1
|
Sprenger RR, Bilgin M, Ostenfeld MS, Bjørnshave A, Rasmussen JT, Ejsing CS. Dietary intake of a MFGM/EV-rich concentrate promotes accretion of very long odd-chain sphingolipids and increases lipid metabolic turnover at the whole-body level. Food Res Int 2024; 190:114601. [PMID: 38945615 DOI: 10.1016/j.foodres.2024.114601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/28/2024] [Accepted: 06/03/2024] [Indexed: 07/02/2024]
Abstract
Lipids from cow milk fat globule membranes (MFGMs) and extracellular vesicles (EVs) are considered beneficial for neurodevelopment, cognitive maintenance and human health in general. Nevertheless, it is largely unknown whether intake of infant formulas and medical nutrition products rich in these particles promote accretion of specific lipids and whether this affects metabolic homeostasis. To address this, we carried out a 16-week dietary intervention study where mice were supplemented with a MFGM/EV-rich concentrate, a control diet supplemented with a whey protein concentrate and devoid of milk lipids, or regular chow. Assessment of commonly used markers of metabolic health, including body weight, glucose intolerance and liver microanatomy, demonstrated no differences across the dietary regimes. In contrast, in-depth lipidomic analysis revealed accretion of milk-derived very long odd-chain sphingomyelins and ceramides in blood plasma and multiple tissues of mice fed the MFGM/EV diet. Furthermore, lipidomic flux analysis uncovered that mice fed the MFGM/EV diet have increased lipid metabolic turnover at the whole-body level. These findings help fill a long-lasting knowledge gap between the intake of MFGM/EV-containing foods and the health-promoting effects of their lipid constituents. In addition, the findings suggest that dietary sphingomyelins or ceramide-breakdown products with very long-chains can be used as structural components of cellular membranes, lipoprotein particles and signaling molecules that modulate metabolic homeostasis and health.
Collapse
Affiliation(s)
- Richard R Sprenger
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Mesut Bilgin
- Lipidomics Core Facility, Danish Cancer Institute, Copenhagen, Denmark
| | | | | | - Jan T Rasmussen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Christer S Ejsing
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| |
Collapse
|
2
|
Gopalan AB, van Uden L, Sprenger RR, Fernandez-Novel Marx N, Bogetofte H, Neveu PA, Meyer M, Noh KM, Diz-Muñoz A, Ejsing CS. Lipotype acquisition during neural development is not recapitulated in stem cell-derived neurons. Life Sci Alliance 2024; 7:e202402622. [PMID: 38418090 PMCID: PMC10902711 DOI: 10.26508/lsa.202402622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 03/01/2024] Open
Abstract
During development, different tissues acquire distinct lipotypes that are coupled to tissue function and homeostasis. In the brain, where complex membrane trafficking systems are required for neural function, specific glycerophospholipids, sphingolipids, and cholesterol are highly abundant, and defective lipid metabolism is associated with abnormal neural development and neurodegenerative disease. Notably, the production of specific lipotypes requires appropriate programming of the underlying lipid metabolic machinery during development, but when and how this occurs is unclear. To address this, we used high-resolution MSALL lipidomics to generate an extensive time-resolved resource of mouse brain development covering early embryonic and postnatal stages. This revealed a distinct bifurcation in the establishment of the neural lipotype, whereby the canonical lipid biomarkers 22:6-glycerophospholipids and 18:0-sphingolipids begin to be produced in utero, whereas cholesterol attains its characteristic high levels after birth. Using the resource as a reference, we next examined to which extent this can be recapitulated by commonly used protocols for in vitro neuronal differentiation of stem cells. Here, we found that the programming of the lipid metabolic machinery is incomplete and that stem cell-derived cells can only partially acquire a neural lipotype when the cell culture media is supplemented with brain-specific lipid precursors. Altogether, our work provides an extensive lipidomic resource for early mouse brain development and highlights a potential caveat when using stem cell-derived neuronal progenitors for mechanistic studies of lipid biochemistry, membrane biology and biophysics, which nonetheless can be mitigated by further optimizing in vitro differentiation protocols.
Collapse
Affiliation(s)
- Anusha B Gopalan
- https://ror.org/03mstc592 Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Faculty of Biosciences, Candidate for Joint PhD Degree Between EMBL and Heidelberg University, Heidelberg, Germany
| | - Lisa van Uden
- https://ror.org/03mstc592 Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Richard R Sprenger
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | | | - Helle Bogetofte
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
- Department of Neurobiology Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Pierre A Neveu
- https://ror.org/03mstc592 Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Morten Meyer
- Department of Neurobiology Research, Institute of Molecular Medicine, University of Southern Denmark, Odense, Denmark
- Department of Neurology, Odense University Hospital, Odense, Denmark
- BRIDGE, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Kyung-Min Noh
- https://ror.org/03mstc592 Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Alba Diz-Muñoz
- https://ror.org/03mstc592 Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Christer S Ejsing
- https://ror.org/03mstc592 Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| |
Collapse
|
3
|
Sprenger RR, Ostenfeld MS, Bjørnshave A, Rasmussen JT, Ejsing CS. Lipidomic Characterization of Whey Concentrates Rich in Milk Fat Globule Membranes and Extracellular Vesicles. Biomolecules 2023; 14:55. [PMID: 38254655 PMCID: PMC10813332 DOI: 10.3390/biom14010055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/24/2024] Open
Abstract
Lipids from milk fat globule membranes (MFGMs) and extracellular vesicles (EVs) are considered beneficial for cognitive development and human health. Milk-derived whey concentrates rich in these lipids are therefore used as ingredients in infant formulas to mimic human milk and in medical nutrition products to improve the metabolic fitness of adults and elderly people. In spite of this, there is no consensus resource detailing the multitude of lipid molecules in whey concentrates. To bridge this knowledge gap, we report a comprehensive and quantitative lipidomic resource of different whey concentrates. In-depth lipidomic analysis of acid, sweet, and buttermilk whey concentrates identified 5714 lipid molecules belonging to 23 lipid classes. The data show that the buttermilk whey concentrate has the highest level of fat globule-derived triacylglycerols and that the acid and sweet whey concentrates have the highest proportions of MFGM- and EV-derived membrane lipids. Interestingly, the acid whey concentrate has a higher level of cholesterol whereas sweet whey concentrate has higher levels of lactosylceramides. Altogether, we report a detailed lipid molecular compendium of whey concentrates and lay the groundwork for using in-depth lipidomic technology to profile the nutritional value of milk products and functional foods containing dairy-based concentrates.
Collapse
Affiliation(s)
- Richard R. Sprenger
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark
| | | | | | - Jan T. Rasmussen
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Christer S. Ejsing
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| |
Collapse
|
4
|
Heyen S, Schneider V, Hüppe L, Meyer B, Wilkes H. Variations of intact phospholipid compositions in the digestive system of Antarctic krill, Euphausia superba, between summer and autumn. PLoS One 2023; 18:e0295677. [PMID: 38157351 PMCID: PMC10756546 DOI: 10.1371/journal.pone.0295677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024] Open
Abstract
The biochemical composition of Antarctic krill, Euphausia superba, is largely determined by their feeding behaviour. As they supply energy for animals of a higher trophic level and are also commercialized for human consumption, the interest in research on the species is high. Lipids, especially phospholipids, make up a high proportion of dry weight in krill. Seasonal changes are well documented in the fingerprint of free fatty acids analysed after hydrolysis of phospholipids, but the underlying intact polar lipids are rarely considered. In this study, we evaluated the compositions of intact phospholipids (IPLs) in the stomach, digestive gland and hind gut of Antarctic krill caught in summer and autumn at the Antarctic Peninsula region. Using high-resolution mass spectrometry, the fatty acid composition of 179 intact phospholipids could be resolved. Most IPLs were phosphatidylcholines, followed by phosphatidylethanolamines. Several very long chain polyunsaturated fatty acids up to 38:8, which have not been reported in krill before, were identified. The composition shifted to higher molecular weight IPLs with a higher degree of unsaturation for summer samples, especially for samples of the digestive gland. The data supplied in this paper provides new insights into lipid dynamics between summer and autumn usually described by free fatty acid biomarkers.
Collapse
Affiliation(s)
- Simone Heyen
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Vivien Schneider
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Lukas Hüppe
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
- Julius-Maximilians-University of Würzburg, Würzburg, Germany
| | - Bettina Meyer
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
- Helmholtz Institute for Marine Functional Biodiversity (HIFMB), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Heinz Wilkes
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| |
Collapse
|
5
|
Hussain AA, Bilgin M, Carlsson J, Foged MM, Mortensen EL, Bulik CM, Støving RK, Sjögren JM. Elevated lipid class concentrations in females with anorexia nervosa before and after intensive weight restoration treatment-A lipidomics study. Int J Eat Disord 2023; 56:2260-2272. [PMID: 37715358 DOI: 10.1002/eat.24063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/17/2023]
Abstract
OBJECTIVE To study the plasma lipidome of patients with anorexia nervosa (AN) before and after weight restoration treatment and report associations with AN subtypes and oral contraceptive pill (OCP) usage. METHODS Quantitative shotgun lipidomics analysis was used to study plasma lipids of 50 female patients with AN before and after weight restoration treatment and 50 healthy female controls (HC). The AN group was assessed with blood samples and questionnaires before and after weight restoration. RESULTS In total we quantified 260 lipid species representing 26 lipid classes of which 13 lipid class concentrations were elevated in patients with AN at admission compared with HC. Lipid classes remained elevated after weight restoration treatment of 84 days (median; interquartile range 28), and only the concentration of the ceramide lipid class increased between pre- and post-treatment (p = .03), whereas lysophosphatidylcholine (LPC, p = .02), ether-linked Phosphatidylcholine (LPCO, p = .02), and lysophosphatidylethanolamine (LPE, p = .009) decreased. CONCLUSION In AN, 13 out of 26 lipid class concentrations were elevated at admission and remained elevated post-treatment. Ceramides increased further between pre- and post-weight restoration treatment, which could be related to the rapid weight gain during re-nutrition. Further research is needed to elucidate the effects of weight restoration treatment on short- and long-term lipid profiles in individuals with AN. PUBLIC SIGNIFICANCE STATEMENT Lipidomics research can increase the understanding of AN, a complex and potentially life-threatening eating disorder. By analyzing lipids, or fats, in the body, we can identify biological markers that may inform diagnosis and develop more effective treatments. This research can also shed light on the underlying mechanisms of the disorder, leading to a better understanding of the processes involved in eating behavior.
Collapse
Affiliation(s)
- Alia Arif Hussain
- Eating Disorder Research Unit, Mental Health Center, Ballerup, Copenhagen University Hospital-Mental Health Services CPH, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Mesut Bilgin
- Lipidomics Core Facility, Danish Cancer Institute, Copenhagen, Denmark
| | - Jessica Carlsson
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Competence Centre for Transcultural Psychiatry, Mental Health Centre Ballerup, Mental Health Services of the Capital Region of Denmark, Copenhagen, Denmark
| | - Mads Møller Foged
- Lipidomics Core Facility, Danish Cancer Institute, Copenhagen, Denmark
| | - Erik Lykke Mortensen
- Unit of Medical Psychology, Section of Environmental Health, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
- Center for Healthy Aging, University of Copenhagen, Copenhagen, Denmark
| | - Cynthia M Bulik
- Department of Psychiatry, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - René Klinkby Støving
- Center for Eating Disorders, Odense University Hospital, Odense, Denmark
- Research Unit for Medical Endocrinology, Odense University Hospital, Odense, Denmark
- Research Unit, Child and Adolescent Psychiatry, Mental Health Services in the Region of Southern Denmark, Denmark
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Jan Magnus Sjögren
- Eating Disorder Research Unit, Mental Health Center, Ballerup, Copenhagen University Hospital-Mental Health Services CPH, Copenhagen, Denmark
- Institute of Clinical Science, Department of Psychiatry, Umeå University, Umeå, Sweden
| |
Collapse
|
6
|
Brademan DR, Overmyer KA, He Y, Barshop WD, Canterbury JD, Bills BJ, Anderson BJ, Hutchins PD, Sharma S, Zabrouskov V, McAlister GC, Coon JJ. Improved Structural Characterization of Glycerophospholipids and Sphingomyelins with Real-Time Library Searching. Anal Chem 2023; 95:7813-7821. [PMID: 37172325 PMCID: PMC10840458 DOI: 10.1021/acs.analchem.2c04633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
In mass spectrometry-based lipidomics, complex lipid mixtures undergo chromatographic separation, are ionized, and are detected using tandem MS (MSn) to simultaneously quantify and structurally characterize eluting species. The reported structural granularity of these identified lipids is strongly reliant on the analytical techniques leveraged in a study. For example, lipid identifications from traditional collisionally activated data-dependent acquisition experiments are often reported at either species level or molecular species level. Structural resolution of reported lipid identifications is routinely enhanced by integrating both positive and negative mode analyses, requiring two separate runs or polarity switching during a single analysis. MS3+ can further elucidate lipid structure, but the lengthened MS duty cycle can negatively impact analysis depth. Recently, functionality has been introduced on several Orbitrap Tribrid mass spectrometry platforms to identify eluting molecular species on-the-fly. These real-time identifications can be leveraged to trigger downstream MSn to improve structural characterization with lessened impacts on analysis depth. Here, we describe a novel lipidomics real-time library search (RTLS) approach, which utilizes the lipid class of real-time identifications to trigger class-targeted MSn and to improve the structural characterization of phosphotidylcholines, phosphotidylethanolamines, phosphotidylinositols, phosphotidylglycerols, phosphotidylserine, and sphingomyelins in the positive ion mode. Our class-based RTLS method demonstrates improved selectivity compared to the current methodology of triggering MSn in the presence of characteristic ions or neutral losses.
Collapse
Affiliation(s)
- Dain R. Brademan
- The Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
| | - Katherine A. Overmyer
- The Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
| | - Yuchen He
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
| | | | | | | | - Benton J. Anderson
- Department of Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
| | | | - Seema Sharma
- Thermo Fisher Scientific, San Jose, CA 95134, USA
| | | | | | - Joshua J. Coon
- The Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison WI 53706, USA
| |
Collapse
|
7
|
Mønsted MØ, Bilgin M, Kuzma M, Pelantová H, Pedersen K, Tomášová P, Nazmutdinova A, Šedivá B, Funda D, Castro-Mejía JL, Holm LJ, Nielsen DS, Haupt-Jorgensen M. Reduced phosphatidylcholine level in the intestinal mucus layer of prediabetic NOD mice. APMIS 2023; 131:237-248. [PMID: 36811202 DOI: 10.1111/apm.13302] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023]
Abstract
Type 1 diabetes (T1D) is an autoimmune disease with rising incidence. Pre- and manifest T1D is associated with intestinal barrier dysfunction, skewed microbiota composition, and serum dyslipidemia. The intestinal mucus layer protects against pathogens and its structure and phosphatidylcholine (PC) lipid composition may be compromised in T1D, potentially contributing to barrier dysfunction. This study compared prediabetic Non-Obese Diabetic (NOD) mice to healthy C57BL/6 mice by analyzing the intestinal mucus PC profile by shotgun lipidomics, plasma metabolomics by mass spectrometry and nuclear magnetic resonance, intestinal mucus production by histology, and cecal microbiota composition by 16 S rRNA sequencing. Jejunal mucus PC class levels were decreased in early prediabetic NOD vs C57BL/6 mice. In colonic mucus of NOD mice, the level of several PC species was reduced throughout prediabetes. In plasma, similar reductions of PC species were observed in early prediabetic NOD mice, where also increased beta-oxidation was prominent. No histological alterations were found in jejunal nor colonic mucus between the mouse strains. However, the β-diversity of the cecal microbiota composition differed between prediabetic NOD and C57BL/6 mice, and the bacterial species driving this difference were related to decreased short-chain fatty acid (SCFA)-production in the NOD mice. This study reports reduced levels of PCs in the intestinal mucus layer and plasma of prediabetic NOD mice as well as reduced proportions of SCFA-producing bacteria in cecal content at early prediabetes, possibly contributing to intestinal barrier dysfunction and T1D.
Collapse
Affiliation(s)
- Mia Øgaard Mønsted
- Department of Pathology, Rigshospitalet, The Bartholin Institute, Copenhagen, Denmark
| | - Mesut Bilgin
- Lipidomics Core Facility, Cell Death and Metabolism Unit, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Marek Kuzma
- Institute of Microbiology, Czech Academy of Sciences, Prague, The Czech Republic
| | - Helena Pelantová
- Institute of Microbiology, Czech Academy of Sciences, Prague, The Czech Republic
| | - Kristina Pedersen
- Department of Pathology, Rigshospitalet, The Bartholin Institute, Copenhagen, Denmark
| | - Petra Tomášová
- Institute of Microbiology, Czech Academy of Sciences, Prague, The Czech Republic
| | | | - Blanka Šedivá
- Faculty of Applied Sciences, University of West Bohemia, Plzeň, The Czech Republic
| | - David Funda
- Institute of Microbiology, Czech Academy of Sciences, Prague, The Czech Republic
| | | | - Laurits Juulskov Holm
- Department of Pathology, Rigshospitalet, The Bartholin Institute, Copenhagen, Denmark
| | | | | |
Collapse
|
8
|
Foged MM, Maeda K, Bilgin M. Profiling the Mammalian Lipidome by Quantitative Shotgun Lipidomics. Methods Mol Biol 2023; 2625:89-102. [PMID: 36653635 DOI: 10.1007/978-1-0716-2966-6_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The emerging field of lipidomics presents the systems biology approach to identify and quantify the full lipid repertoire of cells, tissues, and organisms. The importance of the lipidome is demonstrated by a number of biological studies on dysregulation of lipid metabolism in human diseases such as cancer, diabetes, and neurodegenerative diseases. Exploring changes and regulations in the huge networks of lipids and their metabolic pathways requires a lipidomics methodology: advanced mass spectrometry that resolves the complexity of the lipidome. Here, we report a comprehensive protocol of quantitative shotgun lipidomics that enables identification and quantification of hundreds of molecular lipid species, covering a wide range of lipid classes, extracted from cultured mammalian cells.
Collapse
Affiliation(s)
- Mads Møller Foged
- Cell Death and Metabolism Unit, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Kenji Maeda
- Cell Death and Metabolism Unit, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Mesut Bilgin
- Cell Death and Metabolism Unit, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen, Denmark. .,Lipidomics Core Facility, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center , Copenhagen, Denmark.
| |
Collapse
|
9
|
Lipidomics Analysis with Triple Quadrupole Mass Spectrometry. Methods Mol Biol 2023; 2625:103-106. [PMID: 36653636 DOI: 10.1007/978-1-0716-2966-6_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Lipids serve an essential role in multiple cellular functions including signaling, metabolism, energy storage, and membrane constitution. Lipidomics, the study of lipids using analytical chemistry, allows for the study of disease states and cellular metabolism. Shotgun lipidomics is a technique that involves direct-infusion electrospray ionization (ESI) and analysis with a triple quadrupole mass spectrometer. Triple quadrupole mass spectrometry is ideally suited for lipidomics analysis because it allows for class-specific identification of lipids. Individual lipid class can be identified by the adjustment of three parameters-collision energy, ion mode, and scan type. This chapter describes the use of a triple quadrupole mass spectrometer, the TSQ Quantum Access MAX, to perform lipidomics analysis with high sensitivity, accuracy, and precision.
Collapse
|
10
|
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] [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
|
11
|
Renne MF, Bao X, Hokken MWJ, Bierhuizen AS, Hermansson M, Sprenger RR, Ewing TA, Ma X, Cox RC, Brouwers JF, De Smet CH, Ejsing CS, de Kroon AIPM. Molecular species selectivity of lipid transport creates a mitochondrial sink for di-unsaturated phospholipids. EMBO J 2022; 41:e106837. [PMID: 34873731 PMCID: PMC8762554 DOI: 10.15252/embj.2020106837] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 11/09/2022] Open
Abstract
Mitochondria depend on the import of phospholipid precursors for the biosynthesis of phosphatidylethanolamine (PE) and cardiolipin, yet the mechanism of their transport remains elusive. A dynamic lipidomics approach revealed that mitochondria preferentially import di-unsaturated phosphatidylserine (PS) for subsequent conversion to PE by the mitochondrial PS decarboxylase Psd1p. Several protein complexes tethering mitochondria to the endomembrane system have been implicated in lipid transport in yeast, including the endoplasmic reticulum (ER)-mitochondrial encounter structure (ERMES), ER-membrane complex (EMC), and the vacuole and mitochondria patch (vCLAMP). By limiting the availability of unsaturated phospholipids, we created conditions to investigate the mechanism of lipid transfer and the contributions of the tethering complexes in vivo. Under these conditions, inactivation of ERMES components or of the vCLAMP component Vps39p exacerbated accumulation of saturated lipid acyl chains, indicating that ERMES and Vps39p contribute to the mitochondrial sink for unsaturated acyl chains by mediating transfer of di-unsaturated phospholipids. These results support the concept that intermembrane lipid flow is rate-limited by molecular species-dependent lipid efflux from the donor membrane and driven by the lipid species' concentration gradient between donor and acceptor membrane.
Collapse
Affiliation(s)
- Mike F Renne
- Membrane Biochemistry & BiophysicsDepartment of ChemistryUtrecht UniversityUtrechtThe Netherlands
- Present address:
Sir William Dunn School of PathologyUniversity of OxfordOxfordUK
| | - Xue Bao
- Membrane Biochemistry & BiophysicsDepartment of ChemistryUtrecht UniversityUtrechtThe Netherlands
| | - Margriet WJ Hokken
- Membrane Biochemistry & BiophysicsDepartment of ChemistryUtrecht UniversityUtrechtThe Netherlands
- Present address:
Department of Medical MicrobiologyRadboud University Medical CenterRadboud Institute for Molecular Life SciencesNijmegenThe Netherlands
| | - Adolf S Bierhuizen
- Membrane Biochemistry & BiophysicsDepartment of ChemistryUtrecht UniversityUtrechtThe Netherlands
| | - Martin Hermansson
- Department of Biochemistry and Molecular BiologyVILLUM Center for Bioanalytical SciencesUniversity of Southern DenmarkOdenseDenmark
| | - Richard R Sprenger
- Department of Biochemistry and Molecular BiologyVILLUM Center for Bioanalytical SciencesUniversity of Southern DenmarkOdenseDenmark
| | - Tom A Ewing
- Membrane Biochemistry & BiophysicsDepartment of ChemistryUtrecht UniversityUtrechtThe Netherlands
- Present address:
Wageningen Food & Biobased ResearchWageningen University & ResearchWageningenThe Netherlands
| | - Xiao Ma
- Membrane Biochemistry & BiophysicsDepartment of ChemistryUtrecht UniversityUtrechtThe Netherlands
| | - Ruud C Cox
- Membrane Biochemistry & BiophysicsDepartment of ChemistryUtrecht UniversityUtrechtThe Netherlands
| | - Jos F Brouwers
- Biochemistry and Cell BiologyDepartment of Veterinary MedicineUtrecht UniversityUtrechtThe Netherlands
- Present address:
Center for Molecular MedicineUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Cedric H De Smet
- Membrane Biochemistry & BiophysicsDepartment of ChemistryUtrecht UniversityUtrechtThe Netherlands
| | - Christer S Ejsing
- Department of Biochemistry and Molecular BiologyVILLUM Center for Bioanalytical SciencesUniversity of Southern DenmarkOdenseDenmark
- Cell Biology and Biophysics UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
| | - Anton IPM de Kroon
- Membrane Biochemistry & BiophysicsDepartment of ChemistryUtrecht UniversityUtrechtThe Netherlands
| |
Collapse
|
12
|
Khalil SM, Sprenger RR, Hermansson M, Ejsing CS. DDA-imaging with structural identification of lipid molecules on an Orbitrap Velos Pro mass spectrometer. JOURNAL OF MASS SPECTROMETRY : JMS 2022; 57:e4882. [PMID: 36055222 PMCID: PMC9541402 DOI: 10.1002/jms.4882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/05/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) is a useful technique for visualizing the spatial distribution of lipid molecules in tissues. Nevertheless, the use of MSI to investigate local lipid metabolic hallmarks has until recently been hampered by a lack of adequate technology that supports confident lipid identification. This limitation was recently mitigated by the development of DDA-imaging technology where high-resolution MSI is combined with parallel acquisition of lipid tandem MS2 spectra on a hybrid ion trap-Orbitrap Elite mass spectrometer featuring a resolving power of 240,000 and a scan time of 1 s. Here, we report the key tenets related to successful transfer of the DDA-imaging technology onto an Orbitrap Velos Pro instrument featuring a resolving power of 120,000 and a scan time of 2 s. Through meticulous performance assessments and method optimization, we tuned the DDA-imaging method to be able to confidently identify 73 molecular lipid species in mouse brain sections and demonstrate that the performance of the technology is comparable with DDA-imaging on the Orbitrap Elite. Altogether, our work shows that DDA-imaging on the Orbitrap Velos Pro instrument can serve as a robust workhorse for lipid imaging in routine applications.
Collapse
Affiliation(s)
- Saleh M. Khalil
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical SciencesUniversity of Southern DenmarkOdenseDenmark
| | - Richard R. Sprenger
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical SciencesUniversity of Southern DenmarkOdenseDenmark
| | - Martin Hermansson
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical SciencesUniversity of Southern DenmarkOdenseDenmark
| | - Christer S. Ejsing
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical SciencesUniversity of Southern DenmarkOdenseDenmark
- Cell Biology and Biophysics UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
| |
Collapse
|
13
|
Baquer G, Sementé L, Mahamdi T, Correig X, Ràfols P, García-Altares M. What are we imaging? Software tools and experimental strategies for annotation and identification of small molecules in mass spectrometry imaging. MASS SPECTROMETRY REVIEWS 2022:e21794. [PMID: 35822576 DOI: 10.1002/mas.21794] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Mass spectrometry imaging (MSI) has become a widespread analytical technique to perform nonlabeled spatial molecular identification. The Achilles' heel of MSI is the annotation and identification of molecular species due to intrinsic limitations of the technique (lack of chromatographic separation and the difficulty to apply tandem MS). Successful strategies to perform annotation and identification combine extra analytical steps, like using orthogonal analytical techniques to identify compounds; with algorithms that integrate the spectral and spatial information. In this review, we discuss different experimental strategies and bioinformatics tools to annotate and identify compounds in MSI experiments. We target strategies and tools for small molecule applications, such as lipidomics and metabolomics. First, we explain how sample preparation and the acquisition process influences annotation and identification, from sample preservation to the use of orthogonal techniques. Then, we review twelve software tools for annotation and identification in MSI. Finally, we offer perspectives on two current needs of the MSI community: the adaptation of guidelines for communicating confidence levels in identifications; and the creation of a standard format to store and exchange annotations and identifications in MSI.
Collapse
Affiliation(s)
- Gerard Baquer
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
| | - Lluc Sementé
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
| | - Toufik Mahamdi
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
| | - Xavier Correig
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
- Institut D'Investigacio Sanitaria Pere Virgili, Tarragona, Spain
| | - Pere Ràfols
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
- Institut D'Investigacio Sanitaria Pere Virgili, Tarragona, Spain
| | - María García-Altares
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
| |
Collapse
|
14
|
Henriksen NL, Hansen SH, Lycas MD, Pan X, Eriksen T, Johansen LS, Sprenger RR, Ejsing CS, Burrin DG, Skovgaard K, Christensen VB, Thymann T, Pankratova S. Cholestasis alters brain lipid and bile acid composition and compromises motor function in neonatal piglets. Physiol Rep 2022; 10:e15368. [PMID: 35822260 PMCID: PMC9277266 DOI: 10.14814/phy2.15368] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 05/12/2022] [Accepted: 06/06/2022] [Indexed: 11/24/2022] Open
Abstract
Infants with neonatal cholestasis are prone to neurodevelopmental deficits, however, the underlying pathogenesis is unclear. Lipid malabsorption and accumulation of potentially neurotoxic molecules in the blood such as bile acids are important yet relatively unexplored pathways. Here, we developed a translational piglet model to understand how the molecular bile acid and lipid composition of the brain is affected by this disease and relates to motor function. Piglets (8-days old) had bile duct ligation or sham surgery and were fed a formula diet for 3 weeks. Alongside sensory-motor deficits observed in bile duct-ligated animals, we found a shift toward a more hydrophilic and conjugated bile acid profile in the brain. Additionally, comprehensive lipidomics of the cerebellum revealed a decrease in total lipids including phosphatidylinositols and phosphatidylserines and increases in lysophospholipid species. This was paralleled by elevated cerebellar expression of genes related to inflammation and tissue damage albeit without significant impact on the brain transcriptome. This study offers new insights into the developing brain's molecular response to neonatal cholestasis indicating that bile acids and lipids may contribute in mediating motor deficits.
Collapse
Affiliation(s)
- Nicole Lind Henriksen
- Comparative Pediatrics and Nutrition, Department of Veterinary and Animal SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Svend Høime Hansen
- Department of Clinical BiochemistryCopenhagen University Hospital, RigshospitaletCopenhagen ØDenmark
| | | | - Xiaoyu Pan
- Comparative Pediatrics and Nutrition, Department of Veterinary and Animal SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Thomas Eriksen
- Department of Veterinary Clinical SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | | | - Richard R. Sprenger
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical SciencesUniversity of Southern DenmarkOdense MDenmark
| | - Christer Stenby Ejsing
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical SciencesUniversity of Southern DenmarkOdense MDenmark
| | - Douglas G. Burrin
- Department of Pediatrics, United States Department of Agriculture, Agricultural Research ServiceChildren's Nutrition Research Center, Baylor College of MedicineHoustonTexasUSA
| | - Kerstin Skovgaard
- Department of Biotechnology and BiomedicineTechnical University of DenmarkLyngbyDenmark
| | - Vibeke Brix Christensen
- Comparative Pediatrics and Nutrition, Department of Veterinary and Animal SciencesUniversity of CopenhagenFrederiksberg CDenmark
- Department of Pediatrics and Adolescent MedicineCopenhagen University Hospital, RigshospitaletCopenhagen ØDenmark
| | - Thomas Thymann
- Comparative Pediatrics and Nutrition, Department of Veterinary and Animal SciencesUniversity of CopenhagenFrederiksberg CDenmark
| | - Stanislava Pankratova
- Comparative Pediatrics and Nutrition, Department of Veterinary and Animal SciencesUniversity of CopenhagenFrederiksberg CDenmark
| |
Collapse
|
15
|
Henriksen NL, Asmussen KS, Pan X, Jiang PP, Mori Y, Christiansen LI, Sprenger RR, Ejsing CS, Pankratova S, Thymann T. Brain lipidomics and neurodevelopmental outcomes in intrauterine growth restricted piglets fed dairy or vegetable fat diets. Sci Rep 2022; 12:3303. [PMID: 35228576 PMCID: PMC8885751 DOI: 10.1038/s41598-022-07133-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 02/14/2022] [Indexed: 11/18/2022] Open
Abstract
Breast milk has neurodevelopmental advantages compared to infant formula, especially in low-birth-weight infants, which may in part relate to the fat source. This study compared neurodevelopmental outcomes in three-day-old normal birth weight (NBW) and intrauterine growth restricted (IUGR) piglets fed a formula diet with either vegetable oil (VEG) or bovine milk fat sources (MILK) for three weeks in a 2 × 2 factorial design. Behavioural tests, lipidomics, MRI and RNA sequencing analyses of plasma and brain tissue were conducted. The absolute levels of 82% and 11% of lipid molecules were different between dietary groups in plasma and hippocampus, respectively. Of the lipid molecules with differential abundance in the hippocampus, the majority were upregulated in MILK versus VEG, and they mainly belonged to the group of glycerophospholipids. Lower absolute brain weights, absolute grey and white matter volumes and behaviour and motor function scores, and higher relative total brain weights were present in IUGR compared to NBW with minor influence of diet. Cognitive function and cerebellar gene expression profiles were similar for dietary and weight groups, and overall only minor interactive effects between diet and birth weight were observed. Overall, we show that the dietary fat source influences the plasma and to a lesser degree the hippocampal lipidome and is unable to improve on IUGR-induced brain structural and functional impairments.
Collapse
Affiliation(s)
- Nicole L Henriksen
- Section of Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, University of Copenhagen, Dyrlægevej 68, 1870, Frederiksberg C, Denmark
| | - Karina S Asmussen
- Section of Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, University of Copenhagen, Dyrlægevej 68, 1870, Frederiksberg C, Denmark
| | - Xiaoyu Pan
- Section of Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, University of Copenhagen, Dyrlægevej 68, 1870, Frederiksberg C, Denmark
| | - Ping-Ping Jiang
- Section of Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, University of Copenhagen, Dyrlægevej 68, 1870, Frederiksberg C, Denmark
| | - Yuki Mori
- Center for Translational Neuromedicine, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen N, Denmark
| | - Line I Christiansen
- Section of Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, University of Copenhagen, Dyrlægevej 68, 1870, Frederiksberg C, Denmark
| | - Richard R Sprenger
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Christer S Ejsing
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
| | - Stanislava Pankratova
- Section of Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, University of Copenhagen, Dyrlægevej 68, 1870, Frederiksberg C, Denmark
| | - Thomas Thymann
- Section of Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, University of Copenhagen, Dyrlægevej 68, 1870, Frederiksberg C, Denmark.
| |
Collapse
|
16
|
Han X, Gross RW. The foundations and development of lipidomics. J Lipid Res 2022; 63:100164. [PMID: 34953866 PMCID: PMC8953652 DOI: 10.1016/j.jlr.2021.100164] [Citation(s) in RCA: 72] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/15/2022] Open
Abstract
For over a century, the importance of lipid metabolism in biology was recognized but difficult to mechanistically understand due to the lack of sensitive and robust technologies for identification and quantification of lipid molecular species. The enabling technological breakthroughs emerged in the 1980s with the development of soft ionization methods (Electrospray Ionization and Matrix Assisted Laser Desorption/Ionization) that could identify and quantify intact individual lipid molecular species. These soft ionization technologies laid the foundations for what was to be later named the field of lipidomics. Further innovative advances in multistage fragmentation, dramatic improvements in resolution and mass accuracy, and multiplexed sample analysis fueled the early growth of lipidomics through the early 1990s. The field exponentially grew through the use of a variety of strategic approaches, which included direct infusion, chromatographic separation, and charge-switch derivatization, which facilitated access to the low abundance species of the lipidome. In this Thematic Review, we provide a broad perspective of the foundations, enabling advances, and predicted future directions of growth of the lipidomics field.
Collapse
Affiliation(s)
- Xianlin Han
- Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA; Departments of Medicine - Diabetes, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
| | - Richard W Gross
- Division of Bioorganic Chemistry and Molecular Pharmacology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA; Department of Chemistry, Washington University, St. Louis, MO, USA
| |
Collapse
|
17
|
Abstract
The intimate association between obesity and type II diabetes urges for a deeper understanding of adipocyte function. We and others have previously delineated a role for the tumor suppressor p53 in adipocyte biology. Here, we show that mice haploinsufficient for MDM2, a key regulator of p53, in their adipose stores suffer from overt obesity, glucose intolerance, and hepatic steatosis. These mice had decreased levels of circulating palmitoleic acid [non-esterified fatty acid (NEFA) 16:1] concomitant with impaired visceral adipose tissue expression of Scd1 and Ffar4. A similar decrease in Scd and Ffar4 expression was found in in vitro differentiated adipocytes with perturbed MDM2 expression. Lowered MDM2 levels led to nuclear exclusion of the transcriptional cofactors, MORC2 and LIPIN1, and thereby possibly hampered adipocyte function by antagonizing LIPIN1-mediated PPARγ coactivation. Collectively, these data argue for a hitherto unknown interplay between MDM2 and MORC2/LIPIN1 involved in balancing adipocyte function.
Collapse
|
18
|
Byeon SK, Madugundu AK, Pandey A. Automated data-driven mass spectrometry for improved analysis of lipids with dual dissociation techniques. J Mass Spectrom Adv Clin Lab 2021; 22:43-49. [PMID: 34939054 PMCID: PMC8662330 DOI: 10.1016/j.jmsacl.2021.10.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 10/15/2021] [Accepted: 10/17/2021] [Indexed: 11/15/2022] Open
Abstract
Lipidomics is an important component of most multi-Omics systems biology studies and is largely driven by mass spectrometry (MS). Because lipids are tight regulators of multiple cellular functions, including energy homeostasis, membrane structures and cell signaling, lipidomics can provide a deeper understanding of variations underlying disease states and can become an even more powerful platform when combined with other omics, including genomics or proteomics. However, data analysis, especially in lipid annotation, poses challenges due to the heterogeneity of functional head groups and fatty acyl chains of varying hydrocarbon lengths and degrees of unsaturation. As there are various MS/MS fragmentation sites in lipids that are class-dependent, obtaining MS/MS data that includes as many fragment ions as possible is critical for structural characterization of lipids in lipidomics workflow. Here, we report an improved lipidomics methodology that resulted in increased coverage of lipidome using: 1) An automated data-driven MS/MS acquisition scheme in which inclusion and exclusion lists were automatically generated from the full scan MS of sample injections, followed by creation of updated lists over iterative analyses; and, 2) Incorporation of dual dissociation techniques of higher-energy collision dissociation and collision-induced dissociation for more accurate characterization of phosphatidylcholine species. Inclusion lists were created automatically based on full scan MS signals from samples and through iterative analyses, ions in the inclusion list that were fragmented were automatically moved to the exclusion list in subsequent runs. We confirmed that analytes with low MS response that did not undergo MS/MS events in conventional data-dependent analysis were successfully fragmented using this approach. Overall, this automated data-driven data acquisition approach resulted in a higher coverage of lipidome and the use of dual dissociation techniques provided additional information that was critical in characterizing the side chains of phosphatidylcholine species.
Collapse
Affiliation(s)
- Seul Kee Byeon
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester MN 55905 USA
| | - Anil K. Madugundu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester MN 55905 USA
- Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
- Institute of Bioinformatics, International Technology Park, Bangalore 560006, India
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences, Hosur Road, Bangalore 560029, Karnataka, India
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester MN 55905 USA
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| |
Collapse
|
19
|
Barnette BL, Yu Y, Ullrich RL, Emmett MR. Mitochondrial Effects in the Liver of C57BL/6 Mice by Low Dose, High Energy, High Charge Irradiation. Int J Mol Sci 2021; 22:ijms222111806. [PMID: 34769236 PMCID: PMC8584048 DOI: 10.3390/ijms222111806] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/19/2021] [Accepted: 10/25/2021] [Indexed: 12/19/2022] Open
Abstract
Galactic cosmic rays are primarily composed of protons (85%), helium (14%), and high charge/high energy ions (HZEs) such as 56Fe, 28Si, and 16O. HZE exposure is a major risk factor for astronauts during deep-space travel due to the possibility of HZE-induced cancer. A systems biology integrated omics approach encompassing transcriptomics, proteomics, lipidomics, and functional biochemical assays was used to identify microenvironmental changes induced by HZE exposure. C57BL/6 mice were placed into six treatment groups and received the following irradiation treatments: 600 MeV/n 56Fe (0.2 Gy), 1 GeV/n 16O (0.2 Gy), 350 MeV/n 28Si (0.2 Gy), 137Cs (1.0 Gy) gamma rays, 137Cs (3.0 Gy) gamma rays, and sham irradiation. Left liver lobes were collected at 30, 60, 120, 270, and 360 days post-irradiation. Analysis of transcriptomic and proteomic data utilizing ingenuity pathway analysis identified multiple pathways involved in mitochondrial function that were altered after HZE irradiation. Lipids also exhibited changes that were linked to mitochondrial function. Molecular assays for mitochondrial Complex I activity showed significant decreases in activity after HZE exposure. HZE-induced mitochondrial dysfunction suggests an increased risk for deep space travel. Microenvironmental and pathway analysis as performed in this research identified possible targets for countermeasures to mitigate risk.
Collapse
Affiliation(s)
- Brooke L. Barnette
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA;
| | - Yongjia Yu
- Department of Radiation Oncology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA;
| | - Robert L. Ullrich
- The Radiation Effects Research Foundation (RERF), Hiroshima 732-0815, Japan;
| | - Mark R. Emmett
- Department of Radiation Oncology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA;
- Department of Pathology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
- Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
- Correspondence: ; Tel.: +1-(409)-747-1943
| |
Collapse
|
20
|
Köfeler HC, Ahrends R, Baker ES, Ekroos K, Han X, Hoffmann N, Holčapek M, Wenk MR, Liebisch G. Recommendations for good practice in MS-based lipidomics. J Lipid Res 2021; 62:100138. [PMID: 34662536 PMCID: PMC8585648 DOI: 10.1016/j.jlr.2021.100138] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/29/2021] [Accepted: 10/01/2021] [Indexed: 12/17/2022] Open
Abstract
In the last 2 decades, lipidomics has become one of the fastest expanding scientific disciplines in biomedical research. With an increasing number of new research groups to the field, it is even more important to design guidelines for assuring high standards of data quality. The Lipidomics Standards Initiative is a community-based endeavor for the coordination of development of these best practice guidelines in lipidomics and is embedded within the International Lipidomics Society. It is the intention of this review to highlight the most quality-relevant aspects of the lipidomics workflow, including preanalytics, sample preparation, MS, and lipid species identification and quantitation. Furthermore, this review just does not only highlights examples of best practice but also sheds light on strengths, drawbacks, and pitfalls in the lipidomic analysis workflow. While this review is neither designed to be a step-by-step protocol by itself nor dedicated to a specific application of lipidomics, it should nevertheless provide the interested reader with links and original publications to obtain a comprehensive overview concerning the state-of-the-art practices in the field.
Collapse
Affiliation(s)
- Harald C Köfeler
- Core Facility Mass Spectrometry, Medical University of Graz, Graz, Austria.
| | - Robert Ahrends
- Department for Analytical Chemistry, University of Vienna, Vienna, Austria
| | - Erin S Baker
- Department of Chemistry, North Carolina State University, Raleigh, NC, USA
| | - Kim Ekroos
- Lipidomics Consulting Ltd., Esbo, Finland
| | - Xianlin Han
- Barshop Inst Longev & Aging Studies, Univ Texas Hlth Sci Ctr San Antonio, San Antonio, TX, USA
| | - Nils Hoffmann
- Center for Biotechnology, Universität Bielefeld, Bielefeld, Germany
| | - Michal Holčapek
- Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czech Republic
| | - Markus R Wenk
- Singapore Lipidomics Incubator (SLING), Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore, Singapore
| | - Gerhard Liebisch
- Institute of Clinical Chemistry and Laboratory Medicine, Regensburg University Hospital, Regensburg, Germany.
| |
Collapse
|
21
|
Schmidt S, Gallego SF, Zelnik ID, Kovalchuk S, Albæk N, Sprenger RR, Øverup C, Pewzner-Jung Y, Futerman AH, Lindholm MW, Jensen ON, Ejsing CS. Silencing of ceramide synthase 2 in hepatocytes modulates plasma ceramide biomarkers predictive of cardiovascular death. Mol Ther 2021; 30:1661-1674. [PMID: 34400330 PMCID: PMC9077316 DOI: 10.1016/j.ymthe.2021.08.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/26/2021] [Accepted: 08/08/2021] [Indexed: 12/15/2022] Open
Abstract
Emerging clinical data show that three ceramide molecules, Cer d18:1/16:0, Cer d18:1/24:1, and Cer d18:1/24:0, are biomarkers of a fatal outcome in patients with cardiovascular disease. This finding raises basic questions about their metabolic origin, their contribution to disease pathogenesis, and the utility of targeting the underlying enzymatic machinery for treatment of cardiometabolic disorders. Here, we outline the development of a potent N-acetylgalactosamine-conjugated antisense oligonucleotide engineered to silence ceramide synthase 2 specifically in hepatocytes in vivo. We demonstrate that this compound reduces the ceramide synthase 2 mRNA level and that this translates into efficient lowering of protein expression and activity as well as Cer d18:1/24:1 and Cer d18:1/24:0 levels in liver. Intriguingly, we discover that the hepatocyte-specific antisense oligonucleotide also triggers a parallel modulation of blood plasma ceramides, revealing that the biomarkers predictive of cardiovascular death are governed by ceramide biosynthesis in hepatocytes. Our work showcases a generic therapeutic framework for targeting components of the ceramide enzymatic machinery to disentangle their roles in disease causality and to explore their utility for treatment of cardiometabolic disorders.
Collapse
Affiliation(s)
- Steffen Schmidt
- Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Sandra F Gallego
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark
| | - Iris Daphne Zelnik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sergey Kovalchuk
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark
| | - Nanna Albæk
- Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Richard R Sprenger
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark
| | - Charlotte Øverup
- Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Yael Pewzner-Jung
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Anthony H Futerman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Marie W Lindholm
- Roche Pharma Research and Early Development, Roche Innovation Center Copenhagen, 2970 Hørsholm, Denmark
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark
| | - Christer S Ejsing
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense, Denmark; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
| |
Collapse
|
22
|
Minnier J, Emmett MR, Perez R, Ding LH, Barnette BL, Larios RE, Hong C, Hwang TH, Yu Y, Fallgren CM, Story MD, Weil MM, Raber J. Associations between lipids in selected brain regions, plasma miRNA, and behavioral and cognitive measures following 28Si ion irradiation. Sci Rep 2021; 11:14899. [PMID: 34290258 PMCID: PMC8295277 DOI: 10.1038/s41598-021-93869-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 06/29/2021] [Indexed: 11/09/2022] Open
Abstract
The space radiation environment consists of multiple species of charged particles, including 28Si ions, that may impact brain function during and following missions. To develop biomarkers of the space radiation response, BALB/c and C3H female and male mice and their F2 hybrid progeny were irradiated with 28Si ions (350 MeV/n, 0.2 Gy) and tested for behavioral and cognitive performance 1, 6, and 12 months following irradiation. The plasma of the mice was collected for analysis of miRNA levels. Select pertinent brain regions were dissected for lipidomic analyses and analyses of levels of select biomarkers shown to be sensitive to effects of space radiation in previous studies. There were associations between lipids in select brain regions, plasma miRNA, and cognitive measures and behavioral following 28Si ion irradiation. Different but overlapping sets of miRNAs in plasma were found to be associated with cognitive measures and behavioral in sham and irradiated mice at the three time points. The radiation condition revealed pathways involved in neurodegenerative conditions and cancers. Levels of the dendritic marker MAP2 in the cortex were higher in irradiated than sham-irradiated mice at middle age, which might be part of a compensatory response. Relationships were also revealed with CD68 in miRNAs in an anatomical distinct fashion, suggesting that distinct miRNAs modulate neuroinflammation in different brain regions. The associations between lipids in selected brain regions, plasma miRNA, and behavioral and cognitive measures following 28Si ion irradiation could be used for the development of biomarker of the space radiation response.
Collapse
Affiliation(s)
- Jessica Minnier
- Oregon Health & Science University-Portland State University School of Public Health, Knight Cancer Institute Biostatistics Shared Resource, and the Knight Cardiovascular Institute, OR Health & Science University, Portland, OR, 97239, USA
| | - Mark R Emmett
- Department of Biochemistry and Molecular Biology; Radiation Oncology, Pharmacology and Toxicology, Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch Cancer Center, Galveston, TX, 77555, USA
| | - Ruby Perez
- Department of Behavioral Neuroscience, L470, Oregon Health & Science University, 3181SW Sam Jackson Park Road, Portland, OR, 97239, USA
| | - Liang-Hao Ding
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Brooke L Barnette
- Department of Biochemistry and Molecular Biology; Radiation Oncology, Pharmacology and Toxicology, Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch Cancer Center, Galveston, TX, 77555, USA
| | - Rianna E Larios
- Department of Biochemistry and Molecular Biology; Radiation Oncology, Pharmacology and Toxicology, Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch Cancer Center, Galveston, TX, 77555, USA
| | - Changjin Hong
- Lerner Research Institute, Cleveland Clinic Lerner College of Medicine US, Cleveland, OH, 44195, USA
| | - Tae Hyun Hwang
- Lerner Research Institute, Cleveland Clinic Lerner College of Medicine US, Cleveland, OH, 44195, USA
- Department of Molecular Medicine, School of Medicine, GU Malignancies Program, Case Comprehensive Cancer Center, Genomic Medicine Institute, Case Western Reserve University US., Cleveland, OH, 10900, USA
| | - Yongjia Yu
- Department of Biochemistry and Molecular Biology; Radiation Oncology, Pharmacology and Toxicology, Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch Cancer Center, Galveston, TX, 77555, USA
| | - Christina M Fallgren
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Michael D Story
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Michael M Weil
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Jacob Raber
- Department of Behavioral Neuroscience, L470, Oregon Health & Science University, 3181SW Sam Jackson Park Road, Portland, OR, 97239, USA.
- Division of Neuroscience ONPRC, Departments of Neurology, Psychiatry, and Radiation Medicine, Oregon Health & Science University, Portland, OR, 97239, USA.
| |
Collapse
|
23
|
Artibani M, Masuda K, Hu Z, Rauher PC, Mallett G, Wietek N, Morotti M, Chong K, KaramiNejadRanjbar M, Zois CE, Dhar S, El-Sahhar S, Campo L, Blagden SP, Damato S, Pathiraja PN, Nicum S, Gleeson F, Laios A, Alsaadi A, Santana Gonzalez L, Motohara T, Albukhari A, Lu Z, Bast RC, Harris AL, Ejsing CS, Klemm RW, Yau C, Sauka-Spengler T, Ahmed AA. Adipocyte-like signature in ovarian cancer minimal residual disease identifies metabolic vulnerabilities of tumor-initiating cells. JCI Insight 2021; 6:147929. [PMID: 33945502 PMCID: PMC8262282 DOI: 10.1172/jci.insight.147929] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/29/2021] [Indexed: 12/15/2022] Open
Abstract
Similar to tumor-initiating cells (TICs), minimal residual disease (MRD) is capable of reinitiating tumors and causing recurrence. However, the molecular characteristics of solid tumor MRD cells and drivers of their survival have remained elusive. Here we performed dense multiregion transcriptomics analysis of paired biopsies from 17 ovarian cancer patients before and after chemotherapy. We reveal that while MRD cells share important molecular signatures with TICs, they are also characterized by an adipocyte-like gene expression signature and a portion of them had undergone epithelial-mesenchymal transition (EMT). In a cell culture MRD model, MRD-mimic cells showed the same phenotype and were dependent on fatty acid oxidation (FAO) for survival and resistance to cytotoxic agents. These findings identify EMT and FAO as attractive targets to eradicate MRD in ovarian cancer and make a compelling case for the further testing of FAO inhibitors in treating MRD.
Collapse
Affiliation(s)
- Mara Artibani
- Ovarian Cancer Cell Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, and
- Nuffield Department of Women’s & Reproductive Health, University of Oxford, Oxford, United Kingdom
- Gene Regulatory Networks in Development and Disease Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Kenta Masuda
- Ovarian Cancer Cell Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, and
- Nuffield Department of Women’s & Reproductive Health, University of Oxford, Oxford, United Kingdom
| | - Zhiyuan Hu
- Ovarian Cancer Cell Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, and
- Nuffield Department of Women’s & Reproductive Health, University of Oxford, Oxford, United Kingdom
| | - Pascal C. Rauher
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Garry Mallett
- Ovarian Cancer Cell Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, and
- Nuffield Department of Women’s & Reproductive Health, University of Oxford, Oxford, United Kingdom
- Gene Regulatory Networks in Development and Disease Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Nina Wietek
- Ovarian Cancer Cell Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, and
- Nuffield Department of Women’s & Reproductive Health, University of Oxford, Oxford, United Kingdom
- Department of Gynaecological Oncology, Churchill Hospital, Oxford University Hospitals, Oxford, United Kingdom
| | - Matteo Morotti
- Ovarian Cancer Cell Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, and
- Nuffield Department of Women’s & Reproductive Health, University of Oxford, Oxford, United Kingdom
- Department of Gynaecological Oncology, Churchill Hospital, Oxford University Hospitals, Oxford, United Kingdom
| | - Kay Chong
- Ovarian Cancer Cell Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, and
- Nuffield Department of Women’s & Reproductive Health, University of Oxford, Oxford, United Kingdom
| | - Mohammad KaramiNejadRanjbar
- Ovarian Cancer Cell Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, and
- Nuffield Department of Women’s & Reproductive Health, University of Oxford, Oxford, United Kingdom
| | - Christos E. Zois
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Sunanda Dhar
- Department of Histopathology, Oxford University Hospitals, Oxford, United Kingdom
| | - Salma El-Sahhar
- Ovarian Cancer Cell Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, and
- Nuffield Department of Women’s & Reproductive Health, University of Oxford, Oxford, United Kingdom
| | - Leticia Campo
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Sarah P. Blagden
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Stephen Damato
- Department of Histopathology, Oxford University Hospitals, Oxford, United Kingdom
| | - Pubudu N. Pathiraja
- Department of Gynaecological Oncology, Churchill Hospital, Oxford University Hospitals, Oxford, United Kingdom
| | - Shibani Nicum
- Department of Gynaecological Oncology, Churchill Hospital, Oxford University Hospitals, Oxford, United Kingdom
| | - Fergus Gleeson
- Department of Radiology, Churchill Hospital, Oxford University Hospitals, Oxford, United Kingdom
| | - Alexandros Laios
- Department of Gynaecological Oncology, Churchill Hospital, Oxford University Hospitals, Oxford, United Kingdom
| | - Abdulkhaliq Alsaadi
- Ovarian Cancer Cell Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, and
- Nuffield Department of Women’s & Reproductive Health, University of Oxford, Oxford, United Kingdom
| | - Laura Santana Gonzalez
- Ovarian Cancer Cell Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, and
- Nuffield Department of Women’s & Reproductive Health, University of Oxford, Oxford, United Kingdom
| | - Takeshi Motohara
- Department of Obstetrics and Gynecology, Faculty of Life Sciences, Kumamoto University, Chuo-ku, Kumamoto, Japan
| | - Ashwag Albukhari
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Zhen Lu
- Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Robert C. Bast
- Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Adrian L. Harris
- Department of Oncology, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Christer S. Ejsing
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Robin W. Klemm
- Department of Physiology, Anatomy and Genetics, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Christopher Yau
- Division of Informatics, Imaging and Data Sciences, School of Health Sciences, Faculty of Biology Medicine and Health, the University of Manchester, Manchester, United Kingdom
| | - Tatjana Sauka-Spengler
- Gene Regulatory Networks in Development and Disease Laboratory, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Ahmed Ashour Ahmed
- Ovarian Cancer Cell Laboratory, Medical Research Council (MRC) Weatherall Institute of Molecular Medicine, and
- Nuffield Department of Women’s & Reproductive Health, University of Oxford, Oxford, United Kingdom
- Department of Gynaecological Oncology, Churchill Hospital, Oxford University Hospitals, Oxford, United Kingdom
- Oxford National Institute for Health Research (NIHR) Biomedical Research Centre, Oxford, United Kingdom
| |
Collapse
|
24
|
Marchand J, Guitton Y, Martineau E, Royer AL, Balgoma D, Le Bizec B, Giraudeau P, Dervilly G. Extending the Lipidome Coverage by Combining Different Mass Spectrometric Platforms: An Innovative Strategy to Answer Chemical Food Safety Issues. Foods 2021; 10:foods10061218. [PMID: 34071212 PMCID: PMC8230090 DOI: 10.3390/foods10061218] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/20/2021] [Accepted: 05/22/2021] [Indexed: 01/30/2023] Open
Abstract
From a general public health perspective, a strategy combining non-targeted and targeted lipidomics MS-based approaches is proposed to identify disrupted patterns in serum lipidome upon growth promoter treatment in pigs. Evaluating the relative contributions of the platforms involved, the study aims at investigating the potential of innovative analytical approaches to highlight potential chemical food safety threats. Serum samples collected during an animal experiment involving control and treated pigs, whose food had been supplemented with ractopamine, were extracted and characterised using three MS strategies: Non-targeted RP LC-HRMS; the targeted Lipidyzer™ platform (differential ion mobility associated with shotgun lipidomics) and a homemade LC-HRMS triglyceride platform. The strategy enabled highlighting specific lipid profile patterns involving various lipid classes, mainly in relation to cholesterol esters, sphingomyelins, lactosylceramide, phosphatidylcholines and triglycerides. Thanks to the combination of non-targeted and targeted MS approaches, various compartments of the pig serum lipidome could be explored, including commonly characterised lipids (Lipidyzer™), triglyceride isomers (Triglyceride platform) and unique lipid features (non-targeted LC-HRMS). Thanks to their respective characteristics, the complementarity of the three tools could be demonstrated for public health purposes, with enhanced coverage, level of characterization and applicability.
Collapse
Affiliation(s)
- Jérémy Marchand
- LABERCA, Oniris, INRAE, 44307 Nantes, France; (J.M.); (Y.G.); (A.-L.R.); (D.B.); (B.L.B.)
- CEISAM UMR 6230, Université de Nantes, CNRS, 44000 Nantes, France;
| | - Yann Guitton
- LABERCA, Oniris, INRAE, 44307 Nantes, France; (J.M.); (Y.G.); (A.-L.R.); (D.B.); (B.L.B.)
| | - Estelle Martineau
- CEISAM UMR 6230, Université de Nantes, CNRS, 44000 Nantes, France;
- SpectroMaîtrise, CAPACITES SAS, 26 Bd Vincent Gâche, 44200 Nantes, France
| | - Anne-Lise Royer
- LABERCA, Oniris, INRAE, 44307 Nantes, France; (J.M.); (Y.G.); (A.-L.R.); (D.B.); (B.L.B.)
| | - David Balgoma
- LABERCA, Oniris, INRAE, 44307 Nantes, France; (J.M.); (Y.G.); (A.-L.R.); (D.B.); (B.L.B.)
| | - Bruno Le Bizec
- LABERCA, Oniris, INRAE, 44307 Nantes, France; (J.M.); (Y.G.); (A.-L.R.); (D.B.); (B.L.B.)
| | - Patrick Giraudeau
- CEISAM UMR 6230, Université de Nantes, CNRS, 44000 Nantes, France;
- Correspondence: (P.G.); (G.D.); Tel.: +33-251125709 (P.G.); +33-240687880 (G.D.)
| | - Gaud Dervilly
- LABERCA, Oniris, INRAE, 44307 Nantes, France; (J.M.); (Y.G.); (A.-L.R.); (D.B.); (B.L.B.)
- Correspondence: (P.G.); (G.D.); Tel.: +33-251125709 (P.G.); +33-240687880 (G.D.)
| |
Collapse
|
25
|
Züllig T, Köfeler HC. HIGH RESOLUTION MASS SPECTROMETRY IN LIPIDOMICS. MASS SPECTROMETRY REVIEWS 2021; 40:162-176. [PMID: 32233039 PMCID: PMC8049033 DOI: 10.1002/mas.21627] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 03/06/2020] [Indexed: 05/04/2023]
Abstract
The boost of research output in lipidomics during the last decade is tightly linked to improved instrumentation in mass spectrometry. Associated with this trend is the shift from low resolution-toward high-resolution lipidomics platforms. This review article summarizes the state of the art in the lipidomics field with a particular focus on the merits of high mass resolution. Following some theoretical considerations on the benefits of high mass resolution in lipidomics, it starts with a historical perspective on lipid analysis by sector instruments and moves further to today's instrumental approaches, including shotgun lipidomics, liquid chromatography-mass spectrometry, matrix-assisted laser desorption ionization-time-of-flight, and imaging lipidomics. Subsequently, several data processing and data analysis software packages are critically evaluated with all their pros and cons. Finally, this article emphasizes the importance and necessity of quality standards as the field evolves from its pioneering phase into a mature and robust omics technology and lists various initiatives for improving the applicability of lipidomics. © 2020 The Authors. Mass Spectrometry Reviews published by John Wiley & Sons Ltd. Mass Spec Rev.
Collapse
Affiliation(s)
- Thomas Züllig
- Core Facility Mass SpectrometryMedical University of Graz, ZMFGrazAustria
| | - Harald C. Köfeler
- Core Facility Mass SpectrometryMedical University of Graz, ZMFGrazAustria
| |
Collapse
|
26
|
Methods of Lipidomic Analysis: Extraction, Derivatization, Separation, and Identification of Lipids. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021. [PMID: 33791982 DOI: 10.1007/978-3-030-51652-9_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
Lipidomics refers to the large-scale study of pathways and networks of cellular lipids in biological systems. A lipidomic analysis often involves the identification and quantification of the thousands of cellular lipid molecular species within a complex biological sample and therefore requires a well optimized method for lipid profiling. In this chapter, the methods for lipidomic analysis, including sample collection and preparation, lipid derivatization and separation, mass spectrometric identification of lipids, data processing and interpretation, and quality control, are overviewed.
Collapse
|
27
|
Henriksen NL, Aasmul-Olsen K, Venkatasubramanian R, Nygaard MKE, Sprenger RR, Heckmann AB, Ostenfeld MS, Ejsing CS, Eskildsen SF, Müllertz A, Sangild PT, Bering SB, Thymann T. Dairy-Derived Emulsifiers in Infant Formula Show Marginal Effects on the Plasma Lipid Profile and Brain Structure in Preterm Piglets Relative to Soy Lecithin. Nutrients 2021; 13:718. [PMID: 33668360 PMCID: PMC7996312 DOI: 10.3390/nu13030718] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/15/2021] [Accepted: 02/18/2021] [Indexed: 02/06/2023] Open
Abstract
Breastfed infants have higher intestinal lipid absorption and neurodevelopmental outcomes compared to formula-fed infants, which may relate to a different surface layer structure of fat globules in infant formula. This study investigated if dairy-derived emulsifiers increased lipid absorption and neurodevelopment relative to soy lecithin in newborn preterm piglets. Piglets received a formula diet containing soy lecithin (SL) or whey protein concentrate enriched in extracellular vesicles (WPC-A-EV) or phospholipids (WPC-PL) for 19 days. Both WPC-A-EV and WPC-PL emulsions, but not the intact diets, increased in vitro lipolysis compared to SL. The main differences of plasma lipidomics analysis were increased levels of some sphingolipids, and lipid molecules with odd-chain (17:1, 19:1, 19:3) as well as mono- and polyunsaturated fatty acyl chains (16:1, 20:1, 20:3) in the WPC-A-EV and WPC-PL groups and increased 18:2 fatty acyls in the SL group. Indirect monitoring of intestinal triacylglycerol absorption showed no differences between groups. Diffusor tensor imaging measurements of mean diffusivity in the hippocampus were lower for WPC-A-EV and WPC-PL groups compared to SL indicating improved hippocampal maturation. No differences in hippocampal lipid composition or short-term memory were observed between groups. In conclusion, emulsification of fat globules in infant formula with dairy-derived emulsifiers altered the plasma lipid profile and hippocampal tissue diffusivity but had limited effects on other absorptive and learning abilities relative to SL in preterm piglets.
Collapse
Affiliation(s)
- Nicole L. Henriksen
- Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, University of Copenhagen, Dyrlægevej 68, 1870 Frederiksberg C, Denmark; (N.L.H.); (K.A.-O.); (P.T.S.); (S.B.B.)
| | - Karoline Aasmul-Olsen
- Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, University of Copenhagen, Dyrlægevej 68, 1870 Frederiksberg C, Denmark; (N.L.H.); (K.A.-O.); (P.T.S.); (S.B.B.)
| | - Ramakrishnan Venkatasubramanian
- Physiological Pharmaceutics, Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen Ø, Denmark;
| | - Mikkel K. E. Nygaard
- Center of Functionally Integrative Neuroscience, Department of Clinical Medicine, Aarhus University, Universitetsbyen 3, 8000 Aarhus C, Denmark; (M.K.E.N.); (S.F.E.)
| | - Richard R. Sprenger
- VILLUM Center for Bioanalytical Sciences, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark; (R.R.S.); (C.S.E.)
| | - Anne B. Heckmann
- Arla Foods Ingredients, Sønderhøj 10-12, 8260 Viby J, Denmark; (A.B.H.); (M.S.O.)
| | - Marie S. Ostenfeld
- Arla Foods Ingredients, Sønderhøj 10-12, 8260 Viby J, Denmark; (A.B.H.); (M.S.O.)
| | - Christer S. Ejsing
- VILLUM Center for Bioanalytical Sciences, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark; (R.R.S.); (C.S.E.)
| | - Simon F. Eskildsen
- Center of Functionally Integrative Neuroscience, Department of Clinical Medicine, Aarhus University, Universitetsbyen 3, 8000 Aarhus C, Denmark; (M.K.E.N.); (S.F.E.)
| | - Anette Müllertz
- Bioneer:FARMA, Department of Pharmacy, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen Ø, Denmark;
| | - Per T. Sangild
- Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, University of Copenhagen, Dyrlægevej 68, 1870 Frederiksberg C, Denmark; (N.L.H.); (K.A.-O.); (P.T.S.); (S.B.B.)
| | - Stine B. Bering
- Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, University of Copenhagen, Dyrlægevej 68, 1870 Frederiksberg C, Denmark; (N.L.H.); (K.A.-O.); (P.T.S.); (S.B.B.)
| | - Thomas Thymann
- Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, University of Copenhagen, Dyrlægevej 68, 1870 Frederiksberg C, Denmark; (N.L.H.); (K.A.-O.); (P.T.S.); (S.B.B.)
| |
Collapse
|
28
|
Höring M, Ejsing CS, Krautbauer S, Ertl VM, Burkhardt R, Liebisch G. Accurate quantification of lipid species affected by isobaric overlap in Fourier-transform mass spectrometry. J Lipid Res 2021; 62:100050. [PMID: 33600775 PMCID: PMC8010702 DOI: 10.1016/j.jlr.2021.100050] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/21/2021] [Accepted: 02/05/2021] [Indexed: 11/05/2022] Open
Abstract
Lipidomics data require consideration of ions with near-identical masses, which comprises among others the Type-II isotopic overlap. This overlap occurs in series of lipid species differing only by number of double bonds (DBs) mainly because of the natural abundance of 13C-atoms. High-resolution mass spectrometry, such as Fourier-transform mass spectrometry (FTMS), is capable of resolving Type-II overlap depending on mass resolving power. In this work, we evaluated FTMS quantification accuracy of lipid species affected by Type-II overlap. Spike experiments with lipid species pairs of various lipid classes were analyzed by flow injection analysis-FTMS. Accuracy of quantification was evaluated without and with Type-II correction (using relative isotope abundance) as well as utilizing the first isotopic peak (M+1). Isobaric peaks, which were sufficiently resolved, were most accurate without Type-II correction. In cases of partially resolved peaks, we observed peak interference causing distortions in mass and intensity, which is a well-described phenomenon in FTMS. Concentrations of respective species were more accurate when calculated from M+1. Moreover, some minor species, affected by considerable Type-II overlap, could only be quantified by M+1. Unexpectedly, even completely unresolved peaks were substantially overcorrected by Type-II correction because of peak interference. The described method was validated including intraday and interday precisions for human serum and fibroblast samples. Taken together, our results show that accurate quantification of lipid species by FTMS requires resolution-depended data analysis.
Collapse
Affiliation(s)
- Marcus Höring
- Institute of Clinical Chemistry and Laboratory Medicine, Regensburg University Hospital, Regensburg, Germany
| | - Christer S Ejsing
- Department of Biochemistry and Molecular Biology, Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Sabrina Krautbauer
- Institute of Clinical Chemistry and Laboratory Medicine, Regensburg University Hospital, Regensburg, Germany
| | - Verena M Ertl
- Institute of Clinical Chemistry and Laboratory Medicine, Regensburg University Hospital, Regensburg, Germany
| | - Ralph Burkhardt
- Institute of Clinical Chemistry and Laboratory Medicine, Regensburg University Hospital, Regensburg, Germany
| | - Gerhard Liebisch
- Institute of Clinical Chemistry and Laboratory Medicine, Regensburg University Hospital, Regensburg, Germany.
| |
Collapse
|
29
|
Sprenger RR, Hermansson M, Neess D, Becciolini LS, Sørensen SB, Fagerberg R, Ecker J, Liebisch G, Jensen ON, Vance DE, Færgeman NJ, Klemm RW, Ejsing CS. Lipid molecular timeline profiling reveals diurnal crosstalk between the liver and circulation. Cell Rep 2021; 34:108710. [PMID: 33535053 DOI: 10.1016/j.celrep.2021.108710] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/29/2020] [Accepted: 01/08/2021] [Indexed: 12/18/2022] Open
Abstract
Diurnal regulation of whole-body lipid metabolism plays a vital role in metabolic health. Although changes in lipid levels across the diurnal cycle have been investigated, the system-wide molecular responses to both short-acting fasting-feeding transitions and longer-timescale circadian rhythms have not been explored in parallel. Here, we perform time-series multi-omics analyses of liver and plasma revealing that the majority of molecular oscillations are entrained by adaptations to fasting, food intake, and the postprandial state. By developing algorithms for lipid structure enrichment analysis and lipid molecular crosstalk between tissues, we find that the hepatic phosphatidylethanolamine (PE) methylation pathway is diurnally regulated, giving rise to two pools of oscillating phosphatidylcholine (PC) molecules in the circulation, which are coupled to secretion of either very low-density lipoprotein (VLDL) or high-density lipoprotein (HDL) particles. Our work demonstrates that lipid molecular timeline profiling across tissues is key to disentangling complex metabolic processes and provides a critical resource for the study of whole-body lipid metabolism.
Collapse
Affiliation(s)
- Richard R Sprenger
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Martin Hermansson
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Ditte Neess
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Lena Sokol Becciolini
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Signe Bek Sørensen
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Rolf Fagerberg
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Josef Ecker
- ZIEL-Institute for Food & Health, Research Group Lipid Metabolism, Technical University of Munich, Freising, Germany
| | - Gerhard Liebisch
- Institute of Clinical Chemistry and Laboratory Medicine, Regensburg University Hospital, Regensburg, Germany
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Dennis E Vance
- Group on Molecular and Cell Biology of Lipids, University of Alberta, Edmonton, AB, Canada
| | - Nils J Færgeman
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Robin W Klemm
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK
| | - Christer S Ejsing
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| |
Collapse
|
30
|
Abstract
Over the last few decades, MS-based lipidomics has emerged as a powerful tool to study lipids in biological systems. This success is driven by the constant demand for complete and reliable data. The improvement of MS-based lipidomics will continue to be dependent on the advances in the technology of mass spectrometry and related techniques including separation and bioinformatics, and more importantly, on gaining insight into the knowledge of lipid chemistry essential to develop methodology for lipid analysis. It is hoped that the protocols in this book, collected from experts in their fields, can offer the beginner and the advanced user alike, useful tips toward successful lipidomic analysis.
Collapse
Affiliation(s)
- Fong-Fu Hsu
- Mass Spectrometry Resource, Division of Endocrinology, Metabolism, and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
| |
Collapse
|
31
|
Addepalli RV, Mullangi R. A concise review on lipidomics analysis in biological samples. ADMET AND DMPK 2020; 9:1-22. [PMID: 35299875 PMCID: PMC8923307 DOI: 10.5599/admet.913] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/23/2020] [Indexed: 12/13/2022] Open
Abstract
Lipids are a complex and critical heterogeneous molecular entity, playing an intricate and key role in understanding biological activities and disease processes. Lipidomics aims to quantitatively define the lipid classes, including their molecular species. The analysis of the biological tissues and fluids are challenging due to the extreme sample complexity and occurrence of the molecular species as isomers or isobars. This review documents the overview of lipidomics workflow, beginning from the approaches of sample preparation, various analytical techniques and emphasizing the state-of-the-art mass spectrometry either by shotgun or coupled with liquid chromatography. We have considered the latest ion mobility spectroscopy technologies to deal with the vast number of structural isomers, different imaging techniques. All these techniques have their pitfalls and we have discussed how to circumvent them after reviewing the power of each technique with examples..
Collapse
Affiliation(s)
| | - Ramesh Mullangi
- Laxai Life Sciences Pvt Ltd, MN Park, Genome Valley, Shamirpet, Hyderabad-500 078, India
| |
Collapse
|
32
|
Xu T, Hu C, Xuan Q, Xu G. Recent advances in analytical strategies for mass spectrometry-based lipidomics. Anal Chim Acta 2020; 1137:156-169. [PMID: 33153599 PMCID: PMC7525665 DOI: 10.1016/j.aca.2020.09.060] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 12/20/2022]
Abstract
Lipids are vital biological molecules and play multiple roles in cellular function of mammalian organisms such as cellular membrane anchoring, signal transduction, material trafficking and energy storage. Driven by the biological significance of lipids, lipidomics has become an emerging science in the field of omics. Lipidome in biological systems consists of hundreds of thousands of individual lipid molecules that possess complex structures, multiple categories, and diverse physicochemical properties assembled by different combinations of polar headgroups and hydrophobic fatty acyl chains. Such structural complexity poses a huge challenge for comprehensive lipidome analysis. Thanks to the great innovations in chromatographic separation techniques and the continuous advances in mass spectrometric detection tools, analytical strategies for lipidomics have been highly diversified so that the depth and breadth of lipidomics have been greatly enhanced. This review will present the current state of mass spectrometry-based analytical strategies including untargeted, targeted and pseudotargeted lipidomics. Recent typical applications of lipidomics in biomarker discovery, pathogenic mechanism and therapeutic strategy are summarized, and the challenges facing to the field of lipidomics are also discussed.
Collapse
Affiliation(s)
- Tianrun Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunxiu Hu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiuhui Xuan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
33
|
Bukowski MR, Picklo MJ. Simple, Rapid Lipidomic Analysis of Triacylglycerols in Bovine Milk by Infusion-Electrospray Mass Spectrometry. Lipids 2020; 56:243-255. [PMID: 33169389 DOI: 10.1002/lipd.12292] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/08/2020] [Accepted: 10/26/2020] [Indexed: 11/11/2022]
Abstract
Bovine milk is a complex mixture of lipids, proteins, carbohydrates, and other factors of which lipids comprise 3-5% of the total mass. Rapid analysis and characterization of the triacylglycerols (TAG) that comprise about 95% of the total lipid is daunting given the numerous TAG species. In the attached methods paper, we demonstrate an improved method for identifying and quantifying TAG species by infusion-based "shotgun" lipidomics. Because of the broad range of TAG species in milk, a single internal standard was insufficient for the analysis and required sectioning the spectrum into three portions based upon mass range to provide accurate quantitation of TAG species. Isobaric phospholipid interferences were removed using a simple dispersive solid-phase extraction step. Using this method, > 100 TAG species were quantitated by acyl carbon number and desaturation level in a sample of commercially purchased bovine milk.
Collapse
Affiliation(s)
- Michael R Bukowski
- USDA-ARS Grand Forks Human Nutrition Research Center, Grand Forks, ND, 58203, USA
| | - Matthew J Picklo
- USDA-ARS Grand Forks Human Nutrition Research Center, Grand Forks, ND, 58203, USA
| |
Collapse
|
34
|
Uptake of exogenous serine is important to maintain sphingolipid homeostasis in Saccharomyces cerevisiae. PLoS Genet 2020; 16:e1008745. [PMID: 32845888 PMCID: PMC7478846 DOI: 10.1371/journal.pgen.1008745] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 09/08/2020] [Accepted: 07/22/2020] [Indexed: 12/22/2022] Open
Abstract
Sphingolipids are abundant and essential molecules in eukaryotes that have crucial functions as signaling molecules and as membrane components. Sphingolipid biosynthesis starts in the endoplasmic reticulum with the condensation of serine and palmitoyl-CoA. Sphingolipid biosynthesis is highly regulated to maintain sphingolipid homeostasis. Even though, serine is an essential component of the sphingolipid biosynthesis pathway, its role in maintaining sphingolipid homeostasis has not been precisely studied. Here we show that serine uptake is an important factor for the regulation of sphingolipid biosynthesis in Saccharomyces cerevisiae. Using genetic experiments, we find the broad-specificity amino acid permease Gnp1 to be important for serine uptake. We confirm these results with serine uptake assays in gnp1Δ cells. We further show that uptake of exogenous serine by Gnp1 is important to maintain cellular serine levels and observe a specific connection between serine uptake and the first step of sphingolipid biosynthesis. Using mass spectrometry-based flux analysis, we further observed imported serine as the main source for de novo sphingolipid biosynthesis. Our results demonstrate that yeast cells preferentially use the uptake of exogenous serine to regulate sphingolipid biosynthesis. Our study can also be a starting point to analyze the role of serine uptake in mammalian sphingolipid metabolism. Sphingolipids (SPs) are membrane lipids globally required for eukaryotic life. In contrast to other lipid classes, SPs cannot be stored in the cell and therefore their levels have to be tightly regulated. Failure to maintain sphingolipid homeostasis can result in pathologies including neurodegeneration, childhood asthma and cancer. However, we are only starting to understand how SP biosynthesis is adjusted according to need. In this study, we use genetic and biochemical methods to show that the uptake of exogenous serine is necessary to maintain SP homeostasis in Saccharomyces cerevisiae. Serine is one of the precursors of long chain bases in cells, the first intermediate of SP metabolism. Our results suggest that the uptake of serine is directly coupled to SP biosynthesis at ER-plasma membrane contact sites. Overall, our study identifies serine uptake as a novel regulatory factor of SP homeostasis. While we use yeast as a discovery tool, these results also provide valuable insights into mammalian SP biology especially under pathological conditions.
Collapse
|
35
|
Martínez-Montañés F, Casanovas A, Sprenger RR, Topolska M, Marshall DL, Moreno-Torres M, Poad BL, Blanksby SJ, Hermansson M, Jensen ON, Ejsing CS. Phosphoproteomic Analysis across the Yeast Life Cycle Reveals Control of Fatty Acyl Chain Length by Phosphorylation of the Fatty Acid Synthase Complex. Cell Rep 2020; 32:108024. [DOI: 10.1016/j.celrep.2020.108024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/11/2020] [Accepted: 07/21/2020] [Indexed: 12/12/2022] Open
|
36
|
Raetz M, Bonner R, Hopfgartner G. SWATH-MS for metabolomics and lipidomics: critical aspects of qualitative and quantitative analysis. Metabolomics 2020; 16:71. [PMID: 32504120 DOI: 10.1007/s11306-020-01692-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 05/29/2020] [Indexed: 12/19/2022]
Abstract
INTRODUCTION While liquid chromatography coupled to mass spectrometric detection in the selected reaction monitoring detection mode offers the best quantification sensitivity for omics, the number of target analytes is limited, must be predefined and specific methods developed. Data independent acquisition (DIA), including SWATH using quadrupole time of flight or orbitrap mass spectrometers and generic acquisition methods, has emerged as a powerful alternative technique for quantitative and qualitative analyses since it can cover a wide range of analytes without predefinition. OBJECTIVES Here we review the current state of DIA, SWATH-MS and highlight novel acquisition strategies for metabolomics and lipidomics and opportunities for data analysis tools. METHOD Different databases were searched for papers that report developments and applications of DIA and in particular SWATH-MS in metabolomics and lipidomics. RESULTS DIA methods generate digital sample records that can be mined retrospectively as further knowledge is gained and, with standardized acquisition schemes, used in multiple studies. The different chemical spaces of metabolites and lipids require different specificities, hence different acquisition and data processing approaches must be considered for their analysis. CONCLUSIONS Although the hardware and acquisition modes are well defined for SWATH-MS, a major challenge for routine use remains the lack of appropriate software tools capable of handling large datasets and large numbers of analytes.
Collapse
Affiliation(s)
- Michel Raetz
- Life Sciences Mass Spectrometry, Department of Inorganic and Analytical Chemistry, University of Geneva, 24 Quai Ernest Ansermet, CH-1211, Geneva, Switzerland
| | - Ron Bonner
- Ron Bonner Consulting, Newmarket, ON, L3Y 3C7, Canada
| | - Gérard Hopfgartner
- Life Sciences Mass Spectrometry, Department of Inorganic and Analytical Chemistry, University of Geneva, 24 Quai Ernest Ansermet, CH-1211, Geneva, Switzerland.
| |
Collapse
|
37
|
Advancing Target Identification of Nitrated Phospholipids in Biological Systems by HCD Specific Fragmentation Fingerprinting in Orbitrap Platforms. Molecules 2020; 25:molecules25092120. [PMID: 32369981 PMCID: PMC7248851 DOI: 10.3390/molecules25092120] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/24/2020] [Accepted: 04/29/2020] [Indexed: 12/13/2022] Open
Abstract
Nitrated phospholipids have recently been detected in vitro and in vivo and associated with beneficial health effects. They were identified and quantified in biological samples by lipidomics methodologies using liquid chromatography-collision-induced dissociation (CID) tandem mass spectrometry (MS/MS) acquired with the linear ion trap mass spectrometer. Only a few studies have used higher-energy collision dissociation (HCD)-MS/MS in high-resolution Orbitraps to characterize nitrated phosphatidylserines and nitrated cardiolipins, highlighting the marked differences in the fragmentation patterns when using CID or HCD fragmentation methods. In this study, we aimed to evaluate the fragmentation of nitrated phosphatidylcholine and nitrated phosphatidylethanolamine species under HCD-MS/MS. We studied the effect of normalized collision energy (NCE) in the fragmentation pattern to identify the best acquisition conditions and reporter ions to detect nitrated phospholipids. The results showed that the intensity of the typical neutral loss of nitrous acid (HNO2) diminishes with increasing NCE, becoming non-detectable for a higher NCE. Thus, the loss of HNO2 could not be the most suitable ion/fragment for the characterization of nitrated phospholipids under HCD. In HCD-MS/MS new fragment ions were identified, corresponding to the nitrated fatty acyl chains, NO2-RCOO−, (NO2-RCOOH-H2O + H)+, and (NO2-RCOOH + H)+, suggested as potential reporter ions to detect nitrated phospholipids when using the HCD-MS/MS lipidomics analysis.
Collapse
|
38
|
Klein DR, Blevins MS, Macias LA, Douglass MV, Trent MS, Brodbelt JS. Localization of Double Bonds in Bacterial Glycerophospholipids Using 193 nm Ultraviolet Photodissociation in the Negative Mode. Anal Chem 2020; 92:5986-5993. [PMID: 32212719 PMCID: PMC7385702 DOI: 10.1021/acs.analchem.0c00221] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The need for detailed structural characterization of glycerophospholipids (GPLs) for many types of biologically motivated applications has led to the development of novel mass spectrometry-based methodologies that utilize alternative ion activation methods. Ultraviolet photodissociation (UVPD) has shown great utility for localizing sites of unsaturation within acyl chains and to date has predominantly been used for positive mode analysis of GPLs. In the present work, UVPD is used to localize sites of unsaturation in GPL anions. Similar to UVPD mass spectra of GPL cations, UVPD of deprotonated or formate-adducted GPLs yields diagnostic fragment ions spaced 24 Da apart. This method was integrated into a liquid chromatography workflow and used to evaluate profiles of sites of unsaturation of lipids in Escherichia coli (E. coli) and Acinetobacter baumannii (A. baumannii). When assigning sites of unsaturation, E. coli was found to contain all unsaturation elements at the same position relative to the terminal methyl carbon of the acyl chain; the first carbon participating in a site of unsaturation was consistently seven carbons along the acyl chain when counting carbons from the terminal methyl carbon. GPLs from A. baumannii exhibited more variability in locations of unsaturation. For GPLs containing sites of unsaturation in both acyl chains, an MS3 method was devised to assign sites to specific acyl chains.
Collapse
Affiliation(s)
- Dustin R Klein
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Molly S Blevins
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Luis A Macias
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Martin V Douglass
- Department of Infectious Diseases, The University of Georgia, College of Veterinary Medicine, Athens, Georgia 30602, United States
| | - M Stephen Trent
- Department of Infectious Diseases, The University of Georgia, College of Veterinary Medicine, Athens, Georgia 30602, United States
- Department of Microbiology, The University of Georgia, College of Arts and Sciences, Athens, Georgia 30602, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| |
Collapse
|
39
|
Nielsen IØ, Vidas Olsen A, Dicroce-Giacobini J, Papaleo E, Andersen KK, Jäättelä M, Maeda K, Bilgin M. Comprehensive Evaluation of a Quantitative Shotgun Lipidomics Platform for Mammalian Sample Analysis on a High-Resolution Mass Spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:894-907. [PMID: 32129994 DOI: 10.1021/jasms.9b00136] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Shotgun lipidomics is a powerful tool that enables simultaneous and fast quantification of diverse lipid classes through mass spectrometry based analyses of directly infused crude lipid extracts. We present here a shotgun lipidomics platform established to quantify 38 lipid classes belonging to four lipid categories present in mammalian samples and show the fine-tuning and comprehensive evaluation of its experimental parameters and performance. We first determined for all the targeted lipid classes the collision energy levels optimal for the recording of their lipid class- and species-specific fragment ions and fine-tuned the energy levels applied in the platform. We then performed a series of titrations to define the boundaries of linear signal response for the targeted lipid classes, and demonstrated that the dynamic quantification range spanned more than 3 orders of magnitude and reached sub picomole levels for 35 lipid classes. The platform identified 273, 261, and 287 lipid species in brain, plasma, and cultured fibroblast samples, respectively, at the respective optimal working sample amounts. The platform properly quantified the majority of these identified lipid species, while lipid species measured to be below the limit of quantification were efficiently removed from the data sets by the use of statistical analyses of data reproducibility or a cutoff threshold. Finally, we demonstrated that a series of parameters of cell culture conditions influence lipidomics outcomes, including confluency, medium supplements, and use of transfection reagents. The present study provides a guideline for setting up and using a simple and efficient platform for quantitatively exploring the mammalian lipidome.
Collapse
Affiliation(s)
- Inger Ødum Nielsen
- Unit for Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen DK-2100, Denmark
| | - André Vidas Olsen
- Computational Biology Laboratory, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen DK-2100, Denmark
| | - Jano Dicroce-Giacobini
- Unit for Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen DK-2100, Denmark
| | - Elena Papaleo
- Computational Biology Laboratory, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen DK-2100, Denmark
- Translational Disease Systems Biology, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Klaus Kaae Andersen
- Unit for Statistics and Epidemiology, Danish Cancer Society Research Center, Copenhagen DK-2100, Denmark
| | - Marja Jäättelä
- Unit for Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen DK-2100, Denmark
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Kenji Maeda
- Unit for Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen DK-2100, Denmark
| | - Mesut Bilgin
- Unit for Cell Death and Metabolism, Center for Autophagy, Recycling and Disease, Danish Cancer Society Research Center, Copenhagen DK-2100, Denmark
| |
Collapse
|
40
|
Mitchell JM, Flight RM, Moseley HN. Deriving Lipid Classification Based on Molecular Formulas. Metabolites 2020; 10:E122. [PMID: 32214009 PMCID: PMC7143220 DOI: 10.3390/metabo10030122] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 03/02/2020] [Accepted: 03/21/2020] [Indexed: 12/20/2022] Open
Abstract
Despite instrument and algorithmic improvements, the untargeted and accurate assignment of metabolites remains an unsolved problem in metabolomics. New assignment methods such as our SMIRFE algorithm can assign elemental molecular formulas to observed spectral features in a highly untargeted manner without orthogonal information from tandem MS or chromatography. However, for many lipidomics applications, it is necessary to know at least the lipid category or class that is associated with a detected spectral feature to derive a biochemical interpretation. Our goal is to develop a method for robustly classifying elemental molecular formula assignments into lipid categories for an application to SMIRFE-generated assignments. Using a Random Forest machine learning approach, we developed a method that can predict lipid category and class from SMIRFE non-adducted molecular formula assignments. Our methods achieve high average predictive accuracy (>90%) and precision (>83%) across all eight of the lipid categories in the LIPIDMAPS database. Classification performance was evaluated using sets of theoretical, data-derived, and artifactual molecular formulas. Our methods enable the lipid classification of non-adducted molecular formula assignments generated by SMIRFE without orthogonal information, facilitating the biochemical interpretation of untargeted lipidomics experiments. This lipid classification appears insufficient for validating single-spectrum assignments, but could be useful in cross-spectrum assignment validation.
Collapse
Affiliation(s)
- Joshua M. Mitchell
- Department of Molecular & Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA; (J.M.M.); (R.M.F.)
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
- Resource Center for Stable Isotope Resolved Metabolomics, University of Kentucky, Lexington, KY 40536, USA
| | - Robert M. Flight
- Department of Molecular & Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA; (J.M.M.); (R.M.F.)
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
- Resource Center for Stable Isotope Resolved Metabolomics, University of Kentucky, Lexington, KY 40536, USA
| | - Hunter N.B. Moseley
- Department of Molecular & Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA; (J.M.M.); (R.M.F.)
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
- Resource Center for Stable Isotope Resolved Metabolomics, University of Kentucky, Lexington, KY 40536, USA
- Institute for Biomedical Informatics, University of Kentucky, Lexington, KY 40536, USA
- Center for Clinical and Translational Science, University of Kentucky, Lexington, KY 40536, USA
| |
Collapse
|
41
|
Localization of sterols and oxysterols in mouse brain reveals distinct spatial cholesterol metabolism. Proc Natl Acad Sci U S A 2020; 117:5749-5760. [PMID: 32132201 PMCID: PMC7084107 DOI: 10.1073/pnas.1917421117] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The brain is a remarkably complex organ and cholesterol homeostasis underpins brain function. It is known that cholesterol is not evenly distributed across different brain regions; however, the precise map of cholesterol metabolism in the brain remains unclear. If cholesterol metabolism is to be correlated with brain function it is essential to generate such a map. Here we describe an advanced mass spectrometry platform to reveal spatial cholesterol metabolism in situ at 400-µm spot diameter on 10-µm tissue slices from mouse brain. We mapped, not only cholesterol, but also other biologically active sterols arising from cholesterol turnover in both wild type and mice lacking cholesterol 24S-hydroxylase (CYP46A1), the major cholesterol metabolizing enzyme. Dysregulated cholesterol metabolism is implicated in a number of neurological disorders. Many sterols, including cholesterol and its precursors and metabolites, are biologically active and important for proper brain function. However, spatial cholesterol metabolism in brain and the resulting sterol distributions are poorly defined. To better understand cholesterol metabolism in situ across the complex functional regions of brain, we have developed on-tissue enzyme-assisted derivatization in combination with microliquid extraction for surface analysis and liquid chromatography-mass spectrometry to locate sterols in tissue slices (10 µm) of mouse brain. The method provides sterolomic analysis at 400-µm spot diameter with a limit of quantification of 0.01 ng/mm2. It overcomes the limitations of previous mass spectrometry imaging techniques in analysis of low-abundance and difficult-to-ionize sterol molecules, allowing isomer differentiation and structure identification. Here we demonstrate the spatial distribution and quantification of multiple sterols involved in cholesterol metabolic pathways in wild-type and cholesterol 24S-hydroxylase knockout mouse brain. The technology described provides a powerful tool for future studies of spatial cholesterol metabolism in healthy and diseased tissues.
Collapse
|
42
|
Bowman AP, Blakney GT, Hendrickson CL, Ellis SR, Heeren RMA, Smith DF. Ultra-High Mass Resolving Power, Mass Accuracy, and Dynamic Range MALDI Mass Spectrometry Imaging by 21-T FT-ICR MS. Anal Chem 2020; 92:3133-3142. [PMID: 31955581 PMCID: PMC7031845 DOI: 10.1021/acs.analchem.9b04768] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
Detailed characterization
of complex biological surfaces by matrix-assisted
laser desorption/ionization (MALDI) mass spectrometry imaging (MSI)
requires instrumentation that is capable of high mass resolving power,
mass accuracy, and dynamic range. Fourier transform ion cyclotron
resonance mass spectrometry (FT-ICR MS) offers the highest mass spectral
performance for MALDI MSI experiments, and often reveals molecular
features that are unresolved on lower performance instrumentation.
Higher magnetic field strength improves all performance characteristics
of FT-ICR; mass resolving power improves linearly, while mass accuracy
and dynamic range improve quadratically with magnetic field strength.
Here, MALDI MSI at 21T is demonstrated for the first time: mass resolving
power in excess of 1 600 000 (at m/z 400), root-mean-square mass measurement accuracy below
100 ppb, and dynamic range per pixel over 500:1 were obtained from
the direct analysis of biological tissue sections. Molecular features
with m/z differences as small as
1.79 mDa were resolved and identified with high mass accuracy. These
features allow for the separation and identification of lipids to
the underlying structures of tissues. The unique molecular detail,
accuracy, sensitivity, and dynamic range combined in a 21T MALDI FT-ICR
MSI experiment enable researchers to visualize molecular structures
in complex tissues that have remained hidden until now. The instrument
described allows for future innovative, such as high-end studies to
unravel the complexity of biological, geological, and engineered organic
material surfaces with an unsurpassed detail.
Collapse
Affiliation(s)
- Andrew P Bowman
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS) , Maastricht University , Universiteitssingel 50 , Maastricht 6629ER , The Netherlands
| | - Greg T Blakney
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS) , Maastricht University , Universiteitssingel 50 , Maastricht 6629ER , The Netherlands
| | - Christopher L Hendrickson
- National High Magnetic Field Laboratory , Florida State University , 1800 East Paul Dirac Drive , Tallahassee , Florida 32310-4005 , United States.,Department of Chemistry and Biochemistry , Florida State University , 95 Chieftain Way , Tallahassee , Florida 32306 , United States
| | - Shane R Ellis
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS) , Maastricht University , Universiteitssingel 50 , Maastricht 6629ER , The Netherlands
| | - Ron M A Heeren
- Maastricht MultiModal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry (IMS) , Maastricht University , Universiteitssingel 50 , Maastricht 6629ER , The Netherlands
| | - Donald F Smith
- National High Magnetic Field Laboratory , Florida State University , 1800 East Paul Dirac Drive , Tallahassee , Florida 32310-4005 , United States
| |
Collapse
|
43
|
Triebl A, Burla B, Selvalatchmanan J, Oh J, Tan SH, Chan MY, Mellet NA, Meikle PJ, Torta F, Wenk MR. Shared reference materials harmonize lipidomics across MS-based detection platforms and laboratories. J Lipid Res 2020; 61:105-115. [PMID: 31732502 PMCID: PMC6939597 DOI: 10.1194/jlr.d119000393] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 11/13/2019] [Indexed: 12/18/2022] Open
Abstract
Quantitative MS of human plasma lipids is a promising technology for translation into clinical applications. Current MS-based lipidomic methods rely on either direct infusion (DI) or chromatographic lipid separation methods (including reversed phase and hydrophilic interaction LC). However, the use of lipid markers in laboratory medicine is limited by the lack of reference values, largely because of considerable differences in the concentrations measured by different laboratories worldwide. These inconsistencies can be explained by the use of different sample preparation protocols, method-specific calibration procedures, and other experimental and data-reporting parameters, even when using identical starting materials. Here, we systematically investigated the roles of some of these variables in multiple approaches to lipid analysis of plasma samples from healthy adults by considering: 1) different sample introduction methods (separation vs. DI methods); 2) different MS instruments; and 3) between-laboratory differences in comparable analytical platforms. Each of these experimental variables resulted in different quantitative results, even with the inclusion of isotope-labeled internal standards for individual lipid classes. We demonstrated that appropriate normalization to commonly available reference samples (i.e., "shared references") can largely correct for these systematic method-specific quantitative biases. Thus, to harmonize data in the field of lipidomics, in-house long-term references should be complemented by a commonly available shared reference sample, such as NIST SRM 1950, in the case of human plasma.
Collapse
Affiliation(s)
- Alexander Triebl
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore; Departments of Biochemistry, Yong Loo Lin School of Medicine National University of Singapore, Singapore
| | - Bo Burla
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore
| | - Jayashree Selvalatchmanan
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore; Departments of Biochemistry, Yong Loo Lin School of Medicine National University of Singapore, Singapore
| | - Jeongah Oh
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore; National University of Singapore Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
| | - Sock Hwee Tan
- Medicine, Yong Loo Lin School of Medicine National University of Singapore, Singapore; Cardiovascular Research Institute, National University of Singapore, Singapore
| | - Mark Y Chan
- National University of Singapore Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore; Medicine, Yong Loo Lin School of Medicine National University of Singapore, Singapore; Cardiovascular Research Institute, National University of Singapore, Singapore; National University Heart Centre, National University Health System, Singapore
| | | | - Peter J Meikle
- Baker Heart and Diabetes Institute, Melbourne, Australia
| | - Federico Torta
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore; Departments of Biochemistry, Yong Loo Lin School of Medicine National University of Singapore, Singapore.
| | - Markus R Wenk
- Singapore Lipidomics Incubator, Life Sciences Institute, National University of Singapore, Singapore; Departments of Biochemistry, Yong Loo Lin School of Medicine National University of Singapore, Singapore.
| |
Collapse
|
44
|
Wu Z, Bagarolo GI, Thoröe-Boveleth S, Jankowski J. "Lipidomics": Mass spectrometric and chemometric analyses of lipids. Adv Drug Deliv Rev 2020; 159:294-307. [PMID: 32553782 DOI: 10.1016/j.addr.2020.06.009] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 06/03/2020] [Accepted: 06/06/2020] [Indexed: 01/01/2023]
Abstract
Lipids are ubiquitous in the human organism and play essential roles as components of cell membranes and hormones, for energy storage or as mediators of cell signaling pathways. As crucial mediators of the human metabolism, lipids are also involved in metabolic diseases, cardiovascular and renal diseases, cancer and/or hepatological and neurological disorders. With rapidly growing evidence supporting the impact of lipids on both the genesis and progression of these diseases as well as patient wellbeing, the characterization of the human lipidome has gained high interest and importance in life sciences and clinical diagnostics within the last 15 years. This is mostly due to technically advanced molecular identification and quantification methods, mainly based on mass spectrometry. Mass spectrometry has become one of the most powerful tools for the identification of lipids. New lipidic mediators or biomarkers of diseases can be analysed by state-of-the art mass spectrometry techniques supported by sophisticated bioinformatics and biostatistics. The lipidomic approach has developed dramatically in the realm of life sciences and clinical diagnostics due to the available mass spectrometric methods and in particular due to the adaptation of biostatistical methods in recent years. Therefore, the current knowledge of lipid extraction methods, mass-spectrometric approaches, biostatistical data analysis, including workflows for the interpretation of lipidomic high-throughput data, are reviewed in this manuscript.
Collapse
Affiliation(s)
- Zhuojun Wu
- Institute for Molecular Cardiovascular Research, University Hospital RWTH Aachen, Aachen, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Giulia Ilaria Bagarolo
- Institute for Molecular Cardiovascular Research, University Hospital RWTH Aachen, Aachen, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Sven Thoröe-Boveleth
- Institute for Molecular Cardiovascular Research, University Hospital RWTH Aachen, Aachen, Pauwelsstraße 30, 52074 Aachen, Germany
| | - Joachim Jankowski
- Institute for Molecular Cardiovascular Research, University Hospital RWTH Aachen, Aachen, Pauwelsstraße 30, 52074 Aachen, Germany; School for Cardiovascular Diseases, Maastricht University, Universiteitssingel 50, Maastricht, The Netherlands.
| |
Collapse
|
45
|
Lipidomics from sample preparation to data analysis: a primer. Anal Bioanal Chem 2019; 412:2191-2209. [PMID: 31820027 PMCID: PMC7118050 DOI: 10.1007/s00216-019-02241-y] [Citation(s) in RCA: 169] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/09/2019] [Accepted: 10/25/2019] [Indexed: 12/26/2022]
Abstract
Lipids are amongst the most important organic compounds in living organisms, where they serve as building blocks for cellular membranes as well as energy storage and signaling molecules. Lipidomics is the science of the large-scale determination of individual lipid species, and the underlying analytical technology that is used to identify and quantify the lipidome is generally mass spectrometry (MS). This review article provides an overview of the crucial steps in MS-based lipidomics workflows, including sample preparation, either liquid–liquid or solid-phase extraction, derivatization, chromatography, ion-mobility spectrometry, MS, and data processing by various software packages. The associated concepts are discussed from a technical perspective as well as in terms of their application. Furthermore, this article sheds light on recent advances in the technology used in this field and its current limitations. Particular emphasis is placed on data quality assurance and adequate data reporting; some of the most common pitfalls in lipidomics are discussed, along with how to circumvent them.
Collapse
|
46
|
Abstract
In mammalian systems "sterolomics" can be regarded as the quantitative or semi-quantitative profiling of all metabolites derived from cholesterol and its cyclic precursors. The system can be further complicated by metabolites derived from ingested phytosterols or pharmaceuticals, but this is beyond the scope of this article. "Sterolomics" can be performed on either an unbiased global format, or more usually, exploiting a targeted format. Here we discuss the different mass spectrometry-based analytical techniques used in "sterolomics" giving specific examples in the context of neurodegenerative disease and for the diagnosis of inborn errors of metabolism. We pay particular attention to the profiling of cholesterol metabolites in the bile acid biosynthesis pathways, although the analytical techniques discussed are also appropriate for analysis of hormonal steroids.
Collapse
Affiliation(s)
- William J. Griffiths
- Swansea University Medical School, ILS1 Building, Singleton Park, Swansea SA2 8PP, Wales, UK
| | - Yuqin Wang
- Swansea University Medical School, ILS1 Building, Singleton Park, Swansea SA2 8PP, Wales, UK
| |
Collapse
|
47
|
Wolrab D, Jirásko R, Chocholoušková M, Peterka O, Holčapek M. Oncolipidomics: Mass spectrometric quantitation of lipids in cancer research. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.04.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
|
48
|
Hu C, Wang C, He L, Han X. Novel strategies for enhancing shotgun lipidomics for comprehensive analysis of cellular lipidomes. Trends Analyt Chem 2019; 120:115330. [PMID: 32647401 PMCID: PMC7344273 DOI: 10.1016/j.trac.2018.11.028] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Shotgun lipidomics is one of the most powerful tools in analysis of cellular lipidomes in lipidomics, which directly analyzes lipids from lipid extracts of diverse biological samples with high accuracy/precision. However, despite its great advances in high throughput analysis of cellular lipidomes, low coverage of poorly ionized lipids, especially those species in very low abundance, and some types of isomers within complex lipid extracts by shotgun lipidomics remains a huge challenge. In the past few years, many strategies have been developed to enhance shotgun lipidomics for comprehensive analysis of lipid species. Chemical derivatization represents one of the most attractive and effective strategies, already receiving considerable attention. This review focuses on novel advanced derivatization strategies for enhancing shotgun lipidomics. It is anticipated that with the development of enhanced strategies, shotgun lipidomics can make greater contributions to biological and biomedical research.
Collapse
Affiliation(s)
- Changfeng Hu
- College of Basic Medical Sciences, Zhejiang Chinese Medical University, 548 Bingwen Road, Hangzhou, Zhejiang 310053, China
| | - Chunyan Wang
- Barshop Institute for Longevity and Aging Research, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| | - Lijiao He
- College of Basic Medical Sciences, Zhejiang Chinese Medical University, 548 Bingwen Road, Hangzhou, Zhejiang 310053, China
| | - Xianlin Han
- College of Basic Medical Sciences, Zhejiang Chinese Medical University, 548 Bingwen Road, Hangzhou, Zhejiang 310053, China
- Barshop Institute for Longevity and Aging Research, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
- Department of Medicine – Diabetes, University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA
| |
Collapse
|
49
|
MIGA2 Links Mitochondria, the ER, and Lipid Droplets and Promotes De Novo Lipogenesis in Adipocytes. Mol Cell 2019; 76:811-825.e14. [PMID: 31628041 DOI: 10.1016/j.molcel.2019.09.011] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 07/19/2019] [Accepted: 09/04/2019] [Indexed: 12/25/2022]
Abstract
Physical contact between organelles is vital to the function of eukaryotic cells. Lipid droplets (LDs) are dynamic organelles specialized in lipid storage that interact physically with mitochondria in several cell types. The mechanisms coupling these organelles are, however, poorly understood, and the cell-biological function of their interaction remains largely unknown. Here, we discover in adipocytes that the outer mitochondrial membrane protein MIGA2 links mitochondria to LDs. We identify an amphipathic LD-targeting motif and reveal that MIGA2 binds to the membrane proteins VAP-A or VAP-B in the endoplasmic reticulum (ER). We find that in adipocytes MIGA2 is involved in promoting triglyceride (TAG) synthesis from non-lipid precursors. Our data indicate that MIGA2 links reactions of de novo lipogenesis in mitochondria to TAG production in the ER, thereby facilitating efficient lipid storage in LDs. Based on its presence in many tissues, MIGA2 is likely critical for lipid and energy homeostasis in a wide spectrum of cell types.
Collapse
|
50
|
Hybrid SWATH/MS and HR-SRM/MS acquisition for phospholipidomics using QUAL/QUANT data processing. Anal Bioanal Chem 2019; 411:5681-5690. [PMID: 31201456 DOI: 10.1007/s00216-019-01946-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 05/16/2019] [Accepted: 05/24/2019] [Indexed: 10/26/2022]
Abstract
A hybrid SWATH/MS and HR-SRM/MS acquisition approach using multiple unit mass windows and 100 u precursor selection windows has been developed to interface with a chromatographic lipid class separation. The method allows for the simultaneous monitoring of sum compositions in MS1 and up to 48 lipids in MS2 per lipid class. A total of 240 lipid sum compositions from five phospholipid classes could be monitored in MS2 (HR-SRM/MS) while there was no limitation in the number of analytes in MS1 (HR-SIM/MS). On average, 92 lipid sum compositions and 75 lipid species could be quantified in human plasma samples. The robustness and precision of the workflow has been assessed using technical triplicates of the subject samples. Lipid identification was improved using a combined qualitative and quantitative data processing based on prediction instead of library search. Lipid class specific extracted ion currents of precursors and the corresponding molecular species fragments were extracted based on the information obtained from lipid building blocks and a combinatorial strategy. The SWATH/MS approach with the post-acquisition processing is not limited to the analyzed phospholipid classes and can be applied to other analytes and samples of interest. Graphical abstract.
Collapse
|