1
|
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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [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.
Collapse
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
| |
Collapse
|
2
|
Parchem K, Letsiou S, Petan T, Oskolkova O, Medina I, Kuda O, O'Donnell VB, Nicolaou A, Fedorova M, Bochkov V, Gladine C. Oxylipin profiling for clinical research: Current status and future perspectives. Prog Lipid Res 2024:101276. [PMID: 38697517 DOI: 10.1016/j.plipres.2024.101276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 04/24/2024] [Accepted: 04/29/2024] [Indexed: 05/05/2024]
Abstract
Oxylipins are potent lipid mediators with increasing interest in clinical research. They are usually measured in systemic circulation and can provide a wealth of information regarding key biological processes such as inflammation, vascular tone, or blood coagulation. Although procedures still require harmonization to generate comparable oxylipin datasets, performing comprehensive profiling of circulating oxylipins in large studies is feasible and no longer restricted by technical barriers. However, it is essential to improve and facilitate the biological interpretation of complex oxylipin profiles to truly leverage their potential in clinical research. This requires regular updating of our knowledge about the metabolism and the mode of action of oxylipins, and consideration of all factors that may influence circulating oxylipin profiles independently of the studied disease or condition. This review aims to provide the readers with updated and necessary information regarding oxylipin metabolism, their different forms in systemic circulation, the current limitations in deducing oxylipin cellular effects from in vitro bioactivity studies, the biological and technical confounding factors needed to consider for a proper interpretation of oxylipin profiles.
Collapse
Affiliation(s)
- Karol Parchem
- Department of Food Chemistry, Technology and Biotechnology, Faculty of Chemistry, Gdańsk University of Technology, 11/12 Gabriela Narutowicza St., 80-233 Gdańsk, Poland; Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, 53210 Pardubice, Czech Republic
| | - Sophia Letsiou
- Department of Biomedical Sciences, University of West Attica, Ag. Spiridonos St. Egaleo, 12243 Athens, Greece.
| | - Toni Petan
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia.
| | - Olga Oskolkova
- Institute of Pharmaceutical Sciences, University of Graz, Humboldtstrasse 46/III, 8010 Graz, Austria.
| | - Isabel Medina
- Instituto de Investigaciones Marinas-Consejo Superior de Investigaciones Científicas (IIM-CSIC), Eduardo Cabello 6, E-36208 Vigo, Spain.
| | - Ondrej Kuda
- Institute of Physiology, Czech Academy of Sciences, Videnska 1083, 14200 Prague, Czech Republic.
| | - Valerie B O'Donnell
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK.
| | - Anna Nicolaou
- School of Health Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9NT, UK.
| | - Maria Fedorova
- Center of Membrane Biochemistry and Lipid Research, University Hospital and Faculty of Medicine Carl Gustav Carus of TU Dresden, 01307 Dresden, Germany.
| | - Valery Bochkov
- Institute of Pharmaceutical Sciences, University of Graz, Humboldtstrasse 46/III, 8010 Graz, Austria.
| | - Cécile Gladine
- Université Clermont Auvergne, INRAE, UNH, Clermont-Ferrand, France.
| |
Collapse
|
3
|
Ferreira CR, Lima Gomes PCFD, Robison KM, Cooper BR, Shannahan JH. Implementation of multiomic mass spectrometry approaches for the evaluation of human health following environmental exposure. Mol Omics 2024. [PMID: 38623720 DOI: 10.1039/d3mo00214d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Omics analyses collectively refer to the possibility of profiling genetic variants, RNA, epigenetic markers, proteins, lipids, and metabolites. The most common analytical approaches used for detecting molecules present within biofluids related to metabolism are vibrational spectroscopy techniques, represented by infrared, Raman, and nuclear magnetic resonance (NMR) spectroscopies and mass spectrometry (MS). Omics-based assessments utilizing MS are rapidly expanding and being applied to various scientific disciplines and clinical settings. Most of the omics instruments are operated by specialists in dedicated laboratories; however, the development of miniature portable omics has made the technology more available to users for field applications. Variations in molecular information gained from omics approaches are useful for evaluating human health following environmental exposure and the development and progression of numerous diseases. As MS technology develops so do statistical and machine learning methods for the detection of molecular deviations from personalized metabolism, which are correlated to altered health conditions, and they are intended to provide a multi-disciplinary overview for researchers interested in adding multiomic analysis to their current efforts. This includes an introduction to mass spectrometry-based omics technologies, current state-of-the-art capabilities and their respective strengths and limitations for surveying molecular information. Furthermore, we describe how knowledge gained from these assessments can be applied to personalized medicine and diagnostic strategies.
Collapse
Affiliation(s)
- Christina R Ferreira
- Purdue Metabolite Profiling Facility, Purdue University, West Lafayette, IN 47907, USA.
| | | | - Kiley Marie Robison
- School of Health Sciences, College of Health and Human Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Bruce R Cooper
- Purdue Metabolite Profiling Facility, Purdue University, West Lafayette, IN 47907, USA.
| | - Jonathan H Shannahan
- School of Health Sciences, College of Health and Human Sciences, Purdue University, West Lafayette, IN 47907, USA
| |
Collapse
|
4
|
Tsugawa H, Ishihara T, Ogasa K, Iwanami S, Hori A, Takahashi M, Yamada Y, Satoh-Takayama N, Ohno H, Minoda A, Arita M. A lipidome landscape of aging in mice. Nat Aging 2024:10.1038/s43587-024-00610-6. [PMID: 38609525 DOI: 10.1038/s43587-024-00610-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 03/07/2024] [Indexed: 04/14/2024]
Abstract
Understanding the molecular mechanisms of aging is crucial for enhancing healthy longevity. We conducted untargeted lipidomics across 13 biological samples from mice at various life stages (2, 12, 19 and 24 months) to explore the potential link between aging and lipid metabolism, considering sex (male or female) and microbiome (specific pathogen-free or germ-free) dependencies. By analyzing 2,704 molecules from 109 lipid subclasses, we characterized common and tissue-specific lipidome alterations associated with aging. For example, the levels of bis(monoacylglycero)phosphate containing polyunsaturated fatty acids increased in various organs during aging, whereas the levels of other phospholipids containing saturated and monounsaturated fatty acids decreased. In addition, we discovered age-dependent sulfonolipid accumulation, absent in germ-free mice, correlating with Alistipes abundance determined by 16S ribosomal RNA gene amplicon sequencing. In the male kidney, glycolipids such as galactosylceramides, galabiosylceramides (Gal2Cer), trihexosylceramides (Hex3Cer), and mono- and digalactosyldiacylglycerols were detected, with two lipid classes-Gal2Cer and Hex3Cer-being significantly enriched in aged mice. Integrated analysis of the kidney transcriptome revealed uridine diphosphate galactosyltransferase 8A (UGT8a), alkylglycerone phosphate synthase and fatty acyl-coenzyme A reductase 1 as potential enzymes responsible for the male-specific glycolipid biosynthesis in vivo, which would be relevant to sex dependency in kidney diseases. Inhibiting UGT8 reduced the levels of these glycolipids and the expression of inflammatory cytokines in the kidney. Our study provides a valuable resource for clarifying potential links between lipid metabolism and aging.
Collapse
Affiliation(s)
- Hiroshi Tsugawa
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan.
- Metabolome Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan.
- Molecular and Cellular Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan.
| | - Tomoaki Ishihara
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Pharmacy, Nagasaki International University, Sasebo, Japan
| | - Kota Ogasa
- Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, Tokyo, Japan
| | - Seigo Iwanami
- Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, Tokyo, Japan
| | - Aya Hori
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Mikiko Takahashi
- Metabolome Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Yutaka Yamada
- Metabolome Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Naoko Satoh-Takayama
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hiroshi Ohno
- Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Aki Minoda
- Laboratory for Cellular Epigenomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands
| | - Makoto Arita
- Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
- Molecular and Cellular Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan.
- Division of Physiological Chemistry and Metabolism, Graduate School of Pharmaceutical Sciences, Keio University, Tokyo, Japan.
- Human Biology-Microbiome-Quantum Research Center (WPI-Bio2Q), Keio University, Tokyo, Japan.
| |
Collapse
|
5
|
Henne WM. Navigating the omics era of lipid metabolism. Dev Cell 2024; 59:561-565. [PMID: 38471437 DOI: 10.1016/j.devcel.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/28/2023] [Accepted: 02/01/2024] [Indexed: 03/14/2024]
Abstract
In this opinion, Mike Henne discusses the benefits and challenges for the lipid metabolism field as it embraces omics-oriented approaches, and highlights new online databases that make lipid-related "big data" more accessible to the scientific community.
Collapse
Affiliation(s)
- W Mike Henne
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA.
| |
Collapse
|
6
|
Sarkar S, Roy D, Chatterjee B, Ghosh R. Clinical advances in analytical profiling of signature lipids: implications for severe non-communicable and neurodegenerative diseases. Metabolomics 2024; 20:37. [PMID: 38459207 DOI: 10.1007/s11306-024-02100-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 02/06/2024] [Indexed: 03/10/2024]
Abstract
BACKGROUND Lipids play key roles in numerous biological processes, including energy storage, cell membrane structure, signaling, immune responses, and homeostasis, making lipidomics a vital branch of metabolomics that analyzes and characterizes a wide range of lipid classes. Addressing the complex etiology, age-related risk, progression, inflammation, and research overlap in conditions like Alzheimer's Disease, Parkinson's Disease, Cardiovascular Diseases, and Cancer poses significant challenges in the quest for effective therapeutic targets, improved diagnostic markers, and advanced treatments. Mass spectrometry is an indispensable tool in clinical lipidomics, delivering quantitative and structural lipid data, and its integration with technologies like Liquid Chromatography (LC), Magnetic Resonance Imaging (MRI), and few emerging Matrix-Assisted Laser Desorption Ionization- Imaging Mass Spectrometry (MALDI-IMS) along with its incorporation into Tissue Microarray (TMA) represents current advances. These innovations enhance lipidomics assessment, bolster accuracy, and offer insights into lipid subcellular localization, dynamics, and functional roles in disease contexts. AIM OF THE REVIEW The review article summarizes recent advancements in lipidomic methodologies from 2019 to 2023 for diagnosing major neurodegenerative diseases, Alzheimer's and Parkinson's, serious non-communicable cardiovascular diseases and cancer, emphasizing the role of lipid level variations, and highlighting the potential of lipidomics data integration with genomics and proteomics to improve disease understanding and innovative prognostic, diagnostic and therapeutic strategies. KEY SCIENTIFIC CONCEPTS OF REVIEW Clinical lipidomic studies are a promising approach to track and analyze lipid profiles, revealing their crucial roles in various diseases. This lipid-focused research provides insights into disease mechanisms, biomarker identification, and potential therapeutic targets, advancing our understanding and management of conditions such as Alzheimer's Disease, Parkinson's Disease, Cardiovascular Diseases, and specific cancers.
Collapse
Affiliation(s)
- Sutanu Sarkar
- Amity Institute of Biotechnology (AIBNK), Amity University, Rajarhat, Newtown Action Area 2, Kolkata, 700135, West Bengal, India
| | - Deotima Roy
- Amity Institute of Biotechnology (AIBNK), Amity University, Rajarhat, Newtown Action Area 2, Kolkata, 700135, West Bengal, India
| | - Bhaskar Chatterjee
- Amity Institute of Biotechnology (AIBNK), Amity University, Rajarhat, Newtown Action Area 2, Kolkata, 700135, West Bengal, India
| | - Rajgourab Ghosh
- Amity Institute of Biotechnology (AIBNK), Amity University, Rajarhat, Newtown Action Area 2, Kolkata, 700135, West Bengal, India.
| |
Collapse
|
7
|
Lattau SSJ, Borsch LM, Auf dem Brinke K, Klose C, Vinhoven L, Nietert M, Fitzner D. Plasma Lipidomic Profiling Using Mass Spectrometry for Multiple Sclerosis Diagnosis and Disease Activity Stratification (LipidMS). Int J Mol Sci 2024; 25:2483. [PMID: 38473733 DOI: 10.3390/ijms25052483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/02/2024] [Accepted: 02/13/2024] [Indexed: 03/14/2024] Open
Abstract
This investigation explores the potential of plasma lipidomic signatures for aiding in the diagnosis of Multiple Sclerosis (MS) and evaluating the clinical course and disease activity of diseased patients. Plasma samples from 60 patients with MS (PwMS) were clinically stratified to either a relapsing-remitting (RRMS) or a chronic progressive MS course and 60 age-matched controls were analyzed using state-of-the-art direct infusion quantitative shotgun lipidomics. To account for potential confounders, data were filtered for age and BMI correlations. The statistical analysis employed supervised and unsupervised multivariate data analysis techniques, including a principal component analysis (PCA), a partial least squares discriminant analysis (oPLS-DA) and a random forest (RF). To determine whether the significant absolute differences in the lipid subspecies have a relevant effect on the overall composition of the respective lipid classes, we introduce a class composition visualization (CCV). We identified 670 lipids across 16 classes. PwMS showed a significant increase in diacylglycerols (DAG), with DAG 16:0;0_18:1;0 being proven to be the lipid with the highest predictive ability for MS as determined by RF. The alterations in the phosphatidylethanolamines (PE) were mainly linked to RRMS while the alterations in the ether-bound PEs (PE O-) were found in chronic progressive MS. The amount of CE species was reduced in the CPMS cohort whereas TAG species were reduced in the RRMS patients, both lipid classes being relevant in lipid storage. Combining the above mentioned data analyses, distinct lipidomic signatures were isolated and shown to be correlated with clinical phenotypes. Our study suggests that specific plasma lipid profiles are not merely associated with the diagnosis of MS but instead point toward distinct clinical features in the individual patient paving the way for personalized therapy and an enhanced understanding of MS pathology.
Collapse
Affiliation(s)
| | - Lisa-Marie Borsch
- Department of Neurology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | | | | | - Liza Vinhoven
- Department of Medical Bioinformatics, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Manuel Nietert
- Department of Medical Bioinformatics, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Dirk Fitzner
- Department of Neurology, University Medical Center Göttingen, 37075 Göttingen, Germany
| |
Collapse
|
8
|
Gerhardtova I, Jankech T, Majerova P, Piestansky J, Olesova D, Kovac A, Jampilek J. Recent Analytical Methodologies in Lipid Analysis. Int J Mol Sci 2024; 25:2249. [PMID: 38396926 PMCID: PMC10889185 DOI: 10.3390/ijms25042249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/09/2024] [Accepted: 02/11/2024] [Indexed: 02/25/2024] Open
Abstract
Lipids represent a large group of biomolecules that are responsible for various functions in organisms. Diseases such as diabetes, chronic inflammation, neurological disorders, or neurodegenerative and cardiovascular diseases can be caused by lipid imbalance. Due to the different stereochemical properties and composition of fatty acyl groups of molecules in most lipid classes, quantification of lipids and development of lipidomic analytical techniques are problematic. Identification of different lipid species from complex matrices is difficult, and therefore individual analytical steps, which include extraction, separation, and detection of lipids, must be chosen properly. This review critically documents recent strategies for lipid analysis from sample pretreatment to instrumental analysis and data interpretation published in the last five years (2019 to 2023). The advantages and disadvantages of various extraction methods are covered. The instrumental analysis step comprises methods for lipid identification and quantification. Mass spectrometry (MS) is the most used technique in lipid analysis, which can be performed by direct infusion MS approach or in combination with suitable separation techniques such as liquid chromatography or gas chromatography. Special attention is also given to the correct evaluation and interpretation of the data obtained from the lipid analyses. Only accurate, precise, robust and reliable analytical strategies are able to bring complex and useful lipidomic information, which may contribute to clarification of some diseases at the molecular level, and may be used as putative biomarkers and/or therapeutic targets.
Collapse
Affiliation(s)
- Ivana Gerhardtova
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, SK-845 10 Bratislava, Slovakia
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, SK-842 15 Bratislava, Slovakia
| | - Timotej Jankech
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, SK-845 10 Bratislava, Slovakia
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, SK-842 15 Bratislava, Slovakia
| | - Petra Majerova
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, SK-845 10 Bratislava, Slovakia
| | - Juraj Piestansky
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, SK-845 10 Bratislava, Slovakia
- Toxicological and Antidoping Center, Faculty of Pharmacy, Comenius University in Bratislava, Odbojarov 10, SK-832 32 Bratislava, Slovakia
- Department of Galenic Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Odbojarov 10, SK-832 32 Bratislava, Slovakia
| | - Dominika Olesova
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, SK-845 10 Bratislava, Slovakia
- Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, Dubravska cesta 9, SK-845 05 Bratislava, Slovakia
| | - Andrej Kovac
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, SK-845 10 Bratislava, Slovakia
- Department of Pharmacology and Toxicology, University of Veterinary Medicine and Pharmacy in Kosice, Komenskeho 68/73, SK-041 81 Kosice, Slovakia
| | - Josef Jampilek
- Institute of Neuroimmunology, Slovak Academy of Sciences, Dubravska cesta 9, SK-845 10 Bratislava, Slovakia
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovicova 6, SK-842 15 Bratislava, Slovakia
| |
Collapse
|
9
|
Jumel T, Shevchenko A. Multispecies Benchmark Analysis for LC-MS/MS Validation and Performance Evaluation in Bottom-Up Proteomics. J Proteome Res 2024; 23:684-691. [PMID: 38243904 PMCID: PMC10845134 DOI: 10.1021/acs.jproteome.3c00531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 12/04/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024]
Abstract
We present an instrument-independent benchmark procedure and software (LFQ_bout) for the validation and comparative evaluation of the performance of LC-MS/MS and data processing workflows in bottom-up proteomics. The procedure enables a back-to-back comparison of common and emerging workflows, e.g., diaPASEF or ScanningSWATH, and evaluates the impact of arbitrary and inadequately documented settings or black-box data processing algorithms. It enhances the overall performance and quantification accuracy by recognizing and reporting common quantification errors.
Collapse
Affiliation(s)
- Tobias Jumel
- Max Planck Institute of
Molecular Cell Biology and Genetics (MPI-CBG), Pfotenhauerstraße 108, 01307 Dresden, Germany
| | - Andrej Shevchenko
- Max Planck Institute of
Molecular Cell Biology and Genetics (MPI-CBG), Pfotenhauerstraße 108, 01307 Dresden, Germany
| |
Collapse
|
10
|
Peterka O, Maccelli A, Jirásko R, Vaňková Z, Idkowiak J, Hrstka R, Wolrab D, Holčapek M. HILIC/MS quantitation of low-abundant phospholipids and sphingolipids in human plasma and serum: Dysregulation in pancreatic cancer. Anal Chim Acta 2024; 1288:342144. [PMID: 38220279 DOI: 10.1016/j.aca.2023.342144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/09/2023] [Accepted: 12/14/2023] [Indexed: 01/16/2024]
Abstract
A new hydrophilic interaction liquid chromatography - mass spectrometry method is developed for low-abundant phospholipids and sphingolipids in human plasma and serum. The optimized method involves the Cogent Silica type C hydride column, the simple sample preparation by protein precipitation, and the removal of highly abundant lipid classes using the postcolumn valve directed to waste during two elution windows. The method allows a highly confident and sensitive identification of low-abundant lipid classes in human plasma (246 lipid species from 24 lipid subclasses) based on mass accuracy and retention dependencies in both polarity modes. The method is validated for quantitation using two internal standards (if available) for each lipid class and applied to human plasma and serum samples obtained from patients with pancreatic ductal adenocarcinoma (PDAC), healthy controls, and NIST SRM 1950. Multivariate data analysis followed by various statistical projection methods is used to determine the most dysregulated lipids. Significant downregulation is observed for lysophospholipids with fatty acyl composition 16:0, 18:0, 18:1, and 18:2. Distinct trends are observed for phosphatidylethanolamines (PE) in relation to the bonding type of fatty acyls, where most PE with acyl bonds are upregulated, while ether/plasmenyl PE are downregulated. For the sphingolipid category, sphingolipids with very long N-acyl chains are downregulated, while sphingolipids with shorter N-acyl chains were upregulated in PDAC. These changes are consistently observed for various classes of sphingolipids, ranging from ceramides to glycosphingolipids, indicating a possible metabolic disorder in ceramide biosynthesis caused by PDAC.
Collapse
Affiliation(s)
- Ondřej Peterka
- University of Pardubice, Faculty of Chemical Technology, Department of Analytical Chemistry, Studentská 573, 532 10, Pardubice, Czech Republic
| | - Alessandro Maccelli
- University of Pardubice, Faculty of Chemical Technology, Department of Analytical Chemistry, Studentská 573, 532 10, Pardubice, Czech Republic
| | - Robert Jirásko
- University of Pardubice, Faculty of Chemical Technology, Department of Analytical Chemistry, Studentská 573, 532 10, Pardubice, Czech Republic
| | - Zuzana Vaňková
- University of Pardubice, Faculty of Chemical Technology, Department of Analytical Chemistry, Studentská 573, 532 10, Pardubice, Czech Republic
| | - Jakub Idkowiak
- University of Pardubice, Faculty of Chemical Technology, Department of Analytical Chemistry, Studentská 573, 532 10, Pardubice, Czech Republic
| | - Roman Hrstka
- Research Centre for Applied Molecular Oncology, Masaryk Memorial Cancer Institute, Brno, Czech Republic
| | - Denise Wolrab
- University of Pardubice, Faculty of Chemical Technology, Department of Analytical Chemistry, Studentská 573, 532 10, Pardubice, Czech Republic; University of Vienna, Department of Analytical Chemistry, Währinger Strasse 38, 1090, Vienna, Austria
| | - Michal Holčapek
- University of Pardubice, Faculty of Chemical Technology, Department of Analytical Chemistry, Studentská 573, 532 10, Pardubice, Czech Republic.
| |
Collapse
|
11
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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.
| |
Collapse
|
12
|
Conroy MJ, Andrews RM, Andrews S, Cockayne L, Dennis E, Fahy E, Gaud C, Griffiths W, Jukes G, Kolchin M, Mendivelso K, Lopez-Clavijo A, Ready C, Subramaniam S, O’Donnell V. LIPID MAPS: update to databases and tools for the lipidomics community. Nucleic Acids Res 2024; 52:D1677-D1682. [PMID: 37855672 PMCID: PMC10767878 DOI: 10.1093/nar/gkad896] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/20/2023] Open
Abstract
LIPID MAPS (LIPID Metabolites and Pathways Strategy), www.lipidmaps.org, provides a systematic and standardized approach to organizing lipid structural and biochemical data. Founded 20 years ago, the LIPID MAPS nomenclature and classification has become the accepted community standard. LIPID MAPS provides databases for cataloging and identifying lipids at varying levels of characterization in addition to numerous software tools and educational resources, and became an ELIXIR-UK data resource in 2020. This paper describes the expansion of existing databases in LIPID MAPS, including richer metadata with literature provenance, taxonomic data and improved interoperability to facilitate FAIR compliance. A joint project funded by ELIXIR-UK, in collaboration with WikiPathways, curates and hosts pathway data, and annotates lipids in the context of their biochemical pathways. Updated features of the search infrastructure are described along with implementation of programmatic access via API and SPARQL. New lipid-specific databases have been developed and provision of lipidomics tools to the community has been updated. Training and engagement have been expanded with webinars, podcasts and an online training school.
Collapse
Affiliation(s)
- Matthew J Conroy
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Robert M Andrews
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Simon Andrews
- Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Lauren Cockayne
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Edward A Dennis
- Department of Pharmacology, Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0601, USA
| | - Eoin Fahy
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92037, USA
| | - Caroline Gaud
- Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - William J Griffiths
- Swansea University Medical School, Singleton Park, Swansea SA2 8PP, Wales, UK
| | - Geoff Jukes
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Maksim Kolchin
- Boehringer Ingelheim Espana SA, Carrer de Prat de la Riba, 50, 08174 Sant Cugat del Vallès, Barcelona, Spain
| | - Karla Mendivelso
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | | | - Caroline Ready
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Shankar Subramaniam
- Department of Bioengineering, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92037, USA
| | - Valerie B O’Donnell
- Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| |
Collapse
|
13
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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.
| |
Collapse
|
14
|
Vandenbosch M, Mutuku SM, Mantas MJQ, Patterson NH, Hallmark T, Claesen M, Heeren RMA, Hatcher NG, Verbeeck N, Ekroos K, Ellis SR. Toward Omics-Scale Quantitative Mass Spectrometry Imaging of Lipids in Brain Tissue Using a Multiclass Internal Standard Mixture. Anal Chem 2023; 95:18719-18730. [PMID: 38079536 DOI: 10.1021/acs.analchem.3c02724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Mass spectrometry imaging (MSI) has accelerated our understanding of lipid metabolism and spatial distribution in tissues and cells. However, few MSI studies have approached lipid imaging quantitatively and those that have focused on a single lipid class. We overcome this limitation by using a multiclass internal standard (IS) mixture sprayed homogeneously over the tissue surface with concentrations that reflect those of endogenous lipids. This enabled quantitative MSI (Q-MSI) of 13 lipid classes and subclasses representing almost 200 sum-composition lipid species using both MALDI (negative ion mode) and MALDI-2 (positive ion mode) and pixel-wise normalization of each lipid species in a manner analogous to that widely used in shotgun lipidomics. The Q-MSI approach covered 3 orders of magnitude in dynamic range (lipid concentrations reported in pmol/mm2) and revealed subtle changes in distribution compared to data without normalization. The robustness of the method was evaluated by repeating experiments in two laboratories using both timsTOF and Orbitrap mass spectrometers with an ∼4-fold difference in mass resolution power. There was a strong overall correlation in the Q-MSI results obtained by using the two approaches. Outliers were mostly rationalized by isobaric interferences or the higher sensitivity of one instrument for a particular lipid species. These data provide insight into how the mass resolving power can affect Q-MSI data. This approach opens up the possibility of performing large-scale Q-MSI studies across numerous lipid classes and subclasses and revealing how absolute lipid concentrations vary throughout and between biological tissues.
Collapse
Affiliation(s)
- Michiel Vandenbosch
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry, Maastricht University, Maastricht 6229ER, Netherlands
| | - Shadrack M Mutuku
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
| | | | | | | | | | - Ron M A Heeren
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry, Maastricht University, Maastricht 6229ER, Netherlands
| | - Nathan G Hatcher
- Merck & Co., Inc., 770 Sumneytown Pk, West Point, Pennsylvania 19486, United States
| | | | - Kim Ekroos
- Lipidomics Consulting Ltd., Esbo 02230, Finland
| | - Shane R Ellis
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
| |
Collapse
|
15
|
Wei J, Wong LC, Boland S. Lipids as Emerging Biomarkers in Neurodegenerative Diseases. Int J Mol Sci 2023; 25:131. [PMID: 38203300 PMCID: PMC10778656 DOI: 10.3390/ijms25010131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024] Open
Abstract
Biomarkers are molecules that can be used to observe changes in an individual's biochemical or medical status and provide information to aid diagnosis or treatment decisions. Dysregulation in lipid metabolism in the brain is a major risk factor for many neurodegenerative disorders, including frontotemporal dementia, Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. Thus, there is a growing interest in using lipids as biomarkers in neurodegenerative diseases, with the anionic phospholipid bis(monoacylglycerol)phosphate and (glyco-)sphingolipids being the most promising lipid classes thus far. In this review, we provide a general overview of lipid biology, provide examples of abnormal lysosomal lipid metabolism in neurodegenerative diseases, and discuss how these insights might offer novel and promising opportunities in biomarker development and therapeutic discovery. Finally, we discuss the challenges and opportunities of lipid biomarkers and biomarker panels in diagnosis, prognosis, and/or treatment response in the clinic.
Collapse
|
16
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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.)
| |
Collapse
|
17
|
Ly R, Torres LC, Ly N, Britz-McKibbin P. Expanding Lipidomic Coverage in Multisegment Injection-Nonaqueous Capillary Electrophoresis-Mass Spectrometry via a Convenient and Quantitative Methylation Strategy. Anal Chem 2023; 95:17513-17524. [PMID: 37991882 DOI: 10.1021/acs.analchem.3c02605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Orthogonal separation techniques coupled to high-resolution mass spectrometry are required for characterizing the human lipidome, given its inherent chemical and structural complexity. However, electrophoretic separations remain largely unrecognized in contemporary lipidomics research compared to established chromatographic and ion mobility methods. Herein, we introduce a novel derivatization protocol based on 3-methyl-1-p-tolyltriazene (MTT) as a safer alternative to diazomethane for quantitative phospholipid (PL) methylation (∼90%), which enables their rapid analysis by multisegment injection-nonaqueous capillary electrophoresis-mass spectrometry (MSI-NACE-MS). Isobaric interferences and ion suppression effects were minimized by performing an initial reaction using 9-fluorenylmethyoxycarbonyl chloride prior to MTT and a subsequent back extraction in hexane. This charge-switch derivatization strategy expands lipidome coverage when using MSI-NACE-MS under positive ion mode with improved resolution, greater sensitivity, and higher throughput (∼3.5 min/sample), notably for zwitterionic PLs that are analyzed as their cationic phosphate methyl esters. Our method was validated by analyzing methyl-tert-butyl ether extracts of reference human plasma, which enabled a direct comparison of 48 phosphatidylcholine and 27 sphingomyelin species previously reported in an interlaboratory lipidomics harmonization study. The potential for plasma PL quantification by MSI-NACE-MS via a serial dilution of NIST SRM-1950 was also demonstrated based on estimation of relative response factors using their reported consensus concentrations. Moreover, lipid identification was supported by modeling predictable changes in the electrophoretic mobility for cationic PLs in conjunction with MS/MS. Overall, this work offers a practical derivatization protocol to expand lipidome coverage in CE-MS beyond the analysis of hydrophilic/polar metabolites under aqueous buffer conditions.
Collapse
Affiliation(s)
- Ritchie Ly
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4M1
| | - Lucas Christian Torres
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4M1
| | - Nicholas Ly
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4M1
| | - Philip Britz-McKibbin
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario, Canada L8S 4M1
| |
Collapse
|
18
|
Chicanne G, Darcourt J, Bertrand-Michel J, Garcia C, Ribes A, Payrastre B. What can we learn from the platelet lipidome? Platelets 2023; 34:2182180. [PMID: 36880158 DOI: 10.1080/09537104.2023.2182180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Besides their proteome, platelets use, in all responses to the environmental cues, a huge and diverse family of hydrophobic and amphipathic small molecules involved in structural, metabolic and signaling functions; the lipids. Studying how platelet lipidome changes modulate platelet function is an old story constantly renewed through the impressive technical advances allowing the discovery of new lipids, functions and metabolic pathways. Technical progress in analytical lipidomic profiling by top-of-the-line approaches such as nuclear magnetic resonance and gas chromatography or liquid chromatography coupled to mass spectrometry enables either large-scale analysis of lipids or targeted lipidomics. With the support of bioinformatics tools and databases, it is now possible to investigate thousands of lipids over a concentration range of several orders of magnitude. The lipidomic landscape of platelets is considered a treasure trove, not only able to expand our knowledge of platelet biology and pathologies but also to bring diagnostic and therapeutic opportunities. The aim of this commentary article is to summarize the advances in the field and to highlight what lipidomics can tell us about platelet biology and pathophysiology.
Collapse
Affiliation(s)
- Gaëtan Chicanne
- Institute of Metabolic and Cardiovascular Disease, Inserm UMR1297 and University of Toulouse 3, Toulouse, France
| | - Jean Darcourt
- Institute of Metabolic and Cardiovascular Disease, Inserm UMR1297 and University of Toulouse 3, Toulouse, France
| | - Justine Bertrand-Michel
- Institute of Metabolic and Cardiovascular Disease, Inserm UMR1297 and University of Toulouse 3, Toulouse, France.,MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
| | - Cédric Garcia
- Institute of Metabolic and Cardiovascular Disease, Inserm UMR1297 and University of Toulouse 3, Toulouse, France.,Laboratory of Haematology, University Hospital of Toulouse, Toulouse, France
| | - Agnès Ribes
- Institute of Metabolic and Cardiovascular Disease, Inserm UMR1297 and University of Toulouse 3, Toulouse, France.,Laboratory of Haematology, University Hospital of Toulouse, Toulouse, France
| | - Bernard Payrastre
- Institute of Metabolic and Cardiovascular Disease, Inserm UMR1297 and University of Toulouse 3, Toulouse, France.,Laboratory of Haematology, University Hospital of Toulouse, Toulouse, France
| |
Collapse
|
19
|
Kopczynski D, Hoffmann N, Troppmair N, Coman C, Ekroos K, Kreutz MR, Liebisch G, Schwudke D, Ahrends R. LipidSpace: Simple Exploration, Reanalysis, and Quality Control of Large-Scale Lipidomics Studies. Anal Chem 2023; 95:15236-15244. [PMID: 37792961 PMCID: PMC10585661 DOI: 10.1021/acs.analchem.3c02449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/09/2023] [Indexed: 10/06/2023]
Abstract
Lipid analysis gained significant importance due to the enormous range of lipid functions, e.g., energy storage, signaling, or structural components. Whole lipidomes can be quantitatively studied in-depth thanks to recent analytical advancements. However, the systematic comparison of thousands of distinct lipidomes remains challenging. We introduce LipidSpace, a standalone tool for analyzing lipidomes by assessing their structural and quantitative differences. A graph-based comparison of lipid structures is the basis for calculating structural space models and subsequently computing lipidome similarities. When adding study variables such as body weight or health condition, LipidSpace can determine lipid subsets across all lipidomes that describe these study variables well by utilizing machine-learning approaches. The user-friendly GUI offers four built-in tutorials and interactive visual interfaces with pdf export. Many supported data formats allow an efficient (re)analysis of data sets from different sources. An integrated interactive workflow guides the user through the quality control steps. We used this suite to reanalyze and combine already published data sets (e.g., one with about 2500 samples and 576 lipids in one run) and made additional discoveries to the published conclusions with the potential to fill gaps in the current lipid biology understanding. LipidSpace is available for Windows or Linux (https://lifs-tools.org).
Collapse
Affiliation(s)
- Dominik Kopczynski
- Institute
of Analytical Chemistry, University of Vienna, Vienna 1070, Austria
| | - Nils Hoffmann
- Forschungszentrum
Jülich GmbH, Institute for Bio- and Geosciences (IBG-5), Jülich 52428, Germany
| | - Nina Troppmair
- Institute
of Analytical Chemistry, University of Vienna, Vienna 1070, Austria
| | - Cristina Coman
- Institute
of Analytical Chemistry, University of Vienna, Vienna 1070, Austria
| | - Kim Ekroos
- Lipidomics
Consulting Ltd., Esbo 02230, Finland
| | - Michael R. Kreutz
- Leibniz
Group “Dendritic Organelles and Synaptic Function” University
Medical Center Hamburg-Eppendorf, Center
for Molecular Neurobiology, ZMNH, Hamburg 20251, Germany
- RG
Neuroplasticity, Leibniz Institute for Neurobiology, Magdeburg 39118, Germany
| | - Gerhard Liebisch
- Institute
of Clinical Chemistry and Laboratory Medicine, University of Regensburg, Regensburg 93053, Germany
| | - Dominik Schwudke
- German
Center for Infection Research (DZIF), Site
Hamburg-Lübeck-Borstel-Riems, Hamburg 22297, Germany
- Airway
Research Center North (ARCN), German Center
for Lung Research (DZL), Grosshansdorf 22927, Germany
- Bioanalytical
Chemistry, Research Center Borstel, Borstel 23845, Germany
| | - Robert Ahrends
- Institute
of Analytical Chemistry, University of Vienna, Vienna 1070, Austria
| |
Collapse
|
20
|
Abstract
Extracellular vesicles, such as exosomes, can be used as interesting models to study the structure and function of biological membranes as these vesicles contain only one membrane (i.e., one lipid bilayer). In addition to lipids, they contain proteins, nucleic acids, and various other molecules. The lipid composition of exosomes is here compared to HIV particles and detergent-resistant membranes, which also have a high content of sphingolipids, cholesterol, and phosphatidylserine (PS). We discuss interactions between the lipids in the two bilayers, and especially those between PS 18:0/18:1 in the inner leaflet and the very-long-chain sphingolipids in the outer leaflet, and the importance of cholesterol for these interactions. We also briefly discuss the involvement of ether-linked phospholipids (PLs) in such lipid raft-like structures, and the possible involvement of these and other lipid classes in the formation of exosomes. The urgent need to improve the quality of quantitative lipidomic studies is highlighted.
Collapse
Affiliation(s)
- Tore Skotland
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, 0379 Oslo, Norway
- Centre for Cancer Cell Reprogramming, Faculty of Medicine, University of Oslo, 0379 Oslo, Norway
| | - Alicia Llorente
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, 0379 Oslo, Norway
- Centre for Cancer Cell Reprogramming, Faculty of Medicine, University of Oslo, 0379 Oslo, Norway
- Department of Mechanical, Electronics and Chemical Engineering, Oslo Metropolitan University, 0167 Oslo, Norway
| | - Kirsten Sandvig
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital-The Norwegian Radium Hospital, 0379 Oslo, Norway
- Centre for Cancer Cell Reprogramming, Faculty of Medicine, University of Oslo, 0379 Oslo, Norway
- Department of Molecular Biosciences, University of Oslo, 0316 Oslo, Norway
| |
Collapse
|
21
|
McReynolds C, Hammock B, Morisseau C. Regulatory lipid vicinal diols counteract the biological activity of epoxy fatty acids and can act as biomarkers and mechanisms for disease progression. Pharmacol Ther 2023; 248:108454. [PMID: 37268114 PMCID: PMC10529401 DOI: 10.1016/j.pharmthera.2023.108454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/15/2023] [Accepted: 05/22/2023] [Indexed: 06/04/2023]
Abstract
Polyunsaturated fatty acids (PUFAs) are essential fatty acids required for human health and are obtained primarily from food or synthesized in the body by highly regulated processes. The metabolites of these lipids, formed largely through the action of cyclooxygenase, lipoxygenase, or cytochrome P450 (CYP450) enzymes, are responsible for multiple biological functions including inflammation, tissue repair, cell proliferation, blood vessel permeability, and immune cell behavior. The role of these regulatory lipids in disease has been well studied since their discovery as druggable targets; however, the metabolites generated downstream of these pathways have only recently gained attention for regulating biology. Specifically, the biological activity of lipid vicinal diols formed from the metabolism of CYP450-generated epoxy fatty acids (EpFA) by epoxide hydrolases were previously thought to have little biological activity but increasingly are recognized as promoting inflammation and brown fat adipogenesis, and exciting neurons through the regulation of ion channel activity at low concentrations. These metabolites also appear to balance the action of the EpFA precursor. For example, EpFA demonstrate the ability to resolve inflammation and reduce pain, while some lipid diols, through opposing mechanisms, promote inflammation and pain. This review describes recent studies that highlight the role of regulatory lipids, focusing on the balance between EpFA and their diol metabolites in promoting or resolving disease.
Collapse
Affiliation(s)
| | - Bruce Hammock
- EicOsis, Davis, CA, United States of America; University of California, Davis, CA, United States of America
| | | |
Collapse
|
22
|
Hildebrand F, Schoeny H, Rampler E, Koellensperger G. Scrutinizing different ionization responses of polar lipids in a reversed-phase gradient by implementing a counter-gradient. Anal Chim Acta 2023; 1265:341274. [PMID: 37230568 DOI: 10.1016/j.aca.2023.341274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/30/2023] [Accepted: 04/23/2023] [Indexed: 05/27/2023]
Abstract
Lipidomics studies strive for a comprehensive identification and quantification of lipids. While reversed phase (RP) liquid chromatography (LC) coupled to high resolution mass spectrometry (MS) offers unrivalled selectivity and thus is the preferred method for lipid identification, accurate lipid quantification remains challenging. The widely adopted one-point lipid class specific quantification (one internal standard per lipid class) suffers from the fact that ionization of internal standard and target lipid occurs under different solvent composition as a consequence of chromatographic separation. To address this issue, we established a dual flow injection and chromatography setup that allows to control solvent conditions during ionization enabling isocratic ionization while running a RP gradient through the use of a counter-gradient. Using this dual LC pump platform, we investigated the impact of solvent conditions within a RP gradient on ionization response and arising quantification biases. Our results confirmed that changing solvent composition significantly influences ionization response. Quantification of human plasma (SRM 1950) lipids under gradient and isocratic ionization conditions further confirmed these findings as significant differences between the two conditions were found for the majority of lipids. While the quantity of sphingomyelins with >40 C atoms was consistently overestimated under gradient ionization, isocratic ionization improved their recovery compared to consensus values. However, the limitation of consensus values was demonstrated as overall only small changes in z-score were observed because of high uncertainties of the consensus values. Furthermore, we observed a trueness bias between gradient and isocratic ionization when quantifying a panel of lipid species standards which is highly dependent on lipid class and ionization mode. Uncertainty calculations under consideration of the trueness bias as RP gradient uncertainty revealed that especially ceramides with >40 C atoms had a high bias leading to total combined uncertainties of up to 54%. The assumption of isocratic ionization significantly decreases total measurement uncertainty and highlights the importance of studying the trueness bias introduced by a RP gradient to reduce quantification uncertainty.
Collapse
Affiliation(s)
- Felina Hildebrand
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090, Vienna, Austria; Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Vienna, Austria
| | - Harald Schoeny
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090, Vienna, Austria
| | - Evelyn Rampler
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090, Vienna, Austria
| | - Gunda Koellensperger
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 38, 1090, Vienna, Austria; Vienna Metabolomics Center (VIME), University of Vienna, Althanstr. 14, 1090, Vienna, Austria.
| |
Collapse
|
23
|
Liu S, Chen M, Wang Y, Lei Y, Huang T, Zhang Y, Lam SM, Li H, Qi S, Geng J, Lu K. The ER calcium channel Csg2 integrates sphingolipid metabolism with autophagy. Nat Commun 2023; 14:3725. [PMID: 37349354 PMCID: PMC10287731 DOI: 10.1038/s41467-023-39482-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 06/15/2023] [Indexed: 06/24/2023] Open
Abstract
Sphingolipids are ubiquitous components of membranes and function as bioactive lipid signaling molecules. Here, through genetic screening and lipidomics analyses, we find that the endoplasmic reticulum (ER) calcium channel Csg2 integrates sphingolipid metabolism with autophagy by regulating ER calcium homeostasis in the yeast Saccharomyces cerevisiae. Csg2 functions as a calcium release channel and maintains calcium homeostasis in the ER, which enables normal functioning of the essential sphingolipid synthase Aur1. Under starvation conditions, deletion of Csg2 causes increases in calcium levels in the ER and then disturbs Aur1 stability, leading to accumulation of the bioactive sphingolipid phytosphingosine, which specifically and completely blocks autophagy and induces loss of starvation resistance in cells. Our findings indicate that calcium homeostasis in the ER mediated by the channel Csg2 translates sphingolipid metabolism into autophagy regulation, further supporting the role of the ER as a signaling hub for calcium homeostasis, sphingolipid metabolism and autophagy.
Collapse
Affiliation(s)
- Shiyan Liu
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Mutian Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, Med-X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, 610041, China
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu, 641400, China
| | - Yichang Wang
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yuqing Lei
- Department of Pathology, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Ting Huang
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yabin Zhang
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Sin Man Lam
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- LipidALL Technologies Company Limited, Changzhou, 213022, China
| | - Huihui Li
- Department of Pathology, West China Second University Hospital, Sichuan University, Chengdu, 610041, China.
| | - Shiqian Qi
- Department of Urology, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Jia Geng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, Med-X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu, 641400, China.
| | - Kefeng Lu
- Department of Neurosurgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
| |
Collapse
|
24
|
Wang Q, Hoene M, Hu C, Fritsche L, Ahrends R, Liebisch G, Ekroos K, Fritsche A, Birkenfeld AL, Liu X, Zhao X, Li Q, Su B, Peter A, Xu G, Lehmann R. Ex vivo instability of lipids in whole blood: preanalytical recommendations for clinical lipidomics studies. J Lipid Res 2023; 64:100378. [PMID: 37087100 PMCID: PMC10208886 DOI: 10.1016/j.jlr.2023.100378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 04/24/2023] Open
Abstract
Reliability, robustness, and interlaboratory comparability of quantitative measurements is critical for clinical lipidomics studies. Lipids' different ex vivo stability in blood bears the risk of misinterpretation of data. Clear recommendations for the process of blood sample collection are required. We studied by UHPLC-high resolution mass spectrometry, as part of the "Preanalytics interest group" of the International Lipidomics Society, the stability of 417 lipid species in EDTA whole blood after exposure to either 4°C, 21°C, or 30°C at six different time points (0.5 h-24 h) to cover common daily routine conditions in clinical settings. In total, >800 samples were analyzed. 325 and 288 robust lipid species resisted 24 h exposure of EDTA whole blood to 21°C or 30°C, respectively. Most significant instabilities were detected for FA, LPE, and LPC. Based on our data, we recommend cooling whole blood at once and permanent. Plasma should be separated within 4 h, unless the focus is solely on robust lipids. Lists are provided to check the ex vivo (in)stability of distinct lipids and potential biomarkers of interest in whole blood. To conclude, our results contribute to the international efforts towards reliable and comparable clinical lipidomics data paving the way to the proper diagnostic application of distinct lipid patterns or lipid profiles in the future.
Collapse
Affiliation(s)
- Qingqing Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China; University of Chinese Academy of Sciences, Beijing, China
| | - Miriam Hoene
- Department for Diagnostic Laboratory Medicine, Institute for Clinical Chemistry and Pathobiochemistry, University Hospital Tübingen, Tübingen, Germany
| | - Chunxiu Hu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China
| | - Louise Fritsche
- Institute for Diabetes Research and Metabolic Diseases (IDM) of the Helmholtz Zentrum München at the University of Tuebingen, Tuebingen, Germany; German Center for Diabetes Research (DZD), Tübingen, Germany
| | - Robert Ahrends
- Department of Analytical Chemistry, University of Vienna, Vienna, Austria
| | - Gerhard Liebisch
- Institute of Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | - Kim Ekroos
- Lipidomics Consulting Ltd., Espoo, Finland
| | - Andreas Fritsche
- Institute for Diabetes Research and Metabolic Diseases (IDM) of the Helmholtz Zentrum München at the University of Tuebingen, Tuebingen, Germany; German Center for Diabetes Research (DZD), Tübingen, Germany; Internal Medicine 4, University Hospital Tuebingen, Tuebingen, Germany
| | - Andreas L Birkenfeld
- Institute for Diabetes Research and Metabolic Diseases (IDM) of the Helmholtz Zentrum München at the University of Tuebingen, Tuebingen, Germany; German Center for Diabetes Research (DZD), Tübingen, Germany; Internal Medicine 4, University Hospital Tuebingen, Tuebingen, Germany
| | - Xinyu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China
| | - Xinjie Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China
| | - Qi Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China
| | - Benzhe Su
- School of Computer Science & Technology, Dalian University of Technology, Dalian, China
| | - Andreas Peter
- Department for Diagnostic Laboratory Medicine, Institute for Clinical Chemistry and Pathobiochemistry, University Hospital Tübingen, Tübingen, Germany; Institute for Diabetes Research and Metabolic Diseases (IDM) of the Helmholtz Zentrum München at the University of Tuebingen, Tuebingen, Germany; German Center for Diabetes Research (DZD), Tübingen, Germany
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, China.
| | - Rainer Lehmann
- Department for Diagnostic Laboratory Medicine, Institute for Clinical Chemistry and Pathobiochemistry, University Hospital Tübingen, Tübingen, Germany; Institute for Diabetes Research and Metabolic Diseases (IDM) of the Helmholtz Zentrum München at the University of Tuebingen, Tuebingen, Germany; German Center for Diabetes Research (DZD), Tübingen, Germany.
| |
Collapse
|
25
|
Doré E, Boilard E. Bacterial extracellular vesicles and their interplay with the immune system. Pharmacol Ther 2023; 247:108443. [PMID: 37210006 DOI: 10.1016/j.pharmthera.2023.108443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/09/2023] [Accepted: 05/15/2023] [Indexed: 05/22/2023]
Abstract
The mammalian intestinal tract harbors trillions of microorganisms confined within this space by mucosal barriers. Despite these barriers, bacterial components may still be found elsewhere in the body, even in healthy subjects. Bacteria can release small lipid-bound particles, also named bacterial extracellular vesicles (bEV). While bacteria themselves cannot normally penetrate the mucosal defense, bEVs may infiltrate the barrier and disseminate throughout the body. The extremely diverse cargo that bEVs can carry, depending on their parent species, strain, and growth conditions, grant them an equally broad potential to interact with host cells and influence immune functions. Herein, we review the current knowledge of processes underlying the uptake of bEVs by mammalian cells, and their effect on the immune system. Furthermore, we discuss how bEVs could be targeted and manipulated for diverse therapeutic purposes.
Collapse
Affiliation(s)
- Etienne Doré
- Centre de Recherche du Centre Hospitalier Universitaire de Québec - Université Laval, Québec, QC, Canada; Centre de Recherche ARThrite - Arthrite, Recherche, Traitements, Université Laval, Québec, QC, Canada
| | - Eric Boilard
- Centre de Recherche du Centre Hospitalier Universitaire de Québec - Université Laval, Québec, QC, Canada; Centre de Recherche ARThrite - Arthrite, Recherche, Traitements, Université Laval, Québec, QC, Canada.
| |
Collapse
|
26
|
Kvasnička A, Najdekr L, Dobešová D, Piskláková B, Ivanovová E, Friedecký D. Clinical lipidomics in the era of the big data. Clin Chem Lab Med 2023; 61:587-598. [PMID: 36592414 DOI: 10.1515/cclm-2022-1105] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 12/16/2022] [Indexed: 01/03/2023]
Abstract
Lipidomics as a branch of metabolomics provides unique information on the complex lipid profile in biological materials. In clinically focused studies, hundreds of lipids together with available clinical information proved to be an effective tool in the discovery of biomarkers and understanding of pathobiochemistry. However, despite the introduction of lipidomics nearly twenty years ago, only dozens of big data studies using clinical lipidomics have been published to date. In this review, we discuss the lipidomics workflow, statistical tools, and the challenges of standartisation. The consequent summary divided into major clinical areas of cardiovascular disease, cancer, diabetes mellitus, neurodegenerative and liver diseases is demonstrating the importance of clinical lipidomics. In these publications, the potential of lipidomics for prediction, diagnosis or finding new targets for the treatment of selected diseases can be seen. The first of these results have already been implemented in clinical practice in the field of cardiovascular diseases, while in other areas we can expect the application of the results summarized in this review in the near future.
Collapse
Affiliation(s)
- Aleš Kvasnička
- Laboratory for Inherited Metabolic Disorders, Department of Clinical Biochemistry, University Hospital, Olomouc, Czechia
- Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czechia
| | - Lukáš Najdekr
- Institute of Molecular and Translational Medicine, Palacký University Olomouc, Olomouc, Czechia
| | - Dana Dobešová
- Laboratory for Inherited Metabolic Disorders, Department of Clinical Biochemistry, University Hospital, Olomouc, Czechia
- Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czechia
| | - Barbora Piskláková
- Laboratory for Inherited Metabolic Disorders, Department of Clinical Biochemistry, University Hospital, Olomouc, Czechia
- Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czechia
| | - Eliška Ivanovová
- Laboratory for Inherited Metabolic Disorders, Department of Clinical Biochemistry, University Hospital, Olomouc, Czechia
- Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czechia
| | - David Friedecký
- Laboratory for Inherited Metabolic Disorders, Department of Clinical Biochemistry, University Hospital, Olomouc, Czechia
- Faculty of Medicine and Dentistry, Palacký University Olomouc, Olomouc, Czechia
| |
Collapse
|
27
|
Theodoridis G, Gika H, Raftery D, Goodacre R, Plumb RS, Wilson ID. Ensuring Fact-Based Metabolite Identification in Liquid Chromatography-Mass Spectrometry-Based Metabolomics. Anal Chem 2023; 95:3909-3916. [PMID: 36791228 PMCID: PMC9979140 DOI: 10.1021/acs.analchem.2c05192] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Metabolite identification represents a major bottleneck in contemporary metabolomics research and a step where critical errors may occur and pass unnoticed. This is especially the case for studies employing liquid chromatography-mass spectrometry technology, where there is increased concern on the validity of the proposed identities. In the present perspective article, we describe the issue and categorize the errors into two types: identities that show poor biological plausibility and identities that do not comply with chromatographic data and thus to physicochemical properties (usually hydrophobicity/hydrophilicity) of the proposed molecule. We discuss the problem, present characteristic examples, and propose measures to improve the situation.
Collapse
Affiliation(s)
- Georgios Theodoridis
- Department
of Chemistry, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece,Biomic
AUTh, Center for Interdisciplinary Research
and Innovation (CIRI-AUTH), Balkan Center B1.4, 10th km Thessaloniki-Thermi Rd., P.O. Box 8318, Thessaloniki 57001Greece,FoodOmicsGR,
AUTh node, Center for Interdisciplinary
Research and Innovation (CIRI-AUTH), Balkan Center B1.4, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, Thessaloniki 57001, Greece,
| | - Helen Gika
- Biomic
AUTh, Center for Interdisciplinary Research
and Innovation (CIRI-AUTH), Balkan Center B1.4, 10th km Thessaloniki-Thermi Rd., P.O. Box 8318, Thessaloniki 57001Greece,FoodOmicsGR,
AUTh node, Center for Interdisciplinary
Research and Innovation (CIRI-AUTH), Balkan Center B1.4, 10th km Thessaloniki-Thermi Rd, P.O. Box 8318, Thessaloniki 57001, Greece,Laboratory
of Forensic Medicine and Toxicology, Department of Medicine, Aristotle University,
Thessaloniki 54124, Greece
| | - Daniel Raftery
- Northwest
Metabolomics Research Center, 850 Republican St., Seattle, Washington 98109, United States,Mitochondria
Metabolism Center, Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington 98109, United States
| | - Royston Goodacre
- Centre
for Metabolomics Research, Department of Biochemistry and Systems
Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, BioSciences Building, Crown St., Liverpool, L69 7ZB, United Kingdom
| | - Robert S. Plumb
- Scientific
Operations, IMMERSE, Waters Corporation, Cambridge 02142, Massachusetts United States
| | - Ian D. Wilson
- Centre
for Metabolomics Research, Department of Biochemistry and Systems
Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, BioSciences Building, Crown St., Liverpool, L69 7ZB, United Kingdom,Division
of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London W12 0NN, United Kingdom,
| |
Collapse
|
28
|
Shen T, Conway C, Rempfert KR, Kyle JE, Colby SM, Gaul DA, Habra H, Kong F, Bloodsworth KJ, Allen D, Evans BS, Du X, Fernandez FM, Metz TO, Fiehn O, Evans CR. The unknown lipids project: harmonized methods improve compound identification and data reproducibility in an inter-laboratory untargeted lipidomics study. bioRxiv 2023:2023.02.01.526566. [PMID: 36778509 PMCID: PMC9915661 DOI: 10.1101/2023.02.01.526566] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Untargeted lipidomics allows analysis of a broader range of lipids than targeted methods and permits discovery of unknown compounds. Previous ring trials have evaluated the reproducibility of targeted lipidomics methods, but inter-laboratory comparison of compound identification and unknown feature detection in untargeted lipidomics has not been attempted. To address this gap, five laboratories analyzed a set of mammalian tissue and biofluid reference samples using both their own untargeted lipidomics procedures and a common chromatographic and data analysis method. While both methods yielded informative data, the common method improved chromatographic reproducibility and resulted in detection of more shared features between labs. Spectral search against the LipidBlast in silico library enabled identification of over 2,000 unique lipids. Further examination of LC-MS/MS and ion mobility data, aided by hybrid search and spectral networking analysis, revealed spectral and chromatographic patterns useful for classification of unknown features, a subset of which were highly reproducible between labs. Overall, our method offers enhanced compound identification performance compared to targeted lipidomics, demonstrates the potential of harmonized methods to improve inter-site reproducibility for quantitation and feature alignment, and can serve as a reference to aid future annotation of untargeted lipidomics data.
Collapse
|
29
|
Sagini K, Urbanelli L, Buratta S, Emiliani C, Llorente A. Lipid Biomarkers in Liquid Biopsies: Novel Opportunities for Cancer Diagnosis. Pharmaceutics 2023; 15:pharmaceutics15020437. [PMID: 36839759 PMCID: PMC9966160 DOI: 10.3390/pharmaceutics15020437] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 01/31/2023] Open
Abstract
Altered cellular metabolism is a well-established hallmark of cancer. Although most studies have focused on the metabolism of glucose and glutamine, the upregulation of lipid metabolism is also frequent in cells undergoing oncogenic transformation. In fact, cancer cells need to meet the enhanced demand of plasma membrane synthesis and energy production to support their proliferation. Moreover, lipids are precursors of signaling molecules, termed lipid mediators, which play a role in shaping the tumor microenvironment. Recent methodological advances in lipid analysis have prompted studies aimed at investigating the whole lipid content of a sample (lipidome) to unravel the complexity of lipid changes in cancer patient biofluids. This review focuses on the application of mass spectrometry-based lipidomics for the discovery of cancer biomarkers. Here, we have summarized the main lipid alteration in cancer patients' biofluids and uncovered their potential use for the early detection of the disease and treatment selection. We also discuss the advantages of using biofluid-derived extracellular vesicles as a platform for lipid biomarker discovery. These vesicles have a molecular signature that is a fingerprint of their originating cells. Hence, the analysis of their molecular cargo has emerged as a promising strategy for the identification of sensitive and specific biomarkers compared to the analysis of the unprocessed biofluid.
Collapse
Affiliation(s)
- Krizia Sagini
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, 0379 Oslo, Norway
- Centre for Cancer Cell Reprogramming, Faculty of Medicine, University of Oslo, Montebello, 0379 Oslo, Norway
- Correspondence: ; Tel.: +47-22-78-18-13
| | - Lorena Urbanelli
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | - Sandra Buratta
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | - Carla Emiliani
- Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
- CEMIN (Center of Excellence for Innovative Nanostructured Material), University of Perugia, 06123 Perugia, Italy
| | - Alicia Llorente
- Department of Molecular Cell Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, 0379 Oslo, Norway
- Centre for Cancer Cell Reprogramming, Faculty of Medicine, University of Oslo, Montebello, 0379 Oslo, Norway
- Department for Mechanical, Electronics and Chemical Engineering, Oslo Metropolitan University, 0167 Oslo, Norway
| |
Collapse
|
30
|
Zandl-Lang M, Plecko B, Köfeler H. Lipidomics-Paving the Road towards Better Insight and Precision Medicine in Rare Metabolic Diseases. Int J Mol Sci 2023; 24:ijms24021709. [PMID: 36675224 PMCID: PMC9866746 DOI: 10.3390/ijms24021709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
Even though the application of Next-Generation Sequencing (NGS) has significantly facilitated the identification of disease-associated mutations, the diagnostic rate of rare diseases is still below 50%. This causes a diagnostic odyssey and prevents specific treatment, as well as genetic counseling for further family planning. Increasing the diagnostic rate and reducing the time to diagnosis in children with unclear disease are crucial for a better patient outcome and improvement of quality of life. In many cases, NGS reveals variants of unknown significance (VUS) that need further investigations. The delineation of novel (lipid) biomarkers is not only crucial to prove the pathogenicity of VUS, but provides surrogate parameters for the monitoring of disease progression and therapeutic interventions. Lipids are essential organic compounds in living organisms, serving as building blocks for cellular membranes, energy storage and signaling molecules. Among other disorders, an imbalance in lipid homeostasis can lead to chronic inflammation, vascular dysfunction and neurodegenerative diseases. Therefore, analyzing lipids in biological samples provides great insight into the underlying functional role of lipids in healthy and disease statuses. The method of choice for lipid analysis and/or huge assemblies of lipids (=lipidome) is mass spectrometry due to its high sensitivity and specificity. Due to the inherent chemical complexity of the lipidome and the consequent challenges associated with analyzing it, progress in the field of lipidomics has lagged behind other omics disciplines. However, compared to the previous decade, the output of publications on lipidomics has increased more than 17-fold within the last decade and has, therefore, become one of the fastest-growing research fields. Combining multiple omics approaches will provide a unique and efficient tool for determining pathogenicity of VUS at the functional level, and thereby identifying rare, as well as novel, genetic disorders by molecular techniques and biochemical analyses.
Collapse
Affiliation(s)
- Martina Zandl-Lang
- Division of General Pediatrics, Department of Pediatrics and Adolescent Medicine, Medical University of Graz, 8036 Graz, Austria
| | - Barbara Plecko
- Division of General Pediatrics, Department of Pediatrics and Adolescent Medicine, Medical University of Graz, 8036 Graz, Austria
| | - Harald Köfeler
- Core Facility Mass Spectrometry, ZMF, Medical University of Graz, 8036 Graz, Austria
- Correspondence:
| |
Collapse
|
31
|
B O'Donnell V. Lipidomics Moves to Center Stage of Biomedicine. Function (Oxf) 2023; 4:zqac071. [PMID: 36632473 PMCID: PMC9830535 DOI: 10.1093/function/zqac071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 12/23/2022] [Indexed: 01/05/2023]
|
32
|
Belkin TG, Tham YK, McMullen JR. Lipids regulated by exercise and PI3K: potential role as biomarkers and therapeutic targets for cardiovascular disease. Current Opinion in Physiology 2023. [DOI: 10.1016/j.cophys.2023.100633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
|
33
|
Miao H, Li B, Wang Z, Mu J, Tian Y, Jiang B, Zhang S, Gong X, Shui G, Lam SM. Lipidome Atlas of the Developing Heart Uncovers Dynamic Membrane Lipid Attributes Underlying Cardiac Structural and Metabolic Maturation. Research 2022. [DOI: 10.34133/research.0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Precise metabolic rewiring during heart organogenesis underlies normal cardiac development. Herein, we utilized high-coverage, quantitative lipidomic approaches to construct lipidomic atlases of whole hearts (861 lipids; 31 classes) and mitochondria (587 lipids; 27 classes) across prenatal and postnatal developmental stages in mice. We uncovered the progressive formation of docosahexaenoyl-phospholipids and enhanced remodeling of C18:2, C20:3, and C20:4 fatty acyl moieties into cardiolipins as cardiac development progresses. A preferential flow of ceramides toward sphingomyelin biosynthesis over complex glycosphingolipid formation was also noted. Using maSigPro and GPclust algorithms, we identified a repertoire of 448 developmentally dynamic lipids and mapped their expression patterns to a library of 550 biologically relevant developmentally dynamic genes. Our combinatorial transcriptomics and lipidomics approaches identified
Hadha, Lclat1
, and
Lpcat3
as candidate molecular drivers governing the dynamic remodeling of cardiolipins and phospholipids, respectively, in heart development. Our analyses revealed that postnatal cardiolipin remodeling in the heart constitutes a biphasic process, which first accumulates polyunsaturated C78-cardiolipins prior to tetralinoleoyl cardiolipin forming the predominant species. Multiomics analyses supplemented with transmission electron microscopy imaging uncovered enhanced mitochondria–lipid droplet contacts mediated by perilipin-5. Our combinatorial analyses of multiomics data uncovered an association between mitochondrial-resident, docosahexaenoic acid-phospholipids and messenger RNA levels of proton-transporting adenosine triphosphate synthases on inner mitochondrial membranes, which adds credence to the membrane pacemaker theory of metabolism. The current findings offer lipid-centric biological insights potentially important to understanding the molecular basis of cardiac metabolic flexibility and disease pathology.
Collapse
Affiliation(s)
- Huan Miao
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bowen Li
- LipidALL Technologies Company Limited, Changzhou 213022, Jiangsu Province, China
| | - Zehua Wang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinming Mu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanlin Tian
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Binhua Jiang
- LipidALL Technologies Company Limited, Changzhou 213022, Jiangsu Province, China
| | - Shaohua Zhang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xia Gong
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Guanghou Shui
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sin Man Lam
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- LipidALL Technologies Company Limited, Changzhou 213022, Jiangsu Province, China
| |
Collapse
|