101
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Zhang W, Zhang D, Chen Q, Wu J, Ouyang Z, Xia Y. Online photochemical derivatization enables comprehensive mass spectrometric analysis of unsaturated phospholipid isomers. Nat Commun 2019; 10:79. [PMID: 30622271 PMCID: PMC6325166 DOI: 10.1038/s41467-018-07963-8] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 11/30/2018] [Indexed: 11/09/2022] Open
Abstract
Mass spectrometry-based lipidomics is the primary tool for the structural analysis of lipids but the effective localization of carbon-carbon double bonds (C=C) in unsaturated lipids to distinguish C=C location isomers remains challenging. Here, we develop a large-scale lipid analysis platform by coupling online C=C derivatization through the Paternò-Büchi reaction with liquid chromatography-tandem mass spectrometry. This provides rich information on lipid C=C location isomers, revealing C=C locations for more than 200 unsaturated glycerophospholipids in bovine liver among which we identify 55 groups of C=C location isomers. By analyzing tissue samples of patients with breast cancer and type 2 diabetes plasma samples, we find that the ratios of C=C isomers are much less affected by interpersonal variations than their individual abundances, suggesting that isomer ratios may be used for the discovery of lipid biomarkers.
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Affiliation(s)
- Wenpeng Zhang
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry and State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China.,Department of Chemistry, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Donghui Zhang
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry and State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
| | - Qinhua Chen
- Affiliated Dongfeng Hospital, Hubei University of Medicine, Shiyan, Hubei Province, 442000, China
| | - Junhan Wu
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry and State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
| | - Zheng Ouyang
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry and State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China. .,Department of Chemistry, Purdue University, West Lafayette, Indiana, 47907, USA.
| | - Yu Xia
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry and State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China. .,Department of Chemistry, Purdue University, West Lafayette, Indiana, 47907, USA.
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102
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Zhang W, Zhang D, Chen Q, Wu J, Ouyang Z, Xia Y. Online photochemical derivatization enables comprehensive mass spectrometric analysis of unsaturated phospholipid isomers. Nat Commun 2019. [PMID: 30622271 DOI: 10.1038/s41467-01807963-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023] Open
Abstract
Mass spectrometry-based lipidomics is the primary tool for the structural analysis of lipids but the effective localization of carbon-carbon double bonds (C=C) in unsaturated lipids to distinguish C=C location isomers remains challenging. Here, we develop a large-scale lipid analysis platform by coupling online C=C derivatization through the Paternò-Büchi reaction with liquid chromatography-tandem mass spectrometry. This provides rich information on lipid C=C location isomers, revealing C=C locations for more than 200 unsaturated glycerophospholipids in bovine liver among which we identify 55 groups of C=C location isomers. By analyzing tissue samples of patients with breast cancer and type 2 diabetes plasma samples, we find that the ratios of C=C isomers are much less affected by interpersonal variations than their individual abundances, suggesting that isomer ratios may be used for the discovery of lipid biomarkers.
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Affiliation(s)
- Wenpeng Zhang
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry and State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
- Department of Chemistry, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Donghui Zhang
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry and State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
| | - Qinhua Chen
- Affiliated Dongfeng Hospital, Hubei University of Medicine, Shiyan, Hubei Province, 442000, China
| | - Junhan Wu
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry and State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China
| | - Zheng Ouyang
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry and State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China.
- Department of Chemistry, Purdue University, West Lafayette, Indiana, 47907, USA.
| | - Yu Xia
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Department of Chemistry and State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, 100084, China.
- Department of Chemistry, Purdue University, West Lafayette, Indiana, 47907, USA.
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103
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Hussain G, Anwar H, Rasul A, Imran A, Qasim M, Zafar S, Imran M, Kamran SKS, Aziz N, Razzaq A, Ahmad W, Shabbir A, Iqbal J, Baig SM, Ali M, Gonzalez de Aguilar JL, Sun T, Muhammad A, Muhammad Umair A. Lipids as biomarkers of brain disorders. Crit Rev Food Sci Nutr 2019; 60:351-374. [DOI: 10.1080/10408398.2018.1529653] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Ghulam Hussain
- Department of Physiology Faculty of Life Sciences, Government College University, Faisalabad, Pakistan
| | - Haseeb Anwar
- Department of Physiology Faculty of Life Sciences, Government College University, Faisalabad, Pakistan
| | - Azhar Rasul
- Department of Zoology Faculty of Life Sciences, Government College University, Faisalabad, Pakistan
| | - Ali Imran
- Institute of Home and Food Sciences, Government College University, Faisalabad, Pakistan
| | - Muhammad Qasim
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Shamaila Zafar
- Department of Physiology Faculty of Life Sciences, Government College University, Faisalabad, Pakistan
| | - Muhammad Imran
- University Institute of Diet and Nutritional Sciences, Faculty of Allied Health Sciences, The University of Lahore, Lahore, Pakistan
| | - Syed Kashif Shahid Kamran
- Department of Physiology Faculty of Life Sciences, Government College University, Faisalabad, Pakistan
| | - Nimra Aziz
- Department of Physiology Faculty of Life Sciences, Government College University, Faisalabad, Pakistan
| | - Aroona Razzaq
- Department of Physiology Faculty of Life Sciences, Government College University, Faisalabad, Pakistan
| | - Waseem Ahmad
- Department of Physiology Faculty of Life Sciences, Government College University, Faisalabad, Pakistan
| | - Asghar Shabbir
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan
| | - Javed Iqbal
- Department of Neurology, Allied Hospital, Faisalabad, Pakistan
| | - Shahid Mahmood Baig
- Human Molecular Genetics Laboratory, Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), PIEAS, Faisalabad, Pakistan
| | - Muhammad Ali
- Department of Zoology Faculty of Life Sciences, Government College University, Faisalabad, Pakistan
| | - Jose-Luis Gonzalez de Aguilar
- Université de Strasbourg, Strasbourg, France
- Mécanismes Centraux et Péripheriques de la Neurodégénérescence, INSERM, Strasbourg, France
| | - Tao Sun
- Center for Precision Medicine, School of Medicine and School of Biomedical Sciences, Huaqiao University, Xiamen, Fujian Province, China
| | - Atif Muhammad
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, Saudi Arabia
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104
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Abstract
Lipidomics aims at characterizing lipid profiles and their biological role with respect to protein expression involved in lipid metabolism. Specifically, cerebrospinal fluid (CSF) lipidomics is offering a new perspective in the search for surrogate biomarkers to facilitate early diagnosis of psychiatric and neurodegenerative diseases. In this chapter, we describe a nontargeted approach to profile lipid molecular species present in human CSF using ultrahigh-performance liquid chromatography-electrospray ionization-time-of-flight mass spectrometry (UPLC-ESI-ToF-MS). This workflow complements the toolbox useful for the exploration and monitoring neurodegenerative mechanisms associated with a dysregulation in lipid metabolism.
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105
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Brain age and other bodily 'ages': implications for neuropsychiatry. Mol Psychiatry 2019; 24:266-281. [PMID: 29892055 PMCID: PMC6344374 DOI: 10.1038/s41380-018-0098-1] [Citation(s) in RCA: 221] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 04/13/2018] [Accepted: 04/23/2018] [Indexed: 01/07/2023]
Abstract
As our brains age, we tend to experience cognitive decline and are at greater risk of neurodegenerative disease and dementia. Symptoms of chronic neuropsychiatric diseases are also exacerbated during ageing. However, the ageing process does not affect people uniformly; nor, in fact, does the ageing process appear to be uniform even within an individual. Here, we outline recent neuroimaging research into brain ageing and the use of other bodily ageing biomarkers, including telomere length, the epigenetic clock, and grip strength. Some of these techniques, using statistical approaches, have the ability to predict chronological age in healthy people. Moreover, they are now being applied to neurological and psychiatric disease groups to provide insights into how these diseases interact with the ageing process and to deliver individualised predictions about future brain and body health. We discuss the importance of integrating different types of biological measurements, from both the brain and the rest of the body, to build more comprehensive models of the biological ageing process. Finally, we propose seven steps for the field of brain-ageing research to take in coming years. This will help us reach the long-term goal of developing clinically applicable statistical models of biological processes to measure, track and predict brain and body health in ageing and disease.
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106
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Kappler L, Kollipara L, Lehmann R, Sickmann A. Investigating the Role of Mitochondria in Type 2 Diabetes - Lessons from Lipidomics and Proteomics Studies of Skeletal Muscle and Liver. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1158:143-182. [PMID: 31452140 DOI: 10.1007/978-981-13-8367-0_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mitochondrial dysfunction is discussed as a key player in the pathogenesis of type 2 diabetes mellitus (T2Dm), a highly prevalent disease rapidly developing as one of the greatest global health challenges of this century. Data however about the involvement of mitochondria, central hubs in bioenergetic processes, in the disease development are still controversial. Lipid and protein homeostasis are under intense discussion to be crucial for proper mitochondrial function. Consequently proteomics and lipidomics analyses might help to understand how molecular changes in mitochondria translate to alterations in energy transduction as observed in the healthy and metabolic diseases such as T2Dm and other related disorders. Mitochondrial lipids integrated in a tool covering proteomic and functional analyses were up to now rarely investigated, although mitochondrial lipids might provide a possible lynchpin in the understanding of type 2 diabetes development and thereby prevention. In this chapter state-of-the-art analytical strategies, pre-analytical aspects, potential pitfalls as well as current proteomics and lipidomics-based knowledge about the pathophysiological role of mitochondria in the pathogenesis of type 2 diabetes will be discussed.
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Affiliation(s)
- Lisa Kappler
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tuebingen, Tuebingen, Germany
| | - Laxmikanth Kollipara
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany
| | - Rainer Lehmann
- Institute for Clinical Chemistry and Pathobiochemistry, Department for Diagnostic Laboratory Medicine, University Hospital Tuebingen, Tuebingen, Germany.,Institute for Diabetes Research and Metabolic Diseases of the Helmholtz Centre Munich at the University of Tuebingen, Tuebingen, Germany.,German Center for Diabetes Research (DZD e.V.), Tuebingen, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany. .,Medical Proteome Centre, Ruhr Universität Bochum, Bochum, Germany. .,Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, UK.
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107
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Wozny K, Lehmann WD, Wozny M, Akbulut BS, Brügger B. A method for the quantitative determination of glycerophospholipid regioisomers by UPLC-ESI-MS/MS. Anal Bioanal Chem 2018; 411:915-924. [PMID: 30580388 PMCID: PMC6338697 DOI: 10.1007/s00216-018-1517-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 10/31/2018] [Accepted: 11/26/2018] [Indexed: 01/15/2023]
Abstract
Diacyl glycerophospholipids (GPs) belong to the most abundant lipid species in living organisms and consist of a glycerol backbone with fatty acyl groups in sn-1 and sn-2 and a polar head group in the sn-3 position. Regioisomeric mixed diacyl GPs have the same fatty acyl composition but differ in their allocation to sn-1 or sn-2 of the glycerol unit. In-depth analysis of regioisomeric mixed diacyl GP species composed of fatty acyl moieties that are similar in length and degree of saturation typically requires either chemical derivatization or sophisticated analytical instrumentation, since these types of regioisomers are not well resolved under standard ultra-performance liquid chromatography (UPLC) conditions. Here, we introduce a simple and fast method for diacyl GP regioisomer analysis employing UPLC tandem mass spectrometry (MS/MS). This GP regioisomer analysis is based both on minor chromatographic retention time shifts and on major differences in relative abundances of the two fatty acyl anion fragments observed in MS/MS. To monitor these differences with optimal precision, MS/MS spectra are recorded continuously over the UPLC elution profile of the lipid species of interest. Quantification of relative abundances of the regioisomers was performed by algorithms that we have developed for this purpose. The method was applied to commercially available mixed diacyl GP standards and to total lipid extracts of Escherichia coli (E. coli) and bovine liver. To validate our results, we determined regioisomeric ratios of phosphatidylcholine (PC) standards using phospholipase A2-specific release of fatty acids from the sn-2 position of the glycerol backbone. Our results show that most analyzed mixed diacyl GPs of biological origin exhibit significantly higher regioisomeric purity than synthetic lipid standards. In summary, this method can be implemented in routine LC-MS/MS-based lipidomics workflows without the necessity for additional chemical additives, derivatizations, or instrumentation.
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Affiliation(s)
- Katharina Wozny
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - Wolf D Lehmann
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany.,German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Manfred Wozny
- MassMap GmbH & Co. KG, Meichelbeckstraße 13a, 85356, Freising, Germany
| | | | - Britta Brügger
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120, Heidelberg, Germany.
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108
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Leopold J, Popkova Y, Engel KM, Schiller J. Recent Developments of Useful MALDI Matrices for the Mass Spectrometric Characterization of Lipids. Biomolecules 2018; 8:biom8040173. [PMID: 30551655 PMCID: PMC6316665 DOI: 10.3390/biom8040173] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 12/06/2018] [Accepted: 12/10/2018] [Indexed: 12/24/2022] Open
Abstract
Matrix-assisted laser desorption/ionization (MALDI) is one of the most successful “soft” ionization methods in the field of mass spectrometry and enables the analysis of a broad range of molecules, including lipids. Although the details of the ionization process are still unknown, the importance of the matrix is commonly accepted. Both, the development of and the search for useful matrices was, and still is, an empirical process, since properties like vacuum stability, high absorption at the laser wavelength, etc. have to be fulfilled by a compound to become a useful matrix. This review provides a survey of successfully used MALDI matrices for the lipid analyses of complex biological samples. The advantages and drawbacks of the established organic matrix molecules (cinnamic or benzoic acid derivatives), liquid crystalline matrices, and mixtures of common matrices will be discussed. Furthermore, we will deal with nanocrystalline matrices, which are most suitable to analyze small molecules, such as free fatty acids. It will be shown that the analysis of mixtures and the quantitative analysis of small molecules can be easily performed if the matrix is carefully selected. Finally, some basic principles of how useful matrix compounds can be “designed” de novo will be introduced.
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Affiliation(s)
- Jenny Leopold
- Faculty of Medicine, Institute for Medical Physics and Biophysics, Härtelstr. 16/18, Leipzig University, D-04107 Leipzig, Germany.
| | - Yulia Popkova
- Faculty of Medicine, Institute for Medical Physics and Biophysics, Härtelstr. 16/18, Leipzig University, D-04107 Leipzig, Germany.
| | - Kathrin M Engel
- Faculty of Medicine, Institute for Medical Physics and Biophysics, Härtelstr. 16/18, Leipzig University, D-04107 Leipzig, Germany.
| | - Jürgen Schiller
- Faculty of Medicine, Institute for Medical Physics and Biophysics, Härtelstr. 16/18, Leipzig University, D-04107 Leipzig, Germany.
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109
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Ma HF, Wei F, Wu BF, Yang C, Xie Y, Wu ZY, Lv X, Chen H. Profiling and quantification of aminophospholipids based on chemical derivatization coupled with HPLC-MS. J Lipid Res 2018; 60:121-134. [PMID: 30482807 DOI: 10.1194/jlr.m089482] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 11/01/2018] [Indexed: 01/21/2023] Open
Abstract
In this study, a novel strategy based on acetone stable-isotope derivatization coupled with HPLC-MS for profiling and accurate quantification of aminophospholipids (phosphatidylethanolamine and phosphatidylserine) in biological samples was developed. Acetone derivatization leads to alkylation of the primary amino groups of aminophospholipids with an isopropyl moiety; the use of deuterium-labeled acetone (d6-acetone) introduced a 6 Da mass shift that was ideally suited for profiling and quantification analysis with high selectivity and accuracy. After derivatization, significantly increased column efficiency for chromatographic separation and detection sensitivity for MS analysis of aminophospholipids was observed. Furthermore, an accuracy quantification method was developed. Aminophospholipids in biological samples were derivatized with d0-acetone; while more than two aminophospholipid standards were selected for each class of aminophospholipid and derivatized with d6-acetone, which were then used as the internal standards to typically construct a calibration curve for each class to normalize the nonuniformity response caused by the differential fragmentation kinetics resulting from the distinct chemical constitution of individual aminophospholipid species in the biological samples. The excellent applicability of the developed method was validated by profiling and quantification of aminophospholipids presented in liver samples from rats fed with different diets.
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Affiliation(s)
- Hui-Fang Ma
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Oilseeds Processing of Ministry of Agriculture, Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture, and Hubei Key Laboratory of Lipid Chemistry and Nutrition, Wuhan 430062, China
| | - Fang Wei
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Oilseeds Processing of Ministry of Agriculture, Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture, and Hubei Key Laboratory of Lipid Chemistry and Nutrition, Wuhan 430062, China
| | - Bang-Fu Wu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Oilseeds Processing of Ministry of Agriculture, Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture, and Hubei Key Laboratory of Lipid Chemistry and Nutrition, Wuhan 430062, China
| | - Chen Yang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Oilseeds Processing of Ministry of Agriculture, Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture, and Hubei Key Laboratory of Lipid Chemistry and Nutrition, Wuhan 430062, China
| | - Ya Xie
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Oilseeds Processing of Ministry of Agriculture, Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture, and Hubei Key Laboratory of Lipid Chemistry and Nutrition, Wuhan 430062, China
| | - Zong-Yuan Wu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Oilseeds Processing of Ministry of Agriculture, Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture, and Hubei Key Laboratory of Lipid Chemistry and Nutrition, Wuhan 430062, China
| | - Xin Lv
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Oilseeds Processing of Ministry of Agriculture, Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture, and Hubei Key Laboratory of Lipid Chemistry and Nutrition, Wuhan 430062, China
| | - Hong Chen
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Oilseeds Processing of Ministry of Agriculture, Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture, and Hubei Key Laboratory of Lipid Chemistry and Nutrition, Wuhan 430062, China
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110
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Lamont L, Eijkel GB, Jones EA, Flinders B, Ellis SR, Porta Siegel T, Heeren RMA, Vreeken RJ. Targeted Drug and Metabolite Imaging: Desorption Electrospray Ionization Combined with Triple Quadrupole Mass Spectrometry. Anal Chem 2018. [PMID: 30346139 DOI: 10.1021/acs.analchem.8b03857(2018)] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
Mass spectrometry imaging (MSI) has proven to be a valuable tool for drug and metabolite imaging in pharmaceutical toxicology studies and can reveal, for example, accumulation of drug candidates in early drug development. However, the lack of sample cleanup and chromatographic separation can hamper the analysis due to isobaric interferences. Multiple reaction monitoring (MRM) uses unique precursor ion-product ion transitions to add specificity which leads to higher selectivity. Here, we present a targeted imaging platform where desorption electrospray ionization is combined with a triple quadrupole (QqQ) system to perform MRM imaging. The platform was applied to visualize (i) lipids in mouse brain tissue sections and (ii) a drug candidate and metabolite in canine liver tissue. All QqQ modes were investigated to show the increased detection time provided by MRM as well as the possibility to perform dual polarity imaging. This is very beneficial for lipid imaging because some phospholipid classes ionize in opposite polarity (e.g., phosphatidylcholine/sphingomyelin in positive ion mode and phosphatidylserine/phosphatidylethanolamine in negative ion mode). Drug and metabolite images were obtained to show its strength in drug distribution studies. Multiple MRM transitions were used to confirm the local presence and selective detection of pharmaceutical compounds.
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Affiliation(s)
- Lieke Lamont
- Maastricht Multimodal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry , Maastricht University , 6229 ER Maastricht , The Netherlands
| | - Gert B Eijkel
- Maastricht Multimodal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry , Maastricht University , 6229 ER Maastricht , The Netherlands
| | | | - Bryn Flinders
- Maastricht Multimodal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry , Maastricht University , 6229 ER Maastricht , The Netherlands
| | - Shane R Ellis
- Maastricht Multimodal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry , Maastricht University , 6229 ER Maastricht , The Netherlands
| | - Tiffany Porta Siegel
- Maastricht Multimodal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry , Maastricht University , 6229 ER Maastricht , The Netherlands
| | - Ron M A Heeren
- Maastricht Multimodal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry , Maastricht University , 6229 ER Maastricht , The Netherlands
| | - Rob J Vreeken
- Maastricht Multimodal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry , Maastricht University , 6229 ER Maastricht , The Netherlands
- Janssen Research & Development , B-2340 Beerse , Belgium
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111
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Lamont L, Eijkel GB, Jones EA, Flinders B, Ellis SR, Porta Siegel T, Heeren RMA, Vreeken RJ. Targeted Drug and Metabolite Imaging: Desorption Electrospray Ionization Combined with Triple Quadrupole Mass Spectrometry. Anal Chem 2018; 90:13229-13235. [PMID: 30346139 PMCID: PMC6256344 DOI: 10.1021/acs.analchem.8b03857] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
![]()
Mass
spectrometry imaging (MSI) has proven to be a valuable tool
for drug and metabolite imaging in pharmaceutical toxicology studies
and can reveal, for example, accumulation of drug candidates in early
drug development. However, the lack of sample cleanup and chromatographic
separation can hamper the analysis due to isobaric interferences.
Multiple reaction monitoring (MRM) uses unique precursor ion-product
ion transitions to add specificity which leads to higher selectivity.
Here, we present a targeted imaging platform where desorption electrospray
ionization is combined with a triple quadrupole (QqQ) system to perform
MRM imaging. The platform was applied to visualize (i) lipids in mouse
brain tissue sections and (ii) a drug candidate and metabolite in
canine liver tissue. All QqQ modes were investigated to show the increased
detection time provided by MRM as well as the possibility to perform
dual polarity imaging. This is very beneficial for lipid imaging because
some phospholipid classes ionize in opposite polarity (e.g., phosphatidylcholine/sphingomyelin
in positive ion mode and phosphatidylserine/phosphatidylethanolamine
in negative ion mode). Drug and metabolite images were obtained to
show its strength in drug distribution studies. Multiple MRM transitions
were used to confirm the local presence and selective detection of
pharmaceutical compounds.
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Affiliation(s)
- Lieke Lamont
- Maastricht Multimodal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry , Maastricht University , 6229 ER Maastricht , The Netherlands
| | - Gert B Eijkel
- Maastricht Multimodal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry , Maastricht University , 6229 ER Maastricht , The Netherlands
| | | | - Bryn Flinders
- Maastricht Multimodal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry , Maastricht University , 6229 ER Maastricht , The Netherlands
| | - Shane R Ellis
- Maastricht Multimodal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry , Maastricht University , 6229 ER Maastricht , The Netherlands
| | - Tiffany Porta Siegel
- Maastricht Multimodal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry , Maastricht University , 6229 ER Maastricht , The Netherlands
| | - Ron M A Heeren
- Maastricht Multimodal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry , Maastricht University , 6229 ER Maastricht , The Netherlands
| | - Rob J Vreeken
- Maastricht Multimodal Molecular Imaging (M4I) Institute, Division of Imaging Mass Spectrometry , Maastricht University , 6229 ER Maastricht , The Netherlands.,Janssen Research & Development , B-2340 Beerse , Belgium
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112
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Kumar A, Pathak RK, Gayen A, Gupta S, Singh M, Lata C, Sharma H, Roy JK, Gupta SM. Systems biology of seeds: decoding the secret of biochemical seed factories for nutritional security. 3 Biotech 2018; 8:460. [PMID: 30370201 PMCID: PMC6200710 DOI: 10.1007/s13205-018-1483-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 10/16/2018] [Indexed: 11/28/2022] Open
Abstract
Seeds serve as biochemical factories of nutrition, processing, bio-energy and storage related important bio-molecules and act as a delivery system to transmit the genetic information to the next generation. The research pertaining towards delineating the complex system of regulation of genes and pathways related to seed biology and nutrient partitioning is still under infancy. To understand these, it is important to know the genes and pathway(s) involved in the homeostasis of bio-molecules. In recent past with the advent and advancement of modern tools of genomics and genetic engineering, multi-layered 'omics' approaches and high-throughput platforms are being used to discern the genes and proteins involved in various metabolic, and signaling pathways and their regulations for understanding the molecular genetics of biosynthesis and homeostasis of bio-molecules. This can be possible by exploring systems biology approaches via the integration of omics data for understanding the intricacy of seed development and nutrient partitioning. These information can be exploited for the improvement of biologically important chemicals for large-scale production of nutrients and nutraceuticals through pathway engineering and biotechnology. This review article thus describes different omics tools and other branches that are merged to build the most attractive area of research towards establishing the seeds as biochemical factories for human health and nutrition.
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Affiliation(s)
- Anil Kumar
- Rani Lakshmi Bai Central Agricultural University, Jhansi, Uttar Pradesh 284003 India
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Rajesh Kumar Pathak
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
- Department of Biotechnology, G. B. Pant Institute of Engineering and Technology, Pauri Garhwal, Uttarakhand 246194 India
| | - Aranyadip Gayen
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Supriya Gupta
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Manoj Singh
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand 263145 India
| | - Charu Lata
- Council of Scientific and Industrial Research-National Botanical Research Institute, Lucknow, India
| | - Himanshu Sharma
- National Agri-Food Biotechnology Institute, Mohali, Punjab 140306 India
| | - Joy Kumar Roy
- National Agri-Food Biotechnology Institute, Mohali, Punjab 140306 India
| | - Sanjay Mohan Gupta
- Molecular Biology and Genetic Engineering Laboratory, Defence Institute of Bio-Energy Research (DIBER), DRDO, Haldwani, 263139 India
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113
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Barkla BJ, Garibay-Hernández A, Melzer M, Rupasinghe TWT, Roessner U. Single cell-type analysis of cellular lipid remodelling in response to salinity in the epidermal bladder cells of the model halophyte Mesembryanthemum crystallinum. PLANT, CELL & ENVIRONMENT 2018; 41:2390-2403. [PMID: 29813189 DOI: 10.1111/pce.13352] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Revised: 05/22/2018] [Accepted: 05/22/2018] [Indexed: 05/26/2023]
Abstract
Salt stress causes dramatic changes in the organization and dynamic properties of membranes, however, little is known about the underlying mechanisms involved. Modified trichomes, known as epidermal bladder cells (EBC), on the leaves and stems of the halophyte Mesembryanthemum crystallinum can be successfully exploited as a single-cell-type system to investigate salt-induced changes to cellular lipid composition. In this study, alterations in key molecular species from different lipid classes highlighted an increase in phospholipid species, particularly those from phosphatidylcholine and phosphatidic acid (PA), where the latter is central to the synthesis of membrane lipids. Triacylglycerol (TG) species decreased during salinity, while there was little change in plastidic galactolipids. EBC transcriptomic and proteomic data mining revealed changes in genes and proteins involved in lipid metabolism and the upregulation of transcripts for PIPKIB, PI5PII, PIPKIII, and phospholipase D delta suggested the induction of signalling processes mediated by phosphoinositides and PA. TEM and flow cytometry showed the dynamic nature of lipid droplets in these cells under salt stress. Altogether, this work indicates that the metabolism of TG might play an important role in EBC response to salinity as either an energy reserve for sodium accumulation and/or driving membrane biosynthesis for EBC expansion.
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Affiliation(s)
- Bronwyn J Barkla
- Southern Cross Plant Science, Southern Cross University, Lismore, New South Wales, Australia
| | - Adriana Garibay-Hernández
- Instituto de Biotecnología, UNAM, Cuernavaca, Morelos, Mexico
- Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Michael Melzer
- Leibniz Institute of Plant Genetics and Crop Plant Research, Seeland, Germany
| | - Thusitha W T Rupasinghe
- School of BioSciences, University of Melbourne, Parkville, Victoria, Australia
- Metabolomics Australia, School of BioSciences, University of Melbourne, Parkville, Victoria, Australia
| | - Ute Roessner
- School of BioSciences, University of Melbourne, Parkville, Victoria, Australia
- Metabolomics Australia, School of BioSciences, University of Melbourne, Parkville, Victoria, Australia
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114
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Hsu FF. Mass spectrometry-based shotgun lipidomics - a critical review from the technical point of view. Anal Bioanal Chem 2018; 410:6387-6409. [PMID: 30094786 PMCID: PMC6195124 DOI: 10.1007/s00216-018-1252-y] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/03/2018] [Accepted: 07/06/2018] [Indexed: 11/24/2022]
Abstract
Over the past decade, mass spectrometry (MS)-based "shotgun lipidomics" has emerged as a powerful tool for quantitative and qualitative analysis of the complex lipids in the biological system. The aim of this critical review is to give the interested reader a concise overview of the current state of the technology, focused on lipidomic analysis by mass spectrometry. The pros and cons, and pitfalls associated with each available "shotgun lipidomics" method are discussed; and the new strategies for improving the current methods are described. A list of important papers and reviews that are sufficient rather than comprehensive, covering all the aspects of lipidomics including the workflow, methodology, and fundamentals is also compiled for readers to follow. Graphical abstract ᅟ.
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Affiliation(s)
- Fong-Fu Hsu
- Mass Spectrometry Resource, Division of Endocrinology, Diabetes, Metabolism, and Lipid Research, Department of Internal Medicine, Washington University School of Medicine, 660 S Euclid, St. Louis, MO, 63110, USA.
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115
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Wang C, Wang C, Liu F, Rainosek S, Patterson TA, Slikker W, Han X. Lipidomics Reveals Changes in Metabolism, Indicative of Anesthetic-Induced Neurotoxicity in Developing Brains. Chem Res Toxicol 2018; 31:825-835. [PMID: 30132657 DOI: 10.1021/acs.chemrestox.8b00186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Numerous studies have demonstrated that treatment with high dose anesthetics for a prolonged duration induces brain injury in infants. However, whether anesthetic treatment leading to neurotoxicity is associated with alterations in lipid metabolism and homeostasis is still unclear. This review first outlines the lipidomics tools for analysis of lipid molecular species that can inform alterations in lipid species after anesthetic exposure. Then the available data indicating anesthetics cause changes in lipid profiles in the brain and serum of infant monkeys in preclinical studies are summarized, and the potential mechanisms leading to the altered lipid metabolism and their association with anesthetic-induced brain injury are also discussed. Finally, whether lipid changes identified in serum of infant monkeys can serve as indicators for the early detection of anesthetic-induced brain injury is described. We believe extensive studies on alterations in lipids after exposure to anesthetics will allow us to better understand anesthetic-induced neurotoxicity, unravel its underlying biochemical mechanisms, and develop powerful biomarkers for early detection/monitoring of the toxicity.
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Affiliation(s)
| | | | | | - Shuo Rainosek
- Department of Anesthesiology , Central Arkansas Veterans Health System , 4300 West Seventh Street, VA 704-110 , Little Rock , Arkansas 72205 , United States
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Choi TS, Han JY, Heo CE, Lee SW, Kim HI. Electrostatic and hydrophobic interactions of lipid-associated α-synuclein: The role of a water-limited interfaces in amyloid fibrillation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1854-1862. [DOI: 10.1016/j.bbamem.2018.02.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 02/05/2018] [Accepted: 02/05/2018] [Indexed: 12/22/2022]
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Pathak D, Mehendale N, Singh S, Mallik R, Kamat SS. Lipidomics Suggests a New Role for Ceramide Synthase in Phagocytosis. ACS Chem Biol 2018; 13:2280-2287. [PMID: 29963848 PMCID: PMC6102644 DOI: 10.1021/acschembio.8b00438] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Phagocytosis
is an evolutionarily conserved biological process where pathogens
or cellular debris are cleared by engulfing them in a membrane-enclosed
cellular compartment called the phagosome. The formation, maturation,
and subsequent degradation of a phagosome is an important immune response
essential for protection against many pathogens. Yet, the global lipid
profile of phagosomes remains unknown, especially as a function of
their maturation in immune cells. Here, we show using mass spectrometry
based quantitative lipidomics that the ceramide class of lipids, especially
very long chain ceramides, are enriched on maturing phagosomes with
a concomitant decrease in the biosynthetic precursors of ceramides.
We thus posit a new function for the enzyme ceramide synthase during
phagocytosis in mammalian macrophages. Biochemical assays, cellular
lipid feeding experiments, and pharmacological blockade of ceramide
synthase together show that this enzyme indeed controls the flux of
ceramides on maturing phagosomes. We also find similar results in
the primitive eukaryote Dictyostelium discoideum,
suggesting that ceramide enrichment may be evolutionarily conserved
and likely an indispensible step in phagosome maturation.
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Affiliation(s)
- Divya Pathak
- Department of Biological Sciences, Tata Institute of Fundamental Research (TIFR), Homi Bhabha Road, Mumbai 400005, India
| | - Neelay Mehendale
- Department of Biology, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Shubham Singh
- Department of Biology, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Roop Mallik
- Department of Biological Sciences, Tata Institute of Fundamental Research (TIFR), Homi Bhabha Road, Mumbai 400005, India
| | - Siddhesh S. Kamat
- Department of Biology, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune 411008, India
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118
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Paine MRL, Poad BLJ, Eijkel GB, Marshall DL, Blanksby SJ, Heeren RMA, Ellis SR. Mass Spectrometry Imaging with Isomeric Resolution Enabled by Ozone-Induced Dissociation. Angew Chem Int Ed Engl 2018; 57:10530-10534. [PMID: 29787633 PMCID: PMC6100449 DOI: 10.1002/anie.201802937] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/23/2018] [Indexed: 01/05/2023]
Abstract
Mass spectrometry imaging (MSI) enables the spatial distributions of molecules possessing different mass-to-charge ratios to be mapped within complex environments revealing regional changes at the molecular level. Even at high mass resolving power, however, these images often reflect the summed distribution of multiple isomeric molecules, each potentially possessing a unique distribution coinciding with distinct biological function(s) and metabolic origin. Herein, this chemical ambiguity is addressed through an innovative combination of ozone-induced dissociation reactions with MSI, enabling the differential imaging of isomeric lipid molecules directly from biological tissues. For the first time, we demonstrate both double bond- and sn-positional isomeric lipids exhibit distinct spatial locations within tissue. This MSI approach enables researchers to unravel local lipid molecular complexity based on both exact elemental composition and isomeric structure directly from tissues.
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Affiliation(s)
- Martin R. L. Paine
- M4IThe Maastricht Multimodal Molecular Imaging InstituteDivision of Imaging Mass SpectrometryMaastricht UniversityPostbus 616, 6200MDMaastrichtThe Netherlands
| | - Berwyck L. J. Poad
- Central Analytical Research FacilityInstitute for Future EnvironmentsQueensland University of Technology2 George StBrisbaneQLD 4000Australia
| | - Gert B. Eijkel
- M4IThe Maastricht Multimodal Molecular Imaging InstituteDivision of Imaging Mass SpectrometryMaastricht UniversityPostbus 616, 6200MDMaastrichtThe Netherlands
| | - David L. Marshall
- Central Analytical Research FacilityInstitute for Future EnvironmentsQueensland University of Technology2 George StBrisbaneQLD 4000Australia
| | - Stephen J. Blanksby
- Central Analytical Research FacilityInstitute for Future EnvironmentsQueensland University of Technology2 George StBrisbaneQLD 4000Australia
| | - Ron M. A. Heeren
- M4IThe Maastricht Multimodal Molecular Imaging InstituteDivision of Imaging Mass SpectrometryMaastricht UniversityPostbus 616, 6200MDMaastrichtThe Netherlands
| | - Shane R. Ellis
- M4IThe Maastricht Multimodal Molecular Imaging InstituteDivision of Imaging Mass SpectrometryMaastricht UniversityPostbus 616, 6200MDMaastrichtThe Netherlands
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119
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Zhang XC, Zang Q, Zhao H, Ma X, Pan X, Feng J, Zhang S, Zhang R, Abliz Z, Zhang X. Combination of Droplet Extraction and Pico-ESI-MS Allows the Identification of Metabolites from Single Cancer Cells. Anal Chem 2018; 90:9897-9903. [DOI: 10.1021/acs.analchem.8b02098] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
| | - Qingce Zang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | | | | | | | | | | | - Ruiping Zhang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Zeper Abliz
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- Centre for Bioimaging and Systems Biology, Minzu University of China, Beijing 100081, China
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120
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Yeo HC, Chen S, Ho YS, Lee DY. An LC-MS-based lipidomics pre-processing framework underpins rapid hypothesis generation towards CHO systems biotechnology. Metabolomics 2018; 14:98. [PMID: 30830409 DOI: 10.1007/s11306-018-1394-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 07/06/2018] [Indexed: 01/24/2023]
Abstract
INTRODUCTION Given a raw LC-MS dataset, it is often required to rapidly generate initial hypotheses, in conjunction with other 'omics' datasets, without time-consuming lipid verifications. Furthermore, for meta-analysis of many datasets, it may be impractical to conduct exhaustive confirmatory analyses. In other cases, samples for validation may be difficult to obtain, replicate or maintain. Thus, it is critical that the computational identification of lipids is of appropriate accuracy, coverage, and unbiased by a researcher's experience and prior knowledge. OBJECTIVES We aim to prescribe a systematic framework for lipid identifications, without usage of their characteristic retention-time by fully exploiting their underlying mass features. RESULTS Initially, a hybrid technique, for deducing both common and distinctive daughter ions, is used to infer parent lipids from deconvoluted spectra. This is followed by parent confirmation using basic knowledge of their preferred product ions. Using the framework, we could achieve an accuracy of ~ 80% by correctly identified 101 species from 18 classes in Chinese hamster ovary (CHO) cells. The resulting inferences could explain the recombinant-producing capability of CHO-SH87 cells, compared to non-producing CHO-K1 cells. For comparison, a XCMS-based study of the same dataset, guided by a user's ad-hoc knowledge, identified less than 60 species of 12 classes from thousands of possibilities. CONCLUSION We describe a systematic LC-MS-based framework that identifies lipids for rapid hypothesis generation.
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Affiliation(s)
- Hock Chuan Yeo
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Singapore, 138668, Singapore
- Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, Singapore, 117585, Singapore
| | - Shuwen Chen
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Singapore, 138668, Singapore
| | - Ying Swan Ho
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Singapore, 138668, Singapore
| | - Dong-Yup Lee
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, Singapore, 138668, Singapore.
- School of Chemical Engineering, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Republic of Korea.
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121
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Liu Z, Rochfort S, Cocks B. Milk lipidomics: What we know and what we don't. Prog Lipid Res 2018; 71:70-85. [DOI: 10.1016/j.plipres.2018.06.002] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 06/18/2018] [Accepted: 06/19/2018] [Indexed: 02/07/2023]
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122
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Paine MRL, Poad BLJ, Eijkel GB, Marshall DL, Blanksby SJ, Heeren RMA, Ellis SR. Mass Spectrometry Imaging with Isomeric Resolution Enabled by Ozone‐Induced Dissociation. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802937] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Martin R. L. Paine
- M4I The Maastricht Multimodal Molecular Imaging Institute Division of Imaging Mass Spectrometry Maastricht University Postbus 616, 6200 MD Maastricht The Netherlands
| | - Berwyck L. J. Poad
- Central Analytical Research Facility Institute for Future Environments Queensland University of Technology 2 George St Brisbane QLD 4000 Australia
| | - Gert B. Eijkel
- M4I The Maastricht Multimodal Molecular Imaging Institute Division of Imaging Mass Spectrometry Maastricht University Postbus 616, 6200 MD Maastricht The Netherlands
| | - David L. Marshall
- Central Analytical Research Facility Institute for Future Environments Queensland University of Technology 2 George St Brisbane QLD 4000 Australia
| | - Stephen J. Blanksby
- Central Analytical Research Facility Institute for Future Environments Queensland University of Technology 2 George St Brisbane QLD 4000 Australia
| | - Ron M. A. Heeren
- M4I The Maastricht Multimodal Molecular Imaging Institute Division of Imaging Mass Spectrometry Maastricht University Postbus 616, 6200 MD Maastricht The Netherlands
| | - Shane R. Ellis
- M4I The Maastricht Multimodal Molecular Imaging Institute Division of Imaging Mass Spectrometry Maastricht University Postbus 616, 6200 MD Maastricht The Netherlands
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123
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Li S, Yue Q, Zhou S, Yan J, Zhang X, Ma F. Trehalose Contributes to Gamma-Linolenic Acid Accumulation in Cunninghamella echinulata Based on de Novo Transcriptomic and Lipidomic Analyses. Front Microbiol 2018; 9:1296. [PMID: 29963034 PMCID: PMC6013572 DOI: 10.3389/fmicb.2018.01296] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 05/28/2018] [Indexed: 12/26/2022] Open
Abstract
Gamma-linolenic acid (GLA) is essential for the well-being of humans and other animals. People may lack GLA because of aging or diseases, and thus, dietary supplements or medical reagents containing GLA-enriched lipids are in demand. Cunninghamella echinulata is a potential GLA-producing strain. Interestingly, we found that the GLA content of C. echinulata FR3 was up to 21% (proportion of total lipids) when trehalose was used as a carbon source, significantly higher than the 13% found when glucose was used. Trehalose is quite common and can be accumulated in microorganisms under stress conditions. However, little information is available regarding the role of trehalose in GLA synthesis and accumulation. Our study aimed to understand how the metabolism of C. echinulata responds to trehalose as a carbon source for GLA and lipid biosynthesis. We profiled the major sugars, fatty acids, phospholipids, and gene transcripts of C. echinulata FR3 grown in trehalose medium with glucose as a control by de novo transcriptomics, lipidomics, and other methods. The results showed that trehalose could influence the expression of desaturases and that the GLA proportion increased because of delta-6 desaturase upregulation. The increased GLA was transferred to the extracellular environment through the active PI ion channel, which prefers polyunsaturated acyl chains. At the same time, trehalose might prevent GLA from peroxidation by forming a trehalose-polyunsaturated fatty acid (PUFA) complex. Our study provides new insights into the functions of trehalose in GLA accumulation.
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Affiliation(s)
- Shue Li
- Key Laboratory of Molecular Biophysics of MOE, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Qiang Yue
- Key Laboratory of Molecular Biophysics of MOE, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Shuai Zhou
- Key Laboratory of Molecular Biophysics of MOE, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Jing Yan
- Key Laboratory of Molecular Biophysics of MOE, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyu Zhang
- Key Laboratory of Molecular Biophysics of MOE, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Fuying Ma
- Key Laboratory of Molecular Biophysics of MOE, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.,Hubei Key Laboratory of Lipid Chemistry and Nutrition, Wuhan, China
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Le Bon AM, Deprêtre N, Sibille E, Cabaret S, Grégoire S, Soubeyre V, Masson E, Acar N, Bretillon L, Grosmaitre X, Berdeaux O. Comprehensive study of rodent olfactory tissue lipid composition. Prostaglandins Leukot Essent Fatty Acids 2018; 131:32-43. [PMID: 29628048 DOI: 10.1016/j.plefa.2018.03.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 02/20/2018] [Accepted: 03/21/2018] [Indexed: 11/20/2022]
Abstract
The peripheral olfactory tissue (OT) plays a primordial role in the detection and transduction of olfactory information. Recent proteomic and transcriptomic studies have provided valuable insight into proteins and RNAs expressed in this tissue. Paradoxically, there is little information regarding the lipid composition of mammalian OT. To delve further into this issue, using a set of complementary state-of-the-art techniques, we carried out a comprehensive analysis of OT lipid composition in rats and mice fed with standard diets. The results showed that phospholipids are largely predominant, the major classes being phosphatidylcholine and phosphatidylethanolamine. Two types of plasmalogens, plasmenyl-choline and plasmenyl-ethanolamine, as well as gangliosides were also detected. With the exception of sphingomyelin, substantial levels of n-3 polyunsaturated fatty acids, mainly docosahexaenoic acid (22:6n-3; DHA), were found in the different phospholipid classes. These findings demonstrate that the rodent OT shares several features in common with other neural tissues, such as the brain and retina.
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Affiliation(s)
- Anne Marie Le Bon
- Centre des Sciences du Goût et de l'Alimentation, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, 9E Boulevard Jeanne d'Arc, F-21000 Dijon, France.
| | - Nicolas Deprêtre
- Centre des Sciences du Goût et de l'Alimentation, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, 9E Boulevard Jeanne d'Arc, F-21000 Dijon, France
| | - Estelle Sibille
- Centre des Sciences du Goût et de l'Alimentation, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, 9E Boulevard Jeanne d'Arc, F-21000 Dijon, France
| | - Stéphanie Cabaret
- Centre des Sciences du Goût et de l'Alimentation, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, 9E Boulevard Jeanne d'Arc, F-21000 Dijon, France
| | - Stéphane Grégoire
- Centre des Sciences du Goût et de l'Alimentation, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, 9E Boulevard Jeanne d'Arc, F-21000 Dijon, France
| | - Vanessa Soubeyre
- Centre des Sciences du Goût et de l'Alimentation, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, 9E Boulevard Jeanne d'Arc, F-21000 Dijon, France
| | - Elodie Masson
- Centre des Sciences du Goût et de l'Alimentation, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, 9E Boulevard Jeanne d'Arc, F-21000 Dijon, France
| | - Niyazi Acar
- Centre des Sciences du Goût et de l'Alimentation, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, 9E Boulevard Jeanne d'Arc, F-21000 Dijon, France
| | - Lionel Bretillon
- Centre des Sciences du Goût et de l'Alimentation, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, 9E Boulevard Jeanne d'Arc, F-21000 Dijon, France
| | - Xavier Grosmaitre
- Centre des Sciences du Goût et de l'Alimentation, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, 9E Boulevard Jeanne d'Arc, F-21000 Dijon, France
| | - Olivier Berdeaux
- Centre des Sciences du Goût et de l'Alimentation, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, 9E Boulevard Jeanne d'Arc, F-21000 Dijon, France
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125
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Messias MCF, Mecatti GC, Priolli DG, de Oliveira Carvalho P. Plasmalogen lipids: functional mechanism and their involvement in gastrointestinal cancer. Lipids Health Dis 2018. [PMID: 29514688 PMCID: PMC5842581 DOI: 10.1186/s12944-018-0685-9] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The plasmalogens are a class of glycerophospholipids which contain a vinyl-ether and an ester bond at the sn-1 and sn-2 positions, respectively, in the glycerol backbone. They constitute 10 mol% of the total mass of phospholipids in humans, mainly as membrane structure components. Plasmalogens are important for the organization and stability of lipid raft microdomains and cholesterol-rich membrane regions involved in cellular signaling. In addition to their structural roles, a subset of ether lipids are thought to function as endogenous antioxidants and emerging studies suggest that they are involved in cell differentiation and signaling pathways. Although the clinical significance of plasmalogens is linked to peroxisomal disorders, the pathophysiological roles and their possible metabolic pathways are not fully understood since they present unique structural attributes for the different tissue types. Studies suggest that changes in plasmalogen metabolism may contribute to the development of various types of cancer. Here, we review the molecular characteristics of plasmalogens in order to significantly increase our understanding of the plasmalogen molecule and its involvement in gastrointestinal cancers as well as other types of cancers.
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Affiliation(s)
- Márcia Cristina Fernandes Messias
- Laboratory of Multidisciplinary Research, São Francisco University, USF, São Francisco de Assis Avenue, 218, Bragança Paulista, SP, 12916-900, Brazil.
| | - Giovana Colozza Mecatti
- Laboratory of Multidisciplinary Research, São Francisco University, USF, São Francisco de Assis Avenue, 218, Bragança Paulista, SP, 12916-900, Brazil
| | - Denise Gonçalves Priolli
- Laboratory of Multidisciplinary Research, São Francisco University, USF, São Francisco de Assis Avenue, 218, Bragança Paulista, SP, 12916-900, Brazil
| | - Patrícia de Oliveira Carvalho
- Laboratory of Multidisciplinary Research, São Francisco University, USF, São Francisco de Assis Avenue, 218, Bragança Paulista, SP, 12916-900, Brazil.
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126
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Abstract
Cells depend on hugely diverse lipidomes for many functions. The actions and structural integrity of the plasma membrane and most organelles also critically depend on membranes and their lipid components. Despite the biological importance of lipids, our understanding of lipid engagement, especially the roles of lipid hydrophobic alkyl side chains, in key cellular processes is still developing. Emerging research has begun to dissect the importance of lipids in intricate events such as cell division. This review discusses how these structurally diverse biomolecules are spatially and temporally regulated during cell division, with a focus on cytokinesis. We analyze how lipids facilitate changes in cellular morphology during division and how they participate in key signaling events. We identify which cytokinesis proteins are associated with membranes, suggesting lipid interactions. More broadly, we highlight key unaddressed questions in lipid cell biology and techniques, including mass spectrometry, advanced imaging, and chemical biology, which will help us gain insights into the functional roles of lipids.
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Affiliation(s)
- Elisabeth M Storck
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, United Kingdom;
| | - Cagakan Özbalci
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, United Kingdom;
| | - Ulrike S Eggert
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, London SE1 1UL, United Kingdom; .,Department of Chemistry, King's College London, London SE1 1DB, United Kingdom
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127
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Stinson CA, Zhang W, Xia Y. UV Lamp as a Facile Ozone Source for Structural Analysis of Unsaturated Lipids Via Electrospray Ionization-Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:481-489. [PMID: 29235039 PMCID: PMC5839981 DOI: 10.1007/s13361-017-1861-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 11/27/2017] [Accepted: 11/27/2017] [Indexed: 05/05/2023]
Abstract
Ozonolysis of alkene functional groups is a type of highly specific and effective chemical reaction, which has found increasing applications in structural analysis of unsaturated lipids via coupling with mass spectrometry (MS). In this work, we utilized a low-pressure mercury lamp (6 W) to initiate ozonolysis inside electrospray ionization (ESI) sources. By placing the lamp near a nanoESI emitter that partially transmits 185 nm ultraviolet (UV) emission from the lamp, dissolved dioxygen in the spray solution was converted into ozone, which subsequently cleaved the double bonds within fatty acyls of lipids. Solvent conditions, such as presence of water and acid solution pH, were found to be critical in optimizing ozonolysis yields. Fast (on seconds time scale) and efficient (50%-100% yield) ozonolysis was achieved for model unsaturated phospholipids and fatty acids with UV lamp-induced ozonolysis incorporated on a static and an infusion nanoESI source. The method was able to differentiate double bond location isomers and identify the geometry of the double bond based on yield. The analytical utility of UV lamp-induced ozonolysis was further demonstrated by implementation on a liquid chromatography (LC)-MS platform. Ozonolysis was effected in a flow microreactor that was made from ozone permeable tubing, so that ambient ozone produced by the lamp irradiation could diffuse into the reactor and induce online ozonolysis post-LC separation and before ESI-MS. Graphical Abstract ᅟ.
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Affiliation(s)
- Craig A Stinson
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
- Intel Corporation, Hillsboro, OR, 97214, USA
| | - Wenpeng Zhang
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Yu Xia
- Department of Chemistry, Purdue University, West Lafayette, IN, 47907-2084, USA.
- Department of Chemistry, Tsinghua University, Beijing, 100084, China.
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128
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Observation of endoplasmic reticulum tubules via TOF-SIMS tandem mass spectrometry imaging of transfected cells. Biointerphases 2018; 13:03B409. [PMID: 29482330 DOI: 10.1116/1.5019736] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Advances in three-dimensional secondary ion mass spectrometry (SIMS) imaging have enabled visualizing the subcellular distributions of various lipid species within individual cells. However, the difficulty of locating organelles using SIMS limits efforts to study their lipid compositions. Here, the authors have assessed whether endoplasmic reticulum (ER)-Tracker Blue White DPX®, which is a commercially available stain for visualizing the endoplasmic reticulum using fluorescence microscopy, produces distinctive ions that can be used to locate the endoplasmic reticulum using SIMS. Time-of-flight-SIMS tandem mass spectrometry (MS2) imaging was used to identify positively and negatively charged ions produced by the ER-Tracker stain. Then, these ions were used to localize the stain and thus the endoplasmic reticulum, within individual human embryonic kidney cells that contained higher numbers of endoplasmic reticulum-plasma membrane junctions on their surfaces. By performing MS2 imaging of selected ions in parallel with the precursor ion (MS1) imaging, the authors detected a chemical interference native to the cell at the same nominal mass as the pentafluorophenyl fragment from the ER-Tracker stain. Nonetheless, the fluorine secondary ions produced by the ER-Tracker stain provided a distinctive signal that enabled locating the endoplasmic reticulum using SIMS. This simple strategy for visualizing the endoplasmic reticulum in individual cells using SIMS could be combined with existing SIMS methodologies for imaging intracellular lipid distribution and to study the lipid composition within the endoplasmic reticulum.
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129
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Tharkeshwar AK, Gevaert K, Annaert W. Organellar Omics-A Reviving Strategy to Untangle the Biomolecular Complexity of the Cell. Proteomics 2017; 18:e1700113. [PMID: 29125683 DOI: 10.1002/pmic.201700113] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 10/23/2017] [Indexed: 12/18/2022]
Abstract
A eukaryotic cell encompasses many membrane-enclosed organelles, each of these holding several types of biomolecules that exhibit tremendous diversity in terms of their localization and expression. Despite the development of increasingly sensitive analytical tools, the enormous biomolecular complexity that exists within a cell cannot yet be fully resolved as low abundant molecules often remain unrecognized. Moreover, a drawback of whole cell analysis is that it does not provide spatial information and therefore it is not capable of assigning distinct biomolecules to specific compartments or analyzing changes in the composition of these compartments. Reduction of the biomolecular complexity of a sample helps to identify low abundant molecules, but such a reductionist approach requires methods that enable proper isolation and purification of individual cellular organelles. Decades of research have led to the development of a plethora of isolation methods for a broad range of subcellular organelles; yet, in particular, intrinsically dynamic compartments belonging to the endocytic machinery, including the plasma membrane, remain difficult to isolate in a sufficiently pure fraction. In this review, we discuss various methods that are commonly used to isolate subcellular organelles from cells and evaluate their advantages and disadvantages.
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Affiliation(s)
- Arun Kumar Tharkeshwar
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, Leuven, Belgium.,Laboratory for Membrane Trafficking, Department of Neurosciences, KU Leuven, Leuven, Belgium.,Department of Cell Biology, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT, USA
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.,Department of Biochemistry, Ghent University, Belgium
| | - Wim Annaert
- Laboratory for Membrane Trafficking, VIB-Center for Brain and Disease Research, Leuven, Belgium.,Laboratory for Membrane Trafficking, Department of Neurosciences, KU Leuven, Leuven, Belgium
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130
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Distinct lipidomic profiles in models of physiological and pathological cardiac remodeling, and potential therapeutic strategies. Biochim Biophys Acta Mol Cell Biol Lipids 2017; 1863:219-234. [PMID: 29217479 DOI: 10.1016/j.bbalip.2017.12.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 11/04/2017] [Accepted: 12/02/2017] [Indexed: 01/23/2023]
Abstract
Cardiac myocyte membranes contain lipids which remodel dramatically in response to heart growth and remodeling. Lipid species have both structural and functional roles. Physiological and pathological cardiac remodeling have very distinct phenotypes, and the identification of molecular differences represent avenues for therapeutic interventions. Whether the abundance of specific lipid classes is different in physiological and pathological models was largely unknown. The aim of this study was to determine whether distinct lipids are regulated in settings of physiological and pathological remodeling, and if so, whether modulation of differentially regulated lipids could modulate heart size and function. Lipidomic profiling was performed on cardiac-specific transgenic mice with 1) physiological cardiac hypertrophy due to increased Insulin-like Growth Factor 1 (IGF1) receptor or Phosphoinositide 3-Kinase (PI3K) signaling, 2) small hearts due to depressed PI3K signaling (dnPI3K), and 3) failing hearts due to dilated cardiomyopathy (DCM). In hearts of dnPI3K and DCM mice, several phospholipids (plasmalogens) were decreased and sphingolipids increased compared to mice with physiological hypertrophy. To assess whether restoration of plasmalogens could restore heart size or cardiac function, dnPI3K and DCM mice were administered batyl alcohol (BA; precursor to plasmalogen biosynthesis) in the diet for 16weeks. BA supplementation increased a major plasmalogen species (p18:0) in the heart but had no effect on heart size or function. This may be due to the concurrent reduction in other plasmalogen species (p16:0 and p18:1) with BA. Here we show that lipid species are differentially regulated in settings of physiological and pathological remodeling. Restoration of lipid species in the failing heart warrants further examination.
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131
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Veyrat-Durebex C, Bocca C, Chupin S, Kouassi Nzoughet J, Simard G, Lenaers G, Reynier P, Blasco H. Metabolomics and Lipidomics Profiling of a Combined Mitochondrial Plus Endoplasmic Reticulum Fraction of Human Fibroblasts: A Robust Tool for Clinical Studies. J Proteome Res 2017; 17:745-750. [PMID: 29111762 DOI: 10.1021/acs.jproteome.7b00637] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Mitochondria and endoplasmic reticulum (ER) are physically and functionally connected. This close interaction, via mitochondria-associated membranes, is increasingly explored and supports the importance of studying these two organelles as a whole. Metabolomics and lipidomics are powerful approaches for the exploration of metabolic pathways that may be useful to provide deeper information on these organelles' functions, dysfunctions, and interactions. We developed a quick and simple experimental procedure for the purification of a mitochondria-ER fraction from human fibroblasts. We applied combined metabolomics and lipidomics analyses by mass spectrometry with excellent reproducibility. Seventy-two metabolites and 418 complex lipids were detected with a mean coefficient of variation around 12%, among which many were specific to the mitochondrial metabolism. Thus this strategy based on robust mitochondria-ER extraction and "omics" combination will be useful for investigating the pathophysiology of complex diseases.
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Affiliation(s)
- Charlotte Veyrat-Durebex
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire , 49933 Angers, France.,Equipe Mitolab, Institut MITOVASC, UMR CNRS 6015, INSERM 1083, Université d'Angers , 49933 Angers, France
| | - Cinzia Bocca
- Equipe Mitolab, Institut MITOVASC, UMR CNRS 6015, INSERM 1083, Université d'Angers , 49933 Angers, France
| | - Stéphanie Chupin
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire , 49933 Angers, France
| | - Judith Kouassi Nzoughet
- Equipe Mitolab, Institut MITOVASC, UMR CNRS 6015, INSERM 1083, Université d'Angers , 49933 Angers, France
| | - Gilles Simard
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire , 49933 Angers, France
| | - Guy Lenaers
- Equipe Mitolab, Institut MITOVASC, UMR CNRS 6015, INSERM 1083, Université d'Angers , 49933 Angers, France
| | - Pascal Reynier
- Département de Biochimie et Génétique, Centre Hospitalier Universitaire , 49933 Angers, France.,Equipe Mitolab, Institut MITOVASC, UMR CNRS 6015, INSERM 1083, Université d'Angers , 49933 Angers, France
| | - Hélène Blasco
- Equipe Mitolab, Institut MITOVASC, UMR CNRS 6015, INSERM 1083, Université d'Angers , 49933 Angers, France.,Université François-Rabelais , INSERM U930, 37000 Tours, France.,Laboratoire de Biochimie et Biologie Moléculaire, CHRU de Tours , 37044 Tours, France
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132
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Pollard AK, Ortori CA, Stöger R, Barrett DA, Chakrabarti L. Mouse mitochondrial lipid composition is defined by age in brain and muscle. Aging (Albany NY) 2017; 9:986-998. [PMID: 28325886 PMCID: PMC5391243 DOI: 10.18632/aging.101204] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 03/12/2017] [Indexed: 01/22/2023]
Abstract
Functionality of the lipid rich mitochondrial organelle declines with increased age. Recent advances in lipidomic technologies allowed us to perform a global characterisation of lipid composition in two different tissue types and age ranges. Ultra-high performance liquid chromatography coupled with high resolution mass spectrometry was used to establish and compare mitochondrial lipidomes of brain and skeletal muscle from young (4-11 weeks old) and middle age (78 weeks old) healthy mice. In middle age the brain mitochondria had reduced levels of fatty acids, particularly polyunsaturated fatty acids, while skeletal muscle mitochondria had a decreased abundance of phosphatidylethanolamine, but a pronounced increase of triglyceride levels. Reduced levels of phosphatidylethanolamines are known to decrease mitochondrial membrane fluidity and are connected with accelerated ageing. In mitochondria from skeletal muscle we propose that increased age causes a metabolic shift in the conversion of diacylglycerol so that triglycerides predominate compared with phosphatidylethanolamines. This is the first time mitochondrial lipid content in normal healthy mammalian ageing brain and muscle has been catalogued in such detail across all lipid classes. We identify distinct mitochondrial lipid signatures that change with age, revealing tissue-specific lipid pathways as possible targets to ameliorate ageing-related mitochondrial decline.
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Affiliation(s)
- Amelia K Pollard
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, LE12 5RD, UK
| | - Catharine A Ortori
- Centre for Analytical Bioscience, School of Pharmacy, University of Nottingham, NG7 2RD, UK
| | - Reinhard Stöger
- Division of Animal Science, School of Biosciences, University of Nottingham, LE12 5RD, UK
| | - David A Barrett
- Centre for Analytical Bioscience, School of Pharmacy, University of Nottingham, NG7 2RD, UK
| | - Lisa Chakrabarti
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington, LE12 5RD, UK
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133
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3D MALDI Mass Spectrometry Imaging of a Single Cell: Spatial Mapping of Lipids in the Embryonic Development of Zebrafish. Sci Rep 2017; 7:14946. [PMID: 29097697 PMCID: PMC5668422 DOI: 10.1038/s41598-017-14949-x] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/18/2017] [Indexed: 12/11/2022] Open
Abstract
The zebrafish (Danio rerio) has been widely used as a model vertebrate system to study lipid metabolism, the roles of lipids in diseases, and lipid dynamics in embryonic development. Here, we applied high-spatial resolution matrix-assisted laser desorption/ionization (MALDI)-mass spectrometry imaging (MSI) to map and visualize the three-dimensional spatial distribution of phospholipid classes, phosphatidylcholine (PC), phosphatidylethanolamines (PE), and phosphatidylinositol (PI), in newly fertilized individual zebrafish embryos. This is the first time MALDI-MSI has been applied for three dimensional chemical imaging of a single cell. PC molecular species are present inside the yolk in addition to the blastodisc, while PE and PI species are mostly absent in the yolk. Two-dimensional MSI was also studied for embryos at different cell stages (1-, 2-, 4-, 8-, and 16-cell stage) to investigate the localization changes of some lipids at various cell developmental stages. Four different normalization approaches were compared to find reliable relative quantification in 2D- and 3D- MALDI MSI data sets.
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134
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Üretmen Kagıalı ZC, Şentürk A, Özkan Küçük NE, Qureshi MH, Özlü N. Proteomics in Cell Division. Proteomics 2017; 17. [PMID: 28548456 DOI: 10.1002/pmic.201600100] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 04/07/2017] [Indexed: 11/08/2022]
Abstract
Cell division requires a coordinated action of the cell cycle machinery, cytoskeletal elements, chromosomes, and membranes. Cell division studies have greatly benefitted from the mass spectrometry (MS)-based proteomic approaches for probing the biochemistry of highly dynamic complexes and their coordination with each other as a cell progresses into division. In this review, the authors first summarize a wide-range of proteomic studies that focus on the identification of sub-cellular components/protein complexes of the cell division machinery including kinetochores, mitotic spindle, midzone, and centrosomes. The authors also highlight MS-based large-scale analyses of the cellular components that are largely understudied during cell division such as the cell surface and lipids. Then, the authors focus on posttranslational modification analyses, especially phosphorylation and the resulting crosstalk with other modifications as a cell undergoes cell division. Combining proteomic approaches that probe the biochemistry of cell division components with functional genomic assays will lead to breakthroughs toward a systems-level understanding of cell division.
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Affiliation(s)
| | - Aydanur Şentürk
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
| | | | - Mohammad Haroon Qureshi
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey.,Biomedical Sciences and Engineering, Koç University, Istanbul, Turkey
| | - Nurhan Özlü
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
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135
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Lin L, Ding Y, Wang Y, Wang Z, Yin X, Yan G, Zhang L, Yang P, Shen H. Functional lipidomics: Palmitic acid impairs hepatocellular carcinoma development by modulating membrane fluidity and glucose metabolism. Hepatology 2017; 66:432-448. [PMID: 28073184 DOI: 10.1002/hep.29033] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 11/14/2016] [Accepted: 12/26/2016] [Indexed: 01/09/2023]
Abstract
UNLABELLED Lipids are essential cellular components and energy sources of living organisms, and altered lipid composition is increasingly recognized as a signature of cancer. We performed lipidomic analysis in a series of hepatocellular carcinoma (HCC) cells and identified over 1,700 intact lipids originating from three major lipid categories. Comparative lipidomic screening revealed that 93 significantly changed lipids and decreased palmitic acyl (C16:0)-containing glycerophospholipids were positively associated with metastatic abilities of HCC cells. Furthermore, both in vitro and in vivo experiments demonstrated that C16:0 incubation specifically reduced malignant cell proliferation, impaired cell invasiveness, and suppressed tumor growth in mouse xenograft models. Biochemical experiments demonstrated that C16:0 treatment decreased cell membrane fluidity and limited glucose metabolism. A phosphoproteomics approach further revealed such C16:0 incubation attenuated phosphorylation levels of mammalian target of rapamycin (mTOR) and signal transducer and activator of transcription 3 (STAT3) pathway proteins. Multiple reaction monitoring analysis of 443 lipid molecules showed 8 reduced C16:0-containing lipids out of total 10 altered lipids when cancer tissues were compared with adjacent nontumor tissues in a cohort of clinical HCC specimens (P < 0.05). CONCLUSION These data collectively demonstrate the biomedical potential of using altered lipid metabolism as a diagnostic marker for cancerous cells and open an opportunity for treating aggressive HCCs by targeting altered C16:0 metabolism. (Hepatology 2017;66:432-448).
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Affiliation(s)
- Ling Lin
- Department of Systems Biology for Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Institutes of Biomedical Sciences of Shanghai Medical School, Fudan University, Shanghai, China
| | - Ying Ding
- Department of Systems Biology for Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Shanghai Institute for Food and Drug Control, Shanghai, China
| | - Yi Wang
- Department of Systems Biology for Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Institutes of Biomedical Sciences of Shanghai Medical School, Fudan University, Shanghai, China.,Department of Chemistry, Fudan University, Shanghai, China
| | - Zhenxin Wang
- Department of Systems Biology for Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Xuefei Yin
- Department of Systems Biology for Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Department of Chemistry, Fudan University, Shanghai, China
| | - Guoquan Yan
- Department of Chemistry, Fudan University, Shanghai, China
| | - Lei Zhang
- Institutes of Biomedical Sciences of Shanghai Medical School, Fudan University, Shanghai, China
| | - Pengyuan Yang
- Department of Systems Biology for Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Institutes of Biomedical Sciences of Shanghai Medical School, Fudan University, Shanghai, China.,Department of Chemistry, Fudan University, Shanghai, China
| | - Huali Shen
- Department of Systems Biology for Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Institutes of Biomedical Sciences of Shanghai Medical School, Fudan University, Shanghai, China.,Department of Chemistry, Fudan University, Shanghai, China
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136
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Abstract
PURPOSE OF REVIEW Lipid peroxidation has long been established as a key player in the pathophysiology of critical illness. Recent developments in oxidative lipidomics have aided in deciphering the molecular mechanisms of lipid oxidation in health and disease. This review discusses recent achievements and recent developments in oxidative lipidomics and its contribution to the understanding of critical illness. RECENT FINDINGS Most studies involving acute injury focus on identifying the end products of lipid peroxidation. This misses the early events and targets of peroxidation mechanisms. Recent developments in liquid chromatography tandem mass spectrometry-based oxidative lipidomics have enabled the identification of a wide variety of enzymatically generated lipid oxidation products. Such lipid mediators have been found to play an important role in injury, inflammation, and recovery in disease states such as sepsis or head trauma. SUMMARY Multiple lipid oxidation products are formed either through enzymatic pathways or through random chemical reactions. These products are often biologically active and can contribute to the regulation of cellular signaling. Oxidative lipidomics has contributed to the identification and quantification of lipid peroxidation products, the mechanism and time course of their production after injury, and synergistic functioning with other regulatory processes in the body. These advances in knowledge will help guide the future development of interventions in critical illness.
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Affiliation(s)
- Tamil S. Anthonymuthu
- Department of Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, 15213
- Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, PA, 15213
- Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA, 15213
| | - Nahmah Kim-Campbell
- Department of Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, 15213
- Children’s Hospital of Pittsburgh of UPMC, University of Pittsburgh, Pittsburgh, PA, 15213
| | - Hülya Bayır
- Department of Critical Care Medicine, University of Pittsburgh, Pittsburgh, PA, 15213
- Safar Center for Resuscitation Research, University of Pittsburgh, Pittsburgh, PA, 15213
- Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA, 15213
- Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, 15213
- Children’s Hospital of Pittsburgh of UPMC, University of Pittsburgh, Pittsburgh, PA, 15213
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137
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Zhang H, Gao Y, Sun J, Fan S, Yao X, Ran X, Zheng C, Huang M, Bi H. Optimization of lipid extraction and analytical protocols for UHPLC-ESI-HRMS-based lipidomic analysis of adherent mammalian cancer cells. Anal Bioanal Chem 2017; 409:5349-5358. [PMID: 28717896 DOI: 10.1007/s00216-017-0483-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 06/10/2017] [Accepted: 06/21/2017] [Indexed: 12/12/2022]
Abstract
Lipidomics, which reveals comprehensive characterization of molecular lipids, is a rapidly growing technology used in biomedical research. Lipid extraction is a critical step in lipidomic analysis. However, the effectiveness of different lipid extract solvent systems from cellular samples still remains unclear. In the current study, the protocol of reverse-phase liquid chromatography mass spectrometry (LC/MS)-based lipidomics was optimized for extraction and detection of lipids from human pancreatic cancer cell line PANC-1. Four different extraction methods were compared, including methanol/methyl-tert-butyl ether (MTBE)/H2O, methanol/chloroform, methanol/MTBE/chloroform, and hexane/isopropanol. Data were acquired using high-resolution mass spectrometry in positive and negative ion modes respectively. The number of total detected and identified lipids was assessed with the aid of automated lipid identification software LipidSearch. Results demonstrated that methanol/MTBE/H2O provided a better extraction efficiency for different lipid classes, which was chosen as the optimized extraction solvent system. This validated method enables highly sensitive and reproducible analysis for a variety of cellular lipids, which was further applied to an untargeted lipidomic study on human pancreatic cancer PANC-1 cell lines. Moreover, this optimized extraction solvent system can be further applied to other cancer cell lines with similar chemical and physical properties. Graphical abstract Optimized UHPLC-ESI-HRMS-based lipidomic analysis of cancer cells.
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Affiliation(s)
- Huizhen Zhang
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132# Waihuandong Road, Guangzhou University City, Guangzhou, 510006, China
| | - Yue Gao
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132# Waihuandong Road, Guangzhou University City, Guangzhou, 510006, China
| | - Jiahong Sun
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132# Waihuandong Road, Guangzhou University City, Guangzhou, 510006, China
| | - Shicheng Fan
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132# Waihuandong Road, Guangzhou University City, Guangzhou, 510006, China
| | - Xinpeng Yao
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132# Waihuandong Road, Guangzhou University City, Guangzhou, 510006, China
| | | | | | - Min Huang
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132# Waihuandong Road, Guangzhou University City, Guangzhou, 510006, China
| | - Huichang Bi
- School of Pharmaceutical Sciences, Sun Yat-sen University, 132# Waihuandong Road, Guangzhou University City, Guangzhou, 510006, China.
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138
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Imaging and lipidomics methods for lipid analysis in metabolic and cardiovascular disease. J Dev Orig Health Dis 2017; 8:566-574. [PMID: 28697812 DOI: 10.1017/s2040174417000496] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cardiometabolic diseases exhibit changes in lipid biology, which is important as lipids have critical roles in membrane architecture, signalling, hormone synthesis, homoeostasis and metabolism. However, Developmental Origins of Health and Disease studies of cardiometabolic disease rarely include analysis of lipids. This short review highlights some examples of lipid pathology and then explores the technology available for analysing lipids, focussing on the need to develop imaging modalities for intracellular lipids. Analytical methods for studying interactions between the complex endocrine and intracellular signalling pathways that regulate lipid metabolism have been critical in expanding our understanding of how cardiometabolic diseases develop in association with obesity and dietary factors. Biochemical methods can be used to generate detailed lipid profiles to establish links between lifestyle factors and metabolic signalling pathways and determine how changes in specific lipid subtypes in plasma and homogenized tissue are associated with disease progression. New imaging modalities enable the specific visualization of intracellular lipid traffic and distribution in situ. These techniques provide a dynamic picture of the interactions between lipid storage, mobilization and signalling, which operate during normal cell function and are altered in many important diseases. The development of methods for imaging intracellular lipids can provide a dynamic real-time picture of how lipids are involved in complex signalling and other cell biology pathways; and how they ultimately regulate metabolic function/homoeostasis during early development. Some imaging modalities have the potential to be adapted for in vivo applications, and may enable the direct visualization of progression of pathogenesis of cardiometabolic disease after poor growth in early life.
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Kubicek-Sutherland JZ, Vu DM, Mendez HM, Jakhar S, Mukundan H. Detection of Lipid and Amphiphilic Biomarkers for Disease Diagnostics. BIOSENSORS-BASEL 2017; 7:bios7030025. [PMID: 28677660 PMCID: PMC5618031 DOI: 10.3390/bios7030025] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 06/27/2017] [Accepted: 06/30/2017] [Indexed: 12/24/2022]
Abstract
Rapid diagnosis is crucial to effectively treating any disease. Biological markers, or biomarkers, have been widely used to diagnose a variety of infectious and non-infectious diseases. The detection of biomarkers in patient samples can also provide valuable information regarding progression and prognosis. Interestingly, many such biomarkers are composed of lipids, and are amphiphilic in biochemistry, which leads them to be often sequestered by host carriers. Such sequestration enhances the difficulty of developing sensitive and accurate sensors for these targets. Many of the physiologically relevant molecules involved in pathogenesis and disease are indeed amphiphilic. This chemical property is likely essential for their biological function, but also makes them challenging to detect and quantify in vitro. In order to understand pathogenesis and disease progression while developing effective diagnostics, it is important to account for the biochemistry of lipid and amphiphilic biomarkers when creating novel techniques for the quantitative measurement of these targets. Here, we review techniques and methods used to detect lipid and amphiphilic biomarkers associated with disease, as well as their feasibility for use as diagnostic targets, highlighting the significance of their biochemical properties in the design and execution of laboratory and diagnostic strategies. The biochemistry of biological molecules is clearly relevant to their physiological function, and calling out the need for consideration of this feature in their study, and use as vaccine, diagnostic and therapeutic targets is the overarching motivation for this review.
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Affiliation(s)
- Jessica Z Kubicek-Sutherland
- Physical Chemistry and Applied Spectroscopy, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Dung M Vu
- Physical Chemistry and Applied Spectroscopy, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Heather M Mendez
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM 87131, USA.
- The New Mexico Consortium, Los Alamos, NM 87544, USA.
| | - Shailja Jakhar
- Physical Chemistry and Applied Spectroscopy, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Harshini Mukundan
- Physical Chemistry and Applied Spectroscopy, Chemistry Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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Šmidák R, Köfeler HC, Hoeger H, Lubec G. Comprehensive identification of age-related lipidome changes in rat amygdala during normal aging. PLoS One 2017; 12:e0180675. [PMID: 28672041 PMCID: PMC5495493 DOI: 10.1371/journal.pone.0180675] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 06/19/2017] [Indexed: 12/28/2022] Open
Abstract
Brain lipids are integral components of brain structure and function. However, only recent advancements of chromatographic techniques together with mass spectrometry allow comprehensive identification of lipid species in complex brain tissue. Lipid composition varies between the individual areas and the majority of previous reports was focusing on individual lipids rather than a lipidome. Herein, a mass spectrometry-based approach was used to evaluate age-related changes in the lipidome of the rat amygdala obtained from young (3 months) and old (20 months) males of the Sprague-Dawley rat strain. A total number of 70 lipid species with significantly changed levels between the two animal groups were identified spanning four main lipid classes, i.e. glycerolipids, glycerophospholipids, sphingolipids and sterol lipids. These included phospholipids with pleiotropic brain function, such as derivatives of phosphatidylcholine, phosphatidylserine, and phosphatidylethanolamine. The analysis also revealed significant level changes of phosphatidic acid, diacylglycerol, sphingomyelin and ceramide that directly represent lipid signaling and affect amygdala neuronal activity. The amygdala is a crucial brain region for cognitive functions and former studies on rats and humans showed that this region changes its activity during normal aging. As the information on amygdala lipidome is very limited the results obtained in the present study represent a significant novelty and may contribute to further studies on the role of lipid molecules in age-associated changes of amygdala function.
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Affiliation(s)
- Roman Šmidák
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Harald C. Köfeler
- Center for Medical Research (ZMF), Medical University Graz, Graz, Austria
| | - Harald Hoeger
- Core Unit of Biomedical Research, Division of Laboratory Animal Science and Genetics, Medical University of Vienna, Himberg, Austria
| | - Gert Lubec
- Department of Pharmaceutical Chemistry, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Neuroproteomics Laboratory, Science Park, Ilkovicova 8, Bratislava, Slovakia
- * E-mail:
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Ryan E, Nguyen CQN, Shiea C, Reid GE. Detailed Structural Characterization of Sphingolipids via 193 nm Ultraviolet Photodissociation and Ultra High Resolution Tandem Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1406-1419. [PMID: 28455688 DOI: 10.1007/s13361-017-1668-1] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 03/15/2017] [Accepted: 03/16/2017] [Indexed: 05/29/2023]
Abstract
Sphingolipids serve not only as components of cellular membranes but also as bioactive mediators of numerous cellular functions. As the biological activities of these lipids are dependent on their structures, and due to the limitations of conventional ion activation methods employed during tandem mass spectrometry (MS/MS), there is a recognized need for the development of improved structure-specific methods for their comprehensive identification and characterization. Here, positive-ionization mode 193 nm ultraviolet photodissociation (UVPD)-MS/MS has been implemented for the detailed structural characterization of lipid species from a range of sphingolipid classes introduced to the mass spectrometer via electrospray ionization as their lithiated or protonated adducts. These include sphingosine d18:1(4E), dihydrosphingosine (sphinganine) d18:0, sphingadiene d18:2(4E,11Z), the isomeric sphingolipids ceramide d18:1(4E)/18:0 and dihydroceramide d18:0/18:1(9Z), ceramide-1-phosphate d18:1(4Z)/16:0, sphingomyelin d18:1(4E)/18:1(9Z) the glycosphingolipids galactosyl ceramide d18:1(4E)/24:1(15Z) and lactosyl ceramide d18:1(4E)/24:0, and several endogenous lipids present within a porcine brain total lipid extract. In addition to the product ions formed by higher energy collision dissociation (HCD), UVPD is shown to yield a series of novel structurally diagnostic product ions resulting from cleavage of both sphingosine carbon-carbon and acyl chain carbon-carbon double bonds for direct localization of site(s) of unsaturation, as well as via diagnostic cleavages of the sphingosine backbone and N-C amide bond linkages. With activation timescales and dissociation efficiencies similar to those found in conventional MS/MS strategies, this approach is therefore a promising new tool in the arsenal of ion activation techniques toward providing complete structural elucidation in automated, high-throughput lipid analysis workflows. Graphical Abstract ᅟ.
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Affiliation(s)
- Eileen Ryan
- School of Chemistry, University of Melbourne, Parkville, Victoria, 3010, Australia
| | | | - Christopher Shiea
- School of Chemistry, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Gavin E Reid
- School of Chemistry, University of Melbourne, Parkville, Victoria, 3010, Australia.
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, 3010, Australia.
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, 3010, Australia.
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Abstract
PURPOSE OF REVIEW Alzheimer's disease is the most common cause of dementia. There are still no disease modifying treatments that can cure or slow disease progression. Recently, Alzheimer's disease researchers have attempted to improve early detection and diagnostic criteria for Alzheimer's disease, with the rationale that treatment of disease, or even prevention, may be more successful during the early preclinical stages of Alzheimer's disease when neurodegenerative damage is not as widespread. As the brain has a high lipid content, lipidomics may offer novel insights into the underlying pathogenesis of Alzheimer's disease. This review reports on recent developments in the relatively unexplored field of lipidomics in Alzheimer's disease, including novel biomarkers and pathomechanisms of Alzheimer's disease. RECENT FINDINGS Numerous biomarker panels involving phospholipids and sphingolipids have been proposed, indicating perturbed lipid metabolism in early stages of Alzheimer's disease. Future strategies targeting these metabolic changes through dietary supplementation could have therapeutic benefits in at-risk individuals. SUMMARY Dysregulated lipid metabolism could reflect pathological changes in synaptic function and neuronal membranes, leading to cognitive decline. However, extensive validation in large independent cohorts is required before lipid biomarkers can be used clinically to assess Alzheimer's disease risk and progression.
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143
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Dysregulation of lipids in Alzheimer's disease and their role as potential biomarkers. Alzheimers Dement 2017; 13:810-827. [PMID: 28242299 DOI: 10.1016/j.jalz.2017.01.008] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 11/17/2016] [Accepted: 01/03/2017] [Indexed: 12/14/2022]
Abstract
The brain is highly enriched in lipids, and an intensive study of these lipids may be informative, not only of normal brain function but also of changes with age and in disease. In recent years, the development of highly sensitive mass spectrometry platforms and other high-throughput technologies has enabled the discovery of complex changes in the entire lipidome. This lipidomics approach promises to be a particularly useful tool for identifying diagnostic biomarkers for early detection of age-related neurodegenerative disease, such as Alzheimer's disease (AD), which has till recently been limited to protein- and gene-centric approaches. This review highlights known lipid changes affecting the AD brain and presents an update on the progress of lipid biomarker research in AD. Important considerations for designing large-scale lipidomics experiments are discussed to help standardize findings across different laboratories, as well as challenges associated with moving toward clinical application.
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144
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Klein DR, Brodbelt JS. Structural Characterization of Phosphatidylcholines Using 193 nm Ultraviolet Photodissociation Mass Spectrometry. Anal Chem 2017; 89:1516-1522. [PMID: 28105803 PMCID: PMC5480246 DOI: 10.1021/acs.analchem.6b03353] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Advances in mass spectrometry have made it a preferred tool for structural characterization of glycerophospholipids. Collisional activation methods commonly implemented on commercial instruments do not provide fragmentation patterns that allow elucidation of certain structural features, including acyl chain positions on the glycerol backbone and double bond positions within acyl chains. In the present work, 193 nm ultraviolet photodissociation (UVPD) implemented on an Orbitrap mass spectrometer is used to localize double bond positions within phosphatidylcholine (PC) acyl chains. Cleavage of the carbon-carbon bonds adjacent to the double bond provides a diagnostic mass difference of 24 Da and enables differentiation of double-bond positional isomers. The UVPD method was extended to the characterization of PCs in a bovine liver extract via a shotgun strategy. Positive mode higher energy collisional dissociation (HCD) and UVPD, and negative mode HCD were undertaken in a complementary manner to identify species as PCs and to localize double bonds, respectively.
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Affiliation(s)
- Dustin R Klein
- Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
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Tumanov S, Kamphorst JJ. Recent advances in expanding the coverage of the lipidome. Curr Opin Biotechnol 2017; 43:127-133. [PMID: 27915214 PMCID: PMC5312421 DOI: 10.1016/j.copbio.2016.11.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 11/08/2016] [Accepted: 11/14/2016] [Indexed: 11/30/2022]
Abstract
The lipidome comprises a large array of molecules with diverse physicochemical properties. Lipids are structural components of cells, act as a source of energy, and function as signaling mediators. Alterations in lipid metabolism are involved in the onset and progression of a variety of diseases, including metabolic syndrome and cancer. Because of this, interest in lipidomics, the comprehensive characterization of the lipidome by mass spectrometry, has intensified in recent years. However, obtaining a truly complete overview of all lipids in a sample has remained very challenging due to their enormous structural diversity. Here, we provide an overview of the collection of analytical approaches used to study various lipid classes, emphasizing innovations in sample preparation and liquid chromatography-mass spectrometry (LC-MS). Additionally, we provide practical suggestions for increasing the coverage of the lipidome.
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Affiliation(s)
- Sergey Tumanov
- Cancer Metabolism Research Unit, Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK; Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK
| | - Jurre J Kamphorst
- Cancer Metabolism Research Unit, Cancer Research UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK; Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1QH, UK.
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A novel approach to analyze lysosomal dysfunctions through subcellular proteomics and lipidomics: the case of NPC1 deficiency. Sci Rep 2017; 7:41408. [PMID: 28134274 PMCID: PMC5278418 DOI: 10.1038/srep41408] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 12/19/2016] [Indexed: 01/21/2023] Open
Abstract
Superparamagnetic iron oxide nanoparticles (SPIONs) have mainly been used as cellular carriers for genes and therapeutic products, while their use in subcellular organelle isolation remains underexploited. We engineered SPIONs targeting distinct subcellular compartments. Dimercaptosuccinic acid-coated SPIONs are internalized and accumulate in late endosomes/lysosomes, while aminolipid-SPIONs reside at the plasma membrane. These features allowed us to establish standardized magnetic isolation procedures for these membrane compartments with a yield and purity permitting proteomic and lipidomic profiling. We validated our approach by comparing the biomolecular compositions of lysosomes and plasma membranes isolated from wild-type and Niemann-Pick disease type C1 (NPC1) deficient cells. While the accumulation of cholesterol and glycosphingolipids is seen as a primary hallmark of NPC1 deficiency, our lipidomics analysis revealed the buildup of several species of glycerophospholipids and other storage lipids in selectively late endosomes/lysosomes of NPC1-KO cells. While the plasma membrane proteome remained largely invariable, we observed pronounced alterations in several proteins linked to autophagy and lysosomal catabolism reflecting vesicular transport obstruction and defective lysosomal turnover resulting from NPC1 deficiency. Thus the use of SPIONs provides a major advancement in fingerprinting subcellular compartments, with an increased potential to identify disease-related alterations in their biomolecular compositions.
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147
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Ma X, Liu J, Zhang Z, Bo T, Bai Y, Liu H. Drift tube ion mobility and four-dimensional molecular feature extraction enable data-independent tandem mass spectrometric 'omics' analysis without quadrupole selection. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:33-38. [PMID: 27760459 DOI: 10.1002/rcm.7767] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 10/08/2016] [Accepted: 10/14/2016] [Indexed: 06/06/2023]
Abstract
RATIONALE Quadrupole-based tandem mass spectrometry (MS/MS) plays a critical role in 'omics' studies. However, when a particular m/z precursor is selected by the quadrupole, ions other than the precursor are not transmitted through, and the sensitivity and dynamic range thus diminish. Therefore, separation techniques such as ion mobility (IM) are coupled with MS/MS to improve it. METHODS In this workflow, every IM-mass spectrometry (MS) scan was followed by one high-voltage collision energy (CE) scan. The precursors were separated in IM drift time and dissociated after IM; the four-dimensional molecular feature extraction (4D MFE) algorithm was used to align the precursors and their MS/MS spectra based on retention time and drift time distribution. A complicated peptide mixture was selected to exemplify the workflow in a proteomics study. RESULTS The new IM-MS-based workflow achieved similar performance in finding proteins compared to the traditional quadrupole-based MS/MS method. However, a significant difference was found between the proteins found by these two methods. For the four concentration levels analyzed, at least 23% more proteins were found by combining the new methods than only using the traditional quadrupole-based MS/MS method. CONCLUSIONS The established workflow used the 4D MFE algorithm to analyze a complicated 4D dataset and was demonstrated to find more proteins not found by the traditional quadrupole-based MS/MS method in proteomics application. It is thus an important complementary MS/MS mode for 'omics' studies. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Xin Ma
- Agilent Technologies, Beijing, 100102, China
| | - Jing Liu
- Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemistry Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | | | - Tao Bo
- Agilent Technologies, Beijing, 100102, China
| | - Yu Bai
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Huwei Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Institute of Analytical Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
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148
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The role of interfacial lipids in stabilizing membrane protein oligomers. Nature 2017; 541:421-424. [PMID: 28077870 DOI: 10.1038/nature20820] [Citation(s) in RCA: 288] [Impact Index Per Article: 41.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 11/23/2016] [Indexed: 12/20/2022]
Abstract
Oligomerization of membrane proteins in response to lipid binding has a critical role in many cell-signalling pathways but is often difficult to define or predict. Here we report the development of a mass spectrometry platform to determine simultaneously the presence of interfacial lipids and oligomeric stability and to uncover how lipids act as key regulators of membrane-protein association. Evaluation of oligomeric strength for a dataset of 125 α-helical oligomeric membrane proteins reveals an absence of interfacial lipids in the mass spectra of 12 membrane proteins with high oligomeric stability. For the bacterial homologue of the eukaryotic biogenic transporters (LeuT, one of the proteins with the lowest oligomeric stability), we found a precise cohort of lipids within the dimer interface. Delipidation, mutation of lipid-binding sites or expression in cardiolipin-deficient Escherichia coli abrogated dimer formation. Molecular dynamics simulation revealed that cardiolipin acts as a bidentate ligand, bridging across subunits. Subsequently, we show that for the Vibrio splendidus sugar transporter SemiSWEET, another protein with low oligomeric stability, cardiolipin shifts the equilibrium from monomer to functional dimer. We hypothesized that lipids are essential for dimerization of the Na+/H+ antiporter NhaA from E. coli, which has the lowest oligomeric strength, but not for the substantially more stable homologous Thermus thermophilus protein NapA. We found that lipid binding is obligatory for dimerization of NhaA, whereas NapA has adapted to form an interface that is stable without lipids. Overall, by correlating interfacial strength with the presence of interfacial lipids, we provide a rationale for understanding the role of lipids in both transient and stable interactions within a range of α-helical membrane proteins, including G-protein-coupled receptors.
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Dong S, Zhang R, Liang Y, Shi J, Li J, Shang F, Mao X, Sun J. Changes of myocardial lipidomics profiling in a rat model of diabetic cardiomyopathy using UPLC/Q-TOF/MS analysis. Diabetol Metab Syndr 2017; 9:56. [PMID: 28736579 PMCID: PMC5520292 DOI: 10.1186/s13098-017-0249-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 06/28/2017] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Diabetic cardiomyopathy (DCM) is a serious cardiac dysfunction induced by changes in the structure and contractility of the myocardium that are initiated in part by alterations in energy substrates. The underlying mechanisms of DCM are still under controversial. The observation of lipids, especially lipidomics profiling, can provide an insight into the know the biomarkers of DCM. The aim of our research was to detect changes of myocardial lipidomics profiling in a rat model of diabetic cardiomyopathy. METHODS Diabetic cardiomyopathy was induced by feeding a high-sucrose/fat diet (HSFD) for 28 weeks and streptozotocin (30 mg/kg, intraperitoneally). The ultra-high-performance liquid chromatography (UPLC) coupled to quadruple time-of flight (QTOF) mass spectrometer was used to acquire and analyze the lipidomics profiling of myocardial tissue. Meanwhile, parameters of cardiac function were collected using cardiac catheterization, and the cardiac index was calculated, and fasting blood glucose and lipid levels were measured by an ultraviolet spectrophotometric method. RESULTS We detected 3023 positive ion peaks and 300 negative ion peaks. Levels of phosphatidylcholine (PC) (22:6/18:2), PC (22:6/18:1), PC (20:4/16:1), PC (16:1/18:3), phosphatidylethanolamine (PE) (20:4/18:2), and PE (20:4/16:0) were down-regulated, and PC (20:2/18:2), PC (18:0/16:0), and PC (20:4/18:0) were up-regulated in DCM model rats, when compared with control rats. Cardiac functions signed as values of left ventricular systolic pressure, maximal uprising velocity of left ventricular pressure and maximal decreasing velocity of left ventricular pressure were injured by 21-44%, and the cardiac index was increased by 25%, and fasting blood glucose and lipids were increased by 34-368%. Meanwhile, the cardiac lipid-related biomarkers have significant correlation with changes of cardiac function and cardiac index. CONCLUSIONS UPLC/Q-TOF/MS analysis data suggested changes of some potential lipid biomarkers in the development of cardiac dysfunction and hypertrophy of diabetic cardiomyopathy, which may serve as potential important targets for clinical diagnosis and therapeutic intervention of DCM in the future.
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Affiliation(s)
- Shifen Dong
- Department of Pharmacology, School of Chinese Materia Medica, Beijing University of Chinese Medicine, No. 6 Wang Jing Zhong Huan South Road, Chaoyang District, Beijing, 100102 China
| | - Rong Zhang
- Department of Pharmacology, School of Chinese Materia Medica, Beijing University of Chinese Medicine, No. 6 Wang Jing Zhong Huan South Road, Chaoyang District, Beijing, 100102 China
| | - Yaoyue Liang
- Department of Pharmacology, School of Chinese Materia Medica, Beijing University of Chinese Medicine, No. 6 Wang Jing Zhong Huan South Road, Chaoyang District, Beijing, 100102 China
| | - Jiachen Shi
- Department of Pharmacology, School of Chinese Materia Medica, Beijing University of Chinese Medicine, No. 6 Wang Jing Zhong Huan South Road, Chaoyang District, Beijing, 100102 China
| | - Jiajia Li
- Department of Pharmacology, School of Chinese Materia Medica, Beijing University of Chinese Medicine, No. 6 Wang Jing Zhong Huan South Road, Chaoyang District, Beijing, 100102 China
| | - Fei Shang
- Beijing University of Chemical Technology, Beijing, 100029 China
| | - Xuezhou Mao
- Biostatistics and Programming, Sanofi U.S., Bridgewater, NJ 08807 USA
| | - Jianning Sun
- Department of Pharmacology, School of Chinese Materia Medica, Beijing University of Chinese Medicine, No. 6 Wang Jing Zhong Huan South Road, Chaoyang District, Beijing, 100102 China
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Riebeling C, Jungnickel H, Luch A, Haase A. Systems Biology to Support Nanomaterial Grouping. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 947:143-171. [PMID: 28168668 DOI: 10.1007/978-3-319-47754-1_6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The assessment of potential health risks of engineered nanomaterials (ENMs) is a challenging task due to the high number and great variety of already existing and newly emerging ENMs. Reliable grouping or categorization of ENMs with respect to hazards could help to facilitate prioritization and decision making for regulatory purposes. The development of grouping criteria, however, requires a broad and comprehensive data basis. A promising platform addressing this challenge is the systems biology approach. The different areas of systems biology, most prominently transcriptomics, proteomics and metabolomics, each of which provide a wealth of data that can be used to reveal novel biomarkers and biological pathways involved in the mode-of-action of ENMs. Combining such data with classical toxicological data would enable a more comprehensive understanding and hence might lead to more powerful and reliable prediction models. Physico-chemical data provide crucial information on the ENMs and need to be integrated, too. Overall statistical analysis should reveal robust grouping and categorization criteria and may ultimately help to identify meaningful biomarkers and biological pathways that sufficiently characterize the corresponding ENM subgroups. This chapter aims to give an overview on the different systems biology technologies and their current applications in the field of nanotoxicology, as well as to identify the existing challenges.
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Affiliation(s)
- Christian Riebeling
- German Federal Institute for Risk Assessment, Department of Chemical and Product Safety, Berlin, Germany
| | - Harald Jungnickel
- German Federal Institute for Risk Assessment, Department of Chemical and Product Safety, Berlin, Germany
| | - Andreas Luch
- German Federal Institute for Risk Assessment, Department of Chemical and Product Safety, Berlin, Germany
| | - Andrea Haase
- German Federal Institute for Risk Assessment, Department of Chemical and Product Safety, Berlin, Germany.
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