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Martínez S, Fernández-García M, Londoño-Osorio S, Barbas C, Gradillas A. Highly reliable LC-MS lipidomics database for efficient human plasma profiling based on NIST SRM 1950. J Lipid Res 2024:100671. [PMID: 39395790 DOI: 10.1016/j.jlr.2024.100671] [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: 06/27/2024] [Revised: 10/04/2024] [Accepted: 10/07/2024] [Indexed: 10/14/2024] Open
Abstract
Liquid chromatography coupled to high resolution mass spectrometry (LC-HRMS)-based methods have become the gold standard methodology for the comprehensive profiling of the human plasma lipidome. However, both the complexity of lipid chemistry and LC-HRMS-associated data pose challenges to the characterization of this biological matrix. In accordance with the current consensus of quality requirements for LC-HRMS lipidomics data, we aimed to characterize the NIST® Standard Reference Material for Human Plasma (SRM 1950) using an LC-ESI(+/-)-MS method compatible with high-throughput lipidome profiling. We generated a highly curated lipid database with increased coverage, quality, and consistency, including additional quality assurance procedures involving adduct formation, within-method m/z evaluation, retention behavior of species within lipid chain isomers, and expert-driven resolution of isomeric and isobaric interferences. As a proof-of-concept, we showed the utility of our in-house LC-MS lipidomic database -consisting of 592 lipid entries- for the fast, comprehensive, and reliable lipidomic profiling of the human plasma from healthy human volunteers. We are confident that the implementation of this robust resource and methodology will have a significant impact by reducing data redundancy and the current delays and bottlenecks in untargeted plasma lipidomic studies.
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Affiliation(s)
- Sara Martínez
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Miguel Fernández-García
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain; Departamento de Ciencias Médicas Básicas, Facultad de Medicina, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Sara Londoño-Osorio
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain.
| | - Ana Gradillas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, Spain.
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Ferré-González L, Balaguer Á, Roca M, Ftara A, Lloret A, Cháfer-Pericás C. Plasma lipidomics in early APP/PS1 female mouse model and its relationship with brain: Is it affected by the estrous cycle? Alzheimers Res Ther 2024; 16:183. [PMID: 39143583 PMCID: PMC11323474 DOI: 10.1186/s13195-024-01549-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] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 07/31/2024] [Indexed: 08/16/2024]
Abstract
BACKGROUND Alzheimer's disease (AD) is the most prevalent dementia, showing higher incidence in women. Besides, lipids play an essential role in brain, and they could be dysregulated in neurodegeneration. Specifically, impaired plasma lipid levels could predict early AD diagnosis. This work aims to identify the main plasma lipids altered in early AD female mouse model and evaluate their relationship with brain lipidome. Also, the possible involvement of the estrous cycle in lipid metabolism has been evaluated. METHODS Plasma samples of wild-type (n = 10) and APP/PS1 (n = 10) female mice of 5 months of age were collected, processed, and analysed using a lipidomic mass spectrometry-based method. A statistical analysis involving univariate and multivariate approaches was performed to identify significant lipid differences related to AD between groups. Also, cytology tests were conducted to confirm estrous cycle phases. RESULTS Three hundred thirty lipids were detected in plasma, 18 of them showed significant differences between groups; specifically, some triacylglycerols, cholesteryl esters, lysophosphatidylcholines, phosphatidylcholines, and ether-linked phosphatidylcholines, increased in early AD; while other phosphatidylcholines, phosphatidylethanolamines, ceramides, and ether-linked phosphatidylethanolamines decreased in early AD. A multivariate approach was developed from some lipid variables, showing high diagnostic indexes (70% sensitivity, 90% specificity, 80% accuracy). From brain and plasma lipidome, some significant correlations were observed, mainly in the glycerophospholipid family. Also, some differences were found in both plasma and brain lipids, according to the estrous cycle phase. CONCLUSIONS Therefore, lipid alterations can be identified in plasma at early AD stages in mice females, with a relationship with brain lipid metabolism for most of the lipid subfamilies, suggesting some lipids as potential AD biomarkers. In addition, the estrous cycle monitoring could be relevant in female studies.
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Affiliation(s)
- Laura Ferré-González
- Alzheimer's Disease Research Group, Instituto de Investigación Sanitaria La Fe, Avda de Fernando Abril Martorell, 106; 46026, Valencia, Spain
| | - Ángel Balaguer
- Faculty of Mathematics, University of Valencia, Valencia, Spain
| | - Marta Roca
- Analytical Unit, Health Research Institute La Fe, Valencia, Spain
| | - Artemis Ftara
- Department of Physiology, Faculty of Medicine, University of Valencia, Health Research Institute INCLIVA, Valencia, Spain
| | - Ana Lloret
- Department of Physiology, Faculty of Medicine, University of Valencia, Health Research Institute INCLIVA, Valencia, Spain
| | - Consuelo Cháfer-Pericás
- Alzheimer's Disease Research Group, Instituto de Investigación Sanitaria La Fe, Avda de Fernando Abril Martorell, 106; 46026, Valencia, Spain.
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Fernandez Requena B, Gonzalez-Riano C, Barbas C. Addressing the untargeted lipidomics challenge in urine samples: Comparative study of extraction methods by UHPLC-ESI-QTOF-MS. Anal Chim Acta 2024; 1299:342433. [PMID: 38499427 DOI: 10.1016/j.aca.2024.342433] [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: 09/13/2023] [Revised: 02/23/2024] [Accepted: 02/26/2024] [Indexed: 03/20/2024]
Abstract
Urine analysis has remained a fundamental and widely used method in clinical diagnostics for over a century. With its minimal invasive nature and comprehensive range of analytes, urine has established itself as a clinical diagnostic tool for various disorders, including renal, urological, metabolic, and endocrine diseases. Furthermore, urine's unique attributes make it an attractive matrix for biomarker discovery, as well as in assessing the metabolic and physiological states of patients and healthy individuals alike. However, limitations in our knowledge of average values and sources of urinary lipids decrease the wider clinical application of urinary lipidomics. In this context, untargeted lipidomics analysis relies heavily on the extraction and analysis of lipids in biological samples. Nevertheless, this type of analysis presents challenges in lipid identification due to the diverse nature of lipids. Therefore, proper sample treatment before analysis is crucial to obtain robust and reproducible lipidomic profiles. To address this gap, we conducted a comparative study of a urine pool sample collected from twenty healthy volunteers using four different lipid extraction methods: one biphasic and three monophasic protocols. The extracted lipids were then analyzed using UHPLC-MS and MS/MS, and the semi-quantification of all the accurately annotated lipid species was performed for each extraction method.
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Affiliation(s)
- Belen Fernandez Requena
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, España
| | - Carolina Gonzalez-Riano
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, España
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660 Boadilla del Monte, Madrid, España.
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Ferré-González L, Balaguer Á, Roca M, Ftara A, Lloret A, Cháfer-Pericás C. Brain areas lipidomics in female transgenic mouse model of Alzheimer's disease. Sci Rep 2024; 14:870. [PMID: 38195731 PMCID: PMC10776612 DOI: 10.1038/s41598-024-51463-3] [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: 09/14/2023] [Accepted: 01/05/2024] [Indexed: 01/11/2024] Open
Abstract
Lipids are the major component of the brain with important structural and functional properties. Lipid disruption could play a relevant role in Alzheimer's disease (AD). Some brain lipidomic studies showed significant differences compared to controls, but few studies have focused on different brain areas related to AD. Furthermore, AD is more prevalent in females, but there is a lack of studies focusing on this sex. This work aims to perform a lipidomic study in selected brain areas (cerebellum, amygdala, hippocampus, entire cortex) from wild-type (WT, n = 10) and APPswe/PS1dE9 transgenic (TG, n = 10) female mice of 5 months of age, as a model of early AD, to identify alterations in lipid composition. A lipidomic mass spectrometry-based method was optimized and applied to brain tissue. As result, some lipids showed statistically significant differences between mice groups in cerebellum (n = 68), amygdala (n = 49), hippocampus (n = 48), and the cortex (n = 22). In addition, some lipids (n = 15) from the glycerolipid, phospholipid, and sphingolipid families were statistically significant in several brain areas simultaneously between WT and TG. A selection of lipid variables was made to develop a multivariate approach to assess their discriminant potential, showing high diagnostic indexes, especially in cerebellum and amygdala (sensitivity 70-100%, sensibility 80-100%).
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Affiliation(s)
- Laura Ferré-González
- Alzheimer's Disease Research Group, Health Research Institute La Fe, Avda de Fernando Abril Martorell, 106, 46026, Valencia, Spain
| | - Ángel Balaguer
- Faculty of Mathematics, University of Valencia, Valencia, Spain
| | - Marta Roca
- Analytical Unit, Health Research Institute La Fe, Valencia, Spain
| | | | - Ana Lloret
- Department of Physiology, Faculty of Medicine, University of Valencia, Health Research Institute INCLIVA, Valencia, Spain
| | - Consuelo Cháfer-Pericás
- Alzheimer's Disease Research Group, Health Research Institute La Fe, Avda de Fernando Abril Martorell, 106, 46026, Valencia, Spain.
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Fernández Requena B, Nadeem S, Reddy VP, Naidoo V, Glasgow JN, Steyn AJC, Barbas C, Gonzalez-Riano C. LiLA: lipid lung-based ATLAS built through a comprehensive workflow designed for an accurate lipid annotation. Commun Biol 2024; 7:45. [PMID: 38182666 PMCID: PMC10770321 DOI: 10.1038/s42003-023-05680-7] [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: 08/17/2023] [Accepted: 12/06/2023] [Indexed: 01/07/2024] Open
Abstract
Accurate lipid annotation is crucial for understanding the role of lipids in health and disease and identifying therapeutic targets. However, annotating the wide variety of lipid species in biological samples remains challenging in untargeted lipidomic studies. In this work, we present a lipid annotation workflow based on LC-MS and MS/MS strategies, the combination of four bioinformatic tools, and a decision tree to support the accurate annotation and semi-quantification of the lipid species present in lung tissue from control mice. The proposed workflow allowed us to generate a lipid lung-based ATLAS (LiLA), which was then employed to unveil the lipidomic signatures of the Mycobacterium tuberculosis infection at two different time points for a deeper understanding of the disease progression. This workflow, combined with manual inspection strategies of MS/MS data, can enhance the annotation process for lipidomic studies and guide the generation of sample-specific lipidome maps. LiLA serves as a freely available data resource that can be employed in future studies to address lipidomic alterations in mice lung tissue.
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Affiliation(s)
- Belén Fernández Requena
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660, Boadilla del Monte, España
| | - Sajid Nadeem
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Vineel P Reddy
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Joel N Glasgow
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Adrie J C Steyn
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL, USA
- Africa Health Research Institute, Durban, South Africa
- Centers for AIDS Research and Free Radical Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660, Boadilla del Monte, España.
| | - Carolina Gonzalez-Riano
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Urbanización Montepríncipe, 28660, Boadilla del Monte, España.
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