations exhaustively identified potential misannotations. The selection of in-source fragments of highly abundant lipids as features, instead of the correct recognition of trace lipids, can potentially lead to (i) missing the biologically relevant lipids (i.e., a false negative) and/or (ii) incorrect assignation of a phenotype to an incorrect lipid (i.e., false positive). When ISF is not eliminated in the negative ion mode, ∼40% of the 100 most abundant masses corresponding to unique phospholipids measured in plasma were artifacts from ISF. We show that chromatographic separation and ion intensity considerations assist in distinguishing precursor ions from in-source fragments, suggesting ISF may be especially problematic when complex samples are analyzed via shotgun lipidomics. We also conduct a systematic evaluation of electrospray ionization (ESI) source parameters on an Exactive equipped with a heated electrospray ionization (HESI-II) source with the objective of obtaining uniformly appropriate source conditions for a wide range of lipids, while, at the same time, reducing in-source fragmentation.
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Affiliation(s)
- Rose M. Gathungu
- Department of Medicine, Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital and Department of Medicine, Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115
| | - Pablo Larrea
- Department of Medicine, Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital and Department of Medicine, Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115
| | - Matthew J. Sniatynski
- Department of Medicine, Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital and Department of Medicine, Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115
| | - Vasant R. Marur
- Department of Medicine, Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital and Department of Medicine, Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115
| | - John A. Bowden
- Center for Environmental and Human Toxicology, Department of Physiological Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, 32610
- National Institute of Standards and Technology, Hollings Marine Laboratory, Charleston, SC 29412
| | - Jeremy P. Koelmel
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, University of Florida, Gainesville, FL 32610
| | - Pamela Starke-Reed
- Deputy Director, NIH Division of Nutrition Research Coordination, Bethesda, MD 20892
| | - Van S. Hubbard
- Director, NIH Division of Nutrition Research Coordination, Bethesda, MD 20892
| | - Bruce S. Kristal
- Department of Medicine, Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital and Department of Medicine, Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115
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47
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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: 197] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [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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Bowden JA, Ulmer CZ, Jones CM, Koelmel JP, Yost RA. NIST lipidomics workflow questionnaire: an assessment of community-wide methodologies and perspectives. Metabolomics 2018; 14:53. [PMID: 30830346 DOI: 10.1007/s11306-018-1340-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 02/16/2018] [Indexed: 01/08/2023]
Abstract
INTRODUCTION Efforts to harmonize lipidomic methodologies have been limited within the community. Here, we aimed to capitalize on the recent National Institute of Standards and Technology lipidomics interlaboratory comparison exercise by implementing a questionnaire that assessed current methodologies, quantitation strategies, standard operating procedures (SOPs), and quality control activities employed by the lipidomics community. OBJECTIVES Lipidomics is a rapidly developing field with diverse applications. At present, there are no community-vetted methods to assess measurement comparability or data quality. Thus, a major impetus of this questionnaire was to profile current efforts, highlight areas of need, and establish future objectives in an effort to harmonize lipidomics workflows. METHODS The 54-question survey inquired about laboratory demographics, lipidomic methodologies and SOPs, analytical platforms, quantitation, reference materials, quality control procedures, and opinions regarding challenges existing within the community. RESULTS A total of 125 laboratories participated in the questionnaire. A broad overview of results highlighted a wide methodological diversity within current lipidomic workflows. The impact of this diversity on lipid measurement and quantitation is currently unknown and needs to be explored further. While some laboratories do incorporate SOPs and quality control activities, these concepts have not been fully embraced by the community. The top five perceived challenges within the lipidomics community were a lack of standardization amongst methods/protocols, lack of lipid standards, software/data handling and quantification, and over-reporting/false positives. CONCLUSION The questionnaire provided an overview of current lipidomics methodologies and further promoted the need for community-accepted guidelines and protocols. The questionnaire also served as a platform to help determine and prioritize metrological issues to be investigated.
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Affiliation(s)
- John A Bowden
- Marine Biochemical Sciences Group, National Institute of Standards and Technology, Hollings Marine Laboratory, 331 Fort Johnson Road, Charleston, SC, 29412, USA.
| | - Candice Z Ulmer
- Marine Biochemical Sciences Group, National Institute of Standards and Technology, Hollings Marine Laboratory, 331 Fort Johnson Road, Charleston, SC, 29412, USA
| | - Christina M Jones
- Organic Chemical Measurement Science Group, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899, USA
| | - Jeremy P Koelmel
- Department of Chemistry, University of Florida, 214 Leigh Hall, Gainesville, FL, 32611, USA
| | - Richard A Yost
- Department of Chemistry, University of Florida, 214 Leigh Hall, Gainesville, FL, 32611, USA
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Rustam YH, Reid GE. Analytical Challenges and Recent Advances in Mass Spectrometry Based Lipidomics. Anal Chem 2017; 90:374-397. [PMID: 29166560 DOI: 10.1021/acs.analchem.7b04836] [Citation(s) in RCA: 206] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Yepy H Rustam
- Department of Biochemistry and Molecular Biology, University of Melbourne , Parkville, Victoria 3010, Australia
| | - Gavin E Reid
- Department of Biochemistry and Molecular Biology, University of Melbourne , Parkville, Victoria 3010, Australia.,School of Chemistry, University of Melbourne , Parkville, Victoria 3010, Australia.,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne , Parkville, Victoria 3010, Australia
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50
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Cajka T, Smilowitz JT, Fiehn O. Validating Quantitative Untargeted Lipidomics Across Nine Liquid Chromatography-High-Resolution Mass Spectrometry Platforms. Anal Chem 2017; 89:12360-12368. [PMID: 29064229 DOI: 10.1021/acs.analchem.7b03404] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Liquid chromatography-mass spectrometry (LC-MS) methods are most often used for untargeted metabolomics and lipidomics. However, methods have not been standardized as accepted "best practice" documents, and reports lack harmonization with respect to quantitative data that enable interstudy comparisons. Researchers use a wide variety of high-resolution mass spectrometers under different operating conditions, and it is unclear if results would yield different biological conclusions depending on the instrument performance. To this end, we used 126 identical human plasma samples and 29 quality control samples from a nutritional intervention study. We investigated lipidomic data acquisitions across nine different MS instruments (1 single TOF, 1 Q/orbital ion trap, and 7 QTOF instruments). Sample preparations, chromatography conditions, and data processing methods were kept identical. Single-point internal standard calibrations were used to estimate absolute concentrations for 307 unique lipids identified by accurate mass, MS/MS spectral match, and retention times. Quantitative results were highly comparable between the LC-MS platforms tested. Using partial least-squares discriminant analysis (PLS-DA) to compare results between platforms, a 92% overlap for the most discriminating lipids based on variable importance in projection (VIP) scores was achieved for all lipids that were detected by at least two instrument platforms. Importantly, even the relative positions of individual samples on the PLS-DA projections were identical. The key for success in harmonizing results was to avoid ion saturation by carefully evaluating linear dynamic ranges using serial dilutions and adjusting the resuspension volume and/or injection volume before running actual study samples.
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Affiliation(s)
- Tomas Cajka
- West Coast Metabolomics Center, UC Davis Genome Center, University of California, Davis , Davis, California 95616, United States
| | - Jennifer T Smilowitz
- Department of Food Science and Technology, University of California, Davis , Davis, California 95616, United States.,Foods for Health Institute, University of California Davis , Davis, California 95616, United States
| | - Oliver Fiehn
- West Coast Metabolomics Center, UC Davis Genome Center, University of California, Davis , Davis, California 95616, United States.,Biochemistry Department, Faculty of Science, King Abdulaziz University , Jeddah 21589, Saudi Arabia
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