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Busnelli M, Manzini S, Colombo A, Franchi E, Lääperi M, Laaksonen R, Chiesa G. Effect of Diets on Plasma and Aorta Lipidome: A Study in the apoE Knockout Mouse Model. Mol Nutr Food Res 2023; 67:e2200367. [PMID: 36419336 DOI: 10.1002/mnfr.202200367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 09/20/2022] [Indexed: 11/27/2022]
Abstract
SCOPE Specific lipid molecules circulating in plasma at low concentrations have emerged as biomarkers of atherosclerotic risk. The aim of the present study is that of evaluating, in an athero-prone mouse model, how different diets can affect plasma and aorta lipidome. METHODS AND RESULTS Thirty-six apoE knockout mice are divided in three groups and feed 12 weeks with diets differing for cholesterol and fatty acid content. Atherosclerosis is measured at the aortic sinus and aorta. Lipids are quantified in plasma and aorta with mass spectrometry. The cholesterol content of the diets is the main driver of lipid accumulation in plasma and aorta. The fatty acid composition of the diets affects plasma levels both of essential (linoleic acid) and nonessential (myristic and arachidonic acid) ones. Lipidomics show a comparable distribution, in plasma and aorta, of the main lipid components of oxidized LDL, including cholesteryl esters and lysophosphatidylcholines. Interestingly, lactosylceramide, glucosyl/galactosylceramide, and individual ceramide species are found to accumulate in diseased aortic segments. CONCLUSION Both the cholesterol and fatty acid content of the diets profoundly affect plasma lipidome. Aorta lipidome is likewise affected with the accumulation of specific lipids known as markers of atherosclerosis.
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Affiliation(s)
- Marco Busnelli
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, via Balzaretti, 9, Milan, 20133, Italy
| | - Stefano Manzini
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, via Balzaretti, 9, Milan, 20133, Italy
| | - Alice Colombo
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, via Balzaretti, 9, Milan, 20133, Italy
| | - Elsa Franchi
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, via Balzaretti, 9, Milan, 20133, Italy
| | | | - Reijo Laaksonen
- Zora Biosciences Oy, Espoo, 02150, Finland.,Finnish Cardiovascular Research Center, University of Tampere, Tampere, 33520, Finland
| | - Giulia Chiesa
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, via Balzaretti, 9, Milan, 20133, Italy
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Hoffmann N, Mayer G, Has C, Kopczynski D, Al Machot F, Schwudke D, Ahrends R, Marcus K, Eisenacher M, Turewicz M. A Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics. Metabolites 2022; 12:584. [PMID: 35888710 PMCID: PMC9319858 DOI: 10.3390/metabo12070584] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/17/2022] [Accepted: 06/19/2022] [Indexed: 12/13/2022] Open
Abstract
Mass spectrometry is a widely used technology to identify and quantify biomolecules such as lipids, metabolites and proteins necessary for biomedical research. In this study, we catalogued freely available software tools, libraries, databases, repositories and resources that support lipidomics data analysis and determined the scope of currently used analytical technologies. Because of the tremendous importance of data interoperability, we assessed the support of standardized data formats in mass spectrometric (MS)-based lipidomics workflows. We included tools in our comparison that support targeted as well as untargeted analysis using direct infusion/shotgun (DI-MS), liquid chromatography-mass spectrometry, ion mobility or MS imaging approaches on MS1 and potentially higher MS levels. As a result, we determined that the Human Proteome Organization-Proteomics Standards Initiative standard data formats, mzML and mzTab-M, are already supported by a substantial number of recent software tools. We further discuss how mzTab-M can serve as a bridge between data acquisition and lipid bioinformatics tools for interpretation, capturing their output and transmitting rich annotated data for downstream processing. However, we identified several challenges of currently available tools and standards. Potential areas for improvement were: adaptation of common nomenclature and standardized reporting to enable high throughput lipidomics and improve its data handling. Finally, we suggest specific areas where tools and repositories need to improve to become FAIRer.
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Affiliation(s)
- Nils Hoffmann
- Forschungszentrum Jülich GmbH, Institute for Bio- and Geosciences (IBG-5), 52425 Jülich, Germany
| | - Gerhard Mayer
- Institute of Medical Systems Biology, Ulm University, 89081 Ulm, Germany;
| | - Canan Has
- Biological Mass Spectrometry, Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany;
- University Hospital Carl Gustav Carus, 01307 Dresden, Germany
- CENTOGENE GmbH, 18055 Rostock, Germany
| | - Dominik Kopczynski
- Department of Analytical Chemistry, University of Vienna, 1090 Vienna, Austria; (D.K.); (R.A.)
| | - Fadi Al Machot
- Faculty of Science and Technology, Norwegian University for Life Science (NMBU), 1433 Ås, Norway;
| | - Dominik Schwudke
- Bioanalytical Chemistry, Forschungszentrum Borstel, Leibniz Lung Center, 23845 Borstel, Germany;
- Airway Research Center North, German Center for Lung Research (DZL), 23845 Borstel, Germany
- German Center for Infection Research (DZIF), TTU Tuberculosis, 23845 Borstel, Germany
| | - Robert Ahrends
- Department of Analytical Chemistry, University of Vienna, 1090 Vienna, Austria; (D.K.); (R.A.)
| | - Katrin Marcus
- Center for Protein Diagnostics (ProDi), Medical Proteome Analysis, Ruhr University Bochum, 44801 Bochum, Germany; (K.M.); (M.E.)
| | - Martin Eisenacher
- Center for Protein Diagnostics (ProDi), Medical Proteome Analysis, Ruhr University Bochum, 44801 Bochum, Germany; (K.M.); (M.E.)
- Faculty of Medicine, Medizinisches Proteom-Center, Ruhr University Bochum, 44801 Bochum, Germany
| | - Michael Turewicz
- Institute for Clinical Biochemistry and Pathobiochemistry, German Diabetes Center (DDZ), Leibniz Center for Diabetes Research at Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Düsseldorf, 85764 Neuherberg, Germany
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Manzini S, Busnelli M, Colombo A, Franchi E, Grossano P, Chiesa G. reString: an open-source Python software to perform automatic functional enrichment retrieval, results aggregation and data visualization. Sci Rep 2021; 11:23458. [PMID: 34873191 PMCID: PMC8648753 DOI: 10.1038/s41598-021-02528-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 10/28/2021] [Indexed: 11/30/2022] Open
Abstract
Functional enrichment analysis is an analytical method to extract biological insights from gene expression data, popularized by the ever-growing application of high-throughput techniques. Typically, expression profiles are generated for hundreds to thousands of genes/proteins from samples belonging to two experimental groups, and after ad-hoc statistical tests, researchers are left with lists of statistically significant entities, possibly lacking any unifying biological theme. Functional enrichment tackles the problem of putting overall gene expression changes into a broader biological context, based on pre-existing knowledge bases of reference: database collections of known expression regulation, relationships and molecular interactions. STRING is among the most popular tools, providing both protein-protein interaction networks and functional enrichment analysis for any given set of identifiers. For complex experimental designs, manually retrieving, interpreting, analyzing and abridging functional enrichment results is a daunting task, usually performed by hand by the average wet-biology researcher. We have developed reString, a cross-platform software that seamlessly retrieves from STRING functional enrichments from multiple user-supplied gene sets, with just a few clicks, without any need for specific bioinformatics skills. Further, it aggregates all findings into human-readable table summaries, with built-in features to easily produce user-customizable publication-grade clustermaps and bubble plots. Herein, we outline a complete reString protocol, showcasing its features on a real use-case.
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Affiliation(s)
- Stefano Manzini
- Department of Pharmacological and Biomolecular Sciences, Università Degli Studi Di Milano, Milan, Italy.
| | - Marco Busnelli
- Department of Pharmacological and Biomolecular Sciences, Università Degli Studi Di Milano, Milan, Italy
| | - Alice Colombo
- Department of Pharmacological and Biomolecular Sciences, Università Degli Studi Di Milano, Milan, Italy
| | - Elsa Franchi
- Department of Pharmacological and Biomolecular Sciences, Università Degli Studi Di Milano, Milan, Italy
| | - Pasquale Grossano
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Giulia Chiesa
- Department of Pharmacological and Biomolecular Sciences, Università Degli Studi Di Milano, Milan, Italy.
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